Kurt I. Anderson

Volumetric imaging is increasingly important in fields such as neuroscience, where quantifying structure and mapping features are inherently three-dimensional problems. Block-face serial two-photon tomography (STPT) has emerged as a powerful approach for high-resolution, whole-organ volumetric imaging. STPT avoids complex sample preparation and balances image quality, speed, and scalability. However, STPT remains niche, in part because of the absence of flexible, general-purpose control software. Here we present BakingTray, an open-source software platform for STPT that extends ScanImage. BakingTray’s modular framework accommodates diverse hardware configurations and allows users to build systems customised to their needs. Twelve such systems, which we call ‘BrainSaws’, have been constructed worldwide since 2016, with more under construction, and have so far contributed to 35 research papers. The three systems at the Sainsbury Wellcome Centre alone have acquired over 7,000 samples in a busy multi-user facility. We demonstrate the platform across its core neuroscience applications: electrode track localisation, brain-wide cell counting, and bulk projection mapping. Beyond these, we map the cell-type-specific synaptic output of inhibitory neurons in the ventral lateral geniculate nucleus and, with whole-mount staining, amyloid plaques brain-wide in a mouse model of Alzheimer’s disease. BakingTray is a mature platform for groups or facilities needing a customised volumetric imaging solution, whether built new or converted cheaply from an existing two-photon microscope.

Fluorescent biosensors have proven valuable for revealing the spatio-temporal dynamics of protein conformation in live cells and animals. The great majority of biosensors are genetically encoded, but genetic encoding is difficult or impossible to apply in many cases, including cells or animals with poorly understood genomes, no DNA, or sensitive to manipulation. Using biosensors without genetic manipulation could greatly simplify studies in animals, expand the range of accessible organisms, and ultimately enable application in humans. Here we explore using a membrane-permeable small molecule as a fluorescent biosensor. The drug trifluoperazine, which binds only to the active conformation of calmodulin, was covalently linked to an environment-sensing merocyanine dye to create CaMero, a biosensor of calmodulin activation. Simple incubation of CaMero in the extracellular medium, or injection in the tail vein of mice, led to sensitive real time reporting of calmodulin activity. The dye underwent a 12-fold change in fluorescence intensity upon binding to activated calmodulin, revealing waves of activation in peristaltic intestine, localization and kinetics of calmodulin activation during serum stimulation in fibroblasts, and localized activation in the single-celled marine protist foraminifera.

Neuropeptide Y (NPY) is secreted by sympathetic nerves ^1,2 , but its direct impact on thermogenic adipocytes is unknown. Here we uncover the mechanism by which peripheral NPY protects from obesity. Our imaging of cleared murine brown and white adipose tissue (BAT and WAT) established that NPY ⁺ sympathetic axons are only a minority that mostly maps to the peri-vasculature; our analysis of single-cell RNA-sequencing datasets identifies mural cells as the main NPY-responsive cells in adipose tissues. We show that NPY sustains mural cells, which are known to be a source of beige cells in both BAT and WAT ^3–5 and that NPY facilitates the differentiation to thermogenic adipocytes. We found that diet-induced-obesity leads to neuropathy of NPY ⁺ axons and concomitant depletion of the mural cell pool of beige fat progenitors. This defect is replicated in conditional knockout (cKO) mice with NPY specifically abrogated from sympathetic neurons. These cKO mice have whitened BAT with reduced thermogenic ability and lower energy expenditure even before the onset of obesity; they develop adult-onset obesity on a regular chow diet and are more susceptible to diet induced obesity without increasing food consumption. Our results indicate that, relative to central NPY, peripheral NPY produced by the sympathetic nerves has the opposite effect on body weight homeostasis by sustaining the proliferation of the mural cell progenitors of thermogenic adipocytes.

Light microscopy facilities vary in the number of imaging systems and the scope of technologies they support. Each facility must craft an identity through the selection of equipment and development of staff in order to serve the needs of its local research environment. The process of crafting a light microscopy facility can be compared to curation of an art exhibition: great care should be given to the selection and placement of each object in order to make a coherent statement. Lay Description : Light microscopy facilities vary in the number of imaging systems and the scope of technologies they support. Each facility must develop an identity through the selection of equipment and development of staff in order to serve the needs of its local research environment. The process of crafting a light microscopy facility can be compared to curation of an art exhibition: great care should be given to the selection and placement of each object in order to make a coherent statement.

