bluuebunny/crossref_metadata_2025 huggingface dataset:
Distributed illusory figure-ground segmentation signatures across the dorsal and ventral streams
Authors: Arsenovic Ana , Ischebeck Anja , Zaretskaya Natalia
Published: November 2023

Visual illusions give rise to percepts that are more complex than the incoming sensory information, thereby exposing the inferential nature of perception. Early visual cortex (EVC) can represent not only physical input, but also illusory content of perception. Specifically, much like in real shape perception, during perception of an illusory shape the topographic representation of the shape’s surface is enhanced, while the regions surrounding it are suppressed, reflecting the figure-ground segmentation mechanisms on the neural level. It remains unclear whether such topographically specific figure-ground segmentation signatures are present in higher topographic maps along the visual hierarchy. To test this, we measured brain activity of 30 healthy human participants using functional magnetic resonance imaging (fMRI). The participants performed a central fixation task while passively observing a surrounding configuration of four inducers, which either formed or did not form an illusory shape. Using an additional functional localizer scan we could identify voxels uniquely representing the illusory surface and the background in the EVC, posterior parietal topographic region IPS0/V7 and several other maps along the dorsal and ventral streams. Apart from the EVC, we found signatures of figure-ground segmentation in several topographic maps. Illusory surface enhancement was observed in IPS0/V7, but without background suppression. Ventral topographic maps VO1 and VO2 showed background suppression only. Finally, other extrastriate areas, V3a, V3b and hV4, displayed both surface enhancement and background suppression. Our results demonstrate that topographically specific illusory shape responses are distributed along multiple topographic maps beyond the EVC. Furthermore, they point to the difference in neural signatures of figure-ground segmentation at various hierarchical levels and along different processing streams, stressing the independence of the surface enhancement and background suppression mechanisms.
AraMultiOmics: a tool for generating multi-omics features for downstream statistical analysis to infer the molecular basis of symbiosis among non-host plant Arabidopsis thaliana, host plant, and arbuscular mycorrhizal fungi
Authors: Kang Jee Eun
Published: November 2023

Arbuscular mycorrhizal fungi (AMF) are symbiotic microorganisms that colonize plant roots, promoting plant growth and improving soil quality. A large number of studies have focused on investigating the communication between host-plants and AMF. Recent investigation in molecular evolution related to arbuscular mycorrhizal symbiosis in Arabidopsis thaliana (A. thaliana) have enabled scientists to perform comparative multi-omics analyses between A. thaliana and host-plants. Although there is a vast amount of omics data available for A. thaliana, most AM-related information comes from differentially expressed genes (DEG) identified in transcriptome studies. To address this gap, we developed AraMultiOmics, a useful tool for integrative analysis of multi-omics data of A. thaliana. It consists of 10 modules: 1) epigenetic regulations in protein–nucleic acid interaction (PNI), 2) DNA structure and metal binding profile, 3) transcription factor (TF) binding profiles, 4) protein domain–domain interaction (DDI), 5) profiling of interactions of protein-metal and of protein-ligand with complex structures (PLP) based on alignment of similar protein structures, 6) carbohydrate-lipid-protein interaction (CLP)- analysis of lipidome-proteome-glycoscience, 7) metabolic pathway analysis, 8) multiple omics association study, 9) GO/PO analysis, and 10) Medicago COG information. These analyses are conducted in comparison with the COG of Medicago truncatula (M. truncatula). To facilitate the inference of AM-driven changes and of AM derived molecules during AM symbiosis, the program provides a convenient means to generate datasets with important features that can be conjoined with various downstream statistical methods. We have included demonstrations on how to create comparative datasets, and the program codes are freely available for download atwww.artfoundation.kr.
Murine uterine gland branching is necessary for gland function in implantation
Authors: Granger Katrina , Fitch Sarah , Shen May , Lloyd Jarrett , Bhurke Aishwarya , Hancock Jonathan , Ye Xiaoqin , Arora Ripla
Published: November 2023

Uterine glands are branched, tubular structures whose secretions are essential for pregnancy success. It is known that pre-implantation glandular expression of leukemia inhibitory factor (LIF) is crucial for embryo implantation, however contribution of uterine gland structure to gland secretions such as LIF is not known. Here we use mice deficient in estrogen receptor 1 (ESR1) signaling to uncover the role of ESR1 signaling in gland branching and the role of a branched structure in LIF secretion and embryo implantation. We observed that deletion of ESR1 in neonatal uterine epithelium, stroma and muscle using the progesterone receptorPgrCrecauses a block in uterine gland development at the gland bud stage. Embryonic epithelial deletion of ESR1 using a mullerian duct Cre line -Pax2Cre, displays gland bud elongation but a failure in gland branching. Surprisingly, adult uterine epithelial deletion of ESR1 using the lactoferrin-Cre (LtfCre) displays normally branched uterine glands. Intriguingly, unbranched glands fromPax2CreEsr1flox/floxuteri fail to express glandular pre-implantationLif,preventing implantation chamber formation and embryo alignment along the uterine mesometrial-antimesometrial axis. In contrast, branched glands fromLtfCreEsr1flox/floxuteri display reduced expression of glandularLifresulting in delayed implantation chamber formation and embryo-uterine axes alignment but deliver a normal number of pups. Finally, pre-pubertal unbranched glands in control mice expressLifin the luminal epithelium but fail to expressLifin the glandular epithelium even in the presence of estrogen. These data strongly suggest that branched glands are necessary for pre-implantation glandularLifexpression for implantation success. Our study is the first to identify a relationship between the branched structure and secretory function of uterine glands and provides a framework for understanding how uterine gland structure-function contributes to pregnancy success.
Butyrate-producing bacteria as probiotic supplement: beneficial effects on metabolism and modulation of behavior in an obesity mouse model
Authors: Garcia-Serrano Alba M. , Skoug Cecilia , Axling Ulrika , Korhonen Emma Rosmariini , Teixeira Cristina , Ahrén Irini Lazou , Mukhopadhya Indrani , Boteva Nikoleta , Martin Jennifer , Scott Karen , Gratz Silvia , Stenkula Karin G. , Holm Cecilia , Duarte João M.N.
Published: November 2023

