Standardised Measurements for Monitoring and Comparing Multiphoton Microscope Systems.

The goal of this protocol is to enable better characterisation of multiphoton microscopy hardware across a large user base. The scope of this protocol is purposefully limited to focus on hardware, touching on software and data analysis routines only where relevant. The intended audiences are scientists using and building multiphoton microscopes in their laboratories. The goal is that any scientist, not only those with optical expertise, can test whether their multiphoton microscope is performing well and producing consistent data over the lifetime of their system.

Antibody stabilization for thermally accelerated deep immunostaining.

Antibodies have diverse applications due to their high reaction specificities but are sensitive to denaturation when a higher working temperature is required. We have developed a simple, highly scalable and generalizable chemical approach for stabilizing off-the-shelf antibodies against thermal and chemical denaturation. We demonstrate that the stabilized antibodies (termed SPEARs) can withstand up to 4 weeks of continuous heating at 55 °C and harsh denaturants, and apply our method to 33 tested antibodies. SPEARs enable flexible applications of thermocycling and denaturants to dynamically modulate their binding kinetics, reaction equilibrium, macromolecular diffusivity and aggregation propensity. In particular, we show that SPEARs permit the use of a thermally facilitated three-dimensional immunolabeling strategy (termed ThICK staining), achieving whole mouse brain immunolabeling within 72 h, as well as nearly fourfold deeper penetration with threefold less antibodies in human brain tissue. With faster deep-tissue immunolabeling and broad compatibility with tissue processing and clearing methods without the need for any specialized equipment, we anticipate the wide applicability of ThICK staining with SPEARs for deep immunostaining.

Tissue compartmentalization enables Salmonella persistence during chemotherapy.

Antimicrobial chemotherapy can fail to eradicate the pathogen, even in the absence of antimicrobial resistance. Persisting pathogens can subsequently cause relapsing diseases. In vitro studies suggest various mechanisms of antibiotic persistence, but their in vivo relevance remains unclear because of the difficulty of studying scarce pathogen survivors in complex host tissues. Here, we localized and characterized rare surviving Salmonella in mouse spleen using high-resolution whole-organ tomography. Chemotherapy cleared >99.5% of the Salmonella but was inefficient against a small Salmonella subset in the white pulp. Previous models could not explain these findings: drug exposure was adequate, Salmonella continued to replicate, and host stresses induced only limited Salmonella drug tolerance. Instead, antimicrobial clearance required support of Salmonella-killing neutrophils and monocytes, and the density of such cells was lower in the white pulp than in other spleen compartments containing higher Salmonella loads. Neutrophil densities declined further during treatment in response to receding Salmonella loads, resulting in insufficient support for Salmonella clearance from the white pulp and eradication failure. However, adjunctive therapies sustaining inflammatory support enabled effective clearance. These results identify uneven Salmonella tissue colonization and spatiotemporal inflammation dynamics as main causes of Salmonella persistence and establish a powerful approach to investigate scarce but impactful pathogen subsets in complex host environments.

The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue.

Light-sheet microscopy is an ideal technique for imaging large cleared samples; however, the community is still lacking instruments capable of producing volumetric images of centimeter-sized cleared samples with near-isotropic resolution within minutes. Here, we introduce the mesoscale selective plane-illumination microscopy initiative, an open-hardware project for building and operating a light-sheet microscope that addresses these challenges and is compatible with any type of cleared or expanded sample ( www.mesospim.org ).

The logic of single-cell projections from visual cortex.

Neocortical areas communicate through extensive axonal projections, but the logic of information transfer remains poorly understood, because the projections of individual neurons have not been systematically characterized. It is not known whether individual neurons send projections only to single cortical areas or distribute signals across multiple targets. Here we determine the projection patterns of 591 individual neurons in the mouse primary visual cortex using whole-brain fluorescence-based axonal tracing and high-throughput DNA sequencing of genetically barcoded neurons (MAPseq). Projections were highly diverse and divergent, collectively targeting at least 18 cortical and subcortical areas. Most neurons targeted multiple cortical areas, often in non-random combinations, suggesting that sub-classes of intracortical projection neurons exist. Our results indicate that the dominant mode of intracortical information transfer is not based on 'one neuron-one target area' mapping. Instead, signals carried by individual cortical neurons are shared across subsets of target areas, and thus concurrently contribute to multiple functional pathways.

Autoantibodies Affect Brain Density Reduction in Nonneuropsychiatric Systemic Lupus Erythematosus Patients.

