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French, C.

Publications and source records attributed to French, C..

17 recordsLinked to original sources

Training constrains neural routes to knowledge assembly

A hallmark of human intelligence is the ability to rapidly restructure existing knowledge when new information reveals unexpected connections, a capacity termed knowledge assembly. This cognitive flexibility distinguishes human learning from artificial systems, which catastrophically forget when acquiring new relationships. Understanding the mechanisms underlying flexible knowledge reorganization thus has implications for continual learning in both humans and algorithms. Here, using electroencephalography we show that successful knowledge assembly depends on temporally orchestrated reactivation of prior neural representations. Critically, training schedules bias learners toward different representational strategies: blocked training promotes compressed certainty-weighted codes, while interleaved training yields high-dimensional factorized representations. Vanilla recurrent networks failed to develop human-like certainty geometries despite identical training, revealing missing computational principles in current artificial systems. These findings demonstrate that cognitive flexibility emerges through creative reuse of learned representations, with training history constraining available neural routes to reorganization.

neuroscience↗

CRISPR-Induced NUT Suppression Promotes Differentiation and Enhances Trop2-Targeted Immunocytokine Response in NUT Carcinoma

NUT carcinoma (NC) is an aggressive malignancy driven by NUTM1 gene rearrangements with limited therapeutic options. Here, we show that direct suppression of NUTM1 using CRISPR/Cas9 induces squamous-like differentiation and upregulates TROP2 expression in NC cells. Building on this finding, we developed a TROP2-interferon beta (IFN-{beta}) mutein immunocytokine that selectively targets TROP2-expressing tumors. Combined NUTM1 suppression and TROP2-targeted immunotherapy synergistically enhanced cytotoxic and immune-mediated responses in vitro. Transcriptomic and spatial analyses of NC patient tumors revealed that differentiation status correlates with TROP2 expression, upregulated immune pathways, and favorable clinical outcomes. Our results suggest that overcoming differentiation blockade not only alters tumor phenotype but also creates a more immune-permissive microenvironment. These findings highlight the therapeutic potential of sequential tumor reprogramming followed by targeted immunotherapy in treating NC and propose a broader strategy for overcoming differentiation blockade in fusion-driven cancers.

cancer biology↗

Nucleus Basalis of Meynert as a DBS target

Several clinical attempts to use deep brain stimulation applied to nucleus basalis of Meynert to reduce cognitive decline in different types of dementia report inconclusive effects. At the same time, experiments in rodents have largely demonstrated cognitive improvement. The hypothesised basis for this difference was the application of different patterns of stimulation - tonic continuous over multiple sleep-wake cycles in human clinical trials vs intermittent bursts over shorter intervals in animal studies. However, since no systematic testing of the effects of different stimulation patterns applied in different states of vigilance was conducted, it remains unclear what specific attributes of cortical responses are associated with these patterns, and the effect of vigilance state on pattern response. We hypothesised that communication between nucleus basalis and its cortical targets involves frequencies in both low and high ranges, making burst-type intermittent patterns potentially more effective. Therefore we studied preferred frequencies of neuronal synchronization within nucleus basalis as well as between nucleus basalis and its cortical targets in B6 mouse strain (N=9, age 4-6 month) by recording neuronal spiking and local field potentials (LFP) from 2 sites of the nucleus basalis and 4 cortical sites simultaneously across multiple sleep-wake cycles. Spike-field coherence (SFC) analysis revealed natural synchronization tendencies of nucleus basalis - all animals demonstrated significant SFC at delta-theta range and gamma coherence peaking between 57 and 88 Hz (SFC > 95% Jackknife confidence interval at frequency range > 2*bandwidth). SFC between cortical cells and local field potentials of nucleus basalis, which reflects cortical feedback, peaked at delta-theta frequencies. Based on these results we constructed "nested" patterns of stimulation that included both delta-theta and individually assessed gamma peak for each animal (N=8). The effects of nested stimulation were compared to the ones of random and tonic (20Hz) stimulation patterns. These patterns of stimulation were applied across multiple sleep-wake cycles to freely behaving animals, and spectral power density in response to stimulation compared between patterns for different states of vigilance. We report significant reduction of delta power during slow wave sleep and theta power in REM for all three patterns. Slow wave suppression was also present during wakefulness. This indicates all patterns may improve levels of alertness but highlights strong likelihood of sleep disturbances in response to stimulation during sleep. Thus, deep brain stimulation of nucleus basalis may be counterproductive during sleep. The nested pattern of stimulation alone demonstrated preservation or even enhancement of gamma activity in the cortex while suppressing low frequencies. Broad-band suppression of cortical activity was shown in response to tonic stimulation, and to some extent to the random pattern as well, suggesting that tonic stimulation may be unsuitable for deep brain stimulation of the nucleus basalis of Meynert.

