bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrative Electrophysiology and Neuroimaging Approach in Assessing Disorders of Consciousness: A Multimodal Multicentric Machine Learning Study
Authors: Manasova Dragana , Louan Belloli Laouen Mayal , Rosenfelder Martin , Willacker Lina , Flo Rama Emilia , Valota Chiara , Hermann Bertrand , Kaufmann Brigitte Charlotte , Pirastru Alice , Derchi Chiara Camilla , Raiser Theresa , Valente Melanie , Sangare Aude , Türker Başak , Pyatigorskaya Nadya , Béranger Benoît , Colombo Michele , Munoz-Musat Esteban , Escrichs Anira , Atzori Tiziana , Baglio Francesca , Lapa Constantin , Berlis Ansgar , Krüger Kristina , Luther Tina , Perlbarg Vincent , Deco Gustavo , Sanz-Perl Yonathan , Tagliazucchi Enzo , Puybasset Louis , Rohaut Benjamin , Naccache Lionel , Comanducci Angela , Arzi Anat , Rosanova Mario , Bender Andreas , Sitt Jacobo Diego
Published: November 2024

Severely brain-injured patients may enter a spectrum of conditions collectively known as disorders of consciousness (DoC). This spectrum includes clinical categories such as unresponsive wakefulness syndrome or minimally conscious state, where the behavioral assessment of consciousness can often be deceptive.

To bridge this dissociation, neuroimaging techniques are employed to look for the residual brain functions. Each neuroimaging modality imperfectly captures distinct aspects of brain preservation - functional, anatomical, or both. In this study, we adopt a comprehensive approach by integrating the neurophysiology and neuroimaging modalities available from the standard and advanced clinical assessment through interpretable machine learning (ML). The electrophysiological modalities included high-density electroencephalography (EEG) (resting state and task), whereas neuroimaging modalities included anatomical and resting-state functional magnetic resonance imaging (MRI), diffusion MRI, and 18F-fluoro-deoxy-glucose positron emission tomography (FDG PET).

Our investigation reveals that specific modalities, such as functional assessments provide comprehensive insights into the currently evaluated state of consciousness - the diagnosis of the patients. Conversely, structural modalities offer valuable information about the patient’s evolution within the consciousness spectrum. We validate the proposed analysis with data coming from other centers with different acquisition parameters. Importantly, we show that there is an improved model performance with the increase in the number of modalities. We observe a higher inter-modality disagreement for MCS patients and those patients who improve. Lastly, we observe a difference in feature importances in diagnosis and prognosis.

This integrative multimodal and ML methodology presents a promising avenue for a more nuanced understanding of DoC, contributing to enhanced diagnostic precision and prognostic capabilities in clinical practice.
Mapping the endosomal proximity proteome reveals Retromer as a hub for RAB GTPase regulation
Authors: Antón-Plágaro Carlos , Chen Kai-en , Guo Qian , Liu Meihan , Evans Ashley J. , Lewis Philip A. , Heesom Kate J , Wilkinson Kevin A. , Collins Brett M. , Cullen Peter J.
Published: November 2024

Endosomal retrieval and recycling of integral cargo proteins is essential for cell, tissue and organism-level development and homeostasis and is orchestrated through a specialised retrieval sub-domain on the endosomal vacuole. However, although sub-domain dysfunction is associated with human disease our appreciation of the molecular details and functional components of the retrieval sub-domain(s) remains poorly described. Here, using comparative proximity proteomics of critical retrieval sub-domain components Retromer and Retriever, their cargo adaptors, and a component of the opposing ESCRT-degradative sub-domain, we provide a data-rich resource that identifies new molecular details of retrieval sub-domain composition and organization, including an unrecognised complexity in the interface of Retromer with RAB GTPases. Combining X-ray crystallography and in silico predictions with extensive biochemical and cellular analysis, we dissect the direct association of Retromer with RAB10 regulators DENND4A, DENND4C, TBC1D1, and TBC1D4, and the RAB35 regulator TBC1D13. Overall, we conclude that the Retromer retrieval sub-domain constitutes a major hub for the regulated switching of selected RAB GTPases and propose that this constitutes a major component of the role of Retromer in neuroprotection.
Task-induced internal bodily rather than brain states regulate human self-perception
Authors: Xie Musi , Bao Han , Wu Hang , Zhang Yihui , Liu Yueyao , Han Junrong , Zhang Xilin , Qin Pengmin
Published: November 2024

A fundamental ability for us is to identify and distinguish with others, known as the self, whose neural substrate is hard to identify by external self-related stimuli because of possible interference from internal self-related states of both body and brain. Using the same stimuli, we ruled out this dilemma by manipulating human subjects performing own- and celebrity-face discrimination tasks to induce self-related and non-self-related states, respectively. Results showed that stimulus-driven sensory sensory differences among own-, celebrity-, and stranger-faces were independent of task-induced internal states, whereas their perceptual differences were strongly modulated by these states. Intriguingly, we further found that subjects’ bodily (indexed by heartbeat-evoked potentials) rather than brain (indexed by pre-stimulus α-powers) states not only predicated their self-perception but also moderated the relationship between external stimuli and self-perception. Our results reveal for the first time an adaptive self-perception, shaped by not only external stimuli but also internal states, especially the interoception.
Clonal analysis of murine HSC self-renewal and differentiation in native hematopoiesis
Authors: You Chenyu , Zhang Zhen , Lin Li , Sun Jianlong
Published: November 2024

