bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrated, high-dimensional analysis of CD4 T cell epitope specificities and phenotypes reveals unexpected diversity in the response toMycobacterium tuberculosis
Authors: Mead Heather L , Kirschman Jung Hwa , Harms Caroline E , Kelley Erin J , Soria-Bustos Jorge , Nelson Georgia A , Ogongo Paul , Ouma Gregory , Ouma Samuel G , Ernst Joel D , Altin John A
Published: November 2024

Immunity toMycobacterium tuberculosis(Mtb), like many pathogens, is encoded jointly by the antigen specificities and functions of responding CD4 T cells. However, these features span a large two-dimensional possibility space – defined on one axis by theMtbproteome, and on the other by the T cell transcriptome – that exceeds the dimensionality of existing technologies. Here we present an approach (“CRESTA”) that combines highly-multiplexed DNA-barcoded epitope probes, single cell sequencing, and clonal analysis of T Cell Receptors (TCRs) to robustly detect rare antigen-specific CD4 T cells across hundreds of epitopes simultaneously and reveal their transcriptome-wide phenotypes. By comprehensively assaying known epitopes inMtb-infected participants, we reveal polyclonal and multi-epitope responses across a spectrum of differentiation states, uncover previously-unobserved phenotypic diversity within and between epitopes, and increase the total number of knownMtbepitope-mapped TCRα:βs by ∼8-fold. We expect CRESTA to enable high-dimensional analyses of CD4 T cell responses in various settings, including infection, cancer, autoimmunity and allergy.
SysQuan: repurposing SILAC mice for the affordable absolute quantitation of the human proteome
Authors: Mohammed Yassene , Richard Vincent R. , Reyes Madlangsakay M. Immanuel , Lao Ying , Spicer Victor , Popp Robert , Gaither Claudia , Henneken Laura , Kleinekofort Wolfgang , Zahedi René P. , Borchers Christoph H.
Published: November 2024

Relative quantitation, used by most MS-based proteomics laboratories to determine proteinfold-changes, requires samples being processed and analyzed together for best comparability through minimizing batch differences. This limits the adoption of MS-based proteomics in population-wide studies, and the detection of subtle but relevant changes in heterogeneous samples. Absolute quantitation circumvents these limitations and enables comparison of results across laboratories, studies, and longitudinally. However, high costs of the essential stable isotope labeled (SIL) standards prevents widespread access and limits the number of quantifiable proteins.

Our new approach, called “SysQuan”, repurposes SILAC mouse tissues/biofluids as system-wide internal standards for matched human samples to enable absolute quantitation of, theoretically, two-thirds of the human proteome using 157,086 shared tryptic peptides. We demonstrate that SysQuan enables quantification of 70% and 31% of the liver and plasma proteomes, respectively. We demonstrate for 14 metabolic proteins that abundant SIL mouse tissues enable cost-effective reverse absolute quantitation in, theoretically, 1000s of human samples. Moreover, 10,000s of light/heavy doublets in untargeted SysQuan datasets enable unique post-acquisition absolute quantitation.

SysQuan empowers researchers to replace relative quantitation with affordable absolute quantitation at scale, making data comparable across laboratories, diseases and tissues, enabling completely novel study designs and increasing reusability of data in repositories.

TOC Graphic
Optimizing Angiopep-2 Density on Polymeric Nanoparticles for Enhanced Blood-Brain Barrier Penetration and Glioblastoma Targeting: Insights from In Vitro and In Vivo Experiments
Authors: Zhang Weisen , Refaat Ahmed , Li Haoqin , Zhu Douer , Tong Ziqiu , Nicolazzo Joseph A. , Peng Bo , Bai Hua , Esser Lars , Voelcker Nicolas H.
Published: November 2024

The blood-brain barrier (BBB) poses a formidable challenge to efficient drug delivery into the brain. One promising approach involves leveraging receptor-mediated transcytosis facilitated by Angiopep-2 peptide (Ang-2)-conjugated nanoparticles. However, the precise impact of Ang-2 density on BBB penetration remains poorly understood. In this study, we developed a versatile polymeric nanoparticle system with tuneable Ang-2 surface density and systemically examined its influence on BBB penetration through variousin vitroassays and anin vivostudy. Our findings revealed a nuanced relationship between Ang-2 surface density and BBB penetration across the different experimental setups. In 2D cell culture, we observed a positive correlation between Ang-2 surface density and cellular association in hCMEC/D3 cells, characterized by a distinctive inflection point. Conversely, in the Transwell model, higher Ang-2 density correlated negatively with BBB penetration, whereas the BBB-GBM-on-a-chip showed the opposite trend. These disparities may arise from differences in avidity under static versus dynamic conditions, potentially modulating nanoparticle interactions due to fluidic forces.In vivostudies revealed that higher Ang-2 densities facilitated nanoparticle transport across the BBB, consistent with the findings of the BBB-GBM-on-a-chip model. Furthermore, loading doxorubicin into nanoparticles with optimal Ang-2 density resulted in controlled pH-responsive release and enhanced anticancer effect against U87 GBM cells in both 2D cell cultures and a 3D BBB-GBM-on-a-chip model. These results underscore the critical importance of optimizing Ang-2 surface density for efficient BBB penetration and emphasize the utility of dynamic models in preclinicalin vitroassessment of novel nanoparticle formulations for targeted delivery to the brain.
Harnessing micrometer-scale tPA beads for high plasmin generation and accelerated fibrinolysis
Authors: Osmond Matthew J. , Dabertrand Fabrice , Quillinan Nidia , Su Enming J. , Lawrence Daniel A. , Marr David W.M. , Neeves Keith B.
Published: November 2024

