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Habjan E, Lepioshkin A, Charitou V, Egorova A, Kazakova E, Ho VQT, Bitter W, Makarov V, Speer A. Modulating mycobacterial envelope integrity for antibiotic synergy with benzothiazoles. Life Sci Alliance 2024; 7:e202302509. [PMID: 38744470 PMCID: PMC11094368 DOI: 10.26508/lsa.202302509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Developing effective tuberculosis drugs is hindered by mycobacteria's intrinsic antibiotic resistance because of their impermeable cell envelope. Using benzothiazole compounds, we aimed to increase mycobacterial cell envelope permeability and weaken the defenses of Mycobacterium marinum, serving as a model for Mycobacterium tuberculosis Initial hit, BT-08, significantly boosted ethidium bromide uptake, indicating enhanced membrane permeability. It also demonstrated efficacy in the M. marinum-zebrafish embryo infection model and M. tuberculosis-infected macrophages. Notably, BT-08 synergized with established antibiotics, including vancomycin and rifampicin. Subsequent medicinal chemistry optimization led to BT-37, a non-toxic and more potent derivative, also enhancing ethidium bromide uptake and maintaining synergy with rifampicin in infected zebrafish embryos. Mutants of M. marinum resistant to BT-37 revealed that MMAR_0407 (Rv0164) is the molecular target and that this target plays a role in the observed synergy and permeability. This study introduces novel compounds targeting a new mycobacterial vulnerability and highlights their cooperative and synergistic interactions with existing antibiotics.
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Ten Oever S, Titone L, Te Rietmolen N, Martin AE. Phase-dependent word perception emerges from region-specific sensitivity to the statistics of language. Proc Natl Acad Sci U S A 2024; 121:e2320489121. [PMID: 38805278 DOI: 10.1073/pnas.2320489121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024] Open
Abstract
Neural oscillations reflect fluctuations in excitability, which biases the percept of ambiguous sensory input. Why this bias occurs is still not fully understood. We hypothesized that neural populations representing likely events are more sensitive, and thereby become active on earlier oscillatory phases, when the ensemble itself is less excitable. Perception of ambiguous input presented during less-excitable phases should therefore be biased toward frequent or predictable stimuli that have lower activation thresholds. Here, we show such a frequency bias in spoken word recognition using psychophysics, magnetoencephalography (MEG), and computational modelling. With MEG, we found a double dissociation, where the phase of oscillations in the superior temporal gyrus and medial temporal gyrus biased word-identification behavior based on phoneme and lexical frequencies, respectively. This finding was reproduced in a computational model. These results demonstrate that oscillations provide a temporal ordering of neural activity based on the sensitivity of separable neural populations.
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Koloko Ngassie ML, Drake LY, Roos BB, Koenig-Kappes A, Pabelick CM, Gosens R, Brandsma CA, Burgess JK, Prakash YS. Endoplasmic Reticulum Stress Induced Senescence in Human Lung Fibroblasts. Am J Physiol Lung Cell Mol Physiol 2024. [PMID: 38771153 DOI: 10.1152/ajplung.00264.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 05/09/2024] [Indexed: 05/22/2024] Open
Abstract
Loss of proteostasis and cellular senescence have been previously established as characteristics of aging, however their interaction in the context of lung aging and potential contributions to aging-associated lung remodeling remains understudied. In this study we aimed to characterize endoplasmic reticulum (ER) stress response, cellular senescence, and their interaction in relation to extracellular matrix (ECM) production in lung fibroblasts from young (25-45 years) and old (>60 years) humans. Fibroblasts from young and old patients without significant preexisting lung disease were exposed to vehicle, MG132, etoposide or salubrinal. Afterwards, cells and cell lysates or supernatants were analyzed for ER stress, cellular senescence and ECM changes using protein analysis, proliferation assay and senescence-associated beta galactosidase (SA-β-Gal) staining. At baseline, fibroblasts from aging individuals showed increased levels of ER stress (ATF6 and PERK), senescence (p21 and McL-1) and ECM marker (COL1A1) compared to those from young individuals. Upon ER stress induction and etoposide exposure, fibroblasts showed an increase in senescence (SA-β-Gal, p21, Cav-1), ER stress (PERK) and ECM markers (COL1A1 and LUM) compared to vehicle. Additionally, CXCL8 and IL-6 levels were increase in the supernatants of MG132 and etoposide-treated fibroblasts, respectively. Finally, the ER stress inhibitor salubrinal decreased the expression of p21 compared to vehicle and MG132 treatments, however salubrinal inhibited COL1A1 but not p21 expression in MG132-treated fibroblasts. Our study suggests that ER stress response plays an important role in establishment and maintenance of a senescence phenotype in lung fibroblasts and therefore contributes to altered remodeling in the aging lung.
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van Zwieten R, Bierman TV, Klinkhamer PGL, Bezemer TM, Vrieling K, Kodger TE. Mimicking natural deterrent strategies in plants using adhesive spheres. Proc Natl Acad Sci U S A 2024; 121:e2321565121. [PMID: 38739796 PMCID: PMC11127000 DOI: 10.1073/pnas.2321565121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
With a continuous increase in world population and food production, chemical pesticide use is growing accordingly, yet unsustainably. As chemical pesticides are harmful to the environment and developmental resistance in pests is increasing, a sustainable and effective pesticide alternative is needed. Inspired by nature, we mimic one defense strategy of plants, glandular trichomes, to shift away from using chemical pesticides by moving toward a physical immobilization strategy via adhesive particles. Through controlled oxidation of a biobased starting material, triglyceride oils, an adhesive material is created while monitoring the reactive intermediates. After being milled into particles, nanoindentation shows these particles to be adhesive even at low contact forces. A suspension of particles is then sprayed and found to be effective at immobilizing a target pest, thrips, Frankliniella occidentalis. Small arthropod pests, like thrips, can cause crop damage through virus transfer, which is prevented by their immobilization. We show that through a scalable fabrication process, biosourced materials can be used to create an effective, sustainable physical pesticide.
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Patterson JJ, Feola G, Kim RE. Negotiating discord in sustainability transformations. Proc Natl Acad Sci U S A 2024; 121:e2310186121. [PMID: 38662571 PMCID: PMC11127004 DOI: 10.1073/pnas.2310186121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2024] Open
Abstract
Policy action for sustainability transformation faces inherent and ever-present sources of conflict, pushback, and resistance (i.e., discord). However, conceptual frameworks and policy prescriptions for sustainability transformations often reflect an undue image of accord. This involves simplified assumptions about consensus, steering, friction, discreteness, and additiveness of policy action, conferring an unrealistic view of the potential to deliberately realize transformation. Instead, negotiating discord through continuously finding partial political settlements among divided actors needs to become a key focus of policy action for sustainability transformations. Doing so can help to navigate deeply political settings through imperfect but workable steps that loosen deadlock, generate momentum for further policy action, and avoid complete derailment of transformation agendas when discord arises.
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Zhang Y, Zhu X, Wood JA, Lohse D. Threshold current density for diffusion-controlled stability of electrolytic surface nanobubbles. Proc Natl Acad Sci U S A 2024; 121:e2321958121. [PMID: 38748584 PMCID: PMC11126992 DOI: 10.1073/pnas.2321958121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/29/2024] [Indexed: 05/27/2024] Open
Abstract
Understanding the stability mechanism of surface micro/nanobubbles adhered to gas-evolving electrodes is essential for improving the efficiency of water electrolysis, which is known to be hindered by the bubble coverage on electrodes. Using molecular simulations, the diffusion-controlled evolution of single electrolytic nanobubbles on wettability-patterned nanoelectrodes is investigated. These nanoelectrodes feature hydrophobic islands as preferential nucleation sites and allow the growth of nanobubbles in the pinning mode. In these simulations, a threshold current density distinguishing stable nanobubbles from unstable nanobubbles is found. When the current density remains below the threshold value, nucleated nanobubbles grow to their equilibrium states, maintaining their nanoscopic size. However, for the current density above the threshold value, nanobubbles undergo unlimited growth and can eventually detach due to buoyancy. Increasing the pinning length of nanobubbles increases the degree of nanobubble instability. By connecting the current density with the local gas oversaturation, an extension of the stability theory for surface nanobubbles [Lohse and Zhang, Phys. Rev. E 91, 031003(R) (2015)] accurately predicts the nanobubble behavior found in molecular simulations, including equilibrium contact angles and the threshold current density. For larger systems that are not accessible to molecular simulations, continuum numerical simulations with the finite difference method combined with the immersed boundary method are performed, again demonstrating good agreement between numerics and theories.
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Stäter S, Woering EF, Lombeck F, Sommer M, Hildner R. Hexylation Stabilises Twisted Backbone Configurations in the Prototypical Low-Bandgap Copolymer PCDTBT. Chemphyschem 2024; 25:e202300971. [PMID: 38372667 DOI: 10.1002/cphc.202300971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/20/2024]
Abstract
Conjugated donor-acceptor copolymers hold great potential as materials for high-performance organic photovoltaics, organic transistors and organic thermoelectric devices. Their low optical bandgap is achieved by alternation of donor and acceptor moieties along the polymer chain, leading to a pronounced charge-transfer character of electronic excitations. However, the influence of appended side chains and of chemical defects of the backbone on their photophysical and conformational properties remains largely unexplored on the level of individual chains. Here, we employ room temperature single-molecule photoluminescence spectroscopy on four compounds based on the prototypical copolymer PCDTBT with systematically changed chemical structure. Our results show that an increasing density of statistically added hexyl chains to the TBT comonomer distorts the molecular conformation, likely through the increase of average dihedral angles along the backbone. We find that, although the conformation becomes more twisted with high hexyl density, the side chains appear to stabilize the backbone in this twisted conformation. In addition, we demonstrate that homocoupling defects along the backbone barely influence the PL spectra of single chains, and thus intra-chain electronic properties.
