Biology subjects

Brown, L.

Publications and source records attributed to Brown, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Complex patterns of biological connectivity highlight risks of local depletion in an Australian fishery

Sustainable management of commercial and recreational fisheries depends on accurately resolving population connectivity, across both ecological and evolutionary timescales. However, dispersal can vary markedly among life stages, making stock connectivity difficult to resolve using single-method approaches that often differ in spatio-temporal resolution. Here, we integrated population genomics, otolith stable isotope chemistry, and mark-recapture analyses to provide a multi-faceted assessment of stock connectivity in mulloway (Argyrosomus japonicus). Mulloway are a commercially, culturally, and recreationally important estuary associated fish distributed throughout the Indo-Pacific region, including south-eastern Australia where this study was conducted. Genome-wide single nucleotide polymorphism (SNP) analyses revealed significant genetic differentiation between regions influenced by different current systems, but limited structure within regions across distances exceeding 900 km. In contrast, otolith {delta}13C and {delta}18O signatures revealed fine-scale spatial structuring among estuaries, consistent with prolonged occupancy of local habitats. Mark-recapture analyses supported this interpretation, with most fish exhibiting strong estuarine fidelity over extended periods despite occasional long-distance coastal movements. Reconstructed age structures from fish otoliths revealed remarkably similar cohort composition among estuaries, with populations dominated by cohorts originating from a major recruitment pulse centred on 2011-2012, likely associated with a broad-scale flood-driven spawning and recruitment event. Together, our findings indicate that mulloway fisheries function as regionally connected networks of partially independent estuarine assemblages, where strong local residency is periodically offset by dispersive individuals and episodic recruitment events that maintain long-term demographic and genetic connectivity. Consequently, local estuarine populations may be vulnerable to localised depletion despite broader regional connectivity, particularly where sustained fishing pressure coincides with reductions in freshwater flows that constrain spawning and recruitment. More broadly, our study demonstrates the value of integrating complementary approaches to identify biological connections and define meaningful management units in species with complex life histories.

evolutionary biology↗

bioRxiv2026

Genomic history and selection in Roman and early medieval Britain

Leading biomedical resources rely on genome variation in Britain1-3, but the historical processes that shaped present-day fine-scale diversity remain debated4-13. Here we sequenced 1039 ancient shotgun genomes from Britain (median 1.4-fold coverage), primarily dating to the first millennium CE. We imputed [~]660 million variants in the UK Biobank14-16 and employed genealogy-based ancestry reconstruction. We found an association between Iron Age consanguinity and matrilineal burial practices17, later disrupted following the Roman Conquest. Despite this societal impact, only 20% of Roman-period individuals carried detectable ancestry from outside Britain. In contrast, from the 6th century CE we detect widespread influx of ancestry in over 70% of individuals in southernAnglo-Saxon Britain, with limited local admixture. We find previously underappreciated heterogeneity, with ancestries associated with Central and Southern Europe rising in prevalence from the 7th century CE. We demonstrate distinct Scandinavian-related ancestry in many Viking-associated contexts, but show that the population-level impact of the Viking Age in Britain was limited. Finally, we detect pre-medieval selection on variants linked with key immunity genes TLR10-TLR1 and IRF8. These results identify population-level and selective processes that shape variation and disease risk in Britain today.

genomics↗

bioRxiv2026

From Fabrication to Flow: Impact of Print Orientation on Surface Qualities and Capillary-Driven Flow in Laser SLA-based Open Microchannels