Hematopoietic stem cells (HSC) maintain lifelong hematopoiesis. However, in current clonal analyses with unbiased “barcoding” approaches, steady-state hematopoietic clones in young and middle-aged adults rarely have detectable HSCs, which precludes comprehensive interrogation of HSC clonal behaviors. In the current study, we used the previously described Sleeping Beauty transposon model to investigate HSC self-renewal and differentiation at a clonal level following a lifelong chase that significantly enriched HSC-derived clones. From seventeen mice, we detected over seventy thousand clones in native hematopoiesis that reflected the known HSC differentiation biases observed in transplantation. Our data indicated an intimate connection between megakaryocytic-restricted differentiation and HSC self-renewal expansion. By comparing the differentiation patterns of clones derived from transplanted HSCs, we further demonstrated the abilities of HSCs to preserve their cell fates towards self-renewal or multilineage differentiation. Unlike HSCs, clonal expansion in multipotent progenitors was associated with either a differentiation-active or differentiation-indolent state. Moreover, the clonal expansion events in the more differentiated stem and progenitor cells, but not the most primitive HSCs, drove clonal expansion in the megakaryocyte and myeloid cell lineages. Our study provided a comprehensive portrait of native hematopoiesis at a clonal level and revealed the general patterns in which HSCs maintained self-renewal and multi-lineage differentiation.
Transcallosal generation of phase aligned beta-bursts underlies TMS-induced interhemispheric inhibition
Authors: Georgiev Christian , Mongold Scott J. , Cabaraux Pierre , Naeije Gilles , Duque Julie , Bourguignon Mathieu
Published: November 2024

Background

The excitability of the sensorimotor (SM1) cortices is reflected in the bilateral ∼20 Hz beta oscillations. The extent to which these oscillations subtend the interhemispheric inhibition captured by the Transcranial Magnetic Stimulation (TMS) ipsilateral Silent Period (iSP) protocol is unknown.

Objectives

We investigated the relationship between movement-induced beta suppression, iSP, and manual dexterity.

Methods

Forty adults underwent an Electroencephalography assessment of beta oscillations during volitional left hand movement and a TMS assessment of iSP recorded from the right hand. In both cases, left SM1 beta oscillations (contralateral to the activated right SM1), were monitored through a proxy signal – the Electromyography of the contracted right hand. Manual dexterity was assessed with the Purdue Pegboard Test.

Results

Volitional movement caused significant bilateral SM1 beta suppression in nearly all participants (≥ 85 %). ISPs were observed in every participant. In the proxy signal for the left SM1, the iSP coincides with TMS-induced high-amplitude beta bursts. These bursts showed significant phase alignment across participants 10–70 ms after the TMS pulse. There was no significant association between the left-/right-hemisphere beta suppression, iSP, and manual dexterity.

Conclusion

Our results highlight the distinct nature of beta oscillation changes during voluntary movement compared to TMS-iSP and show that TMS induces IHI via transcallosal induction of phase aligned beta bursts. Furthermore, our data suggests that only the initial phase of a beta burst carries an inhibitory effect. It also highlights the possibility of evoking a beta burst with the iSP protocol, opening perspectives for future modeling studies.

Highlights

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Movement-induced beta suppression does not reflect Transcranial Magnetic Stimulation-induced interhemispheric inhibition

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Transcranial Magnetic Stimulation induces interhemispheric inhibition via transcallosal induction of phase aligned high-amplitude beta bursts

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The inhibitory effect of a beta burst appears to be carried by its initial oscillatory cycle

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Beta oscillations and interhemispheric inhibition’s role for motor dexterity need further exploration
Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity
Authors: Lazarova Mariya , Eicher Thomas , Börnsen Clara , Zeng Hui , Athar Mohd , Okada Ui , Yamashita Eiki , Spannaus Inga M. , Borgosch Max , Cha Hi-jea , Vargiu Attilio V. , Murakami Satoshi , Diederichs Kay , Frangakis Achilleas S. , Pos Klaas M.
Published: November 2024

Antibiotic efflux plays a key role for the multidrug resistance in Gram-negative bacteria1–3. Multidrug efflux pumps of the resistance nodulation and cell division (RND) superfamily function as part of cell envelope spanning systems and provide resistance to diverse antibiotics 4,5. Here, we identify two phylogenetic clusters of RND proteins with conserved binding pocket residues. Based on the characterisation of one representative of each cluster,K. pneumoniaeOqxB andE. coliAcrB, we show that the transfer of a single conserved residue between both clusters alters the resistance against a panel of structurally unrelated drugs. The substitution is not only associated with changes in the binding pocket architecture, but also alters the equilibrium between the conformational states of the transport cycle. We show that AcrB and OqxB adopt fundamentally different apo states that suggest different mechanisms of initial substrate binding and might determine the differences between the substrate preferences of both pumps. The observed conformational heterogeneity between different RND clusters is suggested to be phylogenetically conserved and might play a role for the diversification of the resistance phenotype between homologous RND multidrug efflux pumps.
IFNγ-Expressing Myeloid Cells Localize within Lipoproteinosis during Drug-Associated Pulmonary Alveolar Proteinosis occurring in Systemic Juvenile Idiopathic Arthritis
Authors: Delmastro Alea , Liu Candace C. , Ding Xiao-Wen , Tan Serena Y. , Averbukh Inna , Bosse Marc , Keyes Timothy J. , Sharma Surbhi , Deutsch Gail , Angelo Michael , Saper Vivian E. , Mellins Elizabeth D. , McCaffrey Erin F.
Published: November 2024