neuroscience↗

Neural Networks Are Tuned Near Criticality During a Cognitive Task and Distanced from Criticality In a Psychopharmacological Model of Alzheimer's Disease

Dynamical systems exhibit transitions between ordered and disordered states and "criticality" occurs when the system lies at the borderline between these states at which the input is neither strongly damped nor excessively amplified. Impairments in brain function such as dementia or epilepsy could arise from failure of adaptive criticality, and deviation from criticality may be a potential biomarker for cognition-related neurological and psychiatric impairments. Miniscope wide-field calcium imaging of several hundred hippocampal CA1 neurons in freely-behaving mice was studied during rest, a cognitive task of novel object recognition (NOR), and novel object recognition following scopolamine administration that greatly impairs spatial memory encoding. We find that while hippocampal networks exhibit characteristics of a near-critical system at rest, the network activity shifts significantly closer to a critical state when the mice engaged in the NOR task. The dynamics shift away from criticality with impairment of novel object performance due to scopolamine-induced memory impairment. These results support the concept that hippocampal neural networks move closer to criticality when successfully processing increased cognitive load, taking advantage of maximal dynamical range, information content, and transmission that occur in critical regimes.

neuroscience↗

Critical dynamics arise during structured information presentation: analysis of embodied in vitro neuronal networks

AO_SCPLOWBSTRACTC_SCPLOWAmongst the characteristics about information processing in the brain, observations of dynamic near-critical states have generated significant interest. However, theoretical and experimental limitations have precluded a definite answer about when and why neural criticality arises. To explore this topic, we used an in vitro neural network of cortical neurons that was trained to play a simplified game of Pong. We demonstrate that critical dynamics emerge when neural networks receive task-related structured sensory input, reorganizing the system to a near-critical state. Additionally, better task performance correlated with proximity to critical dynamics. However, criticality alone is insufficient for a neuronal network to demonstrate learning in the absence of additional information regarding the consequences of previous actions. These findings have compelling implications for the role of neural criticality.

neuroscience↗

Utilising hippocampal neuronal calcium activity in mouse CA1 for a multimodal optical brain-computer interface

The hippocampus has been proposed to integrate information from multiple sensory modalities, supporting a comprehensive "cognitive map" for both spatial and non-spatial information. Previous studies have demonstrated decoding of hippocampal spatial information in real time by recording neuronal action potentials with electrodes. However, decoding of hippocampal non-spatial information robustly in real-time has not been previously shown. Here, we utilise the advantages of widefield optical calcium imaging to construct an optical brain-computer interface (BCI) driven by calcium activity of large neuronal ensembles ([~]600 neurons) to decode spatial, visual and auditory information effectively in real time. We developed a high speed end-to-end analysis workflow with advanced machine learning techniques for decoding. This methodology achieves high decoding accuracy and provides a "cognitive translation" approach that may be applied to both research and clinical applications to allow direct neural communication with animals and patients with impairment of function.

bioengineering↗

Higher synaptic threshold for NMDA spike generation in human neurons

Neurons receive synaptic input primarily onto their dendrites. While we know much about the electrical properties of dendrites in rodents, we have only just started to describe their properties in the human brain. Here we investigate the capacity of human neurons to generate NMDA spikes. We find that dendritic iontophoresis of glutamate, as well as local dendritic synaptic stimulation, can evoke NMDA spikes in dendrites of human layer 2/3 pyramidal neurons. Surprisingly, however, the capacity to evoke NMDA spikes in human neurons was significantly reduced compared to that in rodent neurons. Simulations in morphologically realistic models indicated that human neurons have a higher synaptic threshold for NMDA spike generation. Using a simplified model, we show that this is primarily due to the larger diameter of human dendrites. In summary, we find reduced NMDA spike generation in human compared to rodent neurons due to the larger diameter of human dendrites.

neuroscience↗

Observations of the Effect of Scopolamine on Hippocampal CA1 Place Cell and Network Properties in Freely Moving Mice Using Miniscope Imaging

