Biology subjects

Ferguson, S.

Publications and source records attributed to Ferguson, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Lysosomal TBK1 Responds to Amino Acid Availability to Relieve Rab7-Dependent mTORC1 Inhibition

Lysosomes play a pivotal role in coordinating macromolecule degradation and regulating cell growth and metabolism. Despite substantial progress in identifying lysosomal signaling proteins, understanding the pathways that synchronize lysosome functions with changing cellular demands remains incomplete. This study uncovers a role for TANK-binding kinase 1 (TBK1), well known for its role in innate immunity and organelle quality control, in modulating lysosomal responsiveness to nutrients. Specifically, we identify a pool of TBK1 that is recruited to lysosomes in response to elevated amino acid levels. At lysosomes, this TBK1 phosphorylates Rab7 on serine 72. This is critical for alleviating Rab7-mediated inhibition of amino acid-dependent mTORC1 activation. Furthermore, a TBK1 mutant (E696K) associated with amyotrophic lateral sclerosis and frontotemporal dementia constitutively accumulates at lysosomes, resulting in elevated Rab7 phosphorylation and increased mTORC1 activation. This data establishes the lysosome as a site of amino acid regulated TBK1 signaling that is crucial for efficient mTORC1 activation. This lysosomal pool of TBK1 has broader implications for lysosome homeostasis, and its dysregulation could contribute to the pathogenesis of ALS-FTD.

cell biology↗

bioRxiv2023

Climate change introduces threatened killer whale populations and conservation challenges to the Arctic

The Arctic is the fastest-warming region on the planet, and sea ice loss has opened new habitat for sub-Arctic species such as the killer whale (Orcinus orca). As apex predators, killer whales can cause significant ecosystem-scale changes, however, we know very little about killer whales in the Arctic. Setting conservation priorities for killer whales and their Arctic prey species requires knowledge of their evolutionary history and demography. We found that there are two highly genetically distinct, non-interbreeding populations of killer whales using the eastern Canadian Arctic--one population is newly identified as globally distinct. The effective sizes of both populations recently declined, and both are vulnerable to inbreeding and reduced adaptive potential. Furthermore, we present evidence that human-caused mortalities, particularly ongoing harvest, pose an ongoing threat to these populations. The certainty of substantial environmental change in the Arctic complicates conservation and management significantly. Killer whales bring top-down pressure to Arctic food webs, however, they also merit conservation concern. The opening of the Arctic to killer whales exemplifies the magnitude of complex decisions surrounding local peoples, wildlife conservation, and resource management as the effects of climate change are realized.

genomics↗

bioRxiv2023

A STING-CASM-GABARAP Pathway Activates LRRK2 at Lysosomes

Mutations that increase LRRK2 kinase activity have been linked to Parkinsons disease and Crohns disease. LRRK2 is also activated by lysosome damage. However, the endogenous cellular mechanisms that control LRRK2 kinase activity are not well understood. In this study, we identify signaling through Stimulator of Interferon Genes (STING) as an activator of LRRK2 via the Conjugation of ATG8 to Single Membranes (CASM) pathway. We furthermore establish that multiple chemical stimuli that perturb lysosomal homeostasis also converge on CASM to activate LRRK2. Although CASM results in the lipidation of multiple ATG8 protein family members, we establish that LRRK2 lysosome recruitment and kinase activation is highly dependent on interactions with the GABARAP member of this family. Collectively these results define a pathway that integrates multiple stimuli at lysosomes to control the kinase activity of LRRK2. Aberrant activation of LRRK2 via this pathway may be of relevance in both Parkinsons and Crohns diseases.

cell biology↗

bioRxiv2023

Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence.