In the United States, approximately one in 1000 children are diagnosed with the autoinflammatory disease, Juvenile Idiopathic Arthritis (JIA). A subset of JIA cases manifests as Systemic JIA (sJIA), which is characterized by joint pain, fevers, rashes, and systemic inflammation. Severe pulmonary complications have not historically been associated with sJIA. Since 2010, inhibitors of interleukin-1 and interleukin 6 (IL-1i/IL-6i) are the recommended course of treatment for sJIA, yet recently studies show evidence of a severe drug hypersensitivity reaction implicating these medications in a subset of those treated. With this reaction, sJIA patients can develop severe lung disease, including pulmonary alveolar proteinosis (PAP). As this drug-associated lung disease has only recently been identified, the etiology of sJIA drug-associated PAP (sJIA-daPAP) is poorly understood. We used multiplexed ion beam imaging by time-of-flight (MIBI-TOF) to define the cellular immune infiltrate and describe pathological features of PAP in sJIA-daPAP patients. We found an enrichment of eosinophils, neutrophils, and M2 macrophages within regions of lipoproteinosis. These enriched subsets all upregulate IFNγ within lipoproteinosis, a signature specific to sJIA-daPAP samples compared to non-sJIA-PAP samples. In a cellular neighborhood analysis, we identified that eosinophils, neutrophils and M2 macrophages frequently co-localize within the same cellular microenvironment, especially in lipoproteinosis regions. Therefore, this spatial coordination may be involved in clearance or persistence of lipoproteinosis in sJIA-daPAP. This study provides a comprehensive overview of sJIA-daPAP immune pathology and suggests cellular mechanisms that drive inflammation in sJIA patients experiencing pulmonary complications associated with delayed drug hypersensitivity during IL-1i/IL-6i treatment.
Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing
Authors: Wei Tianzi , Li Jiaxuan , Lei Xiang , Lin Risheng , Wu Qingyan , Zhang Zhenfeng , Shuai Shimin , Tian Ruilin
Published: November 2024

Adenosine-to-Inosine (A-to-I) RNA editing is a critical post-transcriptional modification that diversifies the transcriptome and influences various cellular processes. Despite its significance, the regulatory mechanisms controlling A-to-I editing remain largely unknown. In this study, we present two complementary CRISPR-based genetic screening platforms: CREDITS (CRISPR-basedRNAEDITing regulatorScreening), which enables genome-scale identification of editing regulators using an RNA recorder-based reporter system, and scCREDIT-seq (single-cellCRISPR-basedRNAEDITingsequencing), which provides multiplexed single-cell characterization of transcriptome and editome changes for pooled perturbations on dozens of selected genes. Through screening 1,350 RNA-binding proteins, we identified a series of known and novel A-to-I editing regulators. Detailed mechanistic investigation revealed DDX39B as a global repressor of A-to-I editing, which functions by preventing double-stranded RNA accumulation through its helicase and ATPase activities. We demonstrate that targeting DDX39B significantly enhances the efficiency of RNA editing-based tools like CellREADR and LEAPER, and represents a promising strategy for anti-HDV therapy by modulating viral genome editing. These technological advances not only expand our understanding of RNA editing regulation but also provide powerful tools for exploring tissue-specific and context-dependent RNA modification mechanisms, with broad implications for therapeutic development.
Computational analysis to assess hemodynamic forces in descending thoracic aortic aneurysms
Authors: Duca Francesca , Bissacco Daniele , Crugnola Luca , Faitini Chiara , Domanin Maurizio , Migliavacca Francesco , Trimarchi Santi , Vergara Christian
Published: November 2024

Descending Thoracic Aortic Aneurysm (DTAA) is a life-threatening disorder, defined as a localized enlargement of the descending portion of the thoracic aorta. In this context, we develop a Fluid-Structure Interaction (FSI) computational framework, with the inclusion of a turbulence model and different material properties for the healthy and the aneurysmatic portions of the vessel, to study the hemodynamics and its relationship with DTAA.

We first provide an analysis on nine ideal scenarios, accounting for different aortic arch types and DTAA ubications, to study changes in blood pressure, flow patterns, turbulence, wall shear stress, drag forces and internal wall stresses. Our findings demonstrate that the hemodynamics in DTAA is profoundly disturbed, with the presence of flow recirculation, formation of vortices and transition to turbulence. In particular, configurations with a more steep aortic arch exhibit a more chaotic hemodynamics. We notice also an increase of pressure values for configurations with less steep aortic arch and of drag forces for configurations with distal DTAA.

Secondly, we replicate our analysis for three patient-specific cases (one for type of arch) obtaining conforting results in terms of accordance with the ideal scenarios. Finally, in a very preliminary way, we try to relate our findings to possible stent-graft migrations after TEVAR procedure to provide predictions on the post-operative state.

