bluuebunny/crossref_metadata_2025 huggingface dataset:
Determinants of genetic diversity in sticklebacks
Authors: Kivikoski Mikko , Feng Xueyun , Löytynoja Ari , Momigliano Paolo , Merilä Juha
Published: March 2023

Understanding what determines species and population differences in levels of genetic diversity has important implications for our understanding of evolution, as well as for the conservation and management of wild populations. Previous comparative studies have emphasized the roles of linked selection, life-history trait variation and genomic properties, rather than pure demography, as important determinants of genetic diversity. However, these findings are based on coarse estimates across a range of highly diverged taxa, and it is unclear how well they represent the processes within individual species. We assessed genome-wide genetic diversity (π) in 45 nine-spined stickleback (Pungitius pungitius) populations and found thatπvaried 15-fold among populations (πmin≈0.00015,πmax≈0.0023) whereas estimates of recent effective population sizes varied 122-fold. Analysis of inbreeding coefficients (FROH) estimated from runs of homozygosity revealed strong negative association betweenπand FROH. Genetic diversity was also negatively correlated with mean body size and longevity, but these associations were not statistically significant after controlling for demographic effects (FROH). The results give strong support for the view that populations’ demographic features, rather than life history differences, are the chief determinants of genetic diversity in the wild.
The Hippo pathway terminal effector TAZ/WWTR1 mediates oxaliplatin sensitivity in colon cancer cells
Authors: Slaninová Věra , Heron-Milhavet Lisa , Robin Mathilde , Jeanson Laura , Kantar Diala , Tosi Diego , Bréhélin Laurent , Gongora Céline , Djiane Alexandre
Published: March 2023

YAP and TAZ, the Hippo pathway terminal transcriptional activators, are frequently upregulated in cancers. In tumor cells, they have been mainly associated with increased tumorigenesis controlling different aspects from cell cycle regulation, stemness, or resistance to chemotherapies. In fewer cases, they have also been shown to oppose cancer progression, including by promoting cell death through the action of the P73/YAP transcriptional complex, in particular after chemotherapeutic drug exposure. Using several colorectal cancer cell lines, we show here that oxaliplatin treatment led to a dramatic core Hippo pathway down-regulation and nuclear accumulation of TAZ. We further show that TAZ was required for the increased sensitivity of HCT116 cells to oxaliplatin, an effect that appeared independent of P73, but which required the nuclear relocalization of TAZ. Accordingly, Verteporfin and CA3, two drugs affecting the activity of YAP and TAZ, showed an antagonistic with oxaliplatin in co-treatments. Our results support thus an early action of TAZ to sensitize cells to oxaliplatin, consistent with a model in which nuclear TAZ in the context of DNA damage and P53 activity pushes cells towards apoptosis.
A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences
Authors: Ordóñez Carlos D. , Mayoral-Campos Carmen , Egas Conceição , Redrejo-Rodríguez Modesto
Published: March 2023

Multiple displacement amplification (MDA) has proven to be a useful technique for obtaining large amounts of DNA from tiny samples in genomics and metagenomics. However, MDA has limitations, such as amplification artifacts and biases that can interfere with subsequent quantitative analysis. To overcome these challenges, alternative methods and engineered DNA polymerase variants have been developed. Here, we present new MDA protocols based on the primer-independent DNA polymerase (piPolB), a replicative-like DNA polymerase endowed with DNA priming and proofreading capacities. These new methods were tested on a genomes mixture containing diverse sequences with high-GC content, followed by deep sequencing. Protocols relying on piPolB as a single enzyme cannot achieve competent amplification due to its limited processivity and the presence ofab initioDNA synthesis. However, an alternative method called piMDA, which combines piPolB with Φ29 DNA polymerases, allows proficient and faithful amplification of the genomes. In addition, the prior denaturation step commonly performed in MDA protocols is dispensable, resulting in a more straightforward protocol. In summary, piMDA outperforms commercial methods in the amplification of metagenomes containing high GC sequences and exhibits similar profiling, error rate, and variant determination as the non-amplified samples.

Graphical abstract

Schematic representation of methods based on multiple displacement amplification (MDA) for whole genome amplification. The diagrams above represent protocols initiated by random primers (RP-MDA) or a DNA primase-generated short DNA primers (PrimPol-MDA) and continued by Φ29DNAP, whereas the schematics below show piPolB-mediated MDA (left) and the piMDA protocol (right), in which piPolB synthesizes DNA strands that are further extended by Φ29DNAP.
Cortical and subcortical substrates of minutes and days-long object value memory in humans
Authors: Farmani Sepideh , Sharifi Kiomars , Ghazizadeh Ali
Published: March 2023

