Discerning behaviours of free-ranging animals allows for quantification of their activity budget, providing important insight into ecology. Over recent years, accelerometers have been used to unveil ...the cryptic lives of animals. The increased ability of accelerometers to store large quantities of high resolution data has prompted a need for automated behavioural classification. We assessed the performance of several machine learning (ML) classifiers to discern five behaviours performed by accelerometer-equipped juvenile lemon sharks (
Negaprion brevirostris
) at Bimini, Bahamas (25°44′N, 79°16′W). The sharks were observed to exhibit chafing, burst swimming, headshaking, resting and swimming in a semi-captive environment and these observations were used to ground-truth data for ML training and testing. ML methods included logistic regression, an artificial neural network, two random forest models, a gradient boosting model and a voting ensemble (VE) model, which combined the predictions of all other (base) models to improve classifier performance. The macro-averaged
F
-measure, an indicator of classifier performance, showed that the VE model improved overall classification (
F
-measure 0.88) above the strongest base learner model, gradient boosting (0.86). To test whether the VE model provided biologically meaningful results when applied to accelerometer data obtained from wild sharks, we investigated headshaking behaviour, as a proxy for prey capture, in relation to the variables: time of day, tidal phase and season. All variables were significant in predicting prey capture, with predations most likely to occur during early evening and less frequently during the dry season and high tides. These findings support previous hypotheses from sporadic visual observations.
Age and growth estimates are essential for life history modeling in elasmobranchs and are used to inform accurate conservation and management decisions. The nurse shark (
Ginglymostoma cirratum
) is ...abundant in coastal waters of the Atlantic Ocean, yet many aspects of their life history remain relatively understudied, aside from their reproductive behavior. We used mark-recapture data of 91 individual
G. cirratum
from Bimini, The Bahamas, from 2003 to 2020, to calculate von Bertalanffy (vB) growth parameters, empirical growth rate, and age derived from the resulting length-at-age estimates. The Fabens method for estimating growth from mark-recapture methods was applied through a Bayesian framework using Markov chain Monte Carlo (MCMC) methods. This provided growth parameters with an asymptotic total length (
L
∞) of 303.28 cm and a growth coefficient (
k
) of 0.04 yr
-1
. The average growth rate for
G. cirratum
was approximately 8.68 ± 6.00 cm yr
-1
. This study also suggests that the previous maximum age for
G. cirratum
is likely underestimated, with the oldest individual predicted to be 43 years old. Our study is the first to present vB growth parameters and a growth curve for
G. cirratum
. It indicates that this species is slow-growing and long-lived, which improves our understanding of their life history.
Leucocyte migration is essential for robust immune and inflammatory responses, and plays a critical role in many human diseases. Chemokines, a family of small secreted protein chemoattractants, are ...of fundamental importance in this process, directing leucocyte trafficking by signalling through heptahelical G-protein-coupled receptors expressed by the migrating cells. However, several mammalian chemokine receptors, including D6 and CCX-CKR (ChemoCentryx chemokine receptor), do not fit existing models of chemokine receptor function, and do not even appear to signal in response to chemokine binding. Instead, these 'atypical' chemokine receptors are biochemically specialized for chemokine sequestration, acting to regulate chemokine bioavailability and thereby influence responses through signalling-competent chemokine receptors. This is of critical importance in vivo, as mice lacking D6 show exaggerated cutaneous inflammatory responses and an increased susceptibility to the development of skin cancer. CCX-CKR, on the other hand, is predicted to modulate homoeostatic lymphocyte and dendritic cell trafficking, key migratory events in acquired immune responses that are directed by CCX-CKR-binding chemokines. Thus studies on 'atypical' chemokine receptors are revealing functional and biochemical diversity within the chemokine receptor family and providing insights into novel mechanisms of chemokine regulation.
