Biology subjects

Jacobs, J.

Publications and source records attributed to Jacobs, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

The Temporal Dynamics of Aperiodic Neural Activity Track Changes in Sleep Architecture

The aperiodic (1/f-like) component of electrophysiological data - whereby power systematically decreases with increasing frequency, as quantified by the aperiodic exponent - has been shown to differentiate sleep stages. Earlier work, however, has typically focused on measuring the aperiodic exponent across a narrow frequency range. In this work, we sought to further investigate aperiodic activity during sleep by extending these analyses across broader frequency ranges and considering alternate model definitions. This included measuring knees in the aperiodic component, which reflect bends in the power spectrum, indicating a change in the exponent. We also sought to evaluate the temporal dynamics of aperiodic activity during sleep. To do so, we analyzed data from two sources: intracranial EEG (iEEG) from 106 epilepsy patients and high-density EEG from 17 healthy individuals, and measured aperiodic activity, explicitly comparing different frequency ranges and model forms. In doing so, we find that fitting broadband aperiodic models and incorporating a knee feature effectively captures sleep-stage-dependent differences in aperiodic activity as well as temporal dynamics that relate to sleep stage transitions and responses to external stimuli. In particular, the knee parameter shows stage-specific variation, suggesting an interpretation of varying timescales across sleep stages. These results demonstrate that examining broader frequency ranges with the more complex aperiodic models reveals novel insights and interpretations for understanding aperiodic neural activity during sleep.

neuroscience↗

bioRxiv2023

Single neurons in the human medial temporal lobe flexibly shift representations across spatial and memory tasks

Investigations into how individual neurons encode behavioral variables of interest have revealed specific representations in single neurons, such as place and object cells, as well as a wide range of cells with conjunctive encodings or mixed selectivity. However, as most experiments examine neural activity within individual tasks, it is currently unclear if and how neural representations change across different task contexts. Within this discussion, the medial temporal lobe is particularly salient, as it is known to be important for multiple behaviors including spatial navigation and memory, however the relationship between these functions is currently unclear. Here, to investigate how representations in single neurons vary across different task contexts in the MTL, we collected and analyzed single-neuron activity from human participants as they completed a paired-task session consisting of a passive-viewing visual working memory and a spatial navigation and memory task. Five patients contributed 22 paired-task sessions, which were spike sorted together to allow for the same putative single neurons to be compared between the different tasks. Within each task, we replicated concept-related activations in the working memory task, as well as target-location and serial-position responsive cells in the navigation task. When comparing neuronal activity between tasks, we first established that a significant number of neurons maintained the same kind of representation, responding to stimuli presentations across tasks. Further, we found cells that changed the nature of their representation across tasks, including a significant number of cells that were stimulus responsive in the working memory task that responded to serial position in the spatial task. Overall, our results support a flexible encoding of multiple, distinct aspects of different tasks by single neurons in the human MTL, whereby some individual neurons change the nature of their feature coding between task contexts.

neuroscience↗

bioRxiv2022

Widespread regulatory specificities between transcriptional corepressors and enhancers in Drosophila

Animal development and homeostasis critically depend on the accurate regulation of gene transcription, which includes the silencing of genes that should not be expressed. Repression is mediated by a specific class of transcription factors (TFs) termed repressors that, via the recruitment of co-repressors (CoRs), can dominantly prevent transcription, even in the presence of activating cues. However, the relationship between specific CoRs and enhancers has remained unclear. Here, we used functional genomics to uncover regulatory specificities between CoRs and enhancers. We show that enhancers can typically be repressed by only a subset of CoRs. Enhancers classified by CoR sensitivity also show distinct biological functions and endogenous chromatin features. Moreover, enhancers that are sensitive or resistant to silencing by specific CoRs differ in TF motif content, and their sensitivity to CoRs can be predicted based on TF motif content. Finally, we identified and validated specific TF motifs that have a direct impact on enhancers sensitivity or resistance towards specific CoRs, using large scale motif mutagenesis and addition experiments. This study reveals the existence of TF motif-based regulatory rules that coordinate CoRs-enhancer compatibilities. These specificities between repressors and activators not only suggest that repression occurs via distinct mechanisms, but also provide an additional layer in transcriptional regulation that allows for differential repression at close genomic distances and offers multiple ways for de-repression.

