A common rule governing differentiation kinetics of mouse cortical progenitors.

The balance between proliferation and differentiation of stem cells and progenitors determines the size of an adult brain region. While the molecular mechanisms regulating proliferation and differentiation of cortical progenitors have been intensively studied, an analysis of the kinetics of progenitor choice between self-renewal and differentiation in vivo is, due to the technical difficulties, still unknown. Here we established a descriptive mathematical model to estimate the probability of self-renewal or differentiation of cortical progenitor behaviors in vivo, a variable we have termed the expansion coefficient. We have applied the model, one which depends only on experimentally measured parameters, to the developing mouse cortex where the expansive neuroepithelial cells and neurogenic radial glial progenitors are coexisting. Surprisingly, we found that the expansion coefficients of both neuroepithelium cells and radial glial progenitors follow the same developmental trajectory during cortical development, suggesting a common rule governing self-renewal/differentiation behaviors in mouse cortical progenitor differentiation.

In vitro analyses of suspected arrhythmogenic thin filament variants as a cause of sudden cardiac death in infants.

Sudden unexpected death of an infant (SUDI) is a devastating occurrence for families. To investigate the genetic pathogenesis of SUDI, we sequenced >70 genes from 191 autopsy-negative SUDI victims. Ten infants sharing a previously unknown variant in troponin I (TnI) were identified. The mutation (TNNI1 R37C+/-) is in the fetal/neonatal paralog of TnI, a gene thought to be expressed in the heart up to the first 24 months of life. Using phylogenetic analysis and molecular dynamics simulations, it was determined that arginine at residue 37 in TNNI1 may play a critical functional role, suggesting that the variant may be pathogenic. We investigated the biophysical properties of the TNNI1 R37C mutation in human reconstituted thin filaments (RTFs) using fluorometry. RTFs reconstituted with the mutant R37C TnI exhibited reduced Ca2+-binding sensitivity due to an increased Ca2+ off-rate constant. Furthermore, we generated TNNI1 R37C+/- mutants in human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) using CRISPR-Cas9. In monolayers of hiPSC-CMs, we simultaneously monitored voltage and Ca2+ transients through optical mapping and compared them to their isogenic controls. We observed normal intrinsic beating patterns under control conditions in TNNI1 R37C+/- at stimulation frequencies of 55 beats/min (bpm), but these cells showed no restitution with increased stimulation frequency to 65 bpm and exhibited alternans at >75 bpm. The WT hiPSC-CMs did not exhibit any sign of arrhythmogenicity even at stimulation frequencies of 120 bpm. The approach used in this study provides critical physiological and mechanistic bases to investigate sarcomeric mutations in the pathogenesis of SUDI.

Conserved features of the primate face code.

A recent paper demonstrated that the pattern of firing rates across ∼100 neurons in the anterior medial face patch is closely related to which human face (of 2,000) had been presented to a monkey [Chang L, Tsao DY (2017) Cell 169:1013-1028]. In addition, the firing rates for these neurons can be predicted for a novel human face. Although it is clear from this work that the firing rates of these face patch neurons encode faces, the properties of the face code have not yet been fully described. Based on an analysis of 98 neurons responding to 2,000 faces, I conclude that the anterior medial face patch uses a combinatorial rate code, one with an exponential distribution of neuron rates that has a mean rate conserved across faces. Thus, the face code is maximally informative (technically, maximum entropy) and is very similar to the code used by the fruit fly olfactory system.

A neural data structure for novelty detection.

Novelty detection is a fundamental biological problem that organisms must solve to determine whether a given stimulus departs from those previously experienced. In computer science, this problem is solved efficiently using a data structure called a Bloom filter. We found that the fruit fly olfactory circuit evolved a variant of a Bloom filter to assess the novelty of odors. Compared with a traditional Bloom filter, the fly adjusts novelty responses based on two additional features: the similarity of an odor to previously experienced odors and the time elapsed since the odor was last experienced. We elaborate and validate a framework to predict novelty responses of fruit flies to given pairs of odors. We also translate insights from the fly circuit to develop a class of distance- and time-sensitive Bloom filters that outperform prior filters when evaluated on several biological and computational datasets. Overall, our work illuminates the algorithmic basis of an important neurobiological problem and offers strategies for novelty detection in computational systems.

Deep(er) Learning.

Animals successfully thrive in noisy environments with finite resources. The necessity to function with resource constraints has led evolution to design animal brains (and bodies) to be optimal in their use of computational power while being adaptable to their environmental niche. A key process undergirding this ability to adapt is the process of learning. Although a complete characterization of the neural basis of learning remains ongoing, scientists for nearly a century have used the brain as inspiration to design artificial neural networks capable of learning, a case in point being deep learning. In this viewpoint, we advocate that deep learning can be further enhanced by incorporating and tightly integrating five fundamental principles of neural circuit design and function: optimizing the system to environmental need and making it robust to environmental noise, customizing learning to context, modularizing the system, learning without supervision, and learning using reinforcement strategies. We illustrate how animals integrate these learning principles using the fruit fly olfactory learning circuit, one of nature's best-characterized and highly optimized schemes for learning. Incorporating these principles may not just improve deep learning but also expose common computational constraints. With judicious use, deep learning can become yet another effective tool to understand how and why brains are designed the way they are.

