bluuebunny/crossref_metadata_2025 huggingface dataset:
Aspergillus latus: a cryptic causative agent of aspergillosis emerging in Japan
Authors: Shibata Saho , Uchida Momotaka , Ban Sayaka , Kamei Katsuhiko , Watanabe Akira , Yaguchi Takashi , Hubka Vit , Takahashi Hiroki
Published: November 2024

Allodiploid hybrid species,Aspergillus latus, belonging to sectionNidulantes, is a hybrid ofA. spinulosporusand unknown species closely related toA. quadrilineatusandA. subltus. This hybrid has often been misidentified as the species in sectionNidulantes, such asA. nidulans,A. spinulosporus,A. sublatus, or other cryptic species. A. latushas not been reported in Japan as well as Asia so far. In this study, we screened 23 clinical strains identified asA. spinulosporusisolated in Japan from 2012 to 2023 and found sevenA. latusstrains. To characterize theA. latusstrains, we conducted comprehensive phenotyping including morphological observation, whole genome sequences and phylogenetic analysis based on calmodulin (CaM) gene. In addition, we conducted antifungal susceptibility testing forA. latusstrains. As a result, the morphological characters ofA. latuswere more similar to those ofA. spinulosporuscompared toA. sublatus. However, the ascospore ofA. latusdiffered from that ofA. spinulosporus.A. latusphylogenetically clustered withA. spinulosporusandA. sublatus. Furthermore,A. latusstrains showed reduced susceptibility to caspofungin and amphotericin B compared toA. spinulosporus, while they were susceptible to azoles. Our results suggest thatA. latushas been a causative pathogen of aspergillosis in Japan since 2013.
Identification of the differences in molecular networks between idiopathic pulmonary fibrosis and lung squamous cell carcinoma using machine learning
Authors: Nojima Yosui , Mizuguchi Kenji
Published: November 2024

Idiopathic pulmonary fibrosis (IPF), a form of idiopathic interstitial pneumonia, is an independent risk factor for lung cancer. The prognosis of IPF patients with lung cancer is poorer than that of IPF patients without lung cancer, and preventive measures for lung cancer remain elusive in patients with IPF. To mitigate lung cancer onset in patients with IPF, understanding the distinct mechanisms that induce both diseases is crucial. We developed highly accurate machine learning (ML) models to classify patients with IPF and lung cancer using public RNA sequencing data. To construct the ML models, the random restart technique was applied to five algorithms, namely,k-nearest neighbors, support vector machines (SVM) with radial basis function kernel, SVM with linear kernel, eXtreme gradient boosting, and random forest. To identify differentially expressed genes between IPF and lung cancer, feature importance was calculated in the classification models. Furthermore, we detected somatic mutations impacting gene expression using lung cancer data. The ML models identifiedVCX2,TMPRSS11B,PRUNE2,PRG4,PZP,SCARA5,DES,HPSE2,HOXD11,S100A7A, andPLA2G2A11as differentially expressed genes. Somatic mutations were detected in four transcription factors,BHLHE40,MYC,STAT1, andE2F4, that regulate the expression of the abovementioned 11 genes. Furthermore, a molecular network was discovered, comprising the four transcription factors and 11 downstream genes. The newly identified molecular network enhances our understanding of the distinct mechanisms underlying IPF and lung cancer onset, providing new insights into the prevention of lung cancer complications in patients with IPF.
DockFormer: Efficient Multi-Modal Receptor-Ligand Interaction Prediction using Pair Transformer
Authors: Shor Ben , Schneidman-Duhovny Dina
Published: November 2024

Protein-small molecule interactions, or receptor-ligand interactions, are essential for understanding biological processes and advancing drug design. In this paper, we introduce DockFormer, a method that leverages multi-modal learning to predict both the binding affinity and structure of these interactions. DockFormer employs fully flexible docking, where no part of the receptor remains rigid, by adapting the AlphaFold2 architecture. Instead of relying on protein sequences and Multiple Sequence Alignments, DockFormer uses predicted receptor structures as input. This modification enables the model to concentrate on ligand docking prediction rather than protein folding, while preserving full receptor flexibility. The streamlined design also reduces the model size to just 8 layers, compared to AlphaFold2’s 48 layers, greatly accelerating the inference process and making it more efficient for large-scale screening. Benchmark tests on the PoseBusters dataset demonstrated a 27% success rate, while on an affinity benchmark, DockFormer achieved a Pearson correlation of 0.91. This optimized architecture offers a valuable tool for rapid and accurate virtual screening in drug discovery.
Single-cell metabolic oscillations are pervasive and may alleviate a proteome constraint
Authors: Wongprommoon Arin , Muñoz Alán F. , Oyarzún Diego A. , Swain Peter S.
Published: November 2024