Stereolithography (SLA) 3D printing has become increasingly popular for fabricating microfluidic devices, with applications including hydrogel patterning and tissue modeling. In open-channel systems with surface tension-driven flow, 3D-printer-induced discrepancies in channel surface texture can significantly impact fluid flow and device performance. While previous work has focused on comparing different 3D printing methods for microchannel fabrication, the effect of device orientation during SLA printing on microchannel morphology and capillary-driven flow has not been systematically evaluated. Furthermore, there is minimal research elucidating the influence of channel surface texture on the flow of biologically relevant hydrogel precursors commonly used in organ-on-a-chip applications. Herein, we investigated the impact of print orientation on channel morphology, fluid wetting behavior, and fluid flow by comparing laser SLA-based parts where the length of the channel was tilted at 0{degrees}, 15{degrees}, 45{degrees}, or 90{degrees} during printing. We demonstrated that channel floor surface texture is greatly affected by print orientation: the highest axial surface roughness was measured in 15{degrees} printed channels, and the highest axial surface tortuosity-which describes the real length along the surface-was measured in 45{degrees} printed channels. Print angles of 15{degrees} and 45{degrees} also resulted in asymmetric roughness of the channel floor, which caused asymmetric wetting of glycerol solution. Surface tension-driven flow of glycerol solution, agarose precursor solution, and collagen precursor solution was affected by print orientation, in which the 45{degrees} printed flow devices had slowest flow for all test fluids. Root mean square roughness was not a reliable predictor of slower flow; instead, surface tortuosity should be considered. Potential alternatives to better theoretically model how print angle-induced surface texture affects open-channel flow are discussed as well. These findings provide a framework of fabrication considerations for laser SLA printing of open microchannels that can also be applied to other layer-by-layer, vat photopolymerization-based 3D printing technologies.

bioengineering↗

bioRxiv2025

Rising, falling, stalling: Complex biodiversity trajectories in UK rivers

Freshwater ecosystems face intense anthropogenic pressures, with global indicators showing steep biodiversity declines in many regions. Yet in parts of Europe, including the UK, several recent analyses of long-term monitoring datasets have documented widespread improvements in macroinvertebrate communities following major water-quality investments. These gains are often interpreted as being nationally uniform, based on spatially aggregated data or simplified effect sizes, despite substantial site-level heterogeneity in temporal dynamics. Consequently, the prevalence, distribution, and causes of local biodiversity dynamics remain poorly resolved. We address this gap using macroinvertebrate time-series data from 803 river sites in Englands Environment Agency monitoring network. We applied an unsupervised, shape-explicit time-series clustering framework to classify sites into distinct shape-based clusters for three complementary metrics: pollution sensitivity of communities (Whalley, Hawkes, Paisley & Trigg (WHPT) Index), total abundance, and Simpsons diversity index. We then characterized taxonomic and environmental differences among clusters using Linear Discriminant Analysis and non-metric multidimensional scaling. Finally, we quantified how temporal trajectories are structured across increasingly aggregated spatial scales (site, water body, catchment, typology, region) using a Bayesian variance-partitioning model, providing the first multi-metric, multi-scale assessment of macroinvertebrate trends in UK rivers. Overall, our analyses reveal substantial heterogeneity in ecological trajectories: although many sites showed improving trends, more than half ([~]53%) were in decline or lacked clear directional change. Sites with consistent increases or declines were strongly differentiated by longitudinal position, channel morphology, and water chemistry, indicating that network placement and local environmental context mediate river biodiversity changes. Variance partitioning showed that most explainable variation lies at the site and typology levels, demonstrating that broader regional or national summaries can obscure a mosaic of non-linear, site-level trajectories and persistent local declines. Collectively, these findings affirm that freshwater biodiversity change in UK rivers cannot be summarized by a national or even regional narratives of recovery, but represents a mosaic of asynchronous, site-specific trajectories. These results illustrate the need for a renewed investment in dense, long-term river monitoring networks capable of resolving biodiversity change across hierarchical spatial scales.

ecology↗

bioRxiv2025

Evaluation of combined root exudate and rhizosphere microbiota sampling approaches to elucidate plant-soil-microbe interaction

O_LIDeciphering the root exudate-driven interplay between plants and the rhizosphere microbiota is essential for understanding plant adaptation to the environment and future-proofing crop production. However, sampling root exudates and rhizosphere soil remains challenging due to the low throughput and destructive nature of the process. C_LIO_LIWe used the staple crop barley [Hordeum vulgare] as a model to benchmark different sampling approaches for simultaneous exudation and microbiota profiling of soil-grown plants. C_LIO_LIExudate profiles and total dissolved organic carbon exudation rates were consistent across different sampling approaches, whereas root biomass, root morphology measurements, and organic nitrogen exudation varied. C_LIO_LIHigh-throughput amplicon sequencing and quantitative PCR (qPCR) of phylogenetic markers and nitrogen cycle-selected genes revealed a protocol-specific footprint in the composition and abundance of rhizosphere bacterial and fungal microbiota. Yet, on average, 75% of microbes enriched in, and differentiating between, barley rhizosphere and unplanted soil controls were recovered across all the sampling approaches evaluated. C_LIO_LIOur results demonstrated that, under the tested conditions, different sampling approaches produced comparable microbiota and exudation patterns, enabling the integrated study of root exudation and microbial profiles from the same plant. The observed differences across sampling approaches must be considered according to the experimental scope. C_LI

plant biology↗

bioRxiv2025

In Vitro Evidence to Support Amphotericin B and Flucytosine Combination Therapy for Talaromycosis

