Biology subjects

Jones, J.

Publications and source records attributed to Jones, J..

67 records · Page 4Linked to original sources

bioRxiv2020

Towards genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles.

Plant-parasitic nematodes are a continuing threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics: forward genetics is largely restricted to studies of natural variation in populations, and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate the progress of research on plant-parasitic nematodes, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic tool kit in plant-parasitic nematodes. We characterise the gonads of male Heterodera schachtii and Meloidogyne hapla in the context of spermatogenesis. We test and optimise various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult, but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of H. schachtii juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, will expedite the development of genetic modification tools for plant-parasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security.

genetics↗

bioRxiv2020

Pre-existing immunity provides a barrier to airborne transmission of influenza viruses

Human-to-human transmission of influenza viruses is a serious public health threat, yet the precise role of immunity from previous infections on the susceptibility to airborne viruses is still unknown. Using human seasonal influenza viruses in a ferret model, we examined the roles of exposure duration and heterosubtypic immunity on influenza transmission. We found that airborne transmission of seasonal influenza strains is abrogated in recipient animals with pre-existing non-neutralizing immunity, indicating that transmissibility of a given influenza virus strain should be examined in the context of ferrets that are not immunologically naive.

microbiology↗

bioRxiv2020

Age and neuroinflammation are important components of the mechanism of cognitive and neurobehavioral deficits in sickle cell disease.

ObjectivesCognitive and neurobehavioral abnormalities are the most common and complex complications of sickle cell disease (SCD). Known risk factors influencing abnormalities are stroke and silent cerebral infarcts, but a majority of cases do not have overt cerebral injury and the underlying mechanism is not well understood. This study aims to determine whether sickle cell mice could recapitulate features of cognitive and neurobehavioral impairment observed in sickle cell patients as well as to determine the underlying cellular mechanism of these SCD complications. MethodsUsing a longitudinal cross-sectional study design, we evaluated cognition and neurobehavioral deficits as an outcome. Six as well as 13 months old male Townes humanized sickle cell (SS) and matched control (AA) mice were tested. The combination of novel object recognition and fear conditioning tests was employed to measure anxiety/depression, learning and memory. Immunohistochemistry was performed to quantify bone marrow-derived microglia (CD45+) and activated microglia (Iba1+) in the dentate and peri-dentate gyrus to determine if these factors were potential pathogenic mechanisms associated with cognitive and neurobehavioral abnormalities. We evaluated neurogenesis by measuring 5Bromodeoxyuridine (BrdU) and doublecortin (DCX) and phenotyped proliferating cells via quantification of glial fibrillary acid protein (GFAP+), neuronal nuclei (NeuN+), CD45+ and Iba1+. In addition, Golgi-Cox staining was used to assess neuroplasticity via measurement of dendritic spine density and morphology, as well as dendrite arbors. ResultsCompared to matched AA, 13 months old SS mice showed significant evidence of anxiety/depression by the shorter distance traveled as well as thigmotaxis. Additionally, SS mice were significantly less likely to recognize the novel object as well as have a reduced preference for the novel object. There were no significant differences between 6 months old SS and AA. But the difference reappeared after the same mice were aged to 13 months. Aged mice exhibited more anxiety/depression behaviors and thigmotaxis and were less likely to recognize or show a lower percent preference for the novel object compared to aged control (AA) mice. Immunohistochemistry analysis shows that sickle cell (SS) mice had significantly more CD45+ and Iba1+ activated microglia cells in the dentate and peri-dentate gyrus area compared to AA mice. SS mice also had a significantly lower dendritic spine density compared with controls. Treatment of aged SS mice with minocycline resulted in significant improvement of cognitive and neurobehavioral function compared to matched vehicle-treated SS mice. Also immunohistochemical and histological analysis showed that treated SS mice had significantly fewer CD45+ cells and activated microglia in the dentate and peri-dentate gyrus area. Furthermore, there was significant improvement in dendritic spine and dendrite arbor density as well as spine maturation in treated sickle cell mice compared with vehicle-treated sickle cell mice. ConclusionTaken together these results indicate that age, neuro-inflammation and neuroplasticity, specifically, spine maturation and density, are possible mechanisms underlying cognition deficits in sickle cell disease. These could also be targeted as a potential approach for prevention and or treatment of cognitive and neurobehavioral deficits in SCD.