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Heim F, Scharff C, Fisher SE, Riebel K, Ten Cate C. Auditory discrimination learning and acoustic cue weighing in female zebra finches with localized FoxP1 knockdowns. J Neurophysiol 2024; 131:950-963. [PMID: 38629163 DOI: 10.1152/jn.00228.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 05/21/2024] Open
Abstract
Rare disruptions of the transcription factor FOXP1 are implicated in a human neurodevelopmental disorder characterized by autism and/or intellectual disability with prominent problems in speech and language abilities. Avian orthologues of this transcription factor are evolutionarily conserved and highly expressed in specific regions of songbird brains, including areas associated with vocal production learning and auditory perception. Here, we investigated possible contributions of FoxP1 to song discrimination and auditory perception in juvenile and adult female zebra finches. They received lentiviral knockdowns of FoxP1 in one of two brain areas involved in auditory stimulus processing, HVC (proper name) or CMM (caudomedial mesopallium). Ninety-six females, distributed over different experimental and control groups were trained to discriminate between two stimulus songs in an operant Go/Nogo paradigm and subsequently tested with an array of stimuli. This made it possible to assess how well they recognized and categorized altered versions of training stimuli and whether localized FoxP1 knockdowns affected the role of different features during discrimination and categorization of song. Although FoxP1 expression was significantly reduced by the knockdowns, neither discrimination of the stimulus songs nor categorization of songs modified in pitch, sequential order of syllables or by reversed playback were affected. Subsequently, we analyzed the full dataset to assess the impact of the different stimulus manipulations for cue weighing in song discrimination. Our findings show that zebra finches rely on multiple parameters for song discrimination, but with relatively more prominent roles for spectral parameters and syllable sequencing as cues for song discrimination.NEW & NOTEWORTHY In humans, mutations of the transcription factor FoxP1 are implicated in speech and language problems. In songbirds, FoxP1 has been linked to male song learning and female preference strength. We found that FoxP1 knockdowns in female HVC and caudomedial mesopallium (CMM) did not alter song discrimination or categorization based on spectral and temporal information. However, this large dataset allowed to validate different cue weights for spectral over temporal information for song recognition.
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Berkvens A, Salinas L, Remeijer M, Planqué R, Teusink B, Bruggeman FJ. Understanding and computational design of genetic circuits of metabolic networks. Essays Biochem 2024; 68:41-51. [PMID: 38662439 PMCID: PMC11065555 DOI: 10.1042/ebc20230045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024]
Abstract
The expression of metabolic proteins is controlled by genetic circuits, matching metabolic demands and changing environmental conditions. Ideally, this regulation brings about a competitive level of metabolic fitness. Understanding how cells can achieve a robust (close-to-optimal) functioning of metabolism by appropriate control of gene expression aids synthetic biology by providing design criteria of synthetic circuits for biotechnological purposes. It also extends our understanding of the designs of genetic circuitry found in nature such as metabolite control of transcription factor activity, promoter architectures and transcription factor dependencies, and operon composition (in bacteria). Here, we review, explain and illustrate an approach that allows for the inference and design of genetic circuitry that steers metabolic networks to achieve a maximal flux per unit invested protein across dynamic conditions. We discuss how this approach and its understanding can be used to rationalize Escherichia coli's strategy to regulate the expression of its ribosomes and infer the design of circuitry controlling gene expression of amino-acid biosynthesis enzymes. The inferred regulation indeed resembles E. coli's circuits, suggesting that these have evolved to maximize amino-acid production fluxes per unit invested protein. We end by an outlook of the use of this approach in metabolic engineering applications.
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Resendes T, Ellenbogen MA, Oldehinkel AJ. Family dysfunction, stressful life events, and mental health problems across development in the offspring of parents with an affective disorder. J Child Psychol Psychiatry 2024. [PMID: 38682166 DOI: 10.1111/jcpp.13991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND Offspring of parents with affective disorders (OAD) are at risk of developing a wide range of mental disorders. Deficits in the rearing environment and high levels of stress are well-known risk factors for negative outcomes in OAD. Building on prior research, we aim to examine the longitudinal relationships between family dysfunction, stressful life events, and mental health in OAD and control offspring of parents with no affective disorder. In the present study, we hypothesized that high levels of family dysfunction would be associated with more internalizing and externalizing problems across time in OAD than in controls, and that family dysfunction would mediate the relationship between stressful life events in adolescence and poor mental health in adulthood, particularly in OAD. METHODS As part of the TRacking Adolescents' Lives Survey (TRAILS), 2230 participants (51% female, Mage = 11.1 years, SD = 0.6, at baseline) and their parents completed measures across six time points, spanning 15 years. Mental health, family dysfunction, and stressful life events were assessed with the Youth and Adult Self-Report, Family Assessment Device, and an in-house measure, respectively. RESULTS Multi-group structured equation modeling revealed that family dysfunction was linked to internalizing and externalizing problems in OAD, but not controls, across time. Risk status did not moderate family dysfunction's mediation of the relationship between stressful life events and negative outcomes in adulthood. CONCLUSIONS OAD show high sensitivity to dysfunction in the rearing environment across childhood and adolescence, which supports the use of family based interventions to prevent the development of mental disorders in high-risk youth.
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Zhong X, Nicolardi S, Ouyang R, Wuhrer M, Du C, van Wezel G, Vijgenboom E, Briegel A, Claessen D. CslA and GlxA from Streptomyces lividans form a functional cellulose synthase complex. Appl Environ Microbiol 2024; 90:e0208723. [PMID: 38557137 PMCID: PMC11022532 DOI: 10.1128/aem.02087-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Filamentous growth of streptomycetes coincides with the synthesis and deposition of an uncharacterized protective glucan at hyphal tips. Synthesis of this glucan depends on the integral membrane protein CslA and the radical copper oxidase GlxA, which are part of a presumably large multiprotein complex operating at growing tips. Here, we show that CslA and GlxA interact by forming a protein complex that is sufficient to synthesize cellulose in vitro. Mass spectrometry analysis revealed that the purified complex produces cellulose chains with a degree of polymerization of at least 80 residues. Truncation analyses demonstrated that the removal of a significant extracellular segment of GlxA had no impact on complex formation, but significantly diminished activity of CslA. Altogether, our work demonstrates that CslA and GlxA form the active core of the cellulose synthase complex and provide molecular insights into a unique cellulose biosynthesis system that is conserved in streptomycetes. IMPORTANCE Cellulose stands out as the most abundant polysaccharide on Earth. While the synthesis of this polysaccharide has been extensively studied in plants and Gram-negative bacteria, the mechanisms in Gram-positive bacteria have remained largely unknown. Our research unveils a novel cellulose synthase complex formed by the interaction between the cellulose synthase-like protein CslA and the radical copper oxidase GlxA from Streptomyces lividans, a soil-dwelling Gram-positive bacterium. This discovery provides molecular insights into the distinctive cellulose biosynthesis machinery. Beyond expanding our understanding of cellulose biosynthesis, this study also opens avenues for exploring biotechnological applications and ecological roles of cellulose in Gram-positive bacteria, thereby contributing to the broader field of microbial cellulose biosynthesis and biofilm research.
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Brummelman E, Bos PA, de Boer E, Nevicka B, Sedikides C. Reciprocal self-disclosure makes children feel more loved by their parents in the moment: A proof-of-concept experiment. Dev Sci 2024:e13516. [PMID: 38623917 DOI: 10.1111/desc.13516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/20/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
Feeling loved by one's parents is critical for children's health and well-being. How can such feelings be fostered? A vital feature of loving interactions is reciprocal self-disclosure, where individuals disclose intimate information about themselves. In a proof-of-concept experiment, we examined whether encouraging reciprocal self-disclosure in parent-child dyads would make children feel more loved during the conversation. Participants were 218 children (ages 8-13, 50% girls, 94% Dutch) and one of their parents (ages 28-56, 62% women, 90% Dutch). Parent-child dyads received a list of 14 questions and took turns asking them each other for 9 min. Dyads were assigned randomly to engage in self-disclosure (questions invoking escalated intimacy) or small talk (questions invoking minimal intimacy). Before and after, children reported how loved they felt by their parent during the conversation. Self-disclosure made children feel more loved during the conversation than did small talk. Compared to small talk, self-disclosure did not instigate conversations that were lengthier or more positive; rather, it instigated conversations that were more emotionally charged (reflecting anger, anxiety, and sadness), social (discussing family and friends), reflective (creating insight), and meaningful (addressing deeply personal topics, including the passing of loved ones). The dyad's gender composition did not significantly moderate these effects. Our research suggests that reciprocal self-disclosure can make children feel more loved in the moment, uncovers linguistic signatures of reciprocal self-disclosure, and offers developmental scientists a tool to examine causal effects of reciprocal self-disclosure in parent-child dyads. Future work should examine long-term effects in everyday parent-child interactions. RESEARCH HIGHLIGHTS: How can parents make children feel more loved by them in the moment? We theorize that these feelings can be cultivated through reciprocal self-disclosure. In a proof-of-concept experiment, we examined effects of reciprocal self-disclosure versus small talk in 218 parent-child dyads, with children aged 8-13. Self-disclosure (vs. small talk) made children feel more loved during the conversation. Linguistically, self-disclosure instigated conversations that were more emotionally charged, social, reflective, and meaningful. This research provides an experimental method to study self-disclosure in parent-child dyads and suggests that self-disclosure can make children feel more loved in the moment.
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Haver D, Acuña D, Janbaz S, Lerner E, Düring G, Coulais C. Elasticity and rheology of auxetic granular metamaterials. Proc Natl Acad Sci U S A 2024; 121:e2317915121. [PMID: 38536751 PMCID: PMC10998574 DOI: 10.1073/pnas.2317915121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/04/2024] [Indexed: 04/08/2024] Open
Abstract
The flowing, jamming, and avalanche behavior of granular materials is satisfyingly universal and vexingly hard to tune: A granular flow is typically intermittent and will irremediably jam if too confined. Here, we show that granular metamaterials made from particles with a negative Poisson's ratio yield more easily and flow more smoothly than ordinary granular materials. We first create a collection of auxetic grains based on a re-entrant mechanism and show that each grain exhibits a negative Poisson's ratio regardless of the direction of compression. Interestingly, we find that the elastic and yielding properties are governed by the high compressibility of granular metamaterials: At a given confinement, they exhibit lower shear modulus, lower yield stress, and more frequent, smaller avalanches than materials made from ordinary grains. We further demonstrate that granular metamaterials promote flow in more complex confined geometries, such as intruder and hopper geometries, even when the packing contains only a fraction of auxetic grains. Moreover, auxetic granular metamaterials exhibit enhanced impact absorption. Our findings blur the boundary between complex fluids and metamaterials and could help in scenarios that involve process, transport, and reconfiguration of granular materials.