The hippocampus and associated cholinergic inputs regulate spatial memory in rodents. Muscarinic blockade with scopolamine results in cognition deficits usually attributed to impaired memory encoding, but effects on memory retrieval are controversial. Here, we simultaneously recorded hundreds of neurons in mouse hippocampal CA1 using calcium imaging with a miniatured fluorescent microscope to study place cell and ensemble neuronal properties in a linear track environment. We found decoding accuracy and ensemble stability were significantly reduced after the administration of scopolamine. Several other parameters including the Ca2+ event rate, number of total cells and place cells observed, spatial information content were affected including a small increase in running speed. This study enhances the understanding of cholinergic blockade on spatial memory impairment.

neuroscience↗

Effects of Antipsychotic Drugs and Potassium Channel Modulators on Cognition-related Local Field Potential Spectral Properties in Mouse Hippocampus and Frontal Cortex

Local field potentials (LFPs) recorded intracranially display a range of location specific oscillatory spectra which have been related to cognitive processes. Although the exact mechanisms producing LFPs are not completely understood, it is likely that voltage-gated ion channels which produce action potentials and patterned discharges play a significant role. It is also known that antipsychotic drugs (APDs) affect LFPs spectra and a direct inhibitory effect on voltage-gated potassium (Kv) channels has been reported. Additionally, Kv channels have been implicated in the pathophysiology of schizophrenia, a disorder for which APDs are primary therapies. In this study we sought to: i) better characterise the effects of two APDs on LFPs and connectivity measures and ii) examine the effects of potassium channel modulators on LFPs and potential overlap of effects with APDs. Intracranial electrodes were implanted in the hippocampus (HIP) and pre-frontal cortex (PFC) of C57BL/6 mice; power spectra, coherence and phase-amplitude cross frequency coupling were measured. Drugs tested were the APDs haloperidol and clozapine as well as voltage-gated potassium channel modulators (KVMs) 4-aminopyridine(4AP), tetraethylammonium (TEA), E-4031 and retigabine. All drugs and vehicle controls were administered intraperitoneally. Both APDs and KVMs significantly reduced gamma power with the exception of 4AP, which conversely increased slow-gamma power. Clozapine and retigabine additionally reduced coherence between HIP and PFC. Phase-amplitude coupling between theta and gamma oscillations in HIP was significantly reduced by the administration of haloperidol and retigabine. These results provide previously undescribed effects of APDs on LFP properties and demonstrate novel modulation of LFP characteristics by KVMs that intriguingly overlaps with the effects of APDs. The possibility of a common mechanism of action deserves further study.

neuroscience↗

The balance hypothesis for the avian lumbosacral organ and an exploration of its morphological variation

ABSTRACTBirds (Aves) exhibit exceptional and diverse locomotor behaviors, including the exquisite ability to balance on two feet. How birds so precisely control their movements may be partly explained by a set of intriguing modifications in their lower spine. These modifications are collectively known as the lumbosacral organ (LSO) and are found in the fused lumbosacral vertebrae called the synsacrum. They include a set of transverse canal-like recesses in the synsacrum that align with lateral lobes of the spinal cord, as well as a dorsal groove in the spinal cord that houses an egg-shaped glycogen body. Based on compelling but primarily observational data, the most recent functional hypotheses for the LSO consider it to be a secondary balance organ, in which the transverse canals are analogous to the semicircular canals of the inner ear. If correct, this hypothesis would reshape our understanding of avian locomotion, yet the LSO has been largely overlooked in the recent literature. Here, we review the current evidence for this hypothesis and then explore a possible relationship between the LSO and balance-intensive locomotor ecologies. Our comparative morphological dataset consists of micro-computed tomography (μ-CT) scans of synsacra from ecologically diverse species. We find that birds that perch tend to have more prominent transverse canals, suggesting that the LSO is useful for balance-intensive behaviors. We then identify the crucial outstanding questions about LSO structure and function. The LSO may be a key innovation that allows independent but coordinated motion of the head and the body, and a full understanding of its function and evolution will require multiple interdisciplinary research efforts.Jargon-Free Birds have an uncanny ability to move their heads independently of their bodies. They can keep their heads remarkably still to focus on their prey while twisting in flight or perched on a bouncing branch. How are they able to do this? Like us, birds have balance organs in their inner ears that act like gyroscopes. Surprisingly, birds may have an additional balance organ known as the “lumbosacral organ” in their spine, right above their legs, which might help them sense the movement of their body separately from their head. This second balance organ may have played a very important role in bird evolution and how birds move, but it has seldom been considered in recent scientific studies. This intriguing hypothesis is based in part on a series of fluid-filled, canal-like recesses in the bone surrounding the spinal cord, which resemble the semicircular canals of the inner ear. We looked for evidence of these canal-like recesses in many different bird species, and we found it in every bird we examined. We also found that birds that perch often have deeper recesses than birds that do not perch, suggesting these canals help maintain balance. This paper presents those findings, reviews the existing research, and identifies some key questions that need to be asked to advance our understanding of this fascinating and mysterious part of the bird spinal cord.View Full Text