Obtaining valuable objects motivates many of our daily decisions. However, the neural underpinnings of object processing based on human value memory are not yet fully understood. Here, we used whole-brain fMRI to examine activations due to value memory as participants passively viewed objects before, minutes after, and 1-70 days following value training. Significant value memory for objects was evident in the behavioral performance, which nevertheless faded over the days following training. Minutes after training, the occipital, ventral temporal, interparietal, and frontal areas showed strong value discrimination. Days after training, activation in the frontal, temporal, and occipital regions decreased, whereas the parietal areas showed sustained activation. In addition, days-long value responses emerged in certain subcortical regions, including the caudate, ventral striatum, and thalamus. Resting-state analysis revealed that these subcortical areas were functionally connected. Furthermore, the activation in the thalamo-striatal cluster was positively correlated with participants’ performance in days-long value memory. These findings shed light on the neural basis of value memory in humans with implications for object habit formation and cross-species comparisons.
Increased drought resistance in state transition mutants is linked to modified plastoquinone pool redox state
Authors: Leverne Lucas , Roach Thomas , Perreau François , Maignan Fabienne , Krieger-Liszkay Anja
Published: March 2023

Identifying traits that exhibit improved drought resistance is highly important to cope with the challenges of predicted climate change. We investigated the response of state transition mutants to drought. Compared with the wild type, state transition mutants were less affected by drought. Photosynthetic parameters in leaves probed by chlorophyll fluorescence confirmed that mutants possess a more reduced plastoquinone (PQ) pool, as expected due to the absence of state transitions. Seedlings of the mutants showed an enhanced growth of the primary root and more lateral root formation. The photosystem II inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, leading to an oxidized PQ pool, inhibited primary root growth in wild type and mutants, while the cytochromeb6fcomplex inhibitor 2,5-dibromo-3-methyl-6-isopropylbenzoquinone, leading to a reduced PQ pool, stimulated root growth. A more reduced state of the PQ pool was associated with a slight but significant increase in singlet oxygen production. Singlet oxygen may trigger a, yet unknown, signaling cascade promoting root growth. We propose that photosynthetic mutants with a deregulated ratio of photosystem II to photosystem I activity can provide a novel path for improving crop drought resistance.

Summary Statement

Arabidopsis thalianamutants affected in state transitions are more drought resistant.
Antibodies generatedin vitroandin vivoelucidate design of a thermostable ADDomer COVID-19 nasal nanoparticle vaccine
Authors: Buzas Dora , Bunzel H Adrian , Staufer Oskar , Milodowski Emily J , Edmunds Grace L , Bufton Joshua C , Vidana Mateo Beatriz V , Yadav Sathish K N , Gupta Kapil , Fletcher Charlotte , Kavanagh Williamson Maia , Harrison Alexandra , Borucu Ufuk , Capin Julien , Francis Ore , Balchin Georgia , Hall Sophie , Vivoli Vega Mirella , Durbesson Fabien , Vincentelli Renaud , Roe Joe , Wooldridge Linda , Burt Rachel , Anderson J L Ross , Mulholland Adrian J ,   Bristol UNCOVER Group, Hare Jonathan , Bailey Mick , Davidson Andrew D , Finn Adam , Morgan David , Mann Jamie , Spatz Joachim , Garzoni Frederic , Schaffitzel Christiane , Berger Imre
Published: March 2023

COVID-19 continues to damage populations, communities and economies worldwide. Vaccines have reduced COVID-19-related hospitalisations and deaths, primarily in developed countries. Persisting infection rates, and highly transmissible SARS-CoV-2 Variants of Concern (VOCs) causing repeat and breakthrough infections, underscore the ongoing need for new treatments to achieve a global solution. Based on ADDomer, a self-assembling protein nanoparticle scaffold, we created ADDoCoV, a thermostable COVID-19 candidate vaccine displaying multiple copies of a SARS-CoV-2 receptor binding motif (RBM)-derived epitope.In vitrogenerated neutralising nanobodies combined with molecular dynamics (MD) simulations and electron cryo-microscopy (cryo-EM) established authenticity and accessibility of the epitopes displayed. A Gigabody comprising multimerized nanobodies prevented SARS-CoV-2 virion attachment with picomolar EC50. Antibodies generated by immunising mice cross-reacted with VOCs including Delta and Omicron. Our study elucidates nasal administration of ADDomer-based nanoparticles for active and passive immunisation against SARS-CoV-2 and provides a blueprint for designing nanoparticle reagents to combat respiratory viral infections.
CRISPR/Cas9-mediated knockout of the ubiquitin variant UbKEKSreveals a role in regulating nucleolar structures and composition
Authors: Frion Julie , Meller Anna , Marbach Gwendoline , Lévesque Dominique , Roucou Xavier , Boisvert François-Michel
Published: March 2023

Ubiquitination is a post-translational modification responsible for one of the most complex multi-layered communication and regulation system in the cell. Over the past decades, new ubiquitin variants and ubiquitin-like proteins arose to further enrich this mechanism. Among them, the recently discovered ubiquitin variant UbKEKScan specifically target several proteins and yet, functional consequences of this new modification remain unknown. The absence of UbKEKSinduces accumulation of lamin A in the nucleoli, highlighting the need for deeper investigations about protein composition and functions regulation of this highly dynamic and membrane-less compartment. By using data independent acquisition mass spectrometry and microscopy, we show here that despite not impacting protein stability, UbKEKSis required to maintain normal nucleolar organization. The absence of UbKEKSincreases nucleoli’s size and accentuate their circularity while disrupting dense fibrillar component and fibrillar center structures. Moreover, depletion of UbKEKSleads to distinct changes in nucleolar composition. Notably, lack of UbKEKSfavors nucleolar sequestration of known apoptotic regulators such as IFI16 or p14ARF, resulting in an increase of apoptosis in UbKEKSknockout cells observed by flow cytometry and real-time cellular growth monitoring. Overall, the results presented here identifies the first cellular functions of the UbKEKSvariant and lay the foundation stone to establish UbKEKSas a new universal layer of regulation in the already complex ubiquitination system.
Dissecting muscle synergies in the task space
Authors: Reilly David Ó’ , Delis Ioannis
Published: March 2023