Obesity is a risk factor for cardio-metabolic and neurological disease. The contribution of gut microbiota to derangements of the gut-brain axis in the context of obesity has been acknowledged, particularly through physiology modulation by short-chain fatty acids (SCFAs). Thus, probiotic interventions and administration of SCFAs have been employed with the purpose of alleviating symptoms in both metabolic and neurological disease. We have tested the effects of four butyrate-producing bacteria from the Lachnospiraceae family on the development of metabolic syndrome and behavioural alterations in a mouse model of diet-induced obesity. Male mice were fed either a high-fat diet (HFD) or an ingredient-matched control diet for 2 months, and bacteria cultures or culture medium were given by gavage to HFD-fed mice every second day. Assessment of the mice through a battery of metabolic and behaviour tests revealed that one of the administered bacteria affords some degree of protection against the development of obesity and its complications.
Genotype combinations drive variability in the microbiome configuration of the rhizosphere of Maize/Bean intercropping system
Authors: Lanzavecchia Giovanna , Frascarelli Giulia , Rocchetti Lorenzo , Bellucci Elisa , Bitocchi Elena , Di Vittori Valerio , Sillo Fabiano , Ferraris Irene , Carta Giada , Delledonne Massimo , Nanni Laura , Papa Roberto
Published: November 2023

In intercropping system, the interplay between cereals and legumes, which is strongly driven by complementarity of below-ground structures and their interactions with the soil microbiome, raises a fundamental query: Can different genotypes alter the configuration of the rhizosphere microbial communities? To address this issue, we conducted a field study, probing the effects of intercropping and diverse maize (Zea maysL.) and beans (Phaseolus vulgarisL.,Phaseolus coccineusL.) genotype combinations. Our results unveil that intercropping condition alters the rhizosphere bacterial communities, but that the degree of this impact is substantially affected by specific genotype combinations. Overall, intercropping allows the recruitment of exclusive bacterial species and enhance community complexity. Nevertheless, combinations of maize and beans genotypes determine two distinct groups characterized by higher or lower bacterial community diversity and complexity, which are influenced by the specific bean line associated. Moreover, intercropped maize lines exhibit varying propensities in recruiting bacterial members with more responsive lines showing preferential interactions with specific microorganisms. Our study conclusively shows that genotype has an impact on the rhizosphere microbiome and that a careful selection of genotype combinations for both species involved is essential to achieve compatibility optimization in intercropping.
AXDND1 is required to balance spermatogonial commitment and for sperm tail formation in mice and humans
Authors: Houston Brendan J. , Nguyen Joseph , Merriner D. Jo , O’Connor Anne E. , Lopes Alexandra M. , Nagirnaja Liina , Friedrich Corinna , Kliesch Sabine , Tüttelmann Frank , Aston Kenneth I. , Conrad Donald F. , Hobbs Robin M. , Dunleavy Jessica EM , O’Bryan Moira K.
Published: November 2023

Dynein complexes are large, multi-unit assemblies involved in many biological processes including male fertility via their critical roles in protein transport and axoneme motility. Previously we identified a pathogenic variant in the dynein geneAXDND1in an infertile man. Subsequently we identified an additional four potentially compound heterozygous variants of unknown significance inAXDND1in two additional infertile men. We thus tested the role of AXDND1 in mammalian male fertility by generating a knockout mouse model.Axdnd1-/-males were sterile at all ages but could undergo one round of histologically complete spermatogenesis. Subsequently, a progressive imbalance of spermatogonial commitment to spermatogenesis over self-renewal occurred, ultimately leading to catastrophic germ cell loss, loss of blood-testis barrier patency and immune cell infiltration. Sperm produced during the first wave of spermatogenesis were immotile due to abnormal axoneme structure, including the presence of ectopic vesicles and abnormalities in outer dense fibres and microtubule doublet structures. Sperm output was additionally compromised by a severe spermiation defect and abnormal sperm individualisation. Collectively, our data highlight the essential roles of AXDND1 as a regulator of spermatogonial commitment to spermatogenesis and during the processes of spermiogenesis where it is essential for sperm tail development, release and motility.
Candida albicanssuppression of neutrophil reactive nitrogen species is rescued by host Hif-1αin vivo
Authors: Burgess Thomas B. , Hammond Ffion R. , Szkuta Piotr T. , Lewis Amy , Christou Stella , Ayscough Kathryn R. , Johnston Simon A. , Condliffe Alison M. , Elks Philip M.
Published: November 2023