Biological rhythms not only coordinate cellular activity with external signals, but may also enable internal coordination. The metabolic cycle in budding yeast is perhaps the most well-studied example. Historically researchers have investigated this cycle in populations growing in chemostats, but more recently time-lapse microscopy has revealed single-cell oscillations in the redox state of enzyme cofactors and in ATP levels. How to relate the results of these two types of assays is however unclear. Here we report single-cell rhythms too in intracellular pH and show that oscillations in the redox state of flavin molecules occur in auxotrophic and prototrophic strains, in nutrients favouring respiration or fermentation, and in deletion mutants for which oscillations in chemostats are either unobservable or disrupted. To explain the pervasiveness of these rhythms, we postulate that cells generate oscillations to alleviate a proteome constraint – amino acids cells use for one class of enzymes are unavailable for others. Using flux balance analysis with an enzyme-constrained genome-scale metabolic model, we show that, with a finite proteome, sequential synthesis of biomass components typically generates a shorter doubling time than synthesising components in parallel. Our results suggest that the metabolic cycle drives growth and is potentially widespread because all cells grow within a proteome constraint.
De novoassembled databases enable species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition
Authors: Klaes Simon , White Christian , Alvarez-Cohen Lisa , Adrian Lorenz , Ding Chang
Published: November 2024

Background

Protein-based stable isotope probing (Protein-SIP) is a powerful approach that can directly link individual taxa to activity and substrate assimilation, elucidating metabolic pathways and trophic relationships within microbiomes. In Protein-SIP, peptides and corresponding taxa are identified by database matches. Thus, database quality is crucial for accurate Protein-SIP analyses. For samples with unknown community composition, Protein-SIP usually employs broad-spectrum or metagenome-derived databases. However, broad-spectrum databases require advanced post-processing strategies and metagenome-derived databases can be costly to acquire. Further, both can inflate database size, negatively impacting peptide identification.

Results

Here, an approach in which we usede novoassembled databases for Protein-SIP on microbiomes with unknown community compositions is introduced. This approach enables databases to be directly generated from the mass spectrometry raw data usingde novopeptide sequencing. We then use the mass spectrometric data from labeled cultures to quantify isotope incorporation into specific peptides. We benchmark our approach against the canonical approach in which a sample-matching database is generated by DNA sequencing on three different datasets: 1) a proteome analysis from a defined microbial community containing13C-labeledE. colicells, 2) time-course data of an anammox-dominated continuous reactor after feeding with13C-labeled bicarbonate, and 3) a model of the human distal gut simulating a high-protein and high-fiber diet cultivated in either2H2O or H218O. Our results show thatde novodatabase assembly is applicable to different isotopes and detects similar amounts of labeled peptides compared to sample-matching databases. Furthermore, we show that peptide-centric Protein-SIP allows species-specific resolution, enabling the assessment of activity related to individual biological processes. Finally, we provide access to our modular Python pipeline to assist thede novoassembly of databases and subsequent peptide-centric Protein-SIP data analysis (https://git.ufz.de/meb/denovo-sip).

Conclusions

De novoassembled databases enable species-specific Protein-SIP of microbiomes without prior knowledge of the community composition.
Identification of regulatory promoter sequences directing MtCP6 transcription at the onset of nodule senescence in Medicago truncatula.
Authors: Yang Li , Frances Lisa , de Carvalho-Niebel Fernanda , Frendo Pierre , Boncompagni Eric
Published: November 2024

The symbiotic association of legumes with rhizobia results in the formation of new root organs called nodules. However, the lifespan of nodules is limited by the senescence process. Increased proteolytic activity is one of the hallmarks of nodule senescence. In Medicago truncatula, a papain cysteine protease encoding gene, MtCP6, is a marker for the onset of nodule senescence under both developmental and stress-induced pathways. To identify promoter regions conferring MtCP6 senescence-related expression, progressive MtCP6 promoter deletions were generated and the resulting sequences were fused with a reporter gene for promoter::GUS fusion analysis in transgenic M. truncatula roots. In planta, a minimal promoter sequence of 67 bp was identified as sufficient for specific spatiotemporal transcriptional activation of MtCP6 in nodules. The functionality of this cis-regulatory sequence, thereafter named Nodule Senescence (NS), was validated by both gain- and loss-of-function approaches. ERF091, an AP2/ERF family transcription factor, was identified in a yeast one-hybrid (Y1H) screen as an NS-box interacting factor, and shown to mediate transcription activation of a NS-box:GUS reporter in transactivation assays in Nicotiana benthamiana. This work uncovered a new senescence-related nodule specific cis-regulatory region (NS-box) and provided evidence for the likely involvement of a stress-related ERF family member in the regulation of MtCP6, at the onset of nodule senescence.
High-resolution 3-dimensional micro-CT imaging of the nucleus pulposus using a novel contrast agent
Authors: Buckles Madison M , Warda Nada H. , Moncher Jacob C. , Ansari Mohammad Yunus
Published: November 2024

Objective

The nucleus pulpous (NP) in the intervertebral disc (IVD) is the first structure to exhibit degenerative changes during IVD degeneration (IDD). Currently, micro-computed tomography (micro-CT) imaging of the NP is a limiting factor in detecting IDD at an early stage. In this study, we used potassium iodide (KI) as a contrast agent to stain the NP in the IVDs of the tails and spines of mice and rats and imaged them with a micro-CT scanner.

Methods

We collected tails and spines from 12-week-old mice and rats and stained them with KI followed by micro-CT imaging. To induce IDD, we performed caudal disc needle puncture surgery (NPS) in age and sex-matched mice (n=5) and stained the tail with KI for imaging with micro-CT to study disc degeneration.

Results

KI successfully stained and helped visualize the 3D structure of the NP, with X-ray attenuation properties comparable to bone. Contrast staining with KI enabled accurate and reproducible quantification of disc height and NP volume. The cross-sectional micro-CT images of NPS discs were indistinguishable from the histological findings of the same sample and showed similar degenerative changes in the NP. Additionally, we estimated that up to 15 sagittal sections, each 5μm thick with 75μm spacing, would be needed to fully assess disc degeneration.

