Biology subjects

Freedman, S.

Publications and source records attributed to Freedman, S..

5 recordsLinked to original sources

bioRxiv2024

Persistent cross-species transmission systems dominate Shiga toxin-producing Escherichia coli O157:H7 epidemiology in a high incidence region: a genomic epidemiology study

BackgroundSeveral areas of the world suffer notably high incidence of Shiga toxin-producing Escherichia coli, among them Alberta, Canada. We assessed the impact of persistent cross-species transmission systems on the epidemiology of E. coli O157:H7 in Alberta. MethodsWe sequenced and assembled 229 E. coli O157:H7 isolates originating from collocated cattle (n=108) and human (n=121) populations from 2007-2015 in Alberta. We constructed a timed phylogeny using BEAST2 using a structured coalescent model. We then extended the tree with human isolates through 2019 (n=430) to assess the long-term disease impact of locally persistent lineages. Shiga toxin gene (stx) profile was determined for all isolates. ResultsDuring 2007 to 2015, we estimated 108 (95% HPD 104, 112) human lineages arose from cattle lineages, and 14 (95% HPD 5, 23) from other human lineages; i.e., 88.5% of human lineages arose from cattle lineages. We identified 11 persistent lineages local to Alberta, which were associated with 38.0% (95% CI 29.3%, 47.3%) of human isolates. Of 117 isolates in locally persistent lineages, 6.0% carried only the Shiga toxin gene stx2a and the rest both stx1a and stx2a. During the later period, six locally persistent lineages continued to be associated with human illness, including 74.7% (95% CI 68.3%, 80.3%) of reported cases in 2018 and 2019. The stx profile of isolates in locally persistent lineages shifted from the earlier period, with 51.2% encoding only stx2a. ConclusionsOur study identified multiple locally evolving lineages transmitted between cattle and humans persistently associated with E. coli O157:H7 illnesses for up to 13 years. Of concern, there was a dramatic shift in locally persistent lineages toward strains with the more virulent stx2a-only profile. Locally persistent lineages may be a principal cause of the high incidence of E. coli O157:H7 in locations such as Alberta and offer opportunities for understanding the disease ecology supporting E. coli O157:H7 persistence, as well as for local prevention efforts.

microbiology↗

bioRxiv2022

Quantitative Analysis of Transcriptome Dynamics Provides Novel Insights into Developmental State Transitions

During embryogenesis, the developmental potential of initially pluripotent cells becomes progressively restricted as they transit to lineage restricted states. The pluripotent cells of Xenopus blastula-stage embryos are an ideal system in which to study cell state transitions during developmental decision-making, as gene expression dynamics can be followed at high temporal resolution. Here we use transcriptomics to interrogate the process by which pluripotent cells transit to four different lineage-restricted states: neural progenitors, epidermis, endoderm and ventral mesoderm, providing quantitative insights into the dynamics of Waddingtons landscape. Our findings shed light on why the neural progenitor state is the default lineage state for pluripotent cells, and uncover novel components of lineage-specific gene regulation. These data reveal an unexpected overlap in the transcriptional responses to BMP4/7 and activin signaling, and provide mechanistic insight into how the timing of signaling inputs such as BMP are temporally controlled to ensure correct lineage decisions. Together these analyses provide quantitative insights into the logic and dynamics of developmental decision making in early embryos.

developmental biology↗

bioRxiv2019

Pancreatic tumor organoids for modeling in vivo drug response and discovering clinically-actionable biomarkers

