bluuebunny/crossref_metadata_2025 huggingface dataset:
Back to the holobiont: ecophysiological and systemic responses of rooted-cuttings inoculated with a synthetic community
Authors: Sandrini Marco , Chitarra Walter , Pagliarani Chiara , Moffa Loredana , Petrozziello Maurizio , Colla Paola , Balestrini Raffaella , Nerva Luca
Published: November 2023

Despite microbe-based products for grapevine protection and growth improvement are already available, a few of them contain microbes directly isolated from vine tissues. For this reason, a collection of endophytic bacterial isolates obtained directly from grapevine woody tissues has been used for producing anad-hocinoculum. The selected bacterial isolates were tested in biocontrol assays against some of the main grapevine pathogens (e.g.,Botrytis cinerea,Guignardia bidwellii,Neofusicoccum parvum) and the best performing ones were screened for plant growth promoting (PGP)-traits (e.g., phosphorous solubilization, indole-acetic acid and siderophore production). Before being planted, rooted cuttings were inoculated with two different synthetic communities: the first one was anad-hocdeveloped microbial community (SynCom), whereas the second was a commercial consortium formed by arbuscular mycorrhizal fungi (AMF) and a rhizosphere bacterial strain (AMF+B). Physiological parameters were monitored to evaluate effects on plant performances, and samples for biochemical and molecular analyses were collected. Integration of physiological data with metabolite profiling and transcriptome sequencing highlighted that the SynCom treatment shaped the plant growth-defence trade-off, by regulating photosynthesis and diverting energy sources towards the activation of defence metabolic pathways. On the other hand, the AMF+B treatment led to a more balanced growth-defence trade-off, though a mild activation of defence mechanisms was also observed in these plants. Our findings suggest that an experimental approach considering both the features of associated microbes and their impacts on plant growth and defence could shed light on the “dark-side effects” of SynCom application, thereby enabling their exploitation with a refined awareness.
A deep learning framework for automated and generalized synaptic event analysis
Authors: O'Neill Philipp Sean , Baccino-Calace Martin , Rupprecht Peter , Friedrich Rainer W , Mueller Martin , Delvendahl Igor
Published: November 2023

Quantitative information about synaptic transmission is key to our understanding of neural function. Spontaneously occurring synaptic events carry fundamental information about synaptic function and plasticity. However, their stochastic nature and low signal-to-noise ratio present major challenges for the reliable and consistent analysis. Here, we introduce miniML, a supervised deep learning-based method for accurate classification and automated detection of spontaneous synaptic events. Comparative analysis using simulated ground-truth data shows that miniML outperforms existing event analysis methods in terms of both precision and recall. miniML enables precise detection and quantification of synaptic events in electrophysiological recordings. We demonstrate that the deep learning approach generalizes easily to diverse synaptic preparations, different electrophysiological and optical recording techniques, and across animal species. miniML provides not only a comprehensive and robust framework for automated, reliable, and standardized analysis of synaptic events, but also opens new avenues for high-throughput investigations of neural function and dysfunction.
Distinct members of theC. elegansCeMbio reference microbiota exert cryptic virulence and infection protection
Authors: Gonzalez Xavier , Irazoqui Javier E.
Published: November 2023

Microbiotas are complex microbial communities that colonize specific niches in the host and provide essential organismal functions that are important in health and disease. A key aspect is the ability of each distinct community member to promote or impair host health, alone or in the context of the community, in hosts with varied levels of immune competence. Understanding such interactions is limited by the complexity and experimental accessibility of current systems and models. Recently, a reference twelve-member microbiota for the model organismC. elegans,known as CeMbio, was defined to aid the dissection of conserved host-microbiota interactions. Understanding the physiological impact of the CeMbio bacteria onC. elegansis in its infancy. Here, we show the differential ability of each CeMbio bacterial species to activate innate immunity through the conserved PMK-1/p38 MAPK, ACh/WNT, and HLH-30/TFEB pathways. Using immunodeficient animals, we uncovered several examples of bacterial ‘cryptic’ virulence, or virulence that was masked by the host defense response. The ability to activate the PMK-1/p38 pathway did not correlate with bacterial virulence in wild type or immunodeficient animals. In contrast, ten out of twelve species activated HLH-30/TFEB, and most showed virulence towardshlh-30-deficient animals. In addition, we identifiedPseudomonas luridaas a pathogen in wild type animals, andAcinetobacter guillouiaeas avirulent despite activating all three pathways. Moreover, short pre-exposure toA. guillouiaepromoted host survival of infection withP. lurida,which was dependent on PMK-1/p38 MAPK and HLH-30/TFEB. These results suggest that the microbiota ofC. elegansis rife with “opportunistic” pathogens, and that HLH-30/TFEB is a fundamental and key host protective factor. Furthermore, they support the idea that bacteria likeA. guillouiaeevolved the ability to induce host innate immunity to improve host fitness when confronted with pathogens, providing new insights into how colonization order impacts host health.
Disturbance-generated competitive coexistence
Authors: Trigos-Raczkowski U. A. , Lyons R. , Delgadino M. G. , Ackleh A. S. , Ostling A.
Published: November 2023

