bluuebunny/crossref_metadata_2025 huggingface dataset:
pyQCM-BraTaDio: A tool for visualization, data mining, and modelling of Quartz crystal microbalance with dissipation data
Authors: Pardi Brandon M. , Ahmed Syeda Tajin , Jonguitud Flores Silvia , Flores Warren , Mears Laura L.E. , Yáñez Soto Bernardo , Andresen Eguiluz Roberto C.
Published: December 2023

Here, we present a Python based software that allows for the rapid visualization, data mining, and basic model applications of quartz crystal microbalance with dissipation data. Our implementation begins with a Tkinter GUI to prompt the user for all required information, such as file name/location, selection of baseline time, and overtones for visualization (with customization capabilities). These inputs are then fed to a workflow that will use the baseline time to scrub and temporally shift data using the Pandas and Numpy libraries and carry out the plot options for visualization. The last stage consists of an interactive plot, that presents the data and allows the user to select ranges in MatPlotLib-generated panels, followed by application of data models, including Sauerbrey, thin films in liquid, among others, that are carried out with NumPy and SciPy. The implementation of this software allows for simple and expedited data analysis,in lieuof time consuming and labor-intensive spreadsheet analysis.

Metadata
A novel integrated extraction protocol for multi-omic studies in heavily degraded samples
Authors: Boggi Byron , Sharpen Jack , Taylor George , Drosou Konstantina
Published: December 2023

The combination of multi-omic techniques, e.g. genomics, transcriptomics, proteomics, metabolomics and epigenomics has revolutionised studies in medical research. These are employed to support biomarker discovery, better understand molecular pathways and identify novel drug targets. Despite concerted efforts in integrating omic datasets, there is an absence for the integration of all four biomolecules in a single extraction protocol. Here, we demonstrate for the first time a novel, minimally destructive integrated protocol for the simultaneous extraction of artificially degraded DNA, proteins, lipids and metabolites from pig brain samples. We used an MTBE-based approach to separate lipids and metabolites, followed by subsequent isolation of DNA and proteins. We have validated this protocol against standalone extraction protocols and show comparable or higher yield of all four biomolecules. This integrated protocol is key towards facilitating preservation of irreplaceable samples while promoting downstream analyses and successful data integration by removing bias from univariate dataset noise and varied distribution characteristics.
Consequences of alternative stable states for short-term model-based control of cyanobacterial blooms
Authors: Jacobs Bas , van Voorn George , van Heijster Peter , Hengeveld Geerten M.
Published: December 2023

Cyanobacteria can form dense blooms in eutrophic lakes that can be toxic to humans and other animals and harmful to the ecosystem’s functioning. While better nutrient management is generally considered the long-term solution to this problem, short-term mitigation efforts (e.g., flushing, algaecides, flocculants) are becoming increasingly necessary to safeguard water quality and the ecosystem services it provides. Here, we explore potential model-based management strategies for these short-term mitigation efforts. We focus on the case where blooms are linked to the existence of alternative stable states, such that, under the same conditions but depending on the past, a lake may be dominated either by cyanobacteria (causing a harmful algal bloom) or by green algae and macrophytes in a clear water state. Changing conditions may cause the favourable clear water state to disappear through a tipping point, causing the lake to switch rapidly to the turbid cyanobacteria state. At the same time, it may take considerable effort to undo this tipping and return to the favourable state. We identify four different strategies for bloom mitigation in this scenario: Doing nothing, reacting to a bloom, resetting the lake at a later point, and preventing the bloom. We explore the different requirements for these strategies along with their associated cost profiles. We also investigate the effect of transition times from one state to another on the efficacy and costs of different strategies.
Experimental Validation of an Organ-on-Chip for Mechanical Stimulation of Cell Cultures
Authors: Testa Maria , Tornabene Salvatore , Di Leonardo Sofia , Burriesci Gaetano , La Carrubba Vincenzo , Lopresti Francesco
Published: December 2023

This paper focuses on the design, fabrication, and characterization of a platform aiming to dynamically culture cells under mechanical stimulation. The platform, made of polymethylmethacrylate (PMMA), allows real-time mechanical stimuli, providing valuable insights for living tissue models. Through mechanical testing and dynamic microfluidic tests, the chip functionality was assessed. The experimental results validation showcases the potential of the device in mimicking physiological conditions, offering a promising avenue for pharmaceutical testing advancement.
Multiplexed gene editing with a multi-intron containingCas9gene in citrus
Authors: Sarkar Poulami , Vazquez Jorge Santiago , Zhou Mingxi , Levy Amit , Mou Zhonglin , Orbović Vladimir
Published: December 2023

The citrus industry holds significant economic importance in Florida, being one of the leading producers of oranges and grapefruits in the United States. However, several diseases, such as canker and huanglongbing along with natural disasters like hurricanes have rigorously affected citrus production, quality, and yield. Improving citrus through traditional breeding methods requires significant challenges due to time constraints and complexity in genetic enhancements. To overcome these limitations, several expression systems have been developed in clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR/Cas9) framework allowing for gene editing of disease-associated genes across diverse citrus varieties. In this study, we present a new approach employing a multi-intron containingCas9gene plus multiple gRNAs separated with tRNA sequences to target the phytoene desaturase (PDS) gene in both ‘Carrizo’ citrange and ‘Duncan’ grapefruit. Notably, using this unified vector significantly boosted editing efficiency in both citrus varieties, showcasing mutations in all three designated targets. The implementation of this multiplex gene editing system with a multi-intron-containingCas9plus a gRNA-tRNA array demonstrates a promising avenue for efficient citrus genome editing, equipping us with potent tools in the ongoing battle against HLB.