The muscle synergy is a guiding concept in motor control research that relies on the general notion of muscles ‘working together’towards task performance. However, although the synergy concept has provided valuable insights into motor coordination, muscle interactions have not been fully characterised with respect to task performance. Here, we address this research gap by proposing a novel perspective to the muscle synergy that assigns specific functional roles to muscle couplings by characterising their task-relevance. Our novel perspective provides nuance to the muscle synergy concept, demonstrating how muscular interactions can ‘work together’in different ways: a) irrespective of the task at hand but also b) redundantly or c) complementarily towards common task-goals. To establish this perspective, we leverage information- and network-theory and dimensionality reduction methods to include discrete and continuous task parameters directly during muscle synergy extraction. Specifically, we introduce co-information as a measure of the task relevance of muscle interactions and use it to categorise such interactions as task-irrelevant (present across tasks), redundant (shared task information) or synergistic (different task information). To demonstrate these types of interactions in real data, we firstly apply the framework in a simple way, revealing its added functional and physiological relevance with respect to current approaches. We then apply the framework to large-scale datasets and extract generalizable and scale-invariant representations consisting of subnetworks of synchronised muscle couplings and distinct temporal patterns. The representations effectively capture the functional interplay between task end-goals and biomechanical affordances and the concurrent processing of functionally similar and complementary task information. The proposed framework unifies the capabilities of current approaches in capturing distinct motor features while providing novel insights and research opportunities through a nuanced perspective to the muscle synergy.
Creation of Advance Construction of CRISPR-Cas9 via using Multi Round Gateway Cloning
Authors: Jameel M. Rizwan
Published: March 2023

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 (CRISPR-associated system) is used to edit specific genomic sequences with precision and efficacy. CRISPR/Cas9 system mediated double strand binding site through error-prone non homologous end joining repair in targeted sequences, which the deletion or insertion can be achieved by knock out gene. Creation advance construct of CRISPR/Cas9 of soluble starch synthase II-1, 2 and 3 (SSSII) genes in single destination binary vector through multi round LR reaction of Gateway technology. Gateway cloning system developed the suitable for the site-specific DNA recombination of lambda-bacteriophage andccdBthe cytotoxic protein, which is poisonous to most E. coli strains. A genetic transformation vector designed with appropriate gRNAs, Cas9, and antibiotic resistance was used to create SSSII knockout mutants.
Uncovering the Morphological Evolution of Language-Relevant Brain Areas
Authors: Gallardo Guillermo , Eichner Cornelius , Sherwood Chet C. , Hopkins William D. , Anwander Alfred , Friederici Angela D.
Published: March 2023

Human language is supported by a cortical network involving Broca’s area which comprises Brodmann Areas 44 and 45 (BA44, BA45). While cytoarchitectonic homolog areas have been identified in nonhuman primates, it remains unknown how these regions evolved to support human language. Here, we use histological data and advanced cortical registration methods to precisely compare the morphology of BA44 and 45 between humans and chimpanzees. We found a general expansion of Broca’s areas in humans, with the left BA44 enlarging the most, growing anteriorly into a region known to process syntax. Together with recent functional studies, our findings show that BA44 evolved from a purely action-related region to a more expanded region in humans, with a posterior portion supporting action and an anterior portion supporting syntactic processes. Furthermore, our findings provide a solution for the longstanding debate concerning the structural and functional evolution of Broca’s area and its role in action and language.
Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples
Authors: Spangenberg Jannes , zu Siederdissen Christian Höner , Žarković Milena , Triebel Sandra , Rose Ruben , Christophersen Christina Martínez , Paltzow Lea , Hegab Mohsen M. , Wansorra Anna , Srivastava Akash , Krumbholz Andi , Marz Manja
Published: March 2023

Oxford Nanopore Technologies (ONT) allows direct sequencing of ribonucleic acids (RNA) and, in addition, detection of possible RNA modifications due to deviations from the expected ONT signal. The software available so far for this purpose can only detect a small number of modifications. Alternatively, two samples can be compared for different RNA modifications. We presentMagnipore, a novel tool to search for significant signal shifts between samples of Oxford Nanopore data from similar or related species.Magniporeclassifies them into mutations and potential modifications. We useMagniporeto compare SARS-CoV-2 samples. Included were representatives of the early 2020s Pango lineages (n=6), samples from Pango lineages B.1.1.7 (n=2, Alpha), B.1.617.2 (n=1, Delta), and B.1.529 (n=7, Omicron).Magniporeutilizes position-wise Gaussian distribution models and a comprehensible significance threshold to find differential signals. In the case of Alpha and Delta,Magniporeidentifies 55 detected mutations and 15 sites that hint at differential modifications. We predicted potential virus-variant and variant-group-specific differential modifications.Magniporecontributes to advancing RNA modification analysis in the context of viruses and virus variants.
CLN3 deficiency leads to neurological and metabolic perturbations during early development
Authors: Heins-Marroquin Ursula , Singh Randolph R. , Perathoner Simon , Gavotto Floriane , Ruiz Carla Merino , Patraskaki Myrto , Gomez-Giro Gemma , Borgmann Felix Kleine , Meyer Melanie , Carpentier Anaïs , Warmoes Marc O. , Jäger Christian , Mittelbronn Michel , Schwamborn Jens C. , Cordero-Maldonado Maria Lorena , Crawford Alexander D. , L. Schymanski Emma , Linster Carole
Published: March 2023