Structural variants (SVs) play a significant role in speciation and adaptation in many species, yet few studies have explored the prevalence and impact of different categories of SVs. We conducted a comparative analysis of long-read assembled reference genomes of closely related Eucalyptus species to identify candidate SVs potentially influencing speciation and adaptation. Interspecies SVs can be either fixed differences, or polymorphic in one or both species. To describe SV patterns, we employed short-read whole-genome sequencing on over 600 individuals of E. melliodora and E. sideroxylon, along with recent high quality genome assemblies. We aligned reads and genotyped interspecies SVs predicted between species reference genomes. Our results revealed that 49,756 of 58,025 and 39,536 of 47,064 interspecies SVs could be typed with short reads, in E. melliodora and E. sideroxylon respectively. Focusing on inversions and translocations, symmetric SVs which are readily genotyped within both populations, 24 were found to be structural divergences, 2,623 structural polymorphisms, and 928 shared structural polymorphisms. We assessed the functional significance of fixed interspecies SVs by examining differences in estimated recombination rates and genetic differentiation between species, revealing a complex history of natural selection. Shared structural polymorphisms displayed enrichment of potentially adaptive genes. Understanding how different classes of genetic mutations contribute to genetic diversity and reproductive barriers is essential for understanding how organisms enhance fitness, adapt to changing environments, and diversify. Our findings reveal the prevalence of interspecies SVs and elucidate their role in genetic differentiation, adaptive evolution, and species divergence within and between populations.

genomics↗

bioRxiv2023

Stabilisation of soil organic matter with rock dust partially counteracted by plants

Soil application of Ca- and Mg-rich silicates can capture and store atmospheric carbon dioxide as inorganic carbon but could also have the potential to stabilise soil organic matter (SOM). Synergies between these two processes have not been investigated. Here, we apply finely ground silicate rock mining residues (basalt and granite blend) to a loamy sand in a pot trial at a rate of 4% (equivalent to 50 t ha-1) and investigate the effects of a wheat plant and two watering regimes on soil carbon sequestration. Rock dust addition increased soil pH, electric conductivity and soil-exchangeable Ca and Mg contents, as expected for weathering, but decreased exchangeable levels of micronutrients Mn and Zn, likely related to soil pH. Importantly, it increased mineral-associated organic matter by 22% due to the supply of secondary minerals and associated sites for SOM sorption. Additionally, in the non-planted treatments, rock supply of Ca and Mg increased soil microaggregation that subsequently stabilised labile particulate organic matter as organic matter occluded in aggregates by 46%. Plants, however, reduced soil exchangeable Mg and Ca contents and hence counteracted the silicate rock effect on microaggregates and carbon within. We attribute this cation loss to plant exudates released to solubilise micronutrients and hence neutralise plant deficiencies. The effect of enhanced silicate rock weathering on SOM stabilisation could substantially boost its carbon sequestration potential when pH and micronutrient effects are considered.

plant biology↗

bioRxiv2023

Plant genome evolution in the genus Eucalyptus driven by structural rearrangements that promote sequence divergence

Genomes have a highly organised architecture (non-random organisation of functional and non-functional genetic elements within chromosomes) that is essential for many biological functions, particularly, gene expression and reproduction. Despite the need to conserve genome architecture, a surprisingly high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. However, within plant genomes, the processes of genome architecture divergence are not well described. Here we use long-read sequencing and de novo assembly of 33 phylogenetically diverse, wild and naturally evolving Eucalyptus species, covering 1-50 million years of diverging genome evolution to measure genome architectural conservation and describe architectural divergence. The investigation of these genomes revealed that following lineage divergence genome architecture is highly fragmented by rearrangements. As genomes continue to diverge, the accumulation of mutations and subsequent divergence beyond recognition of rearrangements becomes the primary driver of genome divergence. The loss of syntenic regions also contribute to genome divergence, but at a slower pace than rearrangements. We hypothesise that duplications and translocations are potentially the greatest contributors to Eucalyptus genome divergence.

genomics↗

bioRxiv2022

LRRK2 Suppresses Lysosome Degradative Activity in Macrophages and Microglia via Transcription Factor E3 Inhibition