neuroscience↗

bioRxiv2020

A machine-vision approach for automated pain measurement at millisecond timescales

Objective and automatic measurement of pain in mice remains a barrier for discovery in both basic and translational neuroscience. Here we capture rapid paw kinematics during pain behavior in mice with high-speed videography and automated paw tracking with machine and deep learning approaches. Our statistical software platform, PAWS (Pain Assessment at Withdrawal Speeds), uses a univariate projection of paw position over time to automatically quantify fast paw dynamics at the onset of paw withdrawal and also lingering pain-related behaviors such as paw guarding and shaking. Applied to innocuous and noxious stimuli across six inbred mouse strains, a linear discriminant analysis reveals a two-dimensional subspace that separates painful from non-painful stimuli on one axis, and further distinguishes the severity of pain on the second axis. Automated paw tracking combined with PAWS reveals behaviorally-divergent mouse strains that display hypo- and hyper-sensitivity to mechanical stimuli. To demonstrate the efficacy of PAWS for detecting hypersensitivity to noxious stimuli, we chemogenetically activated pain-aversion neurons in the amygdala, which further separated the behavioral representation of pain-related behaviors along a low-dimensional path. Taken together, this automated pain quantification approach should increase the ease and objectivity of collecting rigorous behavioral data, and it is compatible with other neural circuit dissection tools for determining the mouse pain state.

neuroscience↗

bioRxiv2020

A Pre-computed Probabilistic Molecular Search Engine for Tandem Mass Spectrometry Proteomics

Mass spectrometry methods of peptide identification involve comparing observed tandem spectra with in-silico derived spectrum models. Presented here is a proteomics search engine that offers a new variation of the standard approach, with improved results. The proposed method employs information theory and probabilistic information retrieval on a pre-computed and indexed fragmentation database generating a peptide-to-spectrum match (PSM) score modeled on fragment ion frequency. As a result, the direct application of modern document mining, allows for treating the collection of peptides as a corpus and corresponding fragment ions as indexable words, leveraging ready-built search engines and common predefined ranking algorithms. Fast and accurate PSM matches are achieved yielding a 5-10% higher rate of peptide identities than current database mining methods. Immediate applications of this search engine are aimed at identifying peptides from large sequence databases consisting of homologous proteins with minor sequence variations, such as genetic variation expected in the human population.Competing Interest StatementThis research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Researchers have commercial interests in applications of the technology described herein.View Full Text

bioinformatics↗

bioRxiv2020

A minimal 3D model of mosquito flight behavior around the human baited bed net

Advances in digitized video-tracking and behavioral analysis have enabled accurate recording and quantification of mosquito flight and host-seeking behaviors, enabling development of Individual (agent) Based Models at much finer spatial scales than previously possible. We used such quantified behavioral parameters to create a novel virtual testing model, capable of accurately simulating indoor flight behavior by a virtual population of host-seeking mosquitoes as it interacts with and responds to simulated stimuli from a human-occupied bed net. We describe the model, including base mosquito behavior, state transitions, environmental representation and host stimulus representation. In the absence of a bed net and human bait, flight distribution of the model population is relatively uniform in the arena. Introducing an unbaited net induces a change in distribution due to landing events on the net surface, predominantly occurring on the sides and edges of the net. Presence of simulated human baited net strongly impacted flight distribution patterns, exploratory foraging, the number and distribution of net landing sites, depending on the bait orientation. As recorded in live mosquito experiments, contact with baited nets (a measure of exposure to the lethal insecticide) occurred predominantly on the top surface of the net. Number of net contacts and height of contacts decreased with increasing attractant dispersal noise. Results generated by the model are an accurate representation of actual mosquito behavior recorded at and around a human-occupied bed net in untreated and insecticide treated nets. In addition to providing insights into host-seeking behavior of endophilic vectors, this fine-grained model is highly flexible and has significant potential for in silico screening of novel bed net designs, accelerating the deployment of new and more effective tools for protecting against malaria in sub-Saharan Africa.

