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Regeneration of neuromuscular connections in crayfish allotransplanted neurons.

Transplantation of whole ganglia was used to study the regeneration of four of the neurons that innervate the superficial flexor muscles of the crayfish Procambarus clarkii. The isolated ganglia containing the somas of these neurons were successfully transplanted from one crayfish to another. Reinnervation proceeded across the muscle surface and by 8 to 10 weeks connections were detected across the entire target field. At different time periods after the transplant, junction potentials (JPs) produced in phase with spontaneous neuronal spikes were recorded. The distribution of JP sizes and their decay times were examined. JPs from transplanted preparations were smaller than JPs from control or normal regeneration animals. These JPs also failed to facilitate when stimulated at 1 and 10 Hz. These are normal characteristics of immature terminals, but in the transplant preparations, once established, they remained stable for the duration of the study. Thus, synaptogenesis appears to be arrested at a stage before synaptic efficacy is established in the allotransplants. In addition, connectivity maps were plotted for each axon over the muscle surface. Some muscle fibers did not receive any contacts, and overall innervation leveled off at around 60% of the muscle fibers, remaining stable for the duration of this study. Despite the incomplete physiological innervation, however, three of the four neurons showed the same medial/lateral preferences observed in control animals, regenerating their original patterns of connectivity across the muscle surface.

Animals↗

A stochastic self-organizing map for proximity data.

We derive an efficient algorithm for topographic mapping of proximity data (TMP), which can be seen as an extension of Kohonen's self-organizing map to arbitrary distance measures. The TMP cost function is derived in a Baysian framework of folded Markov chains for the description of autoencoders. It incorporates the data by a dissimilarity matrix D and the topographic neighborhood by a matrix H of transition probabilities. From the principle of maximum entropy, a nonfactorizing Gibbs distribution is obtained, which is approximated in a mean-field fashion. This allows for maximum likelihood estimation using an expectation-maximization algorithm. In analogy to the transition from topographic vector quantization to the self-organizing map, we suggest an approximation to TMP that is computationally more efficient. In order to prevent convergence to local minima, an annealing scheme in the temperature parameter is introduced, for which the critical temperature of the first phase transition is calculated in terms of D and H. Numerical results demonstrate the working of the algorithm and confirm the analytical results. Finally, the algorithm is used to generate a connection map of areas of the cat's cerebral cortex.

Algorithms↗

Effect of prior cognitive state on resting state networks measured with functional connectivity.

To address the extent to which functional connectivity measures an absolute brain state, we observed the effect of prior performance of a language task on resting-state networks in regions associated with language. Six subjects were imaged during rest before and after a block-design language task. Connectivity maps were generated for each of four language regions (identified from analysis of the language activation portion of the study) in each subject for both rest periods. Conjunction analysis demonstrated distinct networks of voxels for each seed region, indicating separate functional subnetworks associated with the different regions. In a comparison of rest before and after the activation task widespread and significant changes were observed in all individuals, suggesting that the measured resting state network reflects a dynamic image of the current brain state. At the group level, an extended network was observed that was largely persistent over time. Even at the group level an increase in connectivity was observed between left and right middle frontal gyri, and between posterior cingulate cortex and medial frontal cortex in the rest after the language task. These results suggest that functional connectivity may be a powerful measure of cognitive state, sensitive to differences between controls and patients together with the particular cognitive processing occurring during the rest state.

Brain Mapping↗

Agonist-specific structural rearrangements of integrin alpha IIbbeta 3. Confirmation of the bent conformation in platelets at rest and after activation.

Concrete structural features of integrin alpha(IIb)beta(3) on the surface of platelets (at rest and after activation) have been obtained from epitope maps based on cross-competition among monoclonal antibodies directed against the alpha(IIb) subunit calf-2 domain and the beta(3) subunit betaA domain of alpha(IIb)beta(3). At rest, the observed intersubunit interface is formed by the sequence stretches beta(3)-(150-216), alpha(IIb) light chain-(1-92), and alpha(IIb) heavy chain-(826-856); and the alpha(IIb) interchain interface is formed by the two latter sequence stretches, disulfide-bonded between alpha(IIb) heavy chain Cys(826) and alpha(IIb) light chain Cys(9). These structural features agree with those observed in the alpha(IIb)beta(3) rudimentary connectivity map in solution and with the alpha(v)beta(3) V-shaped crystal structure (Xiong, J.-P., Zhang, R., Dunker, R., Scott, D. L., Joachimiak, A., Goodman, S. L., and Arnaout, M. A. (2001) Science 294, 339-345), but they disagree with the domain disposition suggested by the actual ultrastructural model. The epitope maps in platelets activated by ADP, thrombin receptor activation peptide, and arachidonic acid differ not only from those in platelets at rest, but also among themselves. The structural rearrangements observed confirm the presence in activated platelets of the crystallographically observed knee and argue against the switchblade mechanism proposed for activation (Beglova, N., Blacklow, S. C., Takagi, J., and Springer, T. A. (2002) Nat. Struct. Biol. 9, 282-287), demonstrate the existence of alpha(IIb)beta(3) agonist-specific activation states, explain the specificity for ligand binding and functional inhibition for some agonists, and predict the existence of agonist-specific final effectors and receptor activation mechanisms. The distinct non-reciprocal competition patterns observed at rest and after activation support the agonist-specific activation states and the existence of intrasubunit and intersubunit allosteric effects, previously proposed as the mechanism for alpha(IIb)beta(3) transmembrane activation.