Juvenile Neuronal Ceroid Lipofuscinosis (or Batten disease) is an autosomal recessive, rare neurodegenerative disorder that affects mainly children above the age of 5 years and is most commonly caused by mutations in the highly conservedCLN3gene. Here, we generatedcln3morphants and stable mutant lines in zebrafish. Although neither morphant nor mutantcln3larvae showed any obvious developmental or morphological defects, behavioral phenotyping of the mutant larvae revealed higher basal activity, hyposensitivity to abrupt light changes and hypersensitivity to pro-convulsive drugs. Importantly, in-depth metabolomics and lipidomics analyses revealed significant accumulation of several glycerophosphodiesters (GPDs) and a global decrease of bis(monoacylglycero)phosphate (BMP) species, two classes of molecules previously proposed as potential biomarkers forCLN3disease based on independent studies in other organisms. We could also demonstrate GPD accumulation in human-induced pluripotent stem cell-derived cerebral organoids carrying a pathogenic variant forCLN3. Our models revealed that GPDs accumulate at very early stages of life in the absence of functional CLN3 and highlight glycerophosphoinositol and BMP as promising biomarker candidates for pre-symptomaticCLN3disease.
Where and when local adaptation happens: lessons from the European barn owl (Tyto alba)
Authors: Corval Hugo , Cumer Tristan , Topaloudis Alexandros , Roulin Alexandre , Goudet Jérôme
Published: March 2023

Climatic variations subject living species to evolutionary stresses and shape their distributions. Since the Last Glacial Maximum (LGM) and the subsequent temperature rise, species (re-) colonised higher latitudes. Among the evolutionary mechanisms involved during this process, local adaptation is thought to be one of the keystones of species persistence. However, its relative role and location in space remain elusive. The Western Palearctic barn owl (Tyto alba) recolonised Europe after the LGM (from the Italian and Iberic peninsulas) and offers an excellent opportunity to study local adaptation at the continental scale. Here, we modelled the evolution of the barn owl’s ecological niche since LGM and showed that the birds probably followed its shift towards the North during the recolonisation. To identify traces of local adaptation, we scanned the entire genomes of 74 owls from 9 European populations using both Tajima’s D and population-specific FST and associated genomic variants to temperature and precipitation through a Redundancy analysis. The combination of these methods yielded a total of 394 genomic windows putatively involved in the local adaptation distributed over all populations. Interestingly, our results identified a large region under selection in both refugial populations, consistent with climate change and ecological convergence in the two peninsulas. This study shed light on the genomic basis of local adaptation of the European barn owl, emphasised the importance of considering the ecological niche as a dynamic entity and paved the way to a better understanding of where and how local adaptation happens in a context of postglacial recolonisation.
Do inoculated microbial consortia perform better than single strains in living soil? A meta-analysis
Authors: Liu Xipeng , Mei Siyu , Salles Joana Falcão
Published: March 2023

Microbial consortium inoculation has been proposed as a natural-based strategy to safeguard multiple ecosystem services. Still, its empirical effects and comparisons to single-species inoculation have yet to be systematically quantified. In this global meta-analysis of 51 live-soil studies, we compared the impact (mean and variability) of single-species and consortium inoculations on biofertilization and bioremediation. Our results showed that both single-species and consortium inoculations increased plant growth by 29% and 48%, respectively, and pollution remediation by 48% and 80%, respectively, compared with non-inoculated treatments. We revealed the potential mechanisms contributing to the effectiveness of consortium inoculation, which are associated with the diversity of inoculants and the synergistic effect between frequently used inoculums (e.g.,BacillusandPseudomonas). Despite a reduction in efficacy in field settings compared to greenhouse results, consortium inoculation had a more significant overall advantage under various conditions. We recommend increasing original soil organic matter, N, and P content and regulating soil pH to 6-7 to achieve a better inoculation effect. Overall, these findings support the use of microbial consortia for improved biofertilization and bioremediation in living soil and suggest perspectives for constructing and inoculating beneficial microbial consortia.
Norovirus MLKL-like pore forming protein initiates programed cell death for viral egress
Authors: Wang Guoxun , Zhang Di , Orchard Robert , Hancks Dustin C. , Reese Tiffany A.
Published: March 2023

