Biology subjects

Austin, C.

Publications and source records attributed to Austin, C..

8 recordsLinked to original sources

bioRxiv2026

Driving theta-gamma oscillations modulates extrasynaptic GABAergic tone: a tACS-TMS study

BACKGROUNDTheta-gamma phase-amplitude coupled ({theta}{gamma}-PAC) oscillations in primary motor cortex (M1) have been shown to support motor skill acquisition. Past research has shown that driving gamma activity at the theta peak (TGP), but not the theta trough (TGT) using transcranial alternating current stimulation (tACS) enhances motor learning (Akkad et al., 2021). However, the neurophysiological mechanisms underlying this phase-specific effect remain unclear. METHODSIn a double-blind, sham-controlled, cross-over study, twenty-two healthy participants received 20 minutes of 75Hz/6Hz TGP-tACS, TGT-tACS, or sham stimulation over M1. We used paired-pulse transcranial magnetic stimulation (TMS) to assess GABAergic and NMDAR-mediated activity before, during, and after tACS. Outcome measures included short-interval intracortical inhibition at 1ms (SICI1ms; extrasynaptic GABAergic tone) and 2.5ms (SICI2.5ms; synaptic GABAA activity), intracortical facilitation at 12ms (ICF12ms; NMDAR activity), and motor evoked potential (MEP) amplitude (corticospinal excitability). RESULTSTGP-tACS selectively decreased SICI1ms, a putative marker of extrasynaptic GABAergic tone (main effect of Stimulation: p=.021), with significant differences between TGP and TGT during late stimulation (p=.047). No significant effects were observed on corticospinal excitability, synaptic GABAergic activity (SICI2.5ms), or NMDAR signalling (ICF12ms). CONCLUSIONSDriving theta-gamma oscillations at the theta peak using tACS specifically modulates extrasynaptic GABAergic tone in M1 without affecting corticospinal excitability or synaptic inhibition. Given that reductions in GABAergic signalling supports motor learning, these findings provide a neurophysiological mechanism for the phase-specific behavioural effects of {theta}{gamma}-PAC tACS and suggest a potential therapeutic approach for facilitating motor recovery after stroke. HighlightsO_LITheta-gamma peak tACS selectively reduces extrasynaptic GABA in human motor cortex C_LIO_LIOnly gamma at the peak, not trough, of theta stimulation modulates GABA C_LIO_LINo effects on corticospinal excitability, synaptic GABA, or NMDAR signalling C_LIO_LItACS-TMS reveals mechanism for phase-dependent motor learning effects C_LI

neuroscience↗

bioRxiv2025

Combined antagonism of Oncostatin M (OSM) and Interleukin 6 (IL-6) provides both anti-fibrotic and anti-inflammatory benefit in pulmonary fibrosis

Interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF) and systemic sclerosis-associated ILD (SSc-ILD), are irreversible fibrosing diseases with a mean survival time of less than 5 years for IPF. Poorly understood etiology and complex pathogenesis of these diseases have hampered the identification and development of effective therapeutics. Existing treatments can slow progressive fibrosis and lung function decline but do not stop it entirely, resulting in a minimal impact on patient survival. Thus, novel therapeutic interventions are needed. Tocilizumab, an anti-IL-6 receptor antibody, was recently approved by FDA for the treatment of SSc-ILD based on evidence demonstrating a reduction in the rate of lung function decline. In this study, we have characterized an IL-6-driven feed-forward myeloid axis contributing to lung inflammation providing a mechanistic hypothesis for tocilizumab. Concomitantly we have identified an oncostatin M (OSM) orchestrated lung injury response contributing to epithelial and endothelial cell disruption, myofibroblast activation and fibrosis. Despite dysregulated expression of IL11 in IPF, SSc-ILD, and murine models of fibrosis, we found no evidence for a pro-fibrotic role for IL-11 in vitro or in vivo. Instead, in pre-clinical models of IPF we demonstrate that antagonism of OSM alone, or to a greater degree in combination with IL-6, reduced lung fibrosis and inflammation. Translating these observations, we validated gp130:OSMR, rather than gp130:LIFR, as the dominant human receptor complex used by OSM, identifying OSMR as a potential therapeutic target to stall fibrosis.