Explaining how competing species coexist remains a challenge in ecology. A major hypothesis is that disturbance opens up the opportunity for types with different “life history” strategies to coexist, allowing types better at getting to and using recently disturbed patches to coexist with better competitor types. A simple model introduced several decades ago demonstrated this, but its focus on patch dynamics (i.e. the dynamics of the number of patches a species occupies) gives limited insight into how coexistence-enabling variation arises from within-patch demographic strategies. Here we present, and demonstrate how to analyze, a partial differential equation model that captures the emergence of larger-scale competitive dynamics from within-patch population dynamics of species competing for patches subject to disturbance. We analyze key cases of the model framework, with competition acting in turn on each aspect of within-patch demography included in the model: reproduction, offspring-survival, and adult-survival. Insights arising from these analyses include: 1) variation between species on a simple reproduction-adult-survival trade-off can enable disturbance-generated coexistence, 2) variation along trade-offs with species’ robustness-to-competition can also generate coexistence 3) disturbance-generated coexistence may or may not involve classical “successional dynamics” within patches, and 4) coexistence is easier to generate at intermediate disturbance rates. Our work here provides new tools for more complete development of the theory of disturbance-generated coexistence.
Molecular Forecasting of Domoic Acid during a Pervasive Toxic Diatom Bloom
Authors: Brunson John K. , Thukral Monica , Ryan John P. , Anderson Clarissa R. , Kolody Bethany C. , James Chase , Chavez Francisco P. , Leaw Chui Pin , Rabines Ariel J. , Venepally Pratap , Zheng Hong , Kudela Raphael M. , Smith G. Jason , Moore Bradley S. , Allen Andrew E.
Published: November 2023

In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatomPseudo-nitzschia australis, this bloom produced high levels of the neurotoxin domoic acid (DA). Through molecular and transcriptional characterization of 52 near-weekly phytoplankton net-tow samples collected at a bloom hotspot in Monterey Bay, California, we identified active transcription of known DA biosynthesis (dab) genes from the three identified toxigenic species, includingP. australisas the primary origin of toxicity. Elevated expression of silicon transporters (sit1) during the bloom supports the previously hypothesized role of dissolved silica (Si) exhaustion in contributing to bloom physiology and toxicity. We find that co-expression of thedabAandsit1genes serves as a robust predictor of DA one week in advance, potentially enabling the forecasting of DA-producing HABs. We additionally present evidence that low levels of iron could have co-limited the diatom population along with low Si. Iron limitation represents a previously unrecognized driver of both toxin production and ecological success of the low iron adaptedPseudo-nitzschiagenus during the 2015 bloom, and increasing pervasiveness of iron limitation may fuel the escalating magnitude and frequency of toxicPseudo-nitzschiablooms globally. Our results advance understanding of bloom physiology underlying toxin production, bloom prediction, and the impact of global change on toxic blooms.

Significance

Pseudo-nitzschiadiatoms form oceanic harmful algal blooms that threaten human health through production of the neurotoxin domoic acid (DA). DA biosynthetic gene expression is hypothesized to control DA production in the environment, yet what regulates expression of these genes is yet to be discovered. In this study, we uncovered expression of DA biosynthesis genes by multiple toxigenicPseudo-nitzschiaspecies during an economically impactful bloom along the North American West Coast, and identified genes that predict DA in advance of its production. We discovered that iron and silica co-limitation restrained the bloom and likely promoted toxin production. This work suggests that increasing iron limitation due to global change may play a previously unrecognized role in driving bloom frequency and toxicity.
Coordination among leaf and fine root traits across a strong natural soil fertility gradient
Authors: Guilbeault-Mayers Xavier , Lambers Hans , Laliberté Etienne
Published: November 2023

Unravelling how fundamental axes of trait variation correlate among leaves and roots and relate to nutrient availability is crucial for understanding plant distribution. While the leaf trait variation axis is linked to nutrient availability gradients, the response of root trait variation to the same gradients yields inconsistent results.

We studied leaf and root trait variation among 23 co-occurring plant species along a 2-million year soil chronosequence to assess how leaf and root traits coordinate and how this resulting joint axis of variation relates to soil fertility.

Mycorrhizal association types primarily structured the axes of leaf and root trait variation. However, when considering species abundance, soil nutrient availability was an important driver of trait distribution. Leaves that support rapid growth in younger, fertile soils were associated with roots of larger diameter and arbuscular mycorrhizal colonization. In contrast, leaves that favour nutrient conservation in nutrient-impoverished soil were associated with greater root hair length and phosphorus-mobilizing root exudates.

At the species level, the signals deviated from the community-wide results presented above, highlighting the challenge of generalizing a specific set of root trait values that consistently meet the requirements of leaves supporting either rapid growth or survival.
Non-apical plateau potentials and persistent firing induced by metabotropic cholinergic modulation in layer 2/3 pyramidal cells in the rat prefrontal cortex
Authors: Hagger-Vaughan Nicholas , Kolnier Daniel , Storm Johan F.
Published: November 2023

The prefrontal cortex (PFC) is important for executive functions, including attention, planning, decision-making, and memory, and is proposed by some leading theories to be crucial for consciousness. In particular, the global neuronal workspace theory proposes that PFC layer 2/3 pyramidal cells (L2/3PCs) contribute crucially to the ‘global workspace’, and hence to consciousness, due to their long-range connections to other cortical areas.

Plateau potentials, periods of depolarisation with action potential firing outlasting the stimuli that induced them, have been suggested to help maintain working memory and to contribute to executive functions and consciousness.