molecular biology↗

bioRxiv2022

Ripple-locked coactivity of stimulus-specific neurons supports human associative memory

Associative memory is the ability to encode and retrieve relations between different stimuli. To better understand its neural basis, we investigated whether associative memory involves precisely timed spiking of neurons in the medial temporal lobes that exhibit stimulus-specific tuning. Using single-neuron recordings from epilepsy patients performing an associative object-location memory task, we identified the object- and place-specific neurons that encoded the separate elements of each memory. When patients encoded and retrieved particular memories, the relevant object- and place-specific neurons activated synchronously during hippocampal ripples. This ripple-locked coactivity of stimulus-specific neurons emerged over time as the patients associative learning progressed. Our results suggest a cellular account of associative memory, in which hippocampal ripples coordinate the activity of specialized cellular populations to facilitate links between stimuli.

neuroscience↗

bioRxiv2022

Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat

Two homoeologous QTLs for number of spikelets per spike (SPS) were mapped on chromosomes 7AL and 7BL using two wheat MAGIC populations. Sets of lines contrasting for the QTL on 7AL were developed which allowed for the validation and fine mapping of the 7AL QTL and for the identification of a previously described candidate gene, WHEAT ORTHOLOG OF APO1 (WAPO1). Using transgenic overexpression in both a low and a high SPS line, we provide a functional validation for the role of this gene in determining SPS also in hexaploid wheat. We show that the expression levels of this gene positively correlate with SPS in multiple MAGIC founder lines under field conditions as well as in transgenic lines grown in the greenhouse. This work highlights the potential use of WAPO1 in hexaploid wheat for further yield increases. The impact of WAPO1 and SPS on yield depends on other genetic and environmental factors, hence, will require a finely balanced expression level to avoid the development of detrimental pleiotropic phenotypes.

plant biology↗

bioRxiv2022

The direction and timing of theta and alpha traveling waves modulate human memory processing

To support a range of behaviors, the brain must flexibly coordinate neural activity across widespread brain regions. One potential mechanism for this coordination is a traveling wave, in which a neural oscillation propagates across the brain while organizing the order and timing of activity across regions1,2. Although traveling waves are present across the brain in various species3-5, their potential functional relevance remained unknown. Here, using rare direct human brain recordings, we demonstrate two novel functional roles for traveling waves of theta- and alpha-band (2-13 Hz) oscillations in the cortex. First, traveling waves propagate in different directions during separate cognitive processes. In episodic memory, traveling waves tended to propagate in posterior-to-anterior and anterior-to-posterior directions, respectively, during encoding and retrieval. Second, traveling waves are informative about the timing of behavior, with the phase of ongoing traveling waves indicating when subjects would retrieve memories. Because traveling waves of oscillations correspond to local neuronal spiking, these patterns indicate that rhythmic pulses of activity move across the brain with different directions and timing for separate behaviors. More broadly, our results suggest a fundamental role for traveling waves and oscillations in dynamically coordinating neural connectivity, by flexibly organizing the timing and directionality of network interactions across the cortex to support cognition and behavior.

neuroscience↗

bioRxiv2022

Traveling waves in the monkey frontoparietal network predict recent reward memory

Brain function depends on neural communication, but the mechanisms of this communication are not well understood. Recent studies suggest that one form of neural communication is through traveling waves (TWs)--patterns of neural oscillations that propagate within and between areas. We show that TWs appear robustly in microarray recordings in monkey frontal and parietal cortex and encode memory for recent rewards. While making saccades to obtain probabilistic rewards, monkeys were sensitive to the (statistically irrelevant) prior reward, which is consistent with behavioral biases produced by reward history. TWs in frontal and parietal areas were stronger in trials following a prior reward versus a lack of reward and, in the frontal lobe, correlated with the monkeys sensitivity to the prior reward. The findings suggest that neural communication across fronto-parietal areas, reflected by TWs, maintains default reward memories, while communication within the frontal lobe mediates the read out of the memories for prospective expectations.

