Biology subjects

Nimmerjahn, A.

Publications and source records attributed to Nimmerjahn, A..

11 recordsLinked to original sources

bioRxiv2026

Compact red-shifted near-infrared fluorescent proteins enable deep-tissue SWIR imaging with in vivo optical clearing.

Compact fluorescent proteins (FPs) with red-shifted emission are needed for deep-tissue short-wavelength infrared (SWIR) imaging. We engineered a GAF domain from the JSC1 cyanobacteriochrome of thermophilic Leptolyngbya sp. into three monomeric, biliverdin-binding FPs of 19.1 kDa: miRFP729nano, miRFP732nano and miRFP735nano, with excitation/emission maxima of 714/729, 716/732 and 719/735 nm, respectively. Their off-peak fluorescence beyond 1,000 nm was several-fold higher than that of miRFP718nano previously used for SWIR imaging. miRFP732nano functioned as a fusion tag, a component of target-stabilized nanobodies, and a reporter of NF-{kappa}B and AP-1 transcriptional activities. It enabled single-laser, dual-color three-photon imaging with EGFP to depths of [~]950 m in cortex and [~]300 m in spinal cord. In mice, miRFP732nano supported SWIR imaging of skeletal muscle, inflammatory signaling and intracellular targets. Combining SWIR detection with biocompatible 4-aminoantipyrine-based in vivo tissue clearing enhanced signal and image sharpness. These red-shifted NIR FPs expand the genetically encoded toolkit for deep-tissue imaging.

bioengineering↗

bioRxiv2026

AQuA2-Cloud: a web platform for fluorescence bioimaging activity analysis

BackgroundAdvanced biological imaging analysis platforms such as Activity Quantification and Analysis (AQuA2) enable accurate spatiotemporal activity analysis across diverse cell populations within many species. These tools are increasingly important for investigating cellular signaling dynamics and behavior. However, despite advances in the accuracy and species capability of AQuA2, it remains computationally demanding for analysis of long time-series datasets and requires all users to maintain a MATLAB license, which may limit accessibility and large-scale deployment. ResultsTo address these limitations, we have designed and made available AQuA2-Cloud, a portable software stack and web platform developed as an improvement and further evolution of AQuA2. This container-deployable system permits multi-user cloud-based high accuracy activity quantification with intuitive workflows, export of analysis data and project files, and comparable processing times. The platform offers integrated features such as in-browser analysis control interfaces, asynchronous program state control, multiple users and user management, support for unreliable connections, file uploading and downloading via web browsers and File Transfer Protocol, and centralized organization of analysis output. ConclusionAQuA2-Cloud constitutes a cloud-native solution for laboratories or research groups seeking to centralize analysis of spatiotemporal biological imaging datasets while reducing software installation and licensing barriers for end users. The platform enables researchers with minimal technical expertise to perform advanced bioimaging analysis through standard web browsers while maintaining the analytical capabilities of AQuA2. AQuA2-Cloud source code, deployment procedures, and documentation are freely available at (https://github.com/yu-lab-vt/AQuA2-Cloud).

bioinformatics↗

bioRxiv2026

Modeling predicts a biochemical feedback mechanism underlying astrocyte calcium refractory periods

Astrocytes exhibit intracellular calcium fluctuations in response to neuronal activity. Repeated receptor stimulation can induce a transient suppression of calcium signaling--a refractory period--yet the underlying mechanisms and timescales of this phenomenon during behavior remain poorly understood. Here, we present a biophysically grounded computational model of astrocytic calcium signaling that incorporates a novel feedback mechanism mediated by conventional protein kinase C (cPKC) and predicts the refractory phenomenon. Unlike previous models developed in vitro, our model is directly validated using in vivo two-photon calcium imaging data from behaving mice. It closely recapitulates astrocytic calcium dynamics across both time and frequency domains, including the emergence of refractory periods and their negative correlation with inter-stimulus intervals. Simulations further predict the timing of recovery from refractory states, consistent with experimental observations. This work provides a mechanistic explanation for astrocytic refractory behavior and establishes a framework for integrating computational modeling with in vivo functional imaging.

neuroscience↗

bioRxiv2025

Synthetic multicolor antigen-stabilizable nanobody platform for intersectional labelling and functional imaging.