A statistical property of fly odor responses is conserved across odors.

I have reanalyzed the data presented by Hallem and Carlson [Hallem EA, Carlson JR (2006) Cell 125(1):143-160] and shown that the combinatorial odor code supplied by the fruit fly antenna is a very simple one in which nearly all odors produce, statistically, the same neuronal response; i.e., the probability distribution of sensory neuron firing rates across the population of odorant sensory neurons is an exponential for nearly all odors and odor mixtures, with the mean rate dependent on the odor concentration. Between odors, then, the response differs according to which sensory neurons are firing at what individual rates and with what mean population rate, but not in the probability distribution of firing rates. This conclusion is independent of adjustable parameters, and holds both for monomolecular odors and complex mixtures. Because the circuitry in the antennal lobe constrains the mean firing rate to be the same for all odors and concentrations, the odor code is what is known as maximum entropy.

Changes in the dynamics of the cardiac troponin C molecule explain the effects of Ca2+-sensitizing mutations.

Cardiac troponin C (cTnC) is the regulatory protein that initiates cardiac contraction in response to Ca2+ TnC binding Ca2+ initiates a cascade of protein-protein interactions that begins with the opening of the N-terminal domain of cTnC, followed by cTnC binding the troponin I switch peptide (TnISW). We have evaluated, through isothermal titration calorimetry and molecular-dynamics simulation, the effect of several clinically relevant mutations (A8V, L29Q, A31S, L48Q, Q50R, and C84Y) on the Ca2+ affinity, structural dynamics, and calculated interaction strengths between cTnC and each of Ca2+ and TnISW Surprisingly the Ca2+ affinity measured by isothermal titration calorimetry was only significantly affected by half of these mutations including L48Q, which had a 10-fold higher affinity than WT, and the Q50R and C84Y mutants, each of which had affinities 3-fold higher than wild type. This suggests that Ca2+ affinity of the N-terminal domain of cTnC in isolation is insufficient to explain the pathogenicity of these mutations. Molecular-dynamics simulation was used to evaluate the effects of these mutations on Ca2+ binding, structural dynamics, and TnI interaction independently. Many of the mutations had a pronounced effect on the balance between the open and closed conformations of the TnC molecule, which provides an indirect mechanism for their pathogenic properties. Our data demonstrate that the structural dynamics of the cTnC molecule are key in determining myofilament Ca2+ sensitivity. Our data further suggest that modulation of the structural dynamics is the underlying molecular mechanism for many disease mutations that are far from the regulatory Ca2+-binding site of cTnC.

The Zebrafish Heart as a Model of Mammalian Cardiac Function.

Zebrafish (Danio rerio) are widely used as vertebrate model in developmental genetics and functional genomics as well as in cardiac structure-function studies. The zebrafish heart has been increasingly used as a model of human cardiac function, in part, due to the similarities in heart rate and action potential duration and morphology with respect to humans. The teleostian zebrafish is in many ways a compelling model of human cardiac function due to the clarity afforded by its ease of genetic manipulation, the wealth of developmental biological information, and inherent suitability to a variety of experimental techniques. However, in addition to the numerous advantages of the zebrafish system are also caveats related to gene duplication (resulting in paralogs not present in human or other mammals) and fundamental differences in how zebrafish hearts function. In this review, we discuss the use of zebrafish as a cardiac function model through the use of techniques such as echocardiography, optical mapping, electrocardiography, molecular investigations of excitation-contraction coupling, and their physiological implications relative to that of the human heart. While some of these techniques (e.g., echocardiography) are particularly challenging in the zebrafish because of diminutive size of the heart (~1.5 mm in diameter) critical information can be derived from these approaches and are discussed in detail in this article.

What the fly's nose tells the fly's brain.

The fly olfactory system has a three-layer architecture: The fly's olfactory receptor neurons send odor information to the first layer (the encoder) where this information is formatted as combinatorial odor code, one which is maximally informative, with the most informative neurons firing fastest. This first layer then sends the encoded odor information to the second layer (decoder), which consists of about 2,000 neurons that receive the odor information and "break" the code. For each odor, the amplitude of the synaptic odor input to the 2,000 second-layer neurons is approximately normally distributed across the population, which means that only a very small fraction of neurons receive a large input. Each odor, however, activates its own population of large-input neurons and so a small subset of the 2,000 neurons serves as a unique tag for the odor. Strong inhibition prevents most of the second-stage neurons from firing spikes, and therefore spikes from only the small population of large-input neurons is relayed to the third stage. This selected population provides the third stage (the user) with an odor label that can be used to direct behavior based on what odor is present.

