Biology subjects

Johnson, P.

Publications and source records attributed to Johnson, P..

31 records · Page 2Linked to original sources

bioRxiv2022

Multiple lines of evidence indicate survival of the Ivory-billed Woodpecker in Louisiana

The history of decline of the Ivory-billed Woodpecker is long, complex, and controversial. The last widely accepted sighting of this species in continental North America was 1944. Reports of Ivory-billed Woodpeckers have continued, yet in 2021 the U.S. Fish and Wildlife Service proposed declaring the species extinct. We draw on 10 years of search effort, and provide trail camera photos and drone videos suggesting the consistent presence of Ivory-billed Woodpeckers at our study site. Data indicate repeated re-use of foraging sites and core habitat. We offer insights into behaviors of the Ivory-billed Woodpecker that contribute to difficulty in finding this species. We discuss results with regard to the value of accumulated evidence, and what repeated observations may indicate for continued survival of this iconic species.

ecology↗

bioRxiv2021

Ion currents through Kir potassium channels are gated by anionic lipids.

Ion currents through potassium channels are gated. Constriction of the ion conduction pathway at the inner helix bundle, the textbook gate of Kir potassium channels, has been shown to be an ineffective permeation control, creating a rift in our understanding of how these channels are gated. Here we present the first evidence that anionic lipids act as interactive response elements sufficient to gate potassium conduction. We demonstrate the limiting barrier to K+ permeation lies within the ion conduction pathway and show that this gate is operated by the fatty acyl tails of lipids that infiltrate the conduction pathway via fenestrations in the walls of the pore. Acyl tails occupying a surface groove extending from the cytosolic interface to the conduction pathway provide a potential means of relaying cellular signals, mediated by anionic lipid head groups bound at the canonical lipid binding site, to the internal gate.

biochemistry↗

bioRxiv2021

The immunophilin protein FKBPL and its peptide derivatives are novel regulators of vascular integrity and inflammation via NF-kappaB signaling

A breakdown in vascular integrity and excessive inflammation are hallmarks of serious pathological conditions including sepsis, acute respiratory distress syndrome (ARDs) and most recently, severe COVID-19. FK506 - binding protein like (FKBPL) is a member of the immunophilin protein superfamily with potent anti-tumor activity through inhibition of angiogenesis and cancer stemness. An FKBPL-based 23mer peptide, ALM201, displayed a good safety and pharmacokinetic profile in a Phase 1a oncology clinical trial and was subsequently designated orphan drug status by the FDA in ovarian cancer. Here we describe a novel role for FKBPL and its peptides in regulating vascular integrity and cytokine production though modulating NF-{kappa}B signaling. FKBPL knockdown promoted endothelial cell barrier permeability, which was further exacerbated upon stimulation with lipopolysaccharide (LPS) and accompanied by increased expression of TNF mRNA and phosphorylation of p65(RelA). Whilst treatment with the FKBPL based pre-clinical peptide, AD-01, increased VE-cadherin endothelial tight junctions following LPS stimulation. Bone marrow derived macrophages (BMDM) from FKBPL haploinsufficient mice (Fkbpl+/-) also demonstrated increased phosphorylation of p65(RelA) in response to LPS stimulation compared to wild-type mice. Furthermore, treatment with AD-01 inhibited p65(RelA) phosphorylation following LPS stimulation resulting in reduced NF-{kappa}B target gene expression and proinflammatory cytokine production. In an in vivo LPS survival model, Fkbpl+/- mice have reduced survival compared to wild-type mice. Moreover, treatment of wild-type mice with the clinical FKBPL-based peptide, ALM201, following LPS injection resulted in a 100% survival rate in mice at experimental endpoint, as well as an abrogation of production of pro-inflammatory cytokines, TNF and IL-6, in peritoneal lavage washings. Analysis of human genetic biobanks found an association between common genetic variants associated with FKBPL and traits associated with inflammatory disorders such as psoriasis, rheumatoid arthritis and high lymphocyte count. In summary, for the first time, we describe a novel role for FKBPL as a regulator of inflammation and vascular integrity through modulating NF-{kappa}B signaling and FKBPL based therapies demonstrate potent anti-inflammatory activity.

immunology↗

bioRxiv2020

Differences in Chemo-signaling Compound-Evoked Brain Activity in Male and Female Young Adults: A Pilot Study in the Role of Sexual Dimorphism in Olfactory Chemo-Signaling

