Robust Population Single Neuronal Calcium Signal Extraction Using SCOUT Allows for Longitudinal Analysis of Behavior-associated Neural Ensemble Dynamics

SummaryIn vivo calcium imaging enables simultaneous recording of large neuronal ensembles while engaged in operations such as learning and memory. However, such in vivo optical recordings are typically subject to motion artifact and background contamination from neurons and blood vessels. Further, population cell tracking across multiple recordings is complicated by non-rigid transformation induced by cell movements and field shifts. We introduce the novel method SCOUT for Single-Cell SpatiOtemporal LongitUdinal Tracking, consisting of two crucial parts: (1) imposition of spatial constraints on neuronal footprints extracted from individual optical recordings to improve ROI selection and eliminate false discoveries, and (2) application of a predictor-corrector, using spatiotemporal correlation of extracted neurons across sessions, for population cell tracking across multiple sessions. SCOUT empirically outperforms current methods for cell extraction and tracking in long-term multi-session imaging experiments across multiple brain regions. Application of this method allows for robust longitudinal analysis of contextual discrimination associated neural ensemble dynamics in the hippocampus up to 60 days.

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Effective and Efficient Neural Networks for Spike Inference from In Vivo Calcium Imaging

10.1101/2021.08.30.458217 ◽

2021 ◽

Author(s):

Zhanhong Zhou ◽

Chung Tin

Keyword(s):

Calcium Imaging ◽

Signal To Noise Ratio ◽

Large Population ◽

Brain Regions ◽

Spike Rate ◽

Calcium Signal ◽

Calcium Signals ◽

Inference System ◽

Spike Event

AbstractCalcium imaging technique provides irreplaceable advantages in monitoring large population of neuronal activities simultaneously. However, due to the generally low signal to noise ratio (SNR) of the calcium signal and variability in dye properties, it is still challenging to faithfully infer neuronal spikes from these calcium signals, especially from in vivo experiments. In this study, we tackled the problem of both spike-rate and spike-event predictions using a data-driven approach, based on a public pool of dataset with simultaneously recorded calcium and electrophysiological signals using different dyes and recorded from different brain regions. We proposed the ENS2 (effective and efficient neural networks for spike inference from calcium signals) system using raw calcium inputs and it consistently outperforms state-of-the-arts algorithms in both spike-rate and spike-event predictions with reduced computational load. We have also demonstrated that factors such as sampling rates, smoothing window sizes and parametric evaluation metrics could readily bias the interpretation of inference performance. We concluded that optimizing our system for spike-event prediction could produce a more versatile inference system for real neuroscience studies.

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Abstract 019: Evidence that Remodeling of Insular Cortex Neurovascular Unit Contributes to Hypertension-related Sympathoexcitation

Hypertension ◽

10.1161/hyp.68.suppl_1.019 ◽

2016 ◽

Vol 68 (suppl_1) ◽

Author(s):

Fernanda R Marins ◽

Jennifer A Iddings ◽

Marco A Fontes ◽

Jessica A Filosa

Keyword(s):