Allosteric Site↗

Fgf8 regulates the development of intra-neocortical projections.

The process of generating functionally distinct neocortical areas requires the formation of an intra-neocortical connectivity map. Here, we explore the early development of murine intra-neocortical projections and find that axons from rostral and caudal neurons remain, respectively, within large rostral and caudal domains of the neonatal neocortex. Despite evidence that thalamic input can regulate neocortical areal properties, we found that the neonatal intra-neocortical projection pattern was not perturbed when thalamic input was absent in Gbx2 mutants. On the contrary, in Fgf8 hypomorphic mutants, the rostral neocortex of which acquires more caudal molecular properties, caudally located neurons ectopically project axons into the rostral cortex. Therefore, neocortical patterning by Fgf8 also contributes to arealization through mediating early development of intra-neocortical connectivity.

Animals↗

The nature of traumatic memories: a 4-T FMRI functional connectivity analysis.

OBJECTIVE: This study used functional connectivity analyses to assess interregional brain activity correlations during the recall of traumatic memories in traumatized subjects with and without posttraumatic stress disorder (PTSD). METHOD: Both 4-T functional magnetic resonance imaging (fMRI) and functional connectivity analyses were used to assess interregional brain activity correlations during script-driven symptom provocation in traumatized subjects with (N=11) and without (N=13) PTSD. Functional connectivity analyses were carried out by using data for brain regions activated in both the PTSD group and the comparison group. The use of functional connectivity analyses in addition to subtraction analyses allowed assessment of specific brain regions involved in the recall of traumatic events and of the neuronal networks underlying the recall of such events. RESULTS: Significant between-group differences in functional connectivity were found. Comparison of connectivity maps at coordinates x=2, y=20, z=36 (right anterior cingulate gyrus) for the two groups showed that the subjects without PTSD had greater correlation than the PTSD subjects in the left superior frontal gyrus (Brodmann's area 9), left anterior cingulate gyrus (Brodmann's area 32), left striatum (caudate), left parietal lobe (Brodmann's areas 40 and 43), and left insula (Brodmann's area 13). In contrast, the PTSD subjects showed greater correlation than the subjects without PTSD in the right posterior cingulate gyrus (Brodmann's area 29), right caudate, right parietal lobe (Brodmann's areas 7 and 40), and right occipital lobe (Brodmann's area 19). CONCLUSIONS: The differences in brain connectivity between PTSD and comparison subjects may account for the nonverbal nature of traumatic memory recall in PTSD subjects, compared to a more verbal pattern of traumatic memory recall in comparison subjects.

Brain↗

Metabolic mapping of the brain in pregnant, parturient and lactating rats using fos immunohistochemistry.

