Biology subjects

Jones, B.

Publications and source records attributed to Jones, B..

At least 73 records · Page 4Linked to original sources

bioRxiv2020

Computational approaches towards reducing contamination in single-cell RNA-seq data

Single cell RNA sequencing has enabled quantification of single cells and identification of different cell types and subtypes as well as cell functions in different tissues. Single cell RNA sequence analyses assume acquired RNAs correspond to cells, however, RNAs from contamination within the input data are also captured by these assays. The sequencing of background contamination as well as unwanted cells making their way to the final assay Potentially confound the correct biological interpretation of single cell transcriptomic data. Here we demonstrate two approaches to deal with background contamination as well as profiling of unwanted cells in the assays. We use three real-life datasets of whole-cell capture and nucleotide single-cell captures generated by Fluidigm and 10x technologies and show that these methods reduce the effect of contamination, strengthen clustering of cells and improves biological interpretation.

bioinformatics↗

bioRxiv2020

Impact of N-terminally substituted glucagon family receptor agonists on signal bias, trafficking and downstream responses

Receptors for the peptide hormones glucagon-like peptide-1 (GLP-1), glucose-dependent insulinotropic polypeptide (GIP) and glucagon (GCG) are important regulators of insulin secretion and energy metabolism. Recently described GLP-1 receptor agonists showing signal bias in favour of cyclic AMP over {beta}-arrestin-2 recruitment have delivered promising results in preclinical studies. Here we first sought to establish the role of {beta}-arrestins in the control of intracellular signalling and trafficking responses at the closely related GLP-1, GIP and GCG receptors, through studies performed in cells depleted of both {beta}-arrestin isoforms. We also generated analogues of GLP-1, GCG and GIP which in some cases showed selective reduction in {beta}-arrestin-2 recruitment versus cAMP signalling compared to the parent peptide. Despite reduced acute signalling potency and/or efficacy, some biased GLP-1 and GIP analogues increased maximal sustained insulin secretion from INS-1 832/3 clonal beta cells, although only at high agonist concentrations. Biased GCG analogues did not affect maximal insulin release, or glucose output in hepatocytes.

pharmacology and toxicology↗

bioRxiv2020

Multidecadal decline and recovery of aspen experiencing contrasting fire regimes: long-unburned, infrequent and frequent mixed-severity wildfire

Quaking aspen (Populus tremuloides) is a valued, minor component on western landscapes. It provides a wide range of ecosystem services and has been in decline throughout the arid west for the last century. This decline may be explained partially by the lack of fire on the landscape as aspen benefit from fire that eliminates conifer competition and stimulates reproduction through root suckering. Managers are interested in aspen restoration but there is a lack of knowledge about their spatial dynamics in response to fire. Our study area in northeastern California on the Lassen, Modoc and Plumas National Forests has experienced recent large mixed-severity wildfires where aspen was present, providing an opportunity to study the re-introduction of fire. We observed two time periods; a 54-year absence of fire from 1941 to 1993 preceding a 24-year period of wildfire activity from 1993 to 2017. We utilized aerial photos to delineate aspen stand size, location and succession to conifers. We chose aspen stands in areas where wildfires overlapped (twice-burned), where only a single wildfire burned, and areas that did not burn within the recent 24-year period. We looked at these same stands within the first period of fire exclusion for comparison (i.e., 1941-1993). In the absence of fire, all aspen stand areas declined and all stands experienced increases in conifer composition. After wildfire, stands that burned experienced a release from conifer competition and increased in stand area. Stands that burned twice or at high severity experienced a larger removal of conifer competition than stands that burned once at low severity, promoting aspen recovery and expansion. Stands with less edge:area ratio also expanded more with fire present. Across both time periods, stand movement, where aspen stand footprints were mostly in new areas compared to footprints of previous years, was highest in smaller stands. In the fire exclusion period, smaller stands exhibited greater changes in area and location (movement), highlighting their vulnerability to loss in the absence of disturbances that provide adequate growing space for aspen over time.

ecology↗

bioRxiv2020

Larger active site in an ancestral hydroxynitrile lyase increases catalytically promiscuous esterase activity