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Glatz JFC, Heather LC, Luiken JJFP. CD36 as a gatekeeper of myocardial lipid metabolism and therapeutic target for metabolic disease. Physiol Rev 2024; 104:727-764. [PMID: 37882731 DOI: 10.1152/physrev.00011.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/02/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023] Open
Abstract
The multifunctional membrane glycoprotein CD36 is expressed in different types of cells and plays a key regulatory role in cellular lipid metabolism, especially in cardiac muscle. CD36 facilitates the cellular uptake of long-chain fatty acids, mediates lipid signaling, and regulates storage and oxidation of lipids in various tissues with active lipid metabolism. CD36 deficiency leads to marked impairments in peripheral lipid metabolism, which consequently impact on the cellular utilization of multiple different fuels because of the integrated nature of metabolism. The functional presence of CD36 at the plasma membrane is regulated by its reversible subcellular recycling from and to endosomes and is under the control of mechanical, hormonal, and nutritional factors. Aberrations in this dynamic role of CD36 are causally associated with various metabolic diseases, in particular insulin resistance, diabetic cardiomyopathy, and cardiac hypertrophy. Recent research in cardiac muscle has disclosed the endosomal proton pump vacuolar-type H+-ATPase (v-ATPase) as a key enzyme regulating subcellular CD36 recycling and being the site of interaction between various substrates to determine cellular substrate preference. In addition, evidence is accumulating that interventions targeting CD36 directly or modulating its subcellular recycling are effective for the treatment of metabolic diseases. In conclusion, subcellular CD36 localization is the major adaptive regulator of cellular uptake and metabolism of long-chain fatty acids and appears a suitable target for metabolic modulation therapy to mend failing hearts.
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Keijzer N, Priyanka A, Stijf-Bultsma Y, Fish A, Gersch M, Sixma TK. Variety in the USP deubiquitinase catalytic mechanism. Life Sci Alliance 2024; 7:e202302533. [PMID: 38355287 PMCID: PMC10867860 DOI: 10.26508/lsa.202302533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
The ubiquitin-specific protease (USP) family of deubiquitinases (DUBs) controls cellular ubiquitin-dependent signaling events. This generates therapeutic potential, with active-site inhibitors in preclinical and clinical studies. Understanding of the USP active site is primarily guided by USP7 data, where the catalytic triad consists of cysteine, histidine, and a third residue (third critical residue), which polarizes the histidine through a hydrogen bond. A conserved aspartate (fourth critical residue) is directly adjacent to this third critical residue. Although both critical residues accommodate catalysis in USP2, these residues have not been comprehensively investigated in other USPs. Here, we quantitatively investigate their roles in five USPs. Although USP7 relies on the third critical residue for catalysis, this residue is dispensable in USP1, USP15, USP40, and USP48, where the fourth critical residue is vital instead. Furthermore, these residues vary in importance for nucleophilic attack. The diverging catalytic mechanisms of USP1 and USP7 are independent of substrate and retained in cells for USP1. This unexpected variety of catalytic mechanisms in this well-conserved protein family may generate opportunities for selective targeting of individual USPs.
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Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, van der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proc Natl Acad Sci U S A 2024; 121:e2313162121. [PMID: 38451946 PMCID: PMC10945838 DOI: 10.1073/pnas.2313162121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/30/2023] [Indexed: 03/09/2024] Open
Abstract
Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H[Formula: see text]O/D[Formula: see text]O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H[Formula: see text]O and D[Formula: see text]O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D[Formula: see text]O than in H[Formula: see text]O, and collagen in D[Formula: see text]O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H[Formula: see text]O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D[Formula: see text]O is less hydrated than in H[Formula: see text]O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen-water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.
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Beijen EPW, Ohm RA. Genome annotations for the ascomycete fungi Trichoderma harzianum, Trichoderma aggressivum, and Purpureocillium lilacinum. Microbiol Resour Announc 2024; 13:e0115323. [PMID: 38385672 DOI: 10.1128/mra.01153-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
We sequenced and annotated the genomes of the ascomycete fungi Trichoderma harzianum, Trichoderma aggressivum f. europaeum, and Purpureocillium lilacinum. Moreover, we developed a website to allow users to interactively analyze the assemblies, gene predictions, and functional annotations of these species and 70+ previously sequenced fungi.
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Haast RAM, Kashyap S, Ivanov D, Yousif MD, DeKraker J, Poser BA, Khan AR. Insights into hippocampal perfusion using high-resolution, multi-modal 7T MRI. Proc Natl Acad Sci U S A 2024; 121:e2310044121. [PMID: 38446857 PMCID: PMC10945835 DOI: 10.1073/pnas.2310044121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/26/2023] [Indexed: 03/08/2024] Open
Abstract
We present a comprehensive study on the non-invasive measurement of hippocampal perfusion. Using high-resolution 7 tesla arterial spin labeling (ASL) data, we generated robust perfusion maps and observed significant variations in perfusion among hippocampal subfields, with CA1 exhibiting the lowest perfusion levels. Notably, these perfusion differences were robust and already detectable with 50 perfusion-weighted images per subject, acquired in 5 min. To understand the underlying factors, we examined the influence of image quality metrics, various tissue microstructure and morphometric properties, macrovasculature, and cytoarchitecture. We observed higher perfusion in regions located closer to arteries, demonstrating the influence of vascular proximity on hippocampal perfusion. Moreover, ex vivo cytoarchitectonic features based on neuronal density differences appeared to correlate stronger with hippocampal perfusion than morphometric measures like gray matter thickness. These findings emphasize the interplay between microvasculature, macrovasculature, and metabolic demand in shaping hippocampal perfusion. Our study expands the current understanding of hippocampal physiology and its relevance to neurological disorders. By providing in vivo evidence of perfusion differences between hippocampal subfields, our findings have implications for diagnosis and potential therapeutic interventions. In conclusion, our study provides a valuable resource for extensively characterizing hippocampal perfusion.
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Giglio L, Ostarek M, Sharoh D, Hagoort P. Diverging neural dynamics for syntactic structure building in naturalistic speaking and listening. Proc Natl Acad Sci U S A 2024; 121:e2310766121. [PMID: 38442171 PMCID: PMC10945772 DOI: 10.1073/pnas.2310766121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
The neural correlates of sentence production are typically studied using task paradigms that differ considerably from the experience of speaking outside of an experimental setting. In this fMRI study, we aimed to gain a better understanding of syntactic processing in spontaneous production versus naturalistic comprehension in three regions of interest (BA44, BA45, and left posterior middle temporal gyrus). A group of participants (n = 16) was asked to speak about the events of an episode of a TV series in the scanner. Another group of participants (n = 36) listened to the spoken recall of a participant from the first group. To model syntactic processing, we extracted word-by-word metrics of phrase-structure building with a top-down and a bottom-up parser that make different hypotheses about the timing of structure building. While the top-down parser anticipates syntactic structure, sometimes before it is obvious to the listener, the bottom-up parser builds syntactic structure in an integratory way after all of the evidence has been presented. In comprehension, neural activity was found to be better modeled by the bottom-up parser, while in production, it was better modeled by the top-down parser. We additionally modeled structure building in production with two strategies that were developed here to make different predictions about the incrementality of structure building during speaking. We found evidence for highly incremental and anticipatory structure building in production, which was confirmed by a converging analysis of the pausing patterns in speech. Overall, this study shows the feasibility of studying the neural dynamics of spontaneous language production.
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Wang B, van der Kloet F, Kes MBMJ, Luirink J, Hamoen LW. Improving gene set enrichment analysis (GSEA) by using regulation directionality. Microbiol Spectr 2024; 12:e0345623. [PMID: 38294221 PMCID: PMC10913524 DOI: 10.1128/spectrum.03456-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
To infer the biological meaning from transcriptome data, it is useful to focus on genes that are regulated by the same regulator, i.e., regulons. Unfortunately, current gene set enrichment analysis (GSEA) tools do not consider whether a gene is activated or repressed by a regulator. This distinction is crucial when analyzing regulons since a regulator can work as an activator of certain genes and as a repressor of other genes, yet both sets of genes belong to the same regulon. Therefore, simply averaging expression differences of the genes of such a regulon will not properly reflect the activity of the regulator. What makes it more complicated is the fact that many genes are regulated by different transcription factors, and current transcriptome analysis tools are unable to indicate which regulator is most likely responsible for the observed expression difference of a gene. To address these challenges, we developed the gene set enrichment analysis program GINtool. Additional features of GINtool are novel graphical representations to facilitate the visualization of gene set analyses of transcriptome data, the possibility to include functional categories as gene sets for analysis, and the option to analyze expression differences within operons, which is useful when analyzing prokaryotic transcriptome and also proteome data.IMPORTANCEMeasuring the activity of all genes in cells is a common way to elucidate the function and regulation of genes. These transcriptome analyses produce large amounts of data since genomes contain thousands of genes. The analysis of these large data sets is challenging. Therefore, we developed a new software tool called GINtool that can facilitate the analysis of transcriptome data by using prior knowledge of gene sets controlled by the same regulator, the so-called regulons. An important novelty of GINtool is that it can take into account the directionality of gene regulation in these analyses, i.e., whether a gene is activated or repressed, which is crucial to assess whether a regulon or functional category is affected. GINtool also includes new graphical methods to facilitate the visual inspection of regulation events in transcriptome data sets. These and additional analysis methods included in GINtool make it a powerful software tool to analyze transcriptome data.