Rapid restoration of blood flow is critical in treating acute ischemic stroke. Current fibrinolytic therapies using tissue plasminogen activator (tPA) are limited by low recanalization rates and risks of off-target bleeding. Here, we present a strategy using tPA immobilized on micrometer-scale beads to enhance local plasmin generation. We synthesized tPA-functionalized beads of varying sizes (0.1 μm and 1.0 μm) and evaluated their efficacy.In vitroassays demonstrated that 1.0 μm tPA-beads generated higher plasmin generation compared to free tPA and 0.1 μm beads, overcoming antiplasmin inhibition and promoting a self-propagating wave of fibrinolysis. In a murine model of acute ischemic stroke, intravenous administration of 1.0 μm tPA-beads at doses nearly two orders of magnitude lower than the standard free tPA dose led to rapid and near-complete thrombus removal within minutes. This approach addresses kinetic and transport limitations of current therapies and may reduce the risk of hemorrhagic complications.

Teaser

Micrometer-scale tPA beads improve stroke treatment by enhancing local clot-dissolving action.
Behavioral and neural evidence for perceptual predictions in social interactions
Authors: Lu Juanzhi , Riecke Lars , de Gelder Beatrice
Published: November 2024

The ability to predict others’ behavior is crucial for social interactions. The goal of the present study was to test whether predictions are derived during observation of social interactions and whether these predictions influence how the whole-body emotional expressions of the agents are perceived. Using a novel paradigm, we induced social predictions in participants by presenting them with a short video of a social interaction in which a person approached another person and greeted him by touching the shoulder in either a neutral or an aggressive fashion. The video was followed by a still image showing a later stage in the interaction and we measured participants’ behavioral and neural responses to the still image, which was either congruent or incongruent with the emotional valence of the touching. We varied the strength of the induced predictions by parametrically reducing the saliency of emotional cues in the video.

Behaviorally, we found that reducing the emotional cues in the video led to a significant decrease in participants’ ability to correctly judge the appropriateness of the emotional reaction in the image. At the neural level, EEG recordings revealed that observing an angry reaction elicited significantly larger N170 amplitudes than observing a neutral reaction. This emotion effect was only found in the high prediction condition (where the context in the preceding video was intact and clear), not in the mid and low prediction conditions. We further found that incongruent conditions elicited larger N300 amplitudes than congruent conditions only for the neutral images. Our findings provide evidence that viewing the initial stages of social interactions triggers predictions about their outcome in early cortical processing stages.
Effects of live yeasts and their metabolic products on bumble bee microcolony development
Authors: Rukowski Danielle , Weston Makena , Vannette Rachel L.
Published: November 2024

Bumble bees can benefit from fungi, though the mechanisms underlying these benefits remain unknown and could include nutrition, resource supplementation, or pathogen protection. We tested how adding living yeasts or their metabolic products toBombus impatiensdiets in a factorial experiment affects microcolony performance, including survival, reproduction, and pathogen presence. We additionally assessed effects of yeast treatments on diet (nectar and pollen) chemical composition using untargeted metabolomics. Yeasts impacted microcolony reproduction and survival, but effects depended on source colony. Colonies containing the putative pathogenAspergillusshowed reduced reproduction, but yeast treatments reducedAspergillusprevalence. Yeast treatments altered chemical composition of nectar and pollen, but most distinguishing compounds were unidentified. Our results suggest limited direct effects of yeasts via nutrition, resource supplementation, or modification of diets, instead suggesting that yeasts may benefit bees through interactions with the pathogens includingAspergillus. Overall, the effects of yeast supplementation are context-dependent, and more research is necessary to better understand the factors important in determining their impacts on bee hosts.
Sex-specific attenuation of photoreceptor degeneration by reserpine in a rhodopsin P23H rat model of autosomal dominant retinitis pigmentosa
Authors: Song Hyun Beom , Campello Laura , Mondal Anupam , Chen Holly Y , English Milton A , Glen Michael , Vanlandingham Phillip , Farjo Rafal , Swaroop Anand
Published: November 2024