Hydroxynitrile lyases (HNLs) belonging to the /{beta}-hydrolase-fold superfamily evolved from esterases approximately 100 million years ago. Reconstruction of an ancestral hydroxynitrile lyase in the /{beta}-hydrolase fold superfamily yielded a catalytically active hydroxynitrile lyase, HNL1. Several properties of HNL1 differ from the modern HNL from rubber tree (HbHNL). HNL1 favors larger substrates as compared to HbHNL, is two-fold more catalytically promiscuous for ester hydrolysis (p-nitrophenyl acetate) as compared to mandelonitrile cleavage, and resists irreversible heat inactivation to 35 {degrees}C higher than for HbHNL. We hypothesized that the x-ray crystal structure of HNL1 may reveal the molecular basis for the differences in these properties. The x-ray crystal structure solved to 1.96-[A] resolution shows the expected /{beta}-hydrolase fold, but a 60% larger active site as compared to HbHNL. This larger active site echoes its evolution from esterases since related esterase SABP2 from tobacco also has a 38% larger active site than HbHNL. The larger active site in HNL1 likely accounts for its ability to accept larger hydroxynitrile substrates. Site-directed mutagenesis of HbHNL to expand the active site increased its promiscuous esterase activity 50-fold, consistent with the larger active site in HNL1 being the primary cause of its promiscuous esterase activity. Urea-induced unfolding of HNL1 indicates that it unfolds less completely than HbHNL (m-value = 0.63 for HNL1 vs 0.93 kcal/ mol{middle dot}M for HbHNL), which may account for the ability of HNL1 to better resist irreversible inactivation upon heating. The structure of HNL1 shows changes in hydrogen bond networks that may stabilize regions of the folded structure.

biochemistry↗

bioRxiv2020

The influence of peptide context on signalling and trafficking of glucagon-like peptide-1 receptor biased agonists

Signal bias and membrane trafficking have recently emerged as important considerations in the therapeutic targeting of the glucagon-like peptide-1 receptor (GLP-1R) in type 2 diabetes and obesity. In the present study, we have evaluated a peptide series with varying sequence homology between native GLP-1 and exendin-4, the archetypal ligands on which approved GLP-1R agonists are based. We find notable differences in agonist-mediated signalling, endocytosis and recycling, dependent both on the introduction of a His [->] Phe switch at position 1 and the specific mid-peptide helical regions and C-termini of the two agonists. These observations were linked to insulin secretion in a beta cell model and provide insights into how ligand factors influence GLP-1R function at the cellular level. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/961524v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@cb425borg.highwire.dtl.DTLVardef@719e37org.highwire.dtl.DTLVardef@14a45b9org.highwire.dtl.DTLVardef@127afd1_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2020

Interrogating surface versus intracellular transmembrane receptor populations using cell-impermeable SNAP-tag substrates

Employing self-labelling protein tags for the attachment of fluorescent dyes has become a routine and powerful technique in optical microscopy to visualize and track fused proteins. However, membrane permeability of the dyes and the associated background signals can interfere with the analysis of extracellular labeling sites. Here we describe a novel approach to improve extracellular labeling by functionalizing the SNAP-tag substrate benzyl guanine ("BG") with a charged sulfonate ("SBG"). This chemical manipulation improves solubility, reduces non-specific staining and renders the bioconjugation handle impermeable while leaving its cargo untouched. We report SBG-conjugated fluorophores across the visible spectrum, which cleanly label SNAP-fused proteins in the plasma membrane of living cells. We demonstrate the utility of SBG-conjugated fluorophores to interrogate class A, B and C G protein-coupled receptors (GPCRs) using a range of imaging approaches including nanoscopic super-resolution imaging, analysis of GPCR trafficking from intra- and extracellular pools, in vivo labelling in mouse brain and analysis of receptor stoichiometry using single molecule pull down.

physiology↗

bioRxiv2019

Disconnect between signalling potency and in vivo efficacy of pharmacokinetically optimised biased glucagon-like peptide-1 receptor agonists

ObjectiveTo determine how pharmacokinetically advantageous acylation impacts on glucagon-like peptide-1 receptor (GLP-1R) signal bias, trafficking, anti-hyperglycaemic efficacy and appetite suppression. MethodsIn vitro signalling responses were measured using biochemical and biosensor assays. GLP-1 receptor trafficking was determined by confocal microscopy and diffusion-enhanced resonance energy transfer. Pharmacokinetics, glucoregulatory effects and appetite suppression were measured in acute, sub-chronic and chronic settings in mice. ResultsA C-terminally acylated ligand, exendin-phe1-C16, was identified with undetectable {beta}-arrestin recruitment and GLP-1R internalisation. Depending on the cellular system used, this molecule was up to 1000-fold less potent than the comparator exendin-asp-3-C16 for cyclic AMP signalling, yet was considerably more effective in vivo, particularly for glucose regulation. ConclusionsC-terminal acylation of biased GLP-1R agonists increases their degree of signal bias in favour of cAMP production and improves their therapeutic potential.

