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Article: On inferring population trends of mobile waterbirds from aerial transect surveys in variable environments

Caley, Peter / Reid, Julian R. W. / Colloff, Matthew J. / Barry, Simon C.

Environmental and ecological statistics. 2022 Mar., v. 29, no. 1

2022

Abstract: Monitoring waterbird populations in Australia is challenging for reasons of counting logistics, and because population aggregation and dispersion can shift rapidly in response to large spatio-temporal variations in resource availability. The East ... ...

Abstract	Monitoring waterbird populations in Australia is challenging for reasons of counting logistics, and because population aggregation and dispersion can shift rapidly in response to large spatio-temporal variations in resource availability. The East Australian Waterbird survey has conducted annual, aerial, systematic counts of waterbirds over eastern Australia for almost 40 years. It was designed to monitor waterbird populations using design-based inference though for many species this form of inference appears inadequate in the face of these challenges. Here we develop a state-space model-based Bayesian approach that, in addition to explicitly incorporating process noise and observation uncertainty, uses random effects and rainfall-derived covariates to model the year-to-year variation in the proportion of the total (super) population that is present on surveyed wetlands, and available to be counted. We use this model-based approach to estimate the superpopulation size of 45 waterbird species annually, and model the rate of population increase as a function of antecedent rainfall. The results confirm the strong positive effect of antecedent rainfall on population growth rates for nearly all species, and illustrate that species respond to rainfall differently in terms of habitat use, which influences whether they are present on surveyed wetlands. For many species, the year-to-year variation in the estimated proportion of the population on surveyed wetlands is very high. The results have implications for making inferences on population trends from these data, with the ability to model the year-to-year sampling variation a key requirement before the rate of population increase can be estimated with any precision. This study illustrates how to progress this approach, and infers that under average rainfall conditions, the general trend is for estimated superpopulation rates of increase to be negative, though for only a few species is this occurring with strong belief.
Keywords	Bayesian theory ; habitat preferences ; population growth ; rain ; surveys ; uncertainty ; water birds ; Australia
Language	English
Dates of publication	2022-03
Size	p. 3-31.
Publishing place	Springer US
Document type	Article
ZDB-ID	2000906-9
ISSN	1573-3009 ; 1352-8505
ISSN (online)	1573-3009
ISSN	1352-8505
DOI	10.1007/s10651-021-00510-7
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Best practice in alien species risk assessment: a comment on Leung et al. (2012).

Barry, Simon C

Ecology letters

2013 Volume 16, Issue 11, Page(s) 1414, e5

Abstract: The TEASI model is presented in Leung et al. (2012; TEASIng apart alien species risk assessments: a framework for best practices. Ecol. Lett., 15, 1475) as a framework for best practice in alien species risk assessment. This is not supported by the paper' ...

Abstract	The TEASI model is presented in Leung et al. (2012; TEASIng apart alien species risk assessments: a framework for best practices. Ecol. Lett., 15, 1475) as a framework for best practice in alien species risk assessment. This is not supported by the paper's review as it does not define good, bad or best practice and therefore cannot logically make this claim.
MeSH term(s)	Animals ; Introduced Species/statistics & numerical data ; Models, Biological
Language	English
Publishing date	2013-11
Publishing country	England
Document type	Comment ; Journal Article
ZDB-ID	1441608-6
ISSN	1461-0248 ; 1461-023X
ISSN (online)	1461-0248
ISSN	1461-023X
DOI	10.1111/ele.12163
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Article: Crowd surveillance: estimating citizen science reporting probabilities for insects of biosecurity concern : Implications for plant biosecurity surveillance

Caley, Peter / Barry, Simon C / Welvaert, Marijke

Journal of pest science. 2020 Jan., v. 93, no. 1

2020

Abstract: Data streams arising from citizen reporting activities continue to grow, yet the information content within these streams remains unclear, and methods for addressing the inherent reporting biases little developed. Here, we quantify the major influence of ...