Non-enveloped viruses require cell lysis to release new virions from infected cells, suggesting that these viruses require mechanisms to induce cell death. Noroviruses are one such group of viruses, but a mechanism of norovirus-infection triggered cell death and lysis are unknown. Here we have identified a molecular mechanism of norovirus-induced cell death. We found that the norovirus-encoded NTPase contains a N-terminal four helix bundle domain homologous to the pore forming domain of the pseudokinase Mixed Lineage Kinase Domain-Like (MLKL). Norovirus NTPase acquired a mitochondrial localization signal, thereby inducing cell death by targeting mitochondria. NTPase full length (NTPase-FL) and N-terminal fragment (NTPase-NT) bound mitochondrial membrane lipid cardiolipin, permeabilized mitochondrial membrane and induced mitochondrial dysfunction. Both the N-terminal region and the mitochondrial localization motif of NTPase were essential for cell death, virus egress from cells and virus replication in mice. These findings suggest that noroviruses stole a MLKL-like pore forming domain and co-opted it to facilitate viral egress by inducing mitochondrial dysfunction.
Harnessing PROTAC technology to combat stress hormone receptor activation
Authors: Gazorpak Mahshid , Hugentobler Karina M. , Paul Dominique , Germain Pierre-Luc , Matthis Kei , Rudolf Remo , Barrenechea Sergio Mompart , Kretschmer Miriam , Fischer Vincent , Xue Xiaohan , Privitera Mattia , Ivanova Iryna , Hierlemann Andreas , Meijer Onno C. , Carreira Erick M. , Bohacek Johannes , Gapp Katharina
Published: March 2023

Counteracting the overactivation of glucocorticoid receptors (GR) is an important therapeutic goal in stress-related psychiatry and beyond. The only clinically approved GR antagonist lacks selectivity and induces unwanted side effects. To complement existing tools of small-molecule-based inhibitors, we present a highly potent, novel catalytically-driven GR degrader, KH-103, based on proteolysis-targeting chimera technology. This selective degrader enables immediate and reversible GR depletion that is independent of genetic manipulation and circumvents transcriptional adaptations to inhibition. KH-103 achieves passive inhibition, preventing agonistic induction of gene expression, and significantly averts the GR’s genomic effects compared to two currently available inhibitors. Application in primary-neuron cultures revealed the dependency of a glucocorticoid-induced increase in spontaneous calcium activity on GR. Finally, we present a proof of concept for application in-vivo. KH-103 opens opportunities for a more lucid interpretation of GR functions with translational potential.
Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping
Authors: Foran Gregory , Hallam Ryan Douglas , Megaly Marvel , Turgambayeva Anel , Antfolk Daniel , Li Yifeng , Luca Vincent C. , Necakov Aleksandar
Published: March 2023

The Notch receptor is a pleiotropic signaling protein that translates intercellular ligand interactions into changes in gene expressionviathe nuclear localization of the Notch intracellular Domain (NICD). Using a combination of immunohistochemistry, RNAin situ,Optogenetics and super-resolution live imaging of transcription in human cells, we show that the N1ICD can form condensates that positively facilitate Notch target gene expression. We determined that N1ICD undergoes Phase Separation Coupled Percolation (PSCP) into transcriptional condensates, which recruit, enrich, and encapsulate a broad set of core transcriptional proteins. We show that the capacity for condensation is due to the intrinsically disordered transcriptional activation domain of the N1ICD. In addition, the formation of such transcriptional condensates acts to promote Notch-mediated super enhancer-looping and concomitant activation of the MYC protooncogene expression. Overall, we introduce a novel mechanism of Notch1 activity in which discrete changes in nuclear N1ICD abundance are translated into the assembly of transcriptional condensates that facilitate gene expression by enriching essential transcriptional machineries at target genomic loci.
Parallel genetic adaptation ofBacillus subtilisto different plant species
Authors: Hu Guohai , Wang Yue , Blake Christopher , Nordgaard Mathilde , Liu Xin , Wang Bo , Kovács Ákos T.
Published: March 2023

Plant growth-promoting rhizobacteria benefit plants by stimulating their growth or protecting them against phytopathogens. Rhizobacteria must colonise and persist on plant roots to exert their benefits. However, little is known regarding the processes by which rhizobacteria adapt to different plant species, or behave under alternating host plant regimes. Here, we used experimental evolution and whole-population whole-genome sequencing to analyse howBacillus subtilisevolves onArabidopsis thalianaand tomato seedlings, and under an alternating host plant regime, in a static hydroponic setup. We observed parallel evolution across multiple levels of biological organisation in all conditions, which was greatest for the two heterogeneous, multi-resource spatially-structured environments at the genetic level. Species-specific adaptation at the genetic level was also observed, possibly caused by the selection stress imposed by different host plants. Furthermore, a trade-off between motility and biofilm development was supported by mutational changes in motility– and biofilm-related genes. Finally, we identified several condition-specific and common targeted genes in different environments by comparing three differentB. subtilisbiofilm adaptation settings. The results demonstrate a common evolutionary pattern whenB. subtilisis adapting to the plant rhizosphere in similar conditions, and reveal differences in genetic mechanisms between different host plants. These findings will likely support strain improvements for sustainable agriculture.

Data summary

Sequencing data associated with this article are available in the CNGB Sequence Archive (CNSA) [1] of the China National GeneBank DataBase (CNGBdb) [2] under accession numbers CNP0002416 and CNP0003952. Strain data for the DK1042 ancestor are available under accession number CNP0002416.