We therefore investigated plateau potentials and their mechanisms in PFC layer 2/3 pyramidal neurons. Using whole-cell somatic recordings from L2/3PCs in rat PFC brain slices, we found that the metabotropic cholinergic agonist muscarine reliably induced long-lasting plateau potentials with spiking following a train of evoked action potentials. Similar plateaus were induced by a metabotropic glutamate receptor (mGluR) agonist. Pharmacological tests suggested that these plateaus were dependent on transient receptor potential (TRP) cation channels, both TRPC4 and TRPC5, and required the presence of external calcium (Ca2+) and internal Ca2+stores, but not voltage-gated Ca2+channels. Using local Ca2+applications, we found that the responsible Ca2+influx is most likely distributed on the somatic and/or basal dendritic compartments rather than on the (distal) apical dendrite. We used knife cuts to disconnect apical dendrites, sometimes less than 50 µm from the soma, and found that the plateaus did not depend on the distal apical dendrite, since truncated cells generated plateaus with as many spikes as control cells. These results indicate that layer 2/3PCs can generate plateau potentials with sustained spiking independently of distal apical dendrites.
Rapid nongenomic estrogen signaling controls alcohol drinking behavior
Authors: Zallar Lia J. , Rivera-Irizarry Jean K. , Hamor Peter U. , Pigulevskiy Irena , Rico Rozo Ana-Sofia , Mehanna Hajar , Liu Dezhi , Welday Jacqueline P. , Bender Rebecca , Asfouri Joseph J. , Levine Olivia B. , Skelly Mary Jane , Hadley Colleen K. , Fecteau Kristopher M. , Nelson Scottie , Miller John , Ghazal Pasha , Bellotti Peter , Singh Ashna , Hollmer Lauren V. , Erikson David W. , Geri Jacob , Pleil Kristen E.
Published: November 2023

Ovarian-derived estrogen is a key modulator of numerous physiological processes via genomic and nongenomic mechanisms, including signaling non-canonically at membrane-associated estrogen receptors in the brain to rapidly regulate neuronal function. However, the mechanisms mediating estrogen regulation of behaviors such as alcohol consumption remain unclear. Early alcohol drinking confers greater risk for alcohol use disorder in women than men, and binge alcohol drinking is correlated with high circulating estrogen levels, but a causal role for estrogen signaling in driving alcohol drinking in gonadally-intact animals has not been established. We found that female mice displayed greater binge alcohol drinking and reduced avoidance behavior when circulating estrogen was high during the proestrus phase of the estrous cycle than when it was low, contributing to sex differences in these behaviors. The pro-drinking, but not anxiolytic, effect of high endogenous estrogen state occurred via rapid estrogen signaling at membrane-associated estrogen receptor alpha in the bed nucleus of the stria terminalis, which promoted synaptic excitation of corticotropin-releasing factor neurons and facilitated their activity during alcohol drinking behavior. This study is the first to demonstrate a rapid, nongenomic signaling mechanism for ovarian-derived estrogen signaling in the brain controlling behavior in gonadally intact females, and it establishes a causal role for estrogen in an intact hormonal context for driving alcohol consumption that contributes to known sex differences in this behavior.
Glioblastoma and other intracranial tumors elicit systemic sympathetic hyperactivity that limits immunotherapeutic responses
Authors: Lorrey Selena J , Wachsmuth Lucas , Finlay John , Neff Corey , Ayasoufi Katayoun , Waibl Polania Jessica , Hoyt-Miggelbrink Alexandra , Price Mackenzie , Rein Lindsay , Dell Samuel , Reesman Rachael , Cui Xiuyu , Hawley Amelia , Lerner Emily , Wilkinson Daniel , Srinivasan Ethan , Walsh Kyle , Patel Anoop , Ostrom Quinn T , Fecci Peter E
Published: November 2023

Intracranial tumors present unique challenges for immunotherapy. These can include both local and systemic modes of immune suppression whose mechanistic underpinnings are incompletely understood. Here, we reveal that tumors harbored intracranially elicit systemic increases to circulating catecholamine levels, with the resultant chronic sympathetic hyperactivity driving T cell dysfunction and limiting immunotherapeutic success. Conversely, treatment with b-adrenergic blockade increases NF-kB activity in immune cells, restores T cell polyfunctionality, modifies the tumor microenvironment, and licenses immune-based therapies in murine models of glioblastoma (GBM) to extend survival. Extended survival is also observed in GBM patients having received b-adrenergic blockade, as well as in patients with melanoma and lung cancer brain metastases who received b-blockade alongside concomitant immune checkpoint inhibition. While b-blockade also impacts outcomes in the setting of extracranial disease, the benefits are especially pronounced in patients harboring intracranial disease burdens. These data suggest that sympathetic hyperactivity facilitates systemic immune dysfunction in the setting of intracranial tumors, specifically and advance a role for b-adrenergic blockade in licensing immunotherapeutic responses within the intracranial compartment.
BHLHE40 drives protective polyfunctional CD4 T cell differentiation in the female reproductive tract againstChlamydia
Authors: Mercado Miguel A. B. , Li Qiang , Quick Charles M. , Kim Yejin , Palmer Rachel , Huang Lu , Li Lin-Xi
Published: November 2023