This study explores the relationship between autoantibodies and brain density reduction in SLE patients without major neuropsychiatric manifestation (NPSLE). Ninety-five NPSLE patients without obvious cerebral deficits, as determined by conventional MRI, as well as 89 control subjects, underwent high-resolution structural MRI. Whole-brain density of grey matter (GMD) and white matter (WMD) were calculated for each individual, and correlations between the brain density, symptom severity, immunosuppressive agent (ISA), and autoantibody levels were assessed. The GMD and WMD of the SLE group decreased compared to controls. GMD was negatively associated with SLE activity. The WMD of patients who received ISA treatment were higher than that in the patients who did not. The WMD of patients with anticardiolipin (ACL) or anti-SSB/La antibodies was lower than in patients without these antibodies, while the GMD was lower in patients with anti-SM or anti-U1RNP antibodies. Thus, obvious brain atrophy can occur very early even before the development of significant symptoms and specific autoantibodies might contribute to the reduction of GMD or WMD in NPSLE patients. However, ISAs showed protective effects in minimizing GMD and WMD reduction. The presence of these specific autoantibodies might help identify early brain damage in NPSLE patients.

OpenStage: a low-cost motorized microscope stage with sub-micron positioning accuracy.

Recent progress in intracellular calcium sensors and other fluorophores has promoted the widespread adoption of functional optical imaging in the life sciences. Home-built multiphoton microscopes are easy to build, highly customizable, and cost effective. For many imaging applications a 3-axis motorized stage is critical, but commercially available motorization hardware (motorized translators, controller boxes, etc) are often very expensive. Furthermore, the firmware on commercial motor controllers cannot easily be altered and is not usually designed with a microscope stage in mind. Here we describe an open-source motorization solution that is simple to construct, yet far cheaper and more customizable than commercial offerings. The cost of the controller and motorization hardware are under $1000. Hardware costs are kept low by replacing linear actuators with high quality stepper motors. Electronics are assembled from commonly available hobby components, which are easy to work with. Here we describe assembly of the system and quantify the positioning accuracy of all three axes. We obtain positioning repeatability of the order of 1 µm in X/Y and 0.1 µm in Z. A hand-held control-pad allows the user to direct stage motion precisely over a wide range of speeds (10(-1) to 10(2) µm·s(-1)), rapidly store and return to different locations, and execute "jumps" of a fixed size. In addition, the system can be controlled from a PC serial port. Our "OpenStage" controller is sufficiently flexible that it could be used to drive other devices, such as micro-manipulators, with minimal modifications.

Imaging a population code for odor identity in the Drosophila mushroom body.

The brain represents sensory information in the coordinated activity of neuronal ensembles. Although the microcircuits underlying olfactory processing are well characterized in Drosophila, no studies to date have examined the encoding of odor identity by populations of neurons and related it to the odor specificity of olfactory behavior. Here we used two-photon Ca(2+) imaging to record odor-evoked responses from >100 neurons simultaneously in the Drosophila mushroom body (MB). For the first time, we demonstrate quantitatively that MB population responses contain substantial information on odor identity. Using a series of increasingly similar odor blends, we identified conditions in which odor discrimination is difficult behaviorally. We found that MB ensemble responses accounted well for olfactory acuity in this task. Kenyon cell ensembles with as few as 25 cells were sufficient to match behavioral discrimination accuracy. Using a generalization task, we demonstrated that the MB population code could predict the flies' responses to novel odors. The degree to which flies generalized a learned aversive association to unfamiliar test odors depended upon the relative similarity between the odors' evoked MB activity patterns. Discrimination and generalization place different demands on the animal, yet the flies' choices in these tasks were reliably predicted based on the amount of overlap between MB activity patterns. Therefore, these different behaviors can be understood in the context of a single physiological framework.

Distinct molecular underpinnings of Drosophila olfactory trace conditioning.

Trace conditioning is valued as a simple experimental model to assess how the brain associates events that are discrete in time. Here, we adapted an olfactory trace conditioning procedure in Drosophila melanogaster by training fruit flies to avoid an odor that is followed by foot shock many seconds later. The molecular underpinnings of the learning are distinct from the well-characterized simultaneous conditioning, where odor and punishment temporally overlap. First, Rutabaga adenylyl cyclase (Rut-AC), a putative molecular coincidence detector vital for simultaneous conditioning, is dispensable in trace conditioning. Second, dominant-negative Rac expression, thought to sustain early labile memory, significantly enhances learning of trace conditioning, but leaves simultaneous conditioning unaffected. We further show that targeting Rac inhibition to the mushroom body (MB) but not the antennal lobe (AL) suffices to achieve the enhancement effect. Moreover, the absence of trace conditioning learning in D1 dopamine receptor mutants is rescued by restoration of expression specifically in the adult MB. These results suggest the MB as a crucial neuroanatomical locus for trace conditioning, which may harbor a Rac activity-sensitive olfactory "sensory buffer" that later converges with the punishment signal carried by dopamine signaling. The distinct molecular signature of trace conditioning revealed here shall contribute to the understanding of how the brain overcomes a temporal gap in potentially related events.