Impact statement

For rhizobacteria to benefit plant growth and protect against phytopathogens, bacteria must colonise and persist on plant roots. Understanding how rhizobacteria adapt to different plant species will assist strain development in sustainable agriculture. To explore the rhizobacterial adaptation process for different plant species and alternating host regimes,B. subtiliswas experimentally evolved onA. thalianaor tomato roots, or an alternating host regime. Both parallel and species-specific adaptation was revealed at the genetic level. Analysis of the trade-off between motility and biofilm formation revealed several condition-specific and commonly targeted genes based on experimentally evolvingB. subtilisbiofilms.
Adaptive Expression of Engrams by Retroactive Interference
Authors: Autore Livia , O’Leary James D. , Ortega-de San Luis Clara , Ryan Tomás J.
Published: March 2023

Long-term memories are stored as stable configurations of neuronal ensembles, termed engrams. While investigation of engram cell properties and functionality in memory recall has been extensive, less is known about how engram cells are affected by forgetting. We describe a form of interference-based forgetting using an object memory behavioral paradigm. By using activity-dependent cell labelling, we show that although retroactive interference results in decreased engram cell reactivation during recall trials, optogenetic stimulation of the labelled engram cells is sufficient to induce memory retrieval. Forgotten engrams may also be reinstated via the presentation of similar or related environmental information. Furthermore, we demonstrate that engram activity is necessary for interference to occur. Taken together, these findings indicate that retroactive interference modulates engram expression in a manner that is both reversible and updatable. Retroactive inference may constitute a form of adaptive forgetting, where in everyday life new perceptual and environmental inputs modulate the natural forgetting process.
Novel in-silico predicted matrikines are differential mediators of in vitro and in vivo cellular metabolism
Authors: Jariwala Nathan , Ozols Matiss , Eckersley Alexander , Mambwe Bezaleel , Watson Rachel E B , Zeef Leo , Gilmore Andrew , Debelle Laurent , Bell Mike , Bradley Eleanor J , Doush Yegor , Courage Carole , Leroux Richard , Peschard Olivier , Mondon Philippe , Ringenbach Caroline , Bernard Laure , Pitois Aurelien , Sherratt Michael J
Published: March 2023

The exogenous application of small peptides can beneficially affect clinical skin appearance (wrinkles) and architecture (collagen and elastic fibre deposition and epidermal thickness). However, the discovery of new bioactive peptides has not been underpinned by any guiding hypothesis. As endogenous extracellular matrix (ECM)-derived peptides produced during tissue remodelling can act as molecular signals influencing cell metabolism, we hypothesised that protease cleavage site prediction could identify putative novel matrikines with beneficial activities. Here, we present anin silicotoin vivodiscovery pipeline, which enables the prediction and characterisation of peptide matrikines which differentially influence cellular metabolismin vitro. We use this pipeline to further characterise a combination of two novel ECM peptide mimics (GPKG and LSVD) which actin vitroto enhance the transcription of ECM organisation and cell proliferation genes andin vivoto promote epithelial and dermal remodelling. This pipeline approach can both identify new matrikines and provide insights into the mechanisms underpinning tissue homeostasis and repair.
Development of aPlasmodium vivaxbiobank for functionalex vivoassays
Authors: Dash Rashmi , Skillman Kristen M. , Pereira Ligia , Mascarenhas Anjali , Dass Sheena , Walke Jayashri , Almeida Anvily , Fernandes Mezia , Gomes Edwin , White John , Chery-Karschney Laura , Khandeparkar Anar , Rathod Pradipsinh K. , Duraisingh Manoj T. , Kanjee Usheer
Published: March 2023

Background

Plasmodium vivaxis the second most prevalent cause of malaria yet remains challenging to study due to the lack of a continuousin vitroculture system, highlighting the need to establish a biobank of clinical isolates with multiple freezes per sample for use in functional assays. Different methods for cryopreserving parasite isolates were compared and subsequently the most promising one was validated. Enrichment of early- and late-stage parasites and parasite maturation were quantified to facilitate assay planning.

Methods

In order to compare cryopreservation protocols, nine clinicalP. vivaxisolates were frozen with four glycerolyte-based mixtures. Parasite recovery post thaw, post KCl-Percoll enrichment and in short-termin vitroculture was measured via slide microscopy. Enrichment of late-stage parasites by magnetic activated cell sorting (MACS) was measured. Short and long-term storage of parasites at either -80°C or liquid nitrogen were also compared.

Results

Of the four cryopreservation mixtures, one mixture (glycerolyte:serum:RBC at a 2.5:1.5:1 ratio) resulted in improved parasite recovery and statistically significant (P<0.05) enhancement in parasite survival in short-termin vitroculture. A parasite biobank was subsequently generated using this protocol resulting in a collection with 106 clinical isolates, each with 8 vials. The quality of the biobank was validated by measuring several factors from 47 thaws: the average reduction in parasitemia post-thaw (25.3%); the average fold enrichment post KCl-Percoll (6.65-fold); and the average percent recovery of parasites (22.0%, measured from 30 isolates). During short-termin vitroculture, robust maturation of ring stage parasites to later stages (>20% trophozoites, schizonts and gametocytes) was observed in 60.0% of isolates by 48 hours. Enrichment of mature parasite stages via MACS showed good reproducibility, with an average 30.0% post-MACS parasitemia and an average 5.30 × 105parasites/vial. Finally, the effect of storage temperature was tested, and no large impacts from short-term (7 day) or long term (7 – 10 year) storage at -80°C on parasite recovery, enrichment or viability was observed.