BackgroundTalaromyces marneffei causes talaromycosis, a life-threatening fungal disease with limited treatment options. The standard treatment of amphotericin B (AmB) induction followed by itraconazole consolidation still results in 15% to 30% mortality. This study aimed to investigate the potential of AmB and flucytosine (5FC) combination therapy to enhance antifungal activity. MethodsThe in vitro antifungal activity of AmB and 5FC alone and in combination against 60 T. marneffei clinical isolates was evaluated using a validated colorimetric antifungal susceptibility assay and the checkerboard method. The minimum inhibitory concentration (MIC) was defined as the lowest drug concentration inhibiting [≥] 95% fungal growth (MIC95) for both AmB and 5FC. The combination effect between AmB and 5FC against T. marneffei was determined using fractional inhibitory concentration index. Combination effects were further tested using a time-kill assay. ResultsThe MIC95 was 0.25 - 2 g/mL (geometric mean [GM] 0.68 g/mL) for AmB, and 0.03 - 0.5 g/mL (GM 0.28 g/mL) for 5FC. Full synergy was observed in 4 isolates (7%), and indifference was observed in the remaining 56 isolates (93%). The time-kill experiments revealed a concentration-dependent fungicidal activity of AmB, and concentration-independent fungistatic effect of 5FC. Synergy between AmB and 5FC was confirmed, showing greater than 2-log10 reduction in colony forming units when used in combination. No antagonism was observed. ConclusionsOur study demonstrated in vitro evidence of synergistic activity between AmB and 5FC against T. marneffei, providing the evidence to support in vivo and clinical trial testing of AmB and 5FC combination therapy, and dosing reduction strategies of 5FC. Lay SummaryThis study demonstrated in vitro synergy between amphotericin B and flucytosine against Talaromyces marneffei, providing the proof of concept to test this antifungal combination in a clinical trial of talaromycosis.

pharmacology and toxicology↗

bioRxiv2025

Life in the fast lane: Functional consequences of male-female dynamic differences in the renal autoregulation of flow

Tubuloglomerular feedback (TGF) is essential for the renal auto-regulation of flow. TGF is known to induce spontaneous oscillations in single-nephron tubular fluid flow in male kidneys. However, male-female differences in this dynamic behavior have not been studied. Leveraging intravital two-photon microscopy, resting-state magnetic resonance imaging, ultrasound-based and transdermal recordings, we found TGF-mediated oscillations across spatial scales in the rodent kidney, from single-nephron to whole-organ levels, and that male kidneys exhibited higher operating frequencies than females. To understand the mechanisms involved, we developed a dynamical systems model of TGF that agrees with physiological observations. Analysis of the mathematical model indicated that higher reabsorption rate and fluid flow efficiency in male proximal tubules not only result in higher frequencies, but also render male nephrons more susceptible to lose TGF-mediated oscillations. Furosemide abolished TGF-mediated oscillations in male kidneys and upregulated tubular injury marker KIM-1, suggesting that the propensity to lose TGF-mediated oscillations underlies the heightened risk for injury in males. Our analysis also indicated that SGLT-2 inhibition confers renoprotection by preserving TGF-mediated oscillations in hyperglycemia. Combining quantitative imaging and mathematical modeling, this study provides mechanistic insights into the transition from normal physiology to pathophysiology in the kidney.

physiology↗

bioRxiv2025

Identification of natural products and synthetic analogs which inhibit microsporidia spores and prevent infection