Inherited retinal degenerations (IRDs) constitute a group of clinically and genetically diverse vision-impairing disorders. Retinitis pigmentosa (RP), the most common form of IRD, is characterized by gradual dysfunction and degeneration of rod photoreceptors, followed by the loss of cone photoreceptors. Recently, we identified reserpine as a lead molecule for maintaining rod survival in mouse and human retinal organoids as well as in therd16mouse, which phenocopy Leber congenital amaurosis caused by mutations in the cilia-centrosomal geneCEP290(Chenet al.eLife 2023;12:e83205. DOI: https://doi.org/10.7554/eLife.83205). Here, we show the therapeutic potential of reserpine in a rhodopsin P23H rat model of autosomal dominant RP. At postnatal day (P) 68, when males and females are analyzed together, the reserpine-treated rats exhibit higher rod-derived scotopic b-wave amplitudes compared to the controls with little or no change in scotopic a-wave or cone-derived photopic b-wave. Interestingly, the reserpine-treated female rats display enhanced scotopic a- and b-waves and photopic b-wave responses at P68, along with a better contrast threshold and increased outer nuclear layer thickness. The female rats demonstrate better preservation of both rod and cone photoreceptors following reserpine treatment. Retinal transcriptome analysis reveals sex-specific responses to reserpine, with significant upregulation of phototransduction genes and proteostasis-related pathways, and notably, genes associated with stress response. This study builds upon our previously reported results reaffirming the potential of reserpine for gene-agnostic treatment of IRDs and emphasizes the importance of biological sex in retinal disease research and therapy development.
Interplay between autophagy, the unfolded protein response and the cytoplasmic heat stress response during heat stress in maize
Authors: Tang Jie , Li Zhaoxia , Bassham Diane C
Published: November 2024

High temperatures can substantially reduce plant survival and reproduction, and therefore decrease crop productivity. Plants activate several pathways in response to high temperatures, including the endoplasmic reticulum (ER) unfolded protein response (UPR), the cytoplasmic heat stress response, and autophagy, which together aid in stress tolerance by refolding or degrading misfolded and unfolded proteins. The relationship between the UPR and autophagy is known, as ER stress activates the UPR, and a key activator of the UPR, Inositol-requiring enzyme type 1 (IRE1B), upregulates autophagy. To assess the relationship between the distinct responses to heat stress in maize, we analyzed the effect of disruption of the UPR, via abzip60mutant, on autophagy. We found that genes related to autophagy are upregulated in thebzip60mutant, and that autophagy is activated in this mutant even in the absence of stress. We in turn analyzed the effect of loss of autophagy on the UPR. ThebZIP60mRNA spliced form, a marker for the UPR, was increased in mutants inATG10, a core component of the autophagy machinery, during ER stress. By contrast,bZIP60splicing was unaffected inatg10mutants in response to heat, whereas cytoplasmic heat stress components were increased. Loss of autophagy therefore differentially affects other heat stress response pathways, depending on the specific stress conditions leading to the activation of the pathways.
Evolutionarily guided transcription factor design programs novel T cell states
Authors: Takacsi-Nagy Oliver , Hartman Austin , Chen Andy Y. , Yin Yajie , Reeder Gabriella C. , Kernick Courtney , Lu Johnathan , McClellan Alison K. , Raposo Colin J. , Theberath Nicole E. , Yan Patrick K. , Eyquem Justin , Roth Theodore L. , Satpathy Ansuman T.
Published: November 2024

Protein-coding genes in the human genome evolved via modular rearrangement of domains from ancestral genes1. Here, we develop a scalable, evolutionarily guided method to assemble novel protein-coding genes from constituent domains within a protein family, termed DESynR (Domain Engineered via Synthesis and Recombination) genes. Using primary human chimeric antigen receptor T cells as a model system, we find that the expression of DESynR Activator Protein-1 (AP-1) transcription factors (TFs) significantly outperforms the overexpression of natural AP-1 TFs in multiple functional assaysin vitroandin vivo. Top DESynR AP-1 TFs exhibit non-intuitive architectures of constituent domains, including from TFs that are not canonically expressed in T cells. DESynR AP-1 TFs induce broad transcriptional and epigenetic reprogramming of T cells and, in some cases, lead to the development of non-natural T cell states, engaging gene expression modules from disparate human cell types. Taken together, we demonstrate that novel configurations of existing protein domains may uncover non-evolved genes that program cell states with therapeutically relevant functions.
The circadian clock regulates receptor-mediated immune responses to an herbivore-associated molecular pattern
Authors: Guayazán Palacios Natalia , Imaizumi Takato , Steinbrenner Adam D.
Published: November 2024

Plants activate induced defenses through the recognition of molecular patterns. Like pathogen-associated molecular patterns (PAMPs), herbivore-associated molecular patterns (HAMPs) can be recognized by cell surface pattern recognition receptors leading to defensive transcriptional changes in host plants. Herbivore-induced defensive outputs are regulated by the circadian clock, but the underlying molecular mechanisms remain unknown. To investigate how the plant circadian clock regulates transcriptional reprogramming of a specific HAMP-induced pathway, we characterized the daytime and nighttime transcriptional response to caterpillar-derived In11 peptide, in the legume crop cowpea (Vigna unguiculata). Using diurnal and free-running conditions, we found that daytime In11 elicitation resulted in stronger late-induced gene expression than nighttime. Plants with a conditional arrhythmic phenotype in constant light (LL) conditions lost time-of-day dependent responses to In11 treatment, and this was associated with arrhythmic expression of circadian clock core transcription factorLate Elongated Hypocotyl VuLHY1andVuLHY2. Reporter assays with VuLHY homologs indicated that they interact with the promoter of daytime In11-inducedKunitz Trypsin Inhibitor(VuKTI) via a canonical and a polymorphic CCA1/LHY Binding Site (CBS), consistent with a mechanism of direct regulation by circadian clock transcription factors. This study improves our understanding of the time-dependent mechanisms that regulate herbivore-induced gene expression.
Stress from environmental change drives clearance of a persistent enteric virus
Authors: Herrmann Christin , Zaldana Kimberly , Agostino Eva L , Koralov Sergei B , Cadwell Ken
Published: November 2024

