bluuebunny/crossref_metadata_2025 huggingface dataset:
Catching more air: A method to spatially quantify aerial triazole resistance inAspergillus fumigatus
Authors: Kortenbosch Hylke H. , van Leuven Fabienne , van den Heuvel Cathy , Schoustra Sijmen S. , Zwaan Bas J. , Snelders Eveline
Published: November 2022

Airborne triazole-resistant spores of the human fungal pathogenAspergillus fumigatusare a significant human health problem as the agricultural use of triazoles has selected for cross-resistance to life-saving clinical triazoles. However, how to measure the health risk posed by these inhaled spores remains unclear. Here, we describe a method for cost-effective wide-scale outdoor air sampling to measure both spore abundance as well as antifungal resistance fractions. We show that prolonged outdoor exposure of sticky seals placed in delta traps, when combined with a two-layered cultivation approach, can consistently yield sufficient colony-forming units (CFUs) for the quantitative assessment of aerial resistance levels at a spatial scale that was up to now unfeasible. When testing our method in a European pilot sampling of 12 regions, we demonstrate that the triazole-resistant fraction of airborne spores is widespread and varies between 0 and 0.1 for itraconazole (∼4 mg/L) and voriconazole (∼2 mg/L). This method facilitates the assessment of health risks by pinpointing potential hot- and coldspots of environmental resistance selection. This efficient and accessible air sampling protocol opens up extensive options for fine-spatial sampling and surveillance studies.

IMPORTANCE

Aspergillus fumigatusis an opportunistic fungal pathogen which humans and other animals are primarily exposed to through inhalation. Due to the limited availability of antifungals, resistance to the first choice class of antifungals, the triazoles, inA. fumigatuscan make infections by this fungus untreatable and uncurable. Here we describe and validate a method that allows for the quantification of airborne resistance fractions and quick genotyping ofA. fumigatusTR-types. Our pilot study provides proof of concept of the suitability of the method for use by citizen scientists for large-scale spatial air sampling. Spatial air sampling opens up extensive options for surveillance, health-risk assessment, and studying the ecology ofA. fumigatusand the development of triazole resistance.
Shigellainduces epigenetic reprogramming of zebrafish neutrophils
Authors: Gomes Margarida C. , Brokatzky Dominik , Bielecka Magdalena K. , Wardle Fiona C. , Mostowy Serge
Published: November 2022

Trained immunity is a long-term memory of innate immune cells, generating an improved response upon re-infection.Shigellais an important human pathogen and inflammatory paradigm for which there is no effective vaccine. Using zebrafish larvae we demonstrate that afterShigellapriming neutrophils are more efficient at bacterial clearance. We observe thatShigella-induced protection is non-specific and long-lasting, and is unlike training by BCG and β-glucan. Analysis of histone ChIP-seq on primed neutrophils revealed thatShigellatraining deposits the active H3K4me3 mark on promoter regions of 1612 genes, significantly changing the epigenetic landscape of neutrophils towards enhanced microbial recognition and mitochondrial ROS production. Finally, we demonstrate that mitochondrial ROS plays a key role in enhanced antimicrobial activity of trained neutrophils. It is envisioned that signals and mechanisms we discover here can be used in other vertebrates, including humans, to suggest new therapeutic strategies involving neutrophils to control bacterial infection.
Nuclei isolation protocol from diverse angiosperm species
Authors: Li Chenxin , Wood Joshua C. , Deans Natalie C. , Jarrell Anne Frances , Martin Dionne , Mailloux Kathrine , Wang Yi-Wen , Buell C. Robin
Published: November 2022

The ability to generate intact nuclei is crucial to the success of a variety of genomics experiments, such as Assay for Transposase-Accessible Chromatin using sequencing (ATAC- seq), Cleavage Under Targets and Tagmentation (CUT&Tag), and nuclei-based single cell sequencing (e.g., single nuclei ATAC-seq and single nuclei RNA-seq). For plants, the presence of the cell wall presents significant challenges in the isolation of nuclei from tissues. Here, we report an optimized nuclei isolation protocol that can be adapted for diverse angiosperm species, including maize, soybean, tomato, potato, and wheat, starting from fresh or frozen tissues. Nuclei release is achieved through chopping tissue on ice, where a key parameter affecting nuclei integrity is the concentration of detergent TritonX-100 in the nuclei isolation buffer. The method is simple, quick, and largely centrifugation-free, in which debris is removed by serial filtration. Initial nuclei release and filtration can be performed within 20 min. Fluorescence activated nuclei sorting is then used for final nuclei purification to remove other organelles such as plastids. The protocol uses 500 mg or less plant tissue as input and typically yields at least 100,000 – 200,000 purified nuclei per sample, a common input amount for downstream experiments. Throughout the protocol, we provide guidelines for optimization if performing nuclei isolation from a given species and tissue for the first time.
Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock
Authors: Tariq Daniyal , Maurici Nicole , Bartholomai Bradley M. , Chandrasekaran Siddarth , Dunlap Jay C. , Bah Alaji , Crane Brian R.
Published: November 2022