Conclusion

This study demonstrated that KI can be used to positively stain NP in the intact tail or spine and provide qualitative and quantitative data without any adverse effect on the histological processing of the samples.
The general version of Hamilton’s rule
Authors: van Veelen Matthijs
Published: November 2024

The generality of Hamilton’s rule1,2is much debated3–14. In this paper, I show that this debate can be resolved by constructing a general version of Hamilton’s rule, which allows for a large variety of ways in which the fitness of an individual can depend on the social behaviour of oneself and of others. For this, I first derive the Generalized Price equation, which reconnects the Price equation15with the statistics it borrows its terminology from. The Generalized Price equation moreover shows that there is not just one Price equation, but there is a Price-like equation for every possible true model. This implies that there are also multiple, nested rules to describe selection. The simplest rule is the rule for selection of non-social traits with linear fitness effects. This rule is nested in the classical version of Hamilton’s rule, for which there is consensus that it works for social traits with linear, independent fitness effects. The classical version of Hamilton’s rule, in turn, is nested in more general rules, that for instance allow for nonlinear and/or interdependent fitness effects. The general version of Hamilton’s rule therefore is a constructive solution, that allows us to accurately describe when costly cooperation evolves in a wide variety of circumstances.
VaxLLM: Leveraging Fine-tuned Large Language Model for automated annotation ofBrucellaVaccines
Authors: Li Xingxian , Zheng Yuping , Hu Joy , Zheng Jie , Wang Zhigang , He Yongqun
Published: November 2024

Background

Vaccines play a vital role in enhancing immune defense and preventing the hosts against a wide range of diseases. However, research relating to vaccine annotation remains a labor-intensive task due to the ever-increasing volume of scientific literature. This study explores the application of Large Language Models (LLMs) to automate the classification and annotation of scientific literature on vaccines as exemplified onBrucellavaccines.

Results

We developed an automatic pipeline to automatically perform the classification and annotation ofBrucellavaccine-related articles, using abstract and title. The pipeline includes VaxLLM (Vaccine Large Language Model), which is a fine-tuned Llama 3 model. VaxLLM systematically classifies articles by identifying the presence of vaccine formulations and extracts the key information about vaccines, including vaccine antigen, vaccine formulation, vaccine platform, host species used as animal models, and experiments used to investigate the vaccine. The model demonstrated high performance in classification (Precision: 0.90, Recall: 1.0, F1-Score: 0.95) and annotation accuracy (97.9%), significantly outperforming a corresponding non-fine-tuned Llama 3 model. The outputs from VaxLLM are presented in a structured format to facilitate the integration into databases such as the VIOLIN vaccine knowledgebase. To further enhance the accuracy and depth of theBrucellavaccine data annotations, the pipeline also incorporates PubTator, enabling cross comparison with VaxLLM annotations and supporting downstream analyses like gene enrichment.

Conclusion

VaxLLM rapidly and accurately extracted detailed itemized vaccine information from publications, significantly outperforming traditional annotation methods in both speed and precision. VaxLLM also shows great potential in automating knowledge extraction in the domain of vaccine research.

Availability

All data is available athttps://github.com/xingxianli/VaxLLM, and the model was also uploaded to HuggingFace (https://huggingface.co/Xingxian123/VaxLLM).
Lysosomal calcium signalling contributes to the acute α-adrenergic response via calcium-stimulated adenylyl cyclase 1 and 8
Authors: Akerman Emily , Capel Rebecca A , Read Matthew , Song Qianqian , Bose Samuel J , Calamaio Serena , Aston Daniel , Koschinski Andreas , Lloyd Scott , Bell Laura , Rashbrook Victoria S , Keller Marco , Bracher Franz , Potter Barry VL , Rivolta Ilaria , Galione Antony , Sparrow Duncan B , Conti Alana , Terrar Derek A , Zaccolo Manuela , Burton Rebecca AB
Published: November 2024

Inositol trisphosphate (IP3), a calcium (Ca2+)-mobilizing second messenger, releases Ca2+from the sarcoplasmic reticulum (SR) via IP3receptors and modulates adenylyl cyclase (AC) activity in atrial myocytes. Lysosomes participate in Ca2+homeostasis by mobilising Ca2+in response to Nicotinic Acid Adenine Dinucleotide Phosphate (NAADP). We postulate that both downstream activation of Ca2+sensitive AC (AC1 and AC8) and lysosomal Ca2+signalling in response to IP3R activation contribute to atrial myocyte function and pacemaking. Ectopic application of phenylephrine (PE) increased chronotropy and inotropy and this response was reduced in the presence of NAADP pathway inhibitors (BZ-194 and SAN4825) and Bafilomycin A1. PE increased cyclic adenosine 3’-5’ monophosphate (cAMP) activity in neonatal rat atrial myocytes (NRAMs) and this was inhibited by NAADP pathway inhibitors. This inhibition was not observed in neonatal rat ventricular myocytes (NRVMs), revealing specificity of this response to NRAMs. We investigated expression of AC1 and AC8 as a possible explanation to these observations. Genetic perturbation of AC1 and AC8 by double-knockout ofAdcy1andAdcy8in a mouse model showed a decrease in positive chronotropic and inotropic response upon cumulative dose of PE in atrial tissue, reduced PE stimulated amplitude of Ca2+transient in isolated atrial myocytes and presented decreased cytosolic cAMP levels in response to PE in neonatal atrial myocytes that was not inhibited by NAADP pathway inhibitors. Our data identifies a link between NAADP and α-adrenergic signalling pathways in atrial myocytes, highlighting that lysosomal Ca2+is an important component of α-adrenergic stimulation in the cardiac atria and warrants further investigation.
Identification and Classification of Fungal GPCR Gene Families
Authors: Liu Zhiyin , Salamov Asaf , Grigoriev Igor V.
Published: November 2024

