Biology subjects

Crosby, M.

Publications and source records attributed to Crosby, M..

5 recordsLinked to original sources

bioRxiv2025

An innovative approach in identifying a network of priority wetland sites in the East Asian-Australasian Flyway for a new sustainable management investment programme

The East Asian-Australasian Flyway (EAAF) is widely recognised to be the most threatened of the eight flyways in the world, with wetlands rapidly lost due to land cover change, unsustainable use, and the wider impacts of climate change. The recently established Regional Flyway Initiative aims to bring a network of priority wetlands in the EAAF under improved protection, management, and restoration in 10 Asian countries, while mobilising resources for sustainable agriculture, aquaculture, ecotourism, and other livelihoods for local communities. A major step in the development of this initiative is the identification of priority wetland sites through the application of international criteria, based on modern waterbird count data collated from wetland sites across Asia. Through existing analyses and stakeholder consultations, we short-listed 400 internationally important wetlands as candidate sites for further assessment. Count data of EAAF waterbird species was then assessed against international criteria aligned with the Convention on Wetlands (Ramsar Convention), the EAAF Partnerships Flyway Site Network and Important Bird Areas and Biodiversity for each site to iteratively identify a subset of priority sites, drawing on newly available species population thresholds. Each site was scored and ranked using a metric (Prioritisation Criterion1) calculated from the proportions of every occurring EAAF species against published population thresholds. We identified a total of 147 wetland sites of high conservation priority across the 10 countries, thereby representing the full suite of wetland landscapes and habitats in Asia, both freshwater and coastal, all critical sites for the conservation of migratory waterbirds in the flyway. At least 34 threatened species, including significant proportions of their global populations are represented in this network of 147 sites. To ensure that conservation opportunities are maximised for species and ecosystem services, there is a need to ensure that selected sites and landscapes are reconciled with the conservation and development priorities of each country, and to evaluate priority sites for their ecosystem services.

ecology↗

bioRxiv2024

MYT1L deficiency impairs excitatory neuron trajectory during cortical development

Mutations that reduce the function of MYT1L, a neuron-specific transcription factor, are associated with a syndromic neurodevelopmental disorder. Furthermore, MYT1L is routinely used as a proneural factor in fibroblast-to-neuron transdifferentiation. MYT1L has been hypothesized to play a role in the trajectory of neuronal specification and subtype specific maturation, but this hypothesis has not been directly tested, nor is it clear which neuron types are most impacted by MYT1L loss. In this study, we profiled 313,335 nuclei from the forebrains of wild-type and MYT1L-deficient mice at two developmental stages: E14 at the peak of neurogenesis and P21, when neurogenesis is complete, to examine the role of MYT1L levels in the trajectory of neuronal development. We found that MYT1L deficiency significantly disrupted the relative proportion of cortical excitatory neurons at E14 and P21. Significant changes in gene expression were largely concentrated in excitatory neurons, suggesting that transcriptional effects of MYT1L deficiency are largely due to disruption of neuronal maturation programs. Most effects on gene expression were cell autonomous and persistent through development. In addition, while MYT1L can both activate and repress gene expression, the repressive effects were most sensitive to haploinsufficiency, and thus more likely mediate MYT1L syndrome. These findings illuminate the intricate role of MYT1L in orchestrating gene expression dynamics during neuronal development, providing insights into the molecular underpinnings of MYT1L syndrome.