Blood Vessels ◽

Neurovascular Unit ◽

Insular Cortex ◽

Brain Regions ◽

Simultaneous Recording ◽

Vascular Density ◽

Gfap Immunoreactivity ◽

And Function ◽

Process Length

Introduction and Hypothesis: The intermediate region of the posterior insular cortex (intermediate IC) mediates sympathoexcitatory responses to the heart and kidneys. Previous evidence indicates that hypertension alters both structure and function of neurons, blood vessels, astrocytes and microglia, disrupting the architecture of the neurovascular unit (NVU) in specific brain regions. Thus, the goal of this study is to evaluate the functional and anatomical integrity of the NVU in the intermediate IC during hypertension using in vivo and in situ experiments in male hypertensive (SHR) and normotensive (WKY) rats. Methods: Under urethane anesthesia, NMDA microinjection (0.2mM/100nL) was performed in the intermediate IC with simultaneous recording of renal sympathetic nerve activity (RSNA), heart rate (HR) and mean arterial pressure (MAP). NVU structure was investigated by immunofluorescence for NMDA receptors (NR1, NeuN and TOTO), blood vessels (perfused with 70kDa FITC-dextran), astrocytes (GFAP) and microglia (Iba1). Results: NMDA injections into intermediate IC of SHR (n=4) evoked higher amplitude responses of RSNA (Δ= WKY 26 ± 1.5 vs. SHR 44 ± 4.1 % of baseline, P =0.006), MAP (Δ= WKY 9 ± 1.8 vs. SHR 19 ± 2.2 mmHg, P =0.017) and HR (Δ=WKY 40 ± 2.5 vs. SHR 54 ± 4.9 bpm, P =0.044). Immunofluorescence data of the intermediate IC of SHR showed increased NMDA receptor density (WKY 16.67± 1.05% vs. SHR 24.17± 1.68%, n=6, P =0.003). Vascular density (WKY 1.73± 0.13% vs. SHR 2.52± 0.27%, n=10, P =0.015), branch and end-point number were also increased suggesting angiogenesis at the IC of SHR. Additionally, IC of SHR presented greater GFAP immunoreactivity (WKY 9.37± 2.28% vs. SHR 19.51± 3.52%, n=13, P =0.023) and increased contact between astrocyte processes and the vasculature (Δ= 12.8%, n=13, P =0.015). Skeleton analysis indicated enhanced microglia activation in IC of SHR (reduced number of branches, junctions, end-points and process length, n=13), suggesting an inflammatory process in this region. Conclusions: These findings suggest that the neurogenic origin of hypertension in SHR is associated with marked alterations to NVU structure within the IC contributing to enhanced NMDA-mediated sympathoexcitatory responses and maintenance of hypertension.

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Tissue dynamics of the forebrain neural plate

10.1101/016303 ◽

2015 ◽

Cited By ~ 1

Author(s):

Stephen Young ◽

Joel N Jennings ◽

Guy B Blanchard ◽

Alexandre J Kabla ◽

Richard Adams

Keyword(s):

Mechanical Model ◽

Cell Tracking ◽

Complex Shape ◽

Brain Regions ◽

Neural Plate ◽

Planar Polarity ◽

Cell Behaviour ◽

Vertebrate Brain ◽

Convergence And Extension

The forebrain has the most complex shape and structure of the vertebrate brain regions and the mechanisms of its formation remain obscure. Convergence and extension movements are characteristic of the posterior (spinal cord and hindbrain) neural plate (pNP) while tissue de- formations and underlying cellular dynamics during the early shaping of the forebrain neural plate (fNP) are undefined. Here, we apply live imaging, automated cell tracking and compu- tational analysis to quantitatively map cell behaviour in the zebrafish fNP. We demonstrate a novel mechanism in which planar cell rearrangements, with a passive signature, are orthogo- nal to those in the pNP, and cell divisions lacking planar-polarity facilitate thickening from two to three layers. We develop a mechanical model of the fNP in which polarised cell be- haviour arises from interactions with dissimilar bordering tissues rather than from intrinsical- ly polarised cells. The model unifies in vivo observations and provides a mechanistic under- standing of fNP morphogenesis.