Cells maintain optimal levels of lysosome degradative activity to protect against pathogens, clear waste and generate nutrients. Here we show that LRRK2, a protein that is tightly linked to Parkinsons disease, negatively regulates lysosome degradative activity in macrophages and microglia via a transcriptional mechanism. Depletion of LRRK2 and inhibition of LRRK2 kinase activity enhanced lysosomal proteolytic activity and increased the expression of multiple lysosomal hydrolases. Conversely, the kinase hyperactive LRRK2 G2019S Parkinsons disease mutant suppressed lysosomal degradative activity and gene expression. We identified MiT-TFE transcription factors (TFE3, TFEB and MITF) as mediators of LRRK2-dependent control of lysosomal gene expression. LRRK2 negatively regulated the abundance and nuclear localization of these transcription factors and their depletion prevented LRRK2-dependent changes in lysosome protein levels. These discoveries define a role for LRRK2 in controlling lysosome degradative activity and support a model wherein LRRK2 hyperactivity may increase Parkinsons disease risk by suppressing lysosome degradative activity. Significance StatementThis study defines a homeostatic mechanism that allows macrophages and microglia to match the degradative activity of their lysosomes to ongoing changes in cellular demand. It shows that the leucine rich repeat kinase 2 (LRRK2) protein suppresses lysosome degradative activity by inhibiting the expression and nuclear localization of the MiT-TFE family of transcription factors that control the expression of multiple genes that encode lysosome proteins. It further demonstrates that a Parkinsons disease mutation that hyperactivates LRRK2 kinase activity limits the degradative activity of lysosomes more strongly. These findings support a model wherein LRRK2 protects cells from excessive lysosome degradative activity and suggest that overactivation of this pathway may increase Parkinsons disease risk by limiting the degradative activity of lysosomes.

cell biology↗

bioRxiv2022

Linking movement and dive data to prey distribution models: new insights in foraging behaviour and potential pitfalls of movement analyses

BackgroundAnimal movement data are regularly used to infer foraging behaviour and relationships to environmental characteristics, often to help identify critical habitat. To characterize foraging, movement models make a set of assumptions rooted in theory, for example, time spent foraging in an area increases with higher prey density. MethodsWe assessed the validity of these assumptions by associating horizontal movement and diving of satellite-telemetered ringed seals (Pusa hispida) - an opportunistic predator - in Hudson Bay, Canada, to modelled prey data and environmental proxies. ResultsModelled prey biomass data performed better than their environmental proxies (e.g., sea surface temperature) for explaining seal movement, however movement was not related to foraging effort. Counter to theory, seals appeared to forage more in areas with relatively lower prey diversity and biomass, potentially due to reduced foraging efficiency in those areas. ConclusionsOur study highlights the need to validate movement analyses with prey data to effectively estimate the relationship between prey availability and foraging behaviour.

ecology↗

bioRxiv2022

Multiplexed analysis of a single EV (MASEV) reveals unique biomarker composition with diagnostic impact

Exosomes and extracellular vesicles (EV) are increasingly being explored as circulating biomarkers, but their heterogenous composition will likely mandate the development of single EV technologies. Highly multiplexed analyses of single EVs have been challenging to implement beyond a few colors during spectral sensing. We use a multiplexed analysis of the single EV technique (MASEV) to interrogate thousands of individual EVs during 5 cycles of multi-channel fluorescence staining for 15 EV biomarkers. Contrary to the common belief, we show that i) several "ubiquitous" markers are much less common than believed; ii) that multiple biomarkers concur in single vesicles but only in small fractions, iii) that affinity purification can lead to loss of rare EV subtypes, and iv) that deep profiling allows detailed analysis of EV potentially improving the diagnostic content. These findings establish the potential of MASEV for uncovering fundamental EV biology and heterogeneity and increasing diagnostic specificity. O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/496607v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@5ec056org.highwire.dtl.DTLVardef@a589c9org.highwire.dtl.DTLVardef@1f92900org.highwire.dtl.DTLVardef@f2ddc2_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO Multiplexed analysis of single EV (MASEV) allows robust protein profiling at the single EV level, a prerequisite for early cancer detection or organ of origin determination. C_FIG

cancer biology↗

bioRxiv2022

Intracellular Calcium links Milk Stasis to Lysosome Dependent Cell Death during Mammary Gland Involution

