bluuebunny/crossref_metadata_2025 huggingface dataset:
Lateralized Rhythmic Delta Activity and Lateralized Periodic Discharges in Critically Ill Pediatric Patients
Authors: Gupta Siddharth , Ritzl Eva K. , Husari Khalil S.
Published: January 2024

Purpose:

To evaluate the clinical and electrographic characteristics of critically ill pediatric patients with lateralized rhythmic delta activity (LRDA) and compare them with patients with lateralized periodic discharges (LPDs).

Methods:

This was a retrospective study examining consecutive critically ill pediatric patients (1 month–18 years) with LRDA or LPDs monitored on continuous electroencephalography. Clinical, radiologic, and electrographic characteristics; disease severity; and acute sequelae were compared between the two groups.

Results:

Of 668 pediatric patients monitored on continuous electroencephalography during the study period, 12 (1.79%) patients had LRDA and 15 (2.24%) had LPDs. The underlying etiologies were heterogeneous with no difference in the acuity of brain MRI changes between both groups. Lateralized rhythmic delta activity and LPDs were concordant with the side of MRI abnormality in most patients [85.7% (LRDA) and 83.3% (LPD)]. There was no difference in the measures of disease severity between both groups. Seizures were frequent in both groups (42% in the LRDA group and 73% in the LPD group). Patients in the LPD group had a trend toward requiring a greater number of antiseizure medications for seizure control (median of 4 vs. 2 in the LRDA group, p = 0.09), particularly those patients with LPDs qualifying as ictal–interictal continuum compared with those without ictal–interictal continuum (p = 0.02).

Conclusions:

Lateralized rhythmic delta activity and LPDs are uncommon EEG findings in the pediatric population. Seizures occur commonly in patients with these patterns. Seizures in patients with LPDs, especially those qualifying as ictal–interictal continuum, showed a trend toward being more refractory. Larger studies are needed in the future to further evaluate these findings.
The Electrographic Effects of Ketamine on Patients With Refractory Status Epilepticus After Cardiac Arrest: A Single-Center Retrospective Cohort
Authors: Qing Kurt , Alkhachroum Ayham , Claassen Jan , Forgacs Peter , Schiff Nicholas
Published: January 2024

Purpose:

To investigate the effects of ketamine on patients with refractory status epilepticus after cardiac arrest.

Methods:

In this retrospective cohort, selected EEG segments from patients after cardiac arrest were classified into different EEG patterns (based on background continuity and burden of epileptiform discharges) and spectral profiles (based on the presence of frequency components). For patients who received ketamine, EEG data were compared before, during, and after ketamine infusion; for the no-ketamine group, EEG data were compared at three separated time points during recording. Ketamine usage was determined by clinical providers. Electrographic improvement in epileptiform activity was scored, and the odds ratio was calculated using the Fisher exact test. Functional outcome measures at time of discharge were also examined.

Results:

Of a total of 38 patients with postcardiac arrest refractory status epilepticus, 13 received ketamine and 25 did not. All patients were on ≥2 antiseizure medications including at least one sedative infusion (midazolam). For the ketamine group, eight patients had electrographic improvement, compared with only two patients in the no-ketamine group, with an odds ratio of 7.19 (95% confidence interval 1.16–44.65, P value of 0.0341) for ketamine versus no ketamine. Most of the patients who received ketamine had myoclonic status epilepticus, and overall neurologic outcomes were poor with no patients having a favorable outcome.

Conclusions:

For postarrest refractory status epilepticus, ketamine use was associated with electrographic improvement, but with the available data, it is unclear whether ketamine use or EEG improvement can be linked to better functional recovery.
Electrographic Seizure Characteristics and Electrographic Status Epilepticus Prediction
Authors: Fung France W. , Parikh Darshana S. , Donnelly Maureen , Xiao Rui , Topjian Alexis A. , Abend Nicholas S.
Published: January 2024

Purpose:

We aimed to characterize electrographic seizures (ES) and electrographic status epilepticus (ESE) and determine whether a model predicting ESE exclusively could effectively guide continuous EEG monitoring (CEEG) utilization in critically ill children.

Methods:

This was a prospective observational study of consecutive critically ill children with encephalopathy who underwent CEEG. We used descriptive statistics to characterize ES and ESE, and we developed a model for ESE prediction.

Results:

ES occurred in 25% of 1,399 subjects. Among subjects with ES, 23% had ESE, including 37% with continuous seizures lasting >30 minutes and 63% with recurrent seizures totaling 30 minutes within a 1-hour epoch. The median onset of ES and ESE occurred 1.8 and 0.18 hours after CEEG initiation, respectively. The optimal model for ESE prediction yielded an area under the receiver operating characteristic curves of 0.81. A cutoff selected to emphasize sensitivity (91%) yielded specificity of 56%. Given the 6% ESE incidence, positive predictive value was 11% and negative predictive value was 99%. If the model were applied to our cohort, then 53% of patients would not undergo CEEG and 8% of patients experiencing ESE would not be identified.