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Milano CR, Ur SN, Gu Y, Zhang J, Allison R, Brown G, Neale MJ, Tromer EC, Corbett KD, Hochwagen A. Chromatin binding by HORMAD proteins regulates meiotic recombination initiation. EMBO J 2024; 43:836-867. [PMID: 38332377 PMCID: PMC10907721 DOI: 10.1038/s44318-024-00034-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 02/10/2024] Open
Abstract
The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. In S. cerevisiae, the HORMAD protein Hop1 mediates the enrichment of axis proteins at nucleosome-rich islands through a central chromatin-binding region (CBR). Here, we use cryoelectron microscopy to show that the Hop1 CBR directly recognizes bent nucleosomal DNA through a composite interface in its PHD and winged helix-turn-helix domains. Targeted disruption of the Hop1 CBR-nucleosome interface causes a localized reduction of axis protein binding and meiotic DNA double-strand breaks (DSBs) in axis islands and leads to defects in chromosome synapsis. Synthetic effects with mutants of the Hop1 regulator Pch2 suggest that nucleosome binding delays a conformational switch in Hop1 from a DSB-promoting, Pch2-inaccessible state to a DSB-inactive, Pch2-accessible state to regulate the extent of meiotic DSB formation. Phylogenetic analyses of meiotic HORMADs reveal an ancient origin of the CBR, suggesting that the mechanisms we uncover are broadly conserved.
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Laksono BM, Sooksawasdi Na Ayudhya S, Aguilar-Bretones M, Embregts CWE, van Nierop GP, van Riel D. Human B cells and dendritic cells are susceptible and permissive to enterovirus D68 infection. mSphere 2024; 9:e0052623. [PMID: 38259063 PMCID: PMC10900886 DOI: 10.1128/msphere.00526-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Enterovirus D68 (EV-D68) is predominantly associated with mild respiratory infections, but can also cause severe respiratory disease and extra-respiratory complications, including acute flaccid myelitis. Systemic dissemination of EV-D68 is crucial for the development of extra-respiratory diseases, but it is currently unclear how EV-D68 spreads systemically (viremia). We hypothesize that immune cells contribute to the systemic dissemination of EV-D68, as this is a mechanism commonly used by other enteroviruses. Therefore, we investigated the susceptibility and permissiveness of human primary immune cells for different EV-D68 isolates. In human peripheral blood mononuclear cells inoculated with EV-D68, only B cells were susceptible but virus replication was limited. However, in B cell-rich cultures, such as Epstein-Barr virus-transformed B-lymphoblastoid cell line (BLCL) and primary lentivirus-transduced B cells, which better represent lymphoid B cells, were productively infected. Subsequently, we showed that dendritic cells (DCs), particularly immature DCs, are susceptible and permissive for EV-D68 infection and that they can spread EV-D68 to autologous BLCL. Altogether, our findings suggest that immune cells, especially B cells and DCs, could play an important role in the pathogenesis of EV-D68 infection. Infection of these cells may contribute to systemic dissemination of EV-D68, which is an essential step toward the development of extra-respiratory complications.IMPORTANCEEnterovirus D68 (EV-D68) is an emerging respiratory virus that has caused outbreaks worldwide since 2014. EV-D68 infects primarily respiratory epithelial cells resulting in mild respiratory diseases. However, EV-D68 infection is also associated with extra-respiratory complications, including polio-like paralysis. It is unclear how EV-D68 spreads systemically and infects other organs. We hypothesized that immune cells could play a role in the extra-respiratory spread of EV-D68. We showed that EV-D68 can infect and replicate in specific immune cells, that is, B cells and dendritic cells (DCs), and that virus could be transferred from DCs to B cells. Our data reveal a potential role of immune cells in the pathogenesis of EV-D68 infection. Intervention strategies that prevent EV-D68 infection of immune cells will therefore potentially prevent systemic spread of virus and thereby severe extra-respiratory complications.
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Wijdeven RH, Luk SJ, Schoufour TAW, van der Zanden SY, Cabezuelo M, Heemskerk MHM, Neefjes J. Balanced Epigenetic Regulation of MHC Class I Expression in Tumor Cells by the Histone Ubiquitin Modifiers BAP1 and PCGF1. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:446-454. [PMID: 38088808 DOI: 10.4049/jimmunol.2300263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 11/13/2023] [Indexed: 01/18/2024]
Abstract
MHC class I (MHC-I) molecules are critical for CD8+ T cell responses to viral infections and malignant cells, and tumors can downregulate MHC-I expression to promote immune evasion. In this study, using a genome-wide CRISPR screen on a human melanoma cell line, we identified the polycomb repressive complex 1 (PRC1) subunit PCGF1 and the deubiquitinating enzyme BAP1 as opposite regulators of MHC-I transcription. PCGF1 facilitates deposition of ubiquitin at H2AK119 at the MHC-I promoters to silence MHC-I, whereas BAP1 removes this modification to restore MHC-I expression. PCGF1 is widely expressed in tumors and its depletion increased MHC-I expression in multiple tumor lines, including MHC-Ilow tumors. In cells characterized by poor MHC-I expression, PRC1 and PRC2 act in parallel to impinge low transcription. However, PCGF1 depletion was sufficient to increase MHC-I expression and restore T cell-mediated killing of the tumor cells. Taken together, our data provide an additional layer of regulation of MHC-I expression in tumors: epigenetic silencing by PRC1 subunit PCGF1.
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Beerendonk L, Mejías JF, Nuiten SA, de Gee JW, Fahrenfort JJ, van Gaal S. A disinhibitory circuit mechanism explains a general principle of peak performance during mid-level arousal. Proc Natl Acad Sci U S A 2024; 121:e2312898121. [PMID: 38277436 PMCID: PMC10835062 DOI: 10.1073/pnas.2312898121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 12/04/2023] [Indexed: 01/28/2024] Open
Abstract
Perceptual decision-making is highly dependent on the momentary arousal state of the brain, which fluctuates over time on a scale of hours, minutes, and even seconds. The textbook relationship between momentary arousal and task performance is captured by an inverted U-shape, as put forward in the Yerkes-Dodson law. This law suggests optimal performance at moderate levels of arousal and impaired performance at low or high arousal levels. However, despite its popularity, the evidence for this relationship in humans is mixed at best. Here, we use pupil-indexed arousal and performance data from various perceptual decision-making tasks to provide converging evidence for the inverted U-shaped relationship between spontaneous arousal fluctuations and performance across different decision types (discrimination, detection) and sensory modalities (visual, auditory). To further understand this relationship, we built a neurobiologically plausible mechanistic model and show that it is possible to reproduce our findings by incorporating two types of interneurons that are both modulated by an arousal signal. The model architecture produces two dynamical regimes under the influence of arousal: one regime in which performance increases with arousal and another regime in which performance decreases with arousal, together forming an inverted U-shaped arousal-performance relationship. We conclude that the inverted U-shaped arousal-performance relationship is a general and robust property of sensory processing. It might be brought about by the influence of arousal on two types of interneurons that together act as a disinhibitory pathway for the neural populations that encode the available sensory evidence used for the decision.
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Groenen C, Nguyen TA, Paulusma C, van de Graaf S. Bile salt signaling and bile salt-based therapies in cardiometabolic disease. Clin Sci (Lond) 2024; 138:1-21. [PMID: 38180064 PMCID: PMC10767275 DOI: 10.1042/cs20230934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024]
Abstract
Bile salts have an established role in the emulsification and intestinal absorption of dietary lipids, and their homeostasis is tightly controlled by various transporters and regulators in the enterohepatic circulation. Notably, emerging evidence points toward bile salts as major modulators of cardiometabolic disease (CMD), an umbrella disease of disorders affecting the heart and blood vessels that is caused by systemic metabolic diseases such as Type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated steatotic liver disease (MASLD), the latter encompassing also metabolic dysfunction-associated steatohepatitis (MASH). The underlying mechanisms of protective effects of bile salts are their hormonal properties, enabling them to exert versatile metabolic effects by activating various bile salt-responsive signaling receptors with the nuclear farnesoid X receptor (FXR) and the Takeda G-protein-coupled receptor 5 (TGR5) as most extensively investigated. Activation of FXR and TGR5 is involved in the regulation of glucose, lipid and energy metabolism, and inflammation. Bile salt-based therapies directly targeting FXR and TGR5 signaling have been evaluated for their therapeutic potential in CMD. More recently, therapeutics targeting bile salt transporters thereby modulating bile salt localization, dynamics, and signaling, have been developed and evaluated in CMD. Here, we discuss the current knowledge on the contribution of bile salt signaling in the pathogenesis of CMD and the potential of bile salt-based therapies for the treatment of CMD.
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Zhang S, Boers LS, de Brabander J, van den Heuvel LB, Blok SG, Kullberg RFJ, Smids-Dierdorp BS, Dekker T, Aberson HL, Meijboom LJ, Vlaar APJ, Heunks L, Nossent EJ, van der Poll T, Bos LDJ, Duitman J. The alveolar fibroproliferative response in moderate to severe COVID-19-related acute respiratory distress syndrome and 1-yr follow-up. Am J Physiol Lung Cell Mol Physiol 2024; 326:L7-L18. [PMID: 37933449 DOI: 10.1152/ajplung.00156.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/27/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023] Open
Abstract
COVID-19-related acute respiratory distress syndrome (ARDS) can lead to long-term pulmonary fibrotic lesions. Alveolar fibroproliferative response (FPR) is a key factor in the development of pulmonary fibrosis. N-terminal peptide of procollagen III (NT-PCP-III) is a validated biomarker for activated FPR in ARDS. This study aimed to assess the association between dynamic changes in alveolar FPR and long-term outcomes, as well as mortality in COVID-19 ARDS patients. We conducted a prospective cohort study of 154 COVID-19 ARDS patients. We collected bronchoalveolar lavage (BAL) and blood samples for measurement of 17 pulmonary fibrosis biomarkers, including NT-PCP-III. We assessed pulmonary function and chest computed tomography (CT) at 3 and 12 mo after hospital discharge. We performed joint modeling to assess the association between longitudinal changes in biomarker levels and mortality at day 90 after starting mechanical ventilation. 154 patients with 284 BAL samples were analyzed. Of all patients, 40% survived to day 90, of whom 54 completed the follow-up procedure. A longitudinal increase in NT-PCP-III was associated with increased mortality (HR 2.89, 95% CI: 2.55-3.28; P < 0.001). Forced vital capacity and diffusion for carbon monoxide were impaired at 3 mo but improved significantly at one year after hospital discharge (P = 0.03 and P = 0.004, respectively). There was no strong evidence linking alveolar FPR during hospitalization and signs of pulmonary fibrosis in pulmonary function or chest CT images during 1-yr follow-up. In COVID-19 ARDS patients, alveolar FPR during hospitalization was associated with higher mortality but not with the presence of long-term fibrotic lung sequelae within survivors.NEW & NOTEWORTHY This is the first prospective study on the longitudinal alveolar fibroproliferative response in COVID-19 ARDS and its relationship with mortality and long-term follow-up. We used the largest cohort of COVID-19 ARDS patients who had consecutive bronchoalveolar lavages and measured 17 pulmonary fibroproliferative biomarkers. We found that a higher fibroproliferative response during admission was associated with increased mortality, but not correlated with long-term fibrotic lung sequelae in survivors.