Abstract	Data streams arising from citizen reporting activities continue to grow, yet the information content within these streams remains unclear, and methods for addressing the inherent reporting biases little developed. Here, we quantify the major influence of physical insect features (colour, size, morphology, pattern) on the propensity of citizens to upload photographic sightings to online portals, and hence to contribute to biosecurity surveillance. After correcting for species availability, we show that physical features and pestiness are major predictors of reporting probability. The more distinctive the visual features, the higher the reporting probabilities—potentially providing useful surveillance should the species be an unwanted exotic. Conversely, the reporting probability for many small, nondescript high priority pest species is unlikely to be sufficient to contribute meaningfully to biosecurity surveillance, unless they are causing major harm. The lack of citizen reporting of recent incursions of small, nondescript exotic pests supports the model. By examining the types of insects of concern, industries or environmental managers can assess to what extent they can rely on citizen reporting for their surveillance needs. The citrus industry, for example, probably cannot rely on passive unstructured citizen data streams for surveillance of the Asian citrus psyllid (Diaphorina citri). In contrast, the forestry industry may consider that citizen detection and reporting of species of the large and colourful insects such as pine sawyers (Monochamus spp.) may be sufficient for their needs. Incorporating citizen surveillance into the general surveillance framework is an area for further research.
Keywords	biosecurity ; Citrus ; color ; Diaphorina citri ; forest industries ; insects ; introduced species ; models ; monitoring ; Monochamus ; pests ; probability ; streams
Language	English
Dates of publication	2020-01
Size	p. 543-550.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ZDB-ID	2141662-X
ISSN	1612-4766 ; 1439-0280 ; 1612-4758
ISSN (online)	1612-4766 ; 1439-0280
ISSN	1612-4758
DOI	10.1007/s10340-019-01115-7
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Article ; Online: 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk.

Liu, Ning / Sadlon, Timothy / Wong, Ying Y / Pederson, Stephen / Breen, James / Barry, Simon C

Epigenetics & chromatin

2022 Volume 15, Issue 1, Page(s) 24

Abstract: Background: Genome-wide association studies (GWAS) have enabled the discovery of single nucleotide polymorphisms (SNPs) that are significantly associated with many autoimmune diseases including type 1 diabetes (T1D). However, many of the identified ... ...

Abstract	Background: Genome-wide association studies (GWAS) have enabled the discovery of single nucleotide polymorphisms (SNPs) that are significantly associated with many autoimmune diseases including type 1 diabetes (T1D). However, many of the identified variants lie in non-coding regions, limiting the identification of mechanisms that contribute to autoimmune disease progression. To address this problem, we developed a variant filtering workflow called 3DFAACTS-SNP to link genetic variants to target genes in a cell-specific manner. Here, we use 3DFAACTS-SNP to identify candidate SNPs and target genes associated with the loss of immune tolerance in regulatory T cells (Treg) in T1D. Results: Using 3DFAACTS-SNP, we identified from a list of 1228 previously fine-mapped variants, 36 SNPs with plausible Treg-specific mechanisms of action. The integration of cell type-specific chromosome conformation capture data in 3DFAACTS-SNP identified 266 regulatory regions and 47 candidate target genes that interact with these variant-containing regions in Treg cells. We further demonstrated the utility of the workflow by applying it to three other SNP autoimmune datasets, identifying 16 Treg-centric candidate variants and 60 interacting genes. Finally, we demonstrate the broad utility of 3DFAACTS-SNP for functional annotation of all known common (> 10% allele frequency) variants from the Genome Aggregation Database (gnomAD). We identified 9376 candidate variants and 4968 candidate target genes, generating a list of potential sites for future T1D or other autoimmune disease research. Conclusions: We demonstrate that it is possible to further prioritise variants that contribute to T1D based on regulatory function, and illustrate the power of using cell type-specific multi-omics datasets to determine disease mechanisms. Our workflow can be customised to any cell type for which the individual datasets for functional annotation have been generated, giving broad applicability and utility.
MeSH term(s)	Diabetes Mellitus, Type 1/genetics ; Epigenesis, Genetic ; Genome-Wide Association Study ; Humans ; Polymorphism, Single Nucleotide ; T-Lymphocytes, Regulatory/physiology
Language	English
Publishing date	2022-06-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2462129-8
ISSN	1756-8935 ; 1756-8935
ISSN (online)	1756-8935
ISSN	1756-8935
DOI	10.1186/s13072-022-00456-5
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Article ; Online: PKCζ activation promotes maturation of cord blood T cells towards a Th1 IFN-γ propensity.