KEY POINTS

This study employs computational methods to assess hemodynamic forces in descending thoracic aortic aneurysms;

We consider ideal cases by varying aortic arch type and aneurysm location;

Our results show: chaotic hemodynamics for steep aortic arches; increase of pressure values for less steep aortic arches; high risk of plaque in the sac for proximal aneurysms and in the neck for distal aneurysms;

We analyse also 3 patient-specific cases, confirming the major outcomes found for the ideal cases;

We try to suggest how our pre-operative findings may be put in relation to assess the risk of stent-graft migration of a possible TEVAR procedure.
Machine learning outcompetes human assessment in identifying eggs of a conspecific brood parasite
Authors: Hughes Anna E. , Mari Lisandrina , Troscianko Jolyon , Jelínek Václav , Albrecht Tomáš , Šulc Michal
Published: November 2024

Avian brood parasitism provides an exceptional system for studying coevolution. While conspecific brood parasitism (CBP) is more common than interspecific parasitism, it is less studied due to the challenge of detecting parasitic eggs, which closely resemble those of the host. Although molecular genotyping can accurately detect CBP, its high cost has led researchers to explore egg appearance as a more accessible alternative. Barn swallows (Hirundo rustica) are considered conspecific brood parasites, but identifying parasitic eggs has traditionally relied on human visual assessment. Here, we used UV-visible photographs of non-parasitized barn swallow clutches and simulated parasitism to compare the accuracy of human assessment with automated methods. In two games, participants and models identified parasitic eggs from six or two options. While humans performed better than chance (72% and 87% accuracy), they still made significant errors. In contrast, the automated supervised model was far more reliable, achieving 95% and 97% accuracy. We think that the model outperformed humans due to its ability to analyse a broader range of visual information, including UV reflectance, which humans cannot perceive. We recommend using supervised models over human assessment for identifying conspecific parasitic eggs and highlight their potential to advance research on evolution of egg colouration.
Roquin exhibits opposing effects on RNA stem-loop stability through its two ROQ domain binding sites
Authors: Tants Jan-Niklas , Walbrun Andreas , Kollwitz Lucas , Friedrich Katharina , Rief Matthias , Schlundt Andreas
Published: November 2024

The interaction of mRNA and regulatory proteins is critical for post-transcriptional control. For proper function, these interactions as well as the involved protein and RNA structures are highly dynamic and thus, mechanistic insights from structural biology are challenging to obtain. In this study, we employ a multifaceted approach combining single-molecule force spectroscopy with NMR spectroscopy to analyze the concerted interaction of the two RNA-binding interfaces (A-site, B-site) of the immunoregulatory protein Roquin’s ROQ domain with the 3’ untranslated region (UTR) of theOx40mRNA. This 3’UTR contains two specific hairpin structures termed constitutive and alternative decay elements (CDE, ADE), which mediate mRNA degradation via binding of Roquin. Our single-molecule experiments reveal the CDE folds cooperatively, while ADE folding involves at least 3 on-pathway and 3 off-pathway intermediates. Utilizing an integrated microfluidics setup allows to extract binding kinetics to Roquin in real time. Supported by NMR, we find opposing effects of the two Roquin sub-domains on distinct regions of the ADE: while the A-site interacts strongly with the folded apical stem-loop, we find that the B-site has a distinct destabilizing effect on the central stem of the ADE owed to single-strand RNA binding. We propose that RNA-motif nature and Roquin A- and B-sites jointly steer mRNA decay with context-encoded specificity, and we suggest plasticity of stem structures as key determinant for Roquin-RNA complex formation. The unique methodological combination of NMR and single-molecule force spectroscopy reveals an unknown mechanism of a dual-function RNA-binding domain suggesting a new model for target RNA recognition.

SIGNIFICANCE STATEMENT

Local RNA structure is decisive for specific engagement with gene-regulatory proteins and, as a consequence, correct cellular function. However, its existence often appears dynamic and thus, challenging to study. This study shows how NMR and single-molecule force spectroscopy efficiently complement each other to provide high-resolution, time-resolved data on RNA folding intermediates during dynamic complex formation with the immune-regulating protein Roquin, which exploits multiple RNA-binding sites. Our data reveal a dual-mode binding of Roquin to RNA by firmly attaching to the stem-loop and, at the same time, destabilizing other regions making them accessible to downstream interaction partners.
HGTs are not SPRs: In the presence of ghost lineages, series of Horizontal Gene Transfers do not result in series of Subtree Pruning and Regrafting
Authors: Tannier Eric , Tricou Théo , Benali Syrine , de Vienne Damien M.
Published: November 2024

When a gene is horizontally transferred (HGT), under the “replacement” model where the transferred gene replaces its homolog in the recipient genome, the corresponding gene phylogeny departs from the species phylogeny by a Subtree Prune and Regraft (SPR) operation: the recipient branch is moved from its initial position to attach to the donor branch. Based on this observation, various methods have used SPRs to simulate or infer HGTs. We examine this apparent equivalence in the light of ghost lineages,i.e. all related species absent from the phylogeny because they are extinct, unknown or have not been sampled. These absent species branches are much more numerous than the visible ones under most situations, so HGTs have great chances of originating from ghosts. We show that in this case, there is a high probability that series of HGTs do not correspond to series of SPRs. This biases the simulations under SPRs and prevents the inference under SPRs from retrieving the true transfers. For instance if the studied phylogeny represents 1% of all the species susceptible to exchange genetic material with the 100 sampled species, and 11 transfers occurred, then modelling HGTs with SPRs will be misleading in around 50% of the cases. This applies to a certain extent to other phylogenetic simulation or inference methods of HGT, like reconciliation.
Corylus avellananon-specific lipid-transfer protein Cor a 8 is a moonlighting enzyme with a new lipase activity
Authors: Alex Fissore , Giulia Di Napoli , Maria Laura De Sciscio , Valentina Santoro , Edoardo Salladini , Mauro Marengo , Simonetta Oliaro-Bosso , Gaia Vanzetti , Andrea Caratti , Fabrizio Dal Piaz , Francesco Piazza , Maela Manzoli , Giuseppe Genova , Giuseppe Barbiroli Alberto , Stefania Iametti , Franca Fraternali , Salvatore Adinolfi
Published: November 2024