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de Vries E, van Ede F. Microsaccades Track Location-Based Object Rehearsal in Visual Working Memory. eNeuro 2024; 11:ENEURO.0276-23.2023. [PMID: 38176905 PMCID: PMC10849020 DOI: 10.1523/eneuro.0276-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 01/06/2024] Open
Abstract
Besides controlling eye movements, the brain's oculomotor system has been implicated in the control of covert spatial attention and the rehearsal of spatial information in working memory. We investigated whether the oculomotor system also contributes to rehearsing visual objects in working memory when object location is never asked about. To address this, we tracked the incidental use of locations for mnemonic rehearsal via directional biases in microsaccades while participants maintained two visual objects (colored oriented gratings) in working memory. By varying the stimulus configuration (horizontal, diagonal, and vertical) at encoding, we could quantify whether microsaccades were more aligned with the configurational axis of the memory contents, as opposed to the orthogonal axis. Experiment 1 revealed that microsaccades continued to be biased along the axis of the memory content several seconds into the working memory delay. In Experiment 2, we confirmed that this directional microsaccade bias was specific to memory demands, ruling out lingering effects from passive and attentive encoding of the same visual objects in the same configurations. Thus, by studying microsaccade directions, we uncover oculomotor-driven rehearsal of visual objects in working memory through their associated locations.
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Jobbins M, Rücklin M, Sánchez Villagra MR, Lelièvre H, Grogan E, Szrek P, Klug C. Extreme lower jaw elongation in a placoderm reflects high disparity and modularity in early vertebrate evolution. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231747. [PMID: 38298398 PMCID: PMC10827443 DOI: 10.1098/rsos.231747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024]
Abstract
Jaws are a key vertebrate feature that arose early in our evolution. Placoderms are among the first jawed vertebrates; their fossils yield essential knowledge about the early diversification of gnathostome feeding strategies, diets and modularity. Modularity can be expressed through disproportional lengths of lower and upper jaws as in swordfish or halfbeaks. Alienacanthus malkowskii is an arthrodire from the Famennian of Morocco and Poland, whose most remarkable feature is its lower jaw, which is twice as long as the skull. This is the oldest record of such extreme jaw elongation and modularity in vertebrates. The gnathal plates of Alienacanthus possess sharp, posteriorly recurved teeth that continue anterior of the occlusion in the inferognathals. The dentition suggests a catching and trapping live prey function, and the jaw occlusion is unique among placoderms. This armoured 'fish' expands the morphological and ecological diversity during one of the first radiations of jawed vertebrates with a combination of features so far unrecorded for arthrodires.
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Migulina N, de Hilster RHJ, Bartel S, Vedder RHJ, van den Berge M, Nagelkerke A, Timens W, Harmsen MC, Hylkema MN, Brandsma CA, Burgess JK. 3-D culture of human lung fibroblasts decreases proliferative and increases extracellular matrix remodeling genes. Am J Physiol Cell Physiol 2024; 326:C177-C193. [PMID: 37955339 DOI: 10.1152/ajpcell.00374.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/14/2023]
Abstract
Fibroblasts are the main producers of extracellular matrix (ECM) responsible for ECM maintenance and repair, a process often disrupted in chronic lung diseases. The accompanying mechanical changes adversely affect resident cells and overall lung function. Numerous models have been used to elucidate fibroblast behavior that are now evolving toward complex three-dimensional (3-D) models incorporating ECM, aiming to replicate the cells' native environment. Little is known about the cellular changes that occur when moving from two-dimensional (2-D) to 3-D cell culture. This study compared the gene expression profiles of primary human lung fibroblasts from seven subjects with normal lung function, that were cultured for 24 h on 2-D collagen I-coated tissue culture plastic and in 3-D collagen I hydrogels, which are commonly used to mimic ECM in various models, from contraction assays to intricate organ-on-a-chip models. Comparing 3-D with 2-D cell culture, 6,771 differentially expressed genes (2,896 up, 3,875 down) were found; enriched gene sets within the downregulated genes, identified through Gene Set Enrichment Analysis and Ingenuity Pathway Analysis, were involved in the initiation of DNA replication which implied downregulation of fibroblast proliferation in 3-D. Observation of cells for 72 h in 2-D and 3-D environments confirmed the reduced progression through the cell cycle in 3-D. A focused analysis, examining the Hippo pathway and ECM-associated genes, showed differential patterns of gene expression in the 3-D versus 2-D culture. Altogether, the transcriptional response of fibroblasts cultured in 3-D indicated inhibition of proliferation, and alterations in Hippo and ECM pathways indicating a complete switch from proliferation to ECM remodeling.NEW & NOTEWORTHY With the introduction of complex three-dimensional (3-D) lung models, comes a need for understanding cellular behavior in these models. We compared gene expression profiles of human lung fibroblasts grown on two-dimensional (2-D) collagen I-coated surfaces with those in 3-D collagen I hydrogels. RNA sequencing and subsequent pathway analyses showed decreased proliferation, increased extracellular matrix (ECM) remodeling, and altered Hippo signaling and ECM deposition-related gene signatures. These findings highlight unique responses of fibroblasts in 3-D models.
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van der Willigen RF, Versnel H, van Opstal AJ. Spectral-temporal processing of naturalistic sounds in monkeys and humans. J Neurophysiol 2024; 131:38-63. [PMID: 37965933 DOI: 10.1152/jn.00129.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/23/2023] [Accepted: 11/13/2023] [Indexed: 11/16/2023] Open
Abstract
Human speech and vocalizations in animals are rich in joint spectrotemporal (S-T) modulations, wherein acoustic changes in both frequency and time are functionally related. In principle, the primate auditory system could process these complex dynamic sounds based on either an inseparable representation of S-T features or, alternatively, a separable representation. The separability hypothesis implies an independent processing of spectral and temporal modulations. We collected comparative data on the S-T hearing sensitivity in humans and macaque monkeys to a wide range of broadband dynamic spectrotemporal ripple stimuli employing a yes-no signal-detection task. Ripples were systematically varied, as a function of density (spectral modulation frequency), velocity (temporal modulation frequency), or modulation depth, to cover a listener's full S-T modulation sensitivity, derived from a total of 87 psychometric ripple detection curves. Audiograms were measured to control for normal hearing. Determined were hearing thresholds, reaction time distributions, and S-T modulation transfer functions (MTFs), both at the ripple detection thresholds and at suprathreshold modulation depths. Our psychophysically derived MTFs are consistent with the hypothesis that both monkeys and humans employ analogous perceptual strategies: S-T acoustic information is primarily processed separable. Singular value decomposition (SVD), however, revealed a small, but consistent, inseparable spectral-temporal interaction. Finally, SVD analysis of the known visual spatiotemporal contrast sensitivity function (CSF) highlights that human vision is space-time inseparable to a much larger extent than is the case for S-T sensitivity in hearing. Thus, the specificity with which the primate brain encodes natural sounds appears to be less strict than is required to adequately deal with natural images.NEW & NOTEWORTHY We provide comparative data on primate audition of naturalistic sounds comprising hearing thresholds, reaction time distributions, and spectral-temporal modulation transfer functions. Our psychophysical experiments demonstrate that auditory information is primarily processed in a spectral-temporal-independent manner by both monkeys and humans. Singular value decomposition of known visual spatiotemporal contrast sensitivity, in comparison to our auditory spectral-temporal sensitivity, revealed a striking contrast in how the brain encodes natural sounds as opposed to natural images, as vision appears to be space-time inseparable.
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Verhoeven MD, Nielsen PH, Dueholm MKD. Amplicon-guided isolation and cultivation of previously uncultured microbial species from activated sludge. Appl Environ Microbiol 2023; 89:e0115123. [PMID: 38051071 PMCID: PMC10734543 DOI: 10.1128/aem.01151-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Biological wastewater treatment relies on complex microbial communities that assimilate nutrients and break down pollutants in the wastewater. Knowledge about the physiology and metabolism of bacteria in wastewater treatment plants (WWTPs) may therefore be used to improve the efficacy and economy of wastewater treatment. Our current knowledge is largely based on 16S rRNA gene amplicon profiling, fluorescence in situ hybridization studies, and predictions based on metagenome-assembled genomes. Bacterial isolates are often required to validate genome-based predictions as they allow researchers to analyze a specific species without interference from other bacteria and with simple bulk measurements. Unfortunately, there are currently very few pure cultures representing the microbes commonly found in WWTPs. To address this, we introduce an isolation strategy that takes advantage of state-of-the-art microbial profiling techniques to uncover suitable growth conditions for key WWTP microbes. We furthermore demonstrate that this information can be used to isolate key organisms representing global WWTPs.