G protein-coupled receptors (GPCRs) are transmembrane proteins crucial for signal transduction in eu-karyotes, responding to diverse extracellular signals. Researchers have found 14 distinct types of GPCRs in fungi but their distribution among numerous fungal species remained largely unexamined. Our study identified and classified GPCRs in 1,357 fungal species, and shed light on GPCR distribution in fungi. The predominant class detected in fungi was Pth11-like GPCRs, exclusively found in Pezizomycotina and are notably acknowl-edged for their involvement in fungal pathogenicity. Our analysis suggested that Pezizomycotina ancestor possessed a more extensive array of Pth11-like GPCRs, but over time, some species underwent consider-able reductions in these GPCRs in conjunction with genome contractions. Additionally, we identified 2,089 mammalian homologs in Rhodopsin, Glutamate, and Frizzled classes across 594 fungal species, thereby augmenting the recognized fungal GPCR classes by three classes thought to be mammalian-specific. Utilizing a custom-built convolutional neural network (CNN) for the identification of fungal GPCRs, we discovered several potential novel fungal GPCRs. Moreover, anticipated interactions between these prospective new GPCRs and G-alpha proteins, as simulated by AlphaFold Multimer, offered further confirmation for these findings.
Leveraging the Human Panproteome to Enhance Peptide and Protein Identification in Proteomics and Metaproteomics
Authors: Canderan Jamie , Yuan Ruoying , Tang Haixu , Ye Yuzhen
Published: November 2024

In this paper, we developed a novel approach to utilize the human pangenome to improve peptide and protein identification from proteomic data (MS/MS spectra). We propose a new data structure called panproteome graph (PPG), in which nodes are tryptic peptides, to represent the human pangenome. The PPG can be built in linear time and can be utilized via graph traversal using a depth-first search algorithm to generate potential peptides for peptide identification in proteomics. The PPG built using the 47 human proteomes from the Human Pangenome Reference Consortium (HPRC) coupled with UniProt human proteins resulted in more than 4.2M tryptic peptides, a 26% increase as compared to when only the UniProt proteins were included. Graph-based analysis of the PPG revealed a giant disconnected component with about 3M nodes, suggesting substantial sharing of tryptic peptides among proteins. We applied tryptic peptides derived from PPG to characterize three collections of human proteomic and metaproteomic datasets, and our results showed that by exploiting the human pangenome, we were able to increase the number of identified peptides on all datasets we tested (about 8% increase across all three collections). We also showed that using more complete human proteome would be useful for reducing potential misidentification of human peptides as microbial peptides, a problem that was previously studied but based on genomic sequencing data. Our tool for building PPG is available in a GitHub repo PPGpep, and PPG-derived tryptic peptides can be utilized by MetaProD, a pipeline for both human and bacterial peptide and protein identification from (meta)proteomics datasets.
Mitochondrial and Microtubule Defects in Exfoliation Glaucoma
Authors: Venkatesan Arunkumar , Ridilla Marc , Castro Nileyma , Wolosin J Mario , Henty-Ridilla Jessica L. , Knox Barry E , Ganapathy Preethi S , Brown Jamin S , DeVincentis Anthony F , Sieminski Sandra , Bernstein Audrey M
Published: November 2024

Exfoliation Syndrome (XFS) is an age-related systemic condition characterized by large aggregated fibrillar material deposition in the anterior eye tissues. This aggregate formation and deposition on the aqueous humor outflow pathway are significant risk factors for developing Exfoliation Glaucoma (XFG), a secondary open-angle glaucoma. XFG is a complex, multifactorial late-onset disease that shares common features of neurodegenerative diseases, such as altered cellular processes with increased protein aggregation, impaired protein degradation, and oxidative and cellular stress. XFG patients display decreased mitochondrial membrane potential and mitochondrial DNA deletions. Here, using Tenon Capsule Fibroblasts (TFs) from Normal (No Glaucoma) and XFG patients, we found that XFG TFs have impaired mitochondrial bioenergetics and increased reactive oxygen species (ROS) accumulation. These defects are associated with mitochondrial abnormalities as XFG TFs exhibit smaller mitochondria that contain dysmorphic cristae, with an increase in mitochondrial localization to lysosomes and slowed mitophagy flux. Mitochondrial dysfunction in the XFG TFs was associated with an increase in the dynamics of the microtubule cytoskeleton, decreased acetylated tubulin, and increased HDAC6 activity. Treatment of XFG TFs with a mitophagy inducer, Urolithin A, and a mitochondrial biogenesis inducer, NAD+precursor, Nicotinamide Ribose, improved mitochondrial bioenergetics and reduced ROS accumulation. Our results demonstrate abnormal mitochondria in XFG TFs and suggest that mitophagy inducers may represent a potential class of therapeutics for reversing mitochondrial dysfunction in XFG patients.
Constructing Probabilistic Human Mobility Patterns for Estimating Total Exposures and Pathogen Transmission Using Aggregate Mobile Phone Data
Authors: Facelli Julio C. , Gouripeddi Ram
Published: November 2024