Patient-derived models are transforming translational cancer research. It is not clear if the emergence of patient-derived organoid (PDO) models can extend the utility of the widely used patient-derived xenograft (PDX). In addition, the utility of PDO models for serum biomarker discovery is not known. Here, we demonstrate that PDO models recapitulate the genomics, cell biology, glycomics and drug responses observed in PDX models. Furthermore, we demonstrate the applicability of PDO models for identification of N-glycans that are enriched in the glycome of pancreatic ductal adenocarcinoma (PDAC). Surprisingly, among all the glycans observed in PDX and PDOs, a core set of 57 N-glycans represent 50-94% of the relative abundance of all N-glycans detected, suggesting that only a subset of glycans dominate the cell surface landscape in PDAC. In addition, we outline a tumor organoid-based pipeline to identify surface proteins in extracellular vesicles (EV) from media supernatant of PDO cultures. When combined with the affinity-based validation platform, the EV surface proteins discovered in PDOs are effective in differentiating patients with PDAC from those with benign pancreatitis in the clinic, identifying PDO as powerful discovery platform for serum biomarkers. Thus, PDOs extend the utility of the archival collections of PDX models for translational research and function as a powerful platform for identification of clinically-actionable biomarkers in patients blood. Significance statementTumor organoids extend the utility of PDX models as platforms for investigating drug response, glycosylation changes and function as new platforms for discovering blood-based biomarkers

cancer biology↗

bioRxiv2018

Homeostatic Inhibitory Control of Cortical Hyperexcitability in Fragile X Syndrome

In mouse models of Fragile X Syndrome (FXS), cellular and circuit hyperexcitability are a consequence of altered brain development [reviewed in (Contractor et al., 2015)]. Mechanisms that favor or hinder plasticity of synapses could affect neuronal excitability. This includes inhibitory long term depression (I-LTD) - a heterosynaptic form of plasticity that requires the activation of metabotropic glutamate receptors (mGluRs). Differential circuit maturation leads to shifted time points for critical periods of synaptic plasticity across multiple brain regions (Harlow et al., 2010; He et al., 2014), and disruptions of the development of excitatory and inhibitory synaptic function are also observed both during development and into adulthood (Vislay et al., 2013). However, little is known about how this hyperexcitable environment affects inhibitory synaptic plasticity. Our results demonstrate that the somatosensory cortex of the Fmr1 KO mouse model of FXS exhibits increased GABAergic spontaneous activity, a faulty mGluR-mediated inhibitory input and impaired plasticity processes. We find the overall diminished mGluR activation in the Fmr1 KO mice leads to both a decreased spontaneous inhibitory postsynaptic input to principal cells and also to a disrupted form of inhibitory long term depression (I-LTD). In cortical synapses, this I-LTD is dependent on mGluR activation and the mobilization endocannabinoids (eCBs). Notably, these data suggest enhanced hyperexcitable phenotypes in FXS may be homeostatically counterbalanced by the inhibitory drive of the network and its altered response to mGluR modulation.\n\nSignificance StatementFragile X Syndrome is a pervasive neurodevelopmental disorder characterized by intellectual disability, autism, epilepsy, anxiety and altered sensory sensitivity. In both in vitro and in vivo recordings in the somatosensory cortex of the Fmr1 knockout mouse model of Fragile X Syndrome we show that hyperexcitable network activity contributes to ineffective synaptic plasticity at inhibitory synapses. This increased excitability prevents cortical circuits from adapting to sensory information via ineffective plasticity mechanisms.

neuroscience↗

bioRxiv2017

Eyes closed or Eyes open? Exploring the alpha desynchronization hypothesis in resting state functional connectivity networks with intracranial EEG

This paper addresses a fundamental question, are eyes closed and eyes open resting states equivalent baseline conditions, or do they have consistently different electrophysiological signatures? We compare the functional connectivity patterns in an eyes closed resting state with an eyes open resting state, and show that functional connectivity in the alpha band decreases in the eyes open condition compared to eyes closed. This \"alpha desynchronization \" or reduction in the number of connections from eyes closed to eyes open, is here, for the first time, studied with intracranial recordings. We provide two calculations of the wiring cost, local and mesoscopic, defined in terms of the distance between the electrodes and the likelihood that they are functionally connected. We find that, in agreement with the \"alpha desynchronization\" hypothesis, the local wiring cost decreases going from eyes closed to eyes open. However, when the wiring cost calculation takes into account the connectivity pattern, the wiring cost variation from eyes closed to eyes open is not as consistent and shows regional specificity. The wiring cost measure defined here, provides a new avenue for understanding the electrophysiology of resting state.

neuroscience↗