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Over more than 300 years, microscopic imaging keeps providing fundamental insights into the mechanisms of living organisms. Seeing microscopic structures beyond the reach of free-space light-based microscopy, however, requires dissection of the tissue-an intervention seriously disturbing its physiological functions. The hunt for low-invasiveness tools has led a growing community of physicists and engineers into the realm of complex media photonics. One of its activities represents exploiting multimode optical fibers (MMFs) as ultra-thin endoscopic probes. Employing wavefront shaping, these tools only recently facilitated the first peeks at cells and their sub-cellular compartments at the bottom of the mouse brain with the impact of micro-scale tissue damage. Here, we aim to highlight advances in MMF-based holographic endo-microscopy facilitating microscopic imaging throughout the whole depth of the mouse brain. We summarize the important technical and methodological prerequisites for stabile high-resolution imaging . We showcase images of the microscopic building blocks of brain tissue, including neurons, neuronal processes, vessels, intracellular calcium signaling, and red blood cell velocity in individual vessels. This perspective article helps to understand the complexity behind the technology of holographic endo-microscopy, summarizes its recent advances and challenges, and stimulates the mind of the reader for further exploitation of this tool in the neuroscience research.

Investigating cerebral metabolism in vivo at a microscopic level is essential for understanding brain function and its pathological alterations. The intricate signaling and metabolic dynamics between neurons, glia, and microvasculature requires much more detailed understanding to better comprehend the mechanisms governing brain function and its disease-related changes. We recently demonstrated that pharmacologically-induced alterations to different steps of cerebral metabolism can be distinguished utilizing 2-photon fluorescence lifetime imaging of endogenous reduced nicotinamide adenine dinucleotide (NADH) fluorescence in vivo. Here, we evaluate the ability of the phasor analysis method to identify these pharmacological metabolic alterations and compare the method's performance with more conventional nonlinear curve-fitting analysis. Visualization of phasor data, both at the fundamental laser repetition frequency and its second harmonic, enables resolution of pharmacologically-induced alterations to mitochondrial metabolic processes from baseline cerebral metabolism. Compared to our previous classification models based on nonlinear curve-fitting, phasor-based models required fewer parameters and yielded comparable or improved classification accuracy. Fluorescence lifetime imaging of NADH and phasor analysis shows utility for detecting metabolic alterations and will lead to a deeper understanding of cerebral energetics and its pathological changes.

Light-based in-vivo brain imaging relies on light transport over large distances of highly scattering tissues. Scattering gradually reduces imaging contrast and resolution, making it difficult to reach structures at greater depths even with the use of multiphoton techniques. To reach deeper, minimally invasive endo-microscopy techniques have been established. These most commonly exploit graded-index rod lenses and enable a variety of modalities in head-fixed and freely moving animals. A recently proposed alternative is the use of holographic control of light transport through multimode optical fibres promising much less traumatic application and superior imaging performance. We present a 110 μm thin laser-scanning endo-microscope based on this prospect, enabling in-vivo volumetric imaging throughout the whole depth of the mouse brain. The instrument is equipped with multi-wavelength detection and three-dimensional random access options, and it performs at lateral resolution below 1 μm. We showcase various modes of its application through the observations of fluorescently labelled neurones, their processes and blood vessels. Finally, we demonstrate how to exploit the instrument to monitor calcium signalling of neurones and to measure blood flow velocity in individual vessels at high speeds. Controlled light transport through multimode fibres has recently emerged as uniquely atraumatic prospect to study deep brain structures. Here, authors present hair-thin endoscope providing detailed view through the whole depth of living animal brain.

