Biology subjects

Wells, J.

Publications and source records attributed to Wells, J..

45 records · Page 3Linked to original sources

bioRxiv2020

Nanovibrational stimulation of mesenchymal stem cells induces therapeutic reactive oxygen species and inflammation for 3D bone tissue engineering

There is a pressing clinical need to develop cell-based bone therapies due to a lack of viable, autologous bone grafts and a growing demand for bone grafts in musculoskeletal surgery. Such therapies can be tissue engineered and cellular, such as osteoblasts combined with a material scaffold. Because mesenchymal stem cells (MSCs) are both available and fast growing compared to mature osteoblasts, therapies that utilise these progenitor cells are particularly promising. We have developed a nanovibrational bioreactor that can convert MSCs into bone-forming osteoblasts in 2D and 3D but the mechanisms involved in this osteoinduction process remain unclear. Here, to elucidate this mechanism, we use increasing vibrational amplitude, from 30 nm (N30) to 90 nm (N90) amplitudes at 1000 Hz, and assess MSC metabolite, gene and protein changes. These approaches reveal that dose-dependent changes occur in MSCs responses to increased vibrational amplitude, particularly in adhesion and mechanosensitive ion channel expression, and that energetic metabolic pathways are activated, leading to low-level reactive oxygen species (ROS) production and to low-level inflammation, as well as to ROS- and inflammation-balancing pathways. These events are analogous to those that occur in the natural bone-healing processes. We have also developed a tissue engineered MSC-laden scaffold designed using cells mechanical memory, driven by the stronger N90 stimulation. These new mechanistic insights and cell-scaffold design are underpinned by a process that is free of inductive chemicals.

bioengineering↗

bioRxiv2020

An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea and Iran. Phylogenetic analyses of whole genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.

microbiology↗

bioRxiv2020

The use of nanovibration to discover specific and potent bioactive metabolites that stimulate osteogenic differentiation in mesenchymal stem cells

Bioactive metabolites have wide-ranging biological activities and are a potential source of future research and therapeutic tools. Here, we use nanovibrational stimulation to induce the osteogenic differentiation of MSCs, in the absence of off-target differentiation. We show that this differentiation method, which does not rely on the addition of exogenous growth factors to the culture media, provides an artefact-free approach to identifying bioactive metabolites that specifically and potently induce osteogenesis. We first identify a highly specific metabolite as the endogenous steroid, cholesterol sulphate. Next, a screen of other small molecules with a similar steroid scaffold identified fludrocortisone acetate as being both specific and having highly potent osteogenic-inducing activity. These findings demonstrate that physical priciples can be used to identify bioactive metabolites and then metabolite potency can be optimised by examining structure-function relationship.

bioengineering↗

bioRxiv2020

Dissolved oxygen dynamics reveal biogeochemical tipping points driven by river corridor hydrology

Riverbeds can have an important impact on large-scale fluxes of biogeochemically active solutes in river corridor systems. The hyporheic zone is an important area of both hydrology and biogeochemistry, particularly in a hydropeaked river system where rapid variations in river stage height, hydraulic gradients, and residence times occur. We measured several biogeochemical and hydrological parameters at three different subsurface depths in the riverbed of the Columbia River in Washington state, a complex hydropeaked river system with significant subsurface heterogeneity. During the study, episodes of significant dissolved oxygen (DO) change were observed. The DO signal changes were the most apparent, compared to more modest changes in other biogeochemical markers. While DO is often associated with biological activity, we ultimately found that the notable DO excursions were associated with hydrologic gradients. Here we describe hydrologic perturbations and biogeochemical responses in terms of hydrobiogeochemical regimes. Two different forms of DO response to hydraulic gradient perturbation were observed, defining different hydrobiogeochemical regimes. The system tips abruptly from one regime to the other, exhibiting threshold behavior that is uncaptured in current estimations of cumulative influences of subsurface processes from reach to earth system scales. Plain language summaryThe water in a river is constantly flowing in and out of the rivers bed. While it is in the bed, microbes process environmentally and ecologically important nutrients and other compounds. The exchange of water between the river and the riverbed is largely controlled by the stage of the river. Many processes, both natural and human, can cause rapid changes in the river stage. These rapid stage changes can cause abrupt changes in the riverbeds ability to process nutrients and other compounds. In this study, we use dissolved oxygen as a window into riverbed microbial and chemical processing. We see that relatively rapid changes in river stage can cause abrupt changes in the concentrations of chemicals in the riverbed, indicating fundamental changes in how the riverbed processes are occurring. Understanding these abrupt and fundamental changes is important to our overall understanding of the ecological function of river corridor systems. 3 key pointsO_LIA hydrobiogeochemical regime is defined by the functional form of the relationship of a hydrologic perturbation and biogeochemical marker. C_LIO_LIShort-term hydrologic perturbations drive tipping points between distinct hydrobiogeochemical regimes. C_LIO_LILinear and hysteretic dissolved oxygen dynamics define distinct regimes as observed throughout the hyporheic zone. C_LI

biochemistry↗

bioRxiv2020

Carbon limitation leads to thermodynamic regulation of aerobic metabolism

Organic matter (OM) metabolism in freshwater ecosystems is a critical source of uncertainty in global biogeochemical cycles, yet aquatic OM cycling remains poorly understood. Here, we present the first work to explicitly test OM thermodynamics as a key regulator of aerobic respiration, challenging long-held beliefs that organic carbon and oxygen concentrations are the primary determinants of respiration rates. We pair controlled microcosm experiments with ultrahigh-resolution OM characterization to demonstrate a clear relationship between OM thermodynamic favorability and aerobic respiration under carbon limitation. We also demonstrate a shift in the regulation of aerobic respiration from OM thermodynamics to nitrogen content when carbon is in excess, highlighting a central role for OM thermodynamics in aquatic biogeochemical cycling particularly in carbon-limited ecosystems. Our work therefore illuminates a structural gap in aquatic biogeochemical models and presents a new paradigm in which OM thermodynamics and nitrogen content interactively govern aerobic respiration.