Novel neural circuit mechanism for visual edge detection.

The primary visual cortex is organized in a way that assigns a specific collection of neurons the job of providing the rest of the brain with all of the information it needs about each small part of the image present on the retina: Neighboring patches of the visual cortex provide the information about neighboring patches of the visual world. Each one of these cortical patches--often identified as a "pinwheel"--contains thousands of neurons, and its corresponding image patch is centered on a particular location in the retina. For stimuli within their image patch, neurons respond selectively to lines or edges with a particular slope (orientation tuning) and to regions of the patch of different sizes (known as spatial frequency tuning). The same number of neurons is devoted to reporting each possible slope (orientation). For the cells that cover different-sized regions of their image patch, however, the number of neurons assigned depends strongly on their preferred region size. Only a few neurons report on large and small parts of the image patch, but many neurons report visual information from medium-sized areas. I show here that having different numbers of neurons responsible for image regions of different sizes actually carries out a computation: Edges in the image patch are extracted. I also explain how this edge-detection computation is done.

Predicting visual acuity from the structure of visual cortex.

Three decades ago, Rockel et al. proposed that neuronal surface densities (number of neurons under a square millimeter of surface) of primary visual cortices (V1s) in primates is 2.5 times higher than the neuronal density of V1s in nonprimates or many other cortical regions in primates and nonprimates. This claim has remained controversial and much debated. We replicated the study of Rockel et al. with attention to modern stereological precepts and show that indeed primate V1 is 2.5 times denser (number of neurons per square millimeter) than many other cortical regions and nonprimate V1s; we also show that V2 is 1.7 times as dense. As primate V1s are denser, they have more neurons and thus more pinwheels than similar-sized nonprimate V1s, which explains why primates have better visual acuity.

What is memory? The present state of the engram.

The mechanism of memory remains one of the great unsolved problems of biology. Grappling with the question more than a hundred years ago, the German zoologist Richard Semon formulated the concept of the engram, lasting connections in the brain that result from simultaneous "excitations", whose precise physical nature and consequences were out of reach of the biology of his day. Neuroscientists now have the knowledge and tools to tackle this question, however, and this Forum brings together leading contemporary views on the mechanisms of memory and what the engram means today.

Characterization of Zebrafish Cardiac and Slow Skeletal Troponin C Paralogs by MD Simulation and ITC.

Zebrafish, as a model for teleost fish, have two paralogous troponin C (TnC) genes that are expressed in the heart differentially in response to temperature acclimation. Upon Ca(2+) binding, TnC changes conformation and exposes a hydrophobic patch that interacts with troponin I and initiates cardiac muscle contraction. Teleost-specific TnC paralogs have not yet been functionally characterized. In this study we have modeled the structures of the paralogs using molecular dynamics simulations at 18°C and 28°C and calculated the different Ca(2+)-binding properties between the teleost cardiac (cTnC or TnC1a) and slow-skeletal (ssTnC or TnC1b) paralogs through potential-of-mean-force calculations. These values are compared with thermodynamic binding properties obtained through isothermal titration calorimetry (ITC). The modeled structures of each of the paralogs are similar at each temperature, with the exception of helix C, which flanks the Ca(2+) binding site; this region is also home to paralog-specific sequence substitutions that we predict have an influence on protein function. The short timescale of the potential-of-mean-force calculation precludes the inclusion of the conformational change on the ΔG of Ca(2+) interaction, whereas the ITC analysis includes the Ca(2+) binding and conformational change of the TnC molecule. ITC analysis has revealed that ssTnC has higher Ca(2+) affinity than cTnC for Ca(2+) overall, whereas each of the paralogs has increased affinity at 28°C compared to 18°C. Microsecond-timescale simulations have calculated that the cTnC paralog transitions from the closed to the open state more readily than the ssTnC paralog, an unfavorable transition that would decrease the ITC-derived Ca(2+) affinity while simultaneously increasing the Ca(2+) sensitivity of the myofilament. We propose that the preferential expression of cTnC at lower temperatures increases myofilament Ca(2+) sensitivity by this mechanism, despite the lower Ca(2+) affinity that we have measured by ITC.

Structural uniformity of neocortex, revisited.

The number of neurons under a square millimeter of cortical surface has been reported to be the same across five cortical areas and five species [Rockel et al. (1980) Brain 103(2):221-244] despite differences in cortical thickness between the areas. Although the accuracy of this result has been the subject of sharp debate since its publication approximately 30 y ago, the experiments of Rockel et al. have never been directly replicated with modern stereological methods. We have replicated these experiments and confirm the accuracy of the original report. In addition, we have observed that the number of glial cells under a square millimeter of cortical surface depends on cortical thickness, but not on cortical area or species.

