SyConn2: dense synaptic connectivity inference for volume electron microscopy.

The ability to acquire ever larger datasets of brain tissue using volume electron microscopy leads to an increasing demand for the automated extraction of connectomic information. We introduce SyConn2, an open-source connectome analysis toolkit, which works with both on-site high-performance compute environments and rentable cloud computing clusters. SyConn2 was tested on connectomic datasets with more than 10 million synapses, provides a web-based visualization interface and makes these data amenable to complex anatomical and neuronal connectivity queries.

Energy-efficient network activity from disparate circuit parameters.

Neural circuits can produce similar activity patterns from vastly different combinations of channel and synaptic conductances. These conductances are tuned for specific activity patterns but might also reflect additional constraints, such as metabolic cost or robustness to perturbations. How do such constraints influence the range of permissible conductances? Here we investigate how metabolic cost affects the parameters of neural circuits with similar activity in a model of the pyloric network of the crab .

Estimation of skeletal kinematics in freely moving rodents.

Forming a complete picture of the relationship between neural activity and skeletal kinematics requires quantification of skeletal joint biomechanics during free behavior; however, without detailed knowledge of the underlying skeletal motion, inferring limb kinematics using surface-tracking approaches is difficult, especially for animals where the relationship between the surface and underlying skeleton changes during motion. Here we developed a videography-based method enabling detailed three-dimensional kinematic quantification of an anatomically defined skeleton in untethered freely behaving rats and mice. This skeleton-based model was constrained using anatomical principles and joint motion limits and provided skeletal pose estimates for a range of body sizes, even when limbs were occluded.

Connectomic analysis of thalamus-driven disinhibition in cortical layer 4.

Sensory signals are transmitted via the thalamus primarily to layer 4 (L4) of the primary sensory cortices. While information about average neuronal connectivity in L4 is available, its detailed higher-order circuit structure is not known. Here, we used three-dimensional electron microscopy for a connectomic analysis of the thalamus-driven inhibitory network in L4.

Developmental errors in the common marmoset retina.

Although retinal organization is remarkably conserved, morphological anomalies can be found to different extents and varieties across animal species with each presenting unique characteristics and patterns of displaced and misplaced neurons. One of the most widely used non-human primates in research, the common marmoset () could potentially also be of interest for visual research, but is unfortunately not well characterized in this regard. Therefore, the aim of our study was to provide a first time description of structural retinal layering including morphological differences and distinctive features in this species.

Multiple mechanisms mediate the suppression of motion vision during escape maneuvers in flying .

During voluntary behaviors, animals need to disable any reflexes that could interfere with the intended movements. With the optomotor response, flies stabilize a straight flight path by correcting for unintended deviations sensed as the panoramic motion of the surround. HS cells of the fly are thought to mediate optomotor responses to horizontal motion.

No evidence for age-related alterations in the marmoset retina.

The physiological aging process of the retina is accompanied by various and sometimes extensive changes: Macular degeneration, retinopathies and glaucoma are the most common findings in the elderly and can potentially lead to irreversible visual disablements up to blindness. To study the aging process and to identify possible therapeutic targets to counteract these diseases, the use of appropriate animal models is mandatory. Besides the most commonly used rodent species, a non-human primate, the common marmoset () emerged as a promising animal model of human aging over the last years.

Automatically tracking feeding behavior in populations of foraging .

feeds on bacteria and other small microorganisms which it ingests using its pharynx, a neuromuscular pump. Currently, measuring feeding behavior requires tracking a single animal, indirectly estimating food intake from population-level metrics, or using restrained animals. To enable large throughput feeding measurements of unrestrained, crawling worms on agarose plates at a single worm resolution, we developed an imaging protocol and a complementary image analysis tool called PharaGlow.

A Stable Chemokine Gradient Controls Directional Persistence of Migrating Dendritic Cells.

Navigation of dendritic cells (DCs) from the site of infection to lymphoid organs is guided by concentration gradients of CCR7 ligands. How cells interpret chemokine gradients and how they couple directional sensing to polarization and persistent chemotaxis has remained largely elusive. Previous experimental systems were limited in the ability to control fast formation of the final gradient slope, long-lasting stability of the gradient and to expose cells to dynamic stimulation.

The structure of cyclic nucleotide-gated channels in rod and cone photoreceptors.

Cyclic nucleotide-gated (CNG) channels play a central role in rod and cone photoreceptors of the vertebrate retina. In photoreceptors, light triggers a series of biochemical reactions that ultimately close CNG channels and evoke a brief voltage pulse, a signal that is later passed on to the brain. Malfunction of CNG channels can lead to loss of vision.

Visual recognition of social signals by a tectothalamic neural circuit.

Social affiliation emerges from individual-level behavioural rules that are driven by conspecific signals. Long-distance attraction and short-distance repulsion, for example, are rules that jointly set a preferred interanimal distance in swarms. However, little is known about their perceptual mechanisms and executive neural circuits.

A place learning assay for tethered walking Drosophila.

Background: Drosophila shows a range of visually guided memory and learning behaviors, including place learning. Investigating the dynamics of neural circuits underlying such behaviors requires learning assays in tethered animals, compatible with in vivo imaging experiments.

New Method: Here, we introduce an assay for place learning for tethered walking flies.

Genomic integration of transgenes using UV irradiation in .