Involution of the mammary gland after lactation is a dramatic example of coordinated cell death. Weaning causes distension of the alveolar structures due to the accumulation of milk, which, in turn, activates STAT3 and initiates a caspase- independent but lysosome-dependent cell death (LDCD) pathway. Although the importance of STAT3 and LDCD in early mammary involution is well established, it has not been entirely clear how milk stasis activates STAT3. In this report, we demonstrate that protein levels of the PMCA2 calcium pump are significantly downregulated within 2- 4 hours of experimental milk stasis. Reductions in PMCA2 expression correlate with an increase in cytoplasmic calcium in vivo as measured by multiphoton intravital imaging of GCaMP6f fluorescence. These events occur concomitant with the appearance of nuclear pSTAT3 expression but prior to significant activation of LDCD or its previously implicated mediators such as LIF, IL6 and TGF{beta}3, all of which appear to be upregulated by increased intracellular calcium. We also observed that milk stasis, loss of PMCA2 expression and increased intracellular calcium levels activate TFEB, an important regulator of lysosome biogenesis. This is the result of increased TGF{beta} signaling and inhibition of cell cycle progression. Finally, we demonstrate that increased intracellular calcium activates STAT3 by inducing degradation of its negative regulator, SOCS3, a process which also appears to be mediated by TGF{beta} signaling. In summary, these data suggest that intracellular calcium serves as an important proximal biochemical signal linking milk stasis to STAT3 activation, increased lysosomal biogenesis, and lysosome- mediated cell death.

cell biology↗

bioRxiv2022

Scaled-expansion of the membrane associated cytoskeleton requires conserved kinesin adaptors

A periodic lattice of actin rings and spectrin tetramers scaffolds the axonal membrane. How spectrin is delivered to this structure to scale its size to that of the growing axon is unknown. We found that endogenous spectrin, visualized with singe axon resolution in vivo, is delivered to hotspots in the lattice that support its expansion at rates set by axon stretch-growth. Unlike other cytoskeletal proteins, whose apparent slow movement consists of intermittent bouts of fast movements, spectrin moves slowly and processively. We identified a pair of coiled coil proteins that mediate this slow movement and the expansion of the lattice by linking spectrin to kinesin-1. Thus, processive slow transport and local lattice incorporation support scaled cytoskeletal expansion during axon stretch-growth. One-Sentence SummaryKinesin adaptors control spectrin transport and expansion of the membrane periodic skeleton.

cell biology↗

bioRxiv2021

Soil organic carbon fractionation and metagenomics pipeline to link carbon content and stability with microbial composition - First results investigating fungal endophytes

Society needs to capture gigatons of carbon dioxide from the atmosphere annually and then store it long-term to limit and ultimately reverse the effects of climate change. Bringing lost carbon back into agricultural soils should be a priority as it brings the added benefit of improving soil properties. Linking soil organic carbon (SOC) fractions of different stability with soil microbial composition can help understand and subsequently manage SOC storage. Here we develop a pipeline for evaluating the effects of microbial management on SOC content using rapid and low-cost SOC fractionation and metagenomics approaches. We tested the methods in a wheat pot trial inoculated with 17 individual endophytic fungal isolates. Two fungi increased total SOC in the area under the plant stem by ~15%. The fractionation assay showed that the medium stability soil aggregate carbon fraction (AggC) was increased by one of these fungi (+21%) and the chemically recalcitrant proportion (bleach oxidation) of AggC by the other (+35%). Both fungi increased mineral-associated organic carbon (MAOC), the long-term SOC storage, by ~10%. We used rapid, portable, low-cost, whole metagenome long read sequencing to detect a shift in the microbial composition for one of the fungi-inoculated treatments. This treatment showed a more diverse microbial community and a higher quantity of DNA in soil. The results emphasise the link between composition and abundance of soil microorganisms with soil carbon formation. Our dual carbon fractional and metagenomic analysis pipeline can be used to further test the effects of microbial management and ultimately to model the soil factors that influence SOC storage, such as nutrient and water availability, starting SOC content, soil texture and aggregation.