Microsporidiosis, a disease caused by microsporidia, affects many animals, with symptoms ranging from diarrhea to death, especially in immunocompromised individuals. Current treatments, such as albendazole and fumagillin, are limited in efficacy. To address this problem, we utilized Caenorhabditis elegans infected with its natural microsporidian Nematocida parisii to evaluate 4,080 structurally diverse compounds from the Boston University Center for Molecular Discovery (BU-CMD) chemical library. From this screen we identified 34 compounds that effectively inhibited N. parisii infection and restored the reproductive capacity of C. elegans. All 17 compounds we validated prevented N. parisii infection in C. elegans, and 10 were capable of suppressing microsporidia invasion by inactivating mature spores. Additionally, five of the identified compounds were also effective against Pancytospora epiphaga, a species related to human-infecting microsporidia. Together this work identifies and characterizes compounds which inhibit microsporidia infection. ImportanceMicrosporidia are a large group of microbial parasites that infect many animals, including humans. Many agriculturally important animals such as honey bees, shrimp, crabs, and fish are infected by microsporidia, and these infections often result in smaller animals, fewer offspring, and death. Only two drugs are commonly used to treat microsporidia infections; due to some species being resistant and host toxicity there is a need to identify other microsporidia inhibitors. In this study, we screened over 4000 small molecules using a model round worm infected with microsporidia. We identified several dozen inhibitors and characterized how these compounds prevented infection by determining which stage of the parasite they act upon. Together our work identified and characterized compounds that could be used as a starting point to design better microsporidia inhibitors.

microbiology↗

bioRxiv2025

Vascular Biomechanics and Brain Biochemistry in Aged and Alzheimer's Disease Mouse Models

Age-related vascular changes accompany or precede the development of Alzheimers disease (AD) pathology. The comorbidity of AD and arterial stiffening may suggest that vascular changes have a pathogenic role. Carotid artery mechanics and hemodynamics have been associated with age-related cognitive decline. However, the impact of hemodynamics and vascular mechanics on regional vulnerability within the brain have not been thoroughly explored. Despite the venous systems role in transport, the impact of age-related alterations of the brain venous circulation on cognitive impairment is much less understood compared to the arterial system. By studying vascular mechanics and the resulting spatially-resolved brain lipids in young and aged AD mice, we can determine the relationship between vascular stiffening and brain function. Young and aged female 3xTg mice and age-matched controls were imaged using a combination of ultrasound and mass spectrometry. Wall shear stress varied across age and AD (p<0.05). The circumferential cyclic strain values for the carotid arteries and the WSS values for the jugular veins between groups were measured but were not statistically significant. Both mean velocity and pulsatility index (PI) varied across age and AD (p<0.05). Liquid chromatography mass spectrometry (LC-MS) of brain tissue identified several lipids and metabolites with statistically significant quantities (p<0.05). The fold change was computed for young AD vs. young control, aged AD vs. aged control, aged control vs. young control, and aged AD vs. young AD. The abundance of several lipid headgroups changed significantly with respect to age and AD. Phosphatidylcholines (PC), phosphatidylethanolamines (PE), cardiolipins (CL), phosphatidylserines (PS), and lysophosphatidylcholines (LPC) have been shown to decrease with AD in previous studies. However, we observed a statistically significant increase in PC, PE, CL, PS, and LPC in the aged 3xTG mouse model compared to aged controls. Hexosylceramides (HexCer), ceramides (CER) and sphingomyelin (SM), classes of sphingolipids; lysophosphatidylethanolamine (LPE), a class of phospholipids; and onogalactosyl diglycerides (MGDG), a class of glycerolipids, have been shown to increase with AD in previous studies which aligns with the statistically significant increase of LPC, HexCer, CER, SM, LPE, and MDG observed in the aged 3xTg group compared to controls in this work. Combining both ultrasound imaging and mass spectrometry, we were able determine significant differences in the vascular biomechanics and brain biochemistry seen with aging and AD.

neuroscience↗

bioRxiv2024

Hope for Others: Research Results from the University of Pittsburgh Rapid Autopsy Program for Breast Cancer

