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SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape., Competing Interests: ALG reported receiving contract testing from Abbott, Cepheid, Novavax, Pfizer, Janssen and Hologic and research support from Gilead and Merck, outside of the described work. HC reported consulting with Ellume, Pfizer, the Bill & Melinda Gates Foundation, Glaxo Smith Kline, and Merck. She has received research funding from Emergent Ventures, Gates Ventures, Sanofi Pasteur, the Bill & Melinda Gates Foundation, and research support and reagents from Ellume and Cepheid outside of the submitted work. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. All other authors declare no competing interests., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Despite recent advances in our understanding of pathogenic access to the central nervous system (CNS), the mechanisms by which intracellular pathogens disseminate within the dense cellular network of neural tissue remain poorly understood. To address this issue, longitudinal analysis of Toxoplasma gondii dissemination in the brain was conducted using 2-photon imaging through a cranial window in living mice that transgenically express enhanced green fluorescent protein (eGFP)-claudin-5. Extracellular T. gondii parasites were observed migrating slowly (1.37 ± 1.28 μm/min) and with low displacement within the brain. In contrast, a population of highly motile infected cells transported vacuoles of T. gondii significantly faster (6.30 ± 3.09 μm/min) and with a higher displacement than free parasites. Detailed analysis of microglial dynamics using CX3CR1-GFP mice revealed that T. gondii - infected microglia remained stationary, and infection did not increase the extension/retraction of microglial processes. The role of infiltrating immune cells in shuttling T. gondii was examined by labeling of peripheral hematopoietic cells with anti-CD45 antibody. Infected CD45 + cells were found crawling along the CNS vessel walls and trafficked T. gondii within the brain parenchyma at significantly higher speeds (3.35 ± 1.70 μm/min) than extracellular tachyzoites. Collectively, these findings highlight a dual role for immune cells in neuroprotection and in facilitating parasite dissemination within the brain. IMPORTANCE T. gondii is a foodborne parasite that infects the brain and can cause fatal encephalitis in immunocompromised individuals. However, there is a limited understanding of how the parasites disseminate through the brain and evade immune clearance. We utilized intravital imaging to visualize extracellular T. gondii tachyzoites and infected cells migrating within the infected mouse brain during acute infection. The infection of motile immune cells infiltrating the brain from the periphery significantly increased the dissemination of T. gondii in the brain compared to that of free parasites migrating using their own motility: the speed and displacement of these infected cells would enable them to cover nearly 1 cm of distance per day! Among the infiltrating cells, T. gondii predominantly infected monocytes and CD8 + T cells, indicating that the parasite can hijack immune cells that are critical for controlling the infection in order to enhance their dissemination within the brain.

SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape., Competing Interests: Declaration of interests ALG reports contract testing from Abbott, Cepheid, Novavax, Pfizer, Janssen and Hologic and research support from Gilead and Merck, outside of the described work. All other authors declare no competing interests.

Any pathogen worth its salt has mechanisms to evade, subvert, or antagonize host innate immune responses induced by pattern recognition receptors. Resistance against such pathogens therefore requires alternative means to activate protective immune responses. Intriguingly, the receptors that regulate antimicrobial gene expression are coupled to cell death pathways that are activated by blockade of NF-κB and MAPK signaling. In this review, we discuss the regulation of apoptosis in response to pathogen disruption of immune signaling and the role of this cell death response in protection against such pathogens. Stanley often observed that bacterial pathogens are excellent cell biologists and immunologists, and he noted that studying pathogen-host interactions could pave the way to new insights about host biology. Indeed, how Yersinia and other pathogens disrupt innate immune signaling has provided new insight into these pathways and revealed new ways to think about immunogenic properties of apoptosis during bacterial infection., (Copyright © 2020. Published by Elsevier Ltd.)

