Biology subjects

Kurian, D.

Publications and source records attributed to Kurian, D..

10 recordsLinked to original sources

bioRxiv2026

Spermidine enhances metabolic flexibility and attenuates inflammation associated with ageing in farmed Atlantic salmon

Metabolic ageing and associated changes in lipid mobilisation have been most heavily studied in humans and model taxa, yet remain poorly understood in farmed animals, with potentially important uncharacterised implications for health and welfare outcomes in food production systems. Here, we study both processes in domesticated Atlantic salmon (Salmo salar), the worlds most commercially valuable farmed fish, comparing three stages of aquaculture production. Our sampling captures a key life-cycle change where juvenile fish transition from freshwater into seawater (smoltification), followed by the ongoing ageing process during a final period of growth in seawater. Integrating lipidomics and proteomics of visceral adipose and skeletal muscle tissue, we firstly identified a metabolic-ageing profile akin to that observed in humans, which was distinct from lipid-associated remodelling associated with earlier smoltification. This was marked by impaired triglyceride storage, dysfunctional autophagy-lysosomal pathways, inflammation, fibrosis and reduced pathogen clearance pathways in visceral adipose tissue. In skeletal muscle, ageing was accompanied by reduced metabolic flexibility together with triglyceride and fatty acid accumulation, depletion of phospholipids, and a reduction in free fatty acids required for ATP production. We go on to provide experimental in vivo evidence that dietary spermidine supplementation suppresses adipose inflammation and reverses age-associated metabolic flexibility by re-establishing the buffering role of adipose tissue and enhancing fatty acid metabolism in skeletal muscle. Importantly, spermidine appears to reprogram lipid flux to counter metabolic ageing. As farmed Atlantic salmon exhibit key features of metabolic ageing observed in humans that appear linked to its recent domestication history, this species offers a novel model for ageing related studies of vertebrate metabolism.

molecular biology↗

bioRxiv2025

Proteomic characterisation of matrix vesicles from primary osteoblasts indicates a mixed population with both exosomal and ectosomal routes of biogenesis.

Matrix Vesicles are a crucial step in producing a mineralised, healthy skeleton. Released from chondrocytes and osteoblasts, they concentrate calcium and phosphate to establish the deposition of hydroxyapatite around and within the collagen fibrils of the extracellular matrix, becoming embedded in the matrix in the process. In the 55 years since H. Clarke Anderson first described them, blebbing from the surface of chondrocytes, a consensus on their role, contents and their biogenesis, has yet to be reached. This is in part due to the range of cell types from which they are released and the multitude techniques that can be employed to isolate them. In this study, we, for the first time, characterise the proteome of matrix vesicles isolated from primary osteoblasts. By focussing on those vesicles that have become embedded within the matrix, we are able to avoid bias for specific modes of biogenesis and focus only on osteoblast-released vesicles that are associated with the matrix. Moreover, by studying these vesicles over a time course of mineralising activity, we are able to identify changes in the properties of these vesicles, and develop a more accurate picture of which proteins are involved specifically in mineralisation. In particular we identify the presence of markers associated with the ectosomal and exosomal release of matrix vesicles, as well as identifying proteins required for the maintenance and mineralisation of the extracellular matrix. These data portray a heterogeneous population of matrix vesicles, with different roles to play in bone development.

cell biology↗

bioRxiv2025

Characterisation of the Tilapia Lake Virus proteome and identification of an 11th protein, S9-F3