Breast cancer affects 1/8 of women throughout their lifetimes, with over 90% of cancer deaths being caused by metastasis. However, metastasis poses unique challenges to research, as complex changes in the microenvironment in different metastatic sites and difficulty obtaining tissue for study hinder the ability to examine in depth the changes that occur during metastasis. Rapid autopsy programs thus fill a unique need in advancing metastasis research. Here, we describe our protocol and processes for establishing and improving the US-based Hope for OTHERS (Our Tissue Helping Enhance Research and Science) program for organ donation in metastatic breast cancer. As of August 2024, we consented 114 patients and performed 37 autopsies, from which we collected 551 unique metastatic frozen tumor samples, 1244 FFPE blocks, 90 longitudinal liquid biopsy samples and developed 14 patient-derived organoid and 8 patient-derived xenograft models. We report in-depth clinical and histopathological information and discuss extensive new research and novel findings in patient outcomes, metastatic phylogeny, and factors in successful living model development. Our results reveal key logistical and protocol improvements that are uniquely beneficial to certain programs based on identifiable features, such as working closely with patient advocates, methods to rescue RNA quality in cases where tissue quality may degrade due to time delays, as well as guidelines and future expansions of our program. Statement of SignificanceRapid autopsy programs are unique research settings with huge potential for studying metastatic cancer, however, they have complex research challenges. Our work provides a valuable resource in advancing this field of research.

cancer biology↗

bioRxiv2024

Acute and early stress axis modulation in joint disease permanently reduces pain and emotional comorbidities

Chronic pain affects 20-30% of the population and imposes a significant socio-economic burden as it is often accompanied by substantial emotional comorbidities such as anxiety and depression. Yet, the mechanisms underlying the interactions between the sensory and emotional aspects of chronic pain remain poorly understood. Here, we investigated the role of FKBP51, a regulator of the stress response, in mediating both sensory and emotional symptoms of chronic pain. Inhibition of FKBP51, via genetic deletion or pharmacological blockade, in persistent joint pain reduced fast-onset sensory, functional and activity-related symptoms, as well as late anxio-depressive comorbidities. FKBP51 inhibition after the establishment of the hypersensitive state provided only temporary symptoms relief, while acute inhibition at disease onset protected from the full development of sensory and anxio-depressive symptoms for up to 6 months. Our results also indicated that early pain symptoms could predict the late sensory and emotional outcomes of chronic pain. RNA sequencing of spinal cord tissue revealed that late FKBP51 inhibition transiently altered nociceptive genes associated with mechanical hypersensitivity. In contrast, early inhibition persistently downregulated the Naaa gene, a key regulator of the transition to chronic pain, and reorganized spinal cilia. Our results indicate that early FKBP51 inhibition after injury can persistently reduce chronic pain and prevent the onset of associated emotional comorbidities by modulating critical spinal neurobiological pathways that play pivotal roles in the transition to chronic pain. Significance statementOur study reveals that early inhibition of FKBP51, a modulator in the stress axis, at the onset of joint damage provides sustained pain relief and significantly delays or prevents emotional comorbidities in a sex-dependent manner. In contrast, FKBP51 inhibition initiated after chronic pain is established results in only temporary symptoms improvement. These findings highlight a critical therapeutic window during which timely intervention can prevent the transition from acute to chronic pain. By establishing a predictive link between early therapeutic response and long-term outcomes, this work has important clinical implications for proactive and personalized chronic pain management.

neuroscience↗

bioRxiv2024

Your Blood is Out for Delivery: Considerations of Shipping Time and Temperature on Degradation of RNA from Stabilized Whole Blood

Remote research studies are an invaluable tool for reaching populations in geographical regions with limited access to large medical centers or universities. To expand the remote study toolkit, we have previously developed homeRNA, which allows for at-home self-collection and stabilization of blood and demonstrated the feasibility of using homeRNA in high temperature climates. Here, we expand upon this work through a systematic study exploring the effects of high temperature on RNA integrity through in-lab and field experiments. Compared to the frozen controls (overall mean RIN of 8.2, n = 8), samples kept at 37{degrees}C for 2, 4, and 8 days had mean RINs of 7.6, 5.9, and 5.2 (n = 3), respectively, indicating that typical shipping conditions ([~]2 days) yield samples suitable for downstream RNA sequencing. Shorter time intervals (6 hours) resulted in minimal RNA degradation (median RIN of 6.4, n = 3) even at higher temperatures (50{degrees}C) compared to the frozen control (mean RIN of 7.8, n = 3). Additionally, we shipped homeRNA-stabilized blood from a single donor to 14 different states and back during the summer with continuous temperature probes (7.1 median RIN, n = 42). Samples from all locations were analyzed with 3 mRNA-seq to assess differences in gene counts, with the transcriptomic data suggesting that there was no preferential degradation of transcripts as a result of different shipping times, temperatures, and regions. Overall, our data support that homeRNA can be used in elevated temperature conditions, enabling decentralized sample collection for telemedicine, global health, and clinical research.