ecology↗

bioRxiv2019

Discrete virus factories form in the cytoplasm of cells co-infected with two strains of the segmented dsRNA virus, infectious bursal disease virus (IBDV), that subsequently coalesce

The Birnaviridae family, responsible for major economic losses to poultry and aquaculture, are non-enveloped viruses with a segmented double-stranded (ds)RNA genome that replicate in discrete cytoplasmic virus factories (VFs). Reassortment is common, however, the underlying mechanism remains unknown given that VFs may act as a barrier to genome mixing. In order to provide new information on VF trafficking during dsRNA virus co-infection, we rescued two recombinant infectious bursal disease viruses (IBDVs) of strain PBG98 containing either a split GFP11- or Tetracysteine (TC)- tag fused to the VP1 polymerase (PBG98-VP1-GFP11 and PBG98-VP1-TC). DF-1 cells transfected with GFP1-10 prior to PBG98-VP1-GFP11 infection, or stained with ReAsH following PBG98-VP1-TC infection, had green or red foci in the cytoplasm respectively that co-localised with VP3 and dsRNA, consistent with VFs. The average number of VFs decreased from a mean of 60 to 5 per cell between 10 and 24 hours post infection (hpi) (p<0.001), while the average area increased from 1.24 m2 to 45.01m2 (p<0.001), and live cell imaging revealed that the VFs were highly dynamic structures that coalesced in the cytoplasm. Small VFs moved faster than large (average 0.57m/s at 16 hpi compared to 0.22 m/s at 22 hpi), and VF coalescence was dependent on an intact microtubule network and actin cytoskeleton. During co-infection with PBG98-VP1-GFP11 and PBG98-VP1-TC viruses, discrete VFs initially formed from each input virus that subsequently coalesced 10-16 hours post-infection. We speculate that dsRNA virus reassortment requires VF coalescence, and the potential for reassortment increases at later time points in infection. ImportanceReassortment is common in viruses with segmented double stranded (ds)RNA genomes. However, these viruses typically replicate within discrete cytoplasmic virus factories (VFs) that may represent a barrier to genome mixing. We generated the first replication competent tagged reporter birnaviruses, infectious bursal disease viruses (IBDVs) containing a split GFP11 or tetracysteine (TC) tag and used the viruses to track the location and movement of IBDV VFs, in order to better understand the intracellular dynamics of VFs from two different strains of dsRNA virus during a co-infection. Discrete VFs initially formed from each virus that subsequently coalesced from 10 hours pi. We hypothesise that VF coalescence is required for the reassortment of dsRNA viruses and the potential for reassortment increases later in the replication cycle. This study provides new information that adds to our understanding of dsRNA virus VF trafficking.

microbiology↗

bioRxiv2019

A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing, and around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

genomics↗

bioRxiv2019

Nanotopography reveals metabolites that maintain the immunosuppressive phenotype of mesenchymal stem cells

Mesenchymal stem cells (MSCs) are multipotent stem cells that are immunosuppressive and thus of considerable therapeutic potential in transplant operations. However, MSCs rapidly differentiate once in culture, making their large-scale expansion for use in immunosuppressive therapies challenging. Although the differentiation mechanisms of MSCs have been extensively investigated using materials, little is known about how materials can modulate paracrine activities of MSCs. Here, we show for the first time that nanotopography can control the immunomodulatory capacity of MSCs through decreased intracellular tension increasing oxidative glycolysis. We also use the nanotopography to identify bioactive metabolites that modulate intracellular tension, growth and immunomodulatory phenotype of MSCs in standard culture. Our findings show a novel route to support large-scale expansion of functional MSCs for therapeutic purposes

bioengineering↗

bioRxiv2018

Minimizing marine ingredients in diets of farmed Atlantic salmon (Salmo salar): Effects on growth performance and muscle lipid and fatty acid composition

Due to limited fish meal and fish oil resources and their high costs for the aquaculture industry, it is necessary to find alternative sustainable sources of protein and lipids. Therefore, seven different diets were formulated with different protein and lipid sources to feed farmed Atlantic salmon, and their effects on growth performance, muscle lipid class, and fatty acid composition were examined. Growth performance indicated that the diet with the lowest fish meal and fish oil content resulted in the lowest weight gain and final weight, followed by the diet containing the highest level of animal by-products. The lipid class analysis showed no statistical difference in the muscle total lipid content using different diets. However, significant statistical differences were observed among the main lipid classes; triacylglycerols, phospholipids, and sterols. The diet containing 1.4% omega-3 long-chain fatty acids resulted in the highest content of triacylglycerols and phospholipids. Diets containing medium and low levels of fish oil and fish meal, respectively, led to as high a level of {omega}3 fatty acids in muscle as when fish were fed diets with high levels of fish meal and fish oil. The results of this study suggest that feeding a diet containing low levels of fish meal and moderate levels of fish oil does not significantly affect {omega}3 fatty acid composition in muscle. Fish meal could be reduced to 5% without affecting growth as long as there was a minimum of 5% fish oil, and animal by-products did not exceed 26% of the diet.

biochemistry↗