Predicting the synaptic information efficacy in cortical layer 5 pyramidal neurons using a minimal integrate-and-fire model

Synaptic information efficacy (SIE) is a statistical measure to quantify the efficacy of a synapse. It measures how much information is gained, on the average, about the output spike train of a postsynaptic neuron if the input spike train is known. It is a particularly appropriate measure for assessing the input–output relationship of neurons receiving dynamic stimuli. Here, we compare the SIE of simulated synaptic inputs measured experimentally in layer 5 cortical pyramidal neurons in vitro with the SIE computed from a minimal model constructed to fit the recorded data. We show that even with a simple model that is far from perfect in predicting the precise timing of the output spikes of the real neuron, the SIE can still be accurately predicted. This arises from the ability of the model to predict output spikes influenced by the input more accurately than those driven by the background current. This indicates that in this context, some spikes may be more important than others. Lastly we demonstrate another aspect where using mutual information could be beneficial in evaluating the quality of a model, by measuring the mutual information between the model’s output and the neuron’s output. The SIE, thus, could be a useful tool for assessing the quality of models of single neurons in preserving input–output relationship, a property that becomes crucial when we start connecting these reduced models to construct complex realistic neuronal networks

Photosynthesis and calcification in the calcifying algae Halimeda discoidea studied with microsensors

With microsensors, we measured the steady‐state microprofiles of O2, pH and Ca2+ on the topside of young segments of Halimeda discoidea, as well as the surface dynamics upon light–dark shifts. The effect of several inhibitors was studied. The steady‐state measurements showed that under high light intensity, calcium and protons were taken up, while O2 was produced. In the dark, O2 was consumed, the pH decreased to below seawater level and Ca2+ uptake was reduced to 50%. At low light intensity (12 mmol photons m‐2 s‐1), Ca2+ efflux was observed. Upon light–dark shifts, a complicated pattern of both the pH and calcium surface dynamics was observed. Illumination caused an initial pH decrease, followed by a gradual pH increase: this indicated that the surface pH of H. discoidea is determined by more than one light‐induced process. When photosynthesis was inhibited by dichlorophenyl dimethyl urea (DCMU), a strong acidification was observed upon illumination. The nature and physiological function of this putative pump is not known. The calcium dynamics followed all pH dynamics closely, both in the presence and absence of DCMU. The Ca‐channel blockers verapamil and nifedipine had no effect on the Ca2+ dynamics and steady‐state profiles. Thus, in H. discoidea, calcification is not regulated by the alga, but is a consequence of pH increase during photosynthesis. Acetazolamide had no effect on photosynthesis, whereas ethoxyzolamide inhibited photosynthesis at higher light intensities. Therefore, all carbonic anhydrase activity is intracellular. Carbonic anhydrase is required to alleviate the CO2 limitation. Calcification cannot supply sufficient protons and CO2 to sustain photosynthesis

A perspective on cortical layering and layer-spanning neuronal elements

This review article addresses the function of the layers of the cerebral cortex. We develop the perspective that cortical layering needs to be understood in terms of its functional anatomy, i.e., the terminations of synaptic inputs on distinct cellular compartments and their effect on cortical activity. The cortex is a hierarchical structure in which feed forward and feedback pathways have a layer-specific termination pattern. We take the view that the influence of synaptic inputs arriving at different cortical layers can only be understood in terms of their complex interaction with cellular biophysics and the subsequent computation that occurs at the cellular level. We use high-resolution fMRI, which can resolve activity across layers, as a case study for implementing this approach by describing how cognitive events arising from the laminar distribution of inputs can be interpreted by taking into account the properties of neurons that span different layers. This perspective is based on recent advances in measuring subcellular activity in distinct feed-forward and feedback axons and in dendrites as they span across layers

Dendritic calcium spikes are clearly detectable at the cortical surface

Cortical surface recording techniques such as EEG and ECoG are widely used for measuring brain activity. The prevailing assumption is that surface potentials primarily reflect synaptic activity, although non-synaptic events may also contribute. Here we show that dendritic calcium spikes occurring in pyramidal neurons (that we showed previously are cognitively relevant) are clearly detectable in cortical surface potentials. To show this we developed an optogenetic, non-synaptic approach to evoke dendritic calcium spikes in vivo. We found that optogenetically evoked calcium spikes were easily detectable and had an unexpected waveform near the cortical surface. Sensory-evoked dendritic calcium spikes were also clearly detectable with amplitudes that matched the contribution of synaptic input. These results reveal how dendritic calcium spikes appear at the cortical surface and their significant impact on surface potentials, suggesting that long-standing surface recording data may contain information about dendritic activity that is relevant to behavior and cognitive function

Signaling of layer 1 and whisker-evoked Ca2+ and Na+ action potentials in distal and terminal dendrites of rat neocortical pyramidal neurons in vitro and in vivo

Dendritic regenerative potentials play an important role in integrating and amplifying synaptic inputs. To understand how distal synaptic inputs are integrated and amplified, we made multiple simultaneous (double, triple, or quadruple) and sequential (4–12 paired) recordings from different locations of single tufted layer 5 pyramidal neurons in the cortex in vitro and studied the spatial and temporal properties of their dendritic regenerative potential initial zone. Recordings from the soma and from trunk, primary, secondary, tertiary, and quaternary tuft branches of the apical dendrite of these neurons reveal a spatially restricted low-threshold zone ∼550–900 μm from the soma for Ca2+-dependent regenerative potentials. Dendritic regenerative potentials initiated in this zone have a clearly defined threshold and a refractory period, and they can propagate actively along the dendrite before evoking somatic action potentials. The detailed biophysical characterization of this dendritic action potential initiation zone allowed for the further investigation of dendritic potentials in the intact brain and their roles in information processing. By making whole-cell recordings from the soma and varied locations along the apical dendrite of 53 morphologically identified layer 5 pyramidal neurons in anesthetized rats, we found that three of the dendritic potentials characterized in vitro could be induced by spontaneous or whisker inputs in vivo. Thus layer 5 pyramidal neurons of the rat neocortex have a spatially restricted low-threshold zone in the apical dendrite, the activation or interaction of which with the axonal action potential initiation zone is responsible for multiple forms of regenerative potentials critical for integrating and amplifying sensory and modulatory inputs

