Biology subjects

Walker, M. P.

Publications and source records attributed to Walker, M. P..

13 recordsLinked to original sources

bioRxiv2025

REM Sleep Misfires: Intruding Delta Waves Forecast Tau, Amyloid, and Forgetting in Aging

Rapid Eye Movement (REM) sleep degrades with age, and more severely in Alzheimers disease (AD). REM sleep comprises about twenty percent of adult sleep, alternates between phasic and tonic periods, and includes delta waves (1-4Hz) in two forms: fast sawtooth waves and slower, NREM-like waves, whose expression dynamically varies across REM periods. Yet, the functional relevance of these REM sleep delta waves remains unknown. Here, using two independent cohorts, we show that aging is associated with a shift from fast sawtooth to slow NREM-like delta waves, particularly during phasic REM sleep--a period typically marked by high cortical activation. Beyond chronological age, this shift is associated with amyloid-beta and tau burden, suggesting that AD pathology disrupts REM-specific oscillatory patterns. Furthermore, this shift in REM oscillations is linked to impaired overnight memory consolidation, independent of NREM sleep quality. Moreover, variation in ApoE alleles, a major genetic risk factor for AD, was independently associated with a reduction in fast sawtooth wave density, thereby linking a genetic predisposition for AD to these specific REM microstructural changes. These findings identify a novel signature of memory decline in aging and implicate REM sleep as a distinct vulnerable substrate through which AD pathology may impair brain function.

neuroscience↗

bioRxiv2025

Robust Production of Parvalbumin Cortical Interneurons and Fast-Spiking Neurons from Human Medial Ganglionic Eminence Organoids

The medial ganglionic eminence (MGE) gives rise to parvalbumin (PV)-and somatostatin (SST)-expressing cortical interneurons essential for regulating cortical excitability. Although PV interneurons are linked to various neurodevelopmental and neurodegenerative disorders, reliably generating them from human pluripotent stem cells (hPSCs) has been extremely challenging. We present a robust, reproducible protocol for generating single-rosette MGE organoids (MGEOs) from hPSCs. Transcriptomic analyses reveal that MGEOs exhibit MGE regional identity and faithfully model the developing human fetal MGE. As MGEOs mature, they generate abundant PV-expressing cortical interneurons, including putative basket and axoaxonic cells, at a scale not previously achieved in vitro. When fused with human cortical organoids (hCOs), these interneurons rapidly migrate into the hCOs, integrate into excitatory networks, and contribute to complex electrophysiological patterns and the emergence of large numbers of fast-spiking neurons. Using this model, we uncover a previously unreported migration deficit of MGE interneurons in a disease model of SLC6A1 developmental and epileptic encephalopathy, offering potential insights into the developmental contributions to epileptogenesis. MGEOs thus offer a powerful in vitro approach for probing human MGE-lineage cortical and subcortical GABAergic neuron development, modeling various neuropsychiatric disorders, and advancing cell-based therapies for neurodevelopmental and neurodegenerative disorders. HighlightsO_LIGeneration of subpallial organoids highly enriched for MGE lineages C_LIO_LIMGE organoids (MGEOs) robustly produce parvalbumin-expressing cortical interneurons C_LIO_LIComplex network activity and fast-spiking neurons are generated in assembloids C_LIO_LIImpaired interneuron migration in SLC6A1 knockout and patient-derived MGEOs C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/662594v2_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@1fce574org.highwire.dtl.DTLVardef@3c28d2org.highwire.dtl.DTLVardef@19bf737org.highwire.dtl.DTLVardef@834f2b_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Tau pathology leads to lonely non-traveling slow waves that mediate human memory impairment

Memory markedly declines with age, exaggerated in those with Alzheimers disease, yet the mechanisms are still not resolved. Here, we show that frontal lobe tau pathology in humans leads to impaired en masse unity and cortical traveling propagation of NREM slow waves, consequentially impairing memory retention. We elucidate these findings using PET tau brain imaging, and then replicate and extend them using AD pathology markers derived from lumbar puncture CSF in an independent clinical cohort. Thus, tau-associated memory deficits are not wholly direct, but indirectly mediated through consequential "lonely", non-traveling slow-wave events.