neuroscience↗

bioRxiv2023

Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues

Calling Cards is a platform technology to record a cumulative history of transient protein-DNA interactions in the genome of genetically targeted cell types. The record of these interactions is recovered by next generation sequencing. Compared to other genomic assays, whose readout provides a snapshot at the time of harvest, Calling Cards enables correlation of historical molecular states to eventual outcomes or phenotypes. To achieve this, Calling Cards uses the piggyBac transposase to insert self-reporting transposon (SRT) "Calling Cards" into the genome, leaving permanent marks at interaction sites. Calling Cards can be deployed in a variety of in vitro and in vivo biological systems to study gene regulatory networks involved in development, aging, and disease. Out of the box, it assesses enhancer usage but can be adapted to profile specific transcription factor binding with custom transcription factor (TF)-piggyBac fusion proteins. The Calling Cards workflow has five main stages: delivery of Calling Card reagents, sample preparation, library preparation, sequencing, and data analysis. Here, we first present a comprehensive guide for experimental design, reagent selection, and optional customization of the platform to study additional TFs. Then, we provide an updated protocol for the five steps, using reagents that improve throughput and decrease costs, including an overview of a newly deployed computational pipeline. This protocol is designed for users with basic molecular biology experience to process samples into sequencing libraries in 1-2 days. Familiarity with bioinformatic analysis and command line tools is required to set up the pipeline in a high-performance computing environment and to conduct downstream analyses. Basic Protocol 1: Preparation and delivery of Calling Cards reagents Basic Protocol 2: Sample preparation Basic Protocol 3: Sequencing library preparation Basic Protocol 4: Library pooling and sequencing Basic Protocol 5: Data analysis

genomics↗

bioRxiv2023

Spatio-temporal transcriptomic analysis reveals distinct nephrotoxicity, DNA damage and regeneration response after cisplatin

Nephrotoxicity caused by drug or chemical exposure involves different mechanisms and nephron segments as well as a complex temporal integration of injury and repair responses. Distinct cellular transcriptional programs regulate the time-dependent tissue injury and regeneration responses. Whole kidney transcriptome analysis cannot dissect the complex the nephron segment spatio- temporal injury and regeneration responses. Here, we used laser capture microdissection of formalin- fixed paraffin embedded sections followed by whole genome targeted RNA-sequencing-TempO-Seq and co-expression gene-network (module) analysis to determine the spatial-temporal responses in rat kidney glomeruli (GM), cortical proximal tubules (CPT) and outer-medulla proximal tubules (OMPT) comparison with whole kidney, after a single dose of the nephrotoxicant cisplatin. We demonstrate that cisplatin induced early onset of DNA damage in both CPT and OMPT, but not GM. Sustained DNA damage response was strongest in OMPT coinciding with OMPT specific inflammatory signaling, actin cytoskeletal remodeling and increased glycolytic metabolism coincident with suppression of mitochondrial activity. Later responses reflected regeneration-related cell cycle pathway activation and ribosomal biogenesis in the injured OMPT regions. Activation of modules containing kidney injury biomarkers was strongest in the OMPT, with OMPT Clu expression best correlating with urinary clusterin biomarker measurements compared the correlation of Kim1. Our findings also showed that whole kidney responses were less sensitive than OMPT. In conclusion, our LCM-TempO-Seq method reveals a detailed spatial mechanistic understanding of renal injury/regeneration after nephrotoxicant exposure and identifies the most representative mechanism-based nephron segment specific renal injury biomarkers.

pharmacology and toxicology↗

bioRxiv2019

SEMA4C is a novel target to limit osteosarcoma growth, progression, and metastasis

Semaphorins, specifically type IV, are important regulators of axonal guidance and have been increasingly implicated in poor prognoses in a number of different solid cancers. In conjunction with their cognate PLXNB family receptors, type IV members have been increasingly shown to mediate oncogenic functions necessary for tumor development and malignant spread. In this study, we investigated the role of semaphorin 4C (SEMA4C) in osteosarcoma growth, progression, and metastasis. We investigated the expression and localization of SEMA4C in primary osteosarcoma patient tissues and its tumorigenic functions in these malignancies. We demonstrate that overexpression of SEMA4C promotes properties of cellular transformation, while RNAi knockdown of SEMA4C promotes adhesion and reduces cellular proliferation, colony formation, migration, wound healing, tumor growth, and lung metastasis. These phenotypic changes were accompanied by reductions in activated AKT signaling, G1 cell cycle delay, and decreases in expression of mesenchymal marker genes SNAI1, SNAI2, and TWIST1. Lastly, monoclonal antibody blockade of SEMA4C in vitro mirrored that of the genetic studies. Together, our results indicate a multi-dimensional oncogenic role for SEMA4C in metastatic osteosarcoma and more importantly that SEMA4C has actionable clinical potential.

cancer biology↗