Statements and Declarations

Competing interests

The authors declare that they have no competing interests.

Supplementary Information

Supplementary File 1
Benchmarking of AlphaFold2 accuracy self-estimates as empirical quality measures and model ranking indicators and their comparison with independent model quality assessment programs
Authors: Edmunds Nicholas S. , Genc Ahmet G. , McGuffin Liam J.
Published: December 2023

Motivation

Despite an increase in the accuracy of predicted protein structures following the development of AlphaFold2, there remains a gap in the accuracy of predicted model quality assessment scores when compared to those generated with reference to experimental structures. The predictions of model accuracy scores generated by AlphaFold2, plDDT and pTM, have become familiar descriptors of model quality. However, at CASP15 some modelling groups noticed a variation in these scores for models of very similar observed quality, particularly for quaternary structures. There have also been a number of methods describing adaptations of the AlphaFold2 algorithm to purposes such as refinement by custom template recycling and model quality assessment using a similar method of template input. In this study we compare plDDT and pTM to their observed counterparts lDDT (including lDDT-Cα and lDDT-oligo) and TM-score to examine whether they retain their reliability across the whole scoring range for both tertiary and quaternary structures and in situations where the AlphaFold2 algorithm is adapted to customised functionality. In addition, we explore the accuracy with which plDDT and pTM rank AlphaFold2 tertiary and quaternary models and whether these can be improved by the independent model quality assessment programs ModFOLD9 and ModFOLDdock.

Results

For tertiary structures it was found that plDDT was an accurate descriptor of model quality when compared to observed lDDT-Cα scores (Pearson ρ = 0.97). Additionally, plDDT achieved a tertiary structure ranking agreement with observed scores of 0.34 as measured by true positive rate (TPR) and ModFOLD9 offered similar but not improved performance.

However, the accuracy of plDDT (Pearson ρ = 0.67) and pTM (Pearson ρ = 0.70) became more variable for quaternary structures quality assessment where overprediction was seen with both scores for models of lower quality and underprediction was also seen with pTM for models of higher quality. Importantly, ModFOLDdock was able to improve upon AF2-Multimer quaternary structure model ranking as measured by both TM-score (TPR 0.34) and lDDT-oligo (TPR 0.43). Finally, evidence is presented for an increase in variability of both plDDT and pTM when custom template recycling is used, and that this variation is more pronounced for quaternary structures.
MIMt – A curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification
Authors: Cabezas M. Pilar , Fonseca Nuno A. , Muñoz-Mérida Antonio
Published: December 2023

Motivation

Accurate determination and quantification of the taxonomic composition of microbial communities, especially at the species level, is one of the major issues in metagenomics. This is primarily due to the limitations of commonly used 16S rRNA reference databases, which either contain a lot of redundancy, or a high percentage of sequences with missing taxonomic information. The use of these incomplete or biased databases may lead to erroneous identifications and, thus, to erroneous conclusions regarding the ecological role and importance of those microorganisms in the ecosystem.

Results

The current study presents MIMt, a new 16S rRNA database for archaea and bacteria’s identification, encompassing 39 940 sequences, all precisely identified at species level. MIMt aims to be updated at least once a year to include all new sequenced species. We evaluated MIMt against Greengenes, RDP, GTDB and SILVA in terms of sequence distribution and accuracy of taxonomic assignments. Our results showed that MIMt contains less redundancy, and despite being five to 85 times smaller in size than existing databases, outperforms them in completeness and taxonomic accuracy, enabling more precise assignments at lower taxonomic ranks and thus, significantly improving species-level identification.

Availability and Implementation

MIMt is freely available for non-commercial purposes athttps://mimt.bu.biopolis.pt
Dia2 formin controls receptor activity by organizing plasma membrane lipid partitioning at the nanoscale
Authors: Li Changting , Hamon Yannick , Mazaud David , Gonzalez Troncoso Pamela , Dessard Marie , He Hai-tao , Lamaze Christophe , Blouin Cedric M.
Published: December 2023