neuroscience↗

bioRxiv2021

Spontaneous Neuronal Oscillations in the Human Insula are Hierarchically Organized Traveling Waves

The insula plays a fundamental role in a wide range of adaptive human behaviors, but its electrophysiological dynamics are poorly understood. Here we used human intracranial electroencephalographic recordings to investigate the electrophysiological properties and hierarchical organization of spontaneous neuronal oscillations within the insula. We analyzed the neuronal oscillations of the insula directly and found that rhythms in the theta and beta frequency oscillations are widespread and spontaneously present. These oscillations are largely organized along the anterior-posterior axis of the insula. Both the left and right insula showed anterior-to-posterior decreasing gradients for the power of oscillations in the beta frequency band. The left insula also showed a posterior-to-anterior decreasing frequency gradient and an anterior-to-posterior decreasing power gradient in the theta frequency band. In addition to measuring the power of these oscillations, we also examined the phase of these signals across simultaneous recording channels and found that the insula oscillations in the theta and beta bands are traveling waves. The strength of the traveling waves in each frequency was positively correlated with the amplitude of each oscillation. However, the theta and beta traveling waves were uncoupled to each other in terms of phase and amplitude, which suggested that insula traveling waves in the theta and beta bands operate independently. Our findings provide new insights into the spatiotemporal dynamics and hierarchical organization of neuronal oscillations within the insula, which, given its rich connectivity with widespread cortical regions, indicates that oscillations and traveling waves have an important role in intra- and inter-insula communication.

neuroscience↗

bioRxiv2021

Neuronal activity in the human amygdala and hippocampus enhances emotional memory encoding

Emotional events comprise our strongest and most valuable memories, yet it is unknown how the brain prioritizes emotional information for storage. Here, we examined the neural basis of this prioritization using direct brain recording, deep brain stimulation, and psychometric assessment, with human subjects performing an episodic memory task in which they showed improved performance for emotional stimuli. During the task, high-frequency activity (HFA), a correlate of neuronal spiking activity, increased in both the hippocampus and amygdala when subjects successfully encoded emotionally arousing stimuli. Applying inhibitory electrical stimulation to these regions decreased HFA and specifically reversed the enhancement of memory for emotional stimuli, indicating that neuronal activity in the amygdalohippocampal circuit has a direct role in prioritizing emotional memories. Finally, we found abnormal patterns of amygdalohippocampal HFA in depressed individuals which correlated with a bias for negative memories in these subjects. Going forward, targeted modulation that upregulates neuronal excitation in the amygdalohippocampal circuit may have a causal and translational role in modulating emotional memory.

neuroscience↗

bioRxiv2021

Flexibility of Functional Neuronal Assemblies Supports Human Memory

Summary ParagraphEpisodic memories, or consciously accessible memories of unique events, represent a key aspect of human cognition. Evidence from rodent models suggests that the neural representation of these complex memories requires cooperative firing of groups of neurons on short time scales1, organized by gamma oscillations2, 3. These co-firing groups, termed "neuronal assemblies,"4 represent a fundamental neurophysiological unit supporting memory. Using microelectrode data from neurosurgical patients5, we identify neuronal assemblies in the human MTL and show that they exhibit consistent organization in their firing pattern based on gamma phase information. We connect these properties to memory performance across recording sessions. Finally, we describe how human neuronal assemblies flexibly adjust6-9 over longer time scales. Our findings provide key evidence linking assemblies to human episodic memory for the first time.

neuroscience↗

bioRxiv2021

Leakiness at the human-animal interface in Southeast Asia and implications for the spread of antibiotic resistance

International efforts to curb antimicrobial resistance have focused on drug development and limiting unnecessary use. However, in areas where water, sanitation, and hygiene infrastructure is lacking, and where biosecurity in food-animal production is poor, pathogen-flow between humans and animals could exacerbate the emergence and spread of resistant pathogens. Here, we compared mobile resistance elements among Escherichia coli recovered from humans and meat in Cambodia, a country with substantial connectivity between humans and animals, unregulated antibiotic use, and poor environmental controls. We identified multiple resistance-encoding plasmids and a novel, blaCTX-M and qnrS1-encoding transposon that were widely dispersed in both humans and animals, a phenomenon rarely observed in high-income settings. Our findings indicate that plugging leaks at human-animal interfaces should be a critical part of addressing antimicrobial resistance in low and middle-income countries.

