In Vivo Imaging
in vivo imaging
Department of Integrative Biology and Physiology
Assistant Professor
Prof. Tommaso Patriarchi
Our lab is looking for a highly motivated, ambitious, and hard-working research assistant to contribute and lead exciting projects related to the development and/or in vivo application (in mouse brain) of state of the art genetically encoded fluorescent sensors to track the release properties of neurotransmitters and neuromodulators in the context of natural and/or maladaptive behaviors.
Guillermina Lopez Bendito
We are seeking for highly motivated postdoctoral neuroscientists with a strong background in neuroscience to study the functional development of sensory circuits and spontaneous activity programs in mice using in vivo meso-scale and two-photon calcium imaging, and in vivo electrophysiology.
Dr Shuzo Sakata
A fully funded 3-year PhD studentship is available to work with Dr Shuzo Sakata at University of Strathclyde in Glasgow, UK. Our group has been investigating state-dependent information processing in the brain by combining a range of techniques, including in vivo high-density electrophysiological recording, Ca2+ imaging, optogenetics, behavioural analysis and computational approaches. In this PhD project, we will investigate whether and how manipulating brain states can modify Alzheimer’s disease pathology in mice by utilising state-of-the-art neurophotonic technologies. This project is funded by the Strathclyde Research Excellence Award scheme and will be aligned with an international consortium project, DEEPER, funded from the EU’s Horizon 2020 (https://www.deeperproject.eu/) by closely collaborating with Professor Keith Mathieson at the Institute of Photonics.
Dr. Katie Kindt
A staff scientist position is available within the Section on Sensory Cell Development and Function at the National Institute on Deafness and Other Communication Disorders (NIDCD), at the National Institutes of Health (NIH). We are located in the multidisciplinary Neuroscience Research Center (Building 35A) in Bethesda, Maryland just outside of Washington D.C. Our group utilizes the zebrafish system to study hair cells, the specialized mechanoreceptors that are required to reliably transmit auditory and vestibular information to the brain. Specifically, we use this in vivo model to investigate the function and assembly of the hair cell system. Our work uses this relevant model by combining powerful genetics, functional and time-lapse imaging, electrophysiology, and behavioral analyses to comprehensively dissect the molecular and functional requirements underlying the assembly and function of hair cell systems in vivo. The main questions we are currently asking include: 1) how do collections of sensory cells, synapses, and neurons coordinate to encode sensory information; 2) how does sensory activity impact circuit assembly, function and health; and 3) what molecules are required to set up sensory function and synapse specificity?
Hidden nature of seizures
How seizures emerge from the abnormal dynamics of neural networks within the epileptogenic tissue remains an enigma. Are seizures random events, or do detectable changes in brain dynamics precede them? Are mechanisms of seizure emergence identical at the onset and later stages of epilepsy? Is the risk of seizure occurrence stable, or does it change over time? A myriad of questions about seizure genesis remains to be answered to understand the core principles governing seizure genesis. The last decade has brought unprecedented insights into the complex nature of seizure emergence. It is now believed that seizure onset represents the product of the interactions between the process of a transition to seizure, long-term fluctuations in seizure susceptibility, epileptogenesis, and disease progression. During the lecture, we will review the latest observations about mechanisms of ictogenesis operating at multiple temporal scales. We will show how the latest observations contribute to the formation of a comprehensive theory of seizure genesis, and challenge the traditional perspectives on ictogenesis. Finally, we will discuss how combining conventional approaches with computational modeling, modern techniques of in vivo imaging, and genetic manipulation open prospects for exploration of yet hidden mechanisms of seizure genesis.
Astrocytes encode complex behaviorally relevant information
While it is generally accepted that neurons control complex behavior and brain computation, the role of non-neuronal cells in this context remains unclear. Astrocytes, glial cells of the central nervous system, exhibit complex forms of chemical excitation, most prominently calcium transients, evoked by local and projection neuron activity. In this talk, I will provide mechanistic links between astrocytes’ spatiotemporally complex activity patterns, neuronal molecular signaling, and behavior. Using a visual detection task, in vivo calcium imaging, robust statistical analyses, and machine learning approaches, my work shows that cortical astrocytes encode the animal's decision, reward, performance level, and sensory properties. Behavioral context and motor activity-related parameters strongly impact astrocyte responses. Error analysis confirms that astrocytes carry behaviorally relevant information, supporting astrocytes' complementary role to neuronal coding beyond their established homeostatic and metabolic roles.