We present a synthetic toolkit of antigen-stabilizable fluorescent nanobodies (VIS-Fbs) spanning the entire visible spectrum from 450 nm to 660 nm. By engineering over twenty fluorescent proteins (FPs) and biosensors into eight nanobodies, we established a generalizable design of VIS-Fbs, which fluoresce brightly only upon binding to cognate antigens. Our synthetic approach includes constitutive, photoactivatable and photoswitchable FPs, and intensiometric FP-based biosensors. VIS-Fbs carrying biosensors enable simultaneous monitoring of two metabolites at confined locations, while FP-based VIS-Fbs targeting biosensors allow ratiometric functional imaging in the mouse brain. We further used VIS-Fbs to track endogenous {beta}-catenin dynamics in zebrafish embryos during normal development and under Wnt/{beta}-catenin signaling modulation. VIS-Fbs provide background-free visualization of intracellular proteins, multicolor detection of multiple antigens, and selective targeting of defined cell populations and compartments. This synthetic biology-driven platform enables precise studies of protein dynamics, cellular processes, and complex biological systems with high specificity and minimal background.

synthetic biology↗

bioRxiv2024

Fast, Accurate, and Versatile Data Analysis Platform for the Quantification of Molecular Spatiotemporal Signals

Optical recording of intricate molecular dynamics is becoming an indispensable technique for biological studies, accelerated by the development of new or improved biosensors and microscopy technology. This creates major computational challenges to extract and quantify biologically meaningful spatiotemporal patterns embedded within complex and rich data sources, many of which cannot be captured with existing methods. Here, we introduce Activity Quantification and Analysis (AQuA2), a fast, accurate, and versatile data analysis platform built upon advanced machine learning techniques. It decomposes complex live imaging-based datasets into elementary signaling events, allowing accurate and unbiased quantification of molecular activities and identification of consensus functional units. We demonstrate applications across a wide range of biosensors, cell types, organs, animal models, and imaging modalities. As exemplar findings, we show how AQuA2 identified drug-dependent interactions between neurons and astroglia, and distinct sensorimotor signal propagation patterns in the mouse spinal cord.

neuroscience↗

bioRxiv2023

Brainstem Dbh+ Neurons Control Chronic Allergen-Induced Airway Hyperreactivity

Chronic exposure of the lung to irritants such as allergen is a primary cause of asthma characterized by exaggerated airway constriction, also called hyperreactivity, which can be life-threatening. Aside from immune cells, vagal sensory neurons are important for airway hyperreactivity 1-4. However, the identity and signature of the downstream nodes of this adaptive circuit remains poorly understood. Here we show that a single population of Dbh+neurons in the nucleus of the solitary tract (nTS) of the brainstem, and downstream neurons in the nucleus ambiguous (NA), are both necessary and sufficient for chronic allergen-induced airway hyperreactivity. We found that repeated exposures of mice to inhaled allergen activates nTS neurons in a mast cell-, interleukin 4 (IL-4)-and vagal nerve-dependent manner. Single-nucleus RNA-seq of the nTS at baseline and following allergen challenges reveals that a Dbh+ population is preferentially activated. Ablation or chemogenetic inactivation of Dbh+ nTS neurons blunted, while chemogenetic activation promoted hyperreactivity. Viral tracing indicates that Dbh+nTS neurons, capable of producing norepinephrine, project to the NA, and NA neurons are necessary and sufficient to relay allergen signals to postganglionic neurons that then directly drive airway constriction. Focusing on transmitters, delivery of norepinephrine antagonists to the NA blunted allergen-induced hyperreactivity. Together, these findings provide molecular, anatomical and functional definitions of key nodes of a canonical allergen response circuit. The knowledge opens the possibility of targeted neural modulation as an approach to control refractory allergen-induced airway constriction.

cell biology↗

bioRxiv2021

Multiplex, translaminar imaging in the spinal cord of behaving mice

While the spinal cord is known to play critical roles in sensorimotor processing, including pain-related signaling, corresponding activity patterns in genetically defined cell types across spinal laminae have remained elusive. Calcium imaging has enabled cellular activity measurements in behaving rodents but is currently limited to superficial regions. Using chronically implanted microprisms, we imaged sensory and motor evoked activity in regions and at speeds inaccessible by other high-resolution imaging techniques. To enable translaminar imaging in freely behaving animals through implanted microprisms, we additionally developed wearable microscopes with custom-compound microlenses. This new integrated system addresses multiple challenges of previous wearable microscopes, including their limited working distance, resolution, contrast, and achromatic range. The combination of these innovations allowed us to uncover that dorsal horn astrocytes in behaving mice show somatosensory program-dependent and lamina-specific calcium excitation. Additionally, we show that tachykinin precursor 1 (Tac1)-expressing neurons exhibit upper laminae-restricted activity to acute mechanical pain but not locomotion.