The present study was designed to investigate Fos-positive neurons of the female rat brain at various reproductive states in order to analyze the metabolic map connected with pregnancy, parturition and lactation. The number of Fos-positive neurons in each brain nucleus was analyzed with a quantitative immunohistochemical method in virgin, pregnant, parturient, lactating and arrested lactating rats. In parturient rats, a significant number of Fos-positive neurons was observed as compared to virgin or pregnant females in the following brain regions; the bed nucleus of the stria terminalis (BST), lateral septal nucleus (LS), medial preoptic area (MPA), periventricular hypothalamic nucleus (Pe), parvocellular paraventricular hypothalamic nucleus (PaPVN), magnocellular paraventricular hypothalamic nucleus (MaPVN), supraoptic nucleus (SON), paraventricular thalamic nucleus (PV), anterior hypothalamic area (AHA), lateral hypothalamic area (LH), amygdaloid nucleus (AM), supramammillary nucleus (SuM), substantia nigra (SN), central grey (CG), microcellular tegmental nucleus (MiTg), subparafascicular thalamic nucleus (SPF), posterior hypothalamic area (PH), dorsal raphe nucleus (DR), locus coeruleus (LC), dorsal parabrachial nucleus (DPB), nucleus of solitary tract (Sol), and ventrolateral medulla (VLM). Significant differences were found in the number of Fos-positive neurons between parturient and lactating females, although localization of Fos-positive neurons in lactating females was quite similar to parturient ones. Between parturient and lactating rats: (1) In the MPA, PaPVN, AHA, arcuate hypothalamic nucleus (Arc), ventromedial hypothalamic nucleus (VMH), MLT, and Ge, the number of Fos-positive neurons of lactating females were significantly higher than those of parturient ones; (2) In the LS, Pe, PV, LH, AM, SuM, CG, MiTg, SPF, PH, DR, LC, and VLM, there was no significant differences in the number of Fos-positive neurons; (3) In the BST, MaPVN, SON, SN, DPB and Sol, the number of Fos-positive neurons of lactating rats were significantly lower than those of parturient ones. These different patterns of Fos expression among many brain regions may be owing to the functional differences in each region. Fos expression in lactating rats was apparently induced by suckling stimulation because the removal of their litters immediately after parturition completely eliminated expression of Fos protein in each nucleus. These results suggest that the localization of Fos-positive neurons in a number of neural populations throughout the brain may be revealing the neural circuits in response to parturition or lactation.

Animals↗

Abnormal bone marrow stroma in mice deficient for nemo-like kinase, Nlk.

The stromal compartment of the bone marrow is composed of various cell types that provide trophic and instructive signals for hematopoiesis. The mesenchymal stem cell is believed to give rise to all major cellular components of the bone marrow microenvironment. Nemo-like kinase, Nlk, is a serine-threonine kinase that connects MAP kinase and Wnt signaling pathways; its in vivo function in mouse is unknown. We have generated mice with a targeted disruption of Nlk and find that the complex phenotype significantly varies with the genetic background. Whereas C57BL/6 mice lacking Nlk die during the third trimester of pregnancy, the 129/Sv background supports survival into adolescence; such mice are growth retarded and suffer from various neurological abnormalities. We show here that the Nlk deficiency syndrome includes aberrant differentiation of bone marrow stromal cells. Varying degrees of morphological abnormality, such as increased numbers of adipocytes, large blood sinuses and absence of bone-lining cells are observed in the bone marrow of mutant mice. Nlk deficient mice thus provide a novel model to study the genetic requirements for bone marrow stromal differentiation.

Animals↗

A comparison of signal instability in 2D and 3D EPI resting-state fMRI.

Spatiotemporally structured noise, such as physiological noise, is a potential source of artifacts in functional magnetic resonance imaging (fMRI) and is the main limiting factor for the detection of small blood oxygen level-dependent (BOLD) signal variations. fMRI was employed to detect low-frequency BOLD signal fluctuations, which are thought to be related to spontaneous neuronal activity in the resting human brain. The sensitivity to noise, that is, signal variations of non-BOLD origin, was investigated for two- (2D) and three-dimensional (3D) imaging techniques. Incomplete relaxation between subsequent scans increases the level of temporally and spatially correlated signal variations originating from physiological and/or systemic noise. Although inflow effects are suspected to be reduced in 3D echo-planar imaging (EPI) compared with multi-slice 2D EPI, the noise level was higher in the 3D technique. The noise level in 3D fMRI experiments was significantly increased by instabilities of the transverse steady-state magnetization as the repetition time was of the order of T(2). By implementing radiofrequency spoiling, temporal signal fluctuations and erroneous inter-regional correlation in connectivity maps were diminished to a level present in data sets acquired with 2D EPI.

Adult↗

HMSC: simultaneously detected heteronuclear shift correlation through multiple and single bonds.

A new 2D pulse sequence HMSC (heteronuclear multiple-bond and single-bond coupling connectivities) for the simultaneous detection of long-range and one-bond heteronuclear connectivities is proposed which allows the two types of responses to be separated and the corresponding (n)J(CH) and (1)J(CH) connectivity maps to be calculated. (n)J(CH) coherences are selectively labeled in the course of the pulse sequence, the correspondingly acquired data are separately stored, and a simple add/subtract procedure is applied to disentangle and edit (n)J(CH) and (1)J(CH) responses prior to final data processing. Unlike standard methods, which are designed to measure one single type of heteronuclear spin-spin interactions and to efficiently suppress the other, both (n)J(CH) and (1)J(CH) are measured simultaneously in a single experiment with the HMSC pulse sequence. Compared to the common strategy with two standard experiments applied one after the other, e.g., HMBC and HMQC, valuable measuring time may be saved with this single experiment approach. The efficiency of the new pulse sequence and the quality of the corresponding spectra are demonstrated using strychnine. Features such as sensitivity, lineshapes, and the suppression of (1)J(CH) residual peaks in the final (n)J(CH) subspectra are investigated and compared with the corresponding results obtained with standard methods. The attractive and unique single experiment approach, its high efficiency, and its easy experimental setup together with straightforward data processing make HMSC a valuable experimental alternative for the today's more time-consuming "two-step" practice and makes it suitable for standard routine applications.

