Biology subjects

Barnett, E.

Publications and source records attributed to Barnett, E..

4 recordsLinked to original sources

bioRxiv2023

Comparative Genomics Points to Tandem Duplications of SAD Gene Clusters as Drivers of Increased ω-3 Content in S. hispanica Seeds

O_LIA high-quality chromosome-level reference genome of S. hispanica was assembled and analysed. C_LIO_LIAncestral whole-genome duplication events have not promoted the high -linolenic acid content in S. hispanica seeds C_LIO_LITandem duplication of six stearoyl-ACP desaturase genes is a plausible cause for high {omega}-3 content in chia seeds. C_LI Salvia hispanica L. (chia) is an abundant source of {omega}-3 polyunsaturated fatty acids (PUFAs) that are highly beneficial to human health. The genomic basis for this accrued PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica (321.5 Mbp). The highly contiguous 321.5Mbp genome assembly, which covers all six chromosomes enabled the identification of 32,922 protein coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high -linolenic acid (ALA, {omega}-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein (ACP) desaturase (ShSAD) gene family, is the main driver of the abundance of {omega}-3 PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help leveraging advanced genome editing techniques and will greatly support breeding efforts for improving {omega}-3 content in other oil crops.

genomics↗

bioRxiv2022

Biomechanical Stimulation of Muscles Influences Bone Phenotype by Modulating Myokine Secretion

Diabetes is a chronic metabolic disorder that affects 422 million people worldwide and can lead to diabetic myopathy and bone diseases. The etiology of musculoskeletal complications in diabetes and the interplay between the muscular and osseous systems are poorly understood. Exercise training promises to prevent diabetic myopathy and diabetic bone disease and offer protective effects on muscle and bone. Although the muscle-bone interaction is largely biomechanical, the muscle secretome, specifically the myokines, has significant implications for bone biology. Here, we have developed an in vitro model to elucidate the effects of mechanical strain on myokine secretion and its impact on bone metabolism decoupled from physical stimuli. We developed modular bone constructs using crosslinked gelatin hydrogels which facilitated osteogenic differentiation of osteoprogenitor cells. Then muscle constructs were made from fibrin hydrogel, which enabled myoblast differentiation and formed mature myotubes. We investigated the myokine expression by the muscle constructs under strain regimens replicating endurance (END) and high-intensity interval training (HIIT) in hyperglycemic conditions. In monocultures, both regimens induced higher expression of Il15 and Igf1, while END supported more myoblasts differentiation and myotube maturation than HIIT. When cocultured with bone constructs, the HIIT regimen increased Glut4 expression in muscle contructs that END supporting higher glucose uptake. Likewise, the muscle constructs under the HIIT regimen promoted a healthier and matured bone phenotype than END. Interestingly, under static conditions, myostatin (Mstn) expression was significantly downregulated in muscle constructs cocultured with bone constructs compared to monocultures. Our in vivo analysis of the role of myostatin on bone structure and function also showed that myostatin knockout (GDF8-/-) enhanced muscle mass and moderately influenced bone phenotype in adult mice. Together, our in vitro coculture system allowed orthogonal manipulation of mechanical strain on muscle constructs while facilitating biochemical crosstalk between bone and muscle constructs. Such systems can provide an individualized microenvironment and allow decoupled biomechanical manipulation, which is unachievable using traditional models. In the long-term, these in-vitro systems will help identify molecular targets and develop engineered therapies for diabetic bone disease.

bioengineering↗

bioRxiv2022

Rounding up the annual ryegrass genome: high-quality reference genome of Lolium rigidum

The genome of the major agricultural weed species, annual ryegrass (Lolium rigidum) was assembled, annotated and analysed. Annual ryegrass is a major weed in wheat cropping, and has the remarkable capacity to evolve resistance to herbicides with various modes of action. The chromosome-level assembly was achieved using short- and long-read sequencing in combination with Hi-C mapping. The assembly size is 2.44Gb with N50=361.79Mb across 1,764 scaffolds where the seven longest sequences correspond to the seven chromosomes. Genome completeness assessed through BUSCO returned a 99.8% score for complete (unique and duplicated) and fragmented genes using the Viridiplantae set. We found evidence for the expansion of herbicide resistance-related gene families including detoxification genes. The reference genome assembly of L. rigidum is pivotal for the management of this highly problematic weed species which leverages genomic tools to devise new control options.

genomics↗

bioRxiv2021

Evaluation of maternal-infant dyad inflammatory cytokines in pregnancies affected by maternal SARS-CoV-2 infection in early and late gestation.

ObjectiveSARS-CoV-2 infection induces significant inflammatory cytokine production in adults, but infant cytokine signatures in pregnancies affected by maternal SARS-CoV-2 are less well characterized. We aimed to evaluate cytokine profiles of mothers and their infants following COVID-19 in pregnancy. Study DesignSerum samples at delivery from 31 mother-infant dyads with maternal SARS-CoV-2 infection in pregnancy (COVID) were examined in comparison to 29 control dyads (Control). Samples were evaluated using a 13-plex cytokine assay. ResultsIn comparison with controls, interleukin (IL)-6 and interferon gamma-induced protein 10 (IP-10) were higher in COVID maternal and infant samples (p<0.05) and IL-8 uniquely elevated in COVID infant samples (p<0.05). Significant elevations in IL-6, IP-10 and IL-8 were found among both early (1st/2nd Trimester) and late (3rd Trimester) maternal SARS-CoV-2 infections. ConclusionsMaternal SARS-CoV-2 infections throughout gestation are associated with increased maternal and infant inflammatory cytokines at birth with potential to impact long-term infant health.

immunology↗