neuroscience↗

bioRxiv2022

Personalized transcranial alternating current stimulation improves sleep quality: Initial Findings

Insufficient sleep is a major health issue. Inadequate sleep is associated with an array of poor health outcomes, including cardiovascular disease, diabetes, obesity, certain forms of cancer, Alzheimers disease, depression, anxiety, and suicidality. Given concerns with typical sedative hypnotic drugs for treating sleep difficulties, there is a compelling need for added alternative interventions. Here, we report results of a non-invasive electrical brain stimulation approach to optimizing sleep involving transcranial alternating current stimulation (tACS). A total of 25 participants (mean age: 46.3, S.D. {+/-}12.4, 15 females) were recruited for a null-stimulation controlled (Control condition), within subjects, randomized crossed design, that included two variants of an active condition involving 15 minutes pre-sleep tACS stimulation. To evaluate the impact on sleep quality, the two active tACS stimulation conditions were designed to modulate sleep-dependent neural activity in the theta/alpha frequency bands, with both stimulation types applied to all subjects in separate sessions. The first tACS condition used a fixed stimulation pattern across all participants, a pattern composed of stimulation at 5Hz and 10Hz. The second tACS condition used a personalized stimulation approach with the stimulation frequencies determined by each individuals peak EEG frequencies in the 4-6Hz and 9-11Hz bands. Personalized tACS stimulation increased sleep quantity (duration) by 22 minutes compared to a Control condition (p=.04), and 19 minutes compared to Fixed tACS stimulation (p=.03). Fixed stimulation did not significantly increase sleep duration compared to Control (mean: 3 minutes; p=0.75). For sleep onset, the Personalized tACS stimulation resulted in reducing the onset by 28% compared to the Fixed tACS stimulation (6 minutes faster, p=.02). For a Poor Sleep sub-group (n=13) categorized with Clinical Insomnia and with a high insomnia severity, Personalized tACS stimulation improved sleep duration by 33 minutes compared to Fixed stimulation (p=0.02), and 30 minutes compared to Control condition (p<0.1). Together, these results suggest that Personalized stimulation improves sleep quantity and time taken to fall asleep relative to Control and Fixed stimulation providing motivation for larger-scale trials for Personalized tACS as a sleep therapeutic, including for those with insomnia.

neuroscience↗

bioRxiv2022

Human REM sleep controls neural excitability in support of memory formation

Sleep oscillations provide a key substrate to facilitate memory processing, the underlying mechanism of which may involve the overnight homeostatic regulation of plasticity at a synaptic and whole-network level. However, there remains a lack of human data demonstrating if and how sleep enhances memory consolidation and associated neural homeostasis. We combined intracranial recordings and scalp electroencephalography (EEG) in humans to reveal a new role for rapid eye movement (REM) sleep in promoting the homeostatic recalibration of optimal excitation/inhibition-balance. Moreover, the extent of this REM-sleep homeostatic recalibration predicted the success of overnight memory consolidation, expressly the modulation of hippocampal-- neocortical excitability favoring remembering rather than forgetting. The findings describe a novel, fundamental role of human REM sleep in maintaining neural homeostasis, thereby enhancing long-term memory.

neuroscience↗

bioRxiv2022

Direct type I Interferon signaling in hepatocytes control malaria

Malaria is a devastating disease impacting over half of the worlds population. Plasmodium parasites that cause malaria undergo obligatory development and replication in hepatocytes before infecting red blood cells and initiating clinical disease. While type I interferons (IFNs) are known to facilitate innate immune control to Plasmodium in the liver, how they do so has remained unresolved, preventing the manipulation of such responses to combat malaria. Utilizing transcriptomics, infection studies, and a novel transgenic Plasmodium strain that exports and traffics Cre recombinase, we show that direct type I IFN signaling in Plasmodium-infected hepatocytes is necessary and sufficient to control malaria. We also show that the majority of infected hepatocytes naturally eliminate Plasmodium infection, revealing the potential existence of anti-malarial cell-autonomous immune responses in such hepatocytes. These discoveries challenge the existing paradigms in Plasmodium immunobiology and are expected to inspire new anti-malarial drugs and vaccine strategies.