bioengineering↗

bioRxiv2024

Integrin inactivation slows down neutrophils congesting the pre-metastatic lung in a model of breast cancer

Neutrophils are thought to be critical to the process whereby breast cancers establish an immunosuppressive and tumour cell nurturing pre-metastatic niche before overt metastasis can be detected. However, the spatial localization of neutrophils and their interaction with other cell types in the lung pre-metastatic niche is not well described. We used a spontaneously metastatic mammary cancer model combined with a multiplexed three- and four-dimensional imaging approach to investigate the behaviour of neutrophils in the pre-metastatic niche. Volume fixed tissue three-dimensional imaging showed that approximately 40% of CD8+ T cells are adjacent to neutrophils at this stage. In live tissue, we found neutrophils with impaired intravascular motility congested the capillaries of pre-metastatic lungs potentially obstructing CD8+ T cells. Slowed neutrophil transit was dependent on the conformation of {beta}2-integrin and could be recapitulated by treating non-tumour bearing mice with G-CSF, a potent systemic mediator of granulopoiesis. We found a decrease in L-selectin (CD62L) on neutrophils in the lungs of both mammary tumour bearing and G-CSF treated mice. Finally, we observed differential accumulation of intravenously injected micro-beads in the lung, suggestive of transient circulatory dead spaces which were also dependent on {beta}2-integrin inactivation. Overall, our study proposes that integrin-mediated neutrophil congestion of the alveolar capillaries could contribute to the generation of the pulmonary pre-metastatic niche.

immunology↗

bioRxiv2024

MU-BRAIN: MUltiethnic Brain Rna-seq for Alzheimer INitiative

Alzheimers Disease (AD) exhibits a complex molecular and phenotypic profile. Investigating gene expression plays a crucial role in unraveling the diseases etiology and progression. Transcriptome data across ethnic groups lack, negatively impacting equity in intervention and research. We employed 565 brains across six U.S. brain banks (n=399 non-Hispanic Whites, n=113 Hispanics, n=12 African Americans) to generated bulk RNA sequencing from prefrontal cortex. We sought to identify cross-ancestry and ancestry-specific differentially expressed genes (DEG) across Braak stages, adjusting for sex, age at death, and RNA quality metrics. We further validated our findings using the Religious Orders Study/Memory Aging Project brains (ROS/MAP; n=1,095) and performed metanalysis (n=1,660). We conducted Gene Set and Variation and Enrichment analysis (GSVA; GSEA). We employed a machine-learning approach for phenotype prediction and gene prioritization to construct a polytranscriptomics risk score (PTRS) splitting our sample into training and testing sub-samples, either randomly or by ethnicity ("ancestry-agnostic" and "ancestry-aware", respectively). Lastly, we validated top DEG using single-nucleus RNA sequencing (snRNAseq) data. We identified several DEG associated with Braak staging: AD-known genes VGF (Padj =3.78E- 07) and ADAMTS2 (Pad j=1.21E-04) were consistently differentially expressed across statistical models, ethnicities, and replicated in ROS/MAP. Genes from the heat shock protein (HSP) family, e.g. HSPB7 (Padj =3.78E-07), were the top differentially expressed genes and replicated in ROS/MAP. Ethnic-stratified analyses prioritized TNFSF14 and SPOCD1 as top Hispanics DEG. GSEA highlighted "Alzheimer disease" (Padj =4.24E-06) and "TYROBP causal network in microglia" (Padj =1.68E-08) pathways. Up- and down-regulated genes were enriched in several pathways (e.g. "Immune response activation signal pathways", "Vesicle-mediated transport in synapse", "cognition"). Ancestry-agnostic and ancestry-aware PTRS effectively classified brains (AUC=0.77 and 0.73 respectively) and replicated in ROS/MAP. snRNAseq validated prioritized genes, including VGF (downregulated in neurons; Padj=1.1 E-07). This is the largest diverse AD transcriptome in post-mortem brain tissue, to our knowledge. We identified perturbated genes, pathways and network expressions in AD brains resulting in cross- ethnic and ethnic-specific findings, ultimately highlighting the diversity within AD pathogenesis. The latter underscores the need for an integrative and personalized approach in AD studies.