Candidaspp. cause 750,000 cases per annum of invasive disease worldwide, with up to a 50% mortality rate. Poor efficacy of current antifungals, lack of vaccines and rising antifungal resistance rates point towards an urgent need to develop new therapies.Candida albicansis a human commensal fungus that can cause life-threatening invasive infection in immunocompromised individuals.C. albicansis able to manipulate host macrophages and neutrophils to escape phagosomal killing and has previously been shown to suppress reactive nitrogen species (RNS) productionin vitro. However, the effects ofC. albicanson RNSin vivoand the molecular and cellular mechanisms involved remain unclear. Using a zebrafish model, we aimed to characterise RNS suppression byC. albicans in vivo. We demonstrate thatC. albicanssuppressed neutrophil RNS both proximally and distally to the infection site in a partially active process, with heat-killedC. albicansnot reducing RNS to the same extent as live fungi. Using acar1Δ mutant, we show that fungal arginase is partially responsible for the reduction in neutrophil RNS. Stabilisation of Hif-1α, a transcription factor with a key role in immune regulation, rescued neutrophil RNS production duringC. albicansinfection, leading to improved infection outcomes. The protective effect of Hif-1α stabilisation was neutrophil- and nitric oxide synthase-dependent. Together, these data demonstrate that Hif-1α stabilisation can restore the neutrophil RNS response inC. albicansinfection, leading to improved infection outcomes, highlighting the potential of targeting Hif-1α and RNS in host directed therapies against fungal infections.
Assessment of extracellular vesicle protein cargo as neurodegenerative disease biomarkers
Authors: Gilboa Tal , Ter-Ovanesyan Dmitry , Wang Shih-Chin , Whiteman Sara , Kannarkat George T , Church George M , Chen-Plotkin Alice S. , Walt David R
Published: November 2023

Extracellular vesicles (EVs) are released by all cells and hold great promise as a class of biomarkers. As EVs represent a way of capturing molecular information about the proteins inside of cells, EVs from biofluids could be used to better understand and diagnose disease from difficult to access organs such as the brain. This promise has led to increased interest in measuring EV proteins from both total EVs as well as brain-derived EVs isolated from the blood. However, the measurement of cargo proteins in EVs has been challenging because EVs are present at low levels and EV isolation methods are imperfect at separating EVs from free proteins. Thus, it is difficult to know whether a protein measured after EV isolation is truly inside EVs. In this study, we developed methods to measure whether a protein is inside EVs and quantify the ratio of a protein in EVs relative to total plasma. To achieve this, we combined a high-yield size exclusion chromatography (SEC) protocol with an optimized protease protection assay and Single Molecule Array (Simoa) digital ELISA assays for ultrasensitive measurement of proteins inside EVs. We applied these methods to analyze key proteins involved in neurodegenerative diseases: α-synuclein, Tau, Aβ40, and Aβ42. We found that α-synuclein and Tau are present in plasma EVs at a small fraction of the levels in total plasma, whereas Aβ40 and Aβ42 are undetectable in plasma EVs. This work provides a framework for determining the levels of proteins in EVs and represents an important step in the development of EV diagnostics for diseases of the brain, as well as other organs.
Haptenic adducts of β-lactam antibiotics elicit antibody responses with narrow clonality and specificity
Authors: Deimel Lachlan P. , Moynié Lucile , Sun Guoxuan , Lewis Viliyana , Turner Abigail , Buchanan Charles J. , Burnap Sean A. , Kobras Carolin M. , Stracy Mathew , Struwe Weston B. , Baldwin Andrew J. , Naismith James , Davis Benjamin G. , Sattentau Quentin J.
Published: November 2023

Many classes of small-molecule drugs form protein adductsin vivo, which may elicit antibodies via a classical hapten-carrier-type response, with implications for both allergy and drug sequestration. Although β-lactam antibiotics are a drug class long associated with these phenomena, the molecular determinants of drug-protein conjugation and consequent drug-specific immune responses remain incomplete. Here, we interrogated factors influencing penicilloyl adduct formation and immunogenicity, and used penicillin G (PenG) to probe the B and T cell determinants of drug-specific IgG responses in mice. We identify through deep clonotyping a dominant murine penicilloyl-specific clonal antibody class encompassing phylogenetically relatedIGHV1,IGHV5andIGHV10subgroup gene segments. Through protein NMR and x-ray structural analysis, we determined that adduct specific antibody clones—the MIL series—predominantly recognise the variable side-chain moiety (which for PenG is phenylacetamide) via a hydrophobic pocket, while secondary H-bond contacts with both thiazolidine and the adducted lysine residue is made. As a result, the cross-reactivity against other β-lactam antibiotics is limited. These data demonstrate the relationship between the chemistry of protein-reactive drugs such as penicilloyls, and how their predisposition to generating B cell responses can inform the functional implications at the clonal level.

Highlights

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PenG readily forms immunogenic adducts on lysine sidechains of diverse self- and non-self proteins including complete serum under physiological conditions.