Persistent viral infections are associated with long-term health issues and prolonged transmission. How external perturbations after initial exposure affect the duration of infection is unclear. We discovered that murine astrovirus, an enteric RNA virus, persists indefinitely when mice remain unperturbed but is cleared rapidly after cage change. Besides eliminating the external viral reservoir, cage change also induced a transcriptional defense response in the intestinal epithelium. We further identified that displacing infected animals initially caused a temporary period of immune suppression through the stress hormone corticosterone, which was followed by an immune rebound characterized by an increase in CD8 T cells responsible for the epithelial antiviral responses. Our findings show how viral persistence can be disrupted by preventing re-exposure and activating immunity upon stress recovery, indicating that external factors can be manipulated to shorten the duration of a viral infection.
Acetic acid induces osmotic imbalances in drug-resistant bacteria synergistically enhancing cobalt-doped carbon quantum dots bactericidal efficiency
Authors: Truskewycz Adam , Choi Benedict , Pedersen Line , Han Jianhua , Halberg Nils
Published: November 2024

When pathogenic bacteria colonise a wound, they can create an alkaline ecological niche which selects for their survival by creating an inflammatory environment which restricts healthy wound healing to proceed. To aid healing, wound acidification has been exploited to disrupt this process and stimulate fibroblast growth, increase wound oxygen concentrations, minimise proteolytic activity and re-stimulate the host immune system. Within this study, we have developed unique cobalt doped carbon quantum dot nanoparticles which work together with mild acetic acid creating a potent synergistic antimicrobial therapy. The acidic environment alters the osmotic balance of microorganisms forcing them to swell and speed up the internalisation of the ultra-small particles. The particles hyperpolarise the bacterial membranes and generate damaging peroxidase species resulting in cellular lysis. In mice, cobalt doped carbon quantum dots remove MRSA infection while allowing wounds to heal at equivalent rates to uninfected wounds. This work demonstrates how synergistic antimicrobial treatment strategies can be successfully used to combat antimicrobial resistant infections.
Tardigrade Dsup: Interactions with DNA and protection of cells from oxidative stress
Authors: Ni Gavin Shuyang , Su Hetian , Zhu Yingqi , Dhiman Anshika , Zhou Huan-Xiang , Lin Wei , Hao Nan
Published: November 2024

The remarkable capability of Tardigrade to survive under extreme conditions has been partially attributed to Dsup, an intrinsically disordered, highly positively charged protein. Dsup has been shown to bind to DNA in vitro, a property that has been associated with the capability of Dsup to exhibit stress-protective effects when expressed in mammalian cells. However, DNA binding of Dsup has not been visualized in living cells and expression of Dsup in different cell types was associated with either protective or detrimental effects. In addition, the effect of Dsup expression has not been clearly demonstrated at the organism level. Here we combined molecular dynamics (MD) simulations and fluorescence lifetime imaging microscopy (FLIM)-Förster resonance energy transfer (FRET) to interrogate Dsup-DNA interactions and demonstrated Dsup binding to DNA in living mammalian cells. Furthermore, Dsup expression in both HEK293T cells and yeast enhanced cell survival in the presence of hydrogen peroxide, suggesting that the presence of Dsup allows both mammalian and yeast cells to better cope with oxidative stress conditions. This study provides a better understanding of the property and functional role of Dsup and lays a foundation to explore new approaches to enhance stress resistance.
An ocean of opsins
Authors: De Vivo Giacinto , Pelettier Eric , Feuda Roberto , D’Aniello Salvatore
Published: November 2024

In this study, we explored the diversity and evolution of opsins using meta-omic data from the TARA Oceans and TARA Polar Circle expeditions, one of the largest marine datasets available. By using molecular clustering and phylogenetic analyses, we identified and characterized opsins across various taxonomic groups and gene subfamilies. Our results indicate that the majority of opsin sequences belong to arthropods and vertebrates. However, we also detected sequences from all major opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no novel opsin gene families were discovered, suggesting a comprehensive understanding of opsin diversity in marine ecosystems. Additionally, we present novel opsin sequences from less-studied taxa, which may serve as a valuable resource for future research into opsin function and diversity.
Greening rates are sensitive to methodology and biology; comment to Sustained greening of the Antarctic Peninsula observed from satellites
Authors: Bokhorst S. , Huisman S. , de Jonge I.K. , Janssen T.A.J. , Cornelissen J.H.C. , Hughes K. A. , Convey P.
Published: November 2024