IntroductionPrevious studies have shown that putative pheromones 4,16-androstadien-3-one (AND) and estra-1,3,5(10),16-tetraen-3-ol (EST) cause activation in the preoptic area/anterior hypothalamus in men and women. Sex differences in neural activation patterns have been demonstrated when participants are subject to pheromone stimulation; however, whether other compounds give rise to similar neural activity has not been completely investigated. MethodsTwenty-nine young adults [16 female (21.3+/-0.54; mean yrs+/-SE), 13 male (22.85+/-0.42)] participated in a 3-block design, where participants were exposed to a scent (lavender), a synthetic male pheromone (4,16-androstadien-3b-ol; ALD), and a synthetic female pheromone (1,3,5(10),16-Estratetraen-3-ol; EST) via an automated olfactometer. Whole-brain, high-resolution (1.8mm3) functional MRI data from a Siemens Trio 3T MRI scanner were collected during all blocks. Five adults were excluded due to excessive movement. MANOVA analysis, a 2 x 3 multivariate model and analysis of 2x2 effects between sex and subsets of stimuli was done for activation over the whole brain and small volumes involved in olfaction. ResultsExploratory analysis of 2x2 effects between sex and subsets of stimuli exhibited significant interactions when assessing activations over the whole brain, and small volumes involved in olfaction. The left and right frontal poles (LFP, RFP) shows significant interaction when assessing sex with lavender and EST for whole brain analysis. For small volume analysis, the right orbitofrontal cortex (ROFC) exhibited a sex with lavender and ALD interaction, and a sex with lavender and EST interaction was observed in the left inferior frontal gyrus (LIFG). Main effects of sex, stimulus, or interaction show no differences analyzed using a 2 x 3 multivariate model. ConclusionThe study shows there is a sexually dimorphic response in the olfactory system to pheromones not previously studied. Scents like lavender do not have this same response. These distinct functional differences in activation patterns may be a result of neural development and maturation differences between sexes. Future studies should expand this pilot study and involve a younger demographic to accurately determine the age at which the olfactory response differentiates between males and females.

neuroscience↗

bioRxiv2020

KDM5 inhibition offers a novel therapeutic strategy for the treatment of KMT2D mutant lymphomas

Loss-of-function mutations in KMT2D are a striking feature of the germinal centre (GC) lymphomas, resulting in decreased H3K4 methylation and altered gene expression. We hypothesised that inhibition of the KDM5 family, which demethylates H3K4me3/me2, would re-establish H3K4 methylation and restore the expression of genes repressed upon loss of KMT2D. KDM5-inhibition increased H3K4me3 levels and caused an anti-proliferative response in vitro, which was markedly greater in both endogenous and CRISPR-edited KMT2D mutant DLBCL cell lines, whilst tumour growth was inhibited in KMT2D mutant xenografts in vivo. KDM5-inhibition reactivated both KMT2D-dependent and -independent genes, resulting in diminished B-cell receptor signalling and altered expression of BCL2 family members, including BCL2 itself, allowing it to synergise with agents targeting these pathways. KDM5-inhibition may offer an effective therapeutic strategy for ameliorating KMT2D loss-of-function mutations in GC-lymphomas.Statement of significance We detail a novel way of reverting the effects of loss-of-function mutations in the histone methyltransferase KMT2D by inhibiting the KDM5 demethylase family, increasing levels of H3K4me3 and restoring expression of KMT2D regulated genes.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cancer biology↗

bioRxiv2020

Sorcin stimulates Activation Transcription Factor 6α (ATF6) transcriptional activity