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PenG-protein adductionin vitroorin vivois sufficient to elicit penicillin-specific IgG responses.

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Murine B cell clonotypic responses are characterised by near-uniform antibody binding modes of similar immunogenetic origin.

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The dominant murine PenG-specific clonotype is dominated by benzene ring recognition and correlates with serological cross-reactivity profiles.
Non-canonical hepatic androgen receptor mediates glucagon sensitivity in female mice through the PGC1α/ERRα/mitochondria axis
Authors: Chen Jie , Wu Yuanyuan , Hao Wanyu , You Jia , Wu Lianfeng
Published: November 2023

The hormone glucagon plays a crucial role in maintaining normal blood glucose levels and has recently been found to promote liver lipid catabolism in both clinical and basic research studies. However, the mechanisms by which glucagon signaling synchronizes glucose and lipid metabolism in the liver remain poorly understood. Here, we report that hepatic androgen receptor (AR) functions as a critical mediator of glucagon signaling, contributing to sexual dimorphism in hepatic glucagon sensitivity. The inhibition of AR, either through chemical or genetic means, impairs the ability of glucagon to stimulate gluconeogenesis and lipid catabolism in primary hepatocytes. Notably, female mouse hepatocytes express up to three times more AR than their male littermates. Consequently, they respond to glucagon to a much greater extent in terms of glucose production and lipid catabolism outcomes. Moreover, liver-specific AR knockout impairs the effect of glucagon in inducing blood glucose production, especially in female mice. Mechanistically, we demonstrate that hepatic AR drives a PGC1α/ERRα-mitochondria axis to promote lipid catabolism for liver glucose production in response to glucagon treatment. Together, our study sheds light on the role of hepatic AR in mediating glucagon activity in orchestrating glucose and lipid metabolism, particularly in female mice. These findings may help elucidate the factors responsible for sex differences in glucagon sensitivity and the development of fatty liver disease.
Predicting subject traits from brain spectral signatures: an application to brain ageing
Authors: Jarne Cecilia , Griffin Ben , Vidaurre Diego
Published: November 2023

The prediction of subject traits using brain data is an important goal in neuroscience, with relevant applications in clinical research, as well as in the study of differential psychology and cognition. While previous prediction work has predominantly been done on neuroimaging data, our focus is on electroencephalography (EEG), a relatively inexpensive, widely available and non-invasive data modality. However, EEG data is complex and needs some form of feature extraction for subsequent prediction. This process is sometimes done manually, risking biases and suboptimal decisions. Here we investigate the use of data-driven kernel methods for prediction from single-channels using the the EEG spectrogram, which reflects macro-scale neural oscillations in the brain. Specifically, we introduce the idea of reinterpreting the the spectrogram of each channel as a probability distribution, so that we can leverage advanced machine learning techniques that can handle probability distributions with mathematical rigour and without the need for manual feature extraction. We explore how the resulting technique, Kernel Mean Embedding Regression, compares to a standard application of Kernel Ridge Regression as well as to a non-kernelised approach. Overall, we found that the kernel methods exhibit improved performance thanks to their capacity to handle nonlinearities in the relation between the EEG spectrogram and the trait of interest. We leveraged this method to predict biological age in a multinational EEG data set, HarMNqEEG, showing the method’s capacity to generalise across experiments and acquisition setups.
Thein vitrodynamics of pseudo-vascular network formation
Authors: Oraiopoulou Mariam-Eleni , Couturier Dominique-Laurent , Bunce Ellie V. , Cannell Ian , Golinska Monika , Hannon Gregory , Sakkalis Vangelis , Bohndiek Sarah E.
Published: November 2023

Pseudo-vascular network formation capacityin vitrois considered a key characteristic of vasculogenic mimicry. While many cancer cell lines are known to form pseudo-vascular networks, little is known about the spatiotemporal dynamics of these formations. Here, we present a framework for monitoring and characterising the dynamic formation and dissolution of pseudo-vascular networksin vitro. The framework combines time-resolved optical microscopy with open-source image analysis for network feature extraction and statistical modelling. The framework is demonstrated by comparing diverse cancer cell lines associated with vasculogenic mimicry, then in detecting response to drug compounds proposed to affect formation of vasculogenic mimics. Dynamic datasets collected were analysed morphometrically and a descriptive statistical analysis model was developed in order to measure stability and dissimilarity characteristics of the pseudo-vascular networks formed. Melanoma cells formed the most stable pseudo-vascular networks and were selected to evaluate the response of their pseudo-vascular networks to treatment with axitinib, brucine and tivantinib. Our framework is shown to enable quantitative analysis of both the capacity for network formation, linked vasculogenic mimicry, as well as dynamic responses to treatment.
Pericytes promote more angiogenesis and vasculogenesis than mesenchymal stromal cells in microfluidic chips
Authors: Gonzalez-Rubio Julian , Kubiza Hannah , Koenigs-Werner Hiltrud , Jockenhoevel Stefan , Cornelissen Christian G. , Thiebes Anja Lena
Published: November 2023