Roland et al.1claim to provide evidence for a ‘greening trend’ throughout the Antarctic Peninsula region over the last four decades, based on satellite remote sensing data. However, the early period vegetation cover estimates do not match with the likely extent of vegetated areas in this region at that time, raising doubts about the magnitude of any greening trend. Furthermore, growth rates of mosses and higher plants in Antarctica are insufficient to explain the 14-fold green cover expansion claimed, and neither have such changes been observed at long-term monitoring sites or from field warming studies. The reported satellite time series analyses of the presented trend seems biased by satellite image availability, lack of consistency in the areas covered by imagery and processing pitfalls. Antarctic terrestrial ecosystems are indeed predicted to become greener with climate change, but at much slower rates than reported by Roland et al.1.
"Transcriptional Regulation of human NMNAT2: Insights from 3D Genome Sequencing and Bioinformatics"
Authors: Chang Yu Chen , Yang Sen , Cho Minyoung , Nho Kwangsik , Baizabal José-Manuel , Lu Hui-Chen
Published: November 2024

Abstract

Nicotinamide mononucleotide adenylyl transferases 2 (NMNAT2) is a crucial nicotinamide adenine dinucleotide (NAD)-synthesizing enzyme essential for neuronal health. In the Religious Orders Study/Memory and Aging Project (ROSMAP), human brain levels of NMNAT2 mRNA positively correlated with cognitive capabilities in older adults. NMNAT2 mRNA abundance is significantly reduced following various insults or proteinopathies. To elucidate the transcriptional regulation of NMNAT2, we employed circular chromosome conformation capture followed by high-throughput sequencing (4C-seq) to identify potential NMNAT2 enhancer and silencer regions by determining genomic regions interacting with the NMNAT2 promoter in human SH-SY5Y cells. We discovered distinct NMNAT2 promoter interactomes in undifferentiated versus neuron-like SH-SY5Y cells. Utilizing bioinformatics analyses, we identified putative transcriptional factors and NMNAT2-associated genes. Notably, the mRNA levels of many of these genes showed a significant correlation with NMNAT2 mRNA levels in ∼400 single-nuclei RNA-seq datasets from ROSMAP. Additionally, using CRISPR-Cas9 strategies, we confirmed the requirement of two specific genomic regions within the interactomes and four transcription factors in regulating NMNAT2 transcription. In summary, our study identifies genomic loci containing NMNAT2 regulatory elements and predicts associated genes and transcription factors through computational analyses.
YY1 Enhances the Stability of HIF-1α Protein by Interacting with NUSAP1 in Macrophages within the Prostate Cancer Microenvironment
Authors: Li Wenchao , Chen SaiSai , Lu Jian , Mao Weipu , Zheng Shiya , Zhang Minhao , Wu Tiange , Chen Yurui , Lu Kai , Chu Chunyan , Shu Chuanjun , Hou Yue , Yang Xue , Shi Naipeng , Chen Zhijun , Zhang Lihua , Zhang Lei , Na Rong , Chen Ming , Ju Shenghong , Zhang Dingxiao , Ma Yi , Xu Bin
Published: November 2024

Immune checkpoint therapy for prostate cancer (PCa) has failed in clinical trials; however, the precise underlying mechanisms involved remain elusive. PCa, a classic "immune-cold” tumor, is characterized by an immunosuppressive tumor microenvironment. Within this milieu, macrophages, the predominant immune cell population, have a propensity to infiltrate the hypoxic zones of tumors. In a previous study, we showed that Yin Yang 1 (YY1) is highly expressed in macrophages in PCa tissues. Here, through multiplexed imaging mass cytometry (IMC) of a PCa tissue microarray, we further demonstrate that YY1+macrophages aggregate in hypoxic areas of tumors and that hypoxia promotes the phase separation of YY1 in the nucleus by increasing YY1 tyrosine phosphorylation in macrophages. Furthermore, YY1 binds to NUSAP1 and promotes the SUMOylation of HIF-1α, which promotes phase separation and stabilization of the HIF-1α protein. We also demonstrated that either treatment with a small molecule inhibitor (tenapanor) to decrease the YY1–NUSAP1–HIF-1α interaction or myeloid-specific YY1 gene knockout impairs subcutaneous PCa tumor formation. Furthermore, we present a first-generation tetrahedral DNA nanostructure (TDN) based on the proteolysis targeting chimera (PROTAC) technique, named YY1-DcTAC, which targets and degrades YY1 in tumor-associated macrophages. In a PCa mouse model, YY1-DcTAC exhibited prolonged drug efficacy, robust macrophage-specific responsiveness, potent antitumor effects, and increased CD8+T cell tumor infiltration. In summary, our findings underscore the pivotal role of YY1 within the hypoxia/HIF-1α pathway in tumor-associated macrophages and affirm the therapeutic potential of targeting YY1 for treating PCa.
The biotoxin BMAA promotes mesenchymal transition in neuroblastoma cells
Authors: Moore Ellie , Renner Abby , Dowden Taylor , Messer Devin , Hansen Hayes , Mull McKinnely , Goebel Abigail , Mawawa Grace , Burton Bryan , Pawlus Matthew
Published: November 2024