Circadian clocks are composed of molecular oscillators that pace rhythms of gene expression to the diurnal cycle. Therein, transcriptional-translational negative feedback loops (TTFLs) generate oscillating levels of transcriptional repressor proteins that regulate their own gene expression. In the filamentous fungusNeurospora crassa,the proteinsFrequency (FRQ), theFRQ-interacting RNA helicase (FRH) andCasein-Kinase I (CK1) form theFFCcomplex that represses expression of genes activated by the White-Collar complex (WCC). A key question concerns how FRQ orchestrates molecular interactions at the core of the clock despite containing little predicted tertiary structure. We present the reconstitution and biophysical characterization of FRQ and the FFC in unphosphorylated and highly phosphorylated states. Site-specific spin labeling and pulse- dipolar ESR spectroscopy provides domain-specific structural details on the full-length, 989- residue intrinsically disordered FRQ and the FFC. FRQ contains a compact core that associates and organizes FRH and CK1 to coordinate their roles in WCC repression. FRQ phosphorylation increases conformational flexibility and alters oligomeric state but the changes in structure and dynamics are non-uniform. Full-length FRQ undergoes liquid-liquid phase separation (LLPS) to sequester FRH and CK1 and influence CK1 enzymatic activity. Although FRQ phosphorylation favors LLPS, LLPS feeds back to reduce FRQ phosphorylation by CK1 at higher temperatures. Live imaging ofNeurosporahyphae reveals FRQ foci characteristic of condensates near the nuclear periphery. Analogous clock repressor proteins in higher organisms share little position-specific sequence identity with FRQ; yet, they contain amino-acid compositions that promote LLPS. Hence, condensate formation may be a conserved feature of eukaryotic circadian clocks.
EukRibo: a manually curated eukaryotic 18S rDNA reference database to facilitate identification of new diversity
Authors: Berney Cédric , Henry Nicolas , Mahé Frédéric , Richter Daniel J. , de Vargas Colomban
Published: November 2022

EukRibo is a manually curated, public reference database of small-subunit ribosomal RNA gene (18S rDNA) sequences of eukaryotes, specifically aimed at taxonomic annotation of high-throughput metabarcoding datasets. Unlike other reference databases of ribosomal genes, it is not meant to exhaustively capture all publicly available 18S rDNA sequences from the INSDC repositories, but to represent a subset of highly trustable sequences covering the whole known diversity of eukaryotes. EukRibo strives to include only sequences with verified, up-to-date taxonomic identifications, with a strong focus on protists, and relatively low genetic redundancy, to keep the database compact yet comprehensive. Environmental clone sequences representing previously identified novel diversity are accepted as reference sequences only if they have a precise lineage designation, useful for taxonomic annotation. EukRibo is part of a suite of public resources generated by the UniEuk project, which all follow a common taxonomic framework for maximal interoperability. The high level of taxonomic accuracy of EukRibo allows higher confidence in the taxonomic annotation of environmental metabarcodes, and should facilitate identification of new eukaryotic diversity at various taxonomic levels. The database is currently in version 2, and all versions are permanently stored and made available via the FAIR open platform Zenodo. It is our hope that EukRibo will help ongoing curation efforts of other 18S rDNA reference databases, and we welcome suggestions of corrections and new features to be included in subsequent versions.
A condensate forming tether for lariat debranching enzyme is defective in non-photosensitive trichothiodystrophy
Authors: Townley Brittany A. , Buerer Luke , Bacolla Albino , Rusanov Timur , Schmidt Nicolas , Srivatsan Sridhar N. , Clark Nathanial E. , Mansoori Fadhel , Sample Reilly A. , Brickner Joshua R. , McDonald Drew , Tsai Miaw-Sheue , Walter Matthew J. , Wozniak David F. , Holehouse Alex S. , Tainer John A. , Fairbrother William G. , Mosammaparast Nima
Published: November 2022

The pre-mRNA life cycle requires intron processing; yet, how intron processing defects influence splicing and gene expression is unclear. Here, we find TTDN1, which is frequently mutated in non-photosensitive trichothiodystrophy (NP-TTD), functionally links intron lariat processing to the spliceosome. The conserved TTDN1 C-terminal region directly binds lariat debranching enzyme DBR1, while its N-terminal intrinsically disordered region (IDR) binds the intron binding complex (IBC). The IDR forms condensatesin vitroand is needed for IBC interaction. TTDN1 loss causes significant intron lariat accumulation, as well as splicing and gene expression defects, mirroring phenotypes observed in NP-TTD patient cells.Ttdn1Δ/Δmice recapitulate intron processing defects and neurodevelopmental phenotypes seen in NP-TTD. A DBR1-IDR fusion recruits DBR1 to the IBC and circumvents the requirement for TTDN1, indicating this tethering role as its major molecular function. Collectively, our findings unveil key functional connections between lariat processing, splicing outcomes, and NP-TTD molecular pathology.
A stratagem for primary root elongation under moderate salt stress in the halophyteSchrenkiella parvula
Authors: Sekerci Keriman , Higashitani Nahoko , Ozgur Rengin , Uzilday Baris , Higashitani Atsushi , Turkan Ismail
Published: November 2022