zoology↗

Spatiotemporal patterns of high-frequency activity (80-170 Hz) in long-term intracranial EEG

ObjectiveTo assess the variability in the rates and locations of high-frequency activity (HFA) and epileptiform spikes after electrode implantation, and to examine the long-term patterns of HFA using ambulatory intracranial EEG (iEEG) recordings. MethodsContinuous iEEG recordings obtained over an average of 1.4 years from 15 patients with drug-resistant focal epilepsy were used in this study. HFA was defined as high-frequency events with amplitudes clearly larger than the background, which was automatically detected using a custom algorithm. High-frequency oscillations (HFOs) were also visually annotated by three neurologists in randomly sampled segments of the total data. The automatically detected HFA was compared with the visually marked HFOs. The variations of HFA rates were compared with spikes and seizures on patient-specific and electrode-specific bases. ResultsHFA was a more general event that encompassed HFOs manually annotated by different reviewers. HFA and spike rates had high amounts of intra- and inter-patient variability. The rates and locations of HFA and spikes took up to weeks to stabilize after electrode implantation in some patients. Both HFA and spike rates showed strong circadian rhythms in all patients and some also showed multiday cycles. Furthermore, the circadian patterns of HFA and spike rates had patient-specific correlations with seizures, which tended to vary across electrodes. ConclusionsAnalysis of HFA and epileptiform spikes should account for post-implantation variability. Like seizures, HFA and epileptiform spikes show circadian rhythms. However, the circadian profiles can vary spatially within patients and their correlations to seizures are patient-specific.

neuroscience↗

Production of Insoluble Starch-Like Granules in Escherichia coli by Modification of the Glycogen Synthesis Pathway

While investigating the conversion of cellulosic biomass to starch-like materials for industrial use, it was observed that the overexpression of native ADP-glucose pyrophosphorylase GlgC in Escherichia coli led to the formation of insoluble polysaccharide granules within the cytoplasm, occupying a large fraction of the cell volume, as well as causing an overall increase in cellular polysaccharide content. TEM microscopy revealed that the granules did not have the lamellar structure of starch, but rather an irregular, clustered structure. On starvation, cells overexpressing GlgC appeared unable to fully degrade their polysaccharide material and granules were still clearly visible in cultures after 8 days of starvation. Interestingly, the additional overexpression of the branching enzyme GlgB eliminated the production of granules and led to a further increase in cellular polysaccharides. GlgC is generally thought to be responsible for the rate-limiting step of glycogen synthesis. Our interpretation of these results is that excess GlgC activity may cause the elongation of glycogen chains to outpace the addition of side branches, allowing the chains of adjacent glycogen molecules to reach lengths at which they spontaneously intertwine, forming dense clusters that are largely inaccessible to the host. However, upon additional upregulation of the GlgB branching enzyme, the branching of the polysaccharide is able to keep speed with the synthesis of linear chains, eliminating the granule phenotype. This study suggests potential avenues for increasing bacterial polysaccharide production and recovery. ImportanceIn this work, the polysaccharide stores of Escherichia coli were altered through the addition of extra copies of the bacterias own polysaccharide synthesis genes. In this way, bacteria were created that produced over twice the level of storage polysaccharide as a control strain, in the form of a granule that could potentially facilitate easy harvest. Another form of mutant Escherichia coli was created that produced over seven times the normal level of storage polysaccharide, and also grew to higher cell densities in liquid culture. In addition to increasing our understanding of glycogen synthesis, it is proposed that similarly modified bacteria, grown on inexpensive waste materials, may be a useful source of starch-like polysaccharides for industrial or agricultural use. In particular, the use of cyanobacterial glycogen as a carbon source for biofuels has recently been gaining interest, and the work presented here may well be applicable in this field.

microbiology↗

TXO: Transcription-Only genetic circuits as a novel cell-free approach for Synthetic Biology

