bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine learning forecasts for seasonal epidemic peaks: lessons learnt from an atypical respiratory syncytial virus season
Authors: Morbey Roger A. , Todkill Dan , Watson Conall , Elliot Alex J.
Published: July 2023

Seasonal peaks in infectious disease incidence put pressures on health services. Therefore, early warning of the timing and magnitude of peak activity during seasonal epidemics can provide information for public health practitioners to take appropriate action. Whilst many infectious diseases have predictable seasonality, newly emerging diseases and the impact of public health interventions can result in unprecedented seasonal activity. We propose a machine learning process for generating short-term forecasts, where models are selected based on their ability to correctly forecast peaks in activity and can be useful during the aforementioned atypical seasonal activity, in contrast to traditional modelling. We have validated our forecasts using typical and atypical seasonal activity, using respiratory syncytial virus (RSV) activity during 2019-2021 as an example. During the winter of 2020/21 the usual winter peak in RSV activity in England did not occur but was ‘deferred’ until the Spring of 2021.

We compare a range of machine learning regression models, with alternate models including different independent variables, e.g. with or without seasonality or trend variables. We show that the best-fitting model which minimises daily forecast errors is not the best model for forecasting peaks when the selection criterion is based on peak timing and magnitude. Furthermore, we show that best-fitting models for typical seasons contain different variables to those for atypical black swan seasons. Specifically, including seasonality in models improves performance during typical seasons but worsens it for the atypical seasons. In conclusion, we have found that including seasonality in forecast models can result in overfitting, where the models are required to be used out-of-season or during atypical seasons.
Genome-wide Association Study of Long COVID
Authors: Lammi Vilma , Nakanishi Tomoko , Jones Samuel E. , Andrews Shea J. , Karjalainen Juha , Cortés Beatriz , O’Brien Heath E. , Fulton-Howard Brian E. , Haapaniemi Hele H. , Schmidt Axel , Mitchell Ruth E. , Mousas Abdou , Mangino Massimo , Huerta-Chagoya Alicia , Sinnott-Armstrong Nasa , Cirulli Elizabeth T. , Vaudel Marc , Kwong Alex S.F. , Maiti Amit K. , Marttila Minttu , Batini Chiara , Minnai Francesca , Dearman Anna R. , Warmerdam C.A. Robert , Sequeros Celia B. , Winkler Thomas W. , Jordan Daniel M. , Guare Lindsay , Vergasova Ekaterina , Marouli Eirini , Striano Pasquale , Zainulabid Ummu Afeera , Kumar Ashutosh , Ahmad Hajar Fauzan , Edahiro Ryuya , Azekawa Shuhei ,   Long COVID Host Genetics Initiative,   FinnGen,   DBDS Genomic Consortium,   GEN-COVID Multicenter Study, Grzymski Joseph J. , Ishii Makoto , Okada Yukinori , Beckmann Noam D. , Kumari Meena , Wagner Ralf , Heid Iris M. , John Catherine , Short Patrick J. , Magnus Per , Banasik Karina , Geller Frank , Franke Lude H. , Rakitko Alexander , Duncan Emma L. , Renieri Alessandra , Tsilidis Konstantinos K. , de Cid Rafael , Niavarani Ahmadreza , Tusié-Luna Teresa , Verma Shefali S. , Smith George Davey , Timpson Nicholas J. , Daly Mark J. , Ganna Andrea , Schulte Eva C. , Richards J. Brent , Ludwig Kerstin U. , Hultström Michael , Zeberg Hugo , Ollila Hanna M.
Published: July 2023

Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers after human papillomavirus, or rheumatic fever after streptococcal infections1, 2. Similarly, infection by SARS-CoV-2 can result in Long COVID, a condition characterized by symptoms of fatigue and pulmonary and cognitive dysfunction3–5. The biological mechanisms that contribute to the development of Long COVID remain to be clarified. We leveraged the COVID-19 Host Genetics Initiative6, 7to perform a genome-wide association study for Long COVID including up to 6,450 Long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We identified the first genome-wide significant association for Long COVID at theFOXP4locus.FOXP4has been previously associated with COVID-19 severity6, lung function8, and cancers9, suggesting a broader role for lung function in the pathophysiology of Long COVID. While we identify COVID-19 severity as a causal risk factor for Long COVID, the impact of the genetic risk factor located in theFOXP4locus could not be solely explained by its association to severe COVID-19. Our findings further support the role of pulmonary dysfunction and COVID-19 severity in the development of Long COVID.
Regulation of bacterial stringent response by an evolutionary conserved ribosomal protein L11 methylation
Authors: Walukiewicz Hanna E. , Farris Yuliya , Burnet Meagan C. , Feid Sarah C. , You Youngki , Christensen David , Payne Samuel H. , Wolfe Alan J. , Rao Christopher V. , Nakayasu Ernesto S.
Published: July 2023

Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in bacteria. By reanalyzing a large phyloproteomics dataset from 48 bacterial strains representing 6 phyla, we found that almost a quarter of the bacterial proteome is methylated. Many of these methylated proteins are conserved across diverse bacterial lineages, including those involved in central carbon metabolism and translation. Among the proteins with the most conserved methylation sites is ribosomal protein L11 (bL11). bL11 methylation has been a mystery for five decades, as the deletion of its methyltransferase PrmA causes no cell growth defects. A comparative proteomics analysis combined with a guanosine polyphosphate assay of the ΔprmAmutant inEscherichia colirevealed that bL11 methylation is important for stringent response signaling. Moreover, we show that the ΔprmAmutant has an abnormal polysome profile, suggesting a role in ribosomal homeostasis during stationary growth phase. Overall, our investigation demonstrates that the evolutionary conserved bL11 methylation is important for stringent response signaling and ribosomal homeostasis.