While phone location data is widely collected by providers and shared under special agreements with data aggregators, it is not available for research or routine surveillance purposes. Moreover, raw phone data may expose personal travel patterns which would not be ethically or lawful to use. One large data aggregator, Advan (https://advanresearch.com/) provides aggregate traffic patterns at weekly and monthly temporal resolution for many points of interest. This aggregate data is mostly used for commercial applications, but we argue that it can be also used to develop a model of probabilistic human mobility patterns at weekly or monthly resolution. Here we provide a stochastic algorithm that using the aggregate data provides realistic human mobility patterns at the intended temporal resolution. In the proposed model we associate a “person” with both a unique census block as the residence and another census block as the workplace. These human mobility patterns are dynamic and can be used in exposure models and in epidemiological models of epidemic spreads. Because these models do not assume any exposure or pathogen transmission mechanisms, they can be coupled to any external exposure fields or transmission model of infectious disease. Here we show how they can used to build a probabilistic model of exposure for an arbitrary exposure filed E(X, t) and a SIR contagion model. This probabilistic model can be developed at monthly or weekly time resolutions depending on the data source available and the specific programmatic needs.
RNA programmable cell targeting and manipulation with CellREADR
Authors: Yang Xiaolu , Woldemichael Kehali , Hover John , Zhao Shengli , Guo Xiao , Qian Yongjun , Gillis Jesse , Huang Z. Josh
Published: November 2024

Methods that provide specific, easy, and scalable experimental access to animal cell types and cell states will have broad applications in biology and medicine. CellREADR - Cell access through RNA sensing by Endogenous ADAR (adenosine deaminase acting on RNA), is a programmable RNA sensor-actuator technology that couples the detection of a cell-defining RNA to the translation of an effector protein to monitor and manipulate the cell. The CellREADR RNA device consists of a 5’ sensor region complementary to a cellular RNA and a 3’ payload coding region; payload translation is gated by the removal of a STOP codon in the sensor region upon base pairing with the cognate cellular RNA through an ADAR-mediated A- to-I editing mechanism ubiquitous to metazoan cells. CellREADR thus highlights the potential for RNA-based monitoring and manipulation of animal cells in ways that are simple, versatile, and generalizable across tissues and species. Here, we describe a detailed protocol for implementing CellREADR experiments in cell cultures and in animals. The procedure includes sensor and payload design, cloning, validation and characterization in mammalian cell cultures. The in vivo animal protocol focuses on AAV-based delivery of CellREADR using brain tissue as examples. We describe current best practices, various experimental controls and trouble-shooting steps. Beginning from sensor design, the validation of RNA sensor-actuators in cell cultures can be completed in 2-3 weeks. The construction of AAV vectors and their in vivo validation and characterization will take additional 6-8 weeks.
Modeling speech adaptation to altered sensory feedback through continuous learning of internal sensory predictions
Authors: Elie Benjamin , Šimko Juraj , Turk Alice
Published: November 2024

The paper presents a version of an optimization-based model of speech production that reproduces key acoustic and articulatory features of motorsensory adaptation to altered sensory feedback. In the presented approach, the mechanism of motorsensory adaptation is based on regular updates, based on the sensory feedback perceived by the speaker, of two of the speakers’ internal models used for computing (near)-optimal articulation. These internal models, modeled as separate Artificial Neural Networks, are 1) a model that predicts the acoustic consequences of motor (articulatory commands) and 2) a model that predicts the somatosensory sensations from given motor commands. The paper presents simulations of adaptation experiments that successfully reproduce key acoustic and articulatory features of motorsensory adaptation of speech to altered sensory feedback. These include gradual and incomplete motorsensory adaptation when the auditory (or the somatosensory) feedback is suddenly altered (F1-shifted for the altered auditory feedback, forced jaw movement for altered somatosensory feedback). The presented simulations also show that the rate and magnitude of adaptation behavior depend on a small number of parameters. Variation in the values of these parameters can potentially explain inter-speaker differences in terms of adaptation behavior, including sensory preference.
Identification of EcpK, a bacterial tyrosine pseudokinase important for exopolysaccharide biosynthesis inMyxococcus xanthus
Authors: Blöcher Luca , Schwabe Johannes , Glatter Timo , Søgaard-Andersen Lotte
Published: November 2024

Bacteria synthesize and export chemically diverse polysaccharides that function in many physiological processes and are widely used in industrial applications. In the ubiquitous Wzx/Wzy-dependent biosynthetic pathways for these polysaccharides, the polysaccharide co-polymerase (PCP) facilitates the polymerization of repeat units in the periplasm, and in Gram-negative bacteria, also polysaccharide translocation across the outer membrane. These PCPs are integral inner membrane proteins with extended periplasmic domains, and functionally depend on alternating between different oligomeric states. The oligomeric state, in turn, is determined by a cognate cytoplasmic bacterial tyrosine kinase (BYK), which is either part of the PCP or a stand-alone protein. Interestingly, BYK-like proteins, which lack key catalytic residues and/or the phosphorylated Tyr residues, have been described. InMyxococcus xanthus, the exopolysaccharide (EPS) is synthesized and exportedviathe Wzx/Wzy-dependent EPS pathway in which EpsV serves as the PCP. Here, we confirm that EpsV lacks the BYK domain. Using phylogenomics, experiments and computational structural biology, we identify EcpK as important for EPS biosynthesis and show that it structurally resembles canonical BYKs but lacks residues important for catalysis and Tyr phosphorylation. Using proteomic analyses, two-hybrid assays and structural modeling, we demonstrate that EcpK directly interacts with EpsV. Based on these findings, we suggest that EcpK is a BY pseudokinase and functions as a scaffold, which by direct protein-protein interactions, rather than by Tyr phosphorylation, facilitates EpsV function. EcpK and EpsV homologs are present in other bacteria, suggesting a broad conservation of this mechanism.