The protein basic helix-loop-helix family member e40 (BHLHE40) is a transcription factor recently emerged as a key regulator of host immunity to infections, autoimmune diseases and cancer. In this study, we investigated the role ofBhlhe40in protective T cell responses to the intracellular bacteriumChlamydiain the female reproductive tract (FRT). Mice deficient inBhlhe40exhibited severe defects in their ability to controlChlamydia muridarumshedding from the FRT. The heightened bacterial burdens inBhlhe40−/−mice correlated with a marked increase in IL-10-producing T regulatory type 1 (Tr1) cells and decreased polyfunctional CD4 T cells co-producing IFN-γ, IL-17A and GM-CSF. Genetic ablation of IL-10 or functional blockade of IL-10R increased CD4 T cell polyfunctionality and partially rescued the defects in bacterial control inBhlhe40−/−mice. Using single-cell RNA sequencing coupled with TCR profiling, we detected a significant enrichment of stem-like T cell signatures inBhlhe40-deficient CD4 T cells, whereas WT CD4 T cells were further down on the differentiation trajectory with distinct effector functions beyond IFN-γ production by Th1 cells. Altogether, we identifiedBhlhe40as a key molecular driver of CD4 T cell differentiation and polyfunctional responses in the FRT againstChlamydia.
Differential genetic expression within reward-specific ensembles in mice
Authors: Litif Carl G. , Flom Levi T. , Sandum Kathryn L. , Hodgins Skylar L. , Vaccaro Lucio , Stitzel Jerry A. , Blouin Nicolas A. , Mannino Maria Constanza , Gigley Jason P. , Schoborg Todd A. , Bobadilla Ana-Clara
Published: November 2023

Maladaptive reward seeking is a hallmark of cocaine use disorder. To develop therapeutic targets, it is critical to understand the neurobiological changes specific to cocaine-seeking without altering the seeking of natural rewards, e.g., sucrose. The prefrontal cortex (PFC) and the nucleus accumbens core (NAcore) are known regions associated with cocaine- and sucrose-seeking ensembles, i.e., a sparse population of co-activated neurons. Within ensembles, transcriptomic alterations in the PFC and NAcore underlie the learning and persistence of cocaine- and sucrose-seeking behavior. However, transcriptomes exclusively driving cocaine seeking independent from sucrose seeking have not yet been defined using a within-subject approach. Using Ai14:cFos-TRAP2 transgenic mice in a dual cocaine and sucrose self-administration model, we fluorescently sorted (FACS) and characterized (RNAseq) the transcriptomes defining cocaine- and sucrose-seeking ensembles. We found reward- and region-specific transcriptomic changes that will help develop clinically relevant genetic approaches to decrease cocaine-seeking behavior without altering non-drug reward-based positive reinforcement.
Microscale visualization of cellular features in adult macaque visual cortex
Authors: Balaram Pooja , Takasaki Kevin , Hellevik Ayana , Tandukar Jamuna , Turschak Emily , MacLennan Bryan , Ouellette Naveen , Torres Russel , Laughland Connor , Gliko Olga , Seshamani Sharmistaa , Perlman Eric , Taormina Mike , Peterson Erica , Juneau Zoe , Potekhina Lydia , Glaser Adam , Chandrashekar Jayaram , Logsdon Molly , Cao Kevin , Dylla Celeste , Hatanaka Gaku , Chatterjee Soumya , Ting Jonathan , Vumbaco David , Waters Jack , Bair Wyeth , Tsao Doris , Gao Ruixuan , Reid Clay
Published: November 2023

Expansion microscopy and light sheet imaging enable fine-scale resolution of intracellular features that comprise neural circuits. Most current techniques visualize sparsely distributed features across whole brains or densely distributed features within individual brain regions. Here, we visualize dense distributions of immunolabeled proteins across early visual cortical areas in adult macaque monkeys. This process may be combined with multiphoton or magnetic resonance imaging to produce multimodal atlases in large, gyrencephalic brains.
Single-nucleus transcriptomics of epicardial adipose tissue from females reveals exercise control of innate and adaptive immune cells
Authors: Ahmad Irshad , Gupta Shreyan , Faulkner Patricia , Mullens Destiny , Thomas Micah , Sytha Sharanee P. , Ivanov Ivan , Cai James J. , Heaps Cristine L. , Newell-Fugate Annie E.
Published: November 2023

Coronary artery disease (CAD) is a leading cause of death in women. Although exercise mitigates CAD, the mechanisms by which exercise impacts epicardial adipose tissue (EAT) are unknown. We hypothesized that exercise promotes an anti-inflammatory microenvironment in EAT from female pigs. Yucatan pigs (n=7) were assigned to sedentary (Sed) or exercise (Ex) treatments and coronary arteries were occluded (O) with an ameroid to mimic CAD or remained non-occluded (N). EAT was collected for bulk and single nucleus transcriptomic sequencing (snRNA-seq). Exercise upregulated G-protein coupled receptor, S100 family, and FAK pathways and downregulated the coagulation pathway. Exercise increased the interaction between immune, endothelial, and mesenchymal cells in the insulin-like growth factor pathway and between endothelial and other cell types in the platelet endothelial cell adhesion molecule 1 pathway. Sub- clustering revealed nine cell types in EAT with fibroblast and macrophage populations predominant in O-Ex EAT and T cell population predominant in N-Ex EAT. Coronary occlusion impacted the largest number of genes in T and endothelial cells. Genes related to fatty acid metabolism were the most highly upregulated in non-immune cells from O-Ex EAT. Sub-clustering of endothelial cells revealed that N-Ex EAT separated from other treatments. In conclusion, aerobic exercise increased interaction amongst immune and mesenchymal and endothelial cells in female EAT. Exercise was minimally effective at reversing alterations in gene expression in endothelial and mesenchymal cells in EAT surrounding occluded arteries. These findings lay the foundation for future work focused on the impact of exercise on cell types in EAT.