Core Facilities and Technology Platforms are increasingly important components of the science research landscape. However, data on facility operations and staff careers are lacking to inform their development. Here we have surveyed 114 people working in 46 Light Microscopy (LM) facilities within the United Kingdom. Our survey explores issues around Career Progression, Facility Operations, and Funding. The data show that facilities are substantial repositories of equipment and knowledge which adapt to meet the needs of their local environments. Our report highlights the challenges faced by facility managers, institutions, and funders in evaluating facility performance and devising strategies to maximize the return on research funding investment. This article is protected by copyright. All rights reserved

Multiphoton microscopy has recently passed the milestone of its first 30 years of activity in biomedical research. The growing interest around this approach has led to a variety of applications from basic research to clinical practice. Moreover, this technique offers the advantage of label-free multiphoton imaging to analyze samples without staining processes and the need for a dedicated system. Here, we review the state of the art of label-free techniques; then, we focus on two-photon autofluorescence as well as second and third harmonic generation, describing physical and technical characteristics. We summarize some successful applications to a plethora of biomedical research fields and samples, underlying the versatility of this technique. A paragraph is dedicated to an overview of sample preparation, which is a crucial step in every microscopy experiment. Afterwards, we provide a detailed review analysis of the main quantitative methods to extract important information and parameters from acquired images using second harmonic generation. Lastly, we discuss advantages, limitations, and future perspectives in label-free multiphoton microscopy.

RAC1 activity is critical for intestinal homeostasis, and is required for hyperproliferation driven by loss of the tumour suppressor geneApcin the murine intestine. To avoid the impact of direct targeting upon homeostasis, we reasoned that indirect targeting of RAC1 via RAC-GEFs might be effective. Transcriptional profiling ofApcdeficient intestinal tissue identifiedVav3andTiam1as key targets. Deletion of these indicated that while TIAM1 deficiency could suppressApc-driven hyperproliferation, it had no impact upon tumourigenesis, while VAV3 deficiency had no effect. Intriguingly, deletion of either gene resulted in upregulation ofVav2, with subsequent targeting of all three (Vav2^−/−Vav3^−/−Tiam1^−/−), profoundly suppressing hyperproliferation, tumourigenesis and RAC1 activity, without impacting normal homeostasis. Critically, the observed RAC-GEF dependency was negated by oncogenic KRAS mutation. Together, these data demonstrate that while targeting RAC-GEF molecules may have therapeutic impact at early stages, this benefit may be lost in late stage disease.

The Rac-GEF, P-Rex1, activates Rac1 signaling downstream of G protein-coupled receptors and PI3K. Increased P-Rex1 expression promotes melanoma progression; however, its role in breast cancer is complex, with differing reports of the effect of its expression on disease outcome. To address this we analyzed human databases, undertook gene array expression analysis, and generated unique murine models of P-Rex1 gain or loss of function. Analysis of PREX1 mRNA expression in breast cancer cDNA arrays and a METABRIC cohort revealed that higher PREX1 mRNA in ER^+ve/luminal tumors was associated with poor outcome in luminal B cancers. Prex1 deletion in MMTV-neu or MMTV-PyMT mice reduced Rac1 activation in vivo and improved survival. High level MMTV-driven transgenic PREX1 expression resulted in apicobasal polarity defects and increased mammary epithelial cell proliferation associated with hyperplasia and development of de novo mammary tumors. MMTV-PREX1 expression in MMTV-neu mice increased tumor initiation and enhanced metastasis in vivo, but had no effect on primary tumor growth. Pharmacological inhibition of Rac1 or MEK1/2 reduced P-Rex1-driven tumoroid formation and cell invasion. Therefore, P-Rex1 can act as an oncogene and cooperate with HER2/neu to enhance breast cancer initiation and metastasis, despite having no effect on primary tumor growth. Significance Breast cancer is the most common cancer in women and metastasis remains the leading cause of death. P-Rex1, a guanine nucleotide exchange factor, positively regulates Rac1-mediated oncogenic signaling. P-Rex1 is overexpressed in a subset of human breast cancers; however, little is known of its function in vivo. Here we show P-Rex1 regulates Rac1 activation in vivo in the mammary gland. Increased P-Rex1 expression enhances mammary epithelial cell proliferation and is causally associated with tumor initiation. In murine models, P-Rex1 cooperates with the neu oncogene to increase mammary tumor incidence and metastasis but not primary tumor growth. Our studies suggest that inhibiting the P-Rex1–Rac1 signaling axis may be an adjunct therapy for treating invasive cancers which exhibit increased P-Rex1 expression.

Mammalian embryos change shape dramatically upon implantation. The cellular and molecular mechanism underlying this transition are largely unknown. Here, we show that this transition is directed by cross talk between the embryonic epiblast and the first extra-embryonic tissue, the trophectoderm. Specifically, we show via visualisation of a Cdx2-GFP reporter line and pharmacologically mediated loss and gain of function experiments that the epiblast provides FGF signal that results in differential fate acquisition in the multipotent trophectoderm leading to the formation of a tissue boundary within this tissue. The trophectoderm boundary becomes essential for expansion of the tissue into a multi-layered epithelium. Folding of this multi-layered trophectoderm induces spreading of the second extra-embryonic tissue, the primitive endoderm. Together, these events remodel the pre-implantation embryo into its post-implantation cylindrical shape. Our findings uncover how communication between embryonic and extra-embryonic tissues provides positional cues to drive shape changes in mammalian development during implantation.