Activation of JAK/STAT signaling by IFN-γ requires partitioning of IFN-γR into specific lipid nanodomains at the plasma membrane. Using IFN-γR as a proxy, we investigated the role of actin dynamics in the formation and organization of lipid nanodomains, a process that remains poorly understood. We identified formin Dia2/DIAPH3 as a specific and RhoA -dependent regulator of IFN-γ-induced JAK/STAT signaling. Based on lipidomics and specific probes enabling membrane lipid imaging by super resolution microscopy, we demonstrate that Dia2 is required for proper assembly of sphingomyelin and cholesterol lipid complexes. Finally, we show that the disorganization of lipid nanodomains induced by Dia2 depletion results in drastic changes in nano-partitioning and activity of other membrane proteins, such as Thy1 and PD-L1. Our data establish, therefore, the central role of the RhoA-Dia2 axis in the regulation of IFN-γ induced JAK/STAT signaling, and more broadly, in the nanoscale organization of the plasma membrane.
Locus Coeruleus Norepinephrine Neurons Facilitate Orbitofrontal Cortex Remapping and Behavioral Flexibility
Authors: Ogg M. Cameron , Franks Hunter T. , Lansdell Benjamin J. , Hughes Alex C. , Lee Jimin , Nolen Hunter G. , Shirinifard Abbas , Schwarz Lindsay A.
Published: December 2023

To guide behavior, brain regions such as the orbitofrontal cortex (OFC) retain complex information about current tasks and expected outcomes in cellular representations referred to as cognitive maps. When actions produce undesirable results, OFC cognitive maps must update to promote behavioral change. Here, we show that this remapping is driven by the locus coeruleus (LC), a small brainstem nucleus that contains most of the brain’s norepinephrine (NE)-releasing neurons. In a task that tests behavioral flexibility in rodents, LC-NE activity correlated with task acuity and altered depending on trial outcome. Silencing LC neurons caused perseverative behavior and impeded cognitive remapping in OFC, while enhancing LC activity disrupted the ability of new maps to stabilize. These findings reveal a novel role for bidirectional LC-NE signaling in regulation of OFC cognitive map stability and promotion of flexible behavior that differs from the traditional function of this circuit as a global arousal signal.
Analysis of virus-specific B cell epitopes reveals extensive antigen processing prior to recognition
Authors: Ras-Carmona Alvaro , Reche Pedro A.
Published: December 2023

B cell epitopes must be solvent accessible for recognition by cognate B cells and antibodies. Here, we sought to study such premise for B cell epitopes targeted during infection in humans, available at the Immune Epitope Database. Most of these B cell epitopes were virus-specific linear B cell epitopes and so we focused on them, analyzing first the localization of the relevant antigens. Antigen localization could be unequivocally assigned to 26498 linear B cell epitopes. Of those, 18832 B cell epitopes belonged to antigens that remain enclosed in host cells and/or virus particles, hidden to antibody recognition, while just 7666 lie in ectodomains of viral envelope antigens and/or mature secreted antigens, visible to antibody recognition. Next, we selected B cell epitopes that mapped in antigens with known tertiary (3D-)structures and determined residue relative solvent accessibility (rRSA), comparing them with those of conformational B cell epitopes obtained from available 3D-structures of antigen-antibody complexes. rRSA values computed form linear B cell epitopes had a median value of 23.00%, while that of conformational B cell epitopes was 48.50%. Moreover, considering average rRSA values per entire epitopes (eRSA), only 32.72% of the linear B cell epitopes had eRSA values minimally comparable to those of conformational B cell epitopes. In sum, our results point that most virus-specific B cell epitopes targeted during infection are unreachable to antibody recognition on intact viral particles and/or host cells. Hence, we must conclude that antigen recognition by antibodies must be preceded by degradation/processing of viral particles and infected cells.
Vascular microforamina and endocranial surface: normal variation and distribution in adult humans
Authors: Bruner Emiliano , Eisová Stanislava
Published: December 2023

The termcraniovascular traitsrefers to the imprints left by arteries and veins on the skull bones. These features can be used in anthropology and archaeology to investigate the morphology of the vascular network in extinct species and past populations. Generally, the term refers to macrovascular features of the endocranial cavity, like those associated with the middle meningeal artery, venous sinuses, emissary foramina, and diploic channels. However, small vascular passages (here calledmicroforaminaormicrochannels) have been occasionally described on the endocranial surface. In this study, we describe and quantify the amount and distribution of these microforamina in adult humans (N = 45) and, preliminarily, in early to late juvenile subjects (N = 7). Adults display more microchannels than juvenile skulls. Females show more channels than males, and it should be evaluated whether this trait can represent a new described sexual features, influenced by sex biology. The distribution of the microforamina is particularly concentrated on the top of the vault, in particular along the sides of the sagittal, metopic, and coronal sutures, matching the course of major venous sinuses. Nonetheless, the density is lower in the region behind thebregma. A preferential pattern of distribution seems to join diagonally the coronal and dorsal parietal regions. Beyond oxygenation, these features are likely involved in endocranial thermal regulation and immune responses, and their distribution and prevalence can hence be of interest in human biology, evolutionary anthropology, and medicine.
Genetic and environmental determinants of multicellular-like phenotypes in fission yeast
Authors: Kӧvér Bence , Cohen Céleste E. , Ralser Markus , Heineike Benjamin M. , Bähler Jürg
Published: December 2023