neuroscience↗

bioRxiv2021

Trans-segmental imaging in the spinal cord of behaving mice

Spinal cord circuits play crucial roles in transmitting and gating cutaneous somatosensory modalities, such as pain, but the underlying activity patterns within and across spinal segments in behaving mice have remained elusive. To enable such measurements, we developed a wearable widefield macroscope with a 7.9 mm2 field of view, subcellular lateral resolution, 2.7 mm working distance, and <10 g overall weight. We show that highly localized painful mechanical stimuli evoke widespread, coordinated astrocyte excitation across multiple spinal segments.

neuroscience↗

bioRxiv2021

Astrocytes encode complex behaviorally relevant information

Astrocytes, glial cells of the central nervous system, help to regulate neural circuit operation and adaptation. They exhibit complex forms of chemical excitation, most prominently calcium transients, evoked by neuromodulator and -transmitter receptor activation1-4. However, whether and how astrocytes contribute to cortical processing of complex behavior remains unknown1. One of the puzzling features of astrocyte calcium transients is the high degree of variability in their spatial and temporal patterns under behaving conditions. Here, we provide mechanistic links between astrocytes activity patterns, molecular signaling, and behavioral cognitive and motor activity variables by employing a visual detection task that allows for in vivo calcium imaging, robust statistical analyses, and machine learning approaches. We show that trial type and performance levels deterministically shape astrocytes spatial and temporal response properties. Astrocytes encode the animals decision, reward, and sensory properties. Our error analysis confirms that astrocytes carry behaviorally relevant information depending on and complementing neuronal coding. We also report that cell-intrinsic mechanisms curb astrocyte calcium activity. Additionally, we show that motor activity-related parameters strongly impact astrocyte responses and must be considered in sensorimotor study designs. Our data inform and constrain current models of astrocytes contribution to complex behavior and brain computation beyond their established homeostatic and metabolic roles.

neuroscience↗

bioRxiv2020

Electro-optical mechanically flexible coaxial microprobes for minimally invasive interfacing with intrinsic neural circuits

Central to advancing our understanding of neural circuits is the development of minimally invasive, multi-modal interfaces capable of simultaneously recording and modulating neural activity. Recent devices have focused on matching the mechanical compliance of tissue to reduce inflammatory responses1,2. However, reductions in the size of multi-modal interfaces are needed to further improve biocompatibility and long-term recording capabilities1. Here we demonstrate a multi-modal coaxial microprobe design with a minimally invasive footprint (8-12 m diameter over millimeter lengths) that enables efficient electrical and optical interrogation of neural networks. In the brain, the probes allowed robust electrical measurement and optogenetic stimulation. Scalable fabrication strategies can be used with various electrical and optical materials, making the probes highly customizable to experimental requirements, including length, diameter, and mechanical properties. Given their negligible inflammatory response, these probes promise to enable a new generation of readily tunable multi-modal devices for minimally invasive interfacing with neural circuits.

neuroscience↗

bioRxiv2019

Calcium Imaging Reveals Host-Graft Synaptic Network Formation in Spinal Cord Injury

Neural stem/progenitor cell grafts integrate into sites of spinal cord injury (SCI) and form anatomical and electrophysiological neuronal relays across lesions. To determine how grafts become synaptically organized and connect with host systems, we performed calcium imaging of neural progenitor cell grafts within sites of SCI, using both in vivo imaging and spinal cord slices. Stem cell grafts organize into localized synaptic networks that are spontaneously active. Following optogenetic stimulation of host corticospinal tract axons regenerating into grafts, distinct and segregated neuronal networks respond throughout the graft. Moreover, optogenetic stimulation of graft axons extending out from the lesion into the denervated spinal cord also trigger responses in local host neuronal networks. In vivo imaging reveals that behavioral stimulation of host elicits focal synaptic responses within grafts. Thus, remarkably, neural progenitor cell grafts form functional synaptic subnetworks in patterns paralleling the normal spinal cord.

neuroscience↗