Importance

Bacteria produce a variety of polysaccharides with important biological functions. In Wzx/Wzy-dependent pathways for the biosynthesis of secreted and capsular polysaccharides in Gram-negative bacteria, the polysaccharide co-polymerase (PCP) is a key protein that facilitates repeat unit polymerization and polysaccharide translocation across the outer membrane. PCP function depends on assembly/disassembly cycles that are determined by the phosphorylation/dephosphorylation cycles of an associated bacterial tyrosine kinase (BYK). Here, we identify the BY pseudokinase EcpK as essential for exopolysaccharide biosynthesis inMyxococcus xanthus. Based on experiments and computational structural biology, we suggest that EcpK is a scaffold protein, guiding the assembly/disassembly cycles of the partner PCPviabinding/unbinding cycles independently of Tyr phosphorylation/dephosphorylation cycles. We suggest that this novel mechanism is broadly conserved.
Epistasis in the receptor binding domain of contemporary H3N2 viruses that reverted to bind sialylated diLacNAc repeats
Authors: Liang Ruonan , Peccati Francesca , Ponse Niels L.D. , Uslu Elif , Boons Geert-Jan , Unione Luca , de Vries Robert P.
Published: November 2024

Since the introduction of H3N2 influenza A viruses in the human population, these viruses have continuously evolved to escape human immunity, with mutations occurring in and around the receptor binding site. This process, called antigenic drift, recently resulted in viruses that recognize elongated glycans that are not abundantly displayed in the human respiratory tract. Such receptor specificities hampered our ability to pick and propagate vaccine strains. Using ELISA, glycan array, tissue staining, flow cytometry, and hemagglutinin assays, this study revealed that the most recent H3N2 viruses have expanded receptor specificity by regaining effective recognition to shorter glycans. In recent H3 strains, Y159 and T160 are responsible for restricted binding to elongated glycans; in contemporary strains, however, Y159N and T160I dominate with a consequent loss of strength in receptor binding. Yet, effective receptor interaction is rescued by a remote mutation in the 190-helix, Y195F. The results demonstrate epistasis of critical residues in three of the four structural elements composing the HA receptor-binding site (the 130-loop, 150-loop, and 190-helix), which synergistically contribute to shape receptor binding specificity. Interestingly, a positive correlation exists between binding to an asymmetrical N-glycan containing an α2,6 sialylated tri-LacNAc arm and binding to human and ferret respiratory tract tissues. Together, these results elucidate the epistatic nature of receptor binding specificity during influenza A virus H3N2 evolution.
Colour morphs as alternative solutions to the trade-off predicted by the Immuno-Competence Handicap Hypothesis
Authors: Sacchi Roberto , Coladonato Alan J. , Scali Stefano , Zuffi Marco A. L. , Palme Rupert , Mangiacotti Marco
Published: November 2024

Colour morphs in polymorphic species represent a suite of heritable traits controlled by separate sets of loci, which correspond to alternative peaks in the fitness surfaces. Pleiotropic effects of hormones have been hypothesized to be involved in the maintenance of morphs, but no experiments have been done to test it so far. In this study, we experimentally increased testosterone plasma levels in colour morph of the common wall lizards to test if white and yellow morphs follow two alternative strategies imposed by trade-off depicted in the Immuno-Competence Handicap Hypotheses. Yellow males invest in a more aggressive behaviour at the expense of a reduced immune function, whereas white males invest in greater survival at the expense of a reduced competitiveness. Plasma T levels were increased through transdermal administration. Before and after treatment, we measured i) the immune-response of lizards through phytohaemoagglutinin (PHA), and ii) the aggressive response by the introduction of a small mirror into the plastic enclosure to mimic the intrusion of a stranger male in its own territory. The hormone administration caused a higher immune-suppression in white than yellow males, and a switch to less aggressive behaviour against the mirrored image. Overall, increased plasma testosterone levels resulted in the disappearance of differences between morphs of both immune-response and aggressive behaviour. These results supplied experimental evidence of the existence of morph-specific strategies in common wall lizards depending on the investment in territorial aggression or in a longer survival, as alternative solutions to the trade-off predicted by the Immuno- Competence Handicap Hypothesis.
PyRID: A Brownian dynamics simulator for reacting and interacting particles written in Python
Authors: Becker Moritz , Safari Nahid , Tetzlaff Christian
Published: November 2024