Tilapia Lake Virus (TiLV) is an emerging negative-sense, single-stranded RNA virus that poses a significant threat to global tilapia aquaculture. Of the proteins encoded by its ten genomic segments, the first four, which encode a viral polymerase (segments 1-3) and a nucleoprotein (segment 4) have been characterised. However, the functions of the polypeptides encoded by the remaining segments remain largely unknown. Here, we systematically investigated the expression and subcellular localisation of all ten predicted TiLV-encoded proteins using in vitro translation and expression in mammalian and fish cells as well as mass spectrometry of virus infected cells. These approaches confirmed the synthesis of major polypeptides from each segment and identified an additional 11th protein, S9-F3, translated from an alternative reading frame of segment 9. Microscopy of individually expressed green fluorescent protein (GFP)-tagged constructs revealed that S2 and S10 polypeptides were predominantly nuclear, while S1, S3, S5, S8 and S9-F3 were mostly cytoplasmic with S5 and S6 displaying perinuclear foci. Bioinformatic analysis suggested a potential nuclear export signal in S9-F3 and use of the inhibitor leptomycin B confirmed its CRM1-dependent nuclear export. Evolutionary analyses indicated that both S9 and S9-F3 are under selective pressure, as well as the presence of an S9-F3 homologue in a TiLV-like guppy virus. These findings uncover an alternative translation product and a regulated nuclear export mechanism in TiLV, providing new insights into the molecular biology of this virus and its interaction with host cellular pathways.

microbiology↗

bioRxiv2025

Integrative multi-omics analysis of dietary fibre-induced modulations in the composition and function of chicken caecal microbiota

BackgroundThe sustainability of poultry farming faces significant challenges due to rising feed costs and competition with human food sources. Dietary fibre offers a promising, cost-effective alternative due to its beneficial impact on gut health. We utilised a multi-omics approach to understand the influence of soluble inulin and insoluble cellulose dietary fibres on the composition and function of caecal microbiota in broilers. ResultsHigh inulin significantly altered caecal microbial composition and promoted broader microbial metabolic adaptations, while high cellulose had a minimal impact. ConclusionsThese findings will enhance our understanding of how various fibre types and quantities shape gut microbiota, ultimately leading to improved poultry performance.

microbiology↗

bioRxiv2024

Rapamycin induced autophagy enhances lipid breakdown and ameliorates lipotoxicity in Atlantic salmon cells.

Autophagy is a highly conserved cellular recycling process essential for homeostasis in all eukaryotic cells. Lipid accumulation and its regulation by autophagy are key areas of research for understanding metabolic disorders in human and model mammals. However, the role of autophagy in lipid regulation remains poorly characterised in non-model fish species of importance to food production, which could be important for managing health and welfare in aquaculture. Addressing this knowledge gap, we investigate the role of autophagy in lipid regulation using a macrophage-like cell line (SHK-1) from Atlantic salmon (Salmo salar L.), the worlds most commercially valuable farmed finfish. Multiple lines of experimental evidence reveal that the autophagic pathway responsible for lipid droplet breakdown is conserved in Atlantic salmon cells. We employed global lipidomics and proteomics analyses on SHK-1 cells subjected to lipid overload, followed by treatment with rapamycin to induce autophagy. This revealed that activating autophagy via rapamycin enhances storage of unsaturated triacylglycerols and suppresses key lipogenic proteins, including fatty acid elongase 6 and acid sphingomyelinase. Moreover, fatty acid elongase 6 was identified as cargo for autophagosomes, suggesting a critical role for autophagy in lipid metabolism in fish. Together, this study establishes a novel model of lipotoxicity and advances understanding of lipid autophagy in fish cells, with significant implications for addressing fish health issues in aquaculture.