Despite decades of study, the molecular basis for granuloma formation and restriction of chronic pathogens remains murky. Three articles reveal how Salmonella rewires macrophage polarization (Panagi et al. and Gibbs et al.) to shift the balance between M1 and M2 granuloma macrophages and resist TNF-mediated clearance (Pham et al.)., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Objective: To describe the frequency of renal tubular vacuolization (RTV) as a surrogate of osmotic nephrosis and assess hyperosmolar agents as predictors of RTV severity., Design: Retrospective study (February 2004-October 2014)., Setting: Veterinary teaching hospital., Animals: Fifty-three client-owned, critically ill dogs that had a postmortem examination., Interventions: None., Measurements and Main Results: The frequency, severity, and location of RTV were determined in small group of critically ill dogs postmortem. Logistic regression was performed to assess cumulative 6% HES (670/0.75) and mannitol dose as predictors for RTV severity with presenting serum creatinine concentration, cumulative furosemide dose, and duration of hospitalization as covariates. RTV was noted in 45 (85%) of 53 critically ill dogs and was most commonly located to the medullary rays (68%). Cumulative 6% HES (670/0.75) dose (P = 0.009) and presenting serum creatinine concentration (P = 0.027) were significant predictors of RTV severity. For every 1 mL/kg increase in 6% HES (670/0.75) dose that a dog received, there was 1.6% increased chance of having more severe RTV (OR 1.016; 95% CI 1.004-1.029). In addition, for every 88.4 μmol/L (1 mg/dL) increase in presenting serum creatinine, there was a 22.7% increased chance of having more severe RTV (OR 1.227; 95% CI 1.023-1.472). Cumulative mannitol (P = 0.548) and furosemide (P = 0.136) doses were not significant predictors of RTV severity., Conclusion: In a small group of critically ill dogs, there was a high frequency of RTV identified on postmortem examination. Administration of 6% HES (670/0.75) and presenting serum creatinine concentration were significant predictors of RTV severity. Larger prospective studies are needed to determine the etiology and significance of RTV in dogs., (© Veterinary Emergency and Critical Care Society 2019.)

Although numerous epigenetic aberrancies accumulate in melanoma, their contribution to initiation and progression remain unclear. The epigenetic mark 5-hydroxymethylcytosine (5hmC), generated through TET-mediated DNA modification, is now referred to as the sixth base of DNA and has recently been reported as a potential biomarker for multiple types of cancer. Loss of 5hmC is an epigenetic hallmark of melanoma, but whether a decrease in 5hmc levels contributes directly to pathogenesis or whether it merely results from disease progression-associated epigenetic remodeling remains to be established. Here, we show that NRAS-driven melanomagenesis in mice is accompanied by an overall decrease in 5hmC and specific 5hmC gains in selected gene bodies. Strikingly, genetic ablation of Tet2 in mice cooperated with oncogenic NRAS Q61K to promote melanoma initiation while suppressing specific gains in 5hmC. We conclude that TET2 acts as a barrier to melanoma initiation and progression, partly by promoting 5hmC gains in specific gene bodies. SIGNIFICANCE: This work emphasizes the importance of epigenome plasticity in cancer development and highlights the involvement of druggable epigenetic factors in cancer., (©2018 American Association for Cancer Research.)

Many patients with advanced cancers achieve dramatic responses to a panoply of therapeutics yet retain minimal residual disease (MRD), which ultimately results in relapse. To gain insights into the biology of MRD, we applied single-cell RNA sequencing to malignant cells isolated from BRAF mutant patient-derived xenograft melanoma cohorts exposed to concurrent RAF/MEK-inhibition. We identified distinct drug-tolerant transcriptional states, varying combinations of which co-occurred within MRDs from PDXs and biopsies of patients on treatment. One of these exhibited a neural crest stem cell (NCSC) transcriptional program largely driven by the nuclear receptor RXRG. An RXR antagonist mitigated accumulation of NCSCs in MRD and delayed the development of resistance. These data identify NCSCs as key drivers of resistance and illustrate the therapeutic potential of MRD-directed therapy. They also highlight how gene regulatory network architecture reprogramming may be therapeutically exploited to limit cellular heterogeneity, a key driver of disease progression and therapy resistance., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Caspases regulate cell death programs in response to environmental stresses, including infection and inflammation, and are therefore critical for the proper operation of the mammalian immune system. Caspase-8 is necessary for optimal production of inflammatory cytokines and host defense against infection by multiple pathogens including Yersinia, but whether this is due to death of infected cells or an intrinsic role of caspase-8 in TLR-induced gene expression is unknown. Caspase-8 activation at death signaling complexes results in its autoprocessing and subsequent cleavage and activation of its downstream apoptotic targets. Whether caspase-8 activity is also important for inflammatory gene expression during bacterial infection has not been investigated. Here, we report that caspase-8 plays an essential cell-intrinsic role in innate inflammatory cytokine production in vivo during Yersinia infection. Unexpectedly, we found that caspase-8 enzymatic activity regulates gene expression in response to bacterial infection as well as TLR signaling independently of apoptosis. Using newly-generated mice in which caspase-8 autoprocessing is ablated (Casp8DA/DA), we now demonstrate that caspase-8 enzymatic activity, but not autoprocessing, mediates induction of inflammatory cytokines by bacterial infection and a wide variety of TLR stimuli. Because unprocessed caspase-8 functions in an enzymatic complex with its homolog cFLIP, our findings implicate the caspase-8/cFLIP heterodimer in control of inflammatory cytokines during microbial infection, and provide new insight into regulation of antibacterial immune defense., Competing Interests: The authors have declared that no competing interests exist.