Halophytes are salt-tolerant plants that grow in soil or waters of high salinity.Schrenkiella parvulais one of the halophyte plants that grow around Tuz (Salt) Lake, TURKEY that can survive at 600 mM NaCl. Intriguingly,S. parvulabelongs to the same Brassicaceae family as the model plantArabidopsis thaliana, and its genome is 90% homologous to the Arabidopsis genome. Here, we performed proteomic analysis and physiological studies on the roots ofS. parvulaseedlings cultivated under a moderate salt condition at 100 mM NaCl. Surprisingly, under 100 mM NaCl conditions, the primary roots elongated much faster than under NaCl-free conditions, although up to 200 mM those were reduced. On the other hand, iso-osmotic mannitol did not promote primary root elongation, suggesting a specific response to NaCl. Epidermal cell elongation was promoted in the elongation zone, but meristem size and DNA replication were decreased. In addition, root hair formation and lateral root elongation were suppressed at moderate salinity. Compared withA. thaliana, the cell death and ROS increase of root tip meristem cells under 100 mM NaCl condition were significantly lower inS. parvulaseedlings. The size and starch content of sedimentary amyloplasts/statoliths in columella cells decreased, and gravitropism of primary roots was partially reduced. Gene expression analyses showed that the expression of auxin response and biosynthesis genesIAA1, IAA2, TAA1andYUC8were repressed and theSOS1gene was upregulated two-fold in roots grown under moderate salt conditions. Proteomic analysis showed that co-chaperone and activator of HSPs such as Hop2 and Aha1 domain-containing protein orthologs were upregulated. Moreover, several secondary metabolic process-related proteins, antioxidant proteins, stress response proteins and proline catabolic process-related proteins were also increased. In contrast, enzymes associated with root hair elongation and nucleotide and protein syntheses were downregulated. These changes in auxin-related physiological responses, root architecture, lower ROS signaling, and stress-related protein expression promote primary root penetration into lower-salinity deeper soils as an adaptation ofS. parvula.
kegg_pull: a Software Package for the RESTful Access and Pulling from The Kyoto Encyclopedia of Gene and Genomes
Authors: Huckvale Erik , Moseley Hunter N.B.
Published: November 2022

Background

The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides organized genomic, biomolecular, and metabolic information and knowledge that is reasonably current and highly useful for a wide range of analyses and modeling. KEGG follows the principles of data stewardship to be findable, accessible, interoperable, and reusable (FAIR) by providing RESTful access to their database entries via their web-accessible KEGG API. However, the overall FAIRness of KEGG is often limited by the library and software package support available in a given programming language. While R library support for KEGG is fairly strong, Python library support has been lacking. Moreover, there is no software that provides extensive command line level support for KEGG access and utilization.

Results

We present kegg_pull, a package implemented in the Python programming language that provides better KEGG access and utilization functionality than previous libraries and software packages. Not only does kegg_pull include an application programming interface (API) for Python programming, it also provides a command line interface (CLI) that enables language agnostic utilization of KEGG for a wide range of data analysis pipeline use-cases. As kegg_pull’s name implies, both the API and CLI provide versatile options for pulling (downloading and saving) an arbitrary (user defined) number of database entries from the KEGG API. Moreover, this functionality is implemented to efficiently utilize multiple central processing unit cores. Many options are provided to optimize fault-tolerant performance across a single or multiple processes, with recommendations provided based on extensive testing and practical network considerations.

Conclusions

The new kegg_pull package enables new flexible KEGG retrieval use cases not available in previous software packages. The most notable new feature that kegg_pull provides is its ability to robustly pull an arbitrary number of KEGG entries with a single API method or CLI command, including pulling an entire KEGG database. We provide recommendations to users for the most effective use of kegg_pull according to their network and computational circumstances.
Facemap: a framework for modeling neural activity based on orofacial tracking
Authors: Syeda Atika , Zhong Lin , Tung Renee , Long Will , Pachitariu Marius , Stringer Carsen
Published: November 2022

Recent studies in mice have shown that orofacial behaviors drive a large fraction of neural activity across the brain. To understand the nature and function of these signals, we need better computational models to characterize the behaviors and relate them to neural activity. Here we developed Facemap, a framework consisting of a keypoint tracking algorithm and a deep neural network encoder for predicting neural activity. We used the Facemap keypoints as input for the deep neural network to predict the activity of ∼50,000 simultaneously-recorded neurons and in visual cortex we doubled the amount of explained variance compared to previous methods. Our keypoint tracking algorithm was more accurate than existing pose estimation tools, while the inference speed was several times faster, making it a powerful tool for closed-loop behavioral experiments. The Facemap tracker was easy to adapt to data from new labs, requiring as few as 10 annotated frames for near-optimal performance. We used Facemap to find that the neuronal activity clusters which were highly driven by behaviors were more spatially spread-out across cortex. We also found that the deep keypoint features inferred by the model had time-asymmetrical state dynamics that were not apparent in the raw keypoint data. In summary, Facemap provides a stepping stone towards understanding the function of the brainwide neural signals and their relation to behavior.
Machine learning-guided directed evolution for the development of small-molecule antibiotics originating from antimicrobial peptides
Authors: Zhang Heqian , Wang Yihan , Huang Pengtao , Zhu Yanran , Li Xiaojie , Chen Zhaoying , Liu Yu , Jiang Jiakun , Gao Yuan , Huang Jiaquan , Qin Zhiwei
Published: November 2022