immunology↗

bioRxiv2021

A universal, open-source, high-performance tool for automated sleep staging

The creation of a completely automated sleep-scoring system that is highly accurate, flexible, well validated, free and simple to use by anyone has yet to be accomplished. In part, this is due to the difficulty of use of existing algorithms, algorithms having been trained on too small samples, and paywall demotivation. Here we describe a novel algorithm trained and validated on +27,000 hours of polysomnographic sleep recordings across heterogeneous populations around the world. This tool offers high sleep-staging accuracy matching or exceeding human accuracy and interscorer agreement no matter the population kind. The software is easy to use, computationally low-demanding, open source, and free. Such software has the potential to facilitate broad adoption of automated sleep staging with the hope of becoming an industry standard.

bioinformatics↗

bioRxiv2021

Sleep Loss Impacts the Interconnected Brain-Body-Mood Regulation of Cardiovascular Function in Humans

Poor sleep is associated with hypertension, a major risk factor for cardiovascular disease1,2. However, the mechanism(s) through which sleep loss impacts blood pressure remain largely unknown, including the inter-related brain and peripheral body systems that regulate vascular function3. In a repeated-measures experimental study of 66 healthy adult participants, we demonstrate four core findings addressing this question. First, a night of sleep loss significantly increased blood pressure--both systolic and diastolic, yet this change in vascular tone was independent of any increase in heart rate. Second, sleep loss compromised functional brain connectivity within regions that regulate vascular tone. Third, sleep-loss related changes in brain connectivity and vascular tone were significantly inter-dependent, with changes in brain nodes explaining the shift towards hypertension. Fourth, sleep-loss related changes in mood, specifically reductions in positive and amplification in negative states, each demonstrated an interaction with the impairments in brain connectivity and blood pressure. Together, these findings support an embodied framework in which sleep loss confers increased risk of cardiovascular disease through interactions between brain homeostatic control, mood-state and blood pressure.

neuroscience↗

bioRxiv2019

Extensive Transcriptional and Translational Regulation Occur During the Maturation of Malaria Parasite Sporozoites

Plasmodium sporozoites are transmitted from an infected mosquito to mammals in which they infect the liver. The infectivity profile of sporozoites changes as they egress from oocysts on the mosquito midgut into the hemocoel, and then invade the salivary glands, where they maintain a poised and infectious state until transmission occurs. Upon transmission, the sporozoite must then navigate the host skin, vasculature, and liver. All of these feats require distinct repertoires of proteins and capabilities that are coordinated in an appropriate temporal manner. Here, we report the comprehensive and dynamic transcriptomes and proteomes of both oocyst sporozoite and salivary gland sporozoite stages in both rodent-infectious Plasmodium yoelii parasites and human-infectious Plasmodium falciparum parasites. These data robustly define mRNAs and proteins that are Upregulated in Oocyst Sporozoites (UOS) or Upregulated in Infectious Sporozoites (UIS), which include critical gene products for sporozoite functions, as well as many of unknown importance that are similarly regulated. Moreover, we found that Plasmodium uses two overlapping, extensive, and independent programs of translational repression across sporozoite maturation to temporally regulate specific genes necessary to successfully navigate the mosquito vector and mammalian host environments. Finally, gene-specific validation experiments of selected, translationally repressed transcripts in P. yoelii confirmed the interpretations of the global transcriptomic and proteomic datasets. Together, these data indicate that two waves of translational repression are implemented and relieved at different times in sporozoite maturation to promote its successful life cycle progression.