Conclusions:

ESE was common, but most patients with ESE had recurrent brief seizures rather than long individual seizures. A model predicting ESE might only slightly improve CEEG utilization over models aiming to identify patients at risk for ES but would fail to identify some patients with ESE. Models identifying ES might be more advantageous for preventing ES from evolving into ESE.
Case Series on Trichomonas vaginalis Infections: Impact of Proper Sample Collection and Diagnostic Stewardship
Authors: Agarwal Ashwini , Padhi Abhishek , Chaudhary Anil , Bhise Mayuri , Chauhan Kinjal , Sharma Medhavi , Krishan Ramotra Rohini , Dubey Pankhuri
Published: January 2024

This paper elucidates the transformative impact of a strategic shift in diagnostic practices in the detection of Trichomonas vaginalis (T. vaginalis). It explores five cases where the implementation of a specific diagnostic protocol led to effective identification of the infection. In-depth discussions and a comprehensive literature review underline the necessity for precise diagnosis and the paramount importance of diagnostic stewardship in managing sexually transmitted infections.
Small non-coding RNA content in plasma-derived extracellular vesicles distinguish ataxic SCA3 mutation carriers from pre-ataxic and control subjects
Authors: Santana Magda M , Silva Patrick , Pinto Maria M , Gaspar Laetitia , Nobre Rui , Duarte Sónia , Marques Tânia Monteiro , Gama-Carvalho Margarida , Januário Cristina , Cunha Inês , Ribeiro Joana Afonso , Hübener-Schmid Jeannette , Infante Jon , Raposo Mafalda , Lima Manuela , Garcia-Moreno Hector , Giunti Paola , van de Warrenburg Bart , Synofzik Matthis , Faber Jennifer , Klockgether Thomas ,   ESMI Study Group, Pereira de Almeida Luís
Published: January 2024

Spinocerebellar ataxia type 3 (SCA3), a neurodegenerative disorder caused by a CAG expansion in theATXN3gene, is the most common spinocerebellar ataxia subtype worldwide. Currently, there is no therapy to stop or prevent disease progression. Promising therapeutic strategies are emerging, but their translation into clinical practice requires sensitive and reliable biomarkers. Blood circulating extracellular vesicles constitute a promising source of biomarkers with potential to track alterations of the central nervous system due to their ability to cross the blood brain barrier.

Here, we perform sequencing analysis of small RNAs from plasma-derived extracellular vesicles from SCA3 mutation carriers (10 pre-ataxic and 10 ataxic) and 12 control subjects to identify potential RNA biomarker candidates for this disease.

Data showed that plasma-derived extracellular vesicles from ataxic SCA3 mutation carriers are enriched in mitochondrial, nuclear, and nucleolar RNA biotypes compared to pre-ataxic and control subjects. Moreover, ataxic mutation carriers could be discriminated from control and pre-ataxic subjects based on the miRNAs or piRNAs content, but not tRNA. Furthermore, we identified a subset of differentially expressed miRNAs and piRNAs that clearly differentiate ataxic mutation carriers from pre-ataxic and control subjects.

These findings open new avenues for further investigation on the role of these RNAs in the pathogenesis of SCA3 and their potential as biomarkers for this disease.
PEMPS: A Phylogenetic Software Tool to Model the Evolution of Metabolic Pathways
Authors: McCloskey Nicholas S. , Mammedova Ayna , Liberles David A.
Published: January 2024

Background

Metabolic pathways support the enzyme flux that converts input chemicals into energy and cellular building blocks. With a constant rate of input, steady-state flux is achieved when metabolite concentrations and reaction rates remain constant over time. Individual genes undergo mutation, while selection acts on higher level functions of the pathway, such as steady-state flux where applicable. Modeling the evolution of metabolic pathways through mechanistic sets of ordinary differential equations is a piece of the genotype-phenotype map model for interpreting genetic variation and inter-specific differences. Such models can generate distinct compensatory changes and adaptive changes from directional selection, indicating single nucleotide polymorphisms and fixed differences that could affect phenotype. If used for inference, this would ultimately enable detection of selection on metabolic pathways as well as inference of ancestral states for metabolic pathway function.

Results

A software tool for simulating the evolution of metabolic pathways based upon underlying biochemistry, phylogenetics, and evolutionary considerations is presented. The Python program, Phylogenetic Evolution of Metabolic Pathway Simulator (PEMPS), implements a mutation-selection framework to simulate the evolution of the pathway over a phylogeny by interfacing with COPASI to calculate the steady-state flux of the metabolic network, introducing mutations as alterations in parameter values according to a model, and calculating a fitness score and corresponding probability of fixation based on the change in steady-state flux value(s). Results from simulations are consistent witha prioriexpectations of fixation probabilities and systematic change in model parameters.

Conclusions

The PEMPS program simulates the evolution of a metabolic pathway with a mutation-selection modeling framework based on criteria like steady-state flux that is designed to work with SBML-formatted kinetic models, and Newick-formatted phylogenetic trees. The Python software is run on the Linux command line and is available athttps://github.com/nmccloskey/PEMPS.
Antigen-display exosomes provide adjuvant-free protection against SARS-CoV-2 disease at nanogram levels of spike protein
Authors: Guo Chenxu , Sachithanandham Jaiprasath , Zhong William , Craney Morgan , Villano Jason , Pekosz Andrew , Gould Stephen J.
Published: January 2024

