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The interplay of tissue mechanics and gene regulatory networks in the evolution of morphogenesis.
No full textRecent years have seen the growth of work illuminating the mechanical aspects of morphogenesis, but its relationship to the established ideas and evidence of developmental and evolutionary genetics remains enigmatic. This review aims to re-assess the conceptual relationship between mechanics and genetics in the context of animal morphogenesis. We propose a view in which genetic programs-understood as gene regulatory networks-and processes of physical self-organization are not conflicting models of development, but instead play necessary and complementary causal roles at cellular and supra-cellular length scales, respectively. Current evidence from evolutionary genetics supports the hypothesis that this form of complementarity may be necessary for morphogenesis to be evolvable
Global update on the susceptibilities of influenza viruses to neuraminidase inhibitors and the cap-dependent endonuclease inhibitor baloxavir, 2020-2023.
No full textAntiviral susceptibility of influenza viruses is monitored by the World Health Organization Global Influenza Surveillance and Response System. This study describes a global analysis of the susceptibility of influenza viruses to neuraminidase (NA) inhibitors (NAIs, oseltamivir, zanamivir, peramivir, laninamivir) and the cap-dependent endonuclease inhibitor (CENI, baloxavir) for three periods (May to May for 2020-2021, 2021-2022 and 2022-2023). In particular, global influenza activity declined significantly in 2020-2021 and 2021-2022 when compared to the pre-pandemic period of COVID-19. Combined phenotypic and NA sequence-based analysis revealed that the global frequency of seasonal influenza viruses with reduced or highly reduced inhibition (RI/HRI) by NAIs remained low, 0.09% (2/2224), 0.12% (27/23465) and 0.23% (124/53917) for 2020-2021, 2021-2022 and 2022-2023, respectively. As in previous years, NA-H275Y in A(H1N1)pdm09 viruses was the most frequent substitution causing HRI by oseltamivir and peramivir. Sequence-based analysis of polymerase acidic (PA) protein supplemented with phenotypic testing revealed low global frequencies of seasonal influenza viruses with reduced susceptibility (RS) to baloxavir, 0.07% (1/1376), 0.05% (9/18380) and 0.12% (48/39945) for 2020-2021, 2021-2022 and 2022-2023, respectively; commonly associated substitutions were PA-I38T/M/L. In Japan, the rate was 3.3% (16/488) during 2022-2023, with 11 A(H3N2) viruses having PA-I38T/M substitutions. For zoonotic viruses, 2.7% (3/111) contained substitutions, one each NA-H275Y, NA-S247N and NA-N295S, associated with RI/HRI NAI phenotypes, and none contained PA substitutions associated with RS to baloxavir. In conclusion, the great majority of seasonal and zoonotic influenza viruses remained susceptible to NAIs and CENI baloxavir.</p
Type I IFN drives neutrophil swarming, impeding lung T cell-macrophage interactions and TB control.
No full textThe early immune mechanisms determining Mycobacterium tuberculosis infection outcome are unclear. Using bulk and scRNA-seq over the first weeks of infection, we describe an unexpected, higher early pulmonary type I IFN response in relatively resistant C57BL/6 as compared with highly TB-susceptible C3HeB/FeJ mice. C57BL/6 mice showed pronounced early monocyte-derived macrophage (MDM) accumulation and extensive CD4+ T cell-MDM interactions in lung lesions, accompanied by high expression of T cell-attractant chemokines by MDMs. Conversely, lesions in C3HeB/FeJ mice were dominated by neutrophils with high expression of pro-inflammatory chemokines, from which CD4+ T cells were spatially segregated. Early type I IFN signaling blockade reduced bacterial load and neutrophil swarming within early TB lesions while increasing CD4+ T cell numbers in both C57BL/6 and C3HeB/FeJ mice, with later more pronounced effects on bacterial load in C3HeB/FeJ mice. These data suggest that early type I IFN signaling during M. tuberculosis infection favors neutrophil accumulation and limits CD4+ T cell infiltration into developing lesions
Extended sample size calculations for evaluation of prediction models using a threshold for classification
No full textWhen evaluating the performance of a model for individualised risk prediction, the sample size needs to be large enough to precisely estimate the performance measures of interest. Current sample size guidance is based on precisely estimating calibration, discrimination, and net benefit, which should be the first stage of calculating the minimum required sample size. However, when a clinically important threshold is used for classification, other performance measures are also often reported. We extend the previously published guidance to precisely estimate threshold-based performance measures. We have reported closed-form solutions to estimate the sample size required to target sufficiently precise estimates of accuracy, specificity, sensitivity, positive predictive value (PPV), negative predictive value (NPV), and an iterative method to estimate the sample size required to target a sufficiently precise estimate of the F1-score, in an external evaluation study of a prediction model with a binary outcome. This approach requires the user to pre-specify the target standard error and the expected value for each performance measure alongside the outcome prevalence. We describe how the sample size formulae were derived and demonstrate their use in an example. Extension to time-to-event outcomes is also considered. In our examples, the minimum sample size required was lower than that required to precisely estimate the calibration slope, and we expect this would most often be the case. Our formulae, along with corresponding Python code and updated R, Stata and Python commands (pmvalsampsize), enable researchers to calculate the minimum sample size needed to precisely estimate threshold-based performance measures in an external evaluation study. These criteria should be used alongside previously published criteria to precisely estimate the calibration, discrimination, and net-benefit
Protocol for immunofluorescence detection and quantification of phosphorylated SMAD proteins in human blastocysts.