Perveen, Khalida / Quach, Alex / Stark, Michael J / Prescott, Susan / Barry, Simon C / Hii, Charles S / Ferrante, Antonio

Immunology

2023 Volume 170, Issue 3, Page(s) 359–373

Abstract: A significant number of babies present transiently with low protein kinase C zeta (PKCζ) levels in cord blood T cells (CBTC), associated with reduced ability to transition from a neonatal Th2 to a mature Th1 cytokine bias, leading to a higher risk of ... ...

Abstract	A significant number of babies present transiently with low protein kinase C zeta (PKCζ) levels in cord blood T cells (CBTC), associated with reduced ability to transition from a neonatal Th2 to a mature Th1 cytokine bias, leading to a higher risk of developing allergic sensitisation, compared to neonates whose T cells have 'normal' PKCζ levels. However, the importance of PKCζ signalling in regulating their differentiation from a Th2 to a Th1 cytokine phenotype propensity remains undefined. To define the role of PKCζ signalling in the regulation of CBTC differentiation from a Th2 to a Th1cytokine phenotype we have developed a neonatal T cell maturation model which enables the cells to develop to CD45RA
MeSH term(s)	Infant, Newborn ; Humans ; Interferon-gamma/metabolism ; Th1 Cells/metabolism ; Fetal Blood ; Cytokines/metabolism ; Cell Differentiation ; Leukocyte Common Antigens ; Th2 Cells/metabolism
Chemical Substances	Interferon-gamma (82115-62-6) ; Cytokines ; Leukocyte Common Antigens (EC 3.1.3.48)
Language	English
Publishing date	2023-06-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80124-0
ISSN	1365-2567 ; 0019-2805 ; 0953-4954
ISSN (online)	1365-2567
ISSN	0019-2805 ; 0953-4954
DOI	10.1111/imm.13674
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Article ; Online: RELA governs a network of islet-specific metabolic genes necessary for beta cell function.

Zammit, Nathan W / Wong, Ying Ying / Walters, Stacey N / Warren, Joanna / Barry, Simon C / Grey, Shane T

Diabetologia

2023 Volume 66, Issue 8, Page(s) 1516–1531

Abstract: Aims/hypothesis: NF-κB activation unites metabolic and inflammatory responses in many diseases yet less is known about the role that NF-κB plays in normal metabolism. In this study we investigated how RELA impacts the beta cell transcriptional landscape ...