Recent technological developments in molecular biology led to large data sets providing new insights into the molecular organisation of cells. To fully exploit their potential, these developments have to be complemented by computer simulations that allow to gain in-depth understanding on molecular principles. We developed the Python-based, reaction-diffusion simulator PyRID, integrating many features for the efficient simulation of molecular biological systems. Amongst others, PyRID is capable of simulating unimolecular and bimolecular reactions as well as pairinteractions to assess the dynamics resulting from individual interacting proteins to polydisperse substrates consisting of many different molecules. Furthermore, PyRID supports mesh-based compartments and surface diffusion of particles, enabling analyses of the interaction between (trans-)membrane proteins with intra- and extracellular proteins. PyRID is written entirely in Python, which is a programming language being known for its readability and easy accessibility, such that the scientific community can easily extend PyRID to its current and future needs.
Frontopolar cortex stimulation induces prolonged disruption to counterfactual processing: insights from altered local field potentials
Authors: Ainsworth Matthew , Galeazzi Juan M. , Pedreira Carlos , Stokes Mark G. , Buckley Mark J.
Published: November 2024

Frontopolar cortex (FPC) is a large, anterior sub-region of prefrontal cortex found in both humans and non-human primates (NHPs) and is thought to support monitoring the value of switching between alternative goals. However, the neuronal mechanisms underlying this function are unclear. Here we used multielectrode arrays to record the local field potentials (LFPs) in the FPC of two macaques performing a Wisconsin Card Sorting Test analogue and found that bursts of gamma and beta in FPC tracked counterfactual not current rule value. Moreover, we show that brief high-frequency microstimulation to a single trial causally affects both LFP activity in FPC, as well as rule-guided decision-making across successive trials. Following stimulation of FPC we observed reduced exploration of the counterfactual rule pre-rule-change, as well as a delayed adaptation to the newly relevant following post-rule-change. A similar, multi-trial time-course disturbance to beta and gamma activity within FPC was also induced following single-trial microstimulation. These findings conclusively link neuronal activity in FPC with behavioural monitoring of the value of counterfactual rules and provide neural mechanistic insights into how FPC supports rule-based decision-making.

Significance statement

Increasing evidence from human and non-human primates has prompted theories linking FPC with the control of exploration during decision-making. However, it is current unclear how the neuronal activity within frontal pole supports exploratory decision-making processes. Here we show that rhythmic activity, in the beta and gamma bands, recorded from FPC is correlated both with outcome of the previous choice, and the value of switching to an alternative choice. Furthermore, we show that disrupting beta and gamma activity within FPC causally influences exploratory decision-making: initially decreasing exploration before impairing adaptation to abstract rule changes. Together these findings provide the first mechanistic insight into how the neuronal activity within FPC can support exploratory behaviour.
Growth rate regulates RNA polymerase II transcription elongation inSaccharomyces cerevisiae
Authors: Garrido-Godino A.I. , González R. , Martín-Expósito M. , Chávez S. , Pérez-Ortín J.E. , Navarro F.
Published: November 2024

Cells must adapt to changing environmental conditions to maintain their fitness and to compete with other genotypes during the natural selection process. The growth rate (GR) is a determining factor in this competition, and it influences gene expression. Some genes increase mRNA levels, while others decrease with the GR. mRNA levels depend on the dynamic balance between their synthesis by RNA polymerase II and their degradation rates. RNA polymerase I and III are also influenced by the GR because they transcribe protein synthesis machinery required to make proteins that increase cell mass during growth. Although RNA levels have been extensively studied in relation to the GR in many organisms, synthesis and degradation rates have, however, been much less investigated. In a previous work, we found a positive correlation between RNA polymerase (RNA pol) II transcription and mRNA degradation with GRs in yeast in batch cultures. Here we extend our study under constant growth conditions in a chemostat and find that overall chromatin-associated RNA pol II levels increase in parallel with the GR. This increase appears to involve the accumulation of partially dephosphorylated RNA pol II with a greater tendency to backtracking, which suggests that the GR regulates RNA pol II-dependent transcription at the elongation level. RNA pol I also increases its association with chromatin with the GR, which confirms the general dependence of at least RNA pol I and II transcription on the GR.
Structural Insights into Broad-Range Polyphosphate Kinase 2-II Enzymes Applicable for Pyrimidine Nucleoside Diphosphate Synthesis
Authors: Kuge Marco , Keppler Michael , Friedrich Florian , Saleem-Batcha Raspudin , Winter Juliana , Prucker Isabel , Germer Philipp , Gerhardt Stefan , Einsle Oliver , Jung Manfred , Jessen Henning J. , Andexer Jennifer N.
Published: November 2024

Polyphosphate kinases (PPK) play crucial roles in various biological processes, including energy storage and stress responses, through their interaction with inorganic polyphosphate (polyP) and the intracellular nucleotide pool. Members of the PPK family 2 (PPK2s) catalyse polyP-consuming phosphorylation of nucleotides. In this study, we characterised two PPK2 enzymes fromBacillus cereus(BcPPK2) andLysinibacillus fusiformis(LfPPK2) to investigate their substrate specificity and potential for selective nucleotide synthesis. Both enzymes exhibited a broad substrate scope, selectively converting over 85% of pyrimidine nucleoside monophosphates (NMPs) to nucleoside diphosphates (NDPs), while nucleoside triphosphate (NTP) formation was observed only with purine NMPs. Preparative enzymatic synthesis of cytidine diphosphate (CDP) was applied to achieve an yield of 49%. Finally, structural analysis of five crystal structures ofBcPPK2 andLfPPK2 provided insights into their active sites and substrate interactions. This study highlights PPK2-II enzymes as promising biocatalysts for the efficient and selective synthesis of pyrimidine NDPs.
Sex chromosomes shape the transcriptional landscape of the preimplantation mouse embryo
Authors: Snell Daniel M. , Varsally Wazeer , Courtois Aurélien , Menchero Sergio , Munusamy Prabhakaran , Rietdijk Richelle , Ojarikre Obah A. , Strohbuecker Stephanie , Kaya Haskan , Sangrithi Mahesh N. , Turner James M.A.
Published: November 2024