cell biology↗

bioRxiv2024

Haploinsufficiency of lysosomal enzyme genes in Alzheimers disease

There is growing evidence suggesting that the lysosome or lysosome dysfunction is associated with Alzheimers disease (AD). Pathway analysis of post mortem brain-derived proteomic data from AD patients shows that the lysosomal system is perturbed relative to similarly aged unaffected controls. However, it is unclear if these changes contributed to the pathogenesis or are a response to the disease. Consistent with the hypothesis that lysosome dysfunction contributes to AD pathogenesis, whole genome sequencing data indicate that heterozygous pathogenic mutations and predicted protein-damaging variants in multiple lysosomal enzyme genes are enriched in AD patients compared to matched controls. Heterozygous loss-of-function mutations in the palmitoyl protein thioesterase-1 (PPT1), -L-iduronidase (IDUA), {beta}-glucuronidase (GUSB), N-acetylglucosaminidase (NAGLU), and galactocerebrosidase (GALC) genes have a gene-dosage effect on A{beta}40 levels in brain interstitial fluid in C57BL/6 mice and significantly increase A{beta} plaque formation in the 5xFAD mouse model of AD, thus providing in vivo validation of the human genetic data. A more detailed analysis of PPT1 heterozygosity in 18-month-old mice revealed changes in -, {beta}-, and {gamma}-secretases that favor an amyloidogenic pathway. Proteomic changes in brain tissue from aged PPT1 heterozygous sheep are consistent with both the mouse data and the potential activation of AD pathways. Finally, CNS-directed, AAV-mediated gene therapy significantly decreased A{beta} plaques, increased life span, and improved behavioral performance in 5xFAD/PPT1+/- mice. Collectively, these data strongly suggest that heterozygosity of multiple lysosomal enzyme genes represent risk factors for AD and may identify precise therapeutic targets for a subset of genetically-defined AD patients. Significance StatementLysosomes play a role in the degradation of aggregation-prone proteins such as amyloid {beta} (A{beta}). Homozygous lysosomal enzyme gene defects result in fatal pediatric lysosomal storage diseases and, historically, carriers were considered normal. However, a human genetic analysis identified deleterious heterozygous variants in multiple lysosomal enzyme genes that are enriched in Alzheimers disease (AD) patients. Those findings were validated in vivo by demonstrating that heterozygous loss-of-function (LoF) mutations in five different lysosomal enzyme genes affect A{beta} processing and exacerbate A{beta} plaque formation. CNS-directed gene therapy ameliorated the effects of a heterozygous LoF mutation in one of those genes in a mouse model of AD. These findings provide insights into the role of lysosomes in AD and have important therapeutic implications.

neuroscience↗

bioRxiv2024

ATP-Binding Cassette Family C member 1 constrains metabolic responses to high-fat diet in male mice

Glucocorticoids modulate glucose homeostasis, acting on metabolically active tissues such as liver, skeletal muscle, and adipose tissue. Intra-cellular regulation of glucocorticoid action in adipose tissue impacts metabolic responses to obesity. ATP-Binding Cassette Family C member 1 (ABCC1) is a transmembrane glucocorticoid transporter known to limit the accumulation of exogenously administered corticosterone in adipose tissue. However, the role of ABCC1 in the regulation of endogenous glucocorticoid action and its impact on fuel metabolism has not been studied. Here, we investigate the impact of Abcc1 deficiency on glucocorticoid action and high fat-diet (HFD)-induced obesity. In lean mice, deficiency of Abcc1 increased endogenous corticosterone levels in skeletal muscle and adipose tissue but did not impact insulin sensitivity. In contrast, Abcc1-deficient mice on HFD displayed impaired glucose and insulin tolerance, and fasting hyperinsulinemia, without alterations in tissue corticosterone levels. Proteomics and bulk RNA sequencing in adipose tissue and skeletal muscle revealed that Abcc1 deficiency amplified the transcriptional response to an obesogenic diet in adipose tissue. Moreover, the Abcc1 deficiency impairs key signalling pathways related to glucose metabolism in both skeletal muscle and adipose tissue, in particular those related to OXPHOS machinery and Glut4. Together, our results highlight a role for ABCC1 in regulating glucose homeostasis, demonstrating diet-dependent effects that are not associated with altered tissue glucocorticoid concentrations.

physiology↗

bioRxiv2023

Understanding off-target growth defects introduced to influenza A virus by synonymous recoding