Multicellular fungi have repeatedly given rise to primarily unicellular yeast species. Some of these, includingSchizosaccharomyces pombe, are able to revert to multicellular-like phenotypes (MLP). Our bioinformatic analysis of existing data suggested that, besides some regulatory proteins, most proteins involved in MLP formation are not functionally conserved betweenS. pombeand budding yeast. We developed high-throughput assays for two types of MLP inS. pombe: flocculation and surface adhesion, which correlated in minimal medium, suggesting a common mechanism. Using a library of 57 naturalS. pombeisolates, we found MLP formation to widely vary across different nutrient and drug conditions. Next, in a segregantS. pombelibrary generated from an adhesive natural isolate and the standard laboratory strain, MLP formation correlated with expression levels of the transcription-factor genembx2and several flocculins. Quantitative trait locus mapping of MLP formation located a causal frameshift mutation in thesrb11gene encoding cyclin C, a part of the Cdk8 kinase module (CKM) of the Mediator complex. Other CKM deletions also resulted in MLP formation, consistently through upregulation ofmbx2, and only in minimal media. We screened a library of 3721 gene-deletion strains, uncovering additional genes involved in surface adhesion on minimal media. We identified 31 high-confidence hits, including 19 genes that have not been associated with MLPs in fission or budding yeast. Notably, deletion ofsrb11, unlike deletions of the 31 hits, did not compromise cell growth, which might explain its natural occurrence as a QTL for MLP formation.
Single-cell DNA sequencing reveals pervasive positive selection throughout preleukemic evolution
Authors: Poon Gladys , Vedi Aditi , Sanders Mathijs , Laurenti Elisa , Valk Peter , Blundell Jamie R.
Published: December 2023

The representation of driver mutations in preleukemic haematopoietic stem cells (pHSCs) provides a window into the somatic evolution that precedes Acute Myeloid Leukemia (AML). Here, we isolate pHSCs from the bone marrow of 16 patients diagnosed with AML and perform single-cell DNA sequencing on thousands of cells to reconstruct phylogenetic trees of the major driver clones in each patient. We develop a computational framework that can infer levels of positive selection operating during preleukemic evolution from the statistical properties of these phylogenetic trees. Combining these data with 67 previously published phylogenetic trees, we find that the highly variable structures of preleukemic trees emerge naturally from a simple model of somatic evolution in which there is pervasive positive selection acting throughout the disease trajectory. We infer that selective advantages of preleukemic clones are typically in the range of 9%-24% per year, but vary considerably between individuals. At these level of positive selection, we show that the identification of early multiple-mutant clones identifies individuals at risk of future AML.
SMPD4mediated sphingolipid metabolism regulates brain and primary cilia development
Authors: Inskeep Katherine A. , Crase Bryan , Stottmann Rolf W.
Published: December 2023

Genetic variants in multiple sphingolipid biosynthesis genes cause human brain disorders. A recent study collected patients from twelve unrelated families with variants in the geneSMPD4, a neutral sphingomyelinase which metabolizes sphingomyelin into ceramide at an early stage of the biosynthesis pathway. These patients have severe developmental brain malformations including microcephaly and cerebellar hypoplasia. However, the mechanism ofSMPD4was not known and we pursued a new mouse model. We hypothesized that the role ofSMPD4in producing ceramide is important for making primary cilia, a crucial organelle mediating cellular signaling. We found that the mouse model has cerebellar hypoplasia due to failure of Purkinje cell development. Human induced pluripotent stem cells exhibit neural progenitor cell death and have shortened primary cilia which is rescued by adding exogenous ceramide.SMPD4production of ceramide is crucial for human brain development.
The E3 ubiquitin ligase RNF220 maintains hindbrainHoxexpression patterns through regulation of WDR5 stability
Authors: Wang Huishan , Liu Xingyan , Liu Yamin , Yang Chencheng , Ye Yaxin , Yu Xiaomei , Sheng Nengyin , Zhang Shihua , Mao Bingyu , Ma Pengcheng
Published: December 2023

The spatial and temporal linear expression ofHoxgenes establishes a regionalHoxcode, which is crucial for the antero-posterior (A-P) patterning, segmentation, and neuronal circuit development of the hindbrain. RNF220, an E3 ubiquitin ligase, is widely involved in neural developmentviatargeting of multiple substrates. Here, we found that the expression ofHoxgenes in the pons was markedly up-regulated at the late developmental stage (post-embryonic day E15.5) inRnf220−/−andRnf220+/−mouse embryos. Single-nucleus RNA-seq analysis revealed differentHoxde-repression profiles in different groups of neurons, including the pontine nuclei (PN). TheHoxpattern was disrupted and the neural circuits were affected in the PN ofRnf220+/−mice. We showed that this phenomenon was mediated by WDR5, a key component of the TrxG complex, which can be polyubiquitinated and degraded by RNF220. Intrauterine injection of WDR5 inhibitor (WDR5-IN-4) and genetic ablation ofWdr5inRnf220+/−mice largely recovered the de-repressedHoxexpression pattern in the hindbrain. In P19 embryonal carcinoma cells, the retinoic acid inducedHoxexpression was further stimulated byRnf220knockdown, which can also be rescued byWdr5knockdown. In short, our data suggest a new role of RNF220/WDR5 inHoxpattern maintenance and pons development in mice.
A long-acting prolactin to combat lactation insufficiency
Authors: Kready Kasia , Doiron Kailyn , Redfield Chan Katherine , Way Jeffrey , Justman Quincey , Powe Camille E. , Silver Pamela
Published: December 2023