Levels of the transcription factor ATF6, a key mediator of the unfolded protein response, that provides cellular protection during the progression endoplasmic reticulum (ER) stress, are markedly reduced in the pancreatic islet of patients with type 2 diabetes and in rodent models of the disease, including ob/ob and high fat-fed mice. Sorcin (gene name SRI) is a calcium (Ca2+) binding protein involved in maintaining ER Ca2+ homeostasis. We have previously shown that overexpressing sorcin under the rat insulin promoter in transgenic mice was protective against high fat diet-induced pancreatic beta cell dysfunction, namely preserving intracellular Ca2+ homeostasis and glucose-stimulated insulin secretion during lipotoxic stress. Additionally, sorcin overexpression was apparently activating ATF6 signalling in MIN6 cells despite lowering ER stress. Here, in order to investigate further the relationship between sorcin and ATF6, we describe changes in sorcin expression during ER and lipotoxic stress and changes in ATF6 signalling after sorcin overexpression or inactivation, both in excitable and non-excitable cells. Sorcin mRNA levels were significantly increased in response to the ER stress-inducing agents thapsigargin and tunicamycin, but not by palmitate. On the contrary, palmitate caused a significant decrease in sorcin expression as assessed by both qRT-PCR and Western blotting despite inducing ER stress. Moreover, palmitate prevented the increase in sorcin expression induced by thapsigargin. In addition, sorcin overexpression significantly increased ATF6 transcriptional activity, whereas sorcin inactivation decreased ATF6 signalling. Finally, sorcin overexpression increased levels of ATF6 immunoreactivity and FRET imaging experiments following ER stress induction by thapsigargin showed a direct sorcin-ATF6 interaction. Altogether, our data suggest that sorcin down-regulation during lipotoxicity may prevent full ATF6 activation and a normal UPR during the progression of obesity and insulin resistance, contributing to beta cell failure and type 2 diabetes.

cell biology↗

bioRxiv2019

RNA sequencing and lipidomic analysis of alveolar macrophages from normal and CD44 deficient mice

Alveolar macrophages (AMs) are CD44 expressing cells that reside in the alveolar space where they maintain lung homeostasis by serving critical roles in immunosurveillance and lipid surfactant catabolism. AMs lacking CD44 are unable to bind the glycosaminoglycan, hyaluronan, which compromises their survival and leads to reduced numbers of AMs in the lung. Using RNA sequencing, lipidomics and multiparameter flow cytometry, we demonstrate that CD44-/- mice have impaired AM lipid homeostasis and increased surfactant lipids in the lung. CD44-/- AMs had increased expression of CD36, a lipid scavenger receptor, as well as increased intracellular lipid droplets, giving them a foamy appearance. RNA sequencing revealed the differential expression of genes associated with lipid efflux and metabolism in CD44-/- AMs. Lipidomic analysis showed increased lipids in both the supernatant and cell pellet extracted from the bronchoalveolar lavage of CD44-/- mice. Phosphatidylcholine species, cholesterol, oxidized phospholipids and levels of reactive oxygen species (ROS) were increased in CD44-/- AMs. Oxidized phospholipids were more cytotoxic to CD44-/- AMs and induced greater lung inflammation in CD44-/- mice. Reconstitution of CD44+/+ mice with CD44-/- bone marrow as well as adoptive transfer of CD44-/- AMs into CD44+/+ mice showed that lipid accumulation in CD44-/- AMs occurred irrespective of the lung environment, suggesting a cell intrinsic defect. Administration of colony stimulating factor 2 (CSF-2), a critical factor in AM development and maintenance, increased AM numbers in CD44-/- mice and decreased phosphatidylcholine levels in the bronchoalveolar lavage, but was unable to decrease intracellular lipid accumulation in CD44-/- AMs. Peroxisome proliferator-activated receptor gamma (PPAR{gamma}), downstream of CSF-2 signaling and a regulator of lipid metabolism, was reduced in the nucleus of CD44-/- AMs, and PPAR{gamma} inhibition in normal AMs increased their lipid droplets. Thus, CD44 deficiency causes defects in AMs that lead to abnormal lipid accumulation and oxidation, which exacerbates oxidized lipid-induced lung inflammation. Collectively, these findings implicate CD44 as a regulator of lung homeostasis and inflammation.

immunology↗

bioRxiv2019

Brain morphology predicts long-term placebo response in multiple sclerosis patients

Although significant insights have been gained into the neural mechanisms of acute placebo responses, less is known about the mechanisms of longer-term placebo responses, such as those seen in clinical trials, or the interactions between these mechanisms and brain disease. We examined neuropathological and morphological brain correlates of placebo responses in a randomized clinical trial of a controversial endovascular treatment ("liberation therapy") for multiple sclerosis. Patients were randomized to receive either balloon or sham extracranial venoplasty and followed for 48 weeks. The trial did not support therapeutic efficacy of venoplasty, but a subset of both venoplasty- and sham-treated patients reported an improvement in health-related quality of life that peaked at 12 weeks following treatment, suggesting a placebo response. Placebo responders had higher lesion activity than placebo non-responders. Although placebo responders did not differ from non-responders in terms of total normalized brain volume, regional grey or white matter volume or cortical thickness, graph theoretical analysis of cortical thickness covariance showed that placebo non-responders had a more homogenous cortical thickness topology with a more small-world-like architecture. In placebo non-responders, lesion load inversely predicted cortical thickness in primary somatosensory and motor areas, association areas, precuneus and insula, primarily in the right hemisphere. In placebo responders, lesion load was unrelated to cortical thickness. The neuropathological process in MS may result in a cortical configuration that is less suited to functional integration and less capable of generating a sustained placebo response.