pharmacology and toxicology↗

bioRxiv2019

Differences in signalling, trafficking and glucoregulatory properties of glucagon-like peptide-1 receptor agonists exendin-4 and lixisenatide

Background and purposeAmino acid substitutions at the N-termini of glucagon-like peptide-1 receptor agonist (GLP-1RA) peptides result in distinct patterns of intracellular signalling, sub-cellular trafficking and efficacy in vivo. Here we aimed to determine whether sequence differences at the ligand C-termini of clinically approved GLP-1RAs exendin-4 and lixisenatide lead to similar phenomena. We also sought to establish the impact of the C-terminus on signal bias resulting from modifications elsewhere in the molecule. Experimental approachExendin-4, lixisenatide, and N-terminally substituted analogues with biased signalling characteristics were compared across a range of in vitro trafficking and signalling assays in different cell types. Fluorescent ligands and new time-resolved FRET approaches were developed to study agonist behaviours at the cellular and sub-cellular level. Anti-hyperglycaemic and anorectic effects of each parent ligand, and their biased derivatives, were assessed in mice. Key resultsLixisenatide and exendin-4 showed equal binding affinity, but lixisenatide was 5-fold less potent for cAMP signalling. Both peptides were rapidly endocytosed, but the GLP-1R recycled more slowly to the plasma membrane after lixisenatide treatment. These combined deficits resulted in reduced maximal sustained insulin secretion and reduced anti-hyperglycaemic and anorectic effects in mice. N-terminal substitutions to both ligands had favourable effects on their pharmacology, resulting in improved insulin release and lowering of blood glucose. Conclusion and implicationsChanges to the C-terminus of exendin-4 affect signalling potency and GLP-1R trafficking via mechanisms unrelated to GLP-1R occupancy. These differences were associated with changes in their ability to control blood glucose and therefore may be therapeutically relevant.

pharmacology and toxicology↗

bioRxiv2019

The effects of dyslipidaemia and cholesterol modulation on erythrocyte susceptibility to malaria parasite infection

Malaria disease commences when blood-stage parasites, called merozoites, invade human red blood cells (RBCs). Whilst the process of invasion is traditionally seen as being entirely merozoite-driven, emerging data suggests RBC biophysical properties markedly influence invasion. Cholesterol is a major determinant of cell membrane biophysical properties. We set out to assess whether cholesterol content in the RBC membrane affects susceptibility to merozoite invasion. Here we demonstrate that RBC bending modulus (a measure of deformability) is markedly affected by artificial modulation of cholesterol content and negatively correlated with merozoite invasion efficiency. Contextualising this observation, we tested a mouse model of hypercholesterolemia and human clinical samples from patients with a range of serum cholesterol concentrations for parasite susceptibility. Hypercholesterolaemia in both human and murine subjects had little effect merozoite invasion efficiency. Furthermore, on testing, RBC cholesterol content in both murine and human hypercholesterolaemia settings was found to be unchanged from normal controls. Serum cholesterol is, therefore, unlikely to impact on RBC susceptibility to merozoite entry. Our work, however, suggests that native polymorphisms that affect RBC membrane lipid composition would be expected to affect parasite entry. This supports investigation of RBC biophysical properties in endemic settings, which may yet identify naturally protective lipid-related polymorphisms.

microbiology↗

bioRxiv2019

Liver-Chip: Reproducing Human and Cross-Species Toxicities

Nonclinical rodent and non-rodent toxicity models used to support clinical trials of candidate drugs may produce discordant results or fail to predict complications in humans contributing to drug failures in the clinic. Here we applied microengineered Organ-on-Chip (Organ-Chip) technology to design rat, dog, and human Liver-Chips containing species-specific primary hepatocytes interfaced with liver sinusoidal endothelial cells, with or without Kupffer cells and hepatic stellate cells, cultured under physiological fluid flow. The Liver-Chips detected diverse phenotypes of liver toxicity including hepatocellular injury, steatosis, cholestasis, and fibrosis as well as species-specific toxicities when treated with tool compounds. Multi-species Liver-Chips may provide a useful platform for prediction of liver toxicity and inform human relevance of liver toxicities detected in animal studies to better determine safety and human risk.\n\nOne Sentence SummaryMicroengineered Organ-Chip technology has been used to design rat, dog and human Liver-Chips that recapitulate species-specific liver toxicities.

pharmacology and toxicology↗

bioRxiv2019

Phosphatidylinositol 3,5-Bisphosphate regulates Ca2+ Transport During Yeast Vacuolar Fusion through Activation of the Ca2+ ATPase Pmc1