Abstract	Aims/hypothesis: NF-κB activation unites metabolic and inflammatory responses in many diseases yet less is known about the role that NF-κB plays in normal metabolism. In this study we investigated how RELA impacts the beta cell transcriptional landscape and provides network control over glucoregulation. Methods: We generated novel mouse lines harbouring beta cell-specific deletion of either the Rela gene, encoding the canonical NF-κB transcription factor p65 (βp65KO mice), or the Ikbkg gene, encoding the NF-κB essential modulator NEMO (βNEMOKO mice), as well as βA20Tg mice that carry beta cell-specific and forced transgenic expression of the NF-κB-negative regulator gene Tnfaip3, which encodes the A20 protein. Mouse studies were complemented by bioinformatics analysis of human islet chromatin accessibility (assay for transposase-accessible chromatin with sequencing [ATAC-seq]), promoter capture Hi-C (pcHi-C) and p65 binding (chromatin immunoprecipitation-sequencing [ChIP-seq]) data to investigate genome-wide control of the human beta cell metabolic programme. Results: Rela deficiency resulted in complete loss of stimulus-dependent inflammatory gene upregulation, consistent with its known role in governing inflammation. However, Rela deletion also rendered mice glucose intolerant because of functional loss of insulin secretion. Glucose intolerance was intrinsic to beta cells as βp65KO islets failed to secrete insulin ex vivo in response to a glucose challenge and were unable to restore metabolic control when transplanted into secondary chemical-induced hyperglycaemic recipients. Maintenance of glucose tolerance required Rela but was independent of classical NF-κB inflammatory cascades, as blocking NF-κB signalling in vivo by beta cell knockout of Ikbkg (NEMO), or beta cell overexpression of Tnfaip3 (A20), did not cause severe glucose intolerance. Thus, basal p65 activity has an essential and islet-intrinsic role in maintaining normal glucose homeostasis. Genome-wide bioinformatic mapping revealed the presence of p65 binding sites in the promoter regions of specific metabolic genes and in the majority of islet enhancer hubs (~70% of ~1300 hubs), which are responsible for shaping beta cell type-specific gene expression programmes. Indeed, the islet-specific metabolic genes Slc2a2, Capn9 and Pfkm identified within the large network of islet enhancer hub genes showed dysregulated expression in βp65KO islets. Conclusions/interpretation: These data demonstrate an unappreciated role for RELA as a regulator of islet-specific transcriptional programmes necessary for the maintenance of healthy glucose metabolism. These findings have clinical implications for the use of anti-inflammatories, which influence NF-κB activation and are associated with diabetes.
MeSH term(s)	Animals ; Humans ; Mice ; Chromatin ; Glucose ; Glucose Intolerance ; NF-kappa B/metabolism ; Transcription Factor RelA/genetics ; Transcription Factor RelA/metabolism
Chemical Substances	Chromatin ; Glucose (IY9XDZ35W2) ; NF-kappa B ; RELA protein, human ; Transcription Factor RelA ; Rela protein, mouse
Language	English
Publishing date	2023-06-14
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1694-9
ISSN	1432-0428 ; 0012-186X
ISSN (online)	1432-0428
ISSN	0012-186X
DOI	10.1007/s00125-023-05931-6
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Article ; Online: A disrupted FOXP3 transcriptional signature underpins systemic regulatory T cell insufficiency in early pregnancy failure.

Moldenhauer, Lachlan M / Foyle, Kerrie L / Wilson, Jasmine J / Wong, Ying Y / Sharkey, David J / Green, Ella S / Barry, Simon C / Hull, M Louise / Robertson, Sarah A

iScience

2024 Volume 27, Issue 2, Page(s) 108994

Abstract: Regulatory T (Treg) cell defects are implicated in disorders of embryo implantation and placental development, but the origins of Treg cell dysfunction are unknown. Here, we comprehensively analyzed the phenotypes and transcriptional profile of ... ...

Abstract	Regulatory T (Treg) cell defects are implicated in disorders of embryo implantation and placental development, but the origins of Treg cell dysfunction are unknown. Here, we comprehensively analyzed the phenotypes and transcriptional profile of peripheral blood Treg cells in individuals with early pregnancy failure (EPF). Compared to fertile subjects, EPF subjects had 32% fewer total Treg cells and 54% fewer CD45RA
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2024.108994
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Article: Injectable Diels–Alder cycloaddition hydrogels with tuneable gelation, stiffness and degradation for the sustained release of T-lymphocytes

Yan, Jie / Gundsambuu, Batjargal / Krasowska, Marta / Platts, Kirsten / Facal Marina, Paula / Gerber, Cobus / Barry, Simon C. / Blencowe, Anton

Journal of materials chemistry B. 2022 May 4, v. 10, no. 17

2022

Abstract: Engineered T-cell therapies have proven highly efficacious for the treatment of haematological cancers, but translation of this success to solid tumours has been limited, in part, due to difficulties in maintaining high doses at specific target sites. ... ...