Significance Statement

Coronary artery disease (CAD) is a leading cause of death in women. However, the role of epicardial adipose tissue (EAT) in the development of CAD in females and how exercise, which is recommended to slow CAD progression, impacts EAT are unknown. The effect of aerobic exercise on gene expression in EAT was investigated with RNA-sequencing, revealing significant alterations in fatty acid processing and immunoregulatory processes. This study provides valuable insights into the molecular and cellular changes induced in EAT by exercise in the context of chronic ischemic heart disease in females. These findings bolster current understanding of the impact of aerobic exercise on cardiac health in females and provide a foundation for future research in the field of exercise science.
Whi5 hypo- and hyper-phosphorylation dynamics control cell cycle entry and progression
Authors: Xiao Jordan , Turner Jonathan J. , Kõivomägi Mardo , Skotheim Jan M.
Published: November 2023

Progression through the cell cycle depends on the phosphorylation of key substrates by cyclin-dependent kinases. In budding yeast, these substrates include the transcriptional inhibitor Whi5 that regulates the G1/S transition. In early G1 phase, Whi5 is hypo-phosphorylated and inhibits the SBF complex that promotes transcription of the cyclinsCLN1andCLN2. In late-G1, Whi5 is rapidly hyper-phosphorylated by Cln1,2 in complex with the cyclin-dependent kinase Cdk1. This hyper-phosphorylation inactivates Whi5 and excludes it from the nucleus. Here, we set out to determine the molecular mechanisms responsible for Whi5’s multi-site phosphorylation and how they regulate the cell cycle. To do this, we first identified the 19 Whi5 sites that are appreciably phosphorylated and then determined which of these sites are responsible for G1 hypo-phosphorylation. Mutation of 7 sites removed G1 hypo-phosphorylation, increased cell size, and delayed the G1/S transition. Moreover, the rapidity of Whi5 hyper-phosphorylation in late G1 depends on ‘priming’ sites that dock the Cks1 subunit of Cln1,2-Cdk1 complexes. Hyper-phosphorylation is crucial for Whi5 nuclear export, normal cell size, full expression of SBF target genes, and timely progression through both the G1/S transition and S/G2/M phases. Thus, our work shows how Whi5 phosphorylation regulates the G1/S transition and how it is required for timely progression through S/G2/M phases and not only G1 as previously thought.
The role of alternative polyadenylation in Epithelial-mesenchymal transition of non-small cell lung cancer
Authors: Wu Sijia , Qin Xinyu , Huang Liyu
Published: November 2023

The metastatic non-small cell lung cancer (NSCLC) is one of the cancers with high incidence, poor survival, and limited treatment. Epithelial-mesenchymal transition (EMT) is the first step by which an early tumor converts to an invasive one. Studying the underlying mechanisms of EMT can help the understanding of cancer metastasis and improve the treatment. In this study, 1,013 NSCLC patients and 123 NSCLC cell lines are deeply analyzed for the potential roles of alternative polyadenylation (APA) in the EMT process. A trend of shorter 3’-UTRs is discovered in the mesenchymal samples. The identification of EMT-related APA events highlights the proximal poly(A) selection ofCARM1. It is a pathological biomarker of mesenchymal tumor and cancer metastasis through losing miRNA binding to upregulate the EMT inducer ofCARM1and releasing miRNAs to downregulate the EMT inhibitor ofRBM47. The crucial role of this APA event in EMT also guides its effect on drug responses. The patients with shorter 3’-UTR ofCARM1are more benefit from chemotherapy drugs, especially cisplatin. A stratification of NSCLC patients based on this APA event is useful for chemotherapy design in future clinics.
An end-to-end approach for protein folding by integrating Cryo-EM maps and sequence evolution
Authors: Li Pan , Guo Liangyue , Liu Haibin , Liu Binghua , Meng Fanhao , Ni Xiaodan , Guo Allen Chunlong
Published: November 2023

Protein structure modeling is an important but challenging task. Recent breakthroughs in Cryo-EM technology have led to rapid accumulation of Cryo-EM density maps, which facilitate scientists to determine protein structures but it remains time-consuming. Fortunately, artificial intelligence has great potential in automating this process. In this study, we present SMARTFold, a deep learning protein structure prediction model combining sequence alignment features and Cryo-EM density map features. First, using density map, we sample representative points along the predicted high confidence areas of protein backbone. Then we extract geometric features of these points and integrate these features with sequence alignment features in our proposed protein folding model. Extensive experiments confirm that our model performs best on both single-chain and multi-chain benchmark dataset compared with state-of-the-art methods, which makes it a reliable tool for protein atomic structure determination from Cryo-EM maps.
MDA5-autoimmunity and Interstitial Pneumonitis Contemporaneous with the COVID-19 Pandemic (MIP-C)
Authors: Iqbal Khizer , Sinha Saptarshi , David Paula , De Marco Gabriele , Taheri Sahar , McLaren Ella , Maisuria Sheetal , Arumugakani Gururaj , Ash Zoe , Buckley Catrin , Coles Lauren , Hettiarachchi Chamila , Smithson Gayle , Slade Maria , Shah Rahul , Marzo-Ortega Helena , Keen Mansoor , Lawson Catherine , Mclorinan Joanna , Nizam Sharmin , Reddy Hanu , Sharif Omer , Sultan Shabina , Tran Gui , Wood Mark , Wood Samuel , Ghosh Pradipta , McGonagle Dennis
Published: November 2023

Background

Anti-MDA5 (Melanoma differentiation-associated protein-5) positive dermatomyositis (MDA5+-DM) is characterised by rapidly progressive interstitial lung disease (ILD) and high mortality. MDA5 senses single-stranded RNA and is a key pattern recognition receptor for the SARS-CoV-2 virus.