Optogenetic silencing of synaptic transmission with a mosquito rhodopsin
Long-range projections link distant circuits in the brain, allowing efficient transfer of information between regions and synchronization of distributed patterns of neural activity. Understanding the functional roles of defined neuronal projection pathways requires temporally precise manipulation of their activity, and optogenetic tools appear to be an obvious choice for such experiments. However, we and others have previously shown that commonly-used inhibitory optogenetic tools have low efficacy and off-target effects when applied to presynaptic terminals. In my talk, I will present a new solution to this problem: a targeting-enhanced mosquito homologue of the vertebrate encephalopsin (eOPN3), which upon activation can effectively suppress synaptic transmission through the Gi/o signaling pathway. Brief illumination of presynaptic terminals expressing eOPN3 triggers a lasting suppression of synaptic output that recovers spontaneously within minutes in vitro and in vivo. The efficacy of eOPN3 in suppressing presynaptic release opens new avenues for functional interrogation of long-range neuronal circuits in vivo.
Imaging the influences of sensory experience on visual system circuit development
Using a combination of in vivo imaging of neuronal circuit functional and structural dynamics, we have investigated the mechanisms by which patterned neural activity and sensory experience alter connectivity in the developing brain. We have identified, in addition to the long-hypothesized Hebbian structural plasticity mechanisms, a kind of plasticity induced by the absence of correlated firing that we dubbed “Stentian plasticity”. In the talk I will discuss the phenomenology and some mechanistic insights regarding Stentian mechanisms in brain development. Further, I will show how glia may have a key role in circuit remodeling during development. These studies have led us to an appreciation of the importance of neuron-glia interactions in early development and the ability of patterned activity to guide circuit wiring.
The interaction of sensory and motor information to shape neuronal representations in mouse cortical networks
The neurons in our brain never function in isolation; they are organized into complex circuits which perform highly specialized information processing tasks and transfer information through large neuronal networks. The aim of Janelle Pakan's research group is to better understand how neural circuits function during the transformation of information from sensory perception to behavioural output. Importantly, they also aim to further understand the cell-type specific processes that interrupt the flow of information through neural circuits in neurodegenerative disorders with dementia. The Pakan group utilizes innovative neuroanatomical tracing techniques, advanced in vivo two-photon imaging, and genetically targeted manipulations of neuronal activity to investigate the cell-type specific microcircuitry of the cerebral cortex, the macrocircuitry of cortical output to subcortical structures, and the functional circuitry underlying processes of sensory perception and motor behaviour.
Vagal sensory neurons that guard the airways
The vagus nerve contains a diversity of sensory neurons that detect peripheral stimuli such as blood pressure changes at the aortic arch, lung expansion during breathing, meal-induced stomach distension, and chemotherapeutics that induce nausea. Underlying vagal sensory mechanisms are largely unresolved at a molecular level, presenting tremendously important problems in sensory biology. We charted vagal sensory neurons by single cell RNA sequencing, identifying novel cell surface receptors and classifying a staggering diversity of sensory neuron types. We then generated a collection of ires-Cre knock-in mice to target each neuron type, and adapted genetic tools for Cre-based anatomical mapping, in vivo imaging, targeted ablation, and optogenetic control of vagal neuron activity. We found different sensory neuron types that innervate the lung and exert powerful effects on breathing, others that monitor and control the digestive system, and yet others that innervate that innervate the larynx and protect the airways. Together with Ardem Patapoutian, we also identified a critical role for Piezo mechanoreceptors in the sensation of airway stretch, which underlies a classical respiratory reflex termed the Hering-Breuer inspiratory reflex, as well as in the neuronal sensation of blood pressure and the baroreceptor reflex.
3-Photon in vivo imaging reveals breakdown of microglia surveillance upon glioma invasion in the corpus callosum
FENS Forum 2024
A new family of multicolor genetically encoded indicators for fast, sensitive, and selective in vivo imaging of norepinephrine
FENS Forum 2024
Three-photon in vivo imaging of neurons and glia in the medial prefrontal cortex at unprecedented depth with sub-cellular resolution
FENS Forum 2024
In vivo imaging of CB1-dependent modulation of brain metabolism
FENS Forum 2024