Unlabelled: The expression of biliary/progenitor markers by hepatocellular carcinoma (HCC) is often associated with poor prognosis and stem cell-like behaviors of tumor cells. Hepatocellular adenomas (HCAs) also often express biliary/progenitor markers and frequently act as precursor lesions for HCC. However, the cell of origin of HCA and HCC that expresses these markers remains unclear. Therefore, to evaluate if mature hepatocytes give rise to HCA and HCC tumors and to understand the molecular pathways involved in tumorigenesis, we lineage-labeled hepatocytes by injecting adeno-associated virus containing thyroxine-binding globulin promoter-driven causes recombination (AAV-TBG-Cre) into Rosa(YFP) mice. Yellow fluorescent protein (YFP) was present in >96% of hepatocytes before exposure to carcinogens. We treated AAV-TBG-Cre; Rosa(YFP) mice with diethylnitrosamine (DEN), followed by multiple injections of carbon tetrachloride to induce carcinogenesis and fibrosis and found that HCA and HCC nodules were YFP(+) lineage-labeled; positive for osteopontin, SRY (sex determining region Y)-box 9, and epithelial cell adhesion molecule; and enriched for transcripts of biliary/progenitor markers such as prominin 1, Cd44, and delta-like 1 homolog. Next, we performed the converse experiment and lineage-labeled forkhead box protein L1(Foxl1)-positive hepatic progenitor cells simultaneously with exposure to carcinogens. None of the tumor nodules expressed YFP, indicating that Foxl1-expressing cells are not the origin for hepatotoxin-induced liver tumors. We confirmed that HCA and HCC cells are derived from mature hepatocytes and not from Foxl1-Cre-marked cells in a second model of toxin-induced hepatic neoplasia, using DEN and 3,3',5,5'-tetrachloro-1,4-bis(pyridyloxy)benzene (TCPOBOP)., Conclusion: Hepatocytes are the cell of origin of HCA and HCC in DEN/carbon tetrachloride and DEN/TCPOBOP induced liver tumors. (Hepatology 2016;64:1163-1177)., (© 2016 by the American Association for the Study of Liver Diseases.)

Host-microbe interactions may play a fundamental role in the pathogenesis of atopic dermatitis, a chronic relapsing inflammatory skin disorder characterized by universal colonization with Staphylococcus species. To examine the relationship between epidermal barrier function and the cutaneous microbiota in atopic dermatitis, this study used a spontaneous model of canine atopic dermatitis. In a cohort of 14 dogs with canine atopic dermatitis, the skin microbiota were longitudinally evaluated with parallel assessment of skin barrier function at disease flare, during antimicrobial therapy, and post-therapy. Sequencing of the bacterial 16S ribosomal RNA gene showed decreased bacterial diversity and increased proportions of Staphylococcus (S. pseudintermedius in particular) and Corynebacterium species compared with a cohort of healthy control dogs (n = 16). Treatment restored bacterial diversity with decreased proportions of Staphylococcus species, concurrent with decreased canine atopic dermatitis severity. Skin barrier function, as measured by corneometry, pH, and transepidermal water loss also normalized with treatment. Bacterial diversity correlated with transepidermal water loss and pH level but not with corneometry results. These findings provide insights into the relationship between the cutaneous microbiome and skin barrier function in atopic dermatitis, show the impact of antimicrobial therapy on the skin microbiome, and highlight the utility of canine atopic dermatitis as a spontaneous nonrodent model of atopic dermatitis., (Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Staphylococcus schleiferi is a known pathogen that can cause canine skin and ear infections. The aim of this study was to determine the molecular epidemiology and antimicrobial susceptibility of clinical veterinary isolates from different geographic regions in the United States., Hypothesis: It was hypothesized that S. schleiferi would maintain genotypic homogeneity across the different geographic regions and that meticillin-resistant (MR) isolates of S. schleiferi would predominate., Methods: Isolates were identified as S. schleiferi by a commercial microbiology identification system and confirmed by nuc gene PCR. Antibiotic susceptibility data were collected and PBP2a latex agglutination testing was performed on MR isolates. Pulsed-field gel electrophoresis (PFGE) was performed and clonal clusters were identified with a Dice coefficient similarity of >80%., Results: There were 116 isolates from the Mid-Atlantic region and 101 from across the United States. Of these 217 isolates, 209 (96%) were obtained from cutaneous sites. Of the Mid-Atlantic isolates, 62% (72 of 116) were MR and 16% (18 of 116) were multidrug-resistant (MDR). Of the isolates from the other geographic regions, 73% (74 of 101) were MR and 24% (24 of 101) were MDR. All MR isolates were positive by PBP2a latex agglutination. PFGE identified 155 individual pulsed-field profiles and three major pulsed-field types (PFT) that contained 61% (133 of 217) of the isolates. These pulsed-field types were geographically heterogeneous., Conclusions: This study demonstrates the dissemination of successful MR pulsed-field types of S. schleiferi across the United States., (© 2015 ESVD and ACVD.)