Mesenchymal-like cancer cells are an indicator of malignant tumors as they exhibit tumorigenic properties including downregulation of differentiation markers, and increased colony-forming potential, motility, and chemoresistance. We have previously demonstrated that the cyanobacterial biotoxin beta-methylamino-L-alanine (BMAA) is capable of influencing neural cell differentiation state through mechanisms involving the Wnt signaling pathway, suggesting the possibility that BMAA may play a role in influencing other Wnt related differentiation processes including mesenchymal transition. In this study we present evidence characterizing the effects of BMAA on mesenchymal transition in a human neuroblastoma cell line and provide support for the hypothesis that the biotoxin can promote this process in these cells by altering differentiation state, inducing changes in gene expression, and changing cellular function in manners consistent with cellular mesenchymal transition. Results of this study indicate that BMAA exposure may promote carcinogenesis through its effects on cell differentiation state in certain contexts. These results suggest that exposure to the biotoxin BMAA may be an influencing factor in chemotherapy resistance and cancer relapse in neuroblastoma.
Thermosensitivity of TREK K2P channels is controlled by a PKA switch and depends on the microtubular network
Authors: Cordeiro Sönke , Musinszki Marianne
Published: November 2024

Temperature sensing is an essential component of animal perception and enables individuals to avoid painful or lethal temperatures. Many temperature sensors in central and peripheral neurons are ion channels. Here, we focus on the thermosensitive TREK/TRAAK subfamily of K2P channels – the only known K+selective thermosensitive channels. The C-terminal domain is essential for the temperature activation of TREK channels, but the mechanism of temperature sensation and the nature of the temperature sensor are unknown. We studied the thermosensitivity of representatives of all K2P channel subfamilies and identified TREK-1 and TREK-2 as the only thermosensitive K2P channels, while TRAAK, the third member of the mechano-gated subfamily, showed no temperature dependence. We transferred the thermosensitivity of TREK-1 to TRAAK channels by exchanging the C-termini, demonstrating that the C-terminal domain is sufficient to confer thermosensitivity. By gradually truncating the C-terminus, we isolated a specific temperature responsive element (TRE) consisting of 18 amino acids that constitutes a unique feature in mammalian thermosensitive channels. Within this TRE lie both the binding domain for microtubule associated protein 2 (MAP2) and the PKA phosphorylation site. Pharmacological disruption of the microtubular network as well as the loss of the MAP2 binding site suppressed the temperature response, and PKA activation completely abolished temperature sensitivity. Thus, the connection to the microtubular network enables the thermosensitivity of TREK channels, which is not intrinsic to the channel itself, while the PKA-mediated phosphorylation status acts as a switch that determines if TREK channels are thermosensitive at all.
Deep Multimodal Representations and Classification of First-Episode Psychosis via Live Face Processing
Authors: Singh Rahul , Zhang Yanlei , Bhaskar Dhananjay , Srihari Vinod , Tek Cenk , Zhang Xian , Noah J. Adam , Krishnaswamy Smita , Hirsch Joy
Published: November 2024

Schizophrenia is a severe psychiatric disorder associated with a wide range of cognitive and neurophysiological dysfunctions and long-term social difficulties. In this paper, we test the hypothesis that integration of multiple simultaneous acquisitions of neuroimaging, behavioral, and clinical information will be better for prediction of early psychosis than unimodal recordings. We propose a novel framework to investigate the neural underpinnings of the early psychosis symptoms (that can develop into Schizophrenia with age) using multimodal acquisitions of neural and behavioral recordings including functional near-infrared spectroscopy (fNIRS) and electroencephalography (EEG), and facial features. Our data acquisition paradigm is based on live face-to-face interaction in order to study the neural correlates of social cognition in first-episode psychosis (FEP). We propose a novel deep representation learning framework, Neural-PRISM, for learning joint multimodal compressed representations combining neural as well as behavioral recordings. These learned representations are subsequently used to describe, classify, and predict the severity of early psychosis in patients, as measured by the Positive and Negative Syndrome Scale (PANSS) and Global Assessment of Functioning (GAF) scores. We found that incorporating joint multimodal representations from fNIRS and EEG along with behavioral recordings enhances classification between typical controls and FEP individuals. Additionally, our results suggest that geometric and topological features such as curvatures and path signatures of the embedded trajectories of brain activity enable detection of discriminatory neural characteristics in early psychosis.
Social information use across trophic guilds
Authors: Muñiz Marie , Meadows Brandon T. , Lopez Pablo , Lichtenberg Elinor M.
Published: November 2024