In Bimini, Bahamas, the consistent employment of longlines, beginning in 1982, provided a rare opportunity to explore population trends for large resident sharks. This study assessed three shallow ...water longline survey periods at this location; 1982–1989, 1992–2002 and 2003–2014, with the aim of determining trends in annual catch per unit effort (CPUE) for an IUCN listed near‐threatened species, the lemon shark Negaprion brevirostris. A general additive model (GAM) was used to analyse the non‐linear annual CPUE values over the entire 32‐year research period. The GAM displayed high variability of annual CPUE, with a peak value of 0·026 N. brevirostris per hook day (hooks day−1) in 2000. The temporal pattern of CPUE indicated an abundance trend with a complete cycle, from trough to trough, occurring over a period of approximately 18 years. The 1982–1989 survey period saw the highest proportion of mature individuals (19·8%) and the smallest average pre‐caudal length (LPC; 124·8 cm). The 1992–2002 survey period had the highest average annual CPUE (0·018 hooks day−1), while the 2003–2014 research period saw largest average LPC size (134·8 cm) and the lowest average CPUE values (0·009 hooks day−1) of the entire research period. The long‐term trend identified in this study provides a baseline for future assessment.
Introduction and ObjectivesInfluenza A virus (IAV) infections contribute significantly to global mortality. Stromal cells may be permanently altered by inflammatory responses, a process known as ...trained immunity. We hypothesize that viral infection induces trained immunity in lung stromal cells, enhancing their protective responses to future lung injury via interactions with local immune cells.MethodsC57BL/6 mice were infected intranasally with IAV (WSN) and after 30 days re-challenged with IAV (X31). Mice were sacrificed at day 0, 2, 30 and 32 post-infection/re-infection. The transcriptional profiles and locations of infection experienced stromal cells were identified by RNAscope, viral nucleoprotein (IAV-NP) was detected by immunofluorescence and flow cytometry. An in vitro co-culture assay measured T cell re-activation by naïve or IAV infected stromal cells. To assess the consequences of T cell depletion on viral load following IAV re-challenge, anti-CD4/CD8 blockade was performed during the memory phase of infection.ResultsIAV infection led to formation of dense clusters of T and B cells. RNAscope revealed high expression of SpiB and Cxcl0 in lung epithelial cells and fibroblasts, specifically at sites near immune cell clusters. SpiB regulates genes involved in antigen processing/presentation, while Cxcl10 facilitates T cell communication, suggesting collaboration between these cell types could facilitate early viral control. However, depletion of CD4 and CD8 T cells prior to a re-challenge infection did not alter enhanced viral control in IAV-memory animals. To investigate whether IAV-memory stromal cells display enhanced intrinsic viral control, we infected stromal cells from naïve and IAV-memory mice with IAV in vitro. Less IAV-Nucleoprotein was found in stromal cells taken from memory than naïve animals, this was independent of type I interferon. Interestingly, the NP+epithelial cells in cultures of IAV-memory stromal cells expressed higher levels of MHCII than NP+epithelial cells from naïve animals. Both populations could present IAV antigens to CD4 and CD8 T cells, although infected IAV-memory stromal cells to a lesser extent than infected naïve-stromal cells, perhaps due to lower levels of antigen.ConclusionsIAV-experienced lung stromal cells can play dual roles in anti-viral control, early cell intrinsic control and a rapid ability to communicate with local T cells.
A longline survey was conducted from 2004 to 2014 to investigate the demographic population structure and seasonal abundance of the blacktip shark Carcharhinus limbatus in the Bimini Islands, the ...Bahamas. All individuals sampled (n = 242) were sub‐adult or adults 70·1–145·1 cm pre‐caudal length (LPC) range with no neonates or YOY recorded in Bimini. Carcharhinus limbatus abundance peaked in September, coincident with the largest ratio of female to male sharks and a peak in fresh mating wounds on females. Mitochondrial control region (mtCR) DNA sequences were obtained from C. limbatus at Bimini to test whether Bimini C. limbatus are most closely related to geographically proximate populations sampled on the south‐eastern coast of the U.S.A., the closest known nursery areas for this species. Nine mtCR haplotypes were observed in 32 individuals sampled at Bimini haplotype diversity (h) = 0·821, nucleotide diversity (π) = 0·0015. Four haplotypes observed from Bimini matched those previously found in the northern Yucatan (Mexico)–Belize and two matched a haplotype previously found in the U.S.A. Four haplotypes were novel but were closely related to the northern Yucatan–Belizean haplotypes. Pair‐wise ΦST analysis showed that Bimini was significantly differentiated from all of the populations previously sampled (U.S.A. Atlantic, U.S.A. Gulf of Mexico, northern Yucatan, Belize and Brazil). This indicates that C. limbatus sampled from Bimini are unlikely from the described, proximate U.S.A. nurseries.