The computational properties of the human brain arise from an intricate interplay between billions of neurons connected in complex networks. However, our ability to study these networks in healthy human brain is limited by the necessity to use non-invasive technologies. This is in contrast to animal models where a rich, detailed view of cellular-level brain function with cell-type-specific molecular identity has become available due to recent advances in microscopic optical imaging and genetics. Thus, a central challenge facing neuroscience today is leveraging these mechanistic insights from animal studies to accurately draw physiological inferences from non-invasive signals in humans. On the essential path towards this goal is the development of a detailed ‘bottom-up’ forward model bridging neuronal activity at the level of cell-type-specific populations to non-invasive imaging signals. The general idea is that specific neuronal cell types have identifiable signatures in the way they drive changes in cerebral blood flow, cerebral metabolic rate of O2 (measurable with quantitative functional Magnetic Resonance Imaging), and electrical currents/potentials (measurable with magneto/electroencephalography). This forward model would then provide the ‘ground truth’ for the development of new tools for tackling the inverse problem—estimation of neuronal activity from multimodal non-invasive imaging data. This article is part of the themed issue ‘Interpreting BOLD: a dialogue between cognitive and cellular neuroscience’.

BRAF inhibitors can delay the progression of metastatic melanoma, but resistance usually emerges, leading to relapse. Drugs simultaneously targeting two or more pathways essential for cancer growth could slow or prevent the development of resistant clones. Here, we identified pyridinyl imidazole compounds SB202190, SB203580, and SB590885 as dual inhibitors of critical proliferative pathways in human melanoma cells bearing the V600E activating mutation of BRAF kinase. We found that the drugs simultaneously disrupt the BRAF V600E-driven extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) activity and the mechanistic target of rapamycin complex 1 (mTORC1) signaling in melanoma cells. Pyridinyl imidazole compounds directly inhibit BRAF V600E kinase. Moreover, they interfere with the endolysosomal compartment, promoting the accumulation of large acidic vacuole-like vesicles and dynamic changes in mTOR signaling. A transient increase in mTORC1 activity is followed by the enrichment of the Ragulator complex protein p18/LAMTOR1 at contact sites of large vesicles and delocalization of mTOR from the lysosomes. The induced disruption of the endolysosomal pathway not only disrupts mTORC1 signaling, but also renders melanoma cells sensitive to endoplasmic reticulum (ER) stress. Our findings identify new activities of pharmacologically relevant small molecule compounds and provide a biological rationale for the development of anti-melanoma therapeutics based on the pyridinyl imidazole core.

Identification of the cellular players and molecular messengers that communicate neuronal activity to the vasculature driving cerebral hemodynamics is important for (1) the basic understanding of cerebrovascular regulation and (2) interpretation of functional Magnetic Resonance Imaging (fMRI) signals. Using a combination of optogenetic stimulation and 2-photon imaging in mice, we demonstrate that selective activation of cortical excitation and inhibition elicits distinct vascular responses and identify the vasoconstrictive mechanism as Neuropeptide Y (NPY) acting on Y1 receptors. The latter implies that task-related negative Blood Oxygenation Level Dependent (BOLD) fMRI signals in the cerebral cortex under normal physiological conditions may be mainly driven by the NPY-positive inhibitory neurons. Further, the NPY-Y1 pathway may offer a potential therapeutic target in cerebrovascular disease. Unlike other cells in the body, brain cells contain almost no energy reserves and rely on blood vessels for continuous supply of oxygen. A change in the brain’s activity can cause these blood vessels to either dilate or constrict, which alters the supply to match the change in demand. However, it is not known which signals cause these changes in the blood vessels. Previous studies have shown that individual blood vessels in an intact brain tend to dilate when the brain’s activity increases, and constrict when brain activity is inhibited. However, these studies were based on correlations, and there was no direct evidence that the inhibitory cells cause blood vessels to constrict. Uhlirova, Kılıç et al. now provide such evidence. The experiments made use of mice that had been genetically modified such that the excitatory or inhibitory nerve cells in their brains could be selectively activated by shining a blue light on the brain’s surface. The vessels in the outer millimeter of the gray matter of each mouse’s brain were imaged in detail, both before and after the blue light was used to activate the nerve cells. The experiments reveal that both excitatory and inhibitory nerve cells can cause blood vessels in the brain to dilate. However, blood vessels in the brain will only constrict in response to inhibitory nerve cells. Uhlirova, Kılıç et al. went on to identify a molecule called Neuropeptide Y (or NPY short) as a signal that triggers the constriction of the blood vessels. This signaling molecule is released by a specific sub-type of inhibitory nerve cell and it binds to a receptor protein on the brain’s blood vessels to make them constrict. These findings suggest that NPY and its receptor on blood vessels may offer promising targets for drugs to treat diseases of the brain’s blood vessels. Further studies are now needed to identify the signals responsible for the dilation of blood vessels in the brain.