As the only bionormal nanovesicle, exosomes have high potential as a nanovesicle for delivering vaccines and therapeutics. We show here that the loading of type-1 membrane proteins into the exosome membrane is induced by exosome membrane anchor domains, EMADs, that maximize protein delivery to the plasma membrane, minimize protein sorting to other compartments, and direct proteins into exosome membranes. Using SARS-CoV-2 spike as an example and EMAD13 as our most effective exosome membrane anchor, we show that cells expressing a spike-EMAD13 fusion protein produced exosomes that carry dense arrays of spike trimers on 50% of all exosomes. Moreover, we find that immunization with spike-EMAD13 exosomes induced strong neutralizing antibody responses and protected hamsters against SARS-CoV-2 disease at doses of just 0.5-5 ng of spike protein, without adjuvant, demonstrating that antigen-display exosomes are particularly immunogenic, with important implications for both structural and expression-dependent vaccines.
Wild bird mass mortalities in eastern Canada associated with the Highly Pathogenic Avian Influenza A(H5N1) virus, 2022
Authors: Avery-Gomm Stephanie , Barychka Tatsiana , English Matthew , Ronconi Robert , Wilhelm Sabina I. , Rail Jean-François , Cormier Tabatha , Beaumont Matthieu , Bowser Campbell , Burt Tori V. , Collins Sydney , Duffy Steven , Giacinti Jolene A. , Gilliland Scott , Giroux Jean-François , Gjerdrum Carina , Guillemette Magella , Hargan Kathryn E. , Jones Megan , Kennedy Andrew , Kusalik Liam , Lair Stéphane , Lang Andrew S. , Lavoie Raphael , Lepage Christine , McPhail Gretchen , Montevecchi William A. , Parsons Glen J. , Provencher Jennifer F. , Rahman Ishraq , Robertson Gregory J. , Seyer Yannick , Soos Catherine , Ward Christopher R. E. , Wells Regina , Wight Jordan
Published: January 2024

In 2022, a severe outbreak of clade 2.3.4.4b Highly Pathogenic Avian Influenza (HPAI) H5N1 virus resulted in unprecedented mortality among wild birds in eastern Canada. Tens of thousands of birds were reported sick or dead, prompting a comprehensive assessment of mortality spanning the breeding season between April 1 and September 30, 2022. Mortality reports were collated from federal, Indigenous, provincial, and municipal agencies, the Canadian Wildlife Health Cooperative, non-governmental organizations, universities, and citizen science platforms. A scenario analysis was conducted to refine mortality estimates, accounting for potential double counts from multiple sources under a range of spatial and temporal overlap. Correcting for double counting, an estimated 40,966 wild birds were reported sick or dead in eastern Canada during the spring and summer of 2022. Seabirds and sea ducks, long-lived species that are slow to recover from perturbations, accounted for 98.7% of reported mortalities. Mortalities were greatest among Northern Gannets(Morus bassanus; 26,193), Common Murres (Uria aalge; 8,133), and American Common Eiders (Somateria mollissima dresseri;1,945), however, these figures underestimate total mortality as they exclude unreported deaths on land and at sea. In addition to presenting mortality estimates, we compare mortalities with known population sizes and trends and make an initial assessment of whether population-level impacts are possible for the Northern Gannet, a species that has suffered significant global mortality, and two harvested species, Common Murre and American Common Eider, to support management decisions. We hypothesize that population-level impacts in eastern Canada are possible for Northern Gannets and American Common Eiders but are unlikely for Common Murres. This study underscores the urgent need for further research to understand the broader ecological ramifications of the HPAI outbreak on wild bird populations.
SanA is an inner membrane protein mediating the early stages of Salmonella infection
Authors: Aleksandrowicz Adrianna , Kolenda Rafał , Thurston Teresa L M , Grzymajło Krzysztof
Published: January 2024

Bacterial membrane proteins, crucial for the interaction with the environment, encompass various functional molecules such as SanA. SanA is pivotal for the physicochemical properties of the bacterial membrane, influencingSalmonella’s antibiotic resistance and infection phenotype. Previous studies identified a link betweensanAmutation and increasedSalmonellainvasiveness, but the mechanisms underlying this phenomenon remain largely unexplored. Therefore, our research investigates SanA’s role duringSalmonellainfection, examining its expression pattern, localization within the cell, and association withSalmonellaPathogenicity Island I (SPI-I). Using subcellular fractionation and Western Blotting we revealed that SanA is predominantly located in the inner membrane. Additionally, we utilized transcriptional fusion to monitor SanA expression under various environmental conditions. We observed that SanA plays a significant role during the late exponential and early stationary growth phase and remains important 24 hours after the bacteria enter host cells. Moreover, our invasion assays demonstrated that deletion ofsanAin bacteria grown to early stationary phase significantly enhances their invasiveness, partly due to increased SPI-I expression, which is regulated in a nutrient availability-dependent manner. Our results highlight SanA’s essential role inSalmonella’s response to environmental stress, critical for its entry and survival in hostile environments. This research underscores the importance of inner membrane proteins in bacterial pathogenicity, particularly in the initial stages of infection.
Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex
Authors: Atapour Nafiseh , Rosa Marcello G. P. , Bai Shi , Bednarek Sylwia , Kulesza Agata , Saworska Gabriela , Worthy Katrina H. , Majka Piotr
Published: January 2024

The calcium-binding protein calbindin is selectively expressed in specific neuronal populations of the cerebral cortex, including major classes of inhibitory interneurons. We have charted the distribution of calbindin-positive (CB+) neurons across areas and layers of the entire marmoset cortex using a combination of immunohistochemistry, AI-based image segmentation, 3-dimensional reconstruction, and cytoarchitecture-aware registration. CB+neurons formed 10-20% of the cortical neuronal population, occurring in higher proportions in areas corresponding to low hierarchical levels of processing, such as sensory cortices. Although CB+neurons concentrated in the supragranular layers, there were clear trends in laminar distribution: the relative density in infragranular layers increased with hierarchical level, and the density in layer 4 was lowest in areas involved in sensorimotor integration and action planning. These results reveal new aspects of the cytoarchitectural organization of the primate cortex and demonstrate an efficient approach to mapping the full distribution of neurochemically distinct cell types throughout the brain, readily applicable to most mammalian species and parts of the nervous system.
High-resolution metabolite imaging: luteolinidin accumulates at the host-cyanobiont interface during cold-acclimation inAzollasymbioses
Authors: Güngör Erbil , Bartels Benjamin , Bolchi Giorgio , Heeren Ron M.A. , Ellis Shane R. , Schluepmann Henriette
Published: January 2024

Aquatic ferns of the genusAzolla(Azolla) form highly productive symbioses with filamentous cyanobacteria fixing N2in their leaf cavities,Nostoc azollae. Stressed symbioses characteristically turn red due to 3-deoxyanthocyanin (DA) accumulation, rare in angiosperms and of unknown function. To reveal DA functions upon cold acclimation and recovery, we integrated laser-desorption-ionization mass-spectrometry-imaging (LDI-MSI), a newA. filiculoidesgenome-assembly and annotation, and dual RNA-sequencing into phenotypic analyses of the symbioses.

Azolla sp.Anzali recovered even when cold-induced DA-accumulation was inhibited by abscisic acid. Cyanobacterial filaments generally disappeared upon cold acclimation, andN. azollaetranscript profiles were unlike those of resting stages formed in cold-resistant sporocarps, yet filaments re-appeared in leaf cavities of newly formed green fronds upon cold-recovery.

The high transcript accumulation upon cold acclimation ofAfDFR1encoding a flavanone 4-reductase activein vitrosuggested that the enzyme of the first step in the DA-pathway may regulate accumulation of DAs in different tissues. However, LDI-MSI highlighted the necessity to describe metabolite accumulation beyond class assignments as individual DA and caffeoylquinic acid metabolites accumulated differentially. For example, luteolinidin accumulated in epithelial cells, including those lining the leaf cavity, supporting a role for the former in the symbiotic interaction during cold acclimation.

Summary statement

During cold acclimation inAzollasymbioses, individual compounds from the same phenolic class accumulated in different host tissues: luteolinidin associated with biotic interactions at the symbiosis interface whilst apigenidin with photooxidative stress mitigation in the mesophyll.
Neural representations of predicted events: Evidence from time-resolved EEG decoding
Authors: Li Ai-Su , Theeuwes Jan , van Moorselaar Dirk
Published: January 2024

Through statistical learning, humans are able to extract temporal regularities, using the past to predict the future. Evidence suggests that learning relational structures makes it possible to anticipate the imminent future; yet, the neural dynamics of predicting the future and its time-course remain elusive. To examine whether future representations are denoted in a temporally discounted fashion, we used the high-temporal-resolution of electroencephalography (EEG). Observers were exposed to a fixed sequence of events at four unique spatial positions within the display. Using multivariate pattern analyses trained on independent pattern estimators, we were able to decode the spatial position of dots within full sequences, and within randomly intermixed partial sequences wherein only a single dot was presented. Crucially, within these partial sequences, subsequent spatial positions could be reliably decoded at their expected moment in time. These findings highlight the dynamic weight changes within the assumed spatial priority map and mark the first implementation of EEG to decode predicted, yet critically omitted events.

Impact statement

Utilizing high-temporal-resolution EEG, the dynamic weight changes of assumed spatial priority map were visualized by decoding the spatial position of expected, yet omitted, events at their expected moment in time.
Surface colonization byFlavobacterium johnsoniaepromotes its survival in a model microbial community
Authors: Magesh Shruthi , Hurley Amanda I. , Nepper Julia F. , Chevrette Marc G. , Schrope Jonathan H. , Li Chao , Beebe David J. , Handelsman Jo
Published: January 2024

Flavobacterium johnsoniaeis a ubiquitous soil and rhizosphere bacterium, but despite its abundance, the factors contributing to its success in communities are poorly understood. Using a model microbial community,TheHitchhikersOf the Rhizosphere (THOR), we determined the effects of colonization on fitness ofF. johnsoniaein the community. Insertion sequencing (INSeq), a massively parallel transposon mutant screen, on sterile sand identified 25 genes likely to be important for surface colonization. We constructed in-frame deletions of nine candidate genes predicted to be involved in cell membrane biogenesis, motility, signal transduction, and transport of amino acids and lipids. All mutants poorly colonized sand, glass, and polystyrene and produced less biofilm than the wild type, indicating the importance of the targeted genes in surface colonization. Eight of the nine colonization-defective mutants were also unable to form motile biofilms, or zorbs, thereby suggesting that the affected genes play a role in group movement and linking stationary and motile biofilm formation genetically. Furthermore, we showed that deletion of colonization genes inF. johnsoniaeaffected its behavior and survival in THOR on surfaces, suggesting that the same traits are required for success in a multispecies microbial community. Our results provide insight into the mechanisms of surface colonization byF. johnsoniaeand form the basis for further understanding its ecology in the rhizosphere.

IMPORTANCE

Microbial communities direct key environmental processes through multispecies interactions. Understanding these interactions is vital for manipulating microbiomes to promote health in human, environmental, and agricultural systems. However, microbiome complexity can hinder our understanding of the underlying mechanisms in microbial community interactions. As a first step towards unraveling these interactions, we explored the role of surface colonization in microbial community interactions using THOR, a genetically tractable model community of three bacterial species,Flavobacterium johnsoniae,Pseudomonas koreensis,andBacillus cereus.We identifiedF. johnsoniaegenes important for surface colonization in solitary conditions and in the THOR community. Understanding the mechanisms that promote success of bacteria in microbial communities brings us closer to targeted manipulations to achieve outcomes that benefit agriculture, the environment, and human health.
Macrophages drive the earliest anti-tumoral response to BCG therapy by directly killing bladder cancer through TNF signaling
Authors: Martinez-Lopez Mayra , de Almeida Cátia Rebelo , Fontes Marcia , Mendes Raquel Valente , Kaufmann Stefan H.E. , Fior Rita
Published: January 2024

The Bacillus Calmette-Guérin (BCG) vaccine is the cancer immunotherapy longest in use. Despite its effectiveness in bladder cancer (BC), its initial mechanisms of action remain largely unknown. Therefore, proper diagnostic assessments to identify patients who will not respond to treatment or develop resistance are lacking. Here, we set-out to unravel the earliest innate cellular mechanisms involved in BCG-induced clearance of tumors. We show that BCG induces a massive recruitment of macrophages to the tumor microenvironment and modulates their morphology and behavior towards a proinflammatory phenotype, while also promoting macrophage fusion-like events. We demonstrate that macrophages directly induce apoptosis and clearance of cancer cells through TNF-signaling and that they are indispensable for this antitumoral response since their depletion completely abrogates the BCG-anti tumor effect. Contrary to the general concept that macrophage antitumoral activities uniquely rely on stimulating an effective adaptive response, we demonstrate that macrophages alone can directly induce tumor killing and clearance; revealing an additional step to the BCG-induced tumor immunity model, that was not previously considered. In addition, we also provide proof-of-concept experiments demonstrating the potential of this uniquein vivopreclinical model to test new innate immunomodulators.
The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks
Authors: Zendrikov Dmitrii , Paraskevov Alexander
Published: January 2024

Thin pancake-like neuronal networks cultured on top of a planar microelectrode array have been extensively tried out in neuroengineering, as a substrate for the mobile robot’s control unit, i.e., as a cyborg’s brain. Most of these attempts failed due to intricate self-organizing dynamics in the neuronal systems. In particular, the networks may exhibit an emergent spatial map of steady nucleation sites (“n-sites”) of spontaneous population spikes. Being unpredictable and independent of the surface electrode locations, the n-sites drastically change local ability of the network to generate spikes. Here, using a spiking neuronal network model with generative spatiallyembedded connectome, we systematically show in simulations that the number, location, and relative activity of spontaneously formed n-sites (“the vitals”) crucially depend on the samplings of three distributions: 1) the network distribution of neuronal excitability, 2) the distribution of connections between neurons of the network, and 3) the distribution of maximal amplitudes of a single synaptic current pulse. Moreover, blocking the dynamics of a small fraction (about 4%) of non-pacemaker neurons having the highest excitability was enough to completely suppress the occurrence of population spikes and their n-sites. This key result is explained theoretically. Remarkably, the n-sites occur taking into account only short-term synaptic plasticity, i.e., without a Hebbian-type plasticity. As the spiking network model used in this study is strictly deterministic, all simulation results can be accurately reproduced. The model, which has already demonstrated a very high richness-to-complexity ratio, can also be directly extended into the three-dimensional case, e.g., for targeting peculiarities of spiking dynamics in cerebral (or brain) organoids. We recommend the model as an excellent illustrative tool for teaching network-level computational neuroscience, complementing a few benchmark models.
The kinetics of SARS-CoV-2 nsp7-11 polyprotein processing and impact on complexation with nsp16
Authors: Schamoni-Kast Kira , Krichel Boris , Damjanović Tomislav , Kierspel Thomas , Toker Sibel , Uetrecht Charlotte
Published: January 2024

In severe-acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, polyproteins (pp1a/pp1ab) are processed into non-structural proteins (nsps), which largely form the replication/transcription complex (RTC). The polyprotein processing and complex formation is critical and offers potential therapeutic targets. However, the interplay of polyprotein processing and RTC-assembly are poorly understood. Here, we studied two key aspects: The influence of the pp1a terminal nsp11 on the order of polyprotein processing by viral main protease Mproand the influence of polyprotein processing on core enzyme complex formation. We established a method based on native MS to determine rate constantskconsidering the structural environment. This enabled us to quantify the multi-reaction kinetics of coronavirus polyprotein processing for the first time. Our results serve as a blueprint for other multi-cleavage reactions. Further, it offers a detailed and quantifiable perspective to the dynamic reactions of SARS-CoV-2 polyprotein processing, which is required for development of novel antivirals.
Machine Learning-based Classification of transcriptome Signatures of non-ulcerative Bladder Pain Syndrome
Authors: Akshay Akshay , Besic Mustafa , Kuhn Annette , Burkhard Fiona C. , Bigger-Allen Alex , Adam Rosalyn M. , Monastyrskaya Katia , Gheinani Ali Hashemi
Published: January 2024

Lower urinary tract dysfunction (LUTD) presents a global health challenge with symptoms impacting a substantial percentage of the population. The absence of reliable biomarkers complicates the accurate classification of LUTD subtypes with shared symptoms such as non- ulcerative Bladder Pain Syndrome (BPS) and overactive bladder caused by bladder outlet obstruction with Detrusor Overactivity (DO). This study introduces a machine learning (ML)- based approach for the identification of mRNA signatures specific to non-ulcerative BPS.

Using next-generation sequencing (NGS) transcriptome data from bladder biopsies of patients with BPS, benign prostatic obstruction with DO and controls, our statistical approach successfully identified 13 candidate genes capable of discerning BPS from control and DO patients. This set was subsequently validated using Quantitative Polymerase Chain Reaction (QPCR) in a larger patient cohort. To confirm our findings, we applied both supervised and unsupervised ML approaches to the QPCR dataset. Notably, a three-mRNA signature TPPP3, FAT1, and NCALD, emerged as a robust classifier, effectively distinguishing patients with non- ulcerative BPS from controls and patients with DO. This signature was universally selected by both supervised and unsupervised approaches.

The ML-based framework used to define BPS classifiers not only establishes a solid foundation for comprehending the specific gene expression changes in the bladder of the patients with BPS but also serves as a valuable resource and methodology for advancing signature identification in other fields. The proposed ML pipeline demonstrates its efficacy in handling challenges associated with limited sample sizes, offering a promising avenue for applications in similar domains.
A choroid plexus apocrine secretion mechanism shapes CSF proteome and embryonic brain development
Authors: Courtney Ya’el , Head Joshua P. , Yimer Elizabeth D. , Dani Neil , Shipley Frederick B. , Libermann Towia A. , Lehtinen Maria K.
Published: January 2024

We discovered that apocrine secretion by embryonic choroid plexus (ChP) epithelial cells contributes to the cerebrospinal fluid (CSF) proteome and influences brain development in mice. The apocrine response relies on sustained intracellular calcium signaling and calpain-mediated cytoskeletal remodeling. It rapidly alters the embryonic CSF proteome, activating neural progenitors lining the brain’s ventricles. Supraphysiological apocrine secretion induced during mouse development by maternal administration of a serotonergic 5HT2C receptor agonist dysregulates offspring cerebral cortical development, alters the fate of CSF-contacting neural progenitors, and ultimately changes adult social behaviors. Critically, exposure to maternal illness or to the psychedelic drug LSD during pregnancy also overactivates the ChP, inducing excessive secretion. Collectively, our findings demonstrate a new mechanism by which maternal exposure to diverse stressors disruptsin uterobrain development.
Inositol polyphosphate multikinase regulates Th1 and Th17 cell differentiation by controlling Akt-mTOR signaling
Authors: Yuk Chae Min , Kim Dongeon , Hong Sehoon , Kim Mingyo , Jeong Hyun-Woo , Park Seung Ju , Min Hyungyu , Kim Wooseob , Kim Sang-Gyu , Seong Rho Hyun , Kim Seyun , Lee Seung-Hyo
Published: January 2024

Activated proinflammatory T helper (Th) cells, such as Th1 and Th17 cells, mediate immune responses against intra- and extra-cellular pathogens as well as cause the development of various autoimmune diseases. Inositol polyphosphate multikinase (IPMK) is a key enzyme essential for inositol phosphate and phosphoinositide metabolism, which is known to control major biological events such as growth; however, its role in the function of Th cells remains unclear. Here we show that the expression of IPMK is highly induced in distinct Th1 and Th17 subsets. Further, while conditional deletion of IPMK in CD4+T cells is dispensable for Th2-dependent immune responses, both Th1- and Th17-mediated immune responses are markedly diminished when this enzyme is absent resulting in reduced resistance toLeishmania majorinfection and attenuation of experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. In addition, IPMK-deficient naive CD4+T cells display aberrant T cell activation and impaired differentiation into Th17 cells, which is associated with reduced activation of Akt, mechanistic target of rapamycin (mTOR), and STAT3. Mechanistically, IPMK as a phosphatidylinositol 3-kinase (PI3-kinase) controls the production of phosphatidylinositol (3,4,5)-trisphosphate, thereby promoting T cell activation, differentiation, and effector functions. Our findings suggest that IPMK acts as a critical regulator of Th1 and Th17 differentiation, highlighting the physiological importance of IPMK in Th1- and Th17-mediated immune homeostasis.
Arm movements increase acoustic markers of expiratory flow
Authors: Werner Raphael , Selen Luc , Pouw Wim
Published: January 2024

The gesture-speech physics theory suggests that there are biomechanical interactions of the voice with the whole body, driving speech to align fluctuations in loudness and F0 with upper-limb movement. This exploratory study offers a possible falsification of the gesture-speech physics theory, which would predict effects of upper-limb movement on voice as well as respiration. We therefore investigate co-movement expiration. Seventeen participants were asked to produce a continuous exhalation for several seconds. After 3s, they execute one of five within-subject movement conditions with their arm with and without a wrist weight (no movement, elbow flexion, elbow extension, internal arm rotation, external arm rotation). We analyzed the smoothed amplitude envelope of the acoustic signal in relation to arm movement. Compared to no movement, all four movements lead to higher positive peaks in the amplitude peaks, while weight did not influence the amplitude. We also found that across movement conditions, positive amplitude peaks are structurally timed relative to peaks in kine-matics (speed, acceleration). We conclude that the reason why upper-limb movements affect voice loudness is still best understood through gesture-speech physics theory, where upper-limb movements affect the voice directly by modulating sub-glottal pressures. Multimodal prosody is therefore partly literally embodied.
MAIT cells protect against sterile lung injury
Authors: Zhang Xiawei , Li Shuailin , Lason Wojciech , Greco Maria , Klenerman Paul , Hinks Timothy SC
Published: January 2024

Mucosal-associated invariant T (MAIT) cells, the most abundant unconventional T cells in the lung, have been recently linked to tissue protection and repair. Their role, especially in sterile lung injury, is unknown. Using single cell RNA sequencing (scRNA-seq), spectral analysis and adoptive transfer in a bleomycin-induced sterile lung injury, we found that bleomycin activates murine pulmonary MAIT cells and induces an accompanying tissue repair programme, associated with a protective role against bleomycin-induced lung injury. MAIT cells drive the accumulation of type 1 conventional dendritic cells (cDC1), limiting tissue damage in a DNGR-1 dependent manner. Human scRNA-seq data revealed that MAIT cells were activated, with increased cDC populations in idiopathic pulmonary fibrosis patients. Thus, MAIT cells enhance defence against sterile lung injury by fostering cDC1-driven anti-fibrotic pathways.
Target-aware Molecule Generation for Drug Design Using a Chemical Language Model*
Authors: Xia Yingce , Wu Kehan , Deng Pan , Liu Renhe , Zhang Yuan , Guo Han , Cui Yumeng , Pei Qizhi , Wu Lijun , Xie Shufang , Chen Si , Lu Xi , Hu Song , Wu Jinzhi , Chan Chi-Kin , Chen Shuo , Zhou Liangliang , Yu Nenghai , Liu Haiguang , Guo Jinjiang , Qin Tao , Liu Tie-Yan
Published: January 2024

Generative drug design facilitates the creation of compounds effective against pathogenic target proteins. This opens up the potential to discover novel compounds within the vast chemical space and fosters the development of innovative therapeutic strategies. However, the practicality of generated molecules is often limited, as many designs focus on a narrow set of drug-related properties, failing to improve the success rate of subsequent drug discovery process. To overcome these challenges, we develop TamGen, a method that employs a GPT-like chemical language model and enables target-aware molecule generation and compound refinement. We demonstrate that the compounds generated by TamGen have improved molecular quality and viability. Additionally, we have integrated TamGen into a drug discovery pipeline and identified 7 compounds showing compelling inhibitory activity against the Tuberculosis ClpP protease, with the most effective compound exhibiting a half maximal inhibitory concentration (IC50) of1.9μM. Our findings underscore the practical potential and real-world applicability of generative drug design approaches, paving the way for future advancements in the field.
Glioblastoma cells imitate neuronal excitability in humans
Authors: Tong T , Ozsvar A , Eschen JT , Elbæk KJ , Cortnum SOS , Sindby AKR , Kristensen BW , Meier K , Mikic N , Sørensen JCH , Ting JT , Capogna M , Hou WH , Korshøj AR
Published: January 2024

Glioblastomas (GBM) are renowned for their pronounced intratumoral heterogeneity, characterized by a diverse array of plastic cell types, which poses a significant challenge to effective targeting and treatment [1]. Recent research has documented the presence of neuronal-progenitor-like transcriptomic cell states of GBM [2, 3], notably in the leading edge of the tumor, where synaptic input from adjacent neurons drives disease proliferation [4]. However, conflicting observations regarding GBM cell excitability, ranging from non-excitable [5] to neuron-like excitability [6], add complexity to our comprehension of the pathophysiological diversity of GBM cells. Here we established a novel experimental workflow enabling comprehensive and selective investigation of the electrophysiological characteristics of cancer cells and neurons within cancer-infiltrated organotypic tissue specimens from GBM patients, using viral genetic labelling to target cellular subtypes. We observed that GBM cells exhibit distinct electrophysiological features in humans, characterized by hyperexcitability and neuron-like action potential generation. Our research provides direct evidence of excitability and a comprehensive description of the electrophysiological characteristics of GBM cells in the cancer-infiltrated cortex of humans, contributing to a deeper understanding of the cellular biology of GBM. These insights have broader implications for understanding cell-cell interactions in malignant tumors and could inform targeted therapies across diverse cancer types, offering a new lens for tackling tumor heterogeneity.
Unraveling wheat endosperm development: epigenetic regulation and novel regulators for enhanced yield and quality
Authors: Zhao Long , Chen Jinchao , Zhang Zhaoheng , Wu Wenying , Lin Xuelei , Gao Mingxiang , Yang Yiman , Zhao Peng , Yao Yingyin , Zhang Aiming , Liu Dongcheng , Wang Dongzhi , Xiao Jun
Published: January 2024

Starch content and seed storage protein (SSP) composition are critical factors influencing wheat grain yield and quality. To uncover the molecular mechanisms governing their biosynthesis, we conducted transcriptome and epigenome profiling across key endosperm developmental stages, revealing that chromatin accessibility, H3K27ac, and H3K27me3 collectively regulate SSP and starch genes with varying impact. Population transcriptome and phenotype analyses highlighted the crucial role of accessible promoter regions as a genetic variation resource, influencing grain yield and quality in a core collection of wheat accessions. By integrating time-serial RNA-seq and ATAC-seq data, we constructed a hierarchical transcriptional regulatory network (TRN) governing starch and SSP biosynthesis, identifying 42 high-confidence novel candidates. These candidates exhibited overlap with genetic regions associated with grain size and quality traits, and their functional significance was validated through expression-phenotype association analysis among wheat accessions and TILLING mutants. In-depth functional analysis ofwheat abscisic acid insensitive 3-A1(TaABI3-A1) with genome editing knock-out lines demonstrated its role in promoting SSP accumulation while repressing starch biosynthesis through transcriptional regulation. An elite haplotype ofTaABI3-A1with higher grain weight was identified during the breeding process in China, and its superior trait was associated with alteredTaABI3-A1expression levels. Additionally, we identified the potential upstream regulator, wheat GAGA-binding transcription factor 1 (TaGBP1), influencingTaABI3-A1expression. Our study provides novel and high-confidence regulators, presenting an effective strategy for understanding the regulation of SSP and starch biosynthesis and contributing to breeding enhancement.
Dynamic evolution of the heterochromatin sensing histone demethylase IBM1
Authors: Zhang Yinwen , Jang Hosung , Luo Ziliang , Dong Yinxin , Xu Yangyang , Kantamneni Yamini , Schmitz Robert J.
Published: January 2024

Heterochromatin constitutes a fundamental aspect of genomes that is crucial for maintaining genome stability. In flowering plants, maintenance of heterochromatin relies on a positive feedback loop involving the histone 3 lysine nine methyltransferase (H3K9), KRYPTONITE (KYP), and the DNA methyltransferase, CHROMOMETHYLASE3 (CMT3). An H3K9 demethylase, INCREASED IN BONSAI METHYLATION 1 (IBM1), has evolved to modulate the activity of KYP-CMT3 within transcribed genes. The absence of IBM1 activity results in aberrant methylation of gene bodies, which is deleterious. This study demonstrates extensive genetic and gene expression variations inKYP,CMT3, andIBM1within and between flowering plant species. IBM1 activity inArabidopsis thalianais uniquely regulated by the abundance of H3K9me2 in a repetitive sequence within an intron preceding the histone demethylase domain. This mechanism enables IBM1 to monitor global levels of H3K9me2. We discovered that the methylated intron is prevalent across flowering plants, however, its underlying sequence exhibits dynamic evolution. Its absence in species lacking gene body DNA methylation suggests its primary role in sensing H3K9me2 and preventing its integration into these constitutively expressed genes. Furthermore, our investigation uncoveredArabidopsis thalianaaccessions resembling weakibm1mutants, several Brassicaceae species with reducedIBM1expression, and a potentialIBM1deletion. Evolution towards reduced IBM1 activity in some flowering plants could explain the frequent natural occurrence of diminished or lost CMT3 activity, ascmt3mutants inA. thalianamitigate the deleterious effects of IBM1.
Epsins oversee smooth muscle cell reprograming by influencing master regulators KLF4 and OCT4
Authors: Wang Beibei , Cui Kui , Zhu Bo , Dong Yunzhou , Wang Donghai , Singh Bandana , Wu Hao , Li Kathryn , Eisa-Beygi Shahram , Sun Yong , Wong Scott , Cowan Douglas B. , Chen Yabing , Du Mulong , Chen Hong
Published: January 2024

Smooth muscle cells in major arteries play a crucial role in regulating coronary artery disease. Conversion of smooth muscle cells into other adverse cell types in the artery propels the pathogenesis of the disease. Curtailing artery plaque buildup by modulating smooth muscle cell reprograming presents us a new opportunity to thwart coronary artery disease. Here, our report how Epsins, a family of endocytic adaptor proteins oversee the smooth muscle cell reprograming by influencing master regulators OCT4 and KLF4. Using single-cell RNA sequencing, we characterized the phenotype of modulated smooth muscle cells in mouse atherosclerotic plaque and found that smooth muscle cells lacking epsins undergo profound reprogramming into not only beneficial myofibroblasts but also endothelial cells for injury repair of diseased endothelium. Our work lays concrete groundwork to explore an uncharted territory as we show that depleting Epsins bolsters smooth muscle cells reprograming to endothelial cells by augmenting OCT4 activity but restrain them from reprograming to harmful foam cells by destabilizing KLF4, a master regulator of adverse reprograming of smooth muscle cells. Moreover, the expression of Epsins in smooth muscle cells positively correlates with the severity of both human and mouse coronary artery disease. Integrating our scRNA- seq data with human Genome-Wide Association Studies (GWAS) identifies pivotal roles Epsins play in smooth muscle cells in the pathological process leading to coronary artery disease. Our findings reveal a previously unexplored direction for smooth muscle cell phenotypic modulation in the development and progression of coronary artery disease and unveil Epsins and their downstream new targets as promising novel therapeutic targets for mitigating metabolic disorders.