genomics↗

bioRxiv2021

Cytotoxicity mechanisms and composition of the glyphosate formulated herbicide RangerPro

Understanding the nature of co-formulants and toxic effects of major glyphosate-based herbicide (GBH) formulations is considered a research priority. Indeed, the toxicity of the co-formulants present in GBHs have been widely discussed and the European Union recently banned the co-formulant polyoxyethylene tallow amine (POEA). We provide a foundation for the development of new environmental epidemiological studies by reporting the presence of the most commonly used POEA, known as POE-15 tallow amine, in the widely used US GBH RangerPro. In order to understand if POE-15 tallow amine is present in RangerPro at a concentration at which it can exert toxic effects, we also tested the cytotoxicity of this GBH compared to glyphosate and POE-15 tallow amine in the human epithelial cell line Caco-2, a representative of the human intestinal epithelium, and the first to be exposed from the human diet to glyphosate herbicides. The lethal concentration 50 for each of these substances was 125 g/ml, 17200 g/ml, and 5.7 g/ml, for RangerPro, glyphosate and POE-15, respectively. The Caco-2 cell cytotoxicity assay indicated that RangerPro is more cytotoxic than glyphosate, suggesting that its toxicity can be due to the presence of the POE-15 surfactant. RangerPro and POE-15 tallow amine but not glyphosate exerted cell necrotic effects, but did not induce oxidative stress. We show that RangerPro contains POE-15 tallow amine at a concentration at which it could exert toxic effects, which offers a starting point for conducting surveys of co-formulant exposure in human populations.

pharmacology and toxicology↗

bioRxiv2021

Genomic constraints to drought adaptation

Global shifts in climate and precipitation patterns are altering the diversity and structure of forests. The ability for species to adapt is especially difficult for long lived foundation species with unknown genetic and trait diversity. We harnessed genomic, physiological, and climate data to determine adaptation constraints. We used denovo assembly and 6.5 million genomic variants with drought related traits from 432 individuals sourced from across the complete range of the foundation tree species Corymbia calophylla. We found genomic variants determining traits predominantly in gene regulatory regions. The ability for populations to adapt was limited by within population genetic diversity associated with traits, and epistatic interactions within traits and pleiotropic interactions among traits. Nevertheless, we could accurately predict adaptive traits using genomic and climate data to guide reforestation. Our study indicated that some populations may contain variation sufficient for the species to adapt to the effects of drought, while other populations will need increased variability from those sources.

evolutionary biology↗

bioRxiv2021

Assessing spatial segregation of beluga whales (Delphinapterus leucas) in Western Hudson Bay estuaries

Segregation of older adult males from females and immature males is known to occur in some beluga whale populations, but it is unclear if adults accompanied by calves segregate in Hudson Bay, where the largest summering population is found. Using imagery from a photographic aerial survey conducted in August 2015, we considered a number of environmental variables that might explain distribution by age class of beluga near two of three main estuaries (Churchill and Seal River) used by Western Hudson Bay belugas in the summer season. Belugas were identified and classified by age manually using an identification decision tree and GPS coordinates were plotted in ArcGIS. Distribution by age class was examined in relation to distance to coastal habitat and bathymetry to test the predation risk hypothesis, sea surface temperature (thermal advantage hypothesis), and extent of river plume (forge-selection hypothesis). Habitat characteristics and the proportion of age classes in both estuaries were similar between age class groups (with and without calves) indicating no segregation and suggesting the environmental data assessed were not driving patterns of distribution and density of age classes at the spatial and temporal scale being investigated. Results provide a greater understanding of spatial patterns of beluga whale habitat use in western Hudson Bay and information useful in conservation and management advice.