The pericyte is a key player in vascularization, protecting endothelial cells from external harm and promoting formation of new vessels and connections when necessary. However, pericytic identity and its relation with other cell types, such as the mesenchymal stromal/stem cells, is highly debated. To compare the behaviour of pericytes and unselected stromal cells in vascularization, we used multichannel microfluidic chips to replicate the two processes of vessel formation: vasculogenesis, thede novovessel formation, and angiogenesis, the sprouting of new vessels from existing ones. In angiogenesis, pericytes promote significantly more and longer sproutings than stromal cells. In vasculogenesis, stromal cells promote the formation of structures ressembling the embryonic capillary plexus, whereas pericytes wrap around the endothelial cells, arresting their division and forcing them into tubulogenesis. Whole-transcriptome sequencing confirms an upregulation of pro-vascularization and cytostatic genes in co-cultures of pericytes and endothelial cells; while stromal cells strongly stimulate mitosis and organelle biogenesis pathways and decrease the release of pro-inflammatory cytokines. In this study, we offer new insights into the pericyte-endothelial cell relation and the mesenchymal stromal cell elusive identity, relevant in both vascular biology and tissue engineering.
aHISplex: an imputation based method for eye, hair and skin colour prediction from low coverage ancient DNA
Authors: Maróti Zoltán , Nyerki Emil , Neparaczki Endre , Török Tibor , Varga Gergely István , Kalmár Tibor
Published: November 2023

The prediction of externally visible traits (eye, hair and skin colours) from DNA can provide valuable information for both contemporary and ancient human populations. The validated HIrisPlex-S method is the primary tool in forensics for phenotyping modern samples. The HIrisPlex-S multiplex PCR assay can handle trace DNA from modern samples, but the analysis of degraded, low coverage ancient DNA (aDNA) presents additional challenges. Genotype imputation has recently proven successful in effectively filling in missing information in aDNA sequences. To assess the feasibility of this approach, we evaluated how key factors, such as genome coverage, minor allele frequency, extent of post mortem damage, and the population origin of the test individual influence the efficiency of imputing HIrisPlex-S markers and predicting phenotypes. We used high coverage sequence data from ancient remains for the evaluation. Our results demonstrate that even with genome coverages as low as 0.1-0.5x, the proposed workflow is capable of predicting phenotypes from degraded ancient (or forensic) WGS data with good accuracy. To aid the archaeogenetics community, we have developed a user-friendly, easily deployable imputation-based framework that includes the new bioinformatics tools and the pre-made reference data sets required for the whole analysis.
HPV and p53 status as precision determinants of head and neck cancer response to DNA-PKcs inhibition in combination with irradiation
Authors: Hayrapetyan Liana , Roth Selina M. , Hovhannisyan Lusine , Medo Matúš , Quintin Aurélie , Ott Julien , Albers Joachim , Aebersold Daniel M. , Zimmer Yitzhak , Medová Michaela
Published: November 2023

Major risk factors of head and neck squamous cell carcinoma (HNSCC) are tobacco use and human papillomavirus (HPV). HPV E6 oncoprotein leads to the degradation of the p53 protein, whereas HPV-negative cancers are frequently associated with TP53 mutations. Peposertib is a potent and selective, orally administered small-molecule inhibitor of the catalytic subunit of the DNA-dependent kinase (DNA-PKcs), a key regulator of non-homologous end joining (NHEJ). NHEJ inhibition along with irradiation (IR)-induced DNA double-strand breaks has the potential to increase antitumor treatment efficacy. Here, we investigated the responses of HNSCC models with distinct HPV and p53 status to treatments with IR, DNA-PKcs inhibition, and their combination.

We observed that IR-induced DNA damage combined with peposertib administration shortly before IR results in decreased cell viability and proliferation and causes DNA repair delay in all the studied HNSCC cell lines. However, our data confirm that the actual cell fate upon this treatment is strongly dependent on cellular p53/HPV status. Cells lacking functional p53 due to its degradation by HPV or due to the presence of a loss-of-function mutation are arrested in the G2 phase of the cell cycle and eliminated by apoptosis whereas p53-proficient HNSCC cell lines undergo senescence. Consequently, HPV+ cancer cell lines and xenografts display stronger and more durable responses and seem to benefit from the combined treatment more than p53-proficient HNSCCs. In conclusion, DNA-PKcs inhibitor peposertib should be further studied as a potential radiosensitizer for HNSCCs, taking into consideration the genetic background and the HPV status of a particular tumor.
Pre-existing Subclones Determine Radioresistance in Rectal Cancer Organoids
Authors: Andel D. , Viergever B.J. , Peters N.A. , Raats D.A.E. , van Schelven S.J. , Intven M.P.W. , Zandvliet M. , Hagendoorn J. , Rinkes I.H.M. Borel , Kranenburg O.
Published: November 2023

More than half of all cancer patients receive radiation therapy, but resistance is commonly observed. Currently, it is unknown whether resistance to radiation therapy is acquired or inherently present. Here, we employed organoids derived from rectal cancer and single-cell whole genome sequencing to investigate the long-term evolution of subclones in response to radiation. Comparing single-cell whole genome karyotypes between unirradiated and irradiated organoids revealed three patterns of subclonal evolution: (i) subclonal persistence, (ii) subclonal extinction, and (iii) subclonal expansion. Only organoids in which subclonal shifts occurred (i.e., expansion or extinction) became more resistant to radiation. Although radioresistant subclones did not share recurrent copy number alterations that could explain their radioresistance, resistance was associated with reduced chromosomal instability; an association that was also observed in 529 human cancer cell lines. These data suggest resistance to radiation is inherently present and associated with reduced chromosomal instability.
Unveiling the Microbial Diversity and Associated Secondary Metabolism on Black Apples
Authors: Cowled Michael S. , Phippen Christopher B. W. , Kromphardt Kresten J. K. , Clemmensen Sidsel E. , Frandsen Rasmus J. N. , Frisvad Jens C. , Larsen Thomas O.
Published: November 2023