No full textThe transforming growth factor β (TGF-β) signaling superfamily includes NODAL and bone morphogenetic protein (BMP) signaling, which lead to the phosphorylation of different SMAD proteins and regulate key developmental events. Here, we present a protocol for immunofluorescence detection of phosphorylated SMAD proteins combined with other transcription factors in pre-implantation human embryos. We describe steps for segmenting the nuclei in human blastocysts and quantifying their immunofluorescence intensity. This protocol can be adapted to investigate TGF-β superfamily signaling activity in other mammalian embryos or in vitro models of their development. For complete details on the use and execution of this protocol, please refer to Brumm et al.1
Inactivation of the PHD3-FOXO3 axis blunts the type I interferon response in microglia and ameliorates Alzheimer's disease progression.
No full textMicroglia respond to Alzheimer's disease (AD) with varied transcriptional responses. We show that oligomeric Aß (oAß) induces the expression of Hif1a and Egln3 in microglia in vitro, together with the transcription of the type I interferon signature (IFNS) genes in a PHD3-dependent manner. We identify FOXO3 as a repressor of IFNS, whose abundance decreases upon PHD3 induction in response to oAß. In vivo, loss of PHD3 correlates with abrogation of the IFNS and activation of the disease-associated microglia signature, an increase in microglia proximity to Aß plaques and phagocytosis of both Aß and small plaques. PHD3 deficiency mitigated the Aß plaque-associated neuropathology and rescued behavioral deficits of an AD mouse model. Last, we demonstrate that microglial PHD3 overexpression in the absence of Aß pathology is sufficient to induce the IFNS and behavioral alterations. Together, our data strongly indicate that the inactivation of the PHD3-FOXO3 axis controls the microglial IFNS in a cell autonomous manner, improving AD outcome
Conserved patterns of transcriptional dysregulation, heterogeneity, and cell states in clear cell kidney cancer.
No full textClear cell kidney cancers are characterized both by conserved oncogenic driver events and by marked intratumor genetic and phenotypic heterogeneity, which help drive tumor progression, metastasis, and resistance to therapy. How these are reflected in transcriptional programs within the cancer and stromal cell components remains an important question with the potential to drive novel therapeutic approaches to treating cancer. To better understand these programs, we perform single-cell transcriptomics on 75 multi-regional biopsies from kidney tumors and normal kidney. We identify conserved patterns of transcriptional dysregulation and their upstream regulators within the tumor and associated vasculature. We describe recurrent subclonal transcriptional consequences of Chr14q loss linked to metastatic potential. We identify prognostically significant conserved patterns of intratumor transcriptional heterogeneity. These reflect co-existing cell states found in both cancer cells and normal kidney cells, indicating that rather than arising from genetic heterogeneity they are a consequence of lineage plasticity
A clinical practice guideline for tuberculous meningitis
No full textTuberculous meningitis is the most severe form of tuberculosis, causing death or disability in around half of those affected. There are no up-to-date international guidelines defining its optimal management. Therefore, the Tuberculous Meningitis International Research Consortium conducted a systematic review of available evidence to address key management questions and to develop practice guidance. The consortium includes representatives from India, Indonesia, South Africa, Uganda, Viet Nam, Australia, the Netherlands, the UK, and the USA. Questions were developed using the Population, Intervention, Comparator, Outcome (PICO) format for tuberculous meningitis diagnosis, anti-tuberculosis chemotherapy, adjunctive anti-inflammatory therapy, and neurocritical and neurosurgical care. A Grading of Recommendations, Assessment, Development and Evaluations approach was used to assess the certainty (or quality) of evidence and establish the direction and strength of recommendations for each PICO-based question. We provide evidence-based recommendations for the optimal treatment and diagnosis of tuberculous meningitis, alongside expert opinion. We expose substantial knowledge and evidence gaps, thereby highlighting current research priorities
Repurposing deep learning models from computer vision to classify drug-resistant cells using autofluorescence lifetime imaging data
No full textAn invasive breast ductal carcinoma cell line is used to explore whether metabolic profiling can be used to classify cell populations that are responsive (wild-type) or resistant to antibody-drug conjugate (ADC) treatment. The metabolic profile is determined by 2-photon autofluorescence lifetime imaging (FLIM) of the live cells. This multi-dimensional data contains both intensity and lifetime information corresponding to the location and interaction status of AD(P)H, a molecule that is a key component of cell metabolism, and its average fluorescence lifetime is a means to probe important indicators of cancer. Poster presented as part of the Crick BioImage Analysis Symposium 2025.Permission has been given by authors to upload to Crick Figshare. Copyright remains with the original authors.</p
Understanding the Foreign Body Response to Implantable Soft Robotic Medical Devices for the Treatment of Chronic Diseases
No full textImplantable medical devices elicit a process called the Foreign Body Response (FBR),in which a fibrotic capsule develops around the devices. This prevents effective device function, which is of particular importance in drug release. Using actuation (soft robotics) can improve drug delivery, but the effect of actuation on the cells needs further exploration.Study 1: Understanding macrophages and the process of NETosis could provide us with a better knowledge of how the FBR progresses to deposit material and form a scar-like Fibrotic Capsule (FC) around the implant using explanted animal tissue (Fig. 1)• Looking at Neutrophil Extracellular Trap-released proteins (granule proteins) we can determine that NETosis is occurring.Study 2:Designing a hydrogel scaffold which would provide support for cells to grow within a 3D matrix would provide amore accurate in-vitro representation of in-vivo growth conditions.• Developing test-beds to understand and analyse biocompatibility would provide greater insights into how we test the efficacy of drug-delivery system before implantation.• Hyaluronic acid based hydrogel with the addition of collagen would provide structural support in-vitro and allow for cell adhesion and proliferation which would help in the creation of test-beds.Poster presented as part of the Crick BioImage Analysis Symposium 2025.Permission has been given by authors to upload to Crick Figshare. Copyright remains with the original authors.</p