Control of organ size: development, regeneration, and the role of theory in biology.

How organs grow to be the right size for the animal is one of the central mysteries of biology. In a paper in BMC Biology, Khammash et al. propose a mechanism for escaping from the deficiencies of feedback control of growth as a mechanism.

Short-term plasticity constrains spatial organization of a hippocampal presynaptic terminal.

Although the CA3-CA1 synapse is critically important for learning and memory, experimental limitations have to date prevented direct determination of the structural features that determine the response plasticity. Specifically, the local calcium influx responsible for vesicular release and short-term synaptic facilitation strongly depends on the distance between the voltage-dependent calcium channels (VDCCs) and the presynaptic active zone. Estimates for this distance range over two orders of magnitude. Here, we use a biophysically detailed computational model of the presynaptic bouton and demonstrate that available experimental data provide sufficient constraints to uniquely reconstruct the presynaptic architecture. We predict that for a typical CA3-CA1 synapse, there are ~70 VDCCs located 300 nm from the active zone. This result is surprising, because structural studies on other synapses in the hippocampus report much tighter spatial coupling. We demonstrate that the unusual structure of this synapse reflects its functional role in short-term plasticity (STP).

NSF workshop report: discovering general principles of nervous system organization by comparing brain maps across species.

Efforts to understand nervous system structure and function have received new impetus from the federal Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. Comparative analyses can contribute to this effort by leading to the discovery of general principles of neural circuit design, information processing, and gene-structure-function relationships that are not apparent from studies on single species. We here propose to extend the comparative approach to nervous system 'maps' comprising molecular, anatomical, and physiological data. This research will identify which neural features are likely to generalize across species, and which are unlikely to be broadly conserved. It will also suggest causal relationships between genes, development, adult anatomy, physiology, and, ultimately, behavior. These causal hypotheses can then be tested experimentally. Finally, insights from comparative research can inspire and guide technological development. To promote this research agenda, we recommend that teams of investigators coalesce around specific research questions and select a set of 'reference species' to anchor their comparative analyses. These reference species should be chosen not just for practical advantages, but also with regard for their phylogenetic position, behavioral repertoire, well-annotated genome, or other strategic reasons. We envision that the nervous systems of these reference species will be mapped in more detail than those of other species. The collected data may range from the molecular to the behavioral, depending on the research question. To integrate across levels of analysis and across species, standards for data collection, annotation, archiving, and distribution must be developed and respected. To that end, it will help to form networks or consortia of researchers and centers for science, technology, and education that focus on organized data collection, distribution, and training. These activities could be supported, at least in part, through existing mechanisms at NSF, NIH, and other agencies. It will also be important to develop new integrated software and database systems for cross-species data analyses. Multidisciplinary efforts to develop such analytical tools should be supported financially. Finally, training opportunities should be created to stimulate multidisciplinary, integrative research into brain structure, function, and evolution.

The fraction of cortical GABAergic neurons is constant from near the start of cortical neurogenesis to adulthood.

Approximately one in five neurons is GABAergic in many neocortical areas and species, forming a critical balance between inhibition and excitation in adult circuits. During development, cortical GABAergic neurons are generated in ventral telencephalon and migrate up to developing cortex where the excitatory glutamatergic neurons are born. We ask here: when during development is the adult GABAergic/glutamatergic neuron ratio first established? To answer this question, we have determined the fraction of all neocortical GABAergic neurons that will become inhibitory (GAD67(+)) in mice from embryonic day 10.5 (E10.5) to postnatal day 28 (P28). We find that this fraction is close to 1/5, the adult value, starting from early in corticogenesis (E14.5, when GAD67(+) neurons are still migrating tangentially to the cortex) and continuing at the same 1/5 value throughout the remainder of brain development. Thus our data indicate the one-in-five fraction of GABAergic neurons is already established during their neuronal migration and well before significant synapse formation.

Chronic Granulomatous Reaction to Semi-permanent Eyebrow Tint.

Eyebrow micropigmentation, also known as eyebrow microblading or embroidery, is a new technique in the field of semi-permanent cosmetics that are used for therapeutic and aesthetic purposes to recreate eyebrow structure and definition. It uses synthetic pigment that is deposited through fine needles into the papillary dermis and remains till the body metabolizes the pigment and clinically fades away by 12-18 months. Similar to other tattooing procedures, microblading involves risks including local inflammation, infection, allergic contact dermatitis, and granulomatous reactions that can occur from months to years after the procedure. We describe herein a case of a 49-year-old female who has persistent erythematous and indurated plaques on both eyebrows after a microblading procedure performed over a year and a half prior to her initial visit.