Transgenes are widely used throughout molecular biology for numerous applications. In stable transgenes are usually generated by microinjection into the germline establishing extrachromosomal arrays. Furthermore, numerous technologies exist to integrate transgenes into the genome.

Barrels XXXIV meeting report: Barrels goes virtual.

: To summarize the state of research in the whisker-to-barrel sensorimotor system based on presentations at the Barrels meeting.: Host the 34th annual Barrels meeting was hosted virtually due to the ongoing Covid-19 pandemic.: The Barrels meeting annually focuses on the latest advances in the rodent sensorimotor research.

Axial motion estimation and correction for simultaneous multi-plane two-photon calcium imaging.

Two-photon imaging in behaving animals is typically accompanied by brain motion. For functional imaging experiments, for example with genetically encoded calcium indicators, such brain motion induces changes in fluorescence intensity. These motion-related intensity changes or motion artifacts can typically not be separated from neural activity-induced signals.

The multivariate analysis of variance as a powerful approach for circular data.

Background: A broad range of scientific studies involve taking measurements on a circular, rather than linear, scale (often variables related to times or orientations). For linear measures there is a well-established statistical toolkit based on linear modelling to explore the associations between this focal variable and potentially several explanatory factors and covariates. In contrast, statistical testing of circular data is much simpler, often involving either testing whether variation in the focal measurements departs from circular uniformity, or whether a single explanatory factor with two levels is supported.

The impact of neuron morphology on cortical network architecture.

The neurons in the cerebral cortex are not randomly interconnected. This specificity in wiring can result from synapse formation mechanisms that connect neurons, depending on their electrical activity and genetically defined identity. Here, we report that the morphological properties of the neurons provide an additional prominent source by which wiring specificity emerges in cortical networks.

Live-Cell Imaging of RNA Transport in Axons of Cultured Primary Neurons.

The use of fluorescent proteins has revolutionized the study of protein localization and transport. However, the visualization of other molecules and specifically RNA during live-cell imaging remains challenging. In this chapter, we provide guidance to the available methods, their advantages and drawbacks as well as provide a detailed protocol for the detection of RNA transport using the MS2/PP7-split-Venus system for background-free RNA imaging.

Mitochondria in Neuronal Health: From Energy Metabolism to Parkinson's Disease.

Mitochondria are the main suppliers of neuronal adenosine triphosphate and play a critical role in brain energy metabolism. Mitochondria also serve as Ca sinks and anabolic factories and are therefore essential for neuronal function and survival. Dysregulation of neuronal bioenergetics is increasingly implicated in neurodegenerative disorders, particularly Parkinson's disease.

IgSF11 homophilic adhesion proteins promote layer-specific synaptic assembly of the cortical interneuron subtype.

The most prominent structural hallmark of the mammalian neocortical circuitry is the layer-based organization of specific cell types and synaptic inputs. Accordingly, cortical inhibitory interneurons (INs), which shape local network activity, exhibit subtype-specific laminar specificity of synaptic outputs. However, the underlying molecular mechanisms remain unknown.

Neuroscience history interview with Professor Bert Sakmann, Nobel Laureate in Physiology or Medicine (1991), Max Planck Society, Germany.

Dr. Bert Sakmann (b. 1942) studied at the Universities of Tuebingen, Freiburg, Berlin, Paris, and Munich, graduating in 1967.

High-frequency burst spiking in layer 5 thick-tufted pyramids of rat primary somatosensory cortex encodes exploratory touch.

Diversity of cell-types that collectively shape the cortical microcircuit ensures the necessary computational richness to orchestrate a wide variety of behaviors. The information content embedded in spiking activity of identified cell-types remain unclear to a large extent. Here, we recorded spike responses upon whisker touch of anatomically identified excitatory cell-types in primary somatosensory cortex in naive, untrained rats.

The dorsoanterior brain of adult amphioxus shares similarities in expression profile and neuronal composition with the vertebrate telencephalon.

Background: The evolutionary origin of the telencephalon, the most anterior part of the vertebrate brain, remains obscure. Since no obvious counterpart to the telencephalon has yet been identified in invertebrate chordates, it is difficult to trace telencephalic origins. One way to identify homologous brain parts between distantly related animal groups is to focus on the combinatorial expression of conserved regionalisation genes that specify brain regions.

Kill one or kill the many: interplay between mitophagy and apoptosis.

Mitochondria are key players of cellular metabolism, Ca homeostasis, and apoptosis. The functionality of mitochondria is tightly regulated, and dysfunctional mitochondria are removed via mitophagy, a specialized form of autophagy that is compromised in hereditary forms of Parkinson's disease. Through mitophagy, cells are able to cope with mitochondrial stress until the damage becomes too great, which leads to the activation of pro-apoptotic BCL-2 family proteins located on the outer mitochondrial membrane.

Neural pathways of olfactory kin imprinting and kin recognition in zebrafish.

Teleost fish exhibit extraordinary cognitive skills that are comparable to those of mammals and birds. Kin recognition based on olfactory and visual imprinting requires neuronal circuits that were assumed to be necessarily dependent on the interaction of mammalian amygdala, hippocampus, and isocortex, the latter being a structure that teleost fish are lacking. We show that teleosts-beyond having a hippocampus and pallial amygdala homolog-also have subpallial amygdalar structures.