immunology↗

bioRxiv2024

TRAIL induces caspase-dependent cleavage of specific components of the clathrin-mediated endocytosis machinery

It has been reported that caspase activation by the proapoptotic ligand Apo2L/TRAIL disrupts the clathrin-mediated endocytosis machinery (CMEM). To confirm whether TRAIL induces caspase-mediated cleavage of specific CMEM components, we examined the temporal and functional relationship between TRAIL-induced processing of the apoptosis-initiating protease, caspase-8, and the apoptosis-executing protease, caspase-3, versus cleavage of specific adaptin (AP) and clathrin heavy chain (CHC) proteins. TRAIL induced time-dependent proteolytic processing of caspase-8 and caspase-3, which coincided with cleavage of AP2 and CHC. The pan caspase inhibitor zVAD-FMK, which blocked caspase processing in response to TRAIL, also prevented the cleavage AP2. Whereas FADD-deficient or caspase-8-deficient cells showed little or no TRAIL-driven cleavage of either AP2 or CHC, Bax-deficient or caspase-3-deficient cell lines retained AP2 cleavage but failed to cleave CHC in response to TRAIL. The DNA-damaging agent doxorubicin also led to processing of caspase-8 and caspase-3 in conjunction ith cleavage of AP2 and CHC. Together, these results confirm that TRAIL induces caspase-dependent cleavage of AP2 and CHC. Whereas TRAIL-driven cleavage of both AP2 and CHC requires caspase-8, cleavage of CHC, but not of AP2, requires caspase-3. MATERIALS AND METHODS Cell lines and cell cultureAll cell lines were obtained from ATCC or as kind gifts from Dr. Bert Vogelstein (HCT116 Bax-/-) and Dr. John Blenis (Jurkat I9.2 and E1). Cell lines were cultured with standard media as previously described (1). Immunoblot analysisCells were lysed in RIPA lysis buffer (20-188, Millipore) supplemented with Halt protease and phosphatase inhibitor cocktail (ThermoFisher Scientific) and kept on ice for 30 min. Lysates were cleared by centrifugation at 13,600 x g for 15 min at 4 {degrees}C, and protein amount was determined by BCA protein assay (ThermoFisher Scientific). Protein was denatured by adding NuPAGE LDS buffer and DTT reducing buffer (Invitrogen) and incubating the samples at 95 {degrees}C for 5 min. Equal amounts of denatured protein were loaded into each well of NuPAGE pre-cast gels (Invitrogen), resolved by SDS-PAGE, and electro-transferred to nitrocellulose membranes using the iBLOT2 system (Invitrogen). Membranes were blocked in a 5% nonfat milk solution for 1 hr at room temperature and probed with the corresponding primary antibody at 1:1,000 dilution overnight at 4 {degrees}C. This was followed by incubation with the corresponding horseradish peroxidase (HRP)- conjugated secondary antibody at 1:10,000 dilution during 1 hr at room temperature. All secondary antibodies were from Jackson Laboratories. The primary antibodies and secondary HRP-conjugated antibodies are listed respectively in Table 1 and Table 2. {beta}-actin IB was used to verify uniformity of protein loading and electro-transfer. O_TBL View this table: org.highwire.dtl.DTLVardef@ed5a65org.highwire.dtl.DTLVardef@c9aecdorg.highwire.dtl.DTLVardef@f31b4aorg.highwire.dtl.DTLVardef@849deaorg.highwire.dtl.DTLVardef@9b847b_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONPrimary antibodies used for IB analysis C_TABLECAPTION C_TBL O_TBL View this table: org.highwire.dtl.DTLVardef@16c33forg.highwire.dtl.DTLVardef@6c6b81org.highwire.dtl.DTLVardef@5efb4org.highwire.dtl.DTLVardef@1bc354forg.highwire.dtl.DTLVardef@15007aa_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2.C_FLOATNO O_TABLECAPTIONHorseradish peroxidase conjugated secondary antibodies used for IB analysis C_TABLECAPTION C_TBL Additional reagentsRecombinant soluble non-tagged human TRAIL (Apo2L.0) and Flag-tagged TRAIL were prepared at Genentech. Flag-tagged TRAIL was crosslinked with anti-Flag M2 antibody at a ligand-to-antibody molar ratio of 1:2. zVAD-FMK was purchased from R & D Systems, FMK001. Doxorubicin was purchased from Sigma Aldrich, D1515.

