Biology subjects

Wagemans, J.

Publications and source records attributed to Wagemans, J..

10 recordsLinked to original sources

bioRxiv2026

Oscillatory traveling waves during visual entrainment in autistic and neurotypical adults

Neural oscillations play a crucial role in cognition, and several studies emphasize the importance of considering them as traveling waves that propagate through brain regions. In scalp EEG, waves typically travel along the anterior-posterior axis: forward waves (occipital-to-frontal) predominate during sensory stimulation, while backward waves (frontal-to-occipital) emerge during rest and top-down modulation. Within the predictive coding framework, backward waves are proposed to convey predictive signals, whereas forward waves reflect sensory processes and feedforward propagation of prediction errors. In this study, we investigated traveling wave dynamics during a visual entrainment task in neurotypical (N=25) and autistic (Autism Spectrum Disorder - ASD) adults (N=24). Our results replicated previous findings in neurotypical participants, as we observed an increase in backward waves during rhythmic visual stimulation, consistent with enhanced top-down predictions. Notably, we observed the opposite pattern in the ASD group, characterized by a pronounced increase in forward waves at the entrained frequency during visual stimulation. These results align with predictive coding accounts of autistic perception, which hypothesize an imbalance between predictions and sensory evidence. Specifically, an increase in forward wave may reflect a bias toward bottom-up sensory signaling over predictive feedback, due to atypical hierarchical communication across brain regions in ASD. Together, our findings shed new light on the oscillatory dynamics involved in visual entrainment in neurotypical adults and provide novel evidence in favor of predictive coding accounts of autistic perception, as well as a consequent bias toward bottom-up sensory signaling over predictive feedback in a context of visual entrainment. Significance statementTraveling waves reflect the spatiotemporal propagation of neural oscillations, providing a window into hierarchical brain communication. By examining traveling wave dynamics during visual entrainment, we show that neurotypical adults exhibit increased backward (frontal-to-occipital) waves, consistent with enhanced top-down predictive signaling. In contrast, adults with Autism Spectrum Disorder (ASD) display a marked increase in forward (occipital-to-frontal) waves, indicating stronger bottom-up sensory drive. These findings provide electrophysiological evidence for atypical predictive processing in ASD, supporting predictive coding theories that propose an imbalance between sensory evidence and prior expectations. Our results highlight traveling waves as a sensitive neural marker of hierarchical signaling and predictive dynamics across typical and atypical perceptual systems.

neuroscience↗

bioRxiv2026

Genomic epidemiology of Ukraine conflict-associated Klebsiella pneumoniae reveals the emergence of a high-risk clone with a hybrid virulence-resistance plasmid vulnerable to lytic phages

As antimicrobial resistance continues to rise and the development of new antimicrobials lags, we face an urgent threat where routine infections could become life-threatening. Armed conflicts, like Russias war on Ukraine, intensify this crisis by accelerating the emergence and spread of resistant organisms across regions and borders. Phage Support Ukraine (Phage Sp UKR) is a collaborative effort to provide phages targeting circulating pathogens in Ukraine for delivery of personalized phage therapies. Within this context, we received multidrug-resistant bacterial isolates belonging to a number of different species. We here focus on Klebsiella pneumoniae, the most concerning pathogen with regard to prevalence, virulence and antibiotic resistance. Among the K. pneumoniae isolates, we identified sequence types (ST) 39, 101, 147, 307 and 395, as well as a predominating clonal group--CG10146 (ST23 KL57), first detected in Moscow--carrying a hybrid virulence-resistance plasmid encoding NDM-1 and aerobactin. Over two years (2023-2025), this clonal group expanded and acquired pan-resistance. When tested in virulence assays, only one isolate (ST395) displayed hypervirulence in a Galleria mellonella though not in a mouse infection model. Several phages isolated from Ukrainian sewage were able to lyse these K. pneumoniae strains, including strains obtained from soldiers displaced in Belgium, Germany, and Latvia. Bacterial resistance was observed during in vitro testing. However, some phage-resistant isolates had mutations in virulence factors, including one that completely lost its hybrid plasmid, resulting in restored antibiotic susceptibility. Strategies like Phage Sp UKR are essential to prevent the selection, persistence, and global spread of these MDR clones.

microbiology↗

bioRxiv2023

Understanding the bacterial imbalance in Hidradenitis Suppurativa patients: Insights into microbial community shifts and colonization by opportunistic pathogens