Animals use social information gathered by observing other individuals to adjust their behavior to better match the environment and improve fitness. Many insects use social information in various contexts. Bees improve their foraging efficiency by using social information from conspecifics to gauge nectar availability. Bees frequently encounter various heterospecific flower visitors, including different trophic groups such as nectaring predators. These heterospecifics may provide valuable information about nectar availability. We determined how bumble bees (Bombus impatiens) use visual social information from predatory lady beetles (Hippodamia convergens), who consume nectar to increase their reproductive output. Using laboratory-maintained bumble bees freely flying in arenas, we tested if bees could (1) innately recognize lady beetles as sources of social information about nectar, and (2) learn to use lady beetles to gauge nectar availability. Bees did not innately recognize lady beetles as a source of social information. They correctly learned to associate conspecifics with the presence and absence of food, but only learned to associate lady beetles with the presence of food and not the absence. Our results demonstrate social learning across species and trophic guilds, but suggest limits to when and how bees generalize social information from diverse heterospecific flower visitors.
The Mla pathway promotesVibrio choleraere-expansion from stationary phase
Authors: Leitner Deborah R. , Zingl Franz G. , Morano Alexander A. , Zhang Hailong , Waldor Matthew K.
Published: November 2024

Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identifyVibrio choleraegenes that promote the pathogen’s fitness in stationary phase. We discovered that the Mla (maintenance of lipidasymmetry) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type andmlaEmutantV. choleraerevealed that the Mla pathway promotes re-expansion from 48h stationary phase cultures. The mutant’s defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48h. However, by 96h the culturability of the mutant and wild-type strains were equivalent. By monitoring the abundances of genomically barcoded libraries of wild-type and ΔmlaEstrains, we observed that a few barcodes dominated the mutant culture at 96h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed themlaEmutant’s defect. Whole genome sequencing revealed thatmlaEsuppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for the maintenance ofV. cholerae’sculturability as it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway.

Importance

Bacteria regularly encounter conditions with nutrient scarcity, where cell growth and division are minimal. Knowledge of the pathways that enable re-growth following nutrient restriction are limited. Here, using the cholera pathogen, we uncovered a role for the Mla pathway, a system that enables phospholipid re-cycling, in promotingVibrio choleraere-expansion from stationary phase cultures. Cells labeled with DNA barcodes or fluorophores were useful to demonstrate that though the abundances of wild-type and Mla mutant cells were similar in stationary phase cultures, they had marked differences in their capacities to regrow on plates. Of note, Mla mutant cells lose cell envelope components including high energy phospholipids due to OMV shedding. Our findings suggest that the defects in cellular energy homeostasis which emerge in the absence of the Mla pathway underlie its importance in maintainingV. choleraeculturability.
An algal nutrient-replete, optimized medium for fast growth and high triacylglycerol accumulation
Authors: Jeffers Tim L , McCombs Ryan , Schmollinger Stefan , Merchant Sabeeha S , Niyogi Krishna K , Roth Melissa S
Published: November 2024

Microalgae are promising sources to sustainably meet the global needs for energy and products. Algae grow under different trophic conditions, where nutritional status regulates biosynthetic pathways, energy production, and growth. The green algaChromochloris zofingiensishas strong economic potential because it co-produces biofuel precursors and the high-value antioxidant astaxanthin while accumulating biomass when grown mixotrophically. As an emerging reference alga for photosynthesis, metabolism, and bioproduction,C. zofingiensisneeds a defined, optimized medium to standardize experiments during fast growth. Because the interplay of glucose consumption (+Glc) and mineral deficiency influences photosynthesis, growth, and the production of lipids and astaxanthin, we designed a replete nutrient medium tailored to theC. zofingiensiscellular ionome. We combined inductively coupled plasma mass spectrometry (ICP-MS) and +Glc growth curves to determine a medium that is nutrient replete for at least 5 days of +Glc logarithmic growth. We found that there are high nutritional needs for phosphorus and sulfur during mixotrophy. Iron was the only element measured for which the cellular concentration correlated with exogenous concentration and was iteratively adjusted until the internal ionome was consistent through the logarithmic growth phase. ThisChromochloris-OptimizedRatio ofElements (CORE) medium supports fast growth and high biomass without causing excess nutrient toxicity. This defined, nutrient-replete standard is important for futureC. zofingiensisinvestigations and can be adapted for other species to support high biomass. The method used to develop CORE medium shows how ionomics informs replicable media design and may be applied in industrial settings to inform cost-effective biofuel production.

Significance Statement

Studying how carbon sources and mineral nutrients interplay to regulate algal metabolism can be exploited to discover and control pathways in photosynthesis and biofuel production. Here we design a medium from the cellular ionome ofChromochloris zofingiensis, a powerful algal model for photosynthesis, metabolism, and bioproducts, to provide a defined, replete standard for mixotrophic and heterotrophic growth of green algae. These media design principles show how accounting for increased nutritional demands based on carbon substrate can ensure experimental replicability when probing diverse algal metabolisms.
Transmembrane coupling accelerates the growth of liquid-like protein condensates
Authors: Lee Yohan , Yuan Feng , Cabriales Jerry L. , Stachowiak Jeanne C.
Published: November 2024