Introduction and ObjectivesInfluenza A virus (IAV) induces respiratory infections resulting in significant global mortality. Stromal cells are essential sources of chemokines and growth factors that ...promote immune cell survival and anti-viral responses. The concept that stromal cells are permanently altered by inflammatory responses is referred to as trained immunity. We hypothesise that IAV infections influence future immune responses via changes to lung stromal cells, enabling rapid communication with immune cells following subsequent infection.MethodsC57BL/6 mice were infected intranasally with IAV (WSN, 150PFU) for 30 days and subsequently re-challenged with IAV (X31, 200PFU) for 2 days. Mice were sacrificed at day 0, 2, 30 and 32 post infection. A Nanostring assay was used to examine the transcriptional profiles of FACS sorted lung fibroblasts and epithelial cells. Differentially expressed genes were validated by qPCR and flow cytometry. The expression of upstream transcriptional drivers of these changes were compared with publicly available RNA-seq and ChIP-seq datasets. The potential impact of these changes on stromal-immune cell communication were assessed using immunohistochemistry and immunofluorescence.ResultsGenes involved in T cell communication were significantly upregulated in lung fibroblasts (Cd274, Cxcl10) and epithelial cells (Tnfsf10, Icam2) following secondary IAV infection (d32), compared to d30. These changes were accompanied by elevated IFN-response genes (Bst2, Ifi47, Irf7). Fibroblasts displayed enrichment in genes involved in biological processes regulating T cell activation, while epithelial cells were enriched for genes that regulate cytokines (IFNα/β, TNFα). After secondary IAV infection, stromal cells rapidly upregulated genes involved in antigen processing and presentation (Tap1, Tapbp), compared to d30. The transcription factor SpiB was identified as a shared upstream regulator of these genes. Interestingly, in contrast to d2 post primary infection, MHCII+ epithelial cells were elevated following secondary infection, while the frequency of IFN-responsive fibroblasts was decreased. T and B cells were located near airway epithelial cells at d30 and were retained following secondary infection, indicating ongoing communication between these cells.ConclusionsOur data, show that lung fibroblasts and epithelial cells can display overlapping and functionally discrete responses to IAV infection, enabling them to rapidly communicate with lung T cells following a subsequent infection.Please refer to page A188 for declarations of interest related to this abstract.
Introduction and ObjectivesInfluenza A virus (IAV) infections are a significant cause of mortality worldwide. The concept that stromal cells are permanently altered by insults is termed trained ...immunity. Whether these cells contribute to protection or pathology is unclear. We hypothesise that trained stromal cells may participate in protective immune responses by rapidly reactivating local memory T cells.MethodsC57BL/6 mice were infected intranasally with IAV (WSN, 150PFU) for 30 days and subsequently re-challenged with IAV (X31, 200PFU) for either 2 or 5 days. Mice were sacrificed at day 0, 2, 5, 30, 32, 35 post infection. To detect infected cells, ex vivo, IAV-Nucleoprotein (NP) expression was measured using flow cytometry and the location of NP+ stromal cells was determined using immunofluorescence. Further phenotyping of infection experienced stromal cell subsets was conducted using RNA-scope, immunohistochemistry, and qPCR. To assess the consequences of T cell depletion on NP expression by lung stromal cells following IAV re-challenge, anti-CD4/CD8 blockade was performed during the memory phase of infection.ResultsFollowing influenza virus infection, NP+ epithelial cells were detected at primary (day 2, 5) and to a lesser extent at recall timepoints (day 32, 35). Importantly, NP+ epithelial cells expressed more MHCII compared to NP-negative cells, suggesting enhanced capability to communicate with T cells via enhanced antigen processing/presentation. Using RNAscope, SpiB, a transcription factor that regulates genes involved in antigen processing/presentation, was detected in lung epithelial cells of infected mice. SpiB+ cells were in close proximity to immune cells that form dense clusters containing a mixture of T/B cells and myeloid populations. Interestingly, these microenvironmental changes were dependent on viral replication. Increased frequencies of Ki67+ lung fibroblasts coincided with significant increases in interferon-responsive fibroblasts at early timepoints post infection, compared to naive controls. These two fibroblasts populations did not express NP. Following IAV re-challenge both fibroblast subsets were reduced compared to primary timepoints, suggesting high numbers of infected cells may be required to promote their expansion post infection.ConclusionsInfection experienced stromal cell subsets may promote immune protection upon re-infection, through antigen presentation to T cells and/or alteration of the local lung microenvironment.Please refer to page A211 for declarations of interest related to this abstract.