Conclusions

Here, an optimized freezing method forP. vivaxclinical isolates is demonstrated as a template for the generation and validation of a parasite biobank for use in functional assays.
Multifaceted luminance gain control beyond photoreceptors inDrosophila
Authors: Ketkar Madhura D. , Shao Shuai , Gjorgjieva Julijana , Silies Marion
Published: March 2023

Animals navigating in natural environments must handle vast changes in their sensory input. Visual systems, for example, handle changes in luminance at many timescales, from slow changes across the day to rapid changes during active behavior. To maintain luminance-invariant perception, visual systems must adapt their sensitivity to changing luminance at different timescales. We demonstrate that luminance gain control in photoreceptors alone is insufficient to explain luminance invariance at both fast and slow timescales and reveal the algorithms that adjust gain past photoreceptors in the fly eye. We combined imaging and behavioral experiments with computational modeling to show that, downstream of photoreceptors, circuitry taking input from the single luminance-sensitive neuron type L3 implements gain control at fast and slow timescales. This computation is bidirectional in that it prevents underestimation of contrasts in low luminance and overestimation in high luminance. An algorithmic model disentangles these multifaceted contributions and shows that the bidirectional gain control occurs at both timescales. The model implements a nonlinear interaction of luminance and contrast to achieve gain correction at fast timescales and a dark-sensitive channel to improve the detection of dim stimuli at slow timescales. Together, our work demonstrates how a single neuronal channel performs diverse computations to implement gain control at multiple timescales that are together important for navigation in natural environments.

Significance Statement

Luminance varies slowly throughout the day, or rapidly during movements. Yet, animals show luminance-invariant behaviors to visual cues across these scenarios. Combining in vivo imaging, behavioral analyses and computational modeling, we here show that diverse luminance gain control operations required for robust visual processing exist in the fly visual circuitry beyond photoreceptors. Despite relying on a single luminance-sensitive neuron type, this luminance gain control is multifaceted, in that it achieves both gain increments and decrements at two different timescales. Overall, the study sheds light on a circuit gain control strategy operating at multiple timescales, which together challenge luminance-invariant visual behaviors in natural environments.
Polθ is phosphorylated by Polo-like kinase 1 (PLK1) to enable repair of DNA double strand breaks in mitosis
Authors: Gelot Camille , Kovacs Marton Tibor , Miron Simona , Mylne Emilie , Ghouil Rania , Popova Tatiana , Dingli Florent , Loew Damarys , Guirouilh-Barbat Josée , Del Nery Elaine , Zinn-Justin Sophie , Ceccaldi Raphael
Published: March 2023

DNA double strand breaks (DSBs) are deleterious lesions that challenge genome integrity. To mitigate this threat, human cells rely on the activity of multiple DNA repair machineries that are tightly regulated throughout the cell cycle1. In interphase, DSBs are mainly repaired by non-homologous end joining (NHEJ) and homologous recombination (HR)2. However, these pathways are completely inhibited in mitosis3–5, leaving the fate of mitotic DSBs unknown. Here we show that DNA polymerase theta (Polθ)6repairs mitotic DSBs and thereby maintains genome integrity. In contrast to other DSB repair factors, Polθ function is activated in mitosis upon phosphorylation by the Polo-like kinase 1 (PLK1). Phosphorylated Polθ is recruited to mitotic DSBs, where it mediates joining of broken DNA ends, while halting mitotic progression. The lack of Polθ leads to a shortening of mitotic duration and defective repair of mitotic DSBs, resulting in a loss of genome integrity. In addition, we identify mitotic Polθ repair as the underlying cause of the synthetic lethality between Polθ and HR. Our findings reveal the critical importance of mitotic DSB repair for maintaining genome stability.
Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer
Authors: Wortmann Esther , Osswald Annika , Wylensek David , Kuhls Stephanie , Coleman Olivia I. , Ducarmon Quinten , Liang Wei , Treichel Nicole , Schumacher Fabian , Volet Colin , Matysik Silke , Kleigrewe Karin , Gigl Michael , Rohn Sascha , Kleuser Burkhard , Liebisch Gerhard , Schnieke Angelika , Bernier-Latmani Rizlan , Zeller Georg , Haller Dirk , Flisikowski Krzysztof , Ocvirk Soeren , Clavel Thomas
Published: March 2023