Timely and precise assembly of protein complexes on membrane surfaces is essential to the physiology of living cells. Recently, protein phase separation has been observed at cellular membranes, suggesting it may play a role in the assembly of protein complexes. Inspired by these findings, we observed that protein condensates on one side of a planar suspended membrane spontaneously colocalized with those on the opposite side. How might this phenomenon contribute to the assembly of stable transmembrane complexes? To address this question, we examined the diffusion and growth of protein condensates on both sides of membranes. Our results reveal that transmembrane coupling of protein condensates on opposite sides of the membrane slows down condensate diffusion while accelerating condensate growth. How can the rate of condensate growth increase simultaneously with a decrease in the rate of condensate diffusion? We provide insights into these seemingly contradictory observations by distinguishing between diffusion-limited and coupling-driven growth processes. While transmembrane coupling slows down diffusion, it also locally concentrates condensates within a confined area. This confinement increases the probability of condensate coalescence and thereby enhances the overall rate of growth for coupled condensates, substantially surpassing the growth rate for uncoupled condensates. These findings suggest that transmembrane coupling could play a role in the assembly of diverse membrane-bound structures by promoting the localization and growth of protein complexes on both membrane surfaces. This phenomenon could help to explain the efficient assembly of transmembrane structures in diverse cellular contexts.

Significance

Protein assemblies that span biological membranes are critical to cellular physiology. In the past decade, liquid-like protein condensates, which are flexible, multivalent protein assemblies, have been discovered on diverse membrane surfaces. Recently, we observed that protein condensates on opposite sides of a membrane spontaneously colocalize to form coupled, transmembrane complexes. Interestingly, while transmembrane coupling slows down the diffusion of membrane-bound condensates, it substantially accelerates their growth by strongly localizing interactions between them. These findings suggest that transmembrane coupling of protein condensates may play a role in promoting the robust assembly of membrane-bound protein complexes in crowded, complex cellular environments.
Jade1 and the HBO1 complex are spatial-selective cofactors of Oct4
Authors: Wu Yifan , Manna Asit K. , Li Li , Handa Hiroshi , Chandrasekharan Mahesh B. , Tantin Dean
Published: November 2024

Oct4 is a master regulator of pluripotency. Potential Oct4 interactors have been cataloged extensively but the manner and significance of these interactions are incompletely defined. Like other POU domain proteins, Oct4 is capable of binding to DNA in multiple configurations, however the relationship between these configurations and cofactor recruitment (and hence transcription output) are unknown. Here, we show that Oct4 interacts with common and unique proteins when bound to DNA in different configurations. One of these proteins is Jade1, a component of the HBO histone acetyltransferase complex. Jade1 preferentially associates with Oct4 when bound toMore palindromicOctamer-RelatedElement (MORE) DNA sequences that bind Oct4 dimers and are associated with strong gene expression. Surprisingly, we find that the Oct4 N-terminal activation domain, rather than facilitating Jade1 binding, serves as an autoinhibitory domain that dampens the interaction. ChIP-seq using HBO1, the enzymatic component of the complex, identifies a preference for binding adjacent to Oct4 at MORE sites. Using purified recombinant proteins and nucleosome complexes, we show that the HBO1 complex acetylates histone H3K9 within nucleosomes more efficiently when Oct4 is co-bound to a MORE site. Histone acetylation is further increased when Oct4 is mutated to favor dimeric MORE binding. Cryo-electron microscopy reveals that Oct4 bound to a MORE near the nucleosome entry/exit site partially unwinds DNA from nucleosome core particles, and identifies additional mass associated with the HBO1 complex. These results identify a novel mechanism of transcriptional regulation by Oct4.
Evidence for a role of extraintestinal pathogenic Escherichia coli, Enterococcus faecalis and Streptococcus gallolyticus in the aetiology of exudative cloacitis in the critically endangered kākāpō (Strigops habroptilus)
Authors: French Rebecca Kay , Waller Stephanie J , Wierenga Janelle R , Grimwood Rebecca M , Hodgkinson-Bean James , Digby Andrew , Uddstrom Lydia , Eason Daryl ,   Kakapo Recovery Team, Argilla Lisa , Biggs Patrick J , Cookson Adrian , French Nigel , Geoghegan Jemma L
Published: November 2024

The kakapo is a critically endangered flightless parrot which suffers from exudative cloacitis, a debilitating disease resulting in inflammation of the vent margin or cloaca. Despite this disease emerging over 20 years ago, the cause of exudative cloacitis remains elusive. We used total RNA sequencing and metatranscriptomic analysis to characterise the infectome of lesions and cloacal swabs from nine kakapo affected with exudative cloacitis, and compared this to cloacal swabs from 45 non-diseased kakapo. We identified three bacterial species - Streptococcus gallolyticus, Enterococcus faecalis and Escherichia coli - as significantly more abundant in diseased kakapo compared to healthy individuals. The genetic diversity observed in both S. gallolyticus and E. faecalis among diseased kakapo suggests that these bacteria originate from exogenous sources rather than from kakapo-to-kakapo transmission. The presence of extraintestinal pathogenic E. coli (ExPEC)-associated virulence factors in the diseased kakapo population suggests that E. coli may play a critical role in disease progression by facilitating iron acquisition and causing DNA damage in host cells, possibly in association with E. faecalis. No avian viral, fungal nor other parasitic species were identified. These results, combined with the consistent presence of one E. coli gnd sequence type across multiple diseased birds, suggests that this species may be the primary cause of exudative cloacitis. These findings shed light on possible causative agents of exudative cloacitis, and offer insights into the interplay of microbial factors influencing the disease.