cell biology↗

bioRxiv2023

Lung-innervating neurons expressing Tmc3 can induce broncho-constriction and dilation with direct consequences for the respiratory cycle

Sensory neurons of the vagal ganglia (VG) innervate lungs and play a critical role in maintaining airway homeostasis. However, the specific VG neurons that innervate lungs, and the mechanisms by which these neurons sense and respond to airway insults, are not well understood. Here, we identify a subpopulation of lung-innervating VG neurons defined by their expression of Tmc3. Single cell transcriptomics illuminated several subpopulations of Tmc3+ sensory neurons, revealing distinct Piezo2- and Trpv1-expressing subclusters. Furthermore, Tmc3 deficiency in VG neurons leads to global and subcluster specific transcriptional changes related to metabolic and ion channel function. Importantly, we show that broncho-constriction and dilation can be modulated through inhibition or activation of Tmc3+ VG neurons resulting in a decrease or increase of end-expiratory lung volume, respectively. Together, our data show that Tmc3 is a marker of lung-innervating neurons and may play a pivotal role in maintaining fundamental inspiratory and expiratory processes. SignificanceHarnessing the neuronal mechanisms that regulate lung function offers potential alternatives to existing corticosteroid treatment regimens for respiratory illness associated with acute bronchoconstriction including asthma, COPD, and emphysema. Our findings define Transmembrane channel-like 3, Tmc3, as a marker of lung-innervating sensory neurons, identify distinct subpopulations of Tmc3+ neurons with unique transcriptional profiles, and show that activation or inhibition of these neurons has a significant impact on airway function. Our work highlights potential avenues of novel targeted intervention in respiratory conditions driven by dysfunctional neuronal reflexes.

neuroscience↗

bioRxiv2023

Oxygen isotopes in orangutan teeth reveal recent and ancient climate variation

Studies of climate variation commonly rely on chemical and isotopic changes recorded in sequentially-produced growth layers, such as in corals, shells and tree rings, as well as in accretionary deposits--ice and sediment cores, and speleothems. Oxygen isotopic compositions ({delta}18O) of tooth enamel are a direct method of reconstructing environmental variation experienced by an individual animal. Here we utilize long-forming orangutan dentitions (Pongo spp.) to probe recent and ancient rainfall trends on a weekly basis over [~] 3-11 years per individual. We first demonstrate the lack of any consistent isotopic enrichment effect during exclusive nursing, supporting the use of primate first molar teeth as environmental proxies. Comparisons of {delta}18O values (n = 2016) in twelve molars from six modern Bornean and Sumatran orangutans reveal a high degree of overlap, with more consistent annual and bimodal rainfall patterns in the Sumatran individuals. Comparisons with fossil orangutan {delta}18O values (n = 955 measurements from six molars) reveal similarities between modern and late Pleistocene fossil Sumatran individuals, but differences between modern and late Pleistocene/early Holocene Bornean orangutans. These suggest drier and more open environments with reduced monsoon intensity during this earlier period in northern Borneo, consistent with other Niah Caves studies and long-term speleothem {delta}18O records in the broader region. This approach can be extended to test hypotheses about the paleoenvironments that early humans encountered in southeast Asia.

paleontology↗

bioRxiv2020

More from less: Genome skimming for nuclear markers for animal phylogenomics, a case study using decapod crustaceans