While synthetic biology represents a promising approach to solve real-world problems, the use of genetically modified organisms is a cause of legal and environmental concerns. Cell-free systems have emerged as a possible solution but much work is needed to optimize their functionality and simplify their usage for Synthetic Biology. Here we present TXO, transcription-only genetic circuits, independent of translation or post-translation maturation. RNA aptamers are used as reaction output allowing the generation of fast, reliable and simple-to-design transcriptional units. TXO cell-free reactions and their possible applications are a promising new tool for fast and simple bench-to-market genetic circuit and biosensor applications.

synthetic biology↗

Joint Universal Modular Plasmids (JUMP): A flexible and comprehensive platform for synthetic biology

Complex multi-gene plasmids can be built from basic DNA parts in a reliable and automation friendly way using modular cloning standards, based on Golden Gate cloning. However, each toolkit or standard is limited to one or a few different vectors, which has led to an overabundance of toolkits with varying degrees of compatibility. Here, we present the Joint Universal Modular Plasmids (JUMP), a vector design that overcomes the limitations of current toolkits by expanding the paradigm of modular cloning: all vectors can be modified using modular cloning in an orthogonal way using multiple cloning sites. This allows researchers to introduce any feature into any JUMP vector and simplifies the Design-Build-Test cycle of synthetic biology. JUMP vectors are compatible with PhytoBrick basic parts, BioBricks and the Registry of Standard Biological Parts, and the Standard European Vector Architecture (SEVA). Due to their flexible design, JUMP vectors have the potential to be a universal platform for synthetic biology regardless of host and application. A collection of JUMP backbones and microbial PhytoBrick basic parts are available for distribution.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC=\"FIGDIR/small/799585v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (38K):\norg.highwire.dtl.DTLVardef@142615forg.highwire.dtl.DTLVardef@106c571org.highwire.dtl.DTLVardef@18cb5a2org.highwire.dtl.DTLVardef@e8cb95_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions

We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci.\n\nAvailability and implementationExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/.\n\nContactmeberle@illumina.com

bioinformatics↗

Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish

Despite the critical role of vascular mural cells (smooth muscle cells and pericytes) in supporting the endothelium of blood vessels, we know little of their early morphogenesis and differentiation. foxc1b:EGFP expressing cells in zebrafish associate with the vascular endothelium (kdrl) and co-express a smooth muscle marker (acta2), but not a pericyte marker (pdgfr{beta}). The expression of foxc1b in early peri-endothelial mesenchymal cells allows us to follow the morphogenesis of mesenchyme into acta2 expressing vascular smooth muscle cells. We show that mural cells expressing different markers associate with vessels of different diameters, depending on their embryonic location and developmental timing, suggesting marker expression is predictive of functional differences. We identify gene expression signatures for an enriched vascular smooth muscle cell population (foxc1b + acta2) and all smooth muscle (acta2) using fluorescence-activated cell sorting and RNA-Seq. Finally, we demonstrate that progressive loss of foxc1a/foxc1b results in decreased smooth muscle cell coverage. Together, our data highlight the early cellular dynamics and transcriptome profiles of smooth muscle cells in vivo, using foxc1b as a unique tool to probe vascular smooth muscle cell differentiation.\n\nSummary StatementTracing the morphogenesis and transcriptome of early vascular smooth muscle cells using foxc1b

developmental biology↗

A Migratory Divide In The Painted Bunting (Passerina ciris)

Divergence in migratory behavior is a potential mechanism of lineage divergence in sympatric populations and a key life history trait used in the identification of demographically independent units for conservation purposes. In the Painted Bunting (Passerina ciris), a North American songbird, populations on the Atlantic coast and interior southern United States are known to be allopatric during the breeding season, but efforts to map connectivity with wintering ranges in Mexico, Florida, and the Caribbean have been largely inconclusive. Using genomic and morphological data from natural history specimens and banded birds, we found evidence of three genetically differentiated populations with distinct wintering ranges and molt-migration phenologies. In addition to confirming that the Atlantic coast population remains allopatric throughout the annual cycle, we identified an unexpected migratory divide within the interior breeding range. Populations breeding in the Lower Mississippi River Valley winter on the Yucatan Peninsula, and are parapatric with other interior populations that winter in mainland Mexico and Central America. Across the interior breeding range, genetic ancestry is also associated with variation in wing length; suggesting that selective pressures may be promoting morphological divergence in populations with different migration strategies.

zoology↗