Biology subjects

Khalaf, A.

Publications and source records attributed to Khalaf, A..

16 recordsLinked to original sources

bioRxiv2026

Twenty-five new microsporidian genomes: Insights into ploidy, reproduction, and the group's pangenome

Microsporidia are single-celled, obligately intracellular eukaryotic parasites of growing importance. Many aspects of their biology remain enigmatic, partly because of difficulties in sampling, culturing, and experimentally manipulating them. Here, we continue efforts to generate microsporidian genomes from serendipitously infected organisms sequenced for biodiversity genomics initiatives, such as the Darwin Tree of Life Project. We present 25 new microsporidian genomes: 14 biologically complete, including several at (near-)chromosome level, and 11 partial. Using RNA-seq data for three published genomes we identify Prokka as a suitable ab initio annotation approach for Microsporidia. Consistently annotating all available genomes, we investigate gene-content diversity across microsporidian clades. We find that the microsporidian pangenome exhibits extreme diversity, and that current genomic data substantially undersample the group's proteome space. Neither GC content nor genome span consistently explains orthogroup number across lineages, suggesting different evolutionary pressures. We find few one-to-one orthogroups in Microsporidia, as well as few orthogroups that are both lineage-specific and conserved across most species within a given lineage. Finally, Hi-C data confirm that tetraploid Amblyosporida microsporidia occur as two equivalent diploid units. In contrast, one Enterocytozoonida tetraploid genome suggests that all four genome copies occur within a single nucleus (a 'monokaryon'), confirming a previous proposal.

genomics↗

bioRxiv2026

Measuring conscious tactile perception without report: pupil, blink, and microsaccade signatures of a tactile no-report paradigm

Conscious perception is often inferred from behavioral reports, which conflate awareness-related neural signals with the motor and decision processes required to respond. No-report paradigms address this by using spontaneous physiological signals, such as eye movements, to infer perception. Although our group developed a no-report visual paradigm, we had not applied this approach to touch. We developed a no-report tactile paradigm using the Galileo stimulation system to deliver pneumatic air puffs to non-thumb fingers on both hands while tracking eye movements. Participants reported sensations from the Report hand while receiving threshold-level puffs on both hands; eye metrics were used to infer perception in the No-Report hand. Perceived threshold-level stimuli elicited greater pupil dilation and more post-stimulus blinking than identical unperceived stimuli, with effects lasting 1 - 2 seconds. Microsaccade rate decreased after stimulus onset, but this suppression did not reach statistical significance. A stacked support vector machine trained on the Report eye-tracking measures was applied to classify No-Report trials and successfully separated [Predicted] Perceived from [Predicted] Not Perceived trials (AUC = .92; cross-validated accuracy = 72%; sensitivity = 90% at 80% specificity; label-permutation p < .001). These findings show that eye tracking can detect conscious tactile perception without overt responses and offer a noninvasive, scalable approach for studying tactile perception in patients with self-reported disabilities, including comatose or intubated patients.

neuroscience↗

bioRxiv2025

Neuroanatomical Basis of Coma in Acute Ischemic Stroke

BackgroundAcute ischemic stroke (AIS) can lead to profound disturbances in consciousness, including coma, which is associated with poor prognosis and increased mortality. Clarifying the lesion patterns that precipitate loss of consciousness can refine pathophysiological models and guide prognosis. ObjectivesIn this study, we aim to identify the brain regions most commonly affected in comatose AIS and determine whether specific combinations of lesions are necessary and sufficient to produce coma. MethodsWe retrospectively analyzed 476 AIS patients (52 comatose) using diffusion-weighted imaging. Infarcts were automatically segmented, manually verified, and normalized to MNI space. Support vector regression lesion-symptom mapping (SVR-LSM) quantified voxel-wise associations with coma, controlling for lesion volume. To assess the necessity and sufficiency of lesion combinations, we employed permutation-based nested logistic regression models comparing all subsets of four anatomical predictors: brainstem, thalamus, cerebellum, and the rest of brain lesions. ResultsSVR-LSM revealed that coma was strongly associated with lesions involving the brainstem, thalamus, and cerebellum, whereas non-comatose patients exhibited predominantly cortical infarcts. Nested model comparisons showed that concurrent lesions to both the brainstem and thalamus were necessary and sufficient for coma. Additional involvement of the cerebellum or cerebral cortex did not improve predictive performance. ConclusionsComa after AIS results from a dual-node subcortical lesion pattern involving both the brainstem and thalamus. Cerebellar and cortical lesions, even when extensive, did not induce coma in the absence of the dual-brainstem and thalamic lesions. These observations emphasize the predominant role of lesion location over lesion volume in the pathogenesis of coma. They also support mechanistic models that position the brainstem and thalamic hubs as central to the neural circuitry underlying arousal. Furthermore, these findings delineate a specific anatomical substrate that may serve as a strategic target for circuit-based neuroprotective and neuromodulatory therapies.