Antimicrobial peptides (AMPs) are valuable alternatives to traditional antibiotics that possess a variety of potent biological activities by exerting immunomodulatory effects to clear difficult-to-treat infections. Understanding the structure-activity relationships (SARs) of AMPs can direct the synthesis of desirable therapeutics. In this study, we use machine learning-guided directed evolution to develop the lipopolysaccharide-binding domain (LBD), which acts as a functional domain of anti-lipopolysaccharide factor (ALF), a family of AMPs, identified fromMarsupenaeus japonicus. We report the identification of LBDA-Das an output of this algorithm with the input of the original LBDMjsequence and show the NMR solution structure of LBDB, which possesses a circular extended structure with a disulfide crosslink in each terminus and two 310-helices and exhibits a broad antimicrobial spectrum. Scanning electron microscopy and transmission electron microscopy showed LBDBinduced the formation of a cluster of bacteria wrapped in a flexible coating that ruptured and consequently killed the bacteria. The co-injection of LBDBandVibrio alginolyticus, Staphylococcus aureusand another major pathogen in shrimp aquaculture white spot syndrome virusin vivoimproved the survival ofM. japonicus, indicating a promising therapeutic role of LBDBfor infectious disease. The findings of this study pave the way for the rational drug design of activity-enhanced peptide antibiotics.
The efficacy of chemotherapy is limited by intratumoural senescent cells that persist through the upregulation of PD-L2
Authors: Chaib Selim , López-Domínguez José Alberto , Lalinde Marta , Prats Neus , Marin Ines , Meyer Kathleen , Muñoz María Isabel , Aguilera Mònica , Mateo Lidia , Attolini Camille Stephan-Otto , Llanos Susana , Pérez-Ramos Sandra , Escorihuela Marta , Al-Shahrour Fatima , Cash Timothy P. , Tchkonia Tamara , Kirkland James L. , Arribas Joaquín , Serrano Manuel
Published: November 2022

Anti-cancer therapies often result in a subset of surviving cancer cells that undergo therapy-induced senescence (TIS). Senescent cancer cells strongly modify the intratumoural microenvironment favoring immunosuppression and, thereby, tumour growth. An emerging strategy to optimise current therapies is to combine them with treatments that eliminate senescent cells. To this end, we undertook an unbiased proteomics approach to identify surface markers contributing to senescent cells immune evasion. Through this approach, we discovered that the immune checkpoint inhibitor PD-L2, but not PD-L1, is upregulated across multiple senescent human and murine cells. Importantly, blockade of PD-L2 strongly synergises with genotoxic chemotherapy, causing remission of solid tumours in mice. We show that PD-L2 inhibition prevents the persistence of chemotherapy-induced senescent cells, which exert cell-extrinsic immunomodulatory actions. In particular, upon chemotherapy, tumours deficient in PD-L2 fail to produce cytokines of the CXCL family, do not recruit myeloid-derived suppressor cells (MDSCs) and are eliminated in a CD8 T cell-dependent manner. We conclude that blockade of PD-L2 improves chemotherapy efficacy by reducing the intratumoural burden of senescent cells and their associated recruitment of immunosuppressive cells. These findings provide a novel strategy to exploit vulnerabilities arising in tumour cells as a result of therapy-induced damage and cellular senescence.
DeepOM: Single-molecule optical genome mapping via deep learning
Authors: Nogin Yevgeni , Detinis Zur Tahir , Margalit Sapir , Barzilai Ilana , Alalouf Onit , Ebenstein Yuval , Shechtman Yoav
Published: November 2022

Efficient tapping into genomic information from a single microscopic image of an intact DNA molecule fragment is an outstanding challenge and its solution will open new frontiers in molecular diagnostics. Here, a new computational method for optical genome mapping utilizing Deep Learning is presented, termed DeepOM. Utilization of a Convolutional Neural Network (CNN), trained on simulated images of labeled DNA molecules, improves the success rate in alignment of DNA images to genomic references. The method is evaluated on acquired images of human DNA molecules stretched in nano-channels. The accuracy of the method is benchmarked against state-of-the-art commercial software Bionano Solve. The results show a significant advantage in alignment success rate for molecules shorter than 50 kb. DeepOM improves yield, sensitivity and throughput of optical genome mapping experiments in applications of human genomics and microbiology.
Measuring factors affecting honey bee attraction to soybeans using bioacoustics monitoring
Authors: Forrester Karlan C. , Lin Chia-Hua , Johnson Reed M.
Published: November 2022

Soybean is an important agricultural crop around the world, and previous studies suggest that honey bees can be a component for optimizing soybean production through pollination. Determining when bees are present in soybean fields is critical for assessing pollination activity and identifying periods when bees are absent so that bee-toxic pesticides may be applied. There are currently several methods for detecting pollinator activity, but these existing methods have substantial limitations, including the bias of pan trappings against large bees and the limited duration of observation possible using manual techniques. This study aimed to develop a new method for detecting honey bees in soybean fields using bioacoustics monitoring. Microphones were placed in soybean fields to record the audible wingbeats of foraging bees. Foraging activity was identified using the wingbeat frequency of honey bees (234±13.9 Hz) through a combination of algorithmic and manual approaches. A total of 243 honey bees were detected over ten days of recording in four soybean fields. Bee activity was significantly greater in blooming fields than in non-blooming fields. Temperature had no significant effect on bee activity, but bee activity differed significantly between soybean varieties, suggesting that soybean attractiveness to honey bees is heavily dependent on varietal characteristics. Refinement of bioacoustics methods, particularly through incorporation of machine learning, could provide a practical tool for measuring activity of honey bees and other flying insects in soybeans as well as other crops and ecosystems.
Enteric Glial Cell Network Function is Required for Epithelial Barrier Restitution following Intestinal Ischemic Injury in the Early Postnatal Period
Authors: Ziegler Amanda L. , Erwin Sara , Caldwell Madison L. , Touvron Melissa S. , Pridgen Tiffany A. , Magness Scott T. , Odle Jack , Van Landeghem Laurianne , Blikslager Anthony T.
Published: November 2022