Western diet is an important risk factor for the development of sporadic colorectal cancer (CRC). Dietary fat stimulates bile acid (BA) production by the host and their conversion to secondary BAs by 7α-dehydroxylating (7αDH+) bacteria, but causal proof of their tumor-promoting effectsin vivois lacking. To address this, we performed feeding studies in a genetically engineered pig model of CRC combined with multi-omics analyses and gnotobiotic mouse studies. Western diet worsened the disease phenotype inAPC1311/+pigs. This was accompanied by microbiota changes, increased levels of the secondary bile acid deoxycholic acid (DCA), and higher colonic epithelial cell proliferation. The latter was counteracted by using the BA-scavenging drug colestyramine. Metagenomic analysis across multiple cohorts revealed higher occurrence ofbai(BA inducible) operons fromClostridium scindensand close relatives in stool of CRC subjects (n = 1,034). Using two gnotobiotic mouse models of CRC, we demonstrate that colonization with 7αDH+ bacteria (C. scindensorExtibacter muris) increased colonic tumor loads. This work provides clear evidence for the causal role of microbiome-derived DCA production in CRC under detrimental dietary conditions, opening avenues for future preventive strategies.
High-level cognition is supported by information-rich but compressible brain activity patterns
Authors: Owen Lucy L. W. , Manning Jeremy R.
Published: March 2023

Brain activity patterns are highly flexible and often complex, but also highly structured. Here we examined how fundamental properties of brain activity patterns relate to ongoing cognitive processes. To this end, we applied dimensionality reduction algorithms and pattern classifiers to functional neuroimaging data collected as participants listened to a story, temporally scrambled versions of the story, or underwent a resting state scanning session. These experimental conditions were intended to require different depths of processing and inspire different levels of cognitive engagement. We considered two primary aspects of the data. First, we treated the maximum achievable decoding accuracy across participants as an indicator of the “informativeness” of the recorded patterns. Second, we treated the number of features (components) required to achieve a threshold decoding accuracy as a proxy for the “compressibility” of the neural patterns (where fewer components indicate greater compression). Overall, we found that the peak decoding accuracy (achievable without restricting the numbers of features) was highest in the intact (unscrambled) story listening condition. However, the number of features required to achieve comparable classification accuracy was also lowest in the intact story listening condition. Taken together, our work suggests that our brain networks flexibly reconfigure according to ongoing task demands, and that the activity patterns associated with higher-order cognition and high engagement are both more informative and more compressible than the activity patterns associated with lower-order tasks and lower levels of engagement.

Significance Statement

How our brains respond to ongoing experiences depends on what we are doing and thinking about, among other factors. To study how brain activity reflects ongoing cognition, we examined two fundamental aspects of brain activity under different cognitive circumstances: informativeness and compressibility. Informativeness refers to the extent to which brain patterns are both temporally specific and consistent across different people. Compressibility refers to how robust the informativeness of brain patterns is to dimensionality reduction. Brain activity evoked by higher-level cognitive tasks are both more informativeandmore compressible than activity evoked by lower-level tasks. Our findings suggest that our brains flexibly reconfigure themselves to optimize different aspects of how they function according to ongoing cognitive demands.
Genome sequence and annotation ofPericonia digitata, a promising biocontrol agent of phytopathogenic oomycetes
Authors: Bovio Elena , Rancurel Corinne , Seassau Aurélie , Magliano Marc , Gislard Marie , Loisier Anaïs , Kuchly Claire , Ponchet Michel , Danchin Etienne G.J. , Van Ghelder Cyril
Published: March 2023

ThePericoniafungal genus belongs to the phylum Ascomycota, order Pleosporales, family Periconiaceae.Periconiaare found in many habitats but little is known about their ecology. Several species from this genus produce bioactive molecules.Periconia digitataextracts were shown to be deadly active against the pine wilt nematode. Furthermore,P. digitatawas shown to inhibit plant pathogenic oomycetePhytophthora parasitica. BecauseP. digitatahas great potential as a biocontrol agent and high quality genomic resources are still lacking in the Periconiaceae family, we generated long-read genomic data forP. digitata. Using the PacBio Hifi sequencing technology, we obtained a highly-contiguous genome assembled in 13 chromosomes and totalling ca. 39 Mb. In addition, we produced a reference transcriptome, based on 12 different culture conditions, and proteomic data to support the genome annotation. Besides representing a new reference genome within the Periconiaceae, this work will contribute to our better understanding of the Eukaryotic tree of life and opens new possibilities in terms of biotechnological applications.
Enveloped viruses pseudotyped with mammalian myogenic cell fusogens target skeletal muscle for gene delivery
Authors: Hindi Sajedah M. , Petrany Michael J. , Greenfeld Elena , Focke Leah C. , Cramer Alyssa A.W. , Whitt Michael A. , Prasad Vikram , Chamberlain Jeffrey S. , Podbilewicz Benjamin , Millay Douglas P.
Published: March 2023

Entry of enveloped viruses into cells is mediated by fusogenic proteins that form a complex between membranes to drive rearrangements needed for fusion. Skeletal muscle development also requires membrane fusion events between progenitor cells to form multinucleated myofibers. Myomaker and Myomerger are muscle-specific cell fusogens, but do not structurally or functionally resemble classical viral fusogens. We asked if the muscle fusogens could functionally substitute for viral fusogens, despite their structural distinctiveness, and fuse viruses to cells. We report that engineering of Myomaker and Myomerger on the membrane of enveloped viruses leads to specific transduction of skeletal muscle. We also demonstrate that locally and systemically injected virions pseudotyped with the muscle fusogens can deliver micro-Dystrophin (μDys) to skeletal muscle of a mouse model of Duchenne muscular dystrophy. Through harnessing the intrinsic properties of myogenic membranes, we establish a platform for delivery of therapeutic material to skeletal muscle.