Human infants are born to breastfeed. While 50% of lactating persons struggle to make enough milk, there are no governmentally-approved drugs to enhance lactation1. Here, we engineer a variant of the naturally-occurring driver of lactation, the hormone Prolactin, to increase its serum half-life and produce a viable drug candidate. Our engineered variant, Prolactin-eXtra Long-acting (Prolactin-XL), is comprised of endogenously active human prolactin fused to an engineered human IgG Fc domain designed to overcome the unique drug development challenges specific to the lactating person-infant dyad. Our Prolactin-XL has a serum half-life of 70.9h in mice, 2,625-fold longer than endogenously active prolactin alone (70.9h v. 0.027h). We demonstrate that Prolactin-XL increases milk production and restores growth of pups fed by dams with pharmacologically-ablated lactation. We show that Prolactin-XL-enhanced lactation is accompanied by reversible, lactocyte-driven changes in mammary gland morphology. This work establishes long-acting prolactins as a potentially powerful pharmacologic means to combat insufficient lactation.
Benchmarking DNA binding affinity models using allele-specific transcription factor binding data
Authors: Li Xiaoting , Melo Lucas A. N. , Bussemaker Harmen J.
Published: December 2023

Transcription factors (TFs) bind to DNA in a highly sequence-specific manner. This specificity can manifest itselfin vivoat heterozygous loci as a difference in TF occupancy between the two alleles. When applied on a genomic scale, functional genomic assays such as ChIP-seq typically lack the statistical power to detect allele-specific binding (ASB) at the level of individual variants. To address this, we propose a framework for benchmarking sequence-to-affinity models for TF binding in terms of their ability to predict allelic imbalances in ChIP-seq counts. We show that a likelihood function based on an over-dispersed binomial distribution can aggregate evidence for allelic preference across the genome without requiring statistical significance for individual variants. This allows us to systematically compare predictive performance when multiple binding models for the same TF are available. We introduce PyProBound, an easily extensible reimplementation of the ProBound biophysically interpretable machine learning framework. Configuring PyProBound to explicitly account for a confounding sequence-specific bias in DNA fragmentation rate yields improved TF binding models when training on ChIP-seq data. We also show how our likelihood function can be leveraged to performde novomotif discovery on the raw allele-aware ChIP-seq counts.
Neuronal Avalanches in Naturalistic Speech and Music Listening
Authors: Neri Matteo , Runfola Claudio , te Rietmolen Noemie , Sorrentino Pierpaolo , Schon Daniele , Morillon Benjamin , Rabuffo Giovanni
Published: December 2023

Neuronal avalanches are cascade-like events ubiquitously observed across imaging modalities and scales. Aperiodic timing and topographic distribution of these events have been related to the systemic physiology of brain states. However, it is still unknown whether neuronal avalanches are correlates of cognition, or purely reflect physiological properties. In this work, we investigate this question by analyzing intracranial recordings of epileptic participants during rest and passive listening of naturalistic speech and music stimuli. During speech or music listening, but not rest, participants’ brains “tick” together, as the timing of neuronal avalanches is stimulus-driven and hence correlated across participants. Auditory regions are strongly participating in coordinated neuronal avalanches, but also associative regions, indicating both the specificity and distributivity of cognitive processing. The subnetworks where such processing takes place during speech and music largely overlap, especially in auditory regions, but also diverge in associative cortical sites. Finally, differential pathways of avalanche propagation across auditory and non-auditory regions differentiate brain network dynamics during speech, music and rest. Overall, these results highlight the potential of neuronal avalanches as a neural index of cognition.

Author’s summary

Neuronal avalanches consist of collective network events propagating across the brain in short-lived and aperiodic instances. These salient events have garnered a great interest for studying the physics of cortical dynamics, and bear potential for studying brain data also in purely neuroscientific contexts. In this work we investigated neuronal avalanches to index cognition, analyzing an intracranial stereo electroencephalography (iEEG) dataset during speech, music listening and resting state in epileptic patients. We show that neuronal avalanches are consistently driven by music and speech stimuli: avalanches co-occur in participants listening to the same auditory stimulus; avalanche topography differs from resting state, presenting partial similarities during speech and music; avalanche propagation changes during speech, music, and rest conditions, especially along the pathways between auditory and non auditory regions. Our work underlines the distributed nature of auditory stimulus processing, supporting neuronal avalanches as a valuable and computationally advantageous framework for the study of cognition in humans.
The role of theC. albicanstranscriptional repressorNRG1during filamentation and disseminated candidiasis is strain-dependent
Authors: Wakade Rohan S. , Wellington Melanie , Krysan Damian J.
Published: December 2023