neuroscience↗

bioRxiv2025

Low and high frequency signatures of impaired consciousness in temporal lobe seizures

Impaired consciousness is a debilitating and unpredictable outcome of mesial temporal lobe seizures whose mechanisms to date remain unclear. Moreover, questions about the relationship between impaired consciousness and lateralization, hemispheric spread and electrophysiological characteristics of seizures are yet to be answered. To address these gaps, we conducted in-depth investigation of behavioral and intracranial EEG data from 186 mesial temporal lobe seizures of 51 patients with intractable mesial temporal lobe epilepsy. We found that bilateral mesial temporal spread of seizures is not a necessary condition for impaired consciousness, although seizures with bilateral mesial temporal involvement were significantly more likely to have impaired consciousness than unilateral seizures. Contrary to prior belief, we found no relationship between the onset side (left vs. right temporal lobe or language dominant vs. non-dominant lobe) of seizures and the probability of impaired consciousness. Lastly, we established that widespread increases in slow-wave activity (delta band) in extratemporal cortical areas, as well as increases in fast activity (beta band) in the temporal lobes were both robust markers of seizures with impaired consciousness and could predict ictal impairment with up to 86% accuracy. Our findings shed new light on networks that underlie impaired consciousness in temporal lobe epilepsy and may help guide deep brain stimulation of such systems (e.g. via thalamic nuclei) as a potential intervention to improve consciousness during seizures.

neuroscience↗

bioRxiv2025

Forty New Genomes Shed Light on Sexual Reproduction and the Origin of Tetraploidy in Microsporidia

Microsporidia are single-celled, obligately intracellular parasites with growing public health, agricultural, and economic importance. Despite this, Microsporidia remain relatively enigmatic, with many aspects of their biology and evolution unexplored. Key questions include whether Microsporidia undergo sexual reproduction, and the nature of the relationship between tetraploid and diploid lineages. While few high-quality microsporidian genomes currently exist to help answer such questions, large-scale biodiversity genomics initiatives, such as the Darwin Tree of Life project, can generate high-quality genome assemblies for microsporidian parasites when sequencing infected host species. Here, we present 40 new microsporidian genome assemblies from infected arthropod hosts that were sequenced to create reference genomes. Out of the 40, 32 are complete genomes, eight of which are chromosome-level, and eight are partial microsporidian genomes. We characterised 14 of these as polyploid and five as diploid. We found that tetraploid genome haplotypes are consistent with autopolyploidy, in that they coalesce more recently than species, and that they likely recombine. Within some genomes, we found large-scale rearrangements between the homeologous genomes. We also observed a high rate of rearrangement between genomes from different microsporidian groups, and a striking tolerance for segmental duplications. Analysis of chromatin conformation capture (Hi-C) data indicated that tetraploid genomes are likely organised into two diploid compartments, similar to dikaryotic cells in fungi, with evidence of recombination within and between compartments. Together, our results provide evidence for the existence of a sexual cycle in Microsporidia, and suggest a model for the microsporidian lifecycle that mirrors fungal reproduction.

genomics↗

bioRxiv2024

Effects of organic and inorganic contaminants and their mixtures on metabolic health and gene expression in developmentally exposed zebrafish