ecology↗

bioRxiv2021

Surf4 Promotes Endoplasmic Reticulum Exit of the Lysosomal Prosaposin-Progranulin Complex

Progranulin is a lysosomal protein whose haploinsufficiency causes frontotemporal dementia while homozygous loss of progranulin causes neuronal ceroid lipofuscinosis, a lysosomal storage disease. The sensitivity of cells to progranulin deficiency raises important questions about how cells coordinate intracellular trafficking of progranulin to ensure its efficient delivery to lysosomes. In this study, we discover that progranulin interacts with prosaposin, another lysosomal protein, within the lumen of the endoplasmic reticulum (ER) and that prosaposin is required for the efficient ER exit of progranulin. Mechanistically, we identify an interaction between prosaposin and Surf4, a receptor that promotes loading of lumenal cargos into COPII coated vesicles, and establish that Surf4 is critical for the efficient export of progranulin and prosaposin from the ER. Collectively, this work demonstrates a network of interactions occurring early in the secretory pathway that promote the ER exit and subsequent lysosomal delivery of newly translated progranulin and prosaposin.

cell biology↗

bioRxiv2020

Nutrient signaling pathways regulate amyloid clearance and synaptic loss in Alzheimer's disease

Extra-cellular accumulation of Amyloid-{beta} (A{beta}) plaques is causatively associated with Alzheimers disease (AD). However, mechanisms that mediate the pre-pathological state of amyloid plaque formation remain elusive. Here, using paired RNAi and kinase inhibitor screens, we discovered that AKT-mediated insulin/nutrient signaling suppresses lysosomal clearance of A{beta} and promotes amyloid formation. This mechanism is cell-autonomous and functions in multiple systems, including iPSC-derived human neurons and in vivo. Nutrient signaling regulates amyloid formation via distinct lysosomal functional mechanisms, while enhanced amino acid signaling promotes amyloid formation by transcriptionally suppressing lysosome biogenesis, and high intracellular cholesterol levels suppress lysosomal clearance of amyloid by increasing the number of non-functional lysosomes. The nutrient signaling pathway, present in both neurons and microglia, regulates lysosomal clearance of amyloid and microglia mediated synapse loss, both in vitro and in vivo. Clinically, older hyperlipidemic patients showed less synapse loss through microglia and performed better in cognitive tests. Thus, our results reveal a bi-partite cellular quality control system regulated by the insulinnutrient signaling that in neurons regulates A{beta} peptide clearance and in microglia regulates synaptic loss, both processes causally associated with AD. Our results also caution against reducing amyloid through such processes as this might also result in synapse loss.

neuroscience↗

bioRxiv2020

Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids

PQLC2, a lysosomal cationic amino acid transporter, also serves as a sensor that responds to scarcity of its substrates by recruiting a protein complex comprised of C9orf72, SMCR8 and WDR41 to the surface of lysosomes. This protein complex controls multiple aspects of lysosome function. Although it is known that this response to changes in cationic amino acid availability depends on an interaction between PQLC2 and WDR41, the underlying mechanism for the regulated interaction is not known. In this study, we establish that the WDR41-PQLC2 interaction is mediated by a short peptide motif in a flexible loop that extends from the WDR41 {beta}-propeller and inserts into a cavity presented by the inward-facing conformation of PQLC2. This data supports a transceptor model wherein conformational changes in PQLC2 related to substrate transport regulate the availability of the WDR41 binding site on PQLC2 and mediate recruitment of the WDR41-SMCR8-C9orf72 complex to the surface of lysosomes.

cell biology↗