Methods

This is a retrospective observational study of a surge in MDA5 autoimmunity, as determined using a 15 muscle-specific autoantibodies (MSAs) panel, between Janurary 2018-December 2022 in Yorkshire, UK. MDA5-positivity was correlated with clinical features and outcome, and regional SARS-CoV-2 positivity and vaccination rates. Gene expression patterns in COVID-19 were compared with autoimmune lung disease and idiopathic pulmonary fibrosis (IPF) to gain clues into the genesis of the observed MDA5+-DM outbreak.

Results

Sixty new anti-MDA5+, but not other MSAs surged between 2020-2022, increasing from 0.4% in 2019 to 2.1% (2020), 4.8% (2021) and 1.7% (2022). Few (8/60) had a prior history of confirmed COVID-19, peak rates overlapped with regional SARS-COV-2 community positivity rates in 2021, and 58% (35/60) had received anti-SARS-CoV-2 RNA vaccines. Few (8/60) had a prior history of COVID-19, whereas 58% (35/60) had received anti-SARS-CoV-2 RNA vaccines. 25/60 cases developed ILD which rapidly progression with death in 8 cases. Among the 35/60 non-ILD cases, 14 had myositis, 17 Raynaud phenomena and 10 had dermatomyositis spectrum rashes. Transcriptomic studies showed strongIFIH1(gene encoding for MDA5) induction in COVID-19 and autoimmune-ILD, but not IPF, andIFIH1strongly correlated with an IL-15-centric type-1 interferon response and an activated CD8+ T cell signature that is an immunologic hallmark of progressive ILD in the setting of systemic autoimmune rheumatic diseases. TheIFIH1rs1990760TT variant blunted such response.

Conclusions

A distinct pattern of MDA5-autoimmunity cases surged contemporaneously with circulation of the SARS-COV-2 virus during COVID-19. Bioinformatic insights suggest a shared immunopathology with known autoimmune lung disease mechanisms.
Genetic analysis and multimodal imaging identify novel mtDNA 12148T>C leading to multisystem dysfunction with tissue-specific heteroplasmy
Authors: Belle Kinsley , Kreymerman Alexander , Vadgama Nirmal , Ji Marco H. , Randhawa Sandeep , Caicedo Juan , Wong Megan , Muscat Stephanie P. , Gifford Casey A. , Lee Richard T. , Nasir Jamal , Young Jill L. , Enns Gregory , Karakikes Ioannis , Mercola Mark , Wood Edward H.
Published: November 2023

Patients with mitochondrial disorders present with clinically diverse symptoms, largely driven by heterogeneous mutations in mitochondrial-encoded and nuclear-encoded mitochondrial genes. These mutations ultimately lead to complex biochemical disorders with a myriad of clinical manifestations, often accumulating during childhood on into adulthood, contributing to life-altering and sometimes fatal events. It is therefore important to diagnose and characterize the associated disorders for each mitochondrial mutation as early as possible since medical management might be able to improve the quality and longevity of life in mitochondrial disease patients. Here we identify a novel mitochondrial variant in a mitochondrial transfer RNA for histidine (mt-tRNA-his) [m.12148T>C], that is associated with the development of ocular, aural, neurological, renal, and muscular dysfunctions. We provide a detailed account of a family harboring this mutation, as well as the molecular underpinnings contributing to cellular and mitochondrial dysfunction. In conclusion, this investigation provides clinical, biochemical, and morphological evidence of the pathogenicity of m.12148T>C. We highlight the importance of multiple tissue testing and in vitro disease modeling in diagnosing mitochondrial disease.
Low density neutrophils and neutrophil extracellular traps (NETs) are new inflammatory players in heart failure
Authors: Dumont Benjamin L. , Neagoe Paul-Eduard , Charles Elcha , Villeneuve Louis , Ninni Sandro , Tardif Jean-Claude , Räkel Agnès , White Michel , Sirois Martin G.
Published: November 2023

Background

Heart failure with reduced (HFrEF) or preserved ejection fraction (HFpEF) is characterized by low-grade chronic inflammation. Circulating neutrophils regroup two subtypes termed high- and low-density neutrophils (HDNs and LDNs). LDNs represent less than 2% of total neutrophil under physiological conditions, but their count increase in multiple pathologies, releasing more inflammatory cytokines and neutrophil extracellular traps (NETs).

Objectives

Assess the differential count and role of HDNs, LDNs and NETs-related activities in HF patients.

Methods

HDNs and LDNs were isolated from human blood by density gradient and purified by FACS and their counts obtained by flow cytometry. NETs formation (NETosis) was quantified by confocal microscopy. Circulating inflammatory and NETosis biomarkers were measured by ELISA. Neutrophil adhesion onto human extracellular matrix (hECM) was assessed by optical microscopy.

Results

A total of 140 individuals were enrolled, including 33 healthy volunteers (HV), 41 HFrEF (19 stable patients and 22 presenting acute decompensated HF; ADHF) and 66 HFpEF patients (36 stable patients and 30 presenting HF decompensation). HDNs and LDNs counts were significantly increased up to 39% and 2740% respectively in HF patients compared to HV. In HF patients, the correlations between LDNs counts and circulating inflammatory (CRP, IL-6 and -8), Troponin T, NT-proBNP and NETosis components were all significant. In vitro, LDNs expressed more H3Cit and NETs and were more pro-adhesive, with ADHFpEF patients presenting the highest pro-inflammatory profile.

Conclusions

HFpEF patients present higher levels of circulating LDNs and NETs related activities, which are the highest in the context of acute HF decompensation.