genetics↗

bioRxiv2024

Ligand binding determines proteolytic stability of Vibrio LuxR/HapR quorum sensing transcription factors

In Vibrio species, quorum sensing signaling culminates in the production of the master transcription factor SmcR that regulates group behavior genes in a density-dependent manner. Previously, we identified a small molecule thiophenesulfonamide inhibitor called PTSP that targets the SmcR family of proteins and blocks activity in vivo. Here, we used structure-function analyses to identify eight PTSP-interacting residues in the ligand binding pocket that are required for PTSP inhibition of Vibrio vulnificus SmcR. Binding of PTSP to SmcR drives allosteric unfolding of the N-terminal DNA-binding domain and, in this state, SmcR is degraded by the ClpAP protease. SmcR degradation controls the timing of the phenotypic switch between high and low cell density, and strains expressing degradation-resistant smcR alleles are impervious to changes in cell density state. These studies implicate ligand binding as a mediator of SmcR protein stability and function, which dictates the timing of quorum sensing gene expression in three Vibrio pathogens. Significance StatementSmcR family proteins were discovered in the 1990s as central regulators of quorum sensing gene expression and later discovered to be conserved in all studied Vibrio species. SmcR homologs regulate a wide range of genes involved in pathogenesis, including but not limited to genes involved in biofilm production and toxin secretion. As archetypal members of the broad class of TetR-type transcription factors, each SmcR type protein has a predicted ligand binding pocket. However, no ligand has been identified for these proteins that control their function as regulators. Here, we used SmcR-specific chemical inhibitors to determine that ligand binding drives proteolytic degradation in vivo, the first demonstration of SmcR function connected to ligand binding for this historical protein family.

microbiology↗

bioRxiv2023

WCRC-25: A novel luminal Invasive Lobular Carcinoma cell line model

Breast cancer is categorized by the molecular and histologic presentation of the tumor, with the major histologic subtypes being No Special Type (NST) and Invasive Lobular Carcinoma (ILC). ILC are characterized by growth in a single file discohesive manner with stromal infiltration attributed to their hallmark pathognomonic loss of E-cadherin (CDH1). Few ILC cell line models are available to researchers. Here we report the successful establishment and characterization of a novel ILC cell line, WCRC-25, from a metastatic pleural effusion from a postmenopausal Caucasian woman with metastatic ILC. WCRC-25 is an ER-negative luminal epithelial ILC cell line with both luminal and Her2-like features. It exhibits anchorage independent growth and haptotactic migration towards Collagen I. Sequencing revealed a CDH1 Q706* truncating mutation, together with mutations in FOXA1, CTCF, BRCA2 and TP53, which were also seen in a series of metastatic lesions from the patient. Copy number analyses revealed amplification and deletion of genes frequently altered in ILC while optical genome mapping revealed novel structural rearrangements. RNA-seq analysis comparing the primary tumor, metastases and the cell line revealed signatures for cell cycle progression and receptor tyrosine kinase signaling. To assess targetability, we treated WCRC-25 with AZD5363 and Alpelisib confirming WCRC-25 as susceptible to PI3K/AKT signaling inhibition as predicted by our RNA sequencing analysis. In conclusion, we report WCRC-25 as a novel ILC cell line with promise as a valuable research tool to advance our understanding of ILC and its therapeutic vulnerabilities. Financial supportThe work was in part supported by a Susan G Komen Leadership Grant to SO (SAC160073) and NCI R01 CA252378 (SO/AVL). AVL and SO are Komen Scholars, Hillman Foundation Fellows and supported by BCRF. This project used the UPMC Hillman Cancer Center and Tissue and Research Pathology/Pitt Biospecimen Core shared resource which is supported in part by award P30CA047904. This research was also supported in part by the University of Pittsburgh Center for Research Computing, RRID:SCR_022735, through the resources provided. Specifically, this work used the HTC cluster, which is supported by NIH award number S10OD028483. Finally, partial support was provided by the Magee-Womens Research Institute and Foundation, The Shear Family Foundation, and The Metastatic Breast Cancer Network.