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Simultaneous recording of fluorescence and electrical signals by photometric patch electrode in deep brain regions in vivo

Journal of Neurophysiology ◽

10.1152/jn.00005.2015 ◽

2015 ◽

Vol 113 (10) ◽

pp. 3930-3942 ◽

Cited By ~ 2

Author(s):

Yasuharu Hirai ◽

Eri Nishino ◽

Harunori Ohmori

Keyword(s):

Brain Function ◽

Metabotropic Glutamate Receptors ◽

Electrical Response ◽

Brain Regions ◽

Simultaneous Recording ◽

Optical Measurements ◽

Fluorescence Signal ◽

Deep Brain ◽

Electrical Responses

Despite its widespread use, high-resolution imaging with multiphoton microscopy to record neuronal signals in vivo is limited to the surface of brain tissue because of limited light penetration. Moreover, most imaging studies do not simultaneously record electrical neural activity, which is, however, crucial to understanding brain function. Accordingly, we developed a photometric patch electrode (PME) to overcome the depth limitation of optical measurements and also enable the simultaneous recording of neural electrical responses in deep brain regions. The PME recoding system uses a patch electrode to excite a fluorescent dye and to measure the fluorescence signal as a light guide, to record electrical signal, and to apply chemicals to the recorded cells locally. The optical signal was analyzed by either a spectrometer of high light sensitivity or a photomultiplier tube depending on the kinetics of the responses. We used the PME in Oregon Green BAPTA-1 AM-loaded avian auditory nuclei in vivo to monitor calcium signals and electrical responses. We demonstrated distinct response patterns in three different nuclei of the ascending auditory pathway. On acoustic stimulation, a robust calcium fluorescence response occurred in auditory cortex (field L) neurons that outlasted the electrical response. In the auditory midbrain (inferior colliculus), both responses were transient. In the brain-stem cochlear nucleus magnocellularis, calcium response seemed to be effectively suppressed by the activity of metabotropic glutamate receptors. In conclusion, the PME provides a powerful tool to study brain function in vivo at a tissue depth inaccessible to conventional imaging devices.

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Optical and genetic tools for in vivo single cell tracking

Journal of Neuroscience Methods ◽

10.1016/j.jneumeth.2021.109192 ◽

2021 ◽

Vol 358 ◽

pp. 109192

Author(s):

Yajie Liang ◽

Liset M. de la Prida

Keyword(s):

Single Cell ◽

Cell Tracking ◽

Genetic Tools

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Growth Factor Therapy for Parkinson’s Disease: Alternative Delivery Systems

Journal of Parkinson s Disease ◽

10.3233/jpd-212662 ◽

2021 ◽

pp. 1-7

Author(s):

Sarah Jarrin ◽

Abrar Hakami ◽

Ben Newland ◽

Eilís Dowd

Keyword(s):

Parkinson’S Disease ◽

Gene Therapy ◽

Parkinson's Disease ◽

Growth Factors ◽

Growth Factor ◽

Ex Vivo ◽

Brain Regions ◽

Delivery Systems ◽

Alternative Delivery

Despite decades of research and billions in global investment, there remains no preventative or curative treatment for any neurodegenerative condition, including Parkinson’s disease (PD). Arguably, the most promising approach for neuroprotection and neurorestoration in PD is using growth factors which can promote the growth and survival of degenerating neurons. However, although neurotrophin therapy may seem like the ideal approach for neurodegenerative disease, the use of growth factors as drugs presents major challenges because of their protein structure which creates serious hurdles related to accessing the brain and specific targeting of affected brain regions. To address these challenges, several different delivery systems have been developed, and two major approaches—direct infusion of the growth factor protein into the target brain region and in vivo gene therapy—have progressed to clinical trials in patients with PD. In addition to these clinically evaluated approaches, a range of other delivery methods are in various degrees of development, each with their own unique potential. This review will give a short overview of some of these alternative delivery systems, with a focus on ex vivo gene therapy and biomaterial-aided protein and gene delivery, and will provide some perspectives on their potential for clinical development and translation.