Ischemic damage to the intestinal epithelial barrier, such as in necrotizing enterocolitis or small intestinal volvulus, is associated with higher mortality rates in younger patients. We have recently reported a powerful pig model to investigate these age-dependent outcomes in which mucosal barrier restitution is strikingly absent in neonates but can be rescued by direct application of homogenized mucosa from older, juvenile pigs by a yet-undefined mechanism. Within the mucosa, a postnatally developing network of enteric glial cells (EGC) is gaining recognition as a key regulator of the mucosal barrier. Therefore, we hypothesized that the developing EGC network may play an important role in coordinating intestinal barrier repair in neonates. Neonatal and juvenile jejunal mucosa recovering from surgically induced intestinal ischemia was visualized by scanning electron microscopy and the transcriptomic phenotypes were assessed by bulk RNA sequencing. EGC network density and gliosis were examined by gene set enrichment analysis, three-dimensional volume imaging and western blot and its function in regulating epithelial restitution assessedex vivoin Ussing chamber using the glia-specific inhibitor fluoroacetate, andin vivoby co-culture assay. Here we refine and elaborate our translational model, confirming a neonatal phenotype characterized by a complete lack of coordinated reparative signaling in the mucosal microenvironment. Further, we report important evidence that the subepithelial EGC network changes significantly over the early postnatal period and demonstrate that EGC function in close proximity to wounded intestinal epithelium is critical to intestinal barrier restitution following ischemic injury.

NEW & NOTEWORTHY

This study refines a powerful translational pig model, defining an age-dependent relationship between enteric glia and the intestinal epithelium during intestinal ischemic injury and confirming an important role of the enteric glial cell activity in driving mucosal barrier restitution. This study suggests that targeting the enteric glial network could lead to novel interventions to improve recovery from intestinal injury in neonatal patients.
Label-guided seed-chain-extend alignment on annotated De Bruijn graphs
Authors: Mustafa Harun , Karasikov Mikhail , Ghiasi Nika Mansouri , Rätsch Gunnar , Kahles André
Published: November 2022

Exponential growth in sequencing databases has motivated scalable De Bruijn graph-based (DBG) indexing for searching these data, using annotations to label nodes with sample IDs. Low-depth sequencing samples correspond to fragmented subgraphs, complicating finding the long contiguous walks required for alignment queries. Aligners that target single-labelled subgraphs reduce alignment lengths due to fragmentation, leading to low recall for long reads. While some (e.g., label-free) aligners partially overcome fragmentation by combining information from multiple samples, biologically-irrelevant combinations in such approaches can inflate the search space or reduce accuracy.

We introduce a new scoring model,multi-labelalignment(MLA), for annotated DBGs. MLA leverages two new operations: To promote biologically-relevant sample combinations,Label Changeincorporates more informative global sample similarity into local scores. To improve connectivity,Node Length Changedynamically adjusts the DBG node length during traversal. Our fast, approximate, yet accurate MLA implementation has two key steps: a single-label seed-chain-extendaligner (SCA) and amulti-labelchainer (MLC).SCAuses a traditional scoring model adapting recent chaining improvements to assembly graphs and provides a curated pool of alignments.MLCextracts seed anchors fromSCA’s alignments, produces multi-label chains using MLA scoring, then finally forms multi-label alignments. We show via substantial improvements in taxonomic classification accuracy that MLA produces biologically-relevant alignments, decreasing average weighted UniFrac errors by 63.1–66.8% and covering 45.5–47.4% (median) more long-read query characters than state-of-the-art aligners. MLA’s runtimes are competitive with label-combining alignment and substantially faster than single-label alignment.
Molecular understanding ofEubacterium limosumchemostat methanol metabolism
Authors: Wood Jamin C. , Gonzalez-Garcia R. Axayacatl , Daygon Dara , Talbo Gert , Plan Manuel R. , Marcellin Esteban , Virdis Bernardino
Published: November 2022