Cellular-resolution population imaging reveals robust sparse coding in the Drosophila mushroom body.

Sensory stimuli are represented in the brain by the activity of populations of neurons. In most biological systems, studying population coding is challenging since only a tiny proportion of cells can be recorded simultaneously. Here we used two-photon imaging to record neural activity in the relatively simple Drosophila mushroom body (MB), an area involved in olfactory learning and memory. Using the highly sensitive calcium indicator GCaMP3, we simultaneously monitored the activity of >100 MB neurons in vivo (∼5% of the total population). The MB is thought to encode odors in sparse patterns of activity, but the code has yet to be explored either on a population level or with a wide variety of stimuli. We therefore imaged responses to odors chosen to evaluate the robustness of sparse representations. Different odors activated distinct patterns of MB neurons; however, we found no evidence for spatial organization of neurons by either response probability or odor tuning within the cell body layer. The degree of sparseness was consistent across a wide range of stimuli, from monomolecular odors to artificial blends and even complex natural smells. Sparseness was mainly invariant across concentrations, largely because of the influence of recent odor experience. Finally, in contrast to sensory processing in other systems, no response features distinguished natural stimuli from monomolecular odors. Our results indicate that the fundamental feature of odor processing in the MB is to create sparse stimulus representations in a format that facilitates arbitrary associations between odor and punishment or reward.

Brief sounds evoke prolonged responses in anesthetized ferret auditory cortex.

Neurons in the auditory cortex of anesthetized animals are generally considered to generate phasic responses to simple stimuli such as tones or noise bursts. In this paper, we show that under ketamine/medetomidine anesthesia, neurons in ferret auditory cortex usually exhibit complex sustained responses. We presented 100-ms broad-band noise bursts at a range of interaural level differences (ILDs) and average binaural levels (ABLs), and used extracellular electrodes to monitor evoked activity over 700 ms poststimulus onset. We estimated the degree of randomness (noise) in the response functions of individual neurons over poststimulus time; we found that neural activity was significantly modulated by sound for up to approximately 500 ms following stimulus offset. Pooling data from all neurons, we found that spiking activity carries significant information about stimulus identity over this same time period. However, information about ILD decayed much more quickly over time compared with information about ABL. In addition, ILD and ABL are coded independently by the neural population even though this is not the case at individual neurons. Though most neurons responded more strongly to ILDs corresponding to the opposite side of space, as a population, they were equally informative about both contra- and ipsilateral stimuli.

Specificity of binaural perceptual learning for amplitude modulated tones: a comparison of two training methods.

The specificity of auditory perceptual learning has been taken as an indicator of the likely locus within the brain at which underlying neuronal changes occur. This study examined interaural level difference (ILD) discrimination learning with sinusoidally amplitude modulated (SAM) tones and whether training-induced threshold improvements generalize from one side of auditory space to the other and to an untrained carrier frequency. A novel, dual-staircase adaptive method was adopted that was designed to prevent participants from identifying the nature of the adaptive track. ILD thresholds obtained with this method were compared with a constant-stimulus technique using otherwise identical stimuli. Adaptive thresholds derived from psychometric functions were found to be biased compared to those obtained from reversals. Although adaptive and constant-stimulus procedures appeared to yield different temporal patterns of learning, no global differences were found between them in terms of training outcomes. These data show that ILD discrimination learning with SAM tones does generalize to an untrained carrier frequency but does not generalize across the midline. This implies that the neural substrate for binaural plasticity is found at a relatively high level of the auditory pathway where information is combined across frequency and where each side of auditory space is represented separately.

Virtual adult ears reveal the roles of acoustical factors and experience in auditory space map development.

Auditory neurons in the superior colliculus (SC) respond preferentially to sounds from restricted directions to form a map of auditory space. The development of this representation is shaped by sensory experience, but little is known about the relative contribution of peripheral and central factors to the emergence of adult responses. By recording from the SC of anesthetized ferrets at different age points, we show that the map matures gradually after birth; the spatial receptive fields (SRFs) become more sharply tuned and topographic order emerges by the end of the second postnatal month. Principal components analysis of the head-related transfer function revealed that the time course of map development is mirrored by the maturation of the spatial cues generated by the growing head and external ears. However, using virtual acoustic space stimuli, we show that these acoustical changes are not by themselves responsible for the emergence of SC map topography. Presenting stimuli to infant ferrets through virtual adult ears did not improve the order in the representation of sound azimuth in the SC. But by using linear discriminant analysis to compare different response properties across age, we found that the SRFs of infant neurons nevertheless became more adult-like when stimuli were delivered through virtual adult ears. Hence, although the emergence of auditory topography is likely to depend on refinements in neural circuitry, maturation of the structure of the SRFs (particularly their spatial extent) can be largely accounted for by changes in the acoustics associated with growth of the head and ears.