The high-fat content of hazelnuts, mainly triglycerides, makes them prone to lipid oxidation during storage, which has a big impact on their sensory and nutritional quality. The chemical pathways leading to hazelnut oxidative rancidity have been well characterized and it are faster on free fatty acids. Lipase(s) enzymes are required, in oilseed, to hydrolyze the ester bond to free the single molecule of fatty acids. This step, necessary for germination, is the first event to trigger rancidity. Identifying the lipase(s) enzyme and the biochemical pathways involved in rancidity would lead to an effective strategy to prevent fat deterioration. Different proteins have been characterized in hazelnut seed and great interest has been risen towards the non-specific lipid transfer protein family because they were identified as human allergens. Here we show that Cor a 8 – a member of nsLTP – is a novel non-regiospecific lipase that is able to bind to oil-water interfaces and hydrolyze the triacylglycerol (TAGs) ester bonds by a non-canonical active site (non-serine dependent). Molecular modelling and molecular dynamics suggest that Cor a 8 is a moonlighting enzyme not only able to catalyze the hydrolysis of TAGs but also to stabilize the resulting free fatty acids and transport it.

Cor a 8 homologues are present in all land plants, but the specific catalytic amino acids are found only in angiosperms, suggesting an evolutionary adaptation for lipid metabolism unique to flowering plants. This study sets the foundation for understanding this new lipid metabolism in plants and its role in rancidity development.
Comparison of genomic assembly and annotation based on two clones of avian pathogenicEscherichia coli
Authors: Zhao Yufei , Olsen John Elmerdahl , Poulsen Louise , Christensen Henrik
Published: November 2024

Methods for assembly and annotation of whole genomic sequences were compared for six strains of avian pathogenicEscherichia coli(APEC). Two vertically transferredE. coliclones, represented by three isolates all belonging to pulse field genome electrophoresis (PFGE) type 65- sequence type (ST)95 and three isolates belonging to PFGE type 47- ST131, were selected for Illumina short read sequencing. There was no significant difference between SPAdes and CLC Genomic Workbench for benchmark parameters to assemble the short reads. The six strains were also sequenced by long read sequencing (Nanopore) and these reads were hybrid assembled with the short reads. Unicycler provided a lower number of contigs and higher N50 compared to Flye. No significant differences between total length of genomes were obtained from the four assemblers. At least 2.1 and 0.9% of coding gene sequences (CDSs) annotated with RAST and PROKKA, respectively were wrongly annotated. The errors were most often associated to CDS of shorter length (< 150 nt) with functions such as transposases, mobile genetic elements or being hypothetical. The investigation points out the importance of controlling automatic annotations and suggest further work to improve annotations in strains not belonging to the K12 or B lineages.
Whole-genome sequencing ofHyphopichia burtoniifrom isolated yeast recovered from zebra dove droppings in Thailand
Authors: Indoang Saowakon , Chumtong Sanicha , Prachantasena Sakaoporn , Wiriyaprom Ratchakul , Surachart Komwit , Promwised Rattanaruji , Ngasaman Ruttayaporn
Published: November 2024

This study aimed to characterise zoonotic yeasts from zebra dove (Geopelia striata) droppings in small farms in Songkhla province, Thailand. Four contaminated isolates were found with morphology and biochemical test results like those of Cryptococcus spp., but they exhibited different results from the positive control in nested polymerase chain reaction (PCR); the first step was negative, but the nested PCR step was positive. All isolates were subjected to antifungal susceptibility testing. The resistance isolate (Tip11) was subjected to whole genome sequencing. Only the Tip11 isolate showed high resistance to itraconazole and ketoconazole, with minimum inhibitory concentrations of >32.0 and 32.0 μg/mL, respectively, corresponding to high levels of minimum fungicidal concentrations for both drugs (>32 μg/mL). Consequently, Tip11 was selected as a representative of the contaminated isolates and subjected to whole-genome sequencing analysis. The results identified the Tip11 isolate as Hyphopichia burtonii (99.30% identity), with a genome length of 12,360,159 bp, a GC content of 35.16%, and 2,146 protein groups closely related to the Saccharomycetaceae family. This is the first report of H. burtonii in zebra doves in Thailand. This yeast has been previously identified as a cause of human infection leading to peritonitis in Thailand, and its resistance to antifungal drugs may pose a public health risk. Therefore, the application of biosecurity measures on farms, such as regular removal of droppings and cage sanitisation, should be implemented according to good agricultural practices. Moreover, further characterisation and functional analysis of the proteins identified should be considered.
Ethanol alters mechanosensory habituation inC. elegansby way of the BK potassium channel through a novel mechanism
Authors: Kokan Nikolas , Lin Conny , Luna Alvaro , Viliunas Joani , Rankin Catharine H.
Published: November 2024