Sex chromosomes are emerging as key regulators of adult health and disease in males (XY) and females (XX), but their impact on embryo development is poorly understood. Using single-cell RNA sequencing (scRNA-seq) on wild type and aneuploid mouse embryos, we show that sex chromosomes significantly shape the preimplantation embryo transcriptional landscape. A hierarchy of effects are identified, distinctly mediated by the Y chromosome, the dosage of X chromosomes, X-chromosome imprinting, and byXist, the non-coding RNA that initiates X-inactivation. The sex chromosomes have strongtranseffects on autosomal gene expression throughout preimplantation development. The Y chromosome has an unexpectedly pronounced impact on the trophectoderm, the precursor of the placenta, and this property is shared with genes expressed from the inactive X chromosome. The paternal and maternal X chromosomes differentially promote preimplantation growth, and we identify multiple novel candidate X-linked imprinted genes mediating this effect. Our findings show that sex chromosomes impact the embryo from the beginning of life, long before the appearance of overt sex differences.
Cortical neural activity during responses to mechanical perturbation: Effects of hand preference and hand used
Authors: Hooks Kevin , Kiani Kimia , Fu Qiushi
Published: November 2024

Handedness, as measured by self-reported hand preference, is an important feature of human behavioral lateralization that has often been associated with hemispheric specialization. We examined the extent to which hand preference and whether the dominant hand is used or not influence the motor and neural response during voluntary unimanual corrective actions. The experimental task involved controlling a robotic manipulandum to move a cursor from a center start point to a target presented above or below the start. In some trials, a mechanical perturbation of the hand was randomly applied by the robot either consistent or against the target direction, while electroencephalography (EEG) was recorded. Twelve left-handers and ten right-handers completed the experiment. Left-handed individuals had a greater negative peak in the frontal event-related potential (ERP) than right-handed participants during the initial response phase (N150) than right-handed individuals. Furthermore, left-handed individuals showed more symmetrical ERP distributions between two hemispheres than right-handed individuals in the frontal and parietal regions during the late voluntary response phase (P390). To the best of our knowledge, this is the first evidence that demonstrates the differences in the cortical control of voluntary corrective actions between left-handers and right-handers.
Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis
Authors: Schärfen Leonard , Vock Isaac W. , Simon Matthew D. , Neugebauer Karla M.
Published: November 2024

An RNA’s catalytic, regulatory, or coding potential depends on RNA structure formation. Because base pairing occurs during transcription, early structural states can govern RNA processing events and dictate the formation of functional conformations. These co-transcriptional states remain unknown. Here, we develop CoSTseq, which detects nascent RNA base pairing within and upon exit from RNA polymerases (Pols) transcriptome-wide in living yeast cells. By monitoring each nucleotide’s base pairing activity during transcription, we identify distinct classes of behaviors. While 47% of rRNA nucleotides remain unpaired, rapid and delayed base pairing – with rates of 48.5 and 13.2 kb-1of transcribed rDNA, respectively – typically completes when Pol I is only 25 bp downstream. We show that helicases act immediately to remodel structures across the rDNA locus and facilitate ribosome biogenesis. In contrast, nascent pre-mRNAs attain local structures indistinguishable from mature mRNAs, suggesting that refolding behind elongating ribosomes resembles co-transcriptional folding behind Pol II.
Adolescent-like Processing of Behaviorally Salient Cues in Sensory and Prefrontal Cortices of Adult Preterm-Born Mice
Authors: McCoy Emily , Pendala Vyshnavi , Fariborzi Mona , Demir Lara Y. , Buell Olivia , Fedde Samuel , Stinger Jacqueline , Elbaum Luciano , Holsworth Troy D. , Amenyo-Awude Phillip , Ribic Adema
Published: November 2024

Abstract

Preterm birth is a leading risk factor for atypicalities in cognitive and sensory processing, but it is unclear how prematurity impacts circuits that support these functions. To address this, we trained adult mice born a day early (preterm mice) on a visual discrimination task and found that they commit more errors and fail to achieve high levels of performance. Usingin vivo electrophysiology, we found that the neurons in the primary visual cortex (V1) and the V1-projecting prefrontal anterior cingulate cortex (ACC) are hyper-responsive to the reward, reminiscent of cue processing in adolescence. Moreover, the non-rewarded cue fails to robustly activate the V1 and V1-projecting ACC neurons during error trials, in contrast to prefrontal fast-spiking (FS) interneurons which show elevated error-related activity, suggesting that preterm birth impairs the function of prefrontal circuits for error monitoring. Finally, environmental enrichment, a well-established paradigm that promotes sensory maturation, failed to improve the performance of preterm mice, suggesting limited capacity of early interventions for reducing the risk of cognitive deficits after preterm birth. Altogether, our study for the first time identifies potential circuit mechanisms of cognitive atypicalities in the preterm population and highlights the vulnerability of prefrontal circuits to advanced onset of extrauterine experience.