Candida albicansis one of the most common causes of superficial and invasive fungal disease in humans. Its ability to cause disease has been closely linked to its ability to undergo a morphological transition from budding yeast to filamentous forms (hyphae and pseudohyphae). The ability ofC. albicansstrains isolated from patients to undergo filamentation varies significantly. In addition, the filamentation phenotypes of mutants involving transcription factors that positively regulate hyphal morphogenesis can also vary from strain to strain. Here, we characterized the virulence, in vitro and in vivo filamentation, and in vitro and in vivo hypha-associated gene expression profiles of four poorly filamentingC. albicansisolates and their corresponding deletion mutants of the repressor of filamentationNRG1. The two most virulent strains, 57055 and 78048, show robust in vivo filamentation while remaining predominately yeast phase exposed to RPMI+10% bovine calf serum at 37°C; the two low virulence strains (94015 and 78042) do not filament well under either condition. Deletion ofNRG1increases hyphae formation in the SC5314 derivative SN250 but only pseudohyphae are formed in the clinical isolates in vivo. Deletion ofNRG1modestly increased the virulence of 78042 which was accompanied by increased expression of hyphae-associated genes without an increase in filamentation. Strikingly, deletion ofNRG1in 78048 reduced filamentation, expression of candidalysin (ECE1) and virulence in vivo without dramatically altering establishment of infection. Thus, the function ofNRG1varies significantly within this set ofC. albicansisolates and can actually suppress filamentation in vivo.

Importance

Clinical isolates of the human fungal pathogenCandida albicansshow significant variation in their ability to undergo in vitro filamentation and in the function of well-characterized transcriptional regulators of filamentation. Here, we show that Nrg1, a key repressor of filamentation and filament specific gene expression in standard reference strains, has strain dependent functions, particularly during infection. Most strikingly, loss ofNRG1function can reduce filamentation, hypha-specific gene expression such as the toxin candidalysin, and virulence in some strains. Our data emphasize that the functions of seemingly fundamental and well-conserved transcriptional regulators such as Nrg1 are contextual with respect to both environment and genetic background.
Diet-driven differential response ofAkkermansia muciniphilamodulates pathogen susceptibility
Authors: Wolter Mathis , Grant Erica T. , Boudaud Marie , Pudlo Nicholas A. , V. Pereira Gabriel , Eaton Kathryn A. , Martens Eric C. , Desai Mahesh S.
Published: December 2023

The erosion of the colonic mucus layer by a dietary fiber-deprived gut microbiota results in heightened susceptibility to an attaching and effacing pathogen,Citrobacter rodentium. Nevertheless, the questions of whether and how specific mucolytic bacteria aid in the increased pathogen susceptibility remain unexplored. Here, we leverage a functionally characterized, 14-member synthetic human microbiota in gnotobiotic mice to deduce which bacteria and functions are responsible for the pathogen susceptibility. Using strain dropouts of mucolytic bacteria from the community, we show thatAkkermansia muciniphilarenders the host more vulnerable to the mucosal pathogen during fiber deprivation. However, the presence ofA. muciniphilareduces pathogen load on a fiber-sufficient diet, highlighting the context-dependent beneficial effects of this mucin specialist. The enhanced pathogen susceptibility is not owing to altered host immune or pathogen responses, but is driven by a combination of increased mucus penetrability and altered activities ofA. muciniphilaand other community members. Our study provides novel insights into the mechanisms of how discrete functional responses of the same mucolytic bacterium either resist or enhance enteric pathogen susceptibility.
PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models
Authors: Mendes Fábio K. , Landis Michael J.
Published: December 2023

We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, through its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data. This paper describes the features of PhyloJunction – which include, but are not limited to, a general implementation of a popular family of phylogenetic diversification models – and, moving forward, how it may be expanded to not only include new models, but to also become a platform for conducting and teaching statistical learning.
Hypoxia drives HIF2-dependent macrophage cell cycle entry and susceptibility to lentiviral transduction
Authors: Meng Bo , Zhao Na , Mlcochova Petra , Ferreira Isabella A.T.M , Ortmann Brian M. , Davis Tanja , Wit Niek , Rehwinkel Jan , Cook Simon , Maxwell Patrick H. , Nathan James A. , Gupta Ravindra K.
Published: December 2023