Clinical Perspective

In comparison to HFrEF, HFpEF patients have higher levels of circulation LDNs and NETs-associated inflammatory cytokines, peaking in acute decompensated clinical condition.

Furthermore, LDNs are producing more NETs and are more adhesive than HDNs, which can contribute to pro-thrombogenesis status described in HF patients

Measurement of circulating NETs-associated biomarkers could become a novel tool to assess the the risk of acute thrombogenesis in hospitalized ADHFpEF patients.

These measurements could lead to future clinical treatments using NETosis inhibitors alone or combined with NETs degradation enzymes (e.g. DNase I).

At this time, additional preclinical studies are required to determine specific cell surface markers that could distinguish LDNs from HDNs in whole blood.

Once available, circulating LDNs levels would be routinely measured and integrated in the complete blood count analysis to better assess patients’ inflammatory status.
link-ancestors: Fast simulation of local ancestry with tree sequence software
Authors: Tsambos Georgia , Kelleher Jerome , Ralph Peter , Leslie Stephen , Vukcevic Damjan
Published: November 2023

It is challenging to simulate realistic tracts of genetic ancestry on a scale suitable for simulation based inference. We present an algorithm that enables this information to be extracted efficiently from tree sequences produced by simulations run with msprime and SLiM.

Availability and Implementation

A C-based implementation of the link-ancestors algorithm is in tskit (https://tskit.dev/tskit/docs/stable/). We also provide a user-friendly wrapper for link-ancestors in tspop, a Python-based utility package.

Contact

gtsambos@uw.edu.

Supplementary information

Technical details of link-ancestors are in the Supplementary Information. Documentation for the tspop package is athttp://tspop.readthedocs.io/.
Interleukin-10-producing monocytes contribute to sex differences in pain resolution in mice and humans
Authors: Sim Jaewon , O’Guin Elizabeth , Monahan Karli , Sugimoto Chiho , McLean Samuel A. , Albertorio-Sáez Liz , Zhao Ying , Laumet Sophie , Dagenais Andrew , Bernard Matthew P. , Folger Joseph K. , Robison Alfred J. , Linnstaedt Sarah D. , Laumet Geoffroy
Published: November 2023

Pain is closely associated with the immune system, which exhibits sexual dimorphism. For these reasons, neuro-immune interactions are suggested to drive sex differences in pain pathophysiology. However, our understanding of peripheral neuro-immune interactions on sex differences in pain resolution remains limited. Here, we have shown, in both a mouse model of inflammatory pain and in humans following traumatic pain, that males had higher levels of interleukin (IL)-10 than females, which were correlated with faster pain resolution. Following injury, we identified monocytes (CD11b+ Ly6C+ Ly6G-F4/80mid) as the primary source of IL-10, with IL-10-producing monocytes being more abundant in males than females. In a mouse model, neutralizing IL-10 signaling through antibodies, genetically ablating IL-10R1 in sensory neurons, or depleting monocytes with clodronate all impaired the resolution of pain hypersensitivity in both sexes. Furthermore, manipulating androgen levels in mice reversed the sexual dimorphism of pain resolution and the levels of IL-10-producing monocytes. These results highlight a novel role for androgen-driven peripheral IL-10-producing monocytes in the sexual dimorphism of pain resolution. These findings add to the growing concept that immune cells play a critical role in resolving pain and preventing the transition into chronic pain.

Graphical abstract
ATF6 activation alters colonic lipid metabolism causing tumor-associated microbial adaptation
Authors: Coleman Olivia I. , Sorbie Adam , Bierwith Sandra , Kövilein Janine , von Stern Miriam , Köhler Nikolai , Wirbel Jakob , Schmidt Christina , Kacprowski Tim , Dunkel Andreas , Pauling Josh K. , Plagge Johannes , Mediel-Cuadra Diego , Wagner Sophia , Peng Tingying , Metzler Thomas , Schafmayer Clemens , Hinz Sebastian , Röder Christian , Röcken Christoph , Stecher Bärbel , Rosenstiel Philip , Steiger Katja , Jesinghaus Moritz , Liebisch Gerhard , Ecker Josef , Zeller Georg , Janssen Klaus-Peter , Haller Dirk
Published: November 2023

The induction of endoplasmic reticulum unfolded protein responses (UPRER) contributes to cancer development and progression. We recently linked microbiota-related triggers to the tumor-promoting role of signal transducer activating transcription factor 6 (ATF6) in the colon. Here we substantiate the clinical relevance of ATF6 and related bacterial genera in colorectal cancer patient cohorts. Spatial and longitudinal bacterial profiling in ATF6 transgenic mice (nATF6IEC) identified tumor-initiating and tumor-progressing shifts in the mucosa-associated microbiota. Transcriptional analysis in intestinal epithelial cells (IEC) of germ-free and specific pathogen-free nATF6IECmice defined bacteria-specific changes in cellular metabolism enriched for fatty acid biosynthesis. Untargeted metabolomics, isotope-labeling in intestinal organoids and FASN inhibition confirmed ATF6-mediated involvement of long-chain fatty acids in tumorigenesis. Multi-omics data integration identified a bacteria-lipid network characterized by fatty acid efflux, catabolism and detoxification. We postulate chronic ATF6 signaling to drive a clinically relevant pathologic response altering lipid metabolism to select for a tumor-promoting microbiota.