Black apples are the late-stage microbial decomposition of apples after having fallen to the ground. This phenomenon is highly comparable from year to year, with the filamentous fungusMonilinia fructigenamost commonly being the first invader, followed byPenicillium expansum. Motivated by the fact that only little chemistry has been reported from apple microbiomes, we set out to investigate the chemical diversity and potential ecological roles of secondary metabolites (SMs) in a total of 38 black apples. Metabolomics analyses were conducted on either whole apples or small excisions of fungal biomass derived from black apples. Annotation of fungal SMs in black apple extracts was aided by cultivation of 15 recently isolated fungal strains on 9 different substrates in an OSMAC approach, leading to identification of 3319 unique chemical features. Only 6.8% were attributable to known compounds based on analysis of HPLC-HRMS/MS data using spectral library matching tools. Of the 1606 features detected in the black apple extracts, 32% could be assigned as fungal-derived, due to their presence in the OSMAC-based training dataset. Notably, the detection of several antifungal compounds clearly indicates the importance of such compounds for invasion of and control of other microbial competitors on apples. In conclusion, the diversity and abundance of microbial SMs on black apples was found to be much higher than that typically observed for other environmental microbiomes. Detection of SMs known to be produced by the six fungal species tested also highlights a succession of fungal growth following the initial invaderM. fructigena.

Importance

Microbial secondary metabolites constitute a significant reservoir of biologically potent and clinically valuable chemical scaffolds. However, their usefulness is hampered by rapidly developing resistance, resulting in reduced profitability of such research endeavours. Hence, it is vital that the ecological role of such microbial secondary metabolites be considered to understand how best to utilise such compounds as chemotherapeutics. Here, we explore an under-investigated environmental microbiome in the case of black apples; a veritable “low-hanging fruit”, with relatively high abundances and diversity of microbially produced secondary metabolites. Using both a targeted and untargeted metabolomics approach, the interplay between metabolites, other microbes and the apple host itself was investigated. This study highlights the surprisingly low incidence of known secondary metabolites in such a system, highlighting the need to study the functionality of secondary metabolites in microbial interactions and complex microbiomes.
Plant-like heliotropism in a photosymbiotic animal
Authors: Lintnerova Eliska , Shaw Callum , Keys Matthew , Brownlee Colin , Modepalli Vengamanaidu
Published: November 2023

Being photosynthetic sessile organisms, plants established heliotropism to track the sun’s position across the sky and allow their vegetative parts to orient accordingly. Here, we report plant-like heliotropic movement in a photosymbiotic sea anemoneAnemonia viridis. Like plants, photosynthesis represents a key energy source in endosymbiotic cnidarians bearing microalgae. We observed thatA. viridisin their natural habitats under sunlight displayed heliotropism or solar tracking by pointing their tentacles towards the sun while remaining sessile, facing east at dawn and west at dusk as they track the sun’s relative position through the day, a phenomenon previously only observed in plants. Solar tracking movements inA. viridisare driven by a light wavelength that prompts photosynthesis in their endosymbionts. The heliotropic response was absent in both bleached (aposymbiotic)A. viridisand in symbioticA. viridiswith chemically inhibited photosynthesis. We revealed a direct correlation between heliotropism and endosymbiont oxygen production inA. viridis. Our findings suggest that photosymbioticA. viridishas likely evolved plant-like heliotropism as an effective way to modulate exposure to solar irradiation for photosynthesis. The study exemplifies how photosynthetic organisms such as plants and photosymbiotic sea anemones, display similar behaviour in response to similar environmental pressures.
Microbial Metamorphosis: Symbiotic bacteria and fungi proliferate during diapause and may enhance overwintering survival in a solitary bee
Authors: Christensen S. M. , Srinivas S. , McFrederick Q. , Danforth B. , Buchmann S. L. , Vannette R. L.
Published: November 2023