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Van Hemelrijck WMJ, Martikainen P, Zengarini N, Costa G, Janssen F. The impact of estimation methods for alcohol-attributable mortality on long-term trends for the general population and by educational level in Finland and Italy (Turin). PLoS One 2023; 18:e0295760. [PMID: 38096271 PMCID: PMC10721192 DOI: 10.1371/journal.pone.0295760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND AND AIMS This paper assesses the impact of estimation methods for general and education-specific trends in alcohol-attributable mortality (AAM), and develops an alternative method that can be used when the data available for study is limited. METHODS We calculated yearly adult (30+) age-standardised and age-specific AAM rates by sex for the general population and by educational level (low, middle, high) in Finland and Turin (Italy) from 1972 to 2017. Furthermore the slope index of inequality and relative inequality index were computed by country and sex. We compared trends, levels, age distributions, and educational inequalities in AAM according to three existing estimation methods: (1) Underlying COD (UCOD), (2) Multiple COD (MCOD) method, and (3) the population attributable fractions (PAF)-method. An alternative method is developed based on the pros and cons of these methods and the outcomes of the comparison. RESULTS The UCOD and MCOD approaches revealed mainly increasing trends in AAM compared to the declining trends according to the PAF approach. These differences are more pronounced when examining AAM trends by educational groups, particularly for Finnish men. Until age 65, age patterns are similar for all methods, and levels nearly identical for MCOD and PAF in Finland. Our novel method assumes a similar trend and age pattern as observed in UCOD, but adjusts its level upwards so that it matches the level of the PAF approach for ages 30-64. Our new method yields levels in-between UCOD and PAF for Turin (Italy), and resembles the MCOD rates in Finland for females. Relative inequalities deviate for the PAF-method (lower levels) compared to other methods, whereas absolute inequalities are generally lower for UCOD than all three methods that combine wholly and partly AAM. CONCLUSIONS The choice of method to estimate AAM affects not only levels, but also general and education-specific trends and inequalities. Our newly developed method constitutes a better alternative for multiple-country studies by educational level than the currently used UCOD-method when the data available for study is limited to underlying causes of death.
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Gaudzinski-Windheuser S, Kindler L, Roebroeks W. Widespread evidence for elephant exploitation by Last Interglacial Neanderthals on the North European plain. Proc Natl Acad Sci U S A 2023; 120:e2309427120. [PMID: 38048457 PMCID: PMC10723128 DOI: 10.1073/pnas.2309427120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/26/2023] [Indexed: 12/06/2023] Open
Abstract
Neanderthals hunted and butchered straight-tusked elephants, the largest terrestrial mammals of the Pleistocene, in a lake landscape on the North European plain, 125,000 years ago, as recently shown by a study of the Last Interglacial elephant assemblage from Neumark-Nord (Germany). With evidence for a remarkable focus on adult males and on their extended utilization, the data from this location are thus far without parallel in the archaeological record. Given their relevance for our knowledge of the Neanderthal niche, we investigated whether the Neumark-Nord subsistence practices were more than a local phenomenon, possibly determined by local characteristics. Analyzing elephant remains from two other Last Interglacial archaeological sites on the North European plain, Gröbern and Taubach, we identified in both assemblages similar butchering patterns as at Neumark-Nord, demonstrating that extended elephant exploitation was a widespread Neanderthal practice during the (early part of the) Last Interglacial. The substantial efforts needed to process these animals, weighing up to 13 metric tons, and the large amounts of food generated suggest that Neanderthals either had ways of storing vast amounts of meat and fat and/or temporarily aggregated in larger groups than commonly acknowledged. The data do not allow us to rule out one of the two explanations, and furthermore both factors, short-term larger group sizes as well as some form of food preservation, may have played a role. What the data do show is that exploitation of large straight-tusked elephants was a widespread and recurring phenomenon amongst Last Interglacial Neanderthals on the North European plain.
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Oskam N, den Boer MA, Lukassen MV, Ooijevaar-de Heer P, Veth TS, van Mierlo G, Lai SH, Derksen NIL, Yin V, Streutker M, Franc V, Šiborová M, Damen MJA, Kos D, Barendregt A, Bondt A, van Goudoever JB, de Haas CJC, Aerts PC, Muts RM, Rooijakkers SHM, Vidarsson G, Rispens T, Heck AJR. CD5L is a canonical component of circulatory IgM. Proc Natl Acad Sci U S A 2023; 120:e2311265120. [PMID: 38055740 PMCID: PMC10723121 DOI: 10.1073/pnas.2311265120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023] Open
Abstract
Immunoglobulin M (IgM) is an evolutionary conserved key component of humoral immunity, and the first antibody isotype to emerge during an immune response. IgM is a large (1 MDa), multimeric protein, for which both hexameric and pentameric structures have been described, the latter additionally containing a joining (J) chain. Using a combination of single-particle mass spectrometry and mass photometry, proteomics, and immunochemical assays, we here demonstrate that circulatory (serum) IgM exclusively exists as a complex of J-chain-containing pentamers covalently bound to the small (36 kDa) protein CD5 antigen-like (CD5L, also called apoptosis inhibitor of macrophage). In sharp contrast, secretory IgM in saliva and milk is principally devoid of CD5L. Unlike IgM itself, CD5L is not produced by B cells, implying that it associates with IgM in the extracellular space. We demonstrate that CD5L integration has functional implications, i.e., it diminishes IgM binding to two of its receptors, the FcαµR and the polymeric Immunoglobulin receptor. On the other hand, binding to FcµR as well as complement activation via C1q seem unaffected by CD5L integration. Taken together, we redefine the composition of circulatory IgM as a J-chain containing pentamer, always in complex with CD5L.
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Gan J, Pinto-Fernández A, Flierman D, Akkermans JJLL, O’Brien DP, Greenwood H, Scott HC, Fritz G, Knobeloch KP, Neefjes J, van Dam H, Ovaa H, Ploegh HL, Kessler BM, Geurink PP, Sapmaz A. USP16 is an ISG15 cross-reactive deubiquitinase that targets pro-ISG15 and ISGylated proteins involved in metabolism. Proc Natl Acad Sci U S A 2023; 120:e2315163120. [PMID: 38055744 PMCID: PMC10722975 DOI: 10.1073/pnas.2315163120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023] Open
Abstract
Interferon-induced ubiquitin (Ub)-like modifier ISG15 covalently modifies host and viral proteins to restrict viral infections. Its function is counteracted by the canonical deISGylase USP18 or Ub-specific protease 18. Notwithstanding indications for the existence of other ISG15 cross-reactive proteases, these remain to be identified. Here, we identify deubiquitinase USP16 as an ISG15 cross-reactive protease by means of ISG15 activity-based profiling. Recombinant USP16 cleaved pro-ISG15 and ISG15 isopeptide-linked model substrates in vitro, as well as ISGylated substrates from cell lysates. Moreover, interferon-induced stimulation of ISGylation was increased by depletion of USP16. The USP16-dependent ISG15 interactome indicated that the deISGylating function of USP16 may regulate metabolic pathways. Targeted enzymes include malate dehydrogenase, cytoplasmic superoxide dismutase 1, fructose-bisphosphate aldolase A, and cytoplasmic glutamic-oxaloacetic transaminase 1. USP16 may thus contribute to the regulation of a subset of metabolism-related proteins during type-I interferon responses.
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Prekovic S, Chalkiadakis T, Roest M, Roden D, Lutz C, Schuurman K, Opdam M, Hoekman L, Abbott N, Tesselaar T, Wajahat M, Dwyer AR, Mayayo‐Peralta I, Gomez G, Altelaar M, Beijersbergen R, Győrffy B, Young L, Linn S, Jonkers J, Tilley W, Hickey T, Vareslija D, Swarbrick A, Zwart W. Luminal breast cancer identity is determined by loss of glucocorticoid receptor activity. EMBO Mol Med 2023; 15:e17737. [PMID: 37902007 PMCID: PMC10701603 DOI: 10.15252/emmm.202317737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/31/2023] Open
Abstract
Glucocorticoid receptor (GR) is a transcription factor that plays a crucial role in cancer biology. In this study, we utilized an in silico-designed GR activity signature to demonstrate that GR relates to the proliferative capacity of numerous primary cancer types. In breast cancer, the GR activity status determines luminal subtype identity and has implications for patient outcomes. We reveal that GR engages with estrogen receptor (ER), leading to redistribution of ER on the chromatin. Notably, GR activation leads to upregulation of the ZBTB16 gene, encoding for a transcriptional repressor, which controls growth in ER-positive breast cancer and associates with prognosis in luminal A patients. In relation to ZBTB16's repressive nature, GR activation leads to epigenetic remodeling and loss of histone acetylation at sites proximal to cancer-driving genes. Based on these findings, epigenetic inhibitors reduce viability of ER-positive breast cancer cells that display absence of GR activity. Our findings provide insights into how GR controls ER-positive breast cancer growth and may have implications for patients' prognostication and provide novel therapeutic candidates for breast cancer treatment.
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Nasrawi R, Boettcher SEP, van Ede F. Prospection of Potential Actions during Visual Working Memory Starts Early, Is Flexible, and Predicts Behavior. J Neurosci 2023; 43:8515-8524. [PMID: 37857486 PMCID: PMC10711698 DOI: 10.1523/jneurosci.0709-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
For visual working memory to serve upcoming behavior, it is crucial that we prepare for the potential use of working-memory contents ahead of time. Recent studies have demonstrated how the prospection and planning for an upcoming manual action starts early after visual encoding, and occurs alongside visual retention. Here, we address whether such "output planning" in visual working memory flexibly adapts to different visual-motor mappings, and occurs even when an upcoming action will only potentially become relevant for behavior. Human participants (female and male) performed a visual-motor working memory task in which they remembered one or two colored oriented bars for later (potential) use. We linked, and counterbalanced, the tilt of the visual items to specific manual responses. This allowed us to track planning of upcoming behavior through contralateral attenuation of β band activity, a canonical motor-cortical EEG signature of manual-action planning. The results revealed how action encoding and subsequent planning alongside visual working memory (1) reflect anticipated task demands rather than specific visual-motor mappings, (2) occur even for actions that will only potentially become relevant for behavior, and (3) are associated with faster performance for the encoded item, at the expense of performance to other working-memory content. This reveals how the potential prospective use of visual working memory content is flexibly planned early on, with consequences for the speed of memory-guided behavior.SIGNIFICANCE STATEMENT It is increasingly studied how visual working memory helps us to prepare for the future, in addition to how it helps us to hold onto the past. Recent studies have demonstrated that the planning of prospective actions occurs alongside encoding and retention in working memory. We show that such early "output planning" flexibly adapts to varying visual-motor mappings, occurs both for certain and potential actions, and predicts ensuing working-memory guided behavior. These results highlight the flexible and future-oriented nature of visual working memory, and provide insight into the neural basis of the anticipatory dynamics that translate visual representations into adaptive upcoming behavior.