Low coverage genome sequencing is rapid and cost-effective for recovering complete mitochondrial genomes for animal phylogenomics. The recovery of high copy number nuclear genes, including histone H3, 18S and 28S ribosomal RNAs, is also possible using this approach. In this study, we explore the potential of the genome skimming (GS) to recover additional nuclear genes from shallow sequencing projects. Using an in silico baited approach, we recover three additional core histone genes (H2A, H2B and H4) from our existing collection of low coverage decapod crustacean dataset (99 species, 69 genera, 38 families, 10 infraorders). Phylogenetic analyses based on various combinations of mitochondrial and nuclear genes for the entire decapod dataset and 40 species of crayfish (Infraorder Astacidea) found that the evolutionary rates for different classes of genes varied widely. The highlight being a very high level of congruence found between trees from the six nuclear genes and those derived from the mitogenome sequences for freshwater crayfish. These findings indicate that nuclear genes recovered from the same genome skimming datasets designed to obtain mitogenomes can be used to support more robust and comprehensive phylogenetic analyses. Further, a search for additional intron-less nuclear genes identified several high copy number genes across the decapod dataset and recovery of NaK, PEPCK and GAPDH gene fragments is possible at slightly elevated coverage, suggesting the potential and utility of GS in recovering even more nuclear genetic information for phylogenetic studies from these inexpensive and increasingly abundant datasets.

evolutionary biology↗

bioRxiv2020

Massive-scale biological activity-based modeling identifies novel antiviral leads against SARS-CoV-2

The recent global pandemic caused by the new coronavirus SARS-CoV-2 presents an urgent need for new therapeutic candidates. While the importance of traditional in silico approaches such as QSAR in such efforts in unquestionable, these models fundamentally rely on structural similarity to infer biological activity and are thus prone to becoming trapped in the very nearby chemical spaces of already known ligands. For novel and unprecedented threats such as COVID-19 much faster and efficient paradigms must be devised to accelerate the identification of new chemical classes for rapid drug development. Here we report the development of a new biological activity-based modeling (BABM) approach that builds on the hypothesis that compounds with similar activity patterns tend to share similar targets or mechanisms of action. In BABM, compound activity profiles established on massive scale across multiple assays are used as signatures to predict compound activity in a new assay or against a new target. We first trained and validated this approach by identifying new antiviral lead candidates for Zika and Ebola based on data from ~0.5 million compounds screened against ~2,000 assays. BABM models were then applied to predict ~300 compounds not previously reported to have activity for SARS-CoV-2, which were then tested in a live virus assay with high (>30%) hit rates. The most potent compounds showed antiviral activities in the nanomolar range. These potent confirmed compounds have the potential to be further developed in novel chemical space into new anti-SARS-CoV-2 therapies. These results demonstrate unprecedented ability using BABM to predict novel structures as chemical leads significantly beyond traditional methods, and its application in rapid drug discovery response in a global public health crisis.

cell biology↗

bioRxiv2019

Better tired than lost: turtle ant trail networks favor coherence over shortest paths

Creating a routing backbone is a fundamental problem in both biology and engineering. The routing backbone of the trail networks of arboreal turtle ants (Cephalotes goniodontus) connects many nests and food sources using trail pheromone deposited by ants as they walk. Unlike species that forage on the ground, the trail networks of arboreal ants are constrained by the vegetation. We examined what objectives the trail networks meet by comparing the observed ant trail networks with networks of random, hypothetical trail networks in the same surrounding vegetation and with trails optimized for four objectives: minimizing path length, minimizing average edge length, minimizing number of nodes, and minimizing opportunities to get lost. The ants trails minimized path length by minimizing the number of nodes traversed rather than choosing short edges. In addition, the ants trails reduced the opportunity for ants to get lost at each node, favoring nodes with 3D configurations most likely to be reinforced by pheromone. Thus, rather than finding the shortest edges, turtle ant trail networks take advantage of natural variation in the environment to favor coherence, keeping the ants together on the trails. Author SummaryWe investigated the trail networks of arboreal turtle ants in the canopy of the tropical forest, to ask what characterizes the colonys choice of foraging paths within the vegetation. We monitored day to day changes in the junctions and edges of trail networks of colonies in the dry forest of western Mexico. We compared the paths used by the ants to simulated random paths in the surrounding vegetation. We found that the paths of turtle ants prioritize coherence, keeping ants together on the trail, over minimizing the average edge length. The choice of paths reduces the number of junctions in the trail where ants could get lost, and favors junctions with a physical configuration that makes it likely that successive ants will reinforce the same path. Our work suggests that design principles that emphasize keeping information flow constrained to streamlined, coherent trails may be useful in human-designed distributed routing and transport networks or robot swarms.

ecology↗