ecology↗

bioRxiv2020

Phase precession in the human hippocampus and entorhinal cortex

Knowing where we are, where we have been, and where we are going is critical to many behaviors, including navigation and memory. One potential neuronal mechanism underlying this ability is phase precession, in which spatially tuned neurons represent sequences of positions by activating at progressively earlier phases of local network theta (~5-10 Hz) oscillations. Phase precession may be a general neural pattern for representing sequential events for learning and memory. However, phase precession has never been observed in humans. By recording human single-neuron activity during spatial navigation, we show that spatially tuned neurons in the human hippocampus and entorhinal cortex exhibit phase precession. Furthermore, beyond the neural representation of locations, we show evidence for phase precession related to specific goal-states. Our findings thus extend theta phase precession to humans and suggest that this phenomenon has a broad functional role for the neural representation of both spatial and non-spatial information.

neuroscience↗

bioRxiv2020

Pan-resistant Candida auris: New York Sub-cluster Susceptible to Antifungal Combinations

Four pan-resistant Candia auris strains from New York outbreak were 100% inhibited in vitro by combinations of two antifungal drugs using fixed concentrations achievable in vivo. Pan-resistant C. auris strains have mutations in eleven gene targets associated with major antifungal drugs, and constituted a distinct sub-cluster among NY strains.

microbiology↗

bioRxiv2020

Correlates of auditory decision making in prefrontal, auditory, and basal lateral amygdala cortical areas

Auditory selective listening and decision making underlies important processes, including attending to a single speaker in a crowded room, often referred to as the cocktail party problem. To examine the neural mechanisms underlying these behaviors, we developed a novel auditory selective listening paradigm for monkeys. In this task, monkeys had to detect a difficult to discriminate target embedded in noise when presented in a pre-cued location (either left or right) and ignore it if it was in the opposite location. While the animals carried out the task we recorded neural activity in primary auditory cortex (AC), dorsal lateral prefrontal cortex (dlPFC) and the basal lateral amygdala (BLA), given that these areas have been implicated in auditory decision making, selective listing, and/or reward-guided decision making. There were two main findings in the neural data. First, primary AC encoded the side of the cue and target, and the monkeys choice, before either dlPFC or the amygdala. The BLA encoded cue and target variables negligibly, but was engaged at the time of the monkeys choice. Second, decoding analyses suggested that errors followed primarily from a failure to encode the target stimulus in both AC and PFC, but earlier in AC. Thus, AC neural activity is poised to represent the sensory volley and decision making during selective listening before dlPFC, and they both precede activity in BLA.

neuroscience↗

bioRxiv2020

A neural code of egocentric spatial information in human medial temporal lobe

Spatial navigation relies on neural systems that encode information about places, distances, and directions in relation to the external world or relative to the navigating organism. Since the proposal of cognitive maps, the neuroscience of navigation has focused on allocentric (world-referenced) neural representations including place, grid, and head-direction cells. Here, using single-neuron recordings during virtual navigation, we identify "anchor cells" in the human brain as a neural code for egocentric (self-centered) spatial maps: Anchor cells represent egocentric directions towards "anchor points" located in the environmental center or periphery. Anchor cells were abundant in parahippocampal cortex, supported full vectorial representations of egocentric space, and were integrated into a neural memory network. Neurons encoding allocentric direction complemented anchor-cell activity, potentially assisting anchor cells in transforming percepts into allocentric representations. Anchor cells may facilitate egocentric navigation strategies, may support route planning from egocentric viewpoints, and may underlie the first-person perspective in episodic memories.

neuroscience↗

bioRxiv2020

Time cells in the human hippocampus and entorhinal cortex support episodic memory

The organization of temporal information is critical for the encoding and retrieval of episodic memories. In the rodent hippocampus and entorhinal cortex, recent evidence suggests that temporal information is encoded by a population of "time cells." We identify time cells in humans using intracranial microelectrode recordings obtained from 27 human epilepsy patients who performed an episodic memory task. We show that time cell activity predicts the temporal organization of episodic memories. A significant portion of these cells exhibits phase precession, a key phenomenon not previously seen in human recordings. These findings establish a cellular mechanism for the representation of temporal information in the human brain needed to form episodic memories.