Macrophages play critical roles across health and disease. Low oxygen conditions (hypoxia) have been associated primarily with cell cycle arrest in cultured dividing cells. Macrophages are typically quiescent in G0, though yolk sac and bone marrow derived macrophages frequently proliferate and monocyte-derived tissue macrophages are able to proliferate in response to tissue signals. Here we show that hypoxia (1% oxygen tension) results in reversible entry into the cell cycle in monocyte derived macrophages (MDM) and mouse peritoneal macrophages. Cell cycle progression is largely limited to G1/S phase with very little progression to G2/M. Mechanistically, this cell cycle transitioning is triggered by a HIF2α-directed transcriptional program. The response is accompanied by increased expression of cell cycle-associated proteins, including CDK1, and reversible activation of the canonical mitogen-activated MEK-ERK proliferation pathway. CDK1 associated SAMHD1 phosphorylation at T592 in hypoxic macrophages renders them hyper-susceptible to lentiviral transduction. Furthermore, PHD inhibitors, which activate HIFs, are able to recapitulate HIF2α-dependent cell cycle entry in macrophages, as well as susceptibility to lentiviral transduction. Finally, we demonstrate that tumour associated macrophages (TAM) in lung cancers exhibit transcriptomic profiles representing responses to low oxygen and cell cycle progression at single cell level. This work uncovers HIF2α driven macrophage cell cycle progression in low oxygen conditions that culminates in SAMHD1 phosphorylation and high susceptibility to lentiviral transduction. These findings have implications for inflammation, neoplasia and pathogen defence.
Towards establishing a rapid constant temperature detection method for canine parvovirus based on endonuclease activities
Authors: Weng Shaoting , Ma Shengming , Xing Yueteng , Zhang Wenhui , Wu Yinrong , Fu Mengyao , Luo Zhongyi , Li Qiuying , Lin Sen , Zhang Longfei , Wang Yao
Published: December 2023

Canine parvovirus can cause a high morbidity and mortality rate in puppies, posing a significant threat to both pet dogs and the breeding industry. Rapid, accurate and convenient detection methods are important for the early intervention and treatment of canine parvovirus. In this study, we propose a visual CPV detection system called nucleic acid mismatch enzyme digestion (NMED). This system combines reverse transcription-loop mediated isothermal amplification (RT-LAMP), endonuclease for gene mismatch detection and colloidal gold lateral chromatography. We demonstrated that NMED can induce the binding of the amplicon from the sample to the specific labeling probe, which in turn triggers digestion by the endonuclease. The sensitivity and visual visibility of RT-LAMP were increased by combining of endonuclease and colloidal gold lateral chromatography assisted by a simple temperature-controlled device. The sensitivity of the NMED assay was 1 copy/μL, which was consistent with qPCR. The method was validated with 10 clinical samples that potentially had CPV infection and achieved 100% accuracy. As a rapid, accurate and convenient molecular diagnostic method, NMED has great potential for application in the field of pathogenic microorganism detection.
STACCato: Supervised Tensor Analysis tool for studying Cell-cell Communication using scRNA-seq data across multiple samples and conditions
Authors: Dai Qile , Epstein Michael P. , Yang Jingjing
Published: December 2023

Research on cell-cell communication (CCC) is crucial for understanding biology and diseases. Many existing CCC inference tools neglect potential confounders, such as batch and demographic variables, when analyzing multi-sample, multi-condition scRNA-seq datasets. To address this significant gap, we introduce STACCato, aSupervisedTensorAnalysis tool for studyingCell-cellCommunication, that identifies CCC events and estimates the effects of biological conditions (e.g., disease status, tissue types) on such events, while adjusting for potential confounders. Application of STACCato to both simulated data and real scRNA-seq data of lupus and autism studies demonstrate that incorporating sample-level variables into CCC inference consistently provides more accurate estimations of disease effects and cell type activity patterns than existing methods that ignore sample-level variables. A computational tool implementing the STACCato framework is available on GitHub.
Thermal tolerance and survival are modulated by a natural gradient of infection in differentially acclimated hosts
Authors: De Bonville Jérémy , Côté Ariane , Binning Sandra A.
Published: December 2023

Wild ectotherms are exposed to multiple stressors, including parasites, which can affect their responses to environmental change. Simultaneously, unprecedented warm temperatures are being recorded worldwide, increasing both the average and maximum temperatures experienced in nature. Understanding how ectotherms, such as fishes, will react to the combined stress of parasites and higher average temperatures can help predict the impact of extreme events such as heat waves on populations. The critical thermal method (CTM), which assesses upper (CTmax) and lower (CTmin) thermal tolerance, is often used in acclimated ectotherms to help predict their tolerance to various temperature scenarios. Yet, few studies have characterized the response of naturally infected fish to extreme temperature events or how acute thermal stress affects subsequent survival. We acclimated naturally infected pumpkinseed sunfish (Lepomis gibbosus), to four ecologically relevant temperatures (10, 15, 20 and 25°C) and one future warming scenario (30°C) for three weeks, before measuring CTmaxand CTmin. We also assessed individual survival the week following CTmax. Interestingly, trematode parasites causing black spot disease were negatively related to CTmax, suggesting that heavily infected fish are less tolerant to acute warming. Moreover, fish infected with yellow grub parasites showed decreased survival in the days following CTmaximplying that the infection load has negative survival consequences on sunfish during extreme warming events. Our findings indicate that parasite infection and high prolonged average temperatures can affect fish thermal tolerance and survival, emphasizing the need to better understand the concomitant effects of stressors on health outcomes in wild populations.