Methanol is a promising renewable energy carrier that can be used as a favourable substrate for biotechnology, due to its high energy efficiency conversion and ease of integration within existing infrastructure. Some acetogenic bacteria have the native ability to utilise methanol, along with other C1substrates such as CO2and formate, to produce valuable chemicals. Continuous cultures favour economically viable bioprocesses, however, the performance of acetogens has not been investigated at the molecular level when grown on methanol. Here we present steady-state chemostat quantification of the metabolism ofEubacterium limosum, finding maximum methanol uptake rates up to 640±22 mmol/gDCW/d, with significant fluxes to butyrate. To better understand metabolism of acetogens under methanol growth conditions, we sampled chemostats for proteomics and metabolomics. Changes in protein expression and intracellular metabolomics highlighted key aspects of methanol metabolism, and highlighted bottleneck conditions preventing formation of the more valuable product, butanol. Interestingly, a small amount of formate in methylotrophic metabolism triggered a cellular state known in other acetogens to correlate with solventogenesis. Unfortunately, this was prevented by post-translation effects including an oxidised NAD pool. There remains uncertainty around ferredoxin balance at the methylene-tetrahydrofolate reductase (MTHFR) and at the Rnf level.
Spatial regulation of the glycocalyx component Podocalyxin is a switch for pro-metastatic function
Authors: Román-Fernández Alvaro , Mansour Mohammed A. , Kugeratski Fernanda G. , Anand Jayanthi , Sandilands Emma , Galbraith Laura , Rakovic Kai , Freckmann Eva C. , Cumming Erin M. , Park Ji , Nikolatou Konstantina , Lilla Sergio , Shaw Robin , Strachan David , Mason Susan , Patel Rachana , McGarry Lynn , Katoch Archana , Campbell Kirsteen J. , Nixon Colin , Miller Crispin J. , Leung Hing Y. , Le Quesne John , Norman James C. , Zanivan Sara , Blyth Karen , Bryant David M.
Published: November 2022

The glycocalyx component and sialomucin Podocalyxin (PODXL) is required for normal tissue development by promoting apical membranes to form between cells, triggering lumen formation. Elevated PODXL expression is also associated with metastasis and poor clinical outcome in multiple tumour types. How PODXL presents this duality in effect remains unknown. We identify an unexpected function of PODXL as a decoy receptor for Galectin-3 (GAL3), whereby the PODXL-GAL3 interaction releases GAL3 repression of integrin-based invasion. Differential cortical targeting of PODXL, regulated by ubiquitination, is the molecular mechanism controlling alternate fates. Both PODXL highversuslow surface levels occur in parallel subpopulations within cancer cells. Orthotopic intraprostatic xenograft of PODXL-manipulated cells or those with different surface levels of PODXL define that this axis controls metastasisin vivo. Clinically, interplay between PODXL-GAL3 stratifies prostate cancer patients with poor outcome. Our studies define the molecular mechanisms and context in which PODXL promotes invasion and metastasis.
Can recent evolutionary history promote resilience to environmental change?
Authors: Bladon Eleanor Kate , Pascoal Sonia , Kilner Rebecca Mary
Published: November 2022

Principles of social evolution have long been used retrospectively to interpret social interactions, but have less commonly been applied predictively to inform conservation and animal husbandry strategies. We investigate whether differences in developmental environment, facilitated by divergent social conditions, can predict resilience to environmental change. Upon exposure to harsh novel environments, populations that previously experienced more benign social environments are predicted either to suffer fitness losses (the “mutation load hypothesis” and “selection filter hypothesis”) or maintain fitness (the “beneficial mutation hypothesis”). We tested these contrasting predictions using populations of burying beetlesNicrophorus vespilloideswe had evolved experimentally for 45 generations under contrasting social environments by manipulating the supply of post-hatching parental care. We exposed sexually immature adults from each population to varying heat stress and measured the effect on survival and reproduction. The greater the level of parental care previously experienced by a population, the better its survival under heat stress during sexual maturation. Although this is consistent with the “beneficial mutation hypothesis”, it is also possible that populations that had evolved without post-hatching care were simply more prone to dying during maturation, regardless of their thermal environment. Overall, we suggest that stochastic genetic variation, probably due to founder effects, had a stronger influence on resilience. We discuss the implications for translocation and captive breeding programmes.

Lay summary

Can we use knowledge of a population’s evolutionary history to predict how individuals might cope with environmental change? We investigated whether burying beetles that had evolved for 45 generations with or without post-hatching parental care differed in their resilience to extreme temperatures as they developed to sexual maturity. We found limited evidence that experimental evolution under different regimes of parental care contributed to thermal resilience, which instead was better explained by chance historical events.
A new take on model-based and model-free influences on mental effort and striatal prediction errors
Authors: da Silva Carolina Feher , Lombardi Gaia , Edelson Micah , Hare Todd A.
Published: November 2022

A standard assumption in neuroscience is that low-effort model-free learning is automatic and continuously employed, while more complex model-based strategies are only used when the rewards they generate are worth the additional effort. We present evidence refuting this assumption. First, we demonstrate flaws in previous reports of combined model-free and model-based reward prediction errors in the ventral striatum that likely led to spurious results. More appropriate analyses yield no evidence of a model-free prediction errors in this region. Second, we find that task instructions generating more correct model-based behaviour reduce rather than increase mental effort. This is inconsistent with cost-benefit arbitration between model-based and model-free strategies. Together, our data suggest that model-free learning may not be automatic. Instead, humans can reduce mental effort by using a model-based strategy alone rather than arbitrating between multiple strategies. Our results call for re-evaluation of the assumptions in influential theories of learning and decision-making.
Prediction of elimination of intrahepatic cccDNA in hepatitis B virus-infected patients by a combination of noninvasive viral markers
Authors: Kim Kwang Su , Iwamoto Masashi , Kitagawa Kosaku , Hayashi Sanae , Tsukuda Senko , Matsui Takeshi , Atsukawa Masanori , Chuaypen Natthaya , Tangkijvanich Pisit , Allweiss Lena , Nishiyama Takara , Nakamura Naotoshi , Fujita Yasuhisa , Kawakami Eiryo , Nakaoka Shinji , Muramatsu Masamichi , Aihara Kazuyuki , Wakita Takaji , Perelson Alan S. , Dandri Maura , Watashi Koichi , Iwami Shingo , Tanaka Yasuhito
Published: November 2022