Host-microbe interactions underlie the development and fitness of many macroorganisms including bees. While many social bees benefit from vertically transmitted gut bacteria, solitary bees, which comprise the vast majority of species diversity within bees, lack a specialized gut microbiome. Here we examine the composition and abundance of bacteria and fungi throughout the complete life cycle of a ground-nesting solitary beeAnthophora bomboides standfordiana. In contrast to expectations, immature bee stages maintain a distinct core microbiome consisting of Actinobacteria and fungi in the genusMoniliella. Diapausing larval bees hosted the most abundant and distinctive bacteria and fungi, attaining 33 and 52 times their initial copy number, respectively. We tested two adaptive hypotheses regarding microbial functions for overwintering bees. First, using isolated bacteria and fungi, we found thatStreptomycesfrom brood cells inhibited the growth of multiple pathogenic filamentous fungi, suggesting a role in pathogen protection during the long period of diapause. Second, sugar alcohol composition changed in tandem with major changes in microbial abundance suggesting links with bee metabolism or overwintering biology. Our results suggest thatAnthophora bomboideshosts a conserved core microbiome that may provide key fitness advantages through larval development and overwintering, and raises the question of how this microbiome is transmitted between generations. The present work suggests that focus on adult gut microbiomes in solitary bees may overlook microbial symbionts within brood cells that could play diverse roles in bee fitness, and that exploration of microbes associated with immature bees may uncover novel microbial effects on insect hosts.
Engineered immunomodulatory extracellular vesicles derived from epithelial cells acquire capacity for positive and negative T cell co-stimulation in cancer and autoimmunity
Authors: Kugeratski Fernanda G. , LeBleu Valerie S. , Dowlatshahi Dara P. , Sugimoto Hikaru , Arian Kent A. , Fan Yibo , Huang Li , Wells Danielle , Lilla Sergio , Hodge Kelly , Zanivan Sara , McAndrews Kathleen M. , Kalluri Raghu
Published: November 2023

Extracellular vesicles (EVs) are generated by all cells and systemic administration of allogenic EVs derived from epithelial and mesenchymal cells have been shown to be safe, despite carrying an array of functional molecules, including thousands of proteins. To address whether epithelial cells derived EVs can be modified to acquire the capacity to induce immune response, we engineered 293T EVs to harbor the immunomodulatory CD80, OX40L and PD-L1 molecules. We demonstrated abundant levels of these proteins on the engineered cells and EVs. Functionally, the engineered EVs efficiently elicit positive and negative co-stimulation in human and murine T cells. In the setting of cancer and auto-immune hepatitis, the engineered EVs modulate T cell functions and alter disease progression. Moreover, OX40L EVs provide additional benefit to anti-CTLA-4 treatment in melanoma-bearing mice. Our work provides evidence that epithelial cell derived EVs can be engineered to induce immune responses with translational potential to modulate T cell functions in distinct pathological settings.
Linking modulation of bio-molecular phase behaviour with collective interactions
Authors: Qian Daoyuan , Ausserwoger Hannes , Arter William E. , Scrutton Rob M. , Welsh Timothy J. , Kartanas Tadas , Ermann Niklas , Qamar Seema , Fischer Charlotte , Sneideris Tomas , George-Hyslop Peter St , Pappu Rohit V. , Knowles Tuomas P. J.
Published: November 2023

Bio-molecular condensates formed in the cytoplasm of cells are increasingly recognised as key spatiotemporal organisers of living matter, and are implicated in a wide range of functional or pathological processes. This discovery opens up a new avenue for condensate-based applications and a crucial step in controlling this process is to understand the underlying interactions driving condensate formation or dissolution. However, these condensates are highly multi-component assemblies and many inter-component interactions are present, rendering it difficult to identify key promoters of phase separation. In this work, we extend the recently formulated dominance analysis to modulations of condensate formation. By carrying out dilute phase concentration measurements of a single target solute, the theoretical framework allows one to deduce whether the modulator acts on the target solute or another unspecified, auxiliary solute, as well as the attractive/repulsive nature of the added interaction. This serve as a general guide towards deducing possible modulation mechanisms on the molecular level, which can be complemented by orthogonal measurements. As a case study, we investigate the modulation of G3BP1/RNA condensates by the small molecule suramin, and the dominance measurements point towards a dissolution mechanism where suramin acts on G3BP1 to disrupt G3BP1/RNA interactions, as confirmed by a diffusional sizing assay. Our approach and the dominance framework have a high degree of adaptability and can be applied in many other condensate-forming systems.
Netrin1 patterns the dorsal spinal cord through modulation of Bmp signaling
Authors: Alvarez Sandy , Gupta Sandeep , Honeychurch Kaitlyn , Mercado-Ayon Yesica , Kawaguchi Riki , Butler Samantha J.
Published: November 2023

We have identified an unexpected role for netrin1 as a suppressor of bone morphogenetic protein (Bmp) signaling in the developing dorsal spinal cord. Using a combination of gain- and loss-of-function approaches in chicken, embryonic stem cell (ESC), and mouse models, we have observed that manipulating the level of netrin1 specifically alters the patterning of the Bmp-dependent dorsal interneurons (dIs), dI1-dI3. Altered netrin1 levels also change Bmp signaling activity, as measured by bioinformatics, and monitoring phosophoSmad1/5/8 activation, the canonical intermediate of Bmp signaling, and Id levels, a known Bmp target. Together, these studies support the hypothesis that netrin1 acts from the intermediate spinal cord to regionally confine Bmp signaling to the dorsal spinal cord. Thus, netrin1 has reiterative activities shaping dorsal spinal circuits, first by regulating cell fate decisions and then acting as a guidance cue to direct axon extension.
A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts
Authors: Graham Emily B. , Camargo Antonio Pedro , Wu Ruonan , Neches Russell Y. , Nolan Matt , Paez-Espino David , Kyrpides Nikos C. , Jansson Janet K. , McDermott Jason E. , Hofmockel Kirsten S. ,   the Soil Virosphere Consortium
Published: November 2023