Summary statement

This study shows that parasites influence thermal tolerance and survival of fish, suggesting that such stressors are important to increase the ecological relevance of thermal tolerance studies of wild animals.
Impact of homologous recombination on core genome evolution and host adaptation ofPectobacterium parmentieri
Authors: Arizala Dario , Arif Mohammad
Published: December 2023

Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability and acquisition of novel virulence traits.Pectobacterium parmentieriis a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution ofP. parmentieri. Analysis ofP. parmentierigenomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified seven lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. FastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging 43 bp - 119 kb and 36 bp - 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides, flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the role of homologous recombination inP. parmentieri’s evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.

Significance

This study explores the influence of homologous recombination on the genomic evolution of the globally distributed plant pathogenP. parmentieri, characterized by highly heterogenous strains from various global locations. Our findings reveal diverse recombinogenic patterns within the core genomes ofP. parmentieriisolates, notably in genomic loci associated with vital cell functions, pathogenicity determinants, and CRISPR-Cas genes. These findings highlight the role of homologous recombination in shaping the genomes ofP. parmentieriand impacting its phytopathogenic lifestyle. Additionally, the data suggest a potential role of recombination in the ecological adaptation of this species across different climates, providing insights into the worldwide presence ofP. parmentieri. This study represents a pioneering exploration of the impact of homologous recombination on the dynamic evolutionary genomics of the soft rot-causing bacteriumP. parmentieri.
Interpretable and Generalizable Strategies for Stably Following Hydrodynamic Trails
Authors: Hang Haotian , Jiao Yusheng , Heydari Sina , Ling Feng , Merel Josh , Kanso Eva
Published: December 2023

Aquatic organisms offer compelling evidence that local flow sensing alone, without vision, is sufficient to guide them to the source of a vortical flow field, be it a swimming or stationary object. However, the feedback mechanisms that allow a flow-sensitive follower to track hydrodynamic trails remain opaque. Here, using high-fidelity fluid simulations and Reinforcement Learning (RL), we discovered two equally effective policies for trail following. While not apriori obvious, the RL policies led to parsimonious response strategies, analogous to Braitenberg’s simplest vehicles, where a follower senses local flow signals and turns away from or towards the direction of stronger signal. We analyzed the stability of the RLinspired strategies in ideal and simulated flows and demonstrated their robustness in tracking unfamiliar flows using diverse types of sensors. Our findings uncovered a surprising connection between the stability of hydrodynamic trail following and sense-to-response time delays, akin to those observed in the sensorimotor systems of aquatic organisms, and could guide future designs of flow-responsive autonomous robots.
Opposing effects of pre-existing antibody and memory T cell help on the dynamics of recall germinal centers
Authors: Schiepers Ariën , van ‘t Wout Marije F. L. , Hobbs Alvaro , Mesin Luka , Victora Gabriel D.
Published: December 2023

Re-exposure to an antigen generates serum antibody responses that greatly exceed in magnitude those elicited by primary antigen encounter, while simultaneously driving the formation of recall germinal centers (GCs). Although recall GCs in mice are composed almost entirely of naïve B cells, recall antibody titers derive overwhelmingly from memory B cells, suggesting a division between cellular and serum compartments. Here, we show that this schism is at least partly explained by a marked decrease in the ability of recall GC B cells to detectably bind antigen. Variant priming and plasmablast ablation experiments show that this decrease is largely due to suppression by preexisting antibody, whereas hapten-carrier experiments reveal a role for memory T cell help in allowing B cells with undetectable antigen binding to access GCs. We propose a model in which antibody-mediated feedback steers recall GC B cells away from previously targeted epitopes, thus enabling specific targeting of variant epitopes.
Evolution of Opsin Genes in Caddisflies (Insecta: Trichoptera)
Authors: Powell Ashlyn , Heckenhauer Jacqueline , Pauls Steffen U. , Ríos-Touma Blanca , Kuranishi Ryoichi B. , Holzenthal Ralph W. , Razuri-Gonzales Ernesto , Bybee Seth , Frandsen Paul B.
Published: December 2023

Insects have evolved complex and diverse visual systems in which light-sensing protein molecules called opsins couple with a chromophore to form photopigments. Insect photopigments group into three major gene families based on wavelength sensitivity: long wavelength (LW), short wavelength (SW), and ultraviolet wavelength (UV). Here, we identified 123 opsin sequences from whole genome assemblies across 25 caddisfly species (Insecta: Trichoptera). We discovered the LW opsins have the most diversity across species and form two separate clades in the opsin gene tree. Conversely, we observed a loss of the SW opsin in half of the trichopteran species in this study, which might be associated with the fact that caddisflies are active during low-light conditions. Lastly, we found a single copy of the UV opsin in all the species in this study, with one exception:Athripsodes cinereushas two copies of the UV opsin and resides within a clade of caddisflies with colorful wing patterns.

Significance

While opsin evolution in some insect groups has been well-characterized, it has never been studied across caddisflies. Our findings provide insight into the diversity of opsins in caddisflies and form a basis for further research into the evolutionary drivers and complex visual systems in Trichoptera.