Importance

Protein methylation in bacteria was first identified over sixty years ago. Since then, its functional role has been identified for only a few proteins. To better understand the functional role of methylation in bacteria, we analyzed a large phyloproteomics dataset encompassing 48 diverse bacteria. Our analysis revealed that ribosomal proteins are often methylated at conserved residues, suggesting that methylation of these sites may have a functional role in translation. Further analysis revealed that methylation of ribosomal protein L11 is important for stringent response signaling and ribosomal homeostasis.
Human Th17- and IgG3-associated autoimmunity induced by a translocating gut pathobiont
Authors: Gronke Konrad , Nguyen Mytien , Santamaria Noemi , Schumacher Julia , Yang Yi , Sonnert Nicole , Leopold Shana , Martin Anjelica L. , Hallet Remy , Richter Kirsten , Schubert David A. , Daniel Guillaume M. , Dylus David , Forkel Marianne , Vieira Silvio Manfredo , Schwinge Dorothee , Schramm Christoph , Lassen Kara G. , Piali Luca , Palm Noah W. , Bieniossek Christoph , Kriegel Martin A.
Published: July 2023

Extraintestinal autoimmune diseases are multifactorial with translocating gut pathobionts implicated as instigators and perpetuators in mice. However, the microbial contributions to autoimmunity in humans remain largely unclear, including whether specific pathological human adaptive immune responses are triggered by such pathobionts. We show here that the translocating pathobiontEnterococcus gallinaruminduces human IFNγ+Th17 differentiation and IgG3 subclass switch of anti-E. gallinarumRNA and correlating anti-human RNA autoantibody responses in patients with systemic lupus erythematosus and autoimmune hepatitis. Human Th17 induction byE. gallinarumis cell-contact dependent and involves TLR8-mediated human monocyte activation. In murine gnotobiotic lupus models,E. gallinarumtranslocation triggers IgG3 anti-RNA autoantibody titers that correlate with renal autoimmune pathophysiology and with disease activity in patients. Overall, we define cellular mechanisms of how a translocating pathobiont induces human T- and B-cell-dependent autoimmune responses, providing a framework for developing host- and microbiota-derived biomarkers and targeted therapies in extraintestinal autoimmune diseases.

One Sentence Summary

Translocating pathobiontEnterococcus gallinarumpromotes human Th17 and IgG3 autoantibody responses linked to disease activity in autoimmune patients.
Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication
Authors: Yang Zemin , Johnson Bryan A. , Meliopoulos Victoria A. , Ju Xiaohui , Zhang Peipei , Hughes Michael P. , Wu Jinjun , Koreski Kaitlin P. , Chang Ti-Cheng , Wu Gang , Hixon Jeff , Duffner Jay , Wong Kathy , Lemieux Rene , Lokugamage Kumari G. , Alvardo Rojelio E. , Crocquet-Valdes Patricia A. , Walker David H. , Plante Kenneth S. , Plante Jessica A. , Weaver Scott C. , Kim Hong Joo , Meyers Rachel , Schultz-Cherry Stacey , Ding Qiang , Menachery Vineet D. , Taylor J. Paul
Published: July 2023

G3BP1/2 are paralogous proteins that promote stress granule formation in response to cellular stresses, including viral infection. G3BP1/2 are prominent interactors of the nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the functional consequences of the G3BP1-N interaction in the context of viral infection remain unclear. Here we used structural and biochemical analyses to define the residues required for G3BP1-N interaction, followed by structure-guided mutagenesis of G3BP1 and N to selectively and reciprocally disrupt their interaction. We found that mutation of F17 within the N protein led to selective loss of interaction with G3BP1 and consequent failure of the N protein to disrupt stress granule assembly. Introduction of SARS-CoV-2 bearing an F17A mutation resulted in a significant decrease in viral replication and pathogenesis in vivo, indicating that the G3BP1-N interaction promotes infection by suppressing the ability of G3BP1 to form stress granules.
MKT1alleles regulate stress responses through post-transcriptional modulation of Puf3 targets in budding yeast
Authors: Chaithanya Koppisetty Viswa , Sinha Himanshu
Published: July 2023

MKT1is a pleiotropic stress response gene identified by several quantitative trait studies withMKT189Gas a causal variant, contributing to growth advantage in multiple stress environments.MKT1has been shown to regulateHOendonuclease post-transcriptionally via the Pbp1-Pab1 complex. RNA-binding protein Puf3 modulates a set of nuclear-encoded mitochondrial transcripts whose expression was found to be affected byMKT1alleles. This study attempts to relate theMKT1allele-derived growth advantage with the stability of Puf3 targets during stress and elucidate the roles of Pbