bluuebunny/crossref_metadata_2025 huggingface dataset:
Creation and Validation of a Proteome-Wide Yeast Library for Protein Detection and Analysis
Authors: Baruch Din , Tsirkas Ioannis , Sass Ehud , Dubreuil Benjamin , Asraf Yeynit , Aharoni Amir , Schuldiner Maya , Klein Ofir
Published: January 2025

A significant challenge in cell biology is to uncover the function of uncharacterized proteins. Surprisingly a quarter of the proteome is still poorly understood even in the most well studied model organisms. Systematic methodologies, including the use of tagged protein collections, have emerged as a powerful approach to address this gap. Despite the availability of proteome- wide collections featuring various fused proteins, the impact of tag size on protein function highlighted the need for using minimally disruptive tags for functional genomic studies. To rise to this challenge, we have created a proteome-wide collection of yeast strains in which proteins are N-terminally tagged with the Hemagglutinin (HA) epitope. The library leverages the compact size of the HA tag to minimize drawbacks associated with larger tags while enabling efficient functional analysis. We showcase the potential uses of our library for systematically evaluating protein size, abundance and localization using anin vivolabeling approach. Our characterization underscores the potential utility of a proteome-wide HA-tagged library in revealing novel aspects of cell biology, providing an additional powerful tool for functional genomics.
Preparation of stagedCaenorhabditis elegansembryos using size filtration
Authors: Jhaveri Nikita S. , Mastronardo Maya K. , Collins J.B. , Andersen Erik C.
Published: January 2025

The free-living nematodeCaenorhabditis eleganshas been routinely used to study gene functions, gene interactions, and conserved signaling pathways. Most experiments require that the animals are synchronized to be at the same specific developmental stage. Bleach synchronization is traditionally used to obtain a population of staged embryos, but the method can have harmful effects on the embryos. The physical separation of differently sized animals is preferred but often difficult to perform because some developmental stages are the same sizes as others. Microfluidic device filters have been used as alternatives, but they are expensive and require customization to scale up the preparation of staged animals. Here, we present a protocol for the synchronization of embryos using mesh filters. Using filtration, we obtained a higher yield of embryos per plate than using standard bleach synchronization protocol and at a scale beyond microfluidic devices. Importantly, filtration does not affect downstream larval development assays as much as bleach synchronization does. In conclusion, we have exploited the differences in the sizes ofC. elegansdevelopmental stages to isolate embryo cultures suitable for use in high-throughput assays.
Functional Characterization of a Novel Long Non-Coding RNA inLeishmania braziliensisIdentified Through Computational Screening for Conserved RNA Structures
Authors: Espada Caroline R. , Anthon Christian , Magalhães Rubens D.M. , Quilles Junior José Carlos , Teles Natalia M.M. , Pais Fabiano , Orsine Lissur A. , de Almeida Letícia , Defina Tânia P. A. , Dowle Adam , Gorodkin Jan , Walrad Pegine B. , Cruz Angela K.
Published: January 2025

Leishmaniaparasites alternate between hosts, facing environmental changes that demand rapid gene expression adaptation. Lacking canonical RNA polymerase II promoters, transcription in these eukaryotes is polycistronic, with gene regulation occurring post-transcriptionally. Although non-coding RNAs (ncRNAs) have been identified inLeishmaniatranscriptomes, their functions remain unclear. Recognizing RNA structure’s importance, we performed a genome-wide alignment ofL. braziliensisand related species, identifying conserved RNA structures, 38 of which overlap with known ncRNAs. One such ncRNA,lncRNA45, was functionally characterized. Using a knockout cell line, we demonstrated thatlncRNA45is crucial for parasite fitness. Reintroducing the wild-typelncRNA45restored fitness, while a version with a single nucleotide substitution in the structured region did not. This mutation also altered RNA-protein interactions. These findings suggest thatlncRNA45’s regulatory role and protein interactions rely on its secondary structure. This study highlights the significance of structured lncRNAs inLeishmaniabiology and their potential as therapeutic targets. Further research into these ncRNAs could uncover new parasite regulation mechanisms and inspire novel treatment strategies.
Evaluation of the Hypertension Surveillance System at Pilot Hypertension Prevention and Control Health Facilities in Addis Ababa, Ethiopia, 2022
Authors: Goshim Nigus
Published: January 2025

Introduction

Hypertension is a major cause of premature death worldwide. Evaluating a surveillance system promotes the best use of data collection resources and ensures that systems operate effectively. It allows us to determine whether a specific system is useful for a particular public health initiative and is achieving the goals of the public health program and the data collection objectives. Ethiopian hypertension control initiatives were recently launched (2019) and implemented in limited health facilities. Therefore, this evaluation is aimed at the hypertension surveillance system of Addis Ababa, Ethiopia.

Method

A descriptive cross-sectional study was conducted from December 21 to 31, 2022. Eight health care facilities were evaluated based on updated CDC guidelines for evaluating public health surveillance systems, and one key informant from each facility was interviewed using semi structured questionnaire. The data were analyzed descriptively. The data were analyzed with Excel 2021 and summarized by the frequency mean, percentage and rate.

Results

The system detected cases (8/8) and monitored the control rate, attendance rate and missed visits. All interviewed staff (8/8) stated that the case definition, diagnosis and treatment algorism of hypertension were easy. Regarding acceptability, all staff believed that stakeholders were engaged, and 7/8 of the facilities recorded and reported data in a timely manner, but there was no acknowledgment given to the staff (0/8). The stability and data quality were 95% and 72.9, respectively. The representativeness was 24% to 36% based on prevalence, and regarding sex, it ranged from 88% to 108%. predictive positive value (31.4%) and zero flexibility.

Conclusion

The system was useful for detecting morbidities and retaining patients on treatment. It has good simplicity, acceptability and stability but requires improvement in its flexibility, representativeness, data quality and positive predictive value. The system is better able to scale up to other health facilities.
Optimizing mouse metatranscriptome profiling by selective removal of redundant nucleic acid sequences
Authors: Roos Morgan , Bunga Samuel , Tan Asako , Maissy Erica , Skola Dylan , Richter Alexander , Whittaker Daniel S. , Desplats Paula , Zarrinpar Amir , Conrad Rick , Kuersten Scott
Published: January 2025

Metatranscriptome (MetaT) sequencing is a critical tool for profiling the dynamic metabolic functions of microbiomes. In addition to taxonomic information, MetaT also provides real-time gene expression data of both host and microbial populations, thus permitting authentic quantification of the functional (enzymatic) output of the microbiome and its host. The main challenge to effective and accurate MetaT analysis is the removal of highly abundant rRNA transcripts from these complex mixtures of microbes, which can number in the thousands of individual species. Regardless of methodology for rRNA depletion, the design of rRNA removal probes based solely upon taxonomic content of the microbiome typically requires very large numbers of individual probes, making this approach complex to commercially manufacture, costly, and frequently technically infeasible. In previous work [1], we designed a set of depletion probes for human stool samples using a design strategy based solely on sequence abundance, completely agnostic of the microbiomal species present. Here, we show that the human-based probes are less effective when used with mouse cecal samples. However, adapting additional rRNA depletion probes specifically to cecal content provides both greater efficiency and consistency for MetaT analysis of mouse samples.

Importance

Sequencing total RNA from microbiome samples is seriously impaired by the overwhelming proportion of rRNA to mRNA content. As much as 99% of sequencing reads can be assigned to the rRNA content, thus removal of these abundant transcripts is critical to MetaT analysis. The use of Ribo Zero Plus rRNA depletion probes designed for human gut microbiomes proved to be less effective and more inconsistent across mouse cecal donor samples, a common experimental system for microbiome studies. In the present work, we have extended and refined a taxonomically-neutral probe design method for mouse cecal content. The additional probes were carefully chosen to limit the number needed for effective depletion to reduce both the cost and risk of introducing bias to MetaT analysis. Our results demonstrate this method as efficient and consistent for rRNA removal in mouse cecal samples, thus providing a significant increase in the number of mRNA-rich sequencing reads for MetaT analysis.
EEG Dynamical Features during Variable-Intensity Cycling Exercise in Parkinson’s Disease
Authors: Alizadeh Zahra , Arasteh Emad , Mirian Maryam S. , Sacheli Matthew A. , Murray Danielle , Appel-Cresswell Silke , McKeown Martin J.
Published: January 2025

1.

1.1.

Background

Exercise is increasingly recognized as a beneficial intervention for Parkinson’s disease (PD), yet the optimal type and intensity of exercise remain unclear. This study investigated the relationship between exercise intensity and neural responses in PD patients, using electroencephalography (EEG) to explore potential neural markers that could be ultimately used to guide exercise intensity.

1.2.

Method

EEG data were collected from 14 PD patients (5 females) and 8 healthy controls (HC) performing stationary pedaling exercises at 60 RPM with resistance adjusted to target heart rates of 30%, 40%, 50%, 60%, and 70% of maximum heart rate. Subjects pedaled for 3 minutes at each intensity level in a counterbalanced order. Canonical Time-series Characteristics (Catch-22) features and Multi-set Canonical Correlation Analysis (MCCA) were utilized to identify common profiles of EEG features at increasing exercise intensity across subjects.

1.3.

Results

We identified a statistically significant MCCA component demonstrating a monotonic relationship with pedaling intensity. The dominant feature in this component was Periodicity Wang (PW), related to the autocorrelation of the EEG. Analysis revealed a consistent trend across features: six features increased with intensity, indicating heightened rhythmic engagement and sustained neural activation, while three features decreased, suggesting reduced variability and enhanced predictability in neural responses. Notably, PD patients exhibited more rigid, consistent response patterns compared to healthy controls (HC), who showed greater flexibility and variability in their neural adaptation across intensities.

1.4.

Conclusion

This study highlights the feasibility of using EEG-derived features to track exercise intensity in PD patients, identifying specific neural markers correlating with varying intensity levels. PD subjects demonstrate less inter-subject variability in motor responses to increasing intensity. Our results suggest that EEG biomarkers can be used to assess differing brain involvement with the same exercise of increasing intensity, potentially useful for guiding targeted therapeutic strategies and maximizing the neurological benefits of exercise in PD.
Impaired glymphatic clearance independently contributes to poor outcomes in Parkinson’s disease
Authors: Zarkali Angeliki , Thomas George , Paterson Ross , Hannaway Naomi , Dobreva Ivelina , Heslegrave Amanda J , Veleva Elena , Zetterberg Henrik , Weil Rimona S
Published: January 2025

Background

Impaired glymphatic clearance may contribute to pathological accumulations in Parkinson’s (PD), but how it interacts with other processes causing dementia and poor outcomes remains unclear.

Objectives

Clarify how glymphatic clearance impacts cognition in PD and its interaction with established imaging markers.

Methods

We used diffusion tensor image analysis along the perivascular space (DTI-ALPS) as an indirect marker of glymphatic clearance in 98 PD patients (31 PD-poor outcomes: dementia, mild cognitive impairment, frailty or death within 3-year follow-up; 67 PD-good outcomes) and 28 controls. We assessed DTI-ALPS relationship to cognition, white matter (fibre cross-section), cortical thickness, iron accumulation (quantitative susceptibility mapping (QSM)), and plasma markers (phosphorylated tau-181 (p-tau181 and neurofilament light (NFL)) cross-sectionally and longitudinally.

Results

DTI-ALPS was lower in PD-poor outcomes compared to PD-good outcomes and controls (p=0.005) with further longitudinal reductions only in PD-poor outcomes (group*time interaction: β=-0.013, p=0.021). Lower DTI-ALPS was associated with lower fibre cross-section in P, at baseline and longitudinally but with different spatial distribution from white matter changes relating to PD cognition. There was no correlation between baseline DTI-ALPS and plasma ptau-181 (p=0.642), NFL (p=0.448) or baseline cortical thickness. Lower DTI-ALPS was associated with accelerated cortical thinning within left precentral gyrus and changes in brain iron distribution.

Conclusions

PD patients who develop poor outcomes show impaired glymphatic clearance at baseline that worsened longitudinally. DTI-ALPS correlated with white matter integrity and brain iron accumulation. However, both showed different spatial distribution than that seen in PD dementia; suggesting impaired glymphatic clearance contributes to cognitive decline in a distinct manner.
Repeated tDCS at clinically-relevant field intensity can boost concurrent motor learning in rats
Authors: Farahani Forouzan , Vöröslakos Mihály , Birnbaum Andrew M. , FallahRad Mohamad , Williams Preston T.J.A. , Martin John H. , Parra Lucas C.
Published: January 2025

Electric fields used in clinical trials with transcranial direct current stimulation (tDCS) are small, with magnitudes that have yet to demonstrate measurable effects in preclinical animal models. We hypothesized that weak stimulation will nevertheless produce sizable effects, provided that it is applied concurrently with behavioral training, and repeated over multiple sessions. We tested this here in a rodent model of dexterous motor-skill learning. We developed a preparation that allows concurrent stimulation during the performance of a pellet-reaching task in freely behaving rats. The task was automated to minimize experimenter bias. We measured field magnitudes intracranially to calibrate the stimulation current. In this study, only male rats were used. Animals were trained for 20 min with concurrent epicranial tDCS over 10 daily sessions. Behavior was recorded with high-speed video to quantify reaching dynamics. We also measured motor-evoked potentials (MEPs) bilaterally with epidural microstimulation. The new electrode montage enabled stable stimulation over 10 sessions with a field intensity of 2V/m at the motor cortex. The number of successful reaches improved across days of training, and the rate of learning was higher in the anodal group as compared to sham-control animals (F(1)=7.12, p=0.008, N=24). MEPs were not systematically affected by tDCS. Posthoc analysis suggests that tDCS modulated motor learning only for right-pawed animals, improving success of reaching, but limiting stereotypy in these animals. Repeated and concurrent anodal tDCS can boost motor-skill learning at clinically-relevant field intensities. In this animal model the effect interacted with paw preference and was not associated with corticospinal excitability.

Significance Statement

The effects of tDCS have been explored in numerous human clinical trials, but the mechanisms of action of weak electric fields remain unclear. In vitro studies show that constant electric fields at 2.5 V/m can enhance the efficacy of synapses undergoing plasticity. This study demonstrates in a rodent model that tDCS of only 2 Vm when applied concurrently to behavioral training can improve motor skill learning, and reduce stereotypy of reaching behavior. These effects accumulated over 10 days of training. Motor evoked potentials (MEP), which are often used to demonstrate plastic effects in humans on a time scale of hours, were not measurably affected by tDCS on this longer time scale.
RB1sequence variants in retinoblastoma. Analysis ofRB1variants in a database for correlation with pRB protein domains and clinical presentation
Authors: Diana Parma , Nicohol Tovar-Martelo , Florencia Giliberto , Irene Szijan
Published: January 2025

Retinoblastoma (RB) is the most common pediatric ocular tumor that occurs due to biallelic inactivation of theRB1tumor suppressor gene. RB may be unilateral or bilateral and is hereditary in 50% of cases. Inactivation of theRB1gene may occur by gross rearrangements (20%) or by small-length changes (80%): single nucleotide substitutions (SNVs) and insertions/deletions (INDELs). We analyzed the SNVs and INDELs of germinal origin, annotated in the databasehttp://rb1-lovd.d-lohmann.de, in order to find the frequency of different variants, their correlation with the protein pRB functional domains and with the clinical presentation. The number of mutation variants analyzed was 2103, 34% of them were nonsense, 34% indels, 22% splice-site and 10% missense. All these variants mainly gave rise to bilateral RB (88%), their frequency and distribution in relation to pRB domains varied between bilateral (Bi) and unilateral hereditary (Ug) RB. Nonsense variants occurred more frequently in Bi vs Ug, whereas missense variants were more frequent in Ug vs Bi. Indels and Splice-site variants were not significantly different between Bi and Ug. The most frequent pRB location of mutation variants was in the Pocket domain (the binding site of the E2F transcription factor), 58% for nonsense, 64% missense, 50% splice site and 45% INDELs. The slice-site of the consensus sequence most mutated was the first nucleotide of the donor, which is the driver of the splicing process.

Conclusions

The highest percentage of variants in RB corresponded to nonsense substitutions and indels, mainly affecting the Pocket domain, which is the major functional site for pRB regulatory process These results indicate the predominance of the most pathogenic variants in retinoblastoma.
Longitudinal wastewater-based surveillance of vancomycin-resistant Enterococci in tertiary-care hospitals
Authors: Au Emily , Acosta Nicole , Waddell Barbara J. , Lee Jangwoo , Du Kristine , Weyant R. Benson , Bautista Maria , McCalder Janine , Van Doorn Jennifer , Low Kashtin , Stefani September , Visser Gail , Clark Rhonda , Pitout Johann , Kim Joseph , Missaghi Bayan , Larios Oscar , Kanji Jamil , Vayalumkal Joseph , Leal Jenine , Westlund Paul , Quinn Robert R. , James Matthew , Lee Bonita , Pang Xiao-Li , Dalton Bruce , Frankowski Kevin , O’Grady Christine , Conly John M. , Hubert Casey R.J. , Parkins Michael D.
Published: January 2025

Vancomycin-resistantEnterococcus(VRE) is an important cause of healthcare-associated infections. We adapted wastewater-based surveillance as a tool to longitudinally monitor VRE in hospitals through the detection of vancomycin resistance genesvanAandvanB.

Methods

Wastewater from four tertiary-care hospitals (three adult and one pediatric, totaling >2300 inpatient beds) and all three municipal wastewater treatment plants (WWTP) in Calgary, Canada (∼1.4 million) was sampled weekly (March to September 2022) and every other week (September 2022 to March 2023). Wastewater pellets were collected, DNA extracted, andvanAandvanBquantified by qPCR.vanAandvanBgene copies were assessed as raw (copies/mL) and normalized with three different fecal biomarkers – total bacterial 16S-rRNA,BacteroidesHF183 16S-rRNA, and human 18S-rRNA. Raw and normalizedvanAandvanBabundance from each site was compared with clinically identified infections, vancomycin prescribing and hemodialysis services.

Findings

vanAabundance was up to1085-fold higher p<0.0001, Mann-Whitney) andvanBup to 32-fold higher (p<0.01, Mann-Whitney) in adult hospitals compared to an aggregate municipal signal and exhibited significantly greater variation. Strong correlations between each method of fecal normalization and raw-measuredvanAandvanBwere observed, and no analysis method proved superior (Spearman’s r=0.50–0.96, p<0.0001).vanAabundance was strongly correlated with hemodialysis provision (Spearman’s r=0.8357, p<0.0001) but not vancomycin prescribing.

Interpretation

Wastewater-based surveillance is a comprehensive, real-time tool capable of longitudinal hospital surveillance with the potential to transform the ability of infection control and antimicrobial stewardship programs to dynamically track, understand, and mitigate nosocomial antimicrobial-resistant pathogens.
Cell cycle-dependent cues regulate temporal patterning of theDrosophilacentral brain neural stem cells
Authors: Chaya Gonzalo N. Morales , Syed Mubarak Hussain
Published: January 2025

During nervous system development, diverse types of neurons and glia are sequentially generated by self-renewing neural stem cells (NSCs). Temporal changes in gene expression within NSCs are thought to regulate neural diversity; however, the mechanisms regulating the timing of these temporal gene transitions remain poorly understood.Drosophilatype II NSCs, like human outer radial glia, divide to self-renew and generate intermediate neural progenitors, amplifying and diversifying the population of neurons innervating the central complex, a brain region required for sensorimotor coordination. Type II NSCs express over a dozen genes temporally, broadly classified as early and late-expressed genes. A conserved gene, Seven-up mediates early to late gene expression by activating ecdysone receptor (EcR) expression. However, what determines the timing of EcR expression and, hence, early to late gene transition is unknown. This study investigates whether intrinsic mechanisms of cell cycle progression and cytokinesis are required to induce the NSC early-late transition. By generating mutant clones that arrest the NSC cell cycle or block cytokinesis, we show that both processes are necessary for the early-to-late transitions. When NSCs are cell cycle or cyto-kinesis arrested, the early gene Imp failed to be down-regulated and persisted into the old NSCs, while the late factors EcR and Syncrip failed to be expressed. Furthermore, we show that the early factor Seven-up is insufficient to drive the transition despite its normal expression in the cell cycle-or cytokinesis-inhibited NSCs. These results suggest that both intrinsic (cell cycle/cytokinesis) and extrinsic (hormone) cues are required for the early-late NSC gene expression transition.
Evolution of functional genomic diversity during a bottleneck
Authors: Schlichta Flávia , Peischl Stephan , Excoffier Laurent
Published: January 2025

Most species have been through population bottlenecks and range expansions, and the impact of these events on patterns of diversity has been well studied. In particular, it has been shown that initially rare neutral variants could readily fix on the front of range expansions or during bottlenecks, giving genomic signatures looking like selective sweeps. Here we expand on previous work by considering the dynamics of genomic diversity in (functional) regions harbouring deleterious variants during bottlenecks or during range expansions modelled as serial founder effects. We find that regions with very low levels of diversity (troughs) looking like selective sweeps can also readily form in these functional regions. Additionally, their properties depend on the dominance level of deleterious mutations. Trough density is higher and increases more rapidly in regions with co-dominant deleterious mutations than in regions with recessive mutations. Interestingly, we find that genetic diversity declines less rapidly in regions with partially recessive mutations than in regions with codominant ones or in regions with only neutral mutations. These features are generally enhanced in low recombination regions and for intermediate selection coefficients. If most deleterious mutations in a genome are partially recessive, it follows that functional low recombination regions should better preserve genetic diversity during range expansions than neutral regions of the genome.

Significance statement

Most research on the effects of selection on genetic diversity have been done in equilibrium populations, leaving a gap in our understanding of how selection acting on functional regions interacts with demographic changes. Our study reveals strikingly different impacts of purifying selection on genetic diversity depending on the dominance coefficient of deleterious mutations. While codominant variants create diversity dips resembling selective sweeps, recessive mutations can preserve genetic diversity during bottlenecks through the relatively understudied phenomenon of pseudo-overdominance. Our findings show how selective and demographic forces interact in more complex ways than previously thought and emphasize the importance of further exploring these dynamics to accurately interpret genetic variation in natural populations.
Repetitive stimulation modifies network characteristics of neural organoid circuits
Authors: Chow Siu Yu A. , Hu Huaruo , Duenki Tomoya , Asakura Takuya , Sugimura Sota , Ikeuchi Yoshiho
Published: January 2025

Neural organoids form complex networks but lack external stimuli and hierarchical structures crucial for refining functional microcircuits. In this study, we modeled the hierarchical and modular network organization by connecting multiple organoids and tested if the connection enhances the external stimuli-induced network refinement. We cultured networks of one, two, or three organoids on high-density microelectrode arrays, applied repetitive stimulation at two input locations from the microelectrodes, and monitored emergence of output signals that can decode the stimulus locations with machine learning algorithms. After two weeks of daily stimulation, networks of three organoids showed significantly higher stimulus decoding capability compared to the simpler one- or two-organoid networks. Long-term stimulation induced pronounced changes in the three-organoid network’s response patterns, spontaneous activity, and inter- and intra-organoid functional connectivity. These findings underscore the importance of hierarchical network organization, e.g. creating distinct subnetworks with specialized roles, for stimuli-induced formation of circuits with robust input-output functionality.
Phage defence system abundances vary across environments and increase with viral density
Authors: Meaden Sean , Westra Edze , Fineran Peter
Published: January 2025

The defence systems bacteria use to protect themselves from their viruses are mechanistically and genetically diverse. Yet the ecological conditions that predict when defences are selected for remain unclear, as substantial variation in defence prevalence has been reported. Experimental work in simple communities suggests ecological factors can determine when specific defence systems are most beneficial, but applying these findings to complex communities has been challenging. Here, we use a comprehensive and environmentally balanced collection of metagenomes to survey the defence landscape across complex microbial communities. We also assess the association between the viral community and the prevalence of defence systems. We identify strong environmental effects in predicting overall defence abundance, with animal-host-associated environments and hot environments harbouring more defences overall. We also find a positive correlation between the density and diversity of viruses in the community and the abundance of defence systems. This study provides insights into the ecological factors that influence the composition and distribution of bacterial defence systems in complex microbial environments and outlines future directions for the study of defence system ecology.
Molecular circuit betweenAspergillus nidulanstranscription factors MsnA and VelB to coordinate fungal stress and developmental responses
Authors: Bastakis Emmanouil , Gerke Jennifer , Özkan Seyma , Harting Rebekka , Lienard Tanja , Sasse Christoph , Xylakis Emmanouil S. , Aden Merle , Strohdiek Anja , Heinrich Gabriele , Grosse Verena , Braus Gerhard H.
Published: January 2025

Development and secondary metabolism of the filamentous fungusAspergillus nidulansare tightly controlled by concerted actions of several master regulator transcription factors. The connection between fungal development and cellular stress response programs is often elusive. Here we show that the MsnA zinc finger transcription factor, which controls salt-stress response, is a novel major player in fungal development. A molecular circuit among MsnA and the velvet domain regulator VelB was discovered, which mutually fosters the actions of both regulatory proteins during development. MsnA controls the expression of several genes encoding master transcriptional regulators of asexual as well as sexual development. In addition, MsnA affects directly and indirectly the synthesis of specific secondary metabolites relevant for fungal defense against other organisms and growth, in addition to salt-stress responses. Moreover, the expression of genes encoding the epigenetic regulators VapA and VipC are also directly controlled by MsnA. These subunits of the VapA-VipC-VapB methyltransferase signal transduction complex promote asexual differentiation. MsnA is therefore placed at a novel prominent position of the central regulatory network, which coordinates stress responses with the developmental and metabolic fate of the fungus.
Human and Rodent Seizures Demonstrate a Dynamic Interplay with Spreading Depolarizations
Authors: Norby Jacob H. , Hummel Daniel , Ricks Noah , Rolston John D. , Rahimpour Shervin , Voipio Juha , Trevelyan Andrew J. , Smith Elliot H. , Parrish R. Ryley
Published: January 2025

Seizure termination has been linked to spreading depolarizations (SDs) in experimental epilepsy models, and SDs have recently been suggested to protect against seizures. The precise mechanism, however, remains unclear. Additionally, the co-occurrence of SDs with human seizures remains debated.

In this study, we found that SDs are a prominent feature following ictal events in both human clinical recordings (n=20 seizures from 7 epilepsy patients) using direct-current amplifiers and in the 0 Mg2+model of ictogenesis from rodent brain slices (n=17).

Approximately one-third of rodent seizure-like events (SLEs) were associated with SDs, while all human seizures analyzed had associated infraslow shifts, a hallmark of SDs. SDs were more prominent in the lateral frontal, medial frontal, and lateral temporal lobes, as well as the insular cortex in human patients, but were observed in all recorded brain regions. In rodents, SDs clustered toward the end of ictal events, resulting in significantly shorter SLEs (SLE without SD: 32.60 ± 5.31 s; SLE with SD: 16.03 ± 4.45 s) and delayed onset of subsequent SLEs. These SDs also caused significant AC band silencing compared to SLEs without SDs. Interestingly, SLEs with SDs displayed significantly more low gamma activity during ictal events. Using ion- selective microelectrodes, we found no significant correlation between extracellular [K+] levels and SLEs ending in SDs, questioning the role of [K+]oin SD induction during seizures.

We observed more heterogeneity in human seizures than in rodent SLEs, with some human seizures showing SD-associated termination and others demonstrating SDs in the middle of ictal events; such intra-seizure SDs were never observed in our rodent model. The human data, collected from patients with intractable epilepsy, demonstrate clear SD propagation during seizures and show that SDs appear and propagate, in multiple brain regions simultaneously with ictal events.

Collectively, these results indicate that SDs are a hallmark of ictal activity and may contribute to seizure termination in both experimental and clinical settings. Furthermore, these findings provide unique insight into the neuronal dynamics that promote SD induction by showing that increased low gamma activity during SLEs is more predictive of SD induction than extracellular [K+] levels. We also add further support for the hypothesis that SDs are both anti- seizure and anti-ictogenic as they not only limit and delay subsequent ictal activity but also reduce the duration of SLEs. Taken together, these findings provide rationale for further exploration of SDs as a means to prematurely terminate life-threatening seizures.
In situ light-driven pH modulation for NMR studies
Authors: Barde Aarav , Han Ruixian , Olson Martin A. , Tonelli Marco , Rienstra Chad M. , Henzler-Wildman Katherine , Ravula Thirupathi
Published: January 2025

Proton exchange is a fundamental chemical event, and NMR provides the most direct readout of protonation events with site-specific resolution. Conventional approaches require manual titration of sample pH to collect a series of NMR spectra at different pH values. This requires extensive sample handling and often results in significant sample loss, leading to reduced signal or the need to prepare additional samples. Here, we introduce a novel approach to control pH in NMR samples using water soluble photoacids, which alter the pH of the solution from near neutral to acidic pH upon in situ photo-illumination. We show that the solution pH can be precisely controlled by choice of illumination wavelength and intensity and sufficient protons are released from the photoacid to achieve meaningful pH change in samples where the molecule of interest has significant buffering capacity, such as a >100 μM protein sample. The pH is monitoredin situusing internal standards with pH-sensitive chemical shifts. This method enables precise, calibrated, non-invasive change of sample pH within an NMR magnet, dramatically reducing the necessary sample handling. These findings highlight the potential of light-induced pH control in NMR experiments and increase the robustness and reliability of pH-dependent studies. With pH playing a key role in modulating chemical behavior in both biological and synthetic systems, the ability to study protonation states and modulate sample pH in a simple and precise manner that is compatible with high-resolution NMR studies of molecular structure and function has wide applications.

Entry for the Table of Contents

In this work, we introduce a novel approach to control pH in NMR samples using light-activated photoacids. By combining light stimuli with pH-sensitive molecules, we demonstrate the ability to precisely modulate pH without physically manipulating the sample. This method enables non-invasive pH titration in NMR studies, where pH plays a key role in protein function. Our findings highlight the potential of light-induced pH control to overcome existing limitations in NMR, providing a powerful tool for advancing protein research under controlled pH conditions.
Persistent large-scale changes in alternative splicing in prefrontal cortical neuron types following psychedelic exposure
Authors: Hsiao Yungyi , Fonseca Marcos AS , Tiemroth Alina S , Vasquez Estefany J , Gomez Andrea M
Published: January 2025

Psychedelics engage the serotonergic system as potent neuromodulators, increasing neuroplasticity in humans and rodents. Persistent changes in cognitive flexibility, emotional regulation, and social cognition are thought to underlie the therapeutic effects of psychedelics. However, the underlying molecular and cellular basis of psychedelic-induced plasticity remains unclear. Here, we identify persistent, cell type-specific alternative splicing changes in the mouse medial prefrontal cortex (mPFC) induced by a single dose of psychedelics. Combining deep RiboTag sequencing and bioinformatics, we find that a single dose of psychedelics modestly alters gene expression while dramatically shifting patterns of alternative splicing lasting at least a month. We connect our functional enrichment and alternative splicing analysis with changes in the extracellular matrix, synaptic physiology, and intrinsic physiology in parvalbumin interneurons days to a week after psychedelic treatment. Our dataset is an essential resource for understanding the persistent, cell type-specific effects of psychedelics on cortical cell types and functions.
Category-biased patches encircle core domain-general regions in the human lateral prefrontal cortex
Authors: Assem Moataz , Shashidhara Sneha , Glasser Matthew , Duncan John
Published: January 2025

The fine-grained functional organization of the human lateral prefrontal cortex (PFC) remains poorly understood. Previous fMRI studies delineated focal domain-general, or multiple-demand (MD), PFC areas that co-activate during diverse cognitively demanding tasks. While there is some evidence for category-selective (face and scene) patches, in human and non-human primate PFC, these have not been systematically assessed. Recent precision fMRI studies have also revealed sensory-biased PFC patches adjacent to MD regions. To investigate if this topographic arrangement extends to other domains, we analysed two independent fMRI datasets (n=449 and n=37) utilizing the high-resolution multimodal MRI approaches of the Human Connectome Project (HCP). Both datasets included cognitive control tasks and stimuli spanning different categories: faces, places, tools and body parts. Contrasting each stimulus category against the remaining ones revealed focal interdigitated patches of activity located adjacent to core MD regions. The results were robust, replicating across different executive tasks, experimental designs (block and event-related) and at the single subject level. Our results paint a refined view of the fine-grained functional organization of the PFC, revealing a recurring motif of interdigitated domain-specific and domain-general circuits. This organization offers new constraints for models of cognitive control, cortical specialization and development.
Apolipoprotein E ε4exacerbates microglia-mediated complement-dependent synapse loss caused by neuronalTpkdeficiency
Authors: Du Pengyue , Jin Boru , Wang Zijie , Zhao Binqiao , Sang Shaoming , Zhong Chunjiu
Published: January 2025

Thiamine pyrophosphokinse-1 (TPK) is a key enzyme that converts thiamine to functional thiamine diphosphate (TDP). TPK insufficiency and hence TDP reduction in neurons induced by amyloid-β deposition and diabetes, an independent risk factor of Alzheimer’s disease (AD), recapitulate multi-pathophysiological features in the brain of mice, similar to those in human AD.Apolipoprotein Eε4 allele(APOE4) is the most well-known genetic risk factor for AD. Clinical trials by boosting TDP using benfotiamine, a derivative of thiamine that significantly elevates TDP level in human encrythrocytes, have shown the inferior clinical efficacies inAPOE4carriers compared to non-APOE4 carriers. Clarifying the relationship between APOE4 and TPK expression and multi-pathophysiological characteristics of AD induced byTpkdeficiency in neurons is imperative. Here, we find that humanizedAPOE4didn’t directly affectTpkexpression of mice, but markedly aggravates behavior abnormalities ofTpk-cKO mice. Pathologically, theTpk-cKO mice with humanizedAPOE4knock-in (AE-cKO mice) exhibit more synapse loss than the mice with only humanizedAPOE4knock-in and theTpk-cKO mice. Transcriptomics and pathologic analysis identified thatAPOE4promoted the overactivation of microglia and the transition of microglia to a disease-associated and phagocytosis stateviaa complement-mediated pathway. Further, the C3aR antagonist significantly repressed microglia phagocytosis and synaptic elimination of the AE-cKO mice. Our results demonstrate thatAPOE4exacerbates behavior dysfunction ofTpk-cKO mice through microglia-mediated complement-dependent synaptic elimination. These findings provide important insights into the role of APOE4 in the pathogenesis of AD.
Loss of excitatory inputs and decreased tonic and evoked activity of locus coeruleus neurons in aged P301S mice
Authors: Downs Anthony M. , Kmiec Gracianne , Catavero Christina M. , McElligott Zoé A.
Published: January 2025

Tau pathology in the locus coeruleus (LC) is associated with several neurodegenerative conditions including Alzheimer’s disease and frontotemporal dementia. Phosphorylated tau accumulates in the LC and results in inflammation, synaptic loss, and eventually cell death as the disease progresses. Loss of LC neurons and noradrenergic innervation is thought to contribute to the symptoms of cognitive decline later in disease. While loss and degeneration of LC neurons has been well studied, less is known about changes in LC physiology at advanced stages of tau pathology that precedes neurodegeneration. In this study, we investigated theex vivoelectrophysiological properties of LC neurons in male and female mice from the P301S mouse model of tauopathy at 9 months of age, a time-point when significant tau accumulation, cell death, and cognitive impairments are observed. We found a reduction in excitatory inputs and changes in excitatory post-synaptic current kinetics in male and female P301S. There was also a decrease in spontaneous discharge of LC neurons and an increase in AP threshold in P301S mice of both sexes. Finally, we observed a decrease in excitability and increase in rheobase current in P301S mice. Despite the decrease in LC activity in slice, we did not identify differences in total tissue norepinephrine (NE) or NE metabolites in prefrontal cortex or hippocampus. Together these findings demonstrate reductions in the activity and excitability of LC neurons at late stages of tau accumulation. However, compensatory mechanisms may maintain normal NE levels in LC projection regionsinvivo.
Mass spectra of full-heavy and double-heavy tetraquark states in the conventional quark model
Authors: Meng Qi , Wang Guang-Juan , Oka Makoto
Published: January 2025

A comprehensive study of the S-wave heavy tetraquark states with identical quarks and antiquarks, specifically QQQ¯′Q¯′ (Q,Q′=c, b), QQs¯s¯/Q¯Q¯ss, and QQq¯q¯/Q¯Q¯qq (q=u, d), are studied in a unified constituent quark model. This model contains the one-gluon exchange and confinement potentials. The latter is modeled as the sum of all two-body linear potentials. We employ the Gaussian expansion method to solve the full four-body Schrödinger equations, and search bound and resonant states using the complex-scaling method. We then identify 3 bound and 62 resonant states. The bound states are all QQq¯q¯ states with the isospin and spin-parity quantum numbers I(JP)=0(1+): two bound bbq¯q¯ states with the binding energies, 153 MeV and 4 MeV below the BB* threshold, and a shallow ccq¯q¯ state at −15  MeV from the DD* threshold. The deeper bbq¯q¯ bound state aligns with the lattice QCD predictions, while ccq¯q¯ bound state, still has a much larger binding energy than the recently observed Tcc+ by LHCb collaboration. No bound states are identified for the QQQ¯′Q¯′, QQs¯s¯, and QQq¯q¯ with I=1. Our analysis shows that the bound QQQ¯′Q¯′ states are more probable with a larger mass ratio, mQ/mQ′. Experimental investigation for these states is desired, which will enrich our understanding of hadron spectroscopy and probe insights into the confinement mechanisms within tetraquarks.

Published by the American Physical Society
2025
Nearly optimal quasienergy estimation and eigenstate preparation of time-periodic Hamiltonians by Sambe space formalism
Authors: Mizuta Kaoru
Published: January 2025

Time-periodic (Floquet) systems are one of the most interesting nonequilibrium systems. As the computation of energy eigenvalues and eigenstates of time-independent Hamiltonians is a central problem in both classical and quantum computation, quasienergy and Floquet eigenstates are the important targets. However, their computation has difficulty of time dependence; the problem can be mapped to a time-independent eigenvalue problem by the Sambe space formalism, but it instead requires additional infinite-dimensional space and seems to yield higher computational cost than the time-independent cases. It is still unclear whether they can be computed with guaranteed accuracy as efficiently as the time-independent cases. We address this issue by rigorously deriving the cutoff of the Sambe space to achieve the desired accuracy and organizing quantum algorithms for computing quasienergy and Floquet eigenstates based on the cutoff. The quantum algorithms return quasienergy and Floquet eigenstates with guaranteed accuracy like quantum phase estimation, which is the optimal algorithm for outputting energy eigenvalues and eigenstates of time-independent Hamiltonians. While the time periodicity provides the additional dimension for the Sambe space and defines two different kinds of eigenstates, the query complexity of the algorithms achieves the near-optimal scaling in allowable errors. In addition, as a by-product of these algorithms, we also organize a quantum algorithm for Floquet eigenstate preparation, in which a preferred gapped Floquet eigenstate can be deterministically implemented with nearly optimal query complexity in the gap. These results show that, despite the difficulty of time dependence, quasienergy and Floquet eigenstates can be computed almost as efficiently as time-independent cases, shedding light on the accurate and fast simulation of nonequilibrium systems on quantum computers.

Published by the American Physical Society
2025
Synthesis and crystal structures of 4,4′-methylenebis(2,6-diethylaniline) and 4,4′-methylenebis(3-chloro-2,6-diethylaniline)
Authors: Smirnov Daniil E. , Morozov Oleg S. , Afanasyeva Ekaterina S. , Avdeev Viktor V.
Published: January 2025

The title compounds 4,4′-methylenebis(2,6-diethylaniline) (C21H30N2, 1) and 4,4′-methylenebis(3-chloro-2,6-diethylaniline) (C21H28Cl2N2, 2) are of significant interest as curing agents for a wide range of resins and as building blocks for sterically demanding compounds in the synthesis of ligands for catalysis. This paper describes their synthesis and the preparation of single crystals, with their structures determined through single-crystal X-ray analysis. The presence of the chlorine substituent slightly affects the twist angle between the two aromatic components. The molecules of compound 1 form a network structure through intermolecular N—H...N bonds and C—H...π interactions, while in the crystal structure of compound 2, the molecules are assembled solely through N—H...π interactions. Consequently, despite their chemical similarity, it is the precise structural data that enables us to explain their differing reactivity and opens up the possibility of evaluating steric properties for the development of new materials and ligands.