The transport of Ca2+ across membranes precedes the fusion and fission of various lipid bilayers. Yeast vacuoles during hyperosmotic shock become fragmented through fission events that require Ca2+ efflux of their luminal stores through the TRP channel Yvc1. This requires the production of the lipid PI(3,5)P2 by Fab1. Ca2+ is also released during vacuole fusion upon trans-SNARE complex assembly, however, the role of PI(3,5)P2 remains unclear. Here we demonstrate that elevated PI(3,5)P2 levels abolish Ca2+ efflux during fusion, indicating that PI(3,5)P2 has opposing effects on Ca2+ transport in fission versus fusion. Notably, Ca2+ efflux was enhanced when PI(3,5)P2 levels were reduced. Importantly, the effect of PI(3,5)P2 on Ca2+ flux was independent of Yvc1. Rather, the effect was dependent on the Ca2+ pump Pmc1. Vacuoles lacking Pmc1 were resistant to the effects of PI(3,5)P2, while those lacking Yvc1 remained sensitive. Furthermore altering PI(3,5)P2 levels affects the interactions of Pmc1 with the Vo component Vph1 and the R-SNARE Nyv1. We now propose a model in which elevated PI(3,5)P2 activates continued Pmc1 function to prevent the accumulation of released extraluminal Ca2+. SummaryDuring osmotic stress PI(3,5)P2 triggers Ca2+ release from vacuoles. Here we show PI(3,5)P2 stimulates Ca2+ uptake by vacuoles during fusion, illustrating that it has a dual role in Ca2+ transport.

biochemistry↗

bioRxiv2018

Agonist binding affinity determines palmitoylation of the glucagon-like peptide-1 receptor and its functional interaction with plasma membrane nanodomains in pancreatic beta cells

The glucagon-like peptide-1 receptor (GLP-1R), a key pharmacological target in type 2 diabetes and obesity, is known to undergo palmitoylation by covalent ligation of an acyl chain to cysteine 438 in its carboxyl-terminal tail. Work with other GPCRs indicates that palmitoylation can be dynamically regulated to allow receptors to partition into plasma membrane nanodomains that act as signaling hotspots. Here, we demonstrate that the palmitoylated state of the GLP-1R is increased by agonist binding, leading to its segregation and clustering into plasma membrane signaling nanodomains before undergoing internalization in a clathrin-dependent manner. Both GLP-1R signaling and trafficking are modulated by strategies targeting nanodomain segregation and cluster formation, including depletion of cholesterol or expression of a palmitoylation-defective GLP-1R mutant. Differences in receptor binding affinity exhibited by biased GLP-1R agonists, and modulation of binding kinetics with the positive allosteric modulator BETP, influence GLP-1R palmitoylation, clustering, nanodomain signaling, and internalization. Downstream effects on insulin secretion from pancreatic beta cells indicate that these processes are relevant to GLP-1R physiological actions and might be therapeutically targetable.

cell biology↗

bioRxiv2018

Facial masculinity is only weakly correlated with handgrip strength in young adult women

ObjectivesAncestrally, strength is likely to have played a critical role in determining the ability to obtain and retain resources and the allocation of social status among humans. Responses to facial cues of strength are therefore thought to play an important role in human social interaction. Although many researchers have proposed that sexually dimorphic facial morphology is reliably correlated with physical strength, evidence for this hypothesis is somewhat mixed. Moreover, to date, only one study has investigated the putative relationship between facial masculinity and physical strength in women. Consequently, we tested for correlations between handgrip strength and objective measures of face-shape masculinity.\n\nMethods531 women took part in the study. We measured each participants handgrip strength (dominant hand). Sexual dimorphism of face shape was objectively measured from each face photograph using two methods: discriminant analysis and vector analysis. These methods use shape components derived from principal component analyses of facial landmarks to measure the probability of the face being classified as male (discriminant analysis method) or to locate the face on a female-male continuum (vector analysis method).\n\nResultsOur analyses revealed that handgrip strength is, at best, only weakly correlated with facial masculinity in women. There was a weak significant association between handgrip strength and one measure of womens facial masculinity. The relationship between handgrip strength and our other measure of womens facial masculinity was not significant.\n\nDiscussionTogether, these results do not support the hypothesis that face-shape masculinity is an important cue of physical strength, at least in women.

animal behavior and cognition↗

bioRxiv2018

Does the interaction between partnership status and average progesterone level reliably predict women’s preferences for facial masculinity? Comment on Marcinkowska et al. (2018)