animal behavior and cognition↗

bioRxiv2019

Bee visitation and fruit quality in berries under protected cropping vary along the length of polytunnels

Wild and managed bees provide effective crop pollination services worldwide. Protected cropping conditions are thought to alter the ambient environmental conditions in which pollinators forage for flowers, yet few studies have compared conditions at the edges and centre of growing tunnels. We measured environmental variables (temperature, relative humidity, wind speed, white light and UV light) and surveyed the activity of managed honeybees Apis mellifera, wild stingless bees Tetragonula carbonaria and sweat bees Homalictus urbanus along the length of 32 multiple open-ended polyethylene growing tunnels. These were spaced across 12 blocks at two commercial berry farms, in Coffs Harbour, New South Wales and Walkamin, North Queensland, Australia. Berry yield, fresh weight and other quality metrics were recorded at discrete increments along the length of the tunnels. We found a higher abundance and greater number of flower visits by stingless bees and honeybees at the end of tunnels, and less frequent visits to flowers toward the middle of tunnels. The centre of tunnels experienced higher temperatures and reduced wind speed. In raspberry, fruit shape was improved with greater pollinator abundance and was susceptible to higher temperatures. In blueberry, per plant yield and mean berry weight were positively associated with pollinator abundance and were lower at the centre of tunnels than at the edge. Fruit quality (crumbliness) in raspberries was improved with a greater number of visits by sweat bees, who were not as susceptible to climatic conditions within tunnels. Understanding bee foraging behaviour and changes to yield under protected cropping conditions is critical to inform the appropriate design of polytunnels and aid pollinator management within them.

ecology↗

bioRxiv2019

PRDM16 establishes lineage-specific transcriptional program to promote temporal progression of neural progenitors in the mouse neocortex

Radial glia (RG) in the neocortex sequentially generate distinct subtypes of projection neurons, accounting for the diversity and complex assembly of cortical neural circuits. Mechanisms that drive the rapid and precise temporal progression of RG are beginning to be elucidated. Here we reveal that the RG-specific transcriptional regulator PRDM16 promotes the transition of early to late phases of neurogenesis in the mouse neocortex. Prdm16 mutant RG delays the timely progression of RG, leading to defective cortical laminar organization. We show that PRDM16 regulates expression of neuronal specification genes and a subset of genes that are dynamically expressed between mid-and late-neurogenesis. Our genomic analysis suggests that PRDM16 suppresses target gene expression through maintaining chromatin accessibility of permissive enhancers. Altogether, our results demonstrate a critical role of PRDM16 in establishing stage-specific gene expression program of RG during cortical neurogenesis. These findings also support a model where progenitor cells are primed with daughter cell gene expression program for rapid cell differentiation.

developmental biology↗

bioRxiv2019

ARBoR: An Identity and Security Solution for Clinical Reporting

MotivationClinical genome sequencing laboratories return reports containing clinical testing results, signed by an Board Certified clinical geneticist, to the ordering physician. This report is often a pdf, but can also be a physical paper copy or a structured data file. The reports are frequently modified and re-issued, due to changes in variant interpretation or clinical attributes. To precisely track report authenticity we developed ARBoR, an application for tracking the lineage of versioned clinical reports even when they are distributed as pdf or paper copies. ARBoR employs a modified blockchain approach and instead of relying on a computationally intensive consensus mechanism for determining authenticity, we allow supervised and digitally signed writes to an encrypted ledger, which is then exactly replicated to many clients.\n\nResultsARBoR was implemented for clinical reporting in the HGSC-CL Clinical Laboratory, initially as part of the NIHs Electronic Medical Record and Genomics (eMERGE) project. To date we have issued 15,205 versioned clinical reports tracked by ARBoR. This system has provided us with a simple and tamper-proof mechanism for tracking clinical reports with a complicated update history.