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Romanuka J, Folkers GE, Gnida M, Kovačič L, Wienk H, Kaptein R, Boelens R. Genetic switching by the Lac repressor is based on two-state Monod-Wyman-Changeux allostery. Proc Natl Acad Sci U S A 2023; 120:e2311240120. [PMID: 38019859 DOI: 10.1073/pnas.2311240120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric Escherichia coli Lac repressor. In the absence of ligands, the dimer exists in a dynamic equilibrium between DNA-bound and inducer-bound conformations. Binding of either effector shifts this equilibrium toward either bound state. Analysis of the ternary complex between repressor, operator DNA, and inducer shows how adding the inducer results in allosteric changes that disrupt the interdomain contacts between the inducer binding and DNA binding domains and how this in turn leads to destabilization of the hinge helices and release of the Lac repressor from the operator. Based on our data, the allosteric mechanism of the induction process is in full agreement with the well-known Monod-Wyman-Changeux model.
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van der Meij A, Elsayed SS, Du C, Willemse J, Wood TM, Martin NI, Raaijmakers JM, van Wezel GP. The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes. Appl Environ Microbiol 2023; 89:e0123923. [PMID: 37902333 PMCID: PMC10686085 DOI: 10.1128/aem.01239-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/21/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE Microorganisms that live on or inside plants can influence plant growth and health. Among the plant-associated bacteria, streptomycetes play an important role in defense against plant diseases, but the underlying mechanisms are not well understood. Here, we demonstrate that the plant hormones jasmonic acid (JA) and methyl jasmonate directly affect the life cycle of streptomycetes by modulating antibiotic synthesis and promoting faster development. Moreover, the plant hormones specifically stimulate the synthesis of the polyketide antibiotic actinorhodin in Streptomyces coelicolor. JA is then modified in the cell by amino acid conjugation, thereby quenching toxicity. Collectively, these results provide new insight into the impact of a key plant hormone on diverse phenotypic responses of streptomycetes.
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Meelen T, Münzel K. The uphill struggles of carsharing in the Netherlands. Proc Natl Acad Sci U S A 2023; 120:e2206197120. [PMID: 37956273 PMCID: PMC10666113 DOI: 10.1073/pnas.2206197120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 01/10/2023] [Indexed: 11/15/2023] Open
Abstract
The current mobility system relies heavily on privately owned cars, which results in high levels of emissions, material use, and use of scarce public space. Carsharing is a mobility innovation offering consumers on-demand, short-term access to cars. By changing consumption patterns and reducing car ownership, carsharing has great potential to contribute to a sustainability transition of the mobility system. Even so, carsharing only satisfies a small portion of today's mobility needs and has difficulties becoming mainstream. This study investigates the upscaling trajectory of carsharing in the Netherlands. We structure the analysis along the lines of the multilevel perspective and include economic, technological, sociocultural, and policy factors that shape carsharing growth. The results demonstrate how car ownership is entrenched in the social and economic fabric, and the specific barriers this poses to carsharing. Moreover, we find some forms of carsharing risk extending private car ownership rather than challenging it. The environmental outcomes of carsharing are not predetermined but depend on the trajectories key actors take during upscaling. Our analysis highlights the importance of studying innovations in the context of the consumption-production systems in which they emerge.
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van der Krift F, Zijlmans DW, Shukla R, Javed A, Koukos PI, Schwarz LLE, Timmermans-Sprang EP, Maas PE, Gahtory D, van den Nieuwboer M, Mol JA, Strous GJ, Bonvin AM, van der Stelt M, Veldhuizen EJ, Weingarth M, Vermeulen M, Klumperman J, Maurice MM. A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance. Life Sci Alliance 2023; 6:e202302058. [PMID: 37591722 PMCID: PMC10435995 DOI: 10.26508/lsa.202302058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Cancer cells make extensive use of the folate cycle to sustain increased anabolic metabolism. Multiple chemotherapeutic drugs interfere with the folate cycle, including methotrexate and 5-fluorouracil that are commonly applied for the treatment of leukemia and colorectal cancer (CRC), respectively. Despite high success rates, therapy-induced resistance causes relapse at later disease stages. Depletion of folylpolyglutamate synthetase (FPGS), which normally promotes intracellular accumulation and activity of natural folates and methotrexate, is linked to methotrexate and 5-fluorouracil resistance and its association with relapse illustrates the need for improved intervention strategies. Here, we describe a novel antifolate (C1) that, like methotrexate, potently inhibits dihydrofolate reductase and downstream one-carbon metabolism. Contrary to methotrexate, C1 displays optimal efficacy in FPGS-deficient contexts, due to decreased competition with intracellular folates for interaction with dihydrofolate reductase. We show that FPGS-deficient patient-derived CRC organoids display enhanced sensitivity to C1, whereas FPGS-high CRC organoids are more sensitive to methotrexate. Our results argue that polyglutamylation-independent antifolates can be applied to exert selective pressure on FPGS-deficient cells during chemotherapy, using a vulnerability created by polyglutamylation deficiency.
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Spaan CN, de Boer RJ, Smit WL, van der Meer JH, van Roest M, Vermeulen JL, Koelink PJ, Becker MA, Go S, Silva J, Faller WJ, van den Brink GR, Muncan V, Heijmans J. Grp78 is required for intestinal Kras-dependent glycolysis proliferation and adenomagenesis. Life Sci Alliance 2023; 6:e202301912. [PMID: 37643866 PMCID: PMC10465924 DOI: 10.26508/lsa.202301912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
In development of colorectal cancer, mutations in APC are often followed by mutations in oncogene KRAS The latter changes cellular metabolism and is associated with the Warburg phenomenon. Glucose-regulated protein 78 (Grp78) is an important regulator of the protein-folding machinery, involved in processing and localization of transmembrane proteins. We hypothesize that targeting Grp78 in Apc and Kras (AK)-mutant intestines interferes with the metabolic phenotype imposed by Kras mutations. In mice with intestinal epithelial mutations in Apc, Kras G12D and heterozygosity for Grp78 (AK-Grp78 HET ) adenoma number and size is decreased compared with AK-Grp78 WT mice. Organoids from AK-Grp78 WT mice exhibited a glycolysis metabolism which was completely rescued by Grp78 heterozygosity. Expression and correct localization of glucose transporter GLUT1 was diminished in AK-Grp78 HET cells. GLUT1 inhibition restrained the increased growth observed in AK-mutant organoids, whereas AK-Grp78 HET organoids were unaffected. We identify Grp78 as a critical factor in Kras-mutated adenomagenesis. This can be attributed to a critical role for Grp78 in GLUT1 expression and localization, targeting glycolysis and the Warburg effect.
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Czukiewska SM, Fan X, Mulder AA, Van Der Helm T, Hillenius S, Van Der Meeren L, Matorras R, Eguizabal C, Lei L, Koning RI, Chuva De Sousa Lopes SM. Cell-cell interactions during the formation of primordial follicles in humans. Life Sci Alliance 2023; 6:e202301926. [PMID: 37643865 PMCID: PMC10465921 DOI: 10.26508/lsa.202301926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
Gametogenesis is a complex and sex-specific multistep process during which the gonadal somatic niche plays an essential regulatory role. One of the most crucial steps during human female gametogenesis is the formation of primordial follicles, the functional unit of the ovary that constitutes the pool of follicles available at birth during the entire reproductive life. However, the relation between human fetal germ cells (hFGCs) and gonadal somatic cells during the formation of the primordial follicles remains largely unexplored. We have discovered that hFGCs can form multinucleated syncytia, some connected via interconnecting intercellular bridges, and that not all nuclei in hFGC-syncytia were synchronous regarding meiotic stage. As hFGCs progressed in development, pre-granulosa cells formed protrusions that seemed to progressively constrict individual hFGCs, perhaps contributing to separate them from the multinucleated syncytia. Our findings highlighted the cell-cell interaction and molecular dynamics between hFGCs and (pre)granulosa cells during the formation of primordial follicles in humans. Knowledge on how the pool of primordial follicle is formed is important to understand human infertility.
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Muok AR, Kurniyati K, Cassidy CK, Olsthoorn FA, Ortega DR, Mabrouk AS, Li C, Briegel A. A new class of protein sensor links spirochete pleomorphism, persistence, and chemotaxis. mBio 2023; 14:e0159823. [PMID: 37607060 PMCID: PMC10653840 DOI: 10.1128/mbio.01598-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 08/24/2023] Open
Abstract
IMPORTANCE A new class of bacterial protein sensors monitors intracellular levels of S-adenosylmethionine to modulate cell morphology, chemotaxis, and biofilm formation. Simultaneous regulation of these behaviors enables bacterial pathogens to survive within their niche. This sensor, exemplified by Treponema denticola CheWS, is anchored to the chemotaxis array and its sensor domain is located below the chemotaxis rings. This position may allow the sensor to directly interact with the chemotaxis histidine kinase CheA. Collectively, these data establish a critical role of CheWS in pathogenesis and further illustrate the impact of studying non-canonical chemotaxis proteins.