microbiology↗

bioRxiv2019

An Electrophysiological Marker of Arousal Level in Humans

Deep non-rapid eye movement sleep (NREM) - also called slow wave sleep (SWS) - and general anesthesia are prominent states of reduced arousal linked to the occurrence of slow oscillations in the electroencephalogram (EEG). Rapid eye movement (REM) sleep, however, is also associated with a diminished arousal level, but is characterized by a desynchronized, wake-like EEG. This observation challenges the notion of oscillations as the main physiological mediator of reduced arousal. Using intracranial and surface EEG recordings in four independent data sets, we establish the 1/f spectral slope as an electrophysiological marker that accurately delineates wakefulness from anesthesia, SWS and REM sleep. The spectral slope reflects the non-oscillatory, scale-free measure of neural activity and has been proposed to index the local balance between excitation and inhibition. Taken together, these findings reconcile the long-standing paradox of reduced arousal in both REM and NREM sleep and provide a common unifying physiological principle -- a shift in local Excitation/ Inhibition balance -- to explain states of reduced arousal such as sleep and anesthesia in humans.\n\nSignificance StatementThe clinical assessment of arousal levels in humans depends on subjective measures such as responsiveness to verbal commands. While non-rapid eye movement (NREM) sleep and general anesthesia share some electrophysiological markers, rapid eye movement sleep (REM) is characterized by a wake-like electroencephalogram. Here, we demonstrate that non-oscillatory, scale-free electrical brain activity -- recorded from both scalp electroencephalogram and intracranial recordings in humans -- reliably tracks arousal levels during both NREM and REM sleep as well as under general anesthesia with propofol. Our findings suggest that non-oscillatory brain activity can be used effectively to monitor vigilance states.

neuroscience↗

bioRxiv2018

Ribozyme-Mediated, Multiplex CRISPR Gene Editing and CRISPRi in Plasmodium yoelii

Functional characterization of genes in Plasmodium parasites often relies on genetic manipulations to disrupt or modify a gene-of-interest. However, these approaches are limited by the time required to generate transgenic parasites for P. falciparum and the availability of a single drug selectable marker for P. yoelii. In both cases, there remains a risk of disrupting native gene regulatory elements with the introduction of exogenous sequences. To address these limitations, we have developed CRISPR-RGR, a SpCas9-based gene editing system for Plasmodium that utilizes a Ribozyme-Guide-Ribozyme (RGR) sgRNA expression strategy. Using this system with P. yoelii, we demonstrate that both gene disruptions and coding sequence insertions are efficiently generated, producing marker-free and scar-free parasites with homology arms as short as 80-100bp. Moreover, we find that the common practice of using one sgRNA can produce both unintended plasmid integration and the desired locus replacement editing events, while the use of two sgRNAs results in only locus replacement editing. Lastly, we show that CRISPR-RGR can be used for CRISPR interference (CRISPRi) by binding dCas9 to targets in the gene control region of a gene-of-interest, resulting in a modest reduction in gene expression. This robust and flexible system should open the door for in-depth and efficient genetic characterizations in both rodent- and human-infectious Plasmodium species.\n\nImportancePlasmodium parasites, the causative agent of malaria, still pose an enormous threat to public health worldwide. Gaining additional insight into the biology of the parasite is essential for generating an effective vaccine and identifying novel drug targets. To this end, CRISPR/Cas9 tools have been developed to more efficiently interrogate the Plasmodium genome than is possible with conventional reverse genetics approaches. Here, we describe CRISPR-RGR as an addition to the CRISPR/Cas9 toolbox for the rodent-infectious Plasmodium parasites. By using multiple ribozyme-flanked single guide RNAs expressed from RNA polymerase II promoters, transgenic parasites can be rapidly generated as designed without leaving selectable markers. Moreover, CRISPR-RGR can be adapted for use as a CRISPR interference (CRISPRi) system to alter gene expression without genome modification. Together, CRISPR-RGR for gene editing and CRISPRi application can hasten investigations into the biology and vulnerabilities of the malaria parasite.

microbiology↗

bioRxiv2018

Plasmodium male gametocyte development and transmission are critically regulated by general and transmission-specific members of the CAF1/CCR4/NOT complex