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Cortical neurons exhibit diverse myelination patterns that scale between mouse brain regions and regenerate after demyelination

Nature Communications ◽

10.1038/s41467-021-25035-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Cody L. Call ◽

Dwight E. Bergles

Keyword(s):

Cortical Neurons ◽

Regional Differences ◽

Brain Regions ◽

Axon Diameter ◽

Neuronal Identity ◽

Cortical Areas ◽

Myelin Sheaths ◽

Parvalbumin Interneurons ◽

Selection Of

ABSTRACTAxons in the cerebral cortex show a broad range of myelin coverage. Oligodendrocytes establish this pattern by selecting a cohort of axons for myelination; however, the distribution of myelin on distinct neurons and extent of internode replacement after demyelination remain to be defined. Here we show that myelination patterns of seven distinct neuron subtypes in somatosensory cortex are influenced by both axon diameter and neuronal identity. Preference for myelination of parvalbumin interneurons was preserved between cortical areas with varying myelin density, suggesting that regional differences in myelin abundance arises through local control of oligodendrogenesis. By imaging loss and regeneration of myelin sheaths in vivo we show that myelin distribution on individual axons was altered but overall myelin content on distinct neuron subtypes was restored. Our findings suggest that local changes in myelination are tolerated, allowing regenerated oligodendrocytes to restore myelin content on distinct neurons through opportunistic selection of axons.

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The pharmacokinetics of [18F]UCB-H revisited in the healthy non-human primate brain

EJNMMI Research ◽

10.1186/s13550-021-00777-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Sébastien Goutal ◽

Martine Guillermier ◽

Guillaume Becker ◽

Mylène Gaudin ◽

Yann Bramoullé ◽

...

Keyword(s):

Slow Component ◽

Specific Binding ◽

Compartment Model ◽

Brain Regions ◽

Volume Of Distribution ◽

Pharmacokinetic Data ◽

Limited Information ◽

Positron Emission ◽

Human Primate

Abstract Background Positron Emission Tomography (PET) imaging of the Synaptic Vesicle glycoprotein (SV) 2A is a new tool to quantify synaptic density. [18F]UCB-H was one of the first promising SV2A-ligands to be labelled and used in vivo in rodent and human, while limited information on its pharmacokinetic properties is available in the non-human primate. Here, we evaluate the reliability of the three most commonly used modelling approaches for [18F]UCB-H in the non-human cynomolgus primate, adding the coupled fit of the non-displaceable distribution volume (VND) as an alternative approach to improve unstable fit. The results are discussed in the light of the current state of SV2A PET ligands. Results [18F]UCB-H pharmacokinetic data was optimally fitted with a two-compartment model (2TCM), although the model did not always converge (large total volume of distribution (VT) or large uncertainty of the estimate). 2TCM with coupled fit K1/k2 across brain regions stabilized the quantification, and confirmed a lower specific signal of [18F]UCB-H compared to the newest SV2A-ligands. However, the measures of VND and the influx parameter (K1) are similar to what has been reported for other SV2A ligands. These data were reinforced by displacement studies using [19F]UCB-H, demonstrating only 50% displacement of the total [18F]UCB-H signal at maximal occupancy of SV2A. As previously demonstrated in clinical studies, the graphical method of Logan provided a more robust estimate of VT with only a small bias compared to 2TCM. Conclusions Modeling issues with a 2TCM due to a slow component have previously been reported for other SV2A ligands with low specific binding, or after blocking of specific binding. As all SV2A ligands share chemical structural similarities, we hypothesize that this slow binding component is common for all SV2A ligands, but only hampers quantification when specific binding is low.

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Non-radioactive imaging strategies for in vivo immune cell tracking

Physical Sciences Reviews ◽

10.1515/psr-2020-0205 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Łukasz Kiraga ◽

Paulina Kucharzewska ◽

Damian Strzemecki ◽

Tomasz P. Rygiel ◽

Magdalena Król

Keyword(s):