cancer biology↗

bioRxiv2023

Assessing the global prevalence of wild birds in trade

Trade represents a significant threat to many wild species and is often clandestine and poorly monitored. Information on which species are most prevalent in trade, and potentially threatened by it, therefore remains fragmentary. We mobilised seven global datasets on birds in trade to identify the species or groups of species that might be at particular risk. These datasets sample different parts of the broad trade spectrum but we nevertheless find a statistically strong congruence between them in which species are recorded in trade. Furthermore, the frequency with which species are recorded within datasets is positively correlated with their occurrence across datasets. This allows us to propose a trade prevalence score that can be applied to all bird species globally. This score discriminates well between species known from semi-independent assessments to be heavily or unsustainably traded and all other species. Globally, 45.1% of all bird species, and 36.7% of globally threatened bird species, were recorded in at least one of the seven datasets. Species listed in Appendices I or II of CITES, species with large geographical distributions and non-songbirds had higher trade prevalence scores. Speciose orders with high mean trade prevalence scores include the Falconiformes, Psittaciformes, Accipitriformes, Anseriformes, Bucerotiformes and Strigiformes. Despite their low mean prevalence score, Passeriformes accounted for the highest overall number of traded species of any order but had low representation in CITES Appendices. Geographical hotspots where large numbers of traded species co-occur differed between songbirds (South-East Asia and Eurasia) and non-songbirds (central South America, sub-Saharan Africa and India). This first attempt to quantify and map the relative prevalence in trade of all bird species globally can be used to identify species and groups of species which may be at particular risk of harm from trade and can inform conservation and policy interventions to reduce its adverse impacts. Article impact statementThe first metric to estimate the prevalence in trade of all the worlds bird species is presented.

ecology↗

bioRxiv2023

Anti-Viral and Anti-Inflammatory Therapeutic Effect of RAGE-Ig Protein Against Multiple SARS-CoV-2 Variants of Concern Demonstrated in K18-hACE2 Mouse and Syrian Golden Hamster Models

SignificanceSARS-CoV-2 Variants of Concern (VOCs) continue to evolve and re-emerge with chronic inflammatory long-COVID sequelae necessitating the development of anti-inflammatory therapeutic molecules. Therapeutic effects of the Receptor for Advanced Glycation End products (RAGE) were reported in many inflammatory diseases. However, a therapeutic effect of the RAGE in COVID-19 has not been reported. In the present study, we investigated whether and how the RAGE-Ig fusion protein would have an anti-viral and anti-inflammatory therapeutic effect in the COVID-19 system. MethodsThe protective therapeutic effect of RAGE-Ig was determined in vitro in K18-hACE2 transgenic mice and Syrian golden hamsters infected with six various VOCs of SARS-CoV-2. The underlying anti-viral mechanism of RAGE-Ig was determined in vitro in SARS-CoV-2-infected human lung epithelial cells (BEAS-2B). ResultsFollowing treatment of K18-hACE2 mice and hamsters infected with various SARS-CoV-2 VOCs with RAGE-Ig, we demonstrated: (i) significant dose-dependent protection (i.e. greater survival, less weight loss, lower virus replication in the lungs); (ii) a reduction of inflammatory macrophages (F4/80+/Ly6C+) and neutrophils (CD11b+/Ly6G+) infiltrating the infected lungs; (iii) a RAGE-Ig dose-dependent increase in the expression of type I interferons (IFN-, and IFN-{beta}) and type III interferon (IFN{lambda}2) and a decrease in the inflammatory cytokines (IL-6 and IL-8) in SARS-CoV-2-infected human lung epithelial cells; and (iv) a dose-dependent decrease in the expression of CD64 (FcgR1) on monocytes and lung epithelial cells from symptomatic COVID-19 patients. ConclusionOur pre-clinical findings revealed type I and III interferons-mediated anti-viral and anti-inflammatory therapeutic effects of RAGE-Ig protein against COVID-19 caused by multiple SARS-CoV-2 VOCs.

immunology↗