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities, and interactions with the soil microbiome remains limited. Here, we present the Global Soil Virus (GSV) Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and comprised of 616,935 uncultivated viral genomes (UViGs) and 38,508 unique viral operational taxonomic units (vOTUs). Rarefaction curves from the GSV Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared vOTUs across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.
Bio-Mol:Pretraining Multimodality Bioactivity Profile for Enhancing Small Molecule Property Prediction
Authors: Yip Hiu Fung , Wei Xiao , Li Zeming , Ren Qing , Cao DongSheng , Zhang Lu , Lu Aiping
Published: November 2023

Non-optimized pharmacokinetic parameters serve as the primary cause of failure in clinical trials of drugs. Therefore, the successful prediction of pharmacokinetic parameters during the pre-clinical stage is crucial for the success of drug candidates. Conventional methods primarily rely on 2D structural information, while advanced models extend the features to other structural-related information or use advanced computational models to improve prediction accuracy. However, to gain a comprehensive understanding of small molecules, integrating bioactivity profiles with chemical structural information is essential. One significant challenge in this integration is the high proportion of missing values within experimentally validated bioactivity profiles for most small molecules. To address this challenge, we introduce Bio-Mol, an artificial intelligence model designed to effectively handle this issue. Bio-Mol utilizes a pretrain and finetune strategy, enabling the incorporation of a large proportion of missing bioactivity profiles during the small molecule representation learning process.

Comprehensive evaluations of Bio-Mol demonstrate a notable improvement in predicting molecule properties. The integration of missing bioactivity profiles enhances the AUROC of average 5.2% compared to the previous state-of-the-art model’s predictions. Furthermore, we explore the potential of Bio-Mol in predicting synergistic drug combinations, highlighting its versatility and broader applications in the field of drug discovery.

The successful implementation of Bio-Mol showcases its efficacy in over-coming the challenges posed by missing bioactivity profile data. This model paves the way for optimizing small molecule pharmacokinetics prediction, providing valuable insights for drug development and discovery processes.
Quantitative Three-dimensional Label-free Digital Holographic Imaging of Cardiomyocyte Size, Ploidy, and Cell Division
Authors: Park Sangsoon , Huang Herman , Ross Ines , Moreno Joseph , Khyeam Sheamin , Simmons Jacquelyn , Huang Guo N. , Payumo Alexander Y.
Published: November 2023

Cardiac regeneration in newborn rodents depends on the ability of pre-existing cardiomyocytes to proliferate and divide. This capacity is lost within the first week of postnatal development when these cells rapidly switch from hyperplasia to hypertrophy, withdraw from the cell cycle, become binucleated, and increase in size. How these dynamic changes in size and ploidy impact cardiomyocyte proliferative potential is not well understood. In this study, we innovate the application of a commercially available digital holographic imaging microscope, the Holomonitor M4, to evaluate the proliferative responses of mononucleated diploid and binucleated tetraploid cardiomyocytes. This instrument coupled with the powerful Holomonitor App Suite software enables long-term label-free quantitative three-dimensional tracking of primary cardiomyocyte dynamics in real-time with single-cell resolution. Our digital holographic imaging results provide direct evidence that mononucleated cardiomyocytes retain significant proliferative potential as most can successfully divide with high frequency. In contrast, binucleated cardiomyocytes exhibit a blunted response to a proliferative stimulus with the majority not attempting to divide at all. Nevertheless, some binucleated cardiomyocytes were capable of complete division, suggesting that these cells still do retain limited proliferative capacity. By quantitatively tracking cardiomyocyte volume dynamics during these proliferative responses, we reveal that both mononucleated and binucleated cells reach a unique size threshold prior to attempted cell division. The absolute threshold is increased by binucleation, which may limit the ability of binucleated cardiomyocytes to divide. By defining the interrelationship between cardiomyocyte size, ploidy, and cell cycle control, we will better understand the cellular mechanisms that drive the loss of mammalian cardiac regenerative capacity after birth.
Prebiotic membrane structures mimic the morphology of purported early traces of life on Earth
Authors: Jordan Seán F. , van Zuilen Mark A. , Rouillard Joti , Martins Zita , Lane Nick
Published: November 2023

Elucidating the most probable compositions of the first cell membranes prior to the origin of life, within a laboratory setting, requires experiments with organic molecules and chemical conditions representative of those present on the early Earth. As such, the membrane forming molecules used in these experiments are described as ‘prebiotically plausible’, i.e., they could have formed through abiotic reactions and be available for membrane formation prior to the emergence of biology. Similarly, the chemical properties of solutions in which these membranes are formed (e.g., pH, temperature, ionic strength) must represent the early Earth environmental conditions under investigation. Here, using a combined confocal and transmission electron microscopy approach, we show that prebiotically plausible organic molecules, in solutions representative of Hadean submarine alkaline hydrothermal vents, form aggregated structures with substantial morphological diversity. The structures hold the potential for use as traces of prebiotic processes in the ancient rock record. In addition, many of the structures are morphologically similar to those which are presented as early microfossils, thus highlighting the limitations of morphological interpretation in these types of studies. Detailed analyses of abiotic organic structures are essential for our understanding of the earliest living organisms on Earth, as well as for our interpretation of any potential biosignatures recovered in the future from extra-terrestrial bodies.