neuroscience↗

bioRxiv2020

Radiation Induced Metabolic Alterations Associate with Tumor Aggressiveness and Poor Outcome in Glioblastoma

Glioblastoma (GBM) is uniformly fatal with a one year median survival rate, despite the best available treatment, including radiotherapy (RT). Impacts of prior RT on tumor recurrence are poorly understood but may increase tumor aggressiveness. Metabolic changes have been investigated in radiation-induced brain injury; however, the tumor-promoting effect following prior radiation is lacking. Since RT is vital to GBM management, we quantified the tumor-promoting effects of prior radiotherapy (RT) on patient-derived intracranial GBM xenografts and characterized the metabolic alterations associated with the protumorigenic microenvironment. Human xenografts (GBM143) were implanted into nude mice 24h following 20Gy cranial radiation vs. sham animals. Tumors in pre-radiated mice were more proliferative and more infiltrative, yielding faster mortality (p<0.0001). Histologic evaluation of tumor associated macrophage/microglia (TAMs) revealed cells with a more fully activated ameboid morphology in pre-radiated animals. Microdialyzates from the radiated brain at the margin of tumor infiltration contralateral to the site of implantation were analyzed by unsupervised liquid chromatography-mass spectrometry (LC-MS). In pre-radiated animals, metabolites known to be associated with tumor progression (like, modified nucleotides and polyols) were identified. Whole-tissue metabolomic analysis of the pre-radiated brain microenvironment for metabolic alterations in a separate cohort of nude mice using 1H-NMR revealed significant decrease in levels of antioxidants (glutathione (GSH) and ascorbate (ASC)), NAD+, TCA intermediates, and increased ATP and GTP. Glutathione and ASC showed highest VIPpred (1.65) in OPLS-DA analysis. Involvement of ASC catabolism was further confirmed by GC-MS. To assess longevity of radiation effects, we compared survival with implantation occuring 2 months vs. 24h following radiation, finding worse survival in animals implanted at 2 months. These radiation-induced alterations are consistent with a chronic disease-like microenvironment characterized by reduced levels of antioxidants and NAD+, as well as elevated extracellular ATP and GTP serving as chemoattractants, promoting cell motility and vesicular secretion with decreased levels of GSH and ASC exacerbating oxidative stress. Taken together, these data suggest that IR induces tumor-permissive changes in the microenvironment with metabolomic alterations that may facilitate tumor aggressiveness with important implications for recurrent glioblastoma. Harnessing these metabolomic insights may provide opportunities to attenuate RT-associated aggressiveness of recurrent GBM.

cancer biology↗

bioRxiv2019

Studying Spatial Memory in Augmented and Virtual reality

Spatial memory is a crucial part of our lives. Spatial memory research and rehabilitation in humans is typically performed either in real environments, which is challenging practically, or in Virtual Reality (VR), which has limited realism. Here we explored the use of Augmented Reality (AR) for studying spatial cognition. AR combines the best features of real and VR paradigms by allowing subjects to learn spatial information in a flexible fashion while walking through a real-world environment. To compare these methods, we had subjects perform the same spatial memory task in VR and AR settings. Although subjects showed good performance in both, subjects reported that the AR task version was significantly easier, more immersive, and more fun than VR. Importantly, memory performance was significantly better in AR compared to VR. Our findings validate that integrating AR can lead to improved techniques for spatial memory research and suggest their potential for rehabilitation.\n\nHighlightsO_LIWe built matching spatial memory tasks in VR and AR\nC_LIO_LISubjectively, subjects find the AR easier, more immersive and more fun\nC_LIO_LIObjectively, subjects are significantly more accurate in AR compared to VR\nC_LIO_LIPointing based tasks did not fully show the same advantages\nC_LIO_LIOnly AR walking significantly correlated with SBSoD, suggesting mobile AR better captures more natural spatial performance\nC_LI

neuroscience↗