Patients suffering from hidradenitis suppurativa (HS) develop painful skin lesions, significantly decreasing their quality of life. This chronic disease is triggered by plugged hair follicles resulting in an aberrant immune response, skin microbiome imbalance and secondary bacterial colonization. As a result, a diversity of treatment options are currently applied, including antibiotics, biologicals like adalimumab and surgery, which often provide only short-term relief. Alternative strategies, like phage therapy, have been proposed but identification of the target bacterium is key. Therefore, a spatial and longitudinal analysis was performed on skin swabs of lesions from 39 HS patients and 18 healthy controls, leading to a total collection of 108 lesional samples and 35 control samples at different time points and locations throughout the body. Samples were subjected to 16S rRNA community analysis, as well as bacterial isolation using aerobic and anaerobic culturing in combination with MALDI-TOF. Our data demonstrate that the bacterial community present in lesions of patients with HS is out of balance compared to healthy individuals, in which the niche of Staphylococcus and Corynebacterium is taken over by Escherichia-Shigella. Overall, three bacterial community profiles of HS lesions and one of healthy individuals could be distinguished. Although the overall bacterial composition was not associated with the disease severity defined by the Hurley classification system, lesions often become colonized with opportunistic pathogens including Staphylococcus aureus and Pseudomonas aeruginosa at increasing disease severities. Furthermore, patients with a concurrent IBD diagnosis did not reveal a significantly different bacterial skin community.

microbiology↗

bioRxiv2023

Hidradenitis suppurativa patients exhibit a distinctive and highly individualized skin virome

Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring painful skin lesions. Despite ongoing research, the exact cause underlying the initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virota, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.

microbiology↗

bioRxiv2023

The statistics of natural shapes predict high-level aftereffects in human vision

Shape perception is essential for numerous everyday behaviors from object recognition to grasping and handling objects. Yet how the brain encodes shape remains poorly understood. Here, we probed shape representations using visual aftereffects--perceptual distortions that occur following extended exposure to a stimulus--to resolve a long-standing debate about shape encoding. We implemented contrasting low-level and high-level computational models of neural adaptation, which made precise and distinct predictions about the illusory shape distortions the observers experience following adaptation. Directly pitting the predictions of the two models against one another revealed that the perceptual distortions are driven by high-level shape attributes derived from the statistics of natural shapes. Our findings suggest that the diverse shape attributes thought to underlie shape encoding (e.g., curvature distributions, skeletons, aspect ratio) are the result of a visual system that learns to encode natural shape geometries based on observing many objects.

neuroscience↗

bioRxiv2021

Unraveling protein interactions between the temperate virus Bam35 and its Bacillus host using an integrative yeast two hybrid-high throughput sequencing approach

AO_SCPLOWBSTRACTC_SCPLOWBacillus virus Bam35 is the model Betatectivirus and member of the Tectiviridae family, which is composed of tailless, icosahedral, and membrane-containing bacteriophages. The interest in these viruses has greatly increased in recent years as they are thought to be an evolutionary link between diverse groups of prokaryotic and eukaryotic viruses. Additionally, betatectiviruses infect bacteria of the Bacillus cereus group, known for their applications in industry and notorious since it contains many pathogens. Here, we present the first protein-protein interactions network for a tectivirus-host system by studying the Bam35-Bacillus thuringiensis model using a novel approach that integrates the traditional yeast two-hybrid system and Illumina high-throughput sequencing. We generated and thoroughly analyzed a genomic library of Bam35s host B. thuringiensis HER1410 and screened interactions with all the viral proteins using different combinations of bait-prey couples. In total, this screen resulted in the detection of over 4,000 potential interactions, of which 183 high-confidence interactions were defined as part of the core virus-host interactome. Overall, host metabolism proteins and peptidases are particularly enriched within the detected interactions, distinguishing this host-phage system from the other reported host-phage protein-protein interaction networks (PPIs). Our approach also suggests biological roles for several Bam35 proteins of unknown function, resulting in a better understanding of the Bam35-B. thuringiensis interaction at the molecular level. AO_SCPLOWUTHORC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSUMMARYC_SCPLOWMembers of the family Tectiviridae, composed of non-tailed icosahedral, membrane-containing bacteriophages, have been increasingly scrutinized in recent years for their possible role in the origin of dsDNA viruses. In particular, the genus Betatectivirus receives increased attention as these phages can infect clinical strains as well as industrially relevant members of the B. cereus group. However, little is known about the interactions between these temperate viruses and their hosts. Here, we present the first high-throughput study of tectivirus-host protein-protein interactions focusing on Bam35, model virus of betatectiviruses, and its host B. thuringiensis, an important entomopathogenic bacterium. We adapted the well-known technique yeast-two-hybrid and integrated high-throughput sequencing and bioinformatics for the downstream analysis of the results which enables large-scale analysis of protein-protein interactions. In total, 182 detected interactions show an enrichment in host metabolic proteins and peptidases, in contrast with the current knowledge on host-phage PPIs. Specific host-viral protein-protein interactions were also detected enabling us to propose functions for uncharacterized proteins.