Journal Article↗

Multi-neuronal signals from the retina: acquisition and analysis.

Throughout the central nervous system, information about the outside world is represented collectively by large groups of cells, often arranged in a series of 2-dimensional maps connected by tracts with many fibers. To understand how such a circuit encodes and processes information, one must simultaneously observe the signals carried by many of its cells. This article describes a new method for monitoring the simultaneous electrical activity of many neurons in a functioning piece of retina. Extracellular action potentials are recorded with a planar array of 61 microelectrodes, which provides a natural match to the flat mosaic of retinal ganglion cells. The voltage signals are processed in real time to extract the spike trains from up to 100 neurons. We also present a method of visual stimulation and data analysis that allows a rapid characterization of each neuron's visual response properties. A randomly flickering display is used to elicit spike trains from the ganglion cell population. Analysis of the correlations between each spike train and the flicker stimulus results in a simple description of each ganglion cell's functional properties. The combination of these tools will allow detailed study of how the population of optic nerve fibers encodes a visual scene.

Action Potentials↗

Topological relation of chick thalamofugal visual projections with hyper pallium revealed by three color tracers.

In birds, there are two visual projections from retina to higher pallium, i.e., tectofugal and thalamofugal pathways. The latter one is lateralized in chick and suggested to be involved in visually evoked social behavior, like recognition of novelty, predator, and conspecific animals. We wanted to establish functionally relevant topological connection map between thalamic nuclei and hyperpallium apicale (HA) and carried out tracing study with three color fluorescent tracers. The tracers were serially injected in HA either along with the medial-lateral (M-L) or anterior-posterior (A-P) axis. We found that M-L axis and A-P axis in HA were transferred into the dorsal-ventral axis and the medial-lateral axis, respectively within the nucleus geniculatus lateralis pars dorsalis (GLd). In another word, the medial part of nucleus dorsolateralis anterior thalami pars lateralis (DLLv) projected to anterior part of HA and the ventral part of nucleus dorsolateralis anterior thalami pars lateralis pas ventralis (DLLd) projects to lateral HA. This result suggests that thalamus would process information in parallel through each subnuclei and elaborate coordination among them in relation to topological map presented in higher pallium.

Animals↗

Measuring functional connectivity during distinct stages of a cognitive task.

The inherently multivariate nature of functional brain imaging data affords the unique opportunity to explore how anatomically disparate brain areas interact during cognitive tasks. We introduce a new method for characterizing inter-regional interactions using event-related functional magnetic resonance imaging (fMRI) data. This method's principle advantage over existing analytical techniques is its ability to model the functional connectivity between brain regions during distinct stages of a cognitive task. The method is implemented by using separate covariates to model the activity evoked during each stage of each individual trial in the context of the general linear model (GLM). The resulting parameter estimates (beta values) are sorted according to the stage from which they were derived to form a set of stage-specific beta series. Regions whose beta series are correlated during a given stage are inferred to be functionally interacting during that stage. To validate the assumption that correlated fluctuations in trial-to-trial beta values imply functional connectivity, we applied the method to an event-related fMRI data set in which subjects performed two sequence-tapping tasks. In concordance with previous electrophysiological and fMRI coherence studies, we found that the task requiring greater bimanual coordination induced stronger correlations between motor regions of the two hemispheres. The method was then applied to an event-related fMRI data set in which subjects performed a delayed recognition task. Distinct functional connectivity maps were generated during the component stages of this task, illustrating how important and novel observations of neural networks within the isolated stages of a cognitive task can be obtained.

Adult↗

Bootstrap white matter tractography (BOOT-TRAC).