With relatively few known specific transcription factors to control the abundance of specific mRNAs, Plasmodium parasites also regulate the stability and turnover of transcripts to provide more comprehensive gene regulation. Plasmodium transmission stages impose translational repression on specific transcripts in part to accomplish this. However, few proteins are known to participate in this process, and those that are characterized primarily affect female gametocytes. We have identified and characterized PyCCR4-1, a putative deadenylase, which plays a role in the development and activation of male gametocytes, regulates the abundance of specific mRNAs in gametocytes, and ultimately increases the efficiency of host-to-vector transmission. We find that when pyccr4-1 is deleted or its protein made catalytically inactive, there is a loss in the initial coordination of male gametocyte maturation and a reduction of parasite infectivity of the mosquito. Expression of only the N-terminal CAF1 domain of the essential CAF1 deadenylase, which prevents PyCCR4-1 association with the complex, leads to a similar phenotype. Comparative RNA-seq revealed that PyCCR4-1 affects transcripts important for transmission-related functions that are associated with male or female gametocytes, some of which directly associate with the immunoprecipitated complex. Finally, circular RT-PCR of one of the bound, dysregulated transcripts showed that PyCCR4-1 does not have gross changes in UTR or poly(A) tail length. We conclude that general and transmission-specialized members of the CAF1/CCR4/NOT complex play critical and intertwined roles in gametocyte maturation and transmission.\n\nAUTHOR SUMMARYMalaria is a disease caused by Plasmodium parasites, which are transmitted during an infectious blood meal by anopheline mosquitoes. Transmission of the sexual stages of the parasite to mosquitoes requires the proper regulation of specific mRNAs. While much work has been done to characterize regulation of mRNAs in female gametocytes, little has been done to assess this regulation in male gametocytes. Here, we demonstrate that PyCCR4-1, a member of the CAF1/CCR4/NOT RNA metabolic complex, acts upon transcripts both directly and indirectly in both male and female parasites, and results in a reduction of male gametocytemia. In gametocytes lacking PyCCR4-1, as well as those expressing a catalytically dead variant, the initial coordinated wave of male gametocyte activation is lost, and these parasites are less able to productively infect mosquitoes. We find that PyCCR4-1 requires its association with PyCAF1 and by proxy, the rest of the complex, in order to perform its functions based upon experiments in both Plasmodium yoelii and Plasmodium falciparum. We also find that the CAF1/CCR4/NOT complex is directly binding some of these transcripts and is likely acting both directly and indirectly to modulate transcript abundance. These findings demonstrate that the combined effects of the CAF1/CCR4/NOT complex upon specific mRNAs are important for both male and female gametocytes, and that this regulation is required for efficient transmission to the mosquito vector.

microbiology↗

bioRxiv2018

Gemin4 is an essential gene in mice, and its overexpression in human cells causes relocalization of the SMN complex to the nucleoplasm

Gemin4 is a member of the Survival Motor Neuron (SMN) protein complex, which is responsible for the assembly and maturation of Sm-class small nuclear ribonucleoproteins (snRNPs). In metazoa, Sm snRNPs are assembled in the cytoplasm and subsequently imported into the nucleus. We previously showed that the SMN complex is required for snRNP import in vitro, although it remains unclear which specific components direct this process. Here, we report that Gemin4 overexpression drives SMN and the other Gemin proteins from the cytoplasm into the nucleus. Moreover, it disrupts the subnuclear localization of the Cajal body marker protein, coilin, in a dose-dependent manner. We identified three putative nuclear localization signal (NLS) motifs within Gemin4, one of which is necessary and sufficient to direct nuclear import. Overexpression of Gemin4 constructs lacking this NLS sequestered Gemin3 and, to a lesser extent Gemin2, in the cytoplasm but had little effect on the nuclear accumulation of SMN. We also investigated the effects of Gemin4 depletion in the laboratory mouse, mus musculus. Gemin4 null mice die early in embryonic development, demonstrating that Gemin4 is an essential mammalian protein. When crossed onto a severe SMA mutant background, heterozygous loss of Gemin4 failed to modify the early postnatal mortality phenotype of SMA type I (Smn-/-;SMN2+/+) mice. We conclude that Gemin4 plays an essential role in mammalian snRNP biogenesis, and may facilitate import of the SMN complex (or subunits thereof) into the nucleus.

cell biology↗