microbiology↗

bioRxiv2019

Host metabolic reprogramming of Pseudomonas aeruginosa by phage-based quorum sensing modulation

The Pseudomonas quinolone signal (PQS) is a multifunctional quorum sensing molecule of key importance to the P. aeruginosa metabolism. We here describe that the lytic Pseudomonas bacterial virus LUZ19 targets this population-density-dependent signaling system by expressing quorum sensing-associated acyltransferase (Qst) during early infection. Qst interacts with a key biosynthesis pathway enzyme PqsD, resulting in decreased metabolites levels of PQS and its precursor 2-heptyl-4(1H)-quinolone. The lack of a functional PqsD enzyme impairs the normal LUZ19 infection but is restored by external supplementation of 2-heptyl-4(1H)-quinolone, showing that LUZ19 exploits PQS to successfully achieve its infection. A functional interaction network, which includes enzymes of the central carbon metabolism (CoaC/ThiD) and a novel non-ribosomal peptide synthetase pathway (PA1217), suggests a broader functional context for Qst, which blocks P. aeruginosa cell division. Qst represents an exquisite example of intricate reprogramming of the bacterium, which may be exploited towards antibiotic target discovery for this bacterial pathogen.

microbiology↗

bioRxiv2019

Protection of phage applications in crop production: a patent landscape.

In agriculture, the prevention and treatment of bacterial infections represents an increasing challenge. Traditional (chemical) methods have been restricted to ensure public health and limit the occurrence of resistant strains. Bacteriophages could be a sustainable alternative. A major hurdle towards the commercial implementation of phage-based biocontrol strategies concerns aspects of regulation and intellectual property protection. Within this study, two datasets have been composed to analyze both scientific publications and patent documents and to get an idea on the focus of R&D by means of an abstract and claim analysis. 137 papers and 49 patent families were found searching public databases, their numbers increasing over time. Within this dataset, the majority of the patent documents were filed by non-profit organizations in Asia. There seems to be a good correlation between the papers and patent documents in terms of targeted bacterial genera. Furthermore, granted patents seem to claim rather broad and cover methods of treatment. This review shows that there is indeed a growing publishing and patenting activity concerning phage biocontrol. Targeted research is needed to further stimulate the exploration of phages within integrated pest management strategies and to deal with bacterial infections in crop production.

microbiology↗

bioRxiv2019

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared to other environments. Here we investigate the origin, evolution, and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboratory, we obtained DNA sequences of crAssphage from over one-third of the worlds countries, and showed that its phylogeography is locally clustered within countries, cities, and individuals. We also found colinear crAssphage-like genomes in both Old-World and New-World primates, challenging genomic mosaicism and suggesting that the association of crAssphage with primates may be millions of years old. We conclude that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage and an integral part of the normal human gut virome.

microbiology↗

bioRxiv2017

Repetitive Transcranial Magnetic Stimulation Increases Phase-Amplitude Coupling

A prominent feature of brain activity with relevance to cognitive processes is Phase-Amplitude Coupling (PAC) between slow and fast oscillatory signals. A newly developed neural mass model of cross-frequency coupling [1] predicts, counter-intuitively, that PAC shows sustained increases after repetitive Transcranial Magnetic Stimulation (rTMS). This is because rTMS leads to simultaneous neuronal firing in distinct regions, thereby enhancing the connectivity that, according to the model, is needed for PAC to be increased. We tested this prediction in healthy human volunteers. Two seconds of 10Hz rTMS were applied to the intraparietal sulcus, temporal-parietal junction, and lateral occipital complex. PAC in the subsequent electro-encephalogram was analyzed for two band pairs, theta-gamma and alpha-gamma, and compared to a sham condition. For all stimulation loci, PAC was higher in both band pairs after rTMS than in the sham condition. These results were found to be conform the model prediction. The perspective for using rTMS to modulate cross-band coupling is discussed.

neuroscience↗