The computational properties of the human brain arise from an intricate interplay between billions of neurons connected in complex networks. However, our ability to study these networks in healthy human brain is limited by the necessity to use non-invasive technologies. This is in contrast to animal models where a rich, detailed view of cellular-level brain function with cell-type-specific molecular identity has become available due to recent advances in microscopic optical imaging and genetics. Thus, a central challenge facing neuroscience today is leveraging these mechanistic insights from animal studies to accurately draw physiological inferences from non-invasive signals in humans. Qn the essential path towards this goal is the development of a detailed 'bottom-up' forward model bridging neuronal activity at the level of cell-type-specific populations to non-invasive imaging signals. The general idea is that specific neuronal cell types have identifiable signatures in the way they drive changes in cerebral blood flow, cerebral metabolic rate of O2 (measurable with quantitative functional Magnetic Resonance Imaging), and electrical currents/potentials (measurable with magneto/electroencephalography). This forward model would then provide the 'ground truth' for the development of new tools for tackling the inverse problem—estimation of neuronal activity from multimodal non-invasive imaging data. This article is part of the themed issue 'Interpreting BOLD: a dialogue between cognitive and cellular neuroscience'.

Sharing of experimental data is of critical importance in neuroscience allowing a close inspection by the research community and facilitating the use of experimental data for modeling. However, with a few exceptions, data from individual studies conducted by regular size neuroscience laboratories are not shared. Previously, we provided an example of seamless and low-cost solution for sharing of such data. Specifically, we created a MATLAB® based Graphical User Interface (GUI) engine, which we called Neurovascular Network Explorer 1.0 (NNE 1.0), to interact with a database of 2-photon measurements of sensory stimulus-induced diameter changes of rat cortical arterioles in vivo (Sridhar et al., 2014). NNE 1.0 and the associated database can be downloaded by the user from our academic website (http://nil.ucsd.edu/data/NNE/NNE1_Tian/). The GUI runs either as a MATLAB script or as a standalone program on a Windows platform. It allows browsing the database according to parameters specified by the user, simple manipulation, and visualization of the retrieved records (such as averaging and peak-normalization), and export of the results. The same website provides the NNE 1.0 source code. With this source code, the user can database their own experimental results, given the appropriate data structure and naming conventions, and thus share their data in a user-friendly format with other investigators.Here, we present a novel database containing 2-photon data from our recently published experimental study (Uhlirova et al., 2016a) and a second generation of our GUI-based software engine that we call NNE 2.0. The data, GUI, and source code are freely available for download from our academic website (http://nil.ucsd.edu/data/NNE/NNE2_HDbase_v1.0/). The database contains 2-photon measurements of arteriolar diameter changes in response to selective optogenetic (OG) activation of cortical inhibitory neurons (INs). All measurements were performed in the mouse primary sensory cortex (SI). In addition to all functionalities of NNE 1.0, NNE 2.0 supports 3D visualization of the structural vascular data and localization of individual measurements within the structural vascular network. This new feature can be utilized by the user for computational reconstruction (“graphing”) of the microvascular network, similar to what was done in our published studies (Sakadzic et al., 2010, 2014; Gagnon et al., 2015). Such reconstructions can provide a realistic foundation for bottom-up modeling of the vascular/hemodynamic responses, which are important for understanding cerebral blood flow regulation and physiological underpinning of non-invasive imaging signals (Gagnon et al., 2015; Uhlirova et al., 2016b).