Evaluation of intrahepatic covalently closed circular DNA (cccDNA) is a key for searching an elimination of hepatitis B virus (HBV) infection. HBV RNA and HBV core-related antigen have been proposed as surrogate markers for evaluating cccDNA activity, although they do not necessarily estimate the amount of cccDNA. Here, we developed a novel multiscale mathematical model describing intra- and inter-cellular viral propagation, based on the experimental quantification data in both HBV-infected cell culture and humanized mouse models. We applied it to HBV-infected patients under treatment and developed a model which can predict intracellular HBV dynamics only by use of noninvasive extracellular surrogate biomarkers. Importantly, the model prediction of the amount of cccDNA in patients over time was confirmed to be well-correlated with the liver biopsy data. Thus, our noninvasive method enables to predict the amount of cccDNA in patients and contributes to determining the treatment endpoint required for elimination of intrahepatic cccDNA.
PRMT5 links lipid metabolism to contractile function of skeletal muscles
Authors: Kim Kun Ho , Jia Zhihao , Snyder Madigan M. , Chen Jingjuan , Qiu Jiamin , Oprescu Stephanie N. , Chen Xiyue , Syed Sabriya A , Yue Feng , Roseguini Bruno T. , Imbalzano Anthony N. , Hu Changdeng , Kuang Shihuan
Published: November 2022

The skeletal muscle plays a key role in systemic energy homeostasis besides its canonical contractile function, but what couples these functions is poorly defined. Protein Arginine MethylTransferase 5 (PRMT5) is a well-known oncoprotein but also expressed in healthy tissues with unclear physiological functions. As adult muscles express high levels ofPrmt5, we generated myocyte-specificPrmt5knockout (Prmt5MKO) mice. We observed reduced muscle mass, oxidative capacity, force production and exercise performance inPrmt5MKOmice. The motor deficiency is associated with scarce lipid droplets in myofibers due to defects in lipid biosynthesis and degradation. First,Prmt5MKOreduced demethylation and stability of Sterol Regulatory Element-Binding Transcription Factor 1a (SREBP1a), a master regulator ofde novolipogenesis. Second,Prmt5MKOimpaired the repressive H4R3Me2s (histone H4 arginine-3 symmetric demethylation) at thePnpla2gene, elevating the level of its encoded protein ATGL, the rate-limiting enzyme catalyzing lipolysis. Accordingly, myocyte-specific double knockout ofPnpla2andPrmt5normalized muscle mass and function. Together, our findings delineate a physiological function of PRMT5 in linking lipid metabolism to contractile function of myofibers.
HIV-1 Vpr induces ciTRAN to prevent transcriptional silencing of the provirus
Authors: Bhardwaj Vipin , Singh Aman , Dalavi Rishikesh , Ralte Lalchhanhima , Chawngthu Richard L. , Kumar Nachimuthu Senthil , Vijay Nagarjun , Chande Ajit
Published: November 2022

The functional relevance of circular RNA (circRNA) expression in HIV-1 infection remains unclear. By developing a customized protocol involving direct RNA nanopore sequencing here, we captured circRNAs in their native state from HIV-1 infected T cells and identified ciTRAN, acircRNA modulator of HIV-1Transcription. We show that HIV-1 infection of monocytic, T cell lines and primary CD4+ T cells induces ciTRAN expression in a Vpr-dependent manner. ciTRAN protein interactome analysis by proximity biotinylation and mass spectrometry identified SRSF-1 as a prominent interactor of the circular RNA. SRSF-1 is known to negatively regulate HIV-1 transcription, which the virus overcomes by a yet unknown mechanism. We demonstrate that HIV-1 Vpr induced ciTRAN sequesters SRSF1 away from the viral transcriptional complex to promote efficient viral transcription. Accordingly, ciTRAN depletion by CRISPR-Cas phenocopied the effects of SRSF1 overexpression and improved SRSF1 association with HIV-1 transcriptional complex. Finally, we show that an SRSF-1-inspired competing peptide can inhibit HIV-1 transcription regardless of ciTRAN induction. The hijacking of a host circRNA thus represents a new facet of primate lentiviruses in overcoming transmission bottlenecks.
Bold but not innovative in an urban exploiter, the red fox (Vulpes vulpes)
Authors: Morton F. Blake , Gartner Marieke , Norrie Ellie-Mae , Haddou Yacob , Soulsbury Carl D. , Adaway Kristy A.
Published: November 2022

Urbanisation is the fastest form of landscape transformation on the planet, but researchers’ understanding of the relationships between urbanisation and animal adaptability is still in its infancy. In terms of foraging, bold and innovative behaviours are proposed to help urban animals access, utilise, and exploit novel anthropogenic food sources. Red foxes (Vulpes vulpes) are one of the best known and widespread urban-dwelling species. However, despite frequent stories, images, and videos portraying them as “pests” due to their exploitation of food-related objects (e.g., raiding the contents of outdoor bins), it is unknown whether they are bolder and more innovative in terms of their likelihood of exploiting these resources compared to rural populations. In the current study, we gave novel food-related objects to foxes from 104 locations (one object per location) across a large urban-rural gradient. To access the food, foxes had to use behaviours necessary for exploiting many food-related objects in the real world (e.g., biting, pushing, pulling, or lifting human-made materials). Despite all foxes acknowledging the objects, foxes from 31 locations touched them, while foxes from 12 locations gained access to the food inside. A principal component analysis of urban and other landscape variables (e.g., road, greenspace, and human population density) revealed that urbanisation was significantly and positively related to the likelihood of foxes touching, but not exploiting, the objects. Thus, while urban foxes may be bolder than rural populations in terms of their willingness to physically touch novel food-related objects, our findings are inconsistent with the notion that they are more innovative and pose a general nuisance to people by exploiting these anthropogenic resources.