bioinformatics↗

bioRxiv2019

A large proportion of poor birth outcomes among Aboriginal Western Australians are attributable to smoking, alcohol and substance misuse, and assault

BackgroundAboriginal infants have poorer birth outcomes than non-Aboriginal infants. Harmful use of tobacco, alcohol, and other substances is higher among Aboriginal women, as is violence, due to factors such as intergenerational trauma and poverty. We estimated the proportion of small for gestational age (SGA) births, preterm births, and perinatal deaths that could be attributed to these risks. MethodsBirth, hospital, mental health, and death records for Aboriginal singleton infants born in Western Australia from 1998-2010 and their parents were linked. Using logistic regression with a generalized estimating equation approach, associations with birth outcomes and population attributable fractions were estimated after adjusting for demographic factors and maternal health during pregnancy. ResultsOf 28,119 births, 16% of infants were SGA, 13% were preterm, and 2% died perinatally. 51% of infants were exposed in utero to at least one of the risk factors and the fractions attributable to them were 37% (SGA), 16% (preterm) and 20% (perinatal death). ConclusionsA large proportion of adverse outcomes were attributable to the modifiable risk factors of substance use and assault. Significant improvements in Aboriginal perinatal health are likely to follow reductions in these risk factors. These results highlight the importance of identifying and implementing risk reduction measures which are effective in, and supported by, Aboriginal women, families, and communities.

epidemiology↗

bioRxiv2018

Nuclear-cytoplasmic compartmentalization of the herpes simplex virus 1 infected cell transcriptome is co-ordinated by the viral endoribonuclease vhs and cofactors to facilitate the translation of late proteins

HSV1 encodes an endoribonuclease termed virion host shutoff (vhs) that is produced late in infection and packaged into virions. Paradoxically, vhs is active against not only host but also virus transcripts, and is involved in host shutoff and the temporal expression of the virus transcriptome. Two other virus proteins - VP22 and VP16 - are proposed to regulate vhs to prevent uncontrolled and lethal mRNA degradation but their mechanism of action is unknown. We have performed dual transcriptomic analysis and single-cell mRNA FISH of human fibroblasts, a cell type where in the absence of VP22, HSV1 infection results in extreme translational shutoff. In Wt infection, host mRNAs exhibited a wide range of susceptibility to vhs ranging from resistance to 1000-fold reduction, a variation that was independent of their relative abundance or transcription rate. However, vhs endoribonuclease activity was not found to be overactive against any of the cell transcriptome in {Delta}22-infected cells but rather was delayed, while its activity against the virus transcriptome and in particular late mRNA was minimally enhanced. Intriguingly, immediate-early and early transcripts exhibited vhs-dependent nuclear retention later in Wt infection but late transcripts were cytoplasmic. However, in the absence of VP22, not only early but also late transcripts were retained in the nucleus, a characteristic that extended to cellular transcripts that were not efficiently degraded by vhs. Moreover, the ability of VP22 to bind VP16 enhanced but was not fundamental to the rescue of vhs-induced nuclear retention of late transcripts. Hence, translational shutoff in HSV1 infection is primarily a result of vhs-induced nuclear retention and not degradation of infected cell mRNA. We have therefore revealed a new mechanism whereby vhs and its co-factors including VP22 elicit a temporal and spatial regulation of the infected cell transcriptome, thus co-ordinating efficient late protein production.\n\nAuthor SummaryHerpesviruses are large DNA viruses that replicate in the nucleus and express their genes by exploiting host cell mRNA biogenesis mechanisms including transcription, nuclear export, translation and turnover. As such, these viruses express multiple factors that enable the appropriation of cellular pathways for optimal virus production, and work in concert to shut off host gene expression and to overexpress virus genes in a well-described cascade that occurs in a temporal pattern of immediate-early, early and late proteins. We have analysed global and single cell changes in the host and virus transcriptome to uncover a novel mechanism by which the viral endoribonuclease, termed vhs, turns off early virus gene expression. This is achieved through the vhs-induced nuclear retention of the entire infected cell transcriptome at the onset of late gene expression. To enable the switch from early to late protein production the virus then requires a second factor called VP22 to specifically inhibit the nuclear retention of late transcripts allowing their translation in the cytoplasm. In this way, HSV1 elicits a temporal and spatial regulation of the infected cell transcriptome to co-ordinate efficient late protein production, a process that may be relevant to herpesviruses in general.