CpG dinucleotides are under-represented in the genomes of most RNA viruses. Synonymously increasing CpG content of a range of RNA viruses reliably causes replication defects due to the recognition of CpG motifs in RNA by cellular Zinc-finger Antiviral Protein (ZAP). Prior to the discovery of ZAP as a CpG sensor, we described an engineered influenza A virus (IAV) enriched for CpGs in segment 5 that displays the expected replication defects. However, we report here that this CpG-high ( CpGH) mutant is not attenuated by ZAP. To understand this, we sought to uncover the alternative attenuation mechanism(s). IAV segment 5 encodes NP, a component of the viral RNA replication complex. Unexpectedly, while CpG enrichment resulted in depleted segment 5 transcript and NP protein abundance, this did not impair viral polymerase activity. A pair of nucleotide changes, introduced as compensatory changes to maintain base frequencies, were instead found to be responsible for the replication defect. These mutations resulted in the encoding of a stretch of eight consecutive adenosines (8A), a phenomenon not seen in natural IAV isolates. Sequencing experiments revealed evidence of viral polymerase slippage at this site, resulting in the production of aberrant peptides and type I interferon induction. When the nucleotides in either of these two positions were restored to wildtype sequence, no viral attenuation was seen, despite the 86 extra CpGs encoded by this virus. Conversely, when these two adenosines were introduced into wildtype virus (thereby introducing the 8A tract), viral attenuation, polymerase slippage, aberrant peptide production and type I interferon induction were apparent. That a single nucleotide change can offset the growth defects in a virus designed to have a formidable barrier to wild-type reversion highlights the importance of understanding the processes underlying viral attenuation. The lessons from this study will inform improved recoding designs in the future.

microbiology↗

bioRxiv2021

Secreted SARS-CoV-2 ORF8 modulates the cytokine expression profile of human macrophages

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still adapting to its new human host. Attention has focussed on the viral spike protein, but substantial variation has been seen in the ORF8 gene. Here, we show that SARS-CoV-2 ORF8 protein undergoes signal peptide-mediated processing through the endoplasmic reticulum and is secreted as a glycosylated, disulphide-linked dimer. The secreted protein from the prototype SARS-CoV-2 virus had no major effect on viability of a variety of cell types, or on IFN or NF-{kappa}B signalling. However, it modulated cytokine expression from primary CSF1-derived human macrophages, most notably by decreasing IL-6 and IL-8 secretion. Furthermore, a sequence polymorphism L84S that appeared early in the pandemic associated with the Clade S lineage of virus, showed a markedly different effect, of increasing IL-6 production. We conclude that ORF8 sequence polymorphisms can potentially affect SARS-CoV-2 virulence and should therefore be monitored in sequencing-based surveillance.

microbiology↗

bioRxiv2018

Pleotropic effects of mutations in the effector domain of influenza A virus NS1 protein

ObjectiveThe multifunctional NS1 protein of influenza A virus has roles in antagonising cellular innate immune responses and promoting viral gene expression. To better understand the interplay between these functions, we tested the effects of NS1 effector domain mutations known to affect homo-dimerisation or interactions with cellular PI3 kinase or Trim25 on NS1 ability to promote nuclear export of viral mRNAs.\n\nResultsThe NS1 dimerisation mutant W187R retained the functions of binding cellular NXF1 as well as stabilising NXF1 interaction with viral segment 7 mRNAs and promoting their nuclear export. Two PI3K-binding mutants, NS1 Y89F and Y89A still bound NXF1 but no longer promoted NXF1 interactions with segment 7 mRNA or its nuclear export. The Trim25-binding mutant NS1 E96A/E97A bound NXF1 and supported NXF1 interactions with segment 7 mRNA but no longer supported mRNA nuclear export. Analysis of WT and mutant NS1 interaction partners identified hsp70 as specifically binding to NS1 E96A/E97A. Whilst these data suggest the possibility of functional links between NS1s effects on intracellular signalling and its role in viral mRNA nuclear export, they also indicate potential pleiotropic effects of the NS1 mutations; in the case of E96A/E97A possibly via disrupted protein folding leading to chaperone recruitment.

microbiology↗