White matter tractography is a noninvasive method for estimating and visualizing the white matter connectivity patterns in the human brain using diffusion tensor imaging (DTI) data. Sources of experimental noise may induce errors in the measured fiber directions, which will reduce the accuracy of the estimated white matter trajectories. In this study, a statistical nonparametric bootstrap method is described for estimating the dispersion and other errors in white matter tractography results. Prior studies have derived models of tractography error using the signal-to-noise ratio (SNR) and diffusion anisotropy of the DTI data. Tractography errors measured using bootstrap methods were generally consistent with an analytic model of tractography error except in areas where branching was evident. White matter tractography with bootstrap resampling is also applied to estimate the probabilities of connection between brain regions. The approach was used to generate probabilistic connectivity maps between the cerebral peduncles and specific cortical regions.

Brain↗

Structure of the GnRH receptor-stimulated signaling network: insights from genomics.

The GnRH receptor influences gene expression in the gonadotrope through activating signaling cascades that modulate transcription factor expression and activity. A longstanding question in neuroendocrinology is how instructions received at the membrane in the form of the pattern of receptor stimulation are processed into specific biosynthetic changes at each gonadotropin promoter. Signal transduction from the membrane to preformed transcription factors relies on recognition of altered conformations. Signal transduction through the layers of the gene network also requires the biosynthesis of new transcription factors. The signal processing of this system depends on its molecular connectivity map and its feedback and feed-forward loops. Review of signal transduction, gene control, and genomic studies provide evidence of key loops that cross between cellular and nuclear compartments. Genomic studies suggest that the signal transduction and gene network form a continuum. We propose that information transfer in the gonadotrope depends on robust signaling modules that serve to integrate events at different time scales across cytoplasmic and nuclear compartments.

Animals↗

Multivariate autoregressive modeling of fMRI time series.

We propose the use of multivariate autoregressive (MAR) models of functional magnetic resonance imaging time series to make inferences about functional integration within the human brain. The method is demonstrated with synthetic and real data showing how such models are able to characterize interregional dependence. We extend linear MAR models to accommodate nonlinear interactions to model top-down modulatory processes with bilinear terms. MAR models are time series models and thereby model temporal order within measured brain activity. A further benefit of the MAR approach is that connectivity maps may contain loops, yet exact inference can proceed within a linear framework. Model order selection and parameter estimation are implemented by using Bayesian methods.

Algorithms↗

AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic illness with a multifactorial etiology and heterogeneous symptomatology, posing major challenges for diagnosis and treatment. Here we present BioMapAI, a supervised deep neural network trained on a 4-year, longitudinal, multi-omics dataset from 249 participants, which integrates gut metagenomics, plasma metabolomics, immune cell profiling, blood laboratory data and detailed clinical symptoms. By simultaneously modeling these diverse data types to predict clinical severity, BioMapAI identifies disease- and symptom-specific biomarkers and classifies ME/CFS in both held-out and independent external cohorts. Using an explainable AI approach, we construct a unique connectivity map spanning the microbiome, immune system and plasma metabolome in health and ME/CFS adjusted for age, gender and additional clinical factors. This map uncovers altered associations between microbial metabolism (for example, short-chain fatty acids, branched-chain amino acids, tryptophan, benzoate), plasma lipids and bile acids, and heightened inflammatory responses in mucosal and inflammatory T cell subsets (MAIT, γδT) secreting IFN-γ and GzA. Overall, BioMapAI provides unprecedented systems-level insights into ME/CFS, refining existing hypotheses and hypothesizing unique mechanisms-specifically, how multi-omics dynamics are associated to the disease's heterogeneous symptoms.

Humans↗

A genetic approach to trace neural circuits.

Mammalian nervous system function involves billions of neurons which are interconnected in a multitude of neural circuits. Here we describe a genetic approach to chart neural circuits. By using an olfactory-specific promoter, we selectively expressed barley lectin in sensory neurons in the olfactory epithelium and vomeronasal organ of transgenic mice. The lectin was transported through the axons of those neurons to the olfactory bulb, transferred to the bulb neurons with which they synapse, and transported through the axons of bulb neurons to the olfactory cortex. The lectin also was retrogradely transported from the bulb to neuromodulatory brain areas. No evidence could be obtained for adverse effects of the lectin on odorant receptor gene expression, sensory axon targeting in the bulb, or the generation or transmission of signals by olfactory sensory neurons. Transneuronal transfer was detected prenatally in the odor-sensing pathway, but only postnatally in the pheromone-sensing pathway, suggesting that odors, but not pheromones, may be sensed in utero. Our studies demonstrate that a plant lectin can serve as a transneuronal tracer when its expression is genetically targeted to a subset of neurons. This technology can potentially be applied to a variety of vertebrate and invertebrate neural systems and may be particularly valuable for mapping connections formed by small subsets of neurons and for studying the development of connectivity as it occurs in utero.

Animals↗