Highlights

The impact of urbanisation on animal adaptability remains unclear

Bold and innovative behaviour may help some urban species thrive

We studied wild red foxes’ responses to novel food-related objects

Urban foxes were bolder, but not more innovative, than rural foxes

Urbanisation may favour bolder, not more innovative, fox behaviour
Optogenetic control of YAP can enhance the rate of wound healing
Authors: Toh Pearlyn Jia Ying , Sudol Marius , Saunders Timothy Edward
Published: November 2022

Background

Tissues need to regenerate to restore function after injury. Yet, this regenerative capacity varies significantly between organs and between species. For example, in the heart, some species retain full regenerative capacity throughout their lifespan but human cardiac cells display limited ability to repair injury. After a myocardial infarction, the function of cardiomyocytes is impaired and reduces the ability of the heart to pump, causing heart failure. Therefore, there is a need to restore the function of an injured heart post myocardial infarction. We investigate in cell culture the role of the YAP, a transcriptional co-regulator with a pivotal role in growth, in driving repair after injury.

Methods

We express optogenetic YAP (optoYAP) in three different cell lines. We characterised the behaviour and function of optoYAP using fluorescence imaging and quantitative real-time PCR of downstream YAP target genes. Mutant constructs were generated using site-directed mutagenesis. Nuclear localised optoYAP was functionally tested using wound healing assay and anchorage-independent colony formation assay.

Results

Utilising optoYAP, which enables precise control of pathway activation, we show that YAP induces the expression of downstream genes involved in proliferation and migration. optoYAP can increase the speed of wound healing in H9c2 cardiomyoblasts. Interestingly, this is not driven by an increase in proliferation, but by collective cell migration. We subsequently dissect specific phosphorylation sites in YAP to identify the molecular driver of accelerated healing.

Conclusions

This study shows that optogenetic YAP is functional in H9c2 cardiomyoblasts and its controlled activation can potentially enhance wound healing in a range of conditions.
Distinct feedforward and feedback pathways for cell-type specific attention effects
Authors: Spyropoulos Georgios , Schneider Marius , van Kempen Jochem , Gieselmann Marc Alwin , Thiele Alexander , Vinck Martin
Published: November 2022

Spatial attention selectively enhances neural responses to visual stimuli. There are two long-standing hypotheses about how top-down feedback enhances sensory responses in areas like V4: First, by amplifying V1-to-V4 feedforward communication via 30-80Hz gamma-coherence. Second, via top-down feedback to V4 supra- and infra-granular layers. To test these hypotheses, we recorded distinct cell-types across macaque V1 and V4 layers. Attention increased both V1-V4 gamma-coherence and V4 spike-rates, yet with distinct laminar and cell-type profiles. Surprisingly, V1 gamma did not engage V4 excitatory neurons, but only Layer-4 fast-spiking interneurons. Similar observations were made in mouse visual-cortex, where feedforward gamma-influences preferentially recruit optogenetically-tagged PV+ and narrowwaveform SSt+ interneurons. By contrast, attention enhanced V4 spike-rates in both excitatory neurons and fast-spiking interneurons, with the strongest and earliest modulation in Layer-2/3, consistent with a feedback influence. These findings reveal distinct feedforward and feedback pathways for the attentional modulation of inter-areal coherence and spike rates, respectively.
Selective degradation of ARF monomers controls auxin response in Marchantia
Authors: Das Shubhajit , de Roij Martijn , Bellows Simon , Kohlen Wouter , Farcot Etienne , Weijers Dolf , Borst Jan Willem
Published: November 2022

The plant signaling molecule auxin controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of a ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and the DNA-binding ARF transcription factors. While extensive qualitative understanding of the pathway and its interactions has been obtained by studying the flowering plantArabidopsis thaliana, it is so far unknown how these translate to quantitative system behaviourin vivo, a problem that is confounded by large NAP gene families in this species. Here we used the minimal NAP of the liverwortMarchantia polymorphato quantitatively map NAP protein accumulation and dynamicsin vivothrough the use of knock-in fluorescent fusion proteins. Beyond revealing the native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs MpARF1 and MpARF2 are proteasomally degraded. This degradation serves two functions: it tunes the stoichiometry of auxin-responsive, positively acting MpARF1 and auxin-independent, negatively acting MpARF2, thereby permitting auxin response. Secondly, through mapping a minimal degradation motif, we found that degradation is likely selective for MpARF2 monomers and favours accumulation of dimers. Interfering with MpARF1:MpARF2 stoichiometry or preventing degradation of MpARF2 monomers caused strong growth defects associated with auxin response defects. Thus, quantitative analysis of the entire Marchantia NAP, allowed to identify a novel regulatory mechanism in auxin response, built on regulated ARF degradation.