neuroscience↗

bioRxiv2019

Genomic interrogation of the burden and transmission of multidrug-resistant pathogens within and across hospital networks

BackgroundMultidrug-resistant organisms (MDROs) disproportionately affect hospitalized patients due to the combination of comorbidities, frequent antimicrobial use, and in-hospital MDRO transmission. Identification of MDRO transmission by hospital microbiology laboratories is difficult due to limitations of existing typing methods.\n\nMethodsWe conducted a prospective multicenter genomics implementation study (8 hospitals, 2800 beds) from 24th April to 18th June 2017 in Melbourne, Australia. Clinical and screening isolates from hospital inpatients were collected for six MDROs (vanA VRE, MRSA, ESBL E. coli [ESBL-Ec] and Klebsiella pneumoniae [ESBL-Kp], and carbapenem-resistant Pseudomonas aeruginosa [CRPa] and Acinetobacter baumannii [CRAb]), sequenced (Illumina NextSeq) and analyzed using open-source tools. MDRO transmission was assessed by genomics (core SNP phylogeny, grouped by species and ST) and compared to epidemiologic data.\n\nResults408 isolates were collected from 358 patients; 47.5% were screening isolates. ESBL-Ec was most common (52.5%), then MRSA (21.6%), vanA VRE (15.7%) and ESBL-Kp (7.6%).\n\nWe define the transmission rate for each MDRO by genomics and epidemiology; 31.6% of all study patients had potential genomic links to other study isolates; 86% of these were confirmed by epidemiologic links (probable or possible transmission). The highest transmission rates occurred with vanA VRE (88.4% of patients).\n\nConclusionsCombining genomics with high-quality epidemiologic data gives substantial insights into the burden and distribution of critical MDROs in hospitals, including in-hospital transmission. By defining transmission rates by genomics, we hope to enable comparisons over time and between sites, and introduce this as a new outcome measure to assess the efficacy of infection control interventions.

genomics↗

bioRxiv2019

Does skin surface temperature variation account for Buruli ulcer lesion distribution?

BackgroundBuruli ulcer is a necrotising infection of skin and soft tissue caused by Mycobacterium ulcerans (M. ulcerans). Buruli ulcer most often occurs on limbs, and it is hypothesized this is explained by direct exposure to the environment. However, even on exposed areas Buruli ulcer is not randomly distributed. M. ulcerans prefers an in vitro temperature of 30-33{degrees}C and growth is inhibited at higher temperatures. This study investigated whether variations in skin surface temperature distribution in healthy volunteers could partly account for Buruli ulcer lesion distribution.\n\nMethodology/Principal FindingsIn this observational study, a thermal camera (FLIR E8) was used to measure skin surface temperature at the sternal notch and at 44 predetermined locations on the limbs of 18 human participants. Body locations of high, middle and low Buruli ulcer incidence were identified from existing density maps of lesion distribution. Skin temperature of the three incidence location groups were compared, and differences in age and sex groups were also analysed.\n\nWe found an inverse relationship between skin temperature and lesion distribution, where high incidence locations were significantly cooler and low incidence locations significantly warmer (Kruskal-Wallis test p<0.0001). Linear mixed effects regression analysis estimated that skin surface temperature accounts for 9.5% of the variance in Buruli ulcer lesion distribution (marginal R-squared = 0.095). Men had warmer upper and lower limbs than females (Mann-Whitney U test p=0.0003 and p<0.0001 respectively).\n\nConclusions/SignificanceWe have found an inverse relationship between skin temperature and Buruli ulcer lesion distribution, however this association is weak. Additional unknown factors are likely to be involved that explain the majority of the variation in Buruli lesion distribution.\n\nAuthor SummaryBuruli ulcer is a destructive soft tissue infection caused by the bacterium Mycobacterium ulcerans. The precise mode of transmission remains unknown. One theory proposes that transmission occurs by direct contact with a contaminated environment. Lesions occur mostly on limbs, and it is hypothesized this is explained by direct exposure to the environment. However even on exposed areas, lesions are not randomly distributed. This study investigated whether skin surface temperature can partly explain Buruli ulcer lesion distribution. We measured the skin surface temperature of 18 healthy participants using a thermal camera and compared temperature distribution to the distribution of Buruli ulcer lesions investigated in a previously published study. We found that there is a negative correlation between skin temperature and Buruli ulcer lesion incidence. However, the association is weak and other factors e.g. clothing choice and insect biting patterns may explain the majority of Buruli ulcer lesion distribution.