In this research, we investigated how alcohol modulates the simplest form of learning, habituation, inCaenorhabditis elegans. We used our high throughput Multi-Worm Tracker to conduct a large scale study of more than 21,000 wild-type worms to assess the effects of different doses of alcohol on habituation of the well-characterized tap withdrawal response. We found that the effect of alcohol on habituation of the reversal response to repeated mechanosensory stimuli (taps) differed depending on the component of the reversal response assessed. Furthermore, we discovered that alcohol shifted the dominant response to tap from a backward reversal to a brief forward movement. Because the large conductance potassium (BK) channel has been shown to be important for alcohol’s effects on behaviour in a variety of organisms, includingC. elegans, we investigated whether theC. elegansBK channel ortholog, SLO-1, mediated the effects of alcohol on habituation. We tested several different strains of worms with mutations inslo-1along with wild-type controls; null mutations inslo-1made animals resistant to alcohol induced changes in learning. However, a mutation in the putative ethanol binding site on SLO-1 did not disrupt ethanol’s impact on habituation. Finally, by degrading SLO-1 in different parts of the nervous system we found that SLO-1’s function in ethanol’s impact on habituation is likely distributed throughout the neural circuit that responds to tap. Based on these results, our main conclusions are 1) ethanol is not a general facilitator or inhibitor of habituation but rather a complex modulator, 2) SLO-1 is required for ethanol’s effect on habituation, 3) ethanol is interacting (directly or indirectly) with SLO-1 through a novel unidentified mechanism to influence response plasticity.
Decoding Motivational States and Craving through Electrical Markers for Neural 'Mind Reading'
Authors: Proverbio Alice Mado , Zanetti Alice
Published: November 2024

The aim of this electroencephalogram (EEG) study was to identify electrical neuro-markers of 12 different motivational and physiological states such as visceral craves, affective and somatosensory states, and secondary needs. Event-related potentials (ERPs) were recorded in 30 right-handed participants while recalling a specific state upon the presentation of an auditory verbal command incorporating an evocative sound background consistent with that state (e.g. the chirping of cicadas associated with the verbal complaint about feeling hot). ERP data showed larger amplitude N400 responses in the affective and somatosensory states, while the P400 component displayed greater amplitudes for the secondary and visceral states. Furthermore, the two components were also discernibly responsive to the 12 micro-categories (e.g., joy vs. pain or hunger), by providing a distinctive electric pattern for mostly all microstates. The reconstruction of the intracranial generators of surface signals revealed common imagery-related activations, including the middle and superior frontal gyri, the fusiform and lingual gyri, supramarginal, and middle occipital regions, as well as the middle temporal region. Additionally, specific regions were identified that were active for distinct mentally represented content, such as that visceral needs were associated with activations in the medial and inferior frontal gyri, uncus, precuneus, and cingulate gyrus. Affective states were associated with activations in the medial frontal, superior temporal, and middle temporal gyri. Somatosensory states (e.g., pain or cold) activated regions in the parietal cortex and the crave for music was linked to activations in the auditory and motor regions. These findings support the use of ERP markers for BCI applications.
diaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling
Authors: Woods Kathryn , Rants’o Thankhoe A. , Chan Alexandria M. , Sapre Tanmay , Mastin Grace E. , Maguire Kathleen M. , Ong Shao-En , Golkowski Martin
Published: November 2024

Protein-protein interactions (PPIs) underlie most biological functions. Devastating human conditions like cancers, neurological disorders, and infections, hijack PPI networks to initiate disease, and to drive disease progression. Understanding precisely how diseases remodel PPI networks can, therefore, help clarify disease mechanisms and identify therapeutic targets. Protein kinases control most cellular processes through protein phosphorylation. The 518 human kinases, known as the kinome, are frequently dysregulated in disease and highly druggable with ATP-competitive inhibitors. Kinase activity, localization, and substrate recognition are regulated by dynamic PPI networks composed of scaffolding and adapter proteins, other signaling enzymes like small GTPases and E3 ligases, and phospho-substrates. Accordingly, mapping kinase PPI networks can help determine kinome activation states, and, in turn, cellular activation states; this information can be used for studying kinase-mediated cell signaling, and for prioritizing kinases for drug discovery. Previously, we have developed a high-throughput method for kinome PPI mapping based on mass spectrometry (MS)-based chemoproteomics that we named kinobead competition and correlation analysis (kiCCA). Here, we introduce 2ndgeneration (gen) kiCCA which utilizes data-independent acquisition (dia) with parallel accumulation serial fragmentation (PASEF) MS and a re-designed CCA algorithm with improved selection criteria and the ability to predict multiple kinase interaction partners of the same proteins. Using neuroblastoma cell line models of the noradrenergic-mesenchymal transition (NMT), we demonstrate that 2ndgen kiCCA(1)identified 6.1-times more kinase PPIs in native cell extracts compared to our 1stgen approach,(2)determined kinase-mediated signaling pathways that underly the neuroblastoma NMT, and(3)accurately predicted pharmacological targets for manipulating NMT states. Our 2ndgen kiCCA method is broadly useful for cell signaling research and kinase drug discovery.
A reference genome forTrichogramma kaykai: A tiny desert-dwelling parasitoid wasp with competing sex-ratio distorters
Authors: Culotta Jack , Lindsey Amelia RI
Published: November 2024