Many studies have attempted to identify biological factors that reliably predict individual differences in womens preferences for masculine male faces. Marcinkowska et al. (2018, Hormones & Behavior) recently reported that womens (N=102) preferences for facial masculinity were predicted by the interaction between their relationship status (partnered versus unpartnered) and average progesterone level. Because previous findings for between-women differences in masculinity preferences have often not replicated well, we attempted to replicate Marcinkowska et als result in an open data set from another recent study that had not tested this hypothesis (Jones et al., 2018 Psychological Science). In this sample of 316 women, we found that facial masculinity preferences were predicted by the interaction between womens relationship status and average progesterone level, consistent with Marcinkowska et als results. Together, these findings suggest that the combined effects of relationship status and average progesterone level may predict facial masculinity preferences relatively reliably.

animal behavior and cognition↗

bioRxiv2017

No evidence for correlations between handgrip strength and sexually dimorphic acoustic properties of voices

ObjectivesRecent research on the signal value of masculine physical characteristics in men has focused on the possibility that such characteristics are valid cues of physical strength. However, evidence that sexually dimorphic vocal characteristics are correlated with physical strength is equivocal. Consequently, we undertook a further test for possible relationships between physical strength and masculine vocal characteristics.\n\nMethodsWe tested the putative relationships between White UK (N=115) and Chinese (N=106) participants handgrip strength (a widely used proxy for general upper-body strength) and five sexually dimorphic acoustic properties of voices: fundamental frequency (F0), fundamental frequencys standard deviation (F0-SD), formant dispersion (Df), formant position (Pf), and estimated vocal-tract length (VTL).\n\nResultsAnalyses revealed no clear evidence that stronger individuals had more masculine voices.\n\nConclusionsOur results do not support the hypothesis that masculine vocal characteristics are a valid cue of physical strength.

evolutionary biology↗

bioRxiv2017

A longitudinal analysis of men’s intrasexual competitiveness, state anxiety, salivary testosterone, and salivary cortisol

Many previous studies have investigated relationships between mens competitiveness and testosterone. For example, the extent of changes in mens testosterone levels following a competitive task predicts the likelihood of them choosing to compete again. Recent work investigating whether individual differences in mens testosterone levels predict individual differences in their competitiveness have produced mixed results. Consequently, we investigated whether mens (N=59) scores on the Intrasexual Competitiveness Scale were related to either within-subject changes or between-subject differences in mens testosterone levels. Mens responses on the Intrasexual Competitiveness Scale did not appear to track within-subject changes in testosterone. By contrast with one recent study, mens Intrasexual Competitiveness Scale also did not appear to be related to between-individual differences in testosterone. Thus, our results present no evidence for associations between mens testosterone and their responses on the Intrasexual Competitiveness Scale.

animal behavior and cognition↗

bioRxiv2017

Hormonal correlates of pathogen disgust: Testing the Compensatory Prophylaxis Hypothesis

Raised progesterone during the menstrual cycle is associated with suppressed physiological immune responses, reducing the probability that the immune system will compromise the blastocysts development. The Compensatory Prophylaxis Hypothesis proposes that this progesterone-linked immunosuppression triggers increased disgust responses to pathogen cues, compensating for the reduction in physiological immune responses by minimizing contact with pathogens. Although a popular and influential hypothesis, there is no direct, within-woman evidence for correlated changes in progesterone and pathogen disgust. To address this issue, we used a longitudinal design to test for correlated changes in salivary progesterone and pathogen disgust (measured using the pathogen disgust subscale of the Three Domain Disgust Scale) in a large sample of women (N=375). Our analyses showed no evidence that pathogen disgust tracked changes in progesterone, estradiol, testosterone, or cortisol. Thus, our results provide no support for the Compensatory Prophylaxis Hypothesis of variation in pathogen disgust.

animal behavior and cognition↗

bioRxiv2017

General sexual desire, but not desire for uncommitted sexual relationships, tracks changes in women’s hormonal status

Several recent longitudinal studies have investigated the hormonal correlates of both young adult womens general sexual desire and, more specifically, their desire for uncommitted sexual relationships. Findings across these studies have been mixed, potentially because each study tested only small samples of women (Ns = 43, 33, and 14). Here we report results from a much larger (N = 375) longitudinal study of hormonal correlates of young adult womens general sexual desire and their desire for uncommitted sexual relationships. Our analyses suggest that within-woman changes in general sexual desire are negatively related to progesterone, but are not related to testosterone or cortisol. We observed some positive relationships for estradiol, but these were generally only significant for solitary sexual desire. By contrast with our results for general sexual desire, analyses showed no evidence that changes in womens desire for uncommitted sexual relationships are related to their hormonal status. Together, these results suggest that changes in hormonal status contribute to changes in womens general sexual desire, but do not influence womens desire for uncommitted sexual relationships.

animal behavior and cognition↗