Organic and inorganic chemicals co-occur in household dust, and these chemicals have been determined to have endocrine and metabolic disrupting effects. While there is increasing study of chemical mixtures, the effects of complex mixtures mimicking household dust and other environmental matrices have not been well studied and their potential metabolism disrupting effects are thus poorly understood. Previous research has demonstrated high potency adipogenic effects of residential household dust extracts using in vitro adipogenesis assays. More recent research simplified this to a mixture relevant to household dust and comprised of common co-occurring organic and inorganic contaminants, finding that these complex combinations often exhibited additive or even synergistic effects in cell models. This study aimed to translate our previous in vitro observation to an in vivo model, the developing zebrafish, to evaluate the metabolic effects of early exposure to organic and inorganic chemicals, individually and in mixtures. Zebrafish embryos were exposed from 1 day post fertilization (dpf) to 6 dpf, then metabolic energy expenditure, swimming behavior and gene expression were measured. Globally, we observed that most mixtures did not reflect the effects of individual chemicals; the BFR mixture produced a less potent effect when compared to the individual chemicals, while the PFAS and the inorganic mixtures seemed to have a more potent effect than the individual chemicals. Finally, the environmental mixture, mimicking household dust proportions, was less potent than the inorganic chemical mix alone. Additional work is necessary to better understand the mixture effect of inorganic and organic chemicals combined.

pharmacology and toxicology↗

bioRxiv2024

Filter bank common spatial pattern and envelope-based features in multimodal EEG-fTCD brain-computer interfaces

Brain-computer interfaces (BCIs) exploit brain activity to bypass neuromuscular control with the aim of providing alternative means of communication with the surrounding environment. Such systems can significantly improve the quality of life for patients suffering from severe motor or speech impairment. Multimodal BCIs have been introduced recently to enhance the performance of BCIs utilizing single modality. In this paper, we aim to improve the performance of multimodal BCIs combining Electroencephalography (EEG) and functional transcranial Doppler ultrasound (fTCD). The BCIs included in the study utilized two different paradigms to infer user intent including motor imagery (MI) and flickering mental rotation (MR)/word generation (WG) paradigms. Filter Bank Common Spatial Pattern (FBCSP) algorithm was used to extract features from the EEG data. Several time series features were extracted from the envelope of the fTCD signals. Wilcoxon rank sum test and linear kernel Support vector machines (SVM) were used for feature selection and classification respectively. Additionally, a probabilistic Bayesian fusion approach was used to fuse the information from EEG and fTCD modalities. Average accuracies of 94.53%, 94.9% and 96.29% were achieved for right arm MI versus baseline, left arm MI versus baseline, and right arm MI versus left arm MI respectively. Whereas average accuracies of 95.27%, 85.93% and 96.97% were achieved for MR versus baseline, WG versus baseline, and MR versus WG respectively. Our results show that EEG- fTCD BCIs with the proposed analysis techniques outperformed the multimodal EEG-fNRIS BCIs in comparison.

bioengineering↗

bioRxiv2024

Shared subcortical arousal systems across sensory modalities during transient modulation of attention

Subcortical arousal systems are known to play a key role in controlling sustained changes in attention and conscious awareness. Recent studies indicate that these systems have a major influence on short-term dynamic modulation of visual attention, but their role across sensory modalities is not fully understood. In this study, we investigated shared subcortical arousal systems across sensory modalities during transient changes in attention using block and event-related fMRI paradigms. We analyzed massive publicly available fMRI datasets collected while 1,561 participants performed visual, auditory, tactile, and taste perception tasks. Our analyses revealed a shared circuit of subcortical arousal systems exhibiting early transient increases in activity in midbrain reticular formation and central thalamus across perceptual modalities, as well as less consistent increases in pons, hypothalamus, basal forebrain, and basal ganglia. Identifying these networks is critical for understanding mechanisms of normal attention and consciousness and may help facilitate subcortical targeting for therapeutic neuromodulation.

neuroscience↗

bioRxiv2024

Neural mechanisms of awareness of action

The origins of awareness of action (AoA), the ability to report an action just performed, remain elusive. Differing theories ascribe AoA to pre-action, efferent motor/volitional mechanisms versus post-action, afferent sensory/perceptual neural mechanisms. To study these two types of mechanisms and others, we developed a paradigm where very similar aware and unaware actions occur repeatedly. Aware actions demonstrated larger neurophysiological signals both preceding and following movement. The differences included well-known volitional and perceptual event related potentials (PMP, N140, P300), as well as frontal midline theta, event-related alpha/beta desynchronization, and post-move blink rates. On longer time scales, we identified a novel event related potential preceding unaware moves, and found behavioral and pupillometric evidence for decreased attention and arousal over minutes concurrent with AoA loss. Our findings suggest that both dynamic, individual action-associated volitional and perceptual neural activity, as well as long-term attention and arousal states play a role in maintaining AoA.

neuroscience↗

bioRxiv2024

The Neural Basis of Attentional Blink as a Selective Control Mechanism in Conscious Perception