microbiology↗

bioRxiv2018

Demographic determinants of biometric heritability

The response of quantitative characters to selection depends on their transmission from parents to offspring. A common estimate of this transmission is the biometric heritability defined as the slope of the regression of offspring phenotype on same-aged mid-parent phenotype (i.e. the ratio of the phenotypic parent-offspring covariance over the parental phenotypic variance). This slope is often interpreted as the percentage of phenotypic variation due to additive genetic effects after accounting for confounding factors such as environment, litter or parental effects. However, researchers seldom account for the possible influence of selection on this estimate. Here we study the effect on biometric heritability of fertility and viability selection, as well as phenotype ontogeny (growth) and inheritance from parents to offspring. We present exact formulas for the elasticities of biometric heritability in age-phenotype-structured integral projection models (IPMs), and illustrate these for two iteroparous long-lived species. We find that both viability and fertility selection can strongly affect heritability, mediated by growth and inheritance. Generally, demographic processes that result in parents reproducing at large phenotypes, regardless of their own birth phenotype, decrease heritability. Analysed at equilibrium, our models imply that a heritable character can show no response to selection, if parental phenotypes affect offspring phenotypes and if phenotypes develop with age. Our results further highlight the importance of accounting for demographic processes when estimating heritability.

ecology↗

bioRxiv2017

Discovery of Resistance Pathways to Fibroblast Growth Factor Receptor inhibition in Bladder Cancer

BackgroundAberrant fibroblast growth factor receptor (FGFR) signaling drives the growth of many bladder cancers. NVP-BGJ398 is a small molecule with potent inhibitory activity of FGFRs 1, 2, and 3, and has been shown to selectively inhibit the growth of bladder cancer cell lines that over-express FGFR3 or have oncogenic FGFR3 fusions. As with many agents targeting receptor tyrosine kinases, resistance is known to develop.\n\nObjectiveWe sought to identify potential mechanisms of resistance to NVP-BGJ398 in cell culture models of bladder cancer.\n\nMethodsRT-112 bladder cancer cell lines were derived that were resistant to growth in 3uM NVP-BGJ398. RNA-sequencing was performed on resistant and parental cell lines to identify potential resistance mechanisms and molecular experiments were carried out to test these predictions.\n\nResultsRNA-seq demonstrated decreased expression of FGFR3 and increased expression of FGFRs 1 and 2 in resistant cell lines. Over-expression of FGFR3 in NVP-BGJ398 resistant cells decreased their proliferation. Pathway analysis of RNA-seq data also implicated PIM kinase signaling, among other pathways, as a potential mediator of resistance. Treatment of BGJ398 resistant cells with the PIM kinase inhibitor SGI-1776 reduced the growth of the cells.\n\nConclusionsOur results suggest that altered FGFR expression and PIM kinase activity could mediate resistance to NVP-BGJ398. These pathways should be investigated in samples from patients resistant to this drug.

cancer biology↗