Abstract	Engineered T-cell therapies have proven highly efficacious for the treatment of haematological cancers, but translation of this success to solid tumours has been limited, in part, due to difficulties in maintaining high doses at specific target sites. Hydrogel delivery systems that provide a sustained release of T-cells at the target site are emerging as a promising strategy. Therefore, in this study we aimed to develop an injectable hydrogel that gels in situ via efficient Diels–Alder cycloaddition (DAC) chemistry and provides a sustained release of T-cells through gradual hydrolysis of the hydrogel matrix. Hydrogels were prepared via the DAC between fulvene and maleimide functionalised poly(ethylene glycol) (PEG) derivatives. By adjusting the concentration and molecular weight of the functionalised PEGs in the hydrogel formulation the in vitro gelation time (Tgₑₗ), initial Young's modulus (E) and degradation time (Td) could be tailored from 15–150 min, 5–179 kPa and 7–114 h, respectively. Prior to gelation, the formulations could be readily injected through narrow gauge (26 G) needles with the working time correlating closely with the Tgₑₗ. A 5 wt% hydrogel formation with conjugated cyclic RGD motif was found to be optimal for the encapsulation and release of CD3⁺ T-cells with a near linear release profile and >70% cell viability over the first 4 d and release continuing out to 7 d. With their tuneable Tgₑₗ, Td and stiffness, the DAC hydrogels provide the opportunity to control the release period and profile of encapsulated cells.
Keywords	T-lymphocytes ; cell viability ; cycloaddition reactions ; encapsulation ; gelation ; hydrogels ; hydrolysis ; modulus of elasticity ; molecular weight
Language	English
Dates of publication	2022-0504
Size	p. 3329-3343.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	2702241-9
ISSN	2050-7518 ; 2050-750X
ISSN (online)	2050-7518
ISSN	2050-750X
DOI	10.1039/d2tb00274d
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Article: Epithelial Ovarian Cancer and the Immune System: Biology, Interactions, Challenges and Potential Advances for Immunotherapy.

Macpherson, Anne M / Barry, Simon C / Ricciardelli, Carmela / Oehler, Martin K

Journal of clinical medicine

2020 Volume 9, Issue 9

Abstract: Recent advances in the understanding of immune function and the interactions with tumour cells have led to the development of various cancer immunotherapies and strategies for specific cancer types. However, despite some stunning successes with some ... ...

Abstract	Recent advances in the understanding of immune function and the interactions with tumour cells have led to the development of various cancer immunotherapies and strategies for specific cancer types. However, despite some stunning successes with some malignancies such as melanomas and lung cancer, most patients receive little or no benefit from immunotherapy, which has been attributed to the tumour microenvironment and immune evasion. Although the US Food and Drug Administration have approved immunotherapies for some cancers, to date, only the anti-angiogenic antibody bevacizumab is approved for the treatment of epithelial ovarian cancer. Immunotherapeutic strategies for ovarian cancer are still under development and being tested in numerous clinical trials. A detailed understanding of the interactions between cancer and the immune system is vital for optimisation of immunotherapies either alone or when combined with chemotherapy and other therapies. This article, in two main parts, provides an overview of: (1) components of the normal immune system and current knowledge regarding tumour immunology, biology and their interactions; (2) strategies, and targets, together with challenges and potential innovative approaches for cancer immunotherapy, with attention given to epithelial ovarian cancer.
Language	English
Publishing date	2020-09-14
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm9092967
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Article ; Online: Injectable Diels-Alder cycloaddition hydrogels with tuneable gelation, stiffness and degradation for the sustained release of T-lymphocytes.

Yan, Jie / Gundsambuu, Batjargal / Krasowska, Marta / Platts, Kirsten / Facal Marina, Paula / Gerber, Cobus / Barry, Simon C / Blencowe, Anton

Journal of materials chemistry. B

2022 Volume 10, Issue 17, Page(s) 3329–3343

Abstract	Engineered T-cell therapies have proven highly efficacious for the treatment of haematological cancers, but translation of this success to solid tumours has been limited, in part, due to difficulties in maintaining high doses at specific target sites. Hydrogel delivery systems that provide a sustained release of T-cells at the target site are emerging as a promising strategy. Therefore, in this study we aimed to develop an injectable hydrogel that gels
MeSH term(s)	Cycloaddition Reaction ; Delayed-Action Preparations/chemistry ; Hydrogels/chemistry ; Polyethylene Glycols/chemistry ; T-Lymphocytes
Chemical Substances	Delayed-Action Preparations ; Hydrogels ; Polyethylene Glycols (3WJQ0SDW1A)
Language	English
Publishing date	2022-05-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2702241-9
ISSN	2050-7518 ; 2050-750X
ISSN (online)	2050-7518
ISSN	2050-750X
DOI	10.1039/d2tb00274d
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