Conscious perception of visual stimuli involves large-scale brain networks with multiple activation-deactivation dynamics. Previous works have shown that early detection networks may be switched off about 200ms to 300ms after presentation of a visual stimulus. We hypothesize that these deactivations represent a selective control mechanism of the brain to conserve resources for post-perceptual processing. To this end, we used attentional blink as a behavioral measure for this mechanism. We showed that attentional blink is more likely to occur when a previous visual stimulus was consciously perceived. Using high-resolution eye-tracking, we found prolonged decrease in pupil diameter and transient decrease in blink probability associated with attentional blink. Using scalp EEG data, we further showed that attentional blink is associated with more pronounced event-related potentials related to visual processing and report. One sentence summaryattentional blink may represent a selective control mechanism of neural processing resources underlying conscious perception.

neuroscience↗

bioRxiv2023

Polyploidy is widespread in Microsporidia

Microsporidia are obligate intracellular eukaryotic parasites with an extremely broad host range. They have both economic and public health importance. Ploidy in microsporidia is variable, with a few species formally identified as diploid and one as polyploid. Given the increase in the number of studies sequencing microsporidian genomes, it is now possible to assess ploidy levels across all currently-explored microsporidian diversity. We estimate ploidy for all microsporidian datasets available on the Sequence Read Archive (SRA) using k-mer-based analyses, and demonstrate that polyploidy is widespread in Microsporidia, and that ploidy change is dynamic in the group. Using genome-wide heterozygosity estimates, we also show that polyploid microsporidian genomes are relatively homozygous, and we discuss the implications of these findings on the timing of polyploidisation events and their origin. Author SummaryMicrosporidia are single-celled intracellular parasites, distantly related to fungi, that can infect a broad range of hosts, from humans all the way to protozoans. Exploiting the wealth of microsporidian genomic data available, we use k-mer based analyses to assess ploidy status across the group. Understanding a genomes ploidy is crucial in order to assemble it effectively, and may also be relevant for better understanding a parasites behaviour and life cycle. We show that tetraploidy is present in at least six species in Microsporidia, and that these polyploidisation events are likely to have occurred independently. We discuss why these findings may be paradoxical, given that Microsporidia, like other intracellular parasites, have extremely small, reduced genomes.

evolutionary biology↗

bioRxiv2023

An adversarial collaboration to critically evaluate theories of consciousness

Different theories explain how subjective experience arises from brain activity1,2. These theories have independently accrued evidence, yet, confirmation bias and dependence on design choices hamper progress in the field3. Here, we present an open science adversarial collaboration which directly juxtaposes Integrated Information Theory (IIT)4,5 and Global Neuronal Workspace Theory (GNWT)6-10, employing a theory-neutral consortium approach11,12. We investigate neural correlates of the content and duration of visual experience. The theory proponents and the consortium developed and preregistered the experimental design, divergent predictions, expected outcomes, and their interpretation12. 256 human subjects viewed suprathreshold stimuli for variable durations while neural activity was measured with functional magnetic resonance imaging, magnetoencephalography, and electrocorticography. We find information about conscious content in visual, ventro-temporal and inferior frontal cortex, with sustained responses in occipital and lateral temporal cortex reflecting stimulus duration, and content-specific synchronization between frontal and early visual areas. These results confirm some predictions of IIT and GNWT, while substantially challenging both theories: for IIT, a lack of sustained synchronization within posterior cortex contradicts the claim that network connectivity specifies consciousness. GNWT is challenged by the general lack of ignition at stimulus offset and limited representation of certain conscious dimensions in prefrontal cortex. Beyond challenging the theories themselves, we present an alternative approach to advance cognitive neuroscience through a principled, theory-driven, collaborative effort. We highlight the challenges to change peoples mind 13 and the need for a quantitative framework integrating evidence for systematic theory testing and building.