Physiological and behavioral studies of spatial coding in the auditory cortex.

Despite extensive subcortical processing, the auditory cortex is believed to be essential for normal sound localization. However, we still have a poor understanding of how auditory spatial information is encoded in the cortex and of the relative contribution of different cortical areas to spatial hearing. We investigated the behavioral consequences of inactivating ferret primary auditory cortex (A1) on auditory localization by implanting a sustained release polymer containing the GABA(A) agonist muscimol bilaterally over A1. Silencing A1 led to a reversible deficit in the localization of brief noise bursts in both the horizontal and vertical planes. In other ferrets, large bilateral lesions of the auditory cortex, which extended beyond A1, produced more severe and persistent localization deficits. To investigate the processing of spatial information by high-frequency A1 neurons, we measured their binaural-level functions and used individualized virtual acoustic space stimuli to record their spatial receptive fields (SRFs) in anesthetized ferrets. We observed the existence of a continuum of response properties, with most neurons preferring contralateral sound locations. In many cases, the SRFs could be explained by a simple linear interaction between the acoustical properties of the head and external ears and the binaural frequency tuning of the neurons. Azimuth response profiles recorded in awake ferrets were very similar and further analysis suggested that the slopes of these functions and location-dependent variations in spike timing are the main information-bearing parameters. Studies of sensory plasticity can also provide valuable insights into the role of different brain areas and the way in which information is represented within them. For example, stimulus-specific training allows accurate auditory localization by adult ferrets to be relearned after manipulating binaural cues by occluding one ear. Reversible inactivation of A1 resulted in slower and less complete adaptation than in normal controls, whereas selective lesions of the descending cortico collicular pathway prevented any improvement in performance. These results reveal a role for auditory cortex in training-induced plasticity of auditory localization, which could be mediated by descending cortical pathways.

Binaural-level functions in ferret auditory cortex: evidence for a continuous distribution of response properties.

Many previous studies have subdivided auditory neurons into a number of physiological classes according to various criteria applied to their binaural response properties. However, it is often unclear whether such classifications represent discrete classes of neurons or whether they merely reflect a potentially convenient but ultimately arbitrary partitioning of a continuous underlying distribution of response properties. In this study we recorded the binaural response properties of 310 units in the auditory cortex of anesthetized ferrets, using an extensive range of interaural level differences (ILDs) and average binaural levels (ABLs). Most recordings were from primary auditory fields on the middle ectosylvian gyrus and from neurons with characteristic frequencies >5 kHz. We used simple multivariate statistics to quantify a fundamental coding feature: the shapes of the binaural response functions. The shapes of all 310 binaural response surfaces were represented as points in a five-dimensional principal component space. This space captured the underlying shape of all the binaural response surfaces. The distribution of binaural level functions was not homogeneous because some shapes were more common than others. Despite this, clustering validation techniques revealed no evidence for the existence of discrete, or partially overlapping, clusters that could serve as a basis for an objective classification of binaural-level functions. We also examined the gradients of the response functions for the population of units; these gradients were greatest near the midline, which is consistent with free-field data showing that cortical neurons are most sensitive to changes in stimulus location in this region of space.

Interaural timing cues do not contribute to the map of space in the ferret superior colliculus: a virtual acoustic space study.

In this study, we used individualized virtual acoustic space (VAS) stimuli to investigate the representation of auditory space in the superior colliculus (SC) of anesthetized ferrets. The VAS stimuli were generated by convolving broadband noise bursts with each animal's own head-related transfer function and presented over earphones. Comparison of the amplitude spectra of the free-field and VAS signals and of the spatial receptive fields of neurons recorded in the inferior colliculus with each form of stimulation confirmed that the VAS provided an accurate simulation of sounds presented in the free field. Units recorded in the deeper layers of the SC responded predominantly to virtual sound directions within the contralateral hemifield. In most cases, increasing the sound level resulted in stronger spike discharges and broader spatial receptive fields. However, the preferred sound directions, as defined by the direction of the centroid vector, remained largely unchanged across different levels and, as observed in previous free-field studies, varied topographically in azimuth along the rostrocaudal axis of the SC. We also examined the contribution of interaural time differences (ITDs) to map topography by digitally manipulating the VAS stimuli so that ITDs were held constant while allowing other spatial cues to vary naturally. The response properties of the majority of units, including centroid direction, remained unchanged with fixed ITDs, indicating that sensitivity to this cue is not responsible for tuning to different sound directions. These results are consistent with previous data suggesting that sensitivity to interaural level differences and spectral cues provides the basis for the map of auditory space in the mammalian SC.

Auditory neuroscience: a time for coincidence?

Mammals and birds appear to encode timing differences between the ears, a major cue for auditory localization, in fundamentally different ways. It now appears that results from different species can be accommodated within a single general framework.