The tiny parasitoid waspTrichogramma kaykaiinhabits the Mojave Desert of the southwest United States. Populations of this tiny insect variably host up to two different sex-distorting genetic elements: (1) the endosymbiotic bacteriumWolbachiawhich induces the parthenogenetic reproduction of females, and (2) a B-chromosome, “Paternal Sex Ratio” (PSR), which converts would-be female offspring to PSR-transmitting males. We report here the genome of aWolbachia-infectedTrichogramma kaykaiisofemale colony KSX58. Using Oxford Nanopore sequencing we produced a final genome assembly of 203 Mbp with 45x coverage, consisting of 213 contigs with an N50 of 1.9 Mbp. The assembly is quite complete, with 91.41% complete BUSCOs recovered: a very high score for Trichogrammatids that have been previously characterized for having high levels of core gene losses. We also report a complete mitochondrial genome forT. kaykai,and an assembly of the associatedWolbachia, strainwTkk. We identified copies of the parthenogenesis-inducing genespifAandpifBin a remnant prophage region of thewTkk genome. TheTrichogramma kaykaiassembly is the highest quality genome assembly for the genus to-date and will serve as a great resource for understanding the evolution of sex and selfish genetic elements.
Buprenorphine Induces Human Fetal Membrane Sterile Inflammation
Authors: Lynn Tatyana , Kelleher Megan E , Georges Hanah M , McCauley Elle M , Logan Ryan W , Yonkers Kimberly A , Abrahams Vikki M
Published: November 2024

Opioid-use disorder (OUD) during pregnancy has increased in the United States to critical levels and is a leading cause of maternal morbidity and mortality. Untreated OUD is associated with pregnancy complications in particular, preterm birth. Medications for OUD, such as buprenorphine, are recommended with the added benefit that treatment during pregnancy increases treatment post-partum. However, the rate of preterm birth in individuals using illicit opioids or being treated with opioid agonist therapeutics is double that of the general population. Since inflammation in the placenta and the associated fetal membranes (FM) is a common underlying cause of preterm birth, we sought to determine if the opioid, buprenorphine, induces sterile inflammation in human FMs and to examine the mechanisms involved. Using an establishedin vitrohuman FM explant system, we report that buprenorphine significantly increased FM secretion of the inflammatory cytokine IL-6; the neutrophilic chemokine IL-8; and the inflammasome-mediated cytokine IL-1β, mirroring the inflammatory profile commonly seen at the maternal-fetal interface in preterm birth. Other factors that were elevated in FMs exposed to buprenorphine included the mediators of membrane weakening, prostaglandin E2 (PGE2), and matrix metalloproteinases, MMP1 and MMP9. Furthermore, this sterile inflammatory and weakening FM response induced by buprenorphine was mediated in part by innate immune Toll-like receptor 4 (TLR4), the NLRP3 inflammasome, the μ-opioid receptor, and downstream NFκB and ERK/JNK/MAPK signaling. This may provide the mechanistic link between opioid use in pregnancy and the elevated risk for preterm birth. Since there are adverse consequences of not treating OUD, our findings may help identify ways to mitigate the impact opioids have on pregnancy outcomes while allowing the continuation of maintenance therapy.
Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring
Authors: Willems Patrick , Thery Fabien , Van Moortel Laura , De Meyer Margaux , Staes An , Gul Adillah , Kovalchuke Lyudmila , Declercq Arthur , Devreese Robbe , Bouwmeester Robbin , Gabriels Ralf , Martens Lennart , Impens Francis
Published: November 2024

Mass spectrometry-based discovery of bacterial immunopeptides presented by infected cells allows untargeted discovery of bacterial antigens that can serve as vaccine candidates. However, reliable identification of bacterial epitopes is challenged by their extreme low abundance. Here, we describe an optimized bioinformatical framework to enhance the confident identification of bacterial immunopeptides. Immunopeptidomics data of cell cultures infected withListeria monocytogeneswere searched by four different search engines, PEAKS, Comet, Sage and MSFragger, followed by data-driven rescoring with MS2Rescore. Compared to individual search engine results, this integrated workflow boosted immunopeptide identification by an average of 27% and led to the high-confidence detection of 18 additional bacterial peptides (+27%) matching 15 differentListeriaproteins (+36%). Despite the strong agreement between the search engines, a small number of spectra (< 1%) had ambiguous matches to multiple peptides and were excluded to ensure high-confident identifications. Finally, we demonstrate our workflow with sensitive timsTOF SCP data acquisition and find that rescoring, now with inclusion of ion mobility features, identifies 76% more peptides compared to Q Exactive HF acquisition. Together, our results demonstrate how integration of multiple search engine results along with data-driven rescoring maximizes immunopeptide identification, boosting the detection of high-confidence bacterial epitopes for vaccine development.
Mechanical coupling between dorsal and ventral surfaces shapes the Drosophila haltere
Authors: Song Yuzhao , Martín Paloma , Sun Tianhui , Sánchez-Herrero Ernesto , Pastor-Pareja José Carlos
Published: November 2024