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Chan HY, Scholz C, Cosme D, Martin RE, Benitez C, Resnick A, Carreras-Tartak J, Cooper N, Paul AM, Falk EB. Neural signals predict information sharing across cultures. Proc Natl Acad Sci U S A 2023; 120:e2313175120. [PMID: 37871199 PMCID: PMC10622920 DOI: 10.1073/pnas.2313175120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
Information sharing influences which messages spread and shape beliefs, behavior, and culture. In a preregistered neuroimaging study conducted in the United States and the Netherlands, we demonstrate replicability, predictive validity, and generalizability of a brain-based prediction model of information sharing. Replicating findings in Scholz et al., Proc. Natl. Acad. Sci. U.S.A. 114, 2881-2886 (2017), self-, social-, and value-related neural signals in a group of individuals tracked the population sharing of US news articles. Preregistered brain-based prediction models trained on Scholz et al. (2017) data proved generalizable to the new data, explaining more variance in population sharing than self-report ratings alone. Neural signals (versus self-reports) more reliably predicted sharing cross-culturally, suggesting that they capture more universal psychological mechanisms underlying sharing behavior. These findings highlight key neurocognitive foundations of sharing, suggest potential target mechanisms for interventions to increase message effectiveness, and advance brain-as-predictor research.
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Bunduc CM, Ding Y, Kuijl C, Marlovits TC, Bitter W, Houben ENG. Reconstitution of a minimal ESX-5 type VII secretion system suggests a role for PPE proteins in the outer membrane transport of proteins. mSphere 2023; 8:e0040223. [PMID: 37747201 PMCID: PMC10597459 DOI: 10.1128/msphere.00402-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 09/26/2023] Open
Abstract
Mycobacteria utilize type VII secretion systems (T7SSs) to secrete proteins across their highly hydrophobic and diderm cell envelope. Pathogenic mycobacteria have up to five different T7SSs, called ESX-1 to ESX-5, which are crucial for growth and virulence. Here, we use a functionally reconstituted ESX-5 system in the avirulent species Mycobacterium smegmatis that lacks ESX-5, to define the role of each esx-5 gene in system functionality. By creating an array of gene deletions and assessing protein levels of components and membrane complex assembly, we observed that only the five components of the inner membrane complex are required for its assembly. However, in addition to these five core components, active secretion also depends on both the Esx and PE/PPE substrates. Tagging the PPE substrates followed by subcellular fractionation, surface labeling and membrane extraction showed that these proteins localize to the mycobacterial outer membrane. This indicates that they could play a role in secretion across this enigmatic outer barrier. These results provide the first full overview of the role of each esx-5 gene in T7SS functionality. IMPORTANCE Pathogenic mycobacteria, such as the notorious Mycobacterium tuberculosis, are highly successful as pathogens, in part due to their specific and diderm cell envelope, with a mycolic acid-containing outer membrane. The architecture of this highly impermeable membrane is little understood and the proteins that populate it even less so. To transport proteins across their cell envelope, mycobacteria employ a specialized transport pathway called type VII secretion. While recent studies have elucidated the type VII secretion membrane channel that mediates transport across the inner membrane, the identity of the outer membrane channel remains a black box. Here, we show evidence that specific substrates of the type VII pathway could form these channels. Elucidating the pathway and mechanism of protein secretion through the mycobacterial outer membrane will allow its exploitation for the development of novel mycobacterial therapeutics.
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van den Bulk J, Verdegaal EM, van der Ploeg M, Visser M, Nunes JB, de Ru AH, Tjokrodirijo RT, Ijsselsteijn ME, Janssen NI, van der Breggen R, de Bruin L, de Kok P, Janssen GM, Ruano D, Kapiteijn EH, van Veelen PA, de Miranda NF, van der Burg SH. Neoantigen Targetability in Progressive Advanced Melanoma. Clin Cancer Res 2023; 29:4278-4288. [PMID: 37540567 PMCID: PMC10570682 DOI: 10.1158/1078-0432.ccr-23-1106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/23/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023]
Abstract
PURPOSE The availability of (neo)antigens and the infiltration of tumors by (neo)antigen-specific T cells are crucial factors in cancer immunotherapy. In this study, we aimed to investigate the targetability of (neo)antigens in advanced progessive melanoma and explore the potential for continued T-cell-based immunotherapy. EXPERIMENTAL DESIGN We examined a cohort of eight patients with melanoma who had sequential metastases resected at early and later time points. Antigen-presenting capacity was assessed using IHC and flow cytometry. T-cell infiltration was quantified through multiplex immunofluorescence. Whole-exome and RNA sequencing were conducted to identify neoantigens and assess the expression of neoantigens and tumor-associated antigens. Mass spectrometry was used to evaluate antigen presentation. Tumor recognition by autologous T cells was assessed by coculture assays with cell lines derived from the metastatic lesions. RESULTS We observed similar T-cell infiltration in paired early and later metastatic (LM) lesions. Although elements of the antigen-presenting machinery were affected in some LM lesions, both the early and later metastasis-derived cell lines were recognized by autologous T cells. At the genomic level, the (neo)antigen landscape was dynamic, but the (neo)antigen load was stable between paired lesions. CONCLUSIONS Our findings indicate that subsequently isolated tumors from patients with late-stage melanoma retain sufficient antigen-presenting capacity, T-cell infiltration, and a stable (neo)antigen load, allowing recognition of tumor cells by T cells. This indicates a continuous availability of T-cell targets in metastases occurring at different time points and supports further exploration of (neo)antigen-specific T-cell-based therapeutic approaches for advanced melanoma.
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Groot JM, Miletic S, Isherwood SJS, Tse DHY, Habli S, Håberg AK, Forstmann BU, Bazin PL, Mittner M. Echoes from Intrinsic Connectivity Networks in the Subcortex. J Neurosci 2023; 43:6609-6618. [PMID: 37562962 PMCID: PMC10538587 DOI: 10.1523/jneurosci.1020-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/11/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
Decades of research have greatly improved our understanding of intrinsic human brain organization in terms of functional networks and the transmodal hubs within the cortex at which they converge. However, substrates of multinetwork integration in the human subcortex are relatively uncharted. Here, we leveraged recent advances in subcortical atlasing and ultra-high field (7 T) imaging optimized for the subcortex to investigate the functional architecture of 14 individual structures in healthy adult males and females with a fully data-driven approach. We revealed that spontaneous neural activity in subcortical regions can be decomposed into multiple independent subsignals that correlate with, or "echo," the activity in functional networks across the cortex. Distinct subregions of the thalamus, striatum, claustrum, and hippocampus showed a varied pattern of echoes from attention, control, visual, somatomotor, and default mode networks, demonstrating evidence for a heterogeneous organization supportive of functional integration. Multiple network activity furthermore converged within the globus pallidus externa, substantia nigra, and ventral tegmental area but was specific to one subregion, while the amygdala and pedunculopontine nucleus preferentially affiliated with a single network, showing a more homogeneous topography. Subregional connectivity of the globus pallidus interna, subthalamic nucleus, red nucleus, periaqueductal gray, and locus coeruleus did not resemble patterns of cortical network activity. Together, these finding describe potential mechanisms through which the subcortex participates in integrated and segregated information processing and shapes the spontaneous cognitive dynamics during rest.SIGNIFICANCE STATEMENT Despite the impact of subcortical dysfunction on brain health and cognition, large-scale functional mapping of subcortical structures severely lags behind that of the cortex. Recent developments in subcortical atlasing and imaging at ultra-high field provide new avenues for studying the intricate functional architecture of the human subcortex. With a fully data-driven analysis, we reveal subregional connectivity profiles of a large set of noncortical structures, including those rarely studied in fMRI research. The results have implications for understanding how the functional organization of the subcortex facilitates integrative processing through cross-network information convergence, paving the way for future work aimed at improving our knowledge of subcortical contributions to intrinsic brain dynamics and spontaneous cognition.
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Aanen DK, van ’t Padje A, Auxier B. Longevity of Fungal Mycelia and Nuclear Quality Checks: a New Hypothesis for the Role of Clamp Connections in Dikaryons. Microbiol Mol Biol Rev 2023; 87:e0002221. [PMID: 37409939 PMCID: PMC10521366 DOI: 10.1128/mmbr.00022-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
This paper addresses the stability of mycelial growth in fungi and differences between ascomycetes and basidiomycetes. Starting with general evolutionary theories of multicellularity and the role of sex, we then discuss individuality in fungi. Recent research has demonstrated the deleterious consequences of nucleus-level selection in fungal mycelia, favoring cheaters with a nucleus-level benefit during spore formation but a negative effect on mycelium-level fitness. Cheaters appear to generally be loss-of-fusion (LOF) mutants, with a higher propensity to form aerial hyphae developing into asexual spores. Since LOF mutants rely on heterokaryosis with wild-type nuclei, we argue that regular single-spore bottlenecks can efficiently select against such cheater mutants. We then zoom in on ecological differences between ascomycetes being typically fast-growing but short-lived with frequent asexual-spore bottlenecks and basidiomycetes being generally slow-growing but long-lived and usually without asexual-spore bottlenecks. We argue that these life history differences have coevolved with stricter nuclear quality checks in basidiomycetes. Specifically, we propose a new function for clamp connections, structures formed during the sexual stage in ascomycetes and basidiomycetes but during somatic growth only in basidiomycete dikaryons. During dikaryon cell division, the two haploid nuclei temporarily enter a monokaryotic phase, by alternatingly entering a retrograde-growing clamp cell, which subsequently fuses with the subapical cell to recover the dikaryotic cell. We hypothesize that clamp connections act as screening devices for nuclear quality, with both nuclei continuously testing each other for fusion ability, a test that LOF mutants will fail. By linking differences in longevity of the mycelial phase to ecology and stringency of nuclear quality checks, we propose that mycelia have a constant and low lifetime cheating risk, irrespective of their size and longevity.
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Geelhoed JS, Thorup CA, Bjerg JJ, Schreiber L, Nielsen LP, Schramm A, Meysman FJR, Marshall IPG. Indications for a genetic basis for big bacteria and description of the giant cable bacterium Candidatus Electrothrix gigas sp. nov. Microbiol Spectr 2023; 11:e0053823. [PMID: 37732806 PMCID: PMC10580974 DOI: 10.1128/spectrum.00538-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence in situ hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name Ca. Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca. Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of Ca. Electrothrix gigas and other giant bacteria. IMPORTANCE In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name Candidatus Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.
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