neuroscience↗

bioRxiv2023

The neural activity of auditory conscious perception

Although recent work has made significant headway in understanding the temporal and spatial dynamics of the neural mechanisms of conscious perception, much of that work has focused on visual paradigms. To determine whether there are shared mechanisms for perceptual consciousness across sensory modalities, here we developed a task to test within the auditory domain. Participants (n=31) completed an auditory perceptual threshold task while undergoing intracranial electroencephalography (icEEG) for intractable epilepsy. Intracranial recordings from over 2,800 grey matter electrodes representing widespread cortical coverage were analyzed for power in the high gamma range (40-115 Hz)--a frequency range that reflects local neural activity. For trials that were perceived, we find activity in early auditory regions which is accompanied by activity in the right caudal middle frontal gyrus, and shortly thereafter by activity in non-auditory thalamus. This is followed by a wave of activity that sweeps through the higher auditory association regions and into parietal and frontal cortices, similar to the wave observed in our visual conscious perception paradigm. However, for not perceived trials, we find that significant activity is restricted to early auditory regions (and areas immediately adjacent to the Sylvian fissure). These findings show that the broad anatomical regions of cortical and subcortical networks involved in auditory perception are similar to the networks observed with vision, suggesting shared general mechanisms for conscious perception.

neuroscience↗

bioRxiv2021

Early neural activity changes associated with visual conscious perception

The neural mechanisms of visual conscious perception have been investigated for decades. However, the spatiotemporal dynamics associated with the earliest neural responses following consciously perceived stimuli are still poorly understood. Using a dataset of intracranial EEG recordings, the current study aims to investigate the neural activity changes associated with the earliest stages of visual conscious perception. Subjects (N=10, 1,693 grey matter electrode contacts) completed a continuous performance task in which individual letters were presented in series and subjects were asked to press a button when they saw a target letter. Broadband gamma power (40-115Hz) dynamics were analyzed in comparison to baseline prior to stimulus and contrasted for target trials with button presses and non-target trials without button presses. Regardless of event type, we observed early gamma power changes within 30-150 ms from stimulus onset in a network including increases in bilateral occipital, fusiform, frontal (including frontal eye fields), and medial temporal cortex, increases in left lateral parietal-temporal cortex, and decreases in the right anterior medial occipital cortex. No significant differences were observed between target and non-target stimuli until >150 ms post-stimulus, when we saw greater gamma power increases in left motor and premotor areas, suggesting a possible role of these later signals in perceptual decision making and/or motor responses with the right hand. The early gamma power findings suggest a broadly distributed cortical visual detection network that is engaged at early times tens of milliseconds after signal transduction from the retina.

neuroscience↗

bioRxiv2021

Brain networks in human conscious visual perception

Consciousness is not explained by a single mechanism, rather it involves multiple specialized neural systems overlapping in space and time. We hypothesize that synergistic, large-scale subcortical and cortical attention and signal processing networks encode conscious experiences. To identify brain activity in conscious perception without overt report, we classified visual stimuli as perceived or not using eye measurements. Report-independent event-related potentials and functional magnetic resonance imaging (fMRI) signals both occurred at early times after stimuli. Direct recordings revealed a novel thalamic awareness potential linked to conscious visual perception based on report. fMRI showed thalamic and cortical detection, arousal, attentional salience, task-positive, and default mode networks were involved independent of overt report. These findings identify a specific sequence of neural mechanisms in human conscious visual perception. One-Sentence SummaryHuman conscious visual perception engages large-scale subcortical and cortical networks even without overt report.

neuroscience↗

bioRxiv2021

Decreased overall neuronal activity in a rodent model of impaired consciousness during absence seizures

Absence seizures are characterized by a brief behavioural impairment including apparent loss of consciousness. Neuronal mechanisms determining the behavioural impairment of absence seizures remain unknown, and their elucidation might highlight therapeutic options for reducing seizure severity. However, recent studies have questioned the similarity of animal spike-wave-discharges (SWD) to human absence seizures both behaviourally and neuronally. Here, we report that Genetic Absence Epilepsy Rats from Strasbourg recapitulate the decreased neuroimaging signals and loss of consciousness characteristic of human absence seizures. Overall neuronal firing is decreased but rhythmic in the somatosensory cortex and thalamus during these seizures. Interestingly, individual neurons in both regions tend to consistently express one of four distinct patterns of seizure-associated activity. These patterns differ in firing rate dynamics and in rhythmicity during seizure. One group of neurons showed a transient initial peak in firing at SWD onset, accounting for the brief initial increase in overall neuronal firing seen in cortex and thalamus. The largest group of neurons in both cortex and thalamus showed sustained decreases in firing during SWD. Other neurons showed either sustained increases or no change in firing. These findings suggest that certain classes of cortical and thalamic neurons may be particularly responsible for the paroxysmal oscillations and consequent loss of consciousness in absence epilepsy.

neuroscience↗