The extracellular matrix is an essential determinant of animal form, enabling organization of cells and tissues into organs with complex 3D shapes. In contrast with the dorso-ventrally flat Drosophila wing, its serial homolog the haltere adopts a globular shape thought to arise from a lack of matrix-mediated adhesion between its dorsal and ventral surfaces. Contradicting this model, however, matrix manipulations are known to deform halteres. To understand haltere morphogenesis, we characterized matrix behavior and monitored metamorphic development of the haltere. We found that, similar to the wing, correct haltere morphogenesis requires Collagen IV degradation, which we show is mediated by ecdysone-controlled expression of Matrix metalloprotease 2 in both wing and haltere. After Collagen IV is degraded, similar again to the wing, dorsal and ventral haltere surfaces establish Laminin-mediated contact through long cytoskeletal projections. Furthermore, time-lapse analysis of shape changes in wild type and mutant halteres indicates that these projections couple the two surfaces through a central tensor, ensuring load distribution across the whole organ to create a globular shape against tissue-wide deforming forces. Our findings reveal an unexpected role for matrix-mediated adhesion in haltere morphogenesis and describe a novel type of matrix-based tensor structure building 3D shape from 2D epithelia.
Depletion of all platelet integrins impacts hemostasis, thrombosis and tumor metastasis
Authors: Janus-Bell Emily , Liboni Cristina , Yakusheva Alexandra , Mittelheisser Vincent , Mouriaux Clarisse , Bourdon Catherine , Bochler Louis , Hyenne Vincent , Garcia-Leon Maria , Lefebvre Olivier , Goetz Jacky G. , Mangin Pierre H.
Published: November 2024

Platelet integrins, in addition to other platelet receptors, are known to control hemostasis, thrombosis but also metastatic progression. Yet, their exclusive but combined deficiency has never been tested in these processes. Taking advantage of PF4Cre-β1−/−/β3−/−mouse strain, we show that platelets are exclusively depleted for all integrins. While they displayed impaired binding to fibrinogen and annexin-V, P-selectin exposure was normal. Platelet adhesion was abrogated on immobilized fibrinogen and fibrillar fibronectin under shear flow. PF4Cre-β1−/−/β3−/−mice presented an increased bleeding time and a profound defect in experimental models of arterial thrombosis. Platelet adhesion to tumor cells was also reduced, with a profound impact on tumor growth and metastatic burden in a model of triple negative breast cancer. Overall, these results confirm the central role of platelet integrins in hemostasis and thrombosis, and define their role in tumor growth and metastasis formation.

40-word summary:Depletion of all platelet integrins in PF4Cre-β1−/−/β3−/−mice leads to increased bleeding time and inhibitsin vivoarterial thrombosis. Integrin-null platelets reduce tumor growth and metastatic burden in orthotopic and experimental metastasis models. Platelet integrins control hemostasis, thrombosis and metastasis.
Phage DisCo: targeted discovery of bacteriophages by co-culture
Authors: Rand Eleanor A. , Owen Siân V. , Quinones-Olvera Natalia , Jean Kesther D. C. , Hernandez-Perez Carmen , Baym Michael
Published: November 2024

Phages interact with many components of bacterial physiology from the surface to the cytoplasm. Although there are methods to determine the receptors and intracellular systems a specified phage interacts with retroactively, finding a phage that interacts with a chosen piece of bacterial physiologya prioriis very challenging. Variation in phage plaque morphology does not to reliably distinguish distinct phages and therefore many potentially redundant phages may need to be isolated, purified, and individually characterized to find phages of interest. Here, we present a method in which multiple bacterial strains are co-cultured on the same screening plate to add an extra dimension to plaque morphology data. In this method, PhageDiscovery byCo-culture (Phage DisCo), strains are isogenic except for fluorescent tags and one perturbation expected to impact phage infection. Differential plaquing on the strains is easily detectable by fluorescent signal and implies that the perturbation made to the surviving strain in a plaque prevents phage infection. We validate the phage DisCo method by showing that characterized phages have the expected plaque morphology on Phage DisCo plates and demonstrate the power of Phage DisCo for multiple targeted discovery applications, from receptors to phage defense systems.
Linking Brain and Behavior States in Zebrafish Larvae Locomotion using Hidden Markov Models
Authors: Dommanget-Kott Mattéo , Fernandez-de-Cossio-Diaz Jorge , Coraggioso Monica , Bormuth Volker , Monasson Rémi , Debrégeas Georges , Cocco Simona
Published: November 2024

Understanding how collective neuronal activity in the brain orchestrates behavior is a central question in integrative neuroscience. Addressing this question requires models that can offer a unified interpretation of multimodal data. In this study, we jointly examine video-recordings of zebrafish larvae freely exploring their environment and calcium imaging of the Anterior Rhombencephalic Turning Region (ARTR) circuit, which is known to control swimming orientation, recordedin vivounder tethered conditions. We show that both behavioral and neural data can be accurately modeled using a Hidden Markov Model (HMM) with three hidden states. In the context of behavior, the hidden states correspond to leftward, rightward, and forward swimming. The HMM robustly captures the key statistical features of the swimming motion, including bout-type persistence and its dependence on bath temperature, while also revealing inter-individual phenotypic variability. For neural data, the three states correspond to left- and right-lateral activation of the ARTR circuit, known to govern the selection of left vs. right reorientation, and a balanced state, which likely corresponds to the behavioral forward state. To further unify the two analysis, we exploit the generative nature of the HMM, using the neural sequences to generate synthetic trajectories whose statistical properties are similar to the behavioral data. Overall, this work demonstrates how state-space models can be used to link neuronal and behavioral data, providing insights into the mechanisms of self-generated action.