Diagnostic Imaging ◽

Contrast Agents ◽

Cell Tracking ◽

Immune Cell ◽

Imaging Techniques ◽

Diagnostic Technique ◽

Cell Labeling ◽

X Ray Imaging ◽

Disease Study

Abstract In vivo tracking of administered cells chosen for specific disease treatment may be conducted by diagnostic imaging techniques preceded by cell labeling with special contrast agents. The most commonly used agents are those with radioactive properties, however their use in research is often impossible. This review paper focuses on the essential aspect of cell tracking with the exclusion of radioisotope tracers, therefore we compare application of different types of non-radioactive contrast agents (cell tracers), methods of cell labeling and application of various techniques for cell tracking, which are commonly used in preclinical or clinical studies. We discuss diagnostic imaging methods belonging to three groups: (1) Contrast-enhanced X-ray imaging, (2) Magnetic resonance imaging, and (3) Optical imaging. In addition, we present some interesting data from our own research on tracking immune cell with the use of discussed methods. Finally, we introduce an algorithm which may be useful for researchers planning leukocyte targeting studies, which may help to choose the appropriate cell type, contrast agent and diagnostic technique for particular disease study.

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Genetic Suppressor Element 1 (GSE1) Promotes the Oncogenic and Recurrent Phenotypes of Castration-Resistant Prostate Cancer by Targeting Tumor-Associated Calcium Signal Transducer 2 (TACSTD2)

Cancers ◽

10.3390/cancers13163959 ◽

2021 ◽

Vol 13 (16) ◽

pp. 3959

Author(s):

Oluwaseun Adebayo Bamodu ◽

Yuan-Hung Wang ◽

Chen-Hsun Ho ◽

Su-Wei Hu ◽

Chia-Da Lin ◽

...

Keyword(s):

Prostate Cancer ◽

Disease Progression ◽

Therapy Resistance ◽

Calcium Signal ◽

Signal Transducer ◽

Castration Resistance ◽

Castration Resistant

Background: prostate cancer (PCa) is a principal cause of cancer-related morbidity and mortality. Castration resistance and metastasis are clinical challenges and continue to impede therapeutic success, despite diagnostic and therapeutic advances. There are reports of the oncogenic activity of genetic suppressor element (GSE)1 in breast and gastric cancers; however, its role in therapy resistance, metastasis, and susceptibility to disease recurrence in PCa patients remains unclear. Objective: this study investigated the role of aberrantly expressed GSE1 in the metastasis, therapy resistance, relapse, and poor prognosis of advanced PCa. Methods: we used a large cohort of multi-omics data and in vitro, ex vivo, and in vivo assays to investigate the potential effect of altered GSE1 expression on advanced/castration-resistant PCa (CRPC) treatment responses, disease progression, and prognosis. Results: using a multi-cohort approach, we showed that GSE1 is upregulated in PCa, while tumor-associated calcium signal transducer 2 (TACSTD2) is downregulated. Moreover, the direct, but inverse, correlation interaction between GSE1 and TACSTD2 drives metastatic disease, castration resistance, and disease progression and modulates the clinical and immune statuses of patients with PCa. Patients with GSE1highTACSTD2low expression are more prone to recurrence and disease-specific death than their GSE1lowTACSTD2high counterparts. Interestingly, we found that the GSE1–TACSTD2 expression profile is associated with the therapy responses and clinical outcomes in patients with PCa, especially those with metastatic/recurrent disease. Furthermore, we demonstrate that the shRNA-mediated targeting of GSE1 (shGSE1) significantly inhibits cell proliferation and attenuates cell migration and tumorsphere formation in metastatic PC3 and DU145 cell lines, with an associated suppression of VIM, SNAI2, and BCL2 and the concomitant upregulation of TACSTD2 and BAX. Moreover, shGSE1 enhances sensitivity to the antiandrogens abiraterone and enzalutamide in vitro and in vivo. Conclusion: these data provide preclinical evidence of the oncogenic role of dysregulated GSE1–TACSTD2 signaling and show that the molecular or pharmacological targeting of GSE1 is a workable therapeutic strategy for inhibiting androgen-driven oncogenic signals, re-sensitizing CRPC to treatment, and repressing the metastatic/recurrent phenotypes of patients with PCa.

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