pathology↗

bioRxiv2019

Influence of genetic variants on gene expression in human pancreatic islets - implications for type 2 diabetes

Most signals detected by genome-wide association studies map to non-coding sequence and their tissue-specific effects influence transcriptional regulation. However, many key tissues and cell-types required for appropriate functional inference are absent from large-scale resources such as ENCODE and GTEx. We explored the relationship between genetic variants influencing predisposition to type 2 diabetes (T2D) and related glycemic traits, and human pancreatic islet transcription using RNA-Seq and genotyping data from 420 islet donors. We find: (a) eQTLs have a variable replication rate across the 44 GTEx tissues (<73%), indicating that our study captured islet-specific cis-eQTL signals; (b) islet eQTL signals show marked overlap with islet epigenome annotation, though eQTL effect size is reduced in the stretch enhancers most strongly implicated in GWAS signal location; (c) selective enrichment of islet eQTL overlap with the subset of T2D variants implicated in islet dysfunction; and (d) colocalization between islet eQTLs and variants influencing T2D or related glycemic traits, delivering candidate effector transcripts at 23 loci, including DGKB and TCF7L2. Our findings illustrate the advantages of performing functional and regulatory studies in tissues of greatest disease-relevance while expanding our mechanistic insights into complex traits association loci activity with an expanded list of putative transcripts implicated in T2D development.

genomics↗

bioRxiv2018

Co-exposure to multiple Ranavirus types enhances viral infectivity and replication in a larval amphibian system

Multiple pathogens commonly co-occur in animal populations, yet few studies demonstrate how co-exposure of individual hosts scales up to affect transmission. Although viruses in the genus Ranavirus are globally widespread and multiple virus species or strains likely co-occur in nature, no studies have examined how co-exposure affects infection dynamics in larval amphibians. We exposed individual Rana aurora (Northern red-legged frog) larvae to Ambystoma tigrinum virus (ATV), frog virus 3 (FV3), or an FV3-like strain isolated from a frog-culturing facility in Georgia, USA (RCV-Z2). We compared single-virus to pairwise co-exposures, while experimentally accounting for dosage. Co-exposure to ATV and FV3-like strains resulted in almost twice as many infected individuals compared to single-virus exposures, suggesting an effect of co-exposure on viral infectivity. The viral load in infected individuals exposed to ATV and FV3 was also higher than the single-dose FV3 treatment, suggesting an effect of co-exposure on viral replication. In a follow-up experiment, we examined how the co-occurrence of ATV and FV3 affected epizootics in mesocosm populations of larval Pseudacris triseriata (Western chorus frog). Although ATV did not generally establish within host populations (<4% prevalence), when ATV and FV3 were both present, this co-exposure resulted in a larger epizootic of FV3. Our results emphasize the importance of multi-pathogen interactions in epizootic dynamics and have management implications for natural and commercial amphibian populations.

ecology↗

bioRxiv2018

Finding CRISPR’s Niche: Oxygen and Temperature Shape the Incidence of Adaptive Immunity

Bacteria and archaea are locked in a near-constant battle with their viral pathogens. Despite previous mechanistic characterization of numerous prokaryotic defense strategies, the underlying ecological drivers of different strategies remain largely unknown and predicting which species will take which strategies remains a challenge. Here, we focus on the CRISPR immune strategy and develop a phylogenetically-corrected machine learning approach to build a predictive model of CRISPR incidence using data on over 100 traits across over 2600 species. We discover a strong but hitherto-unknown negative interaction between CRISPR and aerobicity, which we hypothesize may result from interference between CRISPR associated proteins and non-homologous end-joining DNA repair due to oxidative stress. Our predictive model also quantitatively confirms previous observations of an association between CRISPR and temperature. Finally, we contrast the environmental associations of different CRISPR system types (I, II, III) and restriction modification systems, all of which act as intracellular immune systems.

microbiology↗