Top-down Dendritic Input Increases the Gain of Layer 5 Pyramidal Neurons

The cerebral cortex is organized so that an important component of feedback input from higher to lower cortical areas arrives at the distal apical tufts of pyramidal neurons. Yet, distal inputs are predicted to have much less impact on firing than proximal inputs. Here we show that even weak asynchronous dendritic input to the distal tuft region can significantly increase the gain of layer 5 pyramidal neurons and thereby the output of columns in the primary somatosensory cortex of the rat. Noisy currents injected in ramps at different dendritic locations showed that the initial slope of the frequency-current (f/I) relationship increases with the distance of the current injection from the soma. The increase was due to the interaction of dendritic depolarization with back-propagating APs which activated dendritic calcium conductances. Gain increases were accompanied by a change of firing mode from isolated spikes to bursting where the timing of bursts coded the presence of coincident somatic and dendritic inputs. We propose that this dendritic gain modulation and the timing of bursts may serve to associate top-down and bottom-up input on different time scale

We are Still Learning about the Nature of Species and Their Evolutionary Relationships

Early evolutionary thinkers proposed relatively simple models to describe processes of evolution, and these are the basis of evolutionary models still used today. Recent research has since shown that evolutionary relationships among plants can be complex and difficult to reconstruct even from molecular data. In plants there is a continuum of processes, ranging from reticulate relationships within a sexually reproducing population, incomplete lineage sorting and hybridization between recently diverged species, allopolyploidy between more distantly related species, to symbioses and endosymbiosis. These aspects of plant biology can create practical problems for interpreting bifurcating gene trees and identifying species. The promise of "omics" is that it will provide data and analyses to improve our understanding of the nature of species and their phylogenetic relationships. We highlight the importance of distinguishing evolutionary processes and evolutionary models, and stress that improving the understanding of micro-evolutionary processes is necessary to inform current debate on whether or not to accept paraphyletic species

Identification and characterization of a new Halomicronema species (Cyanobacteria) isolated from the Mediterranean marine sponge Petrosia ficiformis (Porifera)

A filamentous cyanobacterium (strain ITAC101) isolated from a Mediterranean sponge (Petrosia ficiformis) was characterized by a combined phenotypic and genetic approach. Morphological and ultrastructural observations were performed along with growth measurements and pigment characterization. The molecular phylogenetic analyses were based on the sequencing of the 16S rRNA gene. In culture conditions, strain ITAC101 is moderately halophilic and grew in the range 0.3–7.6% (w/v) salinity with the optimum at 3.6%. Cell dimensions, thylakoid arrangement and pigment composition of this cyanobacterium fit the Halomicronema genus description, and phylogenetic analyses evidenced 99.9% similarity with another strain endolithic in tropical corals. The new Halomicronema metazoicum species was established including the two cyanobacteria associated to marine animals

Zooxanthellae expelled from bleached corals at 33°C are photosynthetically competent

While a number of factors have been linked to coral bleaching, such as high light, high temperature, low salinity, and UV exposure, the best explanation for recent coral bleaching events are small temperature excursions of 1 to 2°C above summer sea-surface temperatures in the tropics which induce the dinoflagellate symbionts (zooxanthellae) to be expelled from the host. The mechanism that triggers this expulsion of the algal symbionts is not resolved, but has been attributed to damage to the photosynthetic mechanism of the zooxanthellae. In the present investigation we addressed the question of whether such expelled zooxanthellae are indeed impaired irreversibly in their photosynthesis. We employed a Microscopy Pulse Amplitude-Modulated (PAM) fluorometer, by which individual zooxanthellae can be examined to study photosynthesis in zooxanthellae expelled when corals are subjected to a temperature of 33°C. We show that the expelled zooxanthellae from Cyphastrea serailia were largely unaffected in their photosynthesis and could be heated to 37°C before showing temperature-induced photosynthetic impairment. These results suggest strongly that the early events that trigger temperature-induced expulsion of zooxanthellae involve a dysfunction in the interaction of the zooxanthellae and the coral host tissue, and not a dysfunction in the zooxanthellae per se

Physiology of Layer 5 Pyramidal Neurons in Mouse Primary Visual Cortex: Coincidence Detection through Bursting

L5 pyramidal neurons are the only neocortical cell type with dendrites reaching all six layers of cortex, casting them as one of the main integrators in the cortical column. What is the nature and mode of computation performed in mouse primary visual cortex (V1) given the physiology of L5 pyramidal neurons? First, we experimentally establish active properties of the dendrites of L5 pyramidal neurons of mouse V1 using patch-clamp recordings. Using a detailed multi-compartmental model, we show this physiological setup to be well suited for coincidence detection between basal and apical tuft inputs by controlling the frequency of spike output. We further show how direct inhibition of calcium channels in the dendrites modulates such coincidence detection. To establish the singe-cell computation that this biophysics supports, we show that the combination of frequency-modulation of somatic output by tuft input and (simulated) calcium-channel blockage functionally acts as a composite sigmoidal function. Finally, we explore how this computation provides a mechanism whereby dendritic spiking contributes to orientation tuning in pyramidal neurons