Surgery is the most effective method to cure patients with solid tumors, and 50% of all cancer patients undergo resection. Local recurrences are due to tumor cells remaining in the wound, thus we explore near-infrared (NIR) fluorescence spectroscopy and imaging to identify residual cancer cells after surgery. Fifteen canines and two human patients with spontaneously occurring sarcomas underwent intraoperative imaging. During the operation, the wounds were interrogated with NIR fluorescence imaging and spectroscopy. NIR monitoring identified the presence or absence of residual tumor cells after surgery in 14/15 canines with a mean fluorescence signal-to-background ratio (SBR) of ∼16 . Ten animals showed no residual tumor cells in the wound bed (mean SBR<2 , P<0.001 ). None had a local recurrence at >1-year follow-up. In five animals, the mean SBR of the wound was >15 , and histopathology confirmed tumor cells in the postsurgical wound in four/five canines. In the human pilot study, neither patient had residual tumor cells in the wound bed, and both remain disease free at >1.5-year follow up. Intraoperative NIR fluorescence imaging and spectroscopy identifies residual tumor cells in surgical wounds. These observations suggest that NIR imaging techniques may improve tumor resection during cancer operations.

The human intestine is colonized by an estimated 100 trillion bacteria. Some of these bacteria are essential for normal physiology, whereas others have been implicated in the pathogenesis of multiple inflammatory diseases including IBD and asthma. This review examines the influence of signals from intestinal bacteria on the homeostasis of the mammalian immune system in the context of health and disease. We review the bacterial composition of the mammalian intestine, known bacterial-derived immunoregulatory molecules, and the mammalian innate immune receptors that recognize them. We discuss the influence of bacterial-derived signals on immune cell function and the mechanisms by which these signals modulate the development and progression of inflammatory disease. We conclude with an examination of successes and future challenges in using bacterial communities or their products in the prevention or treatment of human disease.

The multifunctional role for calcium during lymphocyte activation and differentiation is well established; yet how fate-specific changes in calcium concentration are produced, and how these signals are translated into distinct cellular responses, is not known. A critical role has been identified for store-operated calcium release-activated calcium (CRAC) channels; however, the lack of information concerning the structure and mechanism of store-dependent activation has limited our ability to define CRAC's role in the range of calcium-dependent responses of lymphocytes. Moreover, additional calcium-permeant cation channels have been recently identified in lymphocytes. These channels regulate functions distinct from those attributed to CRAC channels. Consequently, this review summarizes well-established mechanisms of calcium signaling and also considers recent findings which suggest that diverse and interacting pathways encode functionally specific calcium signals in lymphocytes. Speculation is also offered about how distinct patterns of calcium signaling are translated into diverse transcriptional responses.

IL-12 is a potent inducer of IFN-gamma production and Th1 responses. Co-stimulation mediated by B7 has been shown to synergize with IL-12 for optimal IFN-gamma production and proliferation in vitro. In this study, we examined the requirement of CD28/B7 interactions for optimal induction of IL-12 receptor(R) beta1 and beta2 expression and IFN-gamma. IL-12-induced IFN-gamma production and STAT4 nuclear translocation were markedly reduced in CD28(-/-) splenocytes compared to that of wild-type (WT) splenocytes. Analysis of IL-12R expression revealed that IL-12 induced similar levels of IL-12R beta2 mRNA expression in WT and CD28(-/-) cells. In contrast, IL-12R beta1 expression was impaired in CD28(-/-) cells, indicating that expression of IL-12R beta1 and beta2 is differentially regulated by CD28. CD28(-/-) CD4(+) but not CD8(+) cells exhibited a defect in IL-12Rbeta1 expression that was associated with a marked decrease in IL-12 binding as well as IL-12-induced IFN-gamma production. IL-2 could restore IL-12R expression to CD28(-/-) CD4(+) cells, however, this occurred independently of IL-2-induced proliferation. Thus, these findings identify distinct requirements for CD28 in the capacity of CD4(+) and CD8(+) cells to respond maximally to IL-12.

Infective third-stage larvae of Strongyloides stercoralis were frozen over liquid nitrogen and remained infective to dogs when thawed. Successful cryopreservation depended on a 30-60-min incubation in a cryoprotectant (10% DMSO and 10% dextran) before freezing and thawing the frozen larvae into RPMI. First-stage larvae could also be frozen by this method. Thawed first-stage larvae remained viable and continued their development to third-stage larvae, which were shown to be infective to dogs.