Introduction and ObjectivesPulmonary fibroblasts respond to environmental signals triggered by injury or infections, shaping subsequent responses in the lung. Fibroblasts may contribute to enhanced ...immune protection, or chronic pathogenic inflammation and fibrosis. We hypothesise that molecules upregulated by lung fibroblasts early following influenza A virus (IAV) infection and bleomycin-induced injury persist, in order to generate/maintain immune memory, via altered stromal-immune cell communication.MethodsTo address this, we performed RNA-seq on FACS sorted lung fibroblasts from naïve animals and at early (day 10) and late time points (day 40) following intranasal IAV infection. Transcriptional changes were compared with the bleomycin model of early lung injury (publicly available RNA-seq). The functional profile and location of injury altered lung stromal and immune cells was determined using flow cytometry and immunohistochemistry.ResultsAnalysis of differentially expressed genes demonstrated an enrichment in cell cycle and extracellular matrix genes at day 10 post IAV infection (FDR < 0.05), consistent with fibroblast activation profiles in the bleomycin-injured lung. Three distinct lung fibroblast populations were identified using flow cytometry: damage-responsive (DRF), interferon-responsive (IRF), and antigen-presenting fibroblasts (APF). DRF were significantly elevated in both models at day 10 post injury, while IRF were only detectable in the IAV lung. Interestingly, APF were reduced in the bleomycin lung compared to naïve controls. Furthermore, immunohistochemistry demonstrated that expression of the immunomodulatory molecule, podoplanin, was found in close proximity to immune cell infiltrates in the lung in both models.ConclusionsThese data have important implications for understanding the altered communications between immune and stromal cells during and following subsequent lung infections and injury/fibrotic responses.
Abstract
Background
ICONIC is the largest prospective multi-country (n = 33) observational study assessing burden in adult ulcerative colitis (UC) patients under routine care. Both patient and ...physician assessments of disease severity, activity and life impact were captured 6 monthly up to 2 years. This local subanalysis evaluates baseline (BL) characteristics and the extent of agreement between patients and physicians in measures of disease activity in UK patients.
Methods
Adults with early UC (diagnosed ≤36 months) were enrolled irrespective of disease severity or treatment. Patient self-assessments include disease severity, Pictorial Representation of Illness and Self-Measure (PRISM, a tool assessing perception of disease-associated suffering; lower scores indicate greater disease burden), Patient Health Questionnaire-9 (PHQ-9), Short inflammatory bowel disease Questionnaire (SIBDQ) and patient-modified Simple Clinical Colitis Activity Index (P-SCCAI). Physician assessments include clinical parameters, PRISM, SCCAI. Correlation between PRISM and SIBDQ, PHQ-9 and SCCAI were evaluated by Spearman correlation. BL characteristics are based on observed data.
Results
BL characteristics of 63 UK patients in ICONIC are shown in Table 1. From BL to 2-years, patient/physician PRISM was moderately/strongly correlated with SIBDQ, PHQ-9, P-SCCAI or SCCAI (Table 2). For 62 patients with self and physician assessments, the level of agreement on disease severity at BL (concordant pairs) was: mild 66.7%, moderate 27.8%, severe 45.5%, in remission 50.0%. The mean ± SD P-SCCAI and physician SCCAI values at 2 years were 2.6 ± 2.6 and 1.5 ± 1.5, respectively; the measures were strongly correlated (Table 2). For patient/physician PRISM assessments at 2 years, scores were 5.2 ± 2.6 and 5.2 ± 2.1, respectively, and were moderately/strongly correlated (Table 2).
Conclusion
Results from this subanalysis of ICONIC demonstrate persistently high UC disease burden over 2-years, despite treatment. EIMs were common and therefore awareness of potential EIM impact is essential. PRISM, used for the first time in UC, was moderately correlated with disease-specific measures (SIBDQ/SCCAI) and a general depression assessment (PHQ-9). Alignment between patients and physicians on disease activity/severity varied according to the instrument used but was greatest for SCCAI.
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