Graphical Abstract

Chronic ATF6 signaling in the colonic epithelium alters lipid metabolism to select a tumor-promoting microbiota

nATF6 expression is induced in intestinal epithelial cells in transgenic mice (nATF6IEC)

Biallelic nATF6IECgerm-free mice (grey circle) and floxed or monoallelic specific pathogen-free mice (black circle) remain in a state of homeostasis (yellow circle), while biallelic specific pathogen-free mice (black circle) develop spontaneous colon tumorigenesis (red circle)

Mechanistically, biallelic nATF6IECmice in the presence of an intestinal microbiota alter colonic lipid metabolism, including the upregulation of Fasn

The microbial lipid-response to the altered lipid milieu results in dysbiosis and the subsequent formation of colon adenomas

Inhibition of FASN in biallelic nATF6IECmice prevents colon tumor formation (yellow arrow)

Created withBioRender.com

nATF6: activated activating transcription factor 6; LCFA: long-chain fatty acids; SAFA: saturated fatty acids; Fasn: fatty acid synthase; C75 i.p.: intraperitoneal injection of the Fasn inhibitor C75.
Pangenomic exploration ofTheobroma cacao: New Insights into Gene Content Diversity and Selection During Domestication
Authors: Argout Xavier , Droc Gaetan , Fouet Olivier , Rouard Mathieu , Labadie Karine , Rhoné Bénédicte , Rey Loor Gaston , Lanaud Claire
Published: November 2023

The Cacao tree (Theobroma cacao L.)is a major cash crop and an important source of income for millions of farmers across Africa, Asia and Latin America. However, cacao farmers and producing countries are facing multiple challenges including pest and disease management, sustainable production under threat of climate changes and diversification of cocoa flavor profiles. Addressing these challenging requires a deeper understanding of the existing genetic diversity of the species. Yet, very little is known about the intraspecific gene content variation.

In this study, we used the genome of 216 accessions ofT. cacao(including 185 newly re-sequenced) covering a broad genetic diversity of the species to construct the first pan-genome of the cacao tree. As a result, we predicted a total of 30,489 pan-genes, enriching the reference Criollo genome with 1,407 new genes.

Our analysis revealed that only a small fraction of these genes (9.2%) is dispensable, being absent in some individuals. However, these genes could represent a valuable resource for breeding efforts aimed at improving disease resistance in the species.

We used this new pangenome resource to gain insights into how diversification and domestication processes have influenced genomic variability within the species. Notably, we observed a significant loss of genes within the domesticated Criollo genetic group. Furthermore, we found evidences suggesting that domestication processes have had an impact on the vigor and disease tolerance of Criollo accessions. In summary, our research has contributed to a better understanding of the cacao tree’s genome diversity. These findings offer new avenues for biological discovery and breeding, ultimately addressing the challenges faced by cacao farmers and producing countries.
Time-dependent Interaction Modification Generated from Plant-soil Feedback
Authors: Zou Heng-Xing , Yan Xinyi , Rudolf Volker H.W.
Published: November 2023

Pairwise interactions between species can be modified by other community members, leading to emergent dynamics contingent on community composition. Despite the prevalence of such higher-order interactions, little is known about how they are linked to the timing and order of species’ arrival. We generate population dynamics from a mechanistic plant-soil feedback model, then apply a general theoretical framework to show that the modification of a pairwise interaction by a third plant depends on its germination phenology. These time-dependent interaction modifications emerge from concurrent changes in plant and microbe populations and are strengthened by higher overlap between plants’ associated microbiomes. The interaction between this overlap and the specificity of microbiomes further determines plant coexistence. Our framework is widely applicable to mechanisms in other systems from which similar time-dependent interaction modifications can emerge, highlighting the need to integrate temporal shifts of species interactions to predict the emergent dynamics of natural communities.
Design rules for efficient endosomal escape
Authors: Zoltek Madeline , Vázquez Angel , Zhang Xizi , Dadina Neville , Lesiak Lauren , Schepartz Alanna
Published: November 2023

The inefficient translocation of proteins across biological membranes limits their application as therapeutic compounds and research tools. In most cases, translocation involves two steps: uptake into the endocytic pathway and endosomal escape. Certain charged or amphiphilic molecules promote protein uptake but few enable efficient endosomal escape. One exception is ZF5.3, a mini-protein that exploits natural endosomal maturation machinery to translocate across endosomal membranes. Although certain ZF5.3-protein conjugates are delivered efficiently into the cytosol or nucleus, overall delivery efficiency varies widely with no obvious design rules. Here we evaluate the role of protein size and thermal stability in the ability to efficiently escape endosomes when attached to ZF5.3. Using fluorescence correlation spectroscopy, a singlemolecule technique that provides a precise measure of intra-cytosolic protein concentration, we demonstrate that delivery efficiency depends on both size and the ease with which a protein unfolds. Regardless of size and pI, low-Tm cargos of ZF5.3 (including intrinsically disordered domains) bias its endosomal escape route toward a high-efficiency pathway that requires the homotypic fusion and protein sorting (HOPS) complex. Small protein domains are delivered with moderate efficiency through the same HOPS portal even if the Tm is high. These findings imply a novel protein- and/or lipid-dependent pathway out of endosomes that is exploited by ZF5.3 and provide clear guidance for the selection or design of optimally deliverable therapeutic cargo.

Significance Statement

The results described in this paper provide new insights into how protein delivery works and how it can be best utilized in the future. Although intracellular protein delivery has been studied for decades, this paper describes the first interrogation of why certain protein cargos are privileged for efficient endosomal escape. These results represent a fundamental advance in the long-awaited goal of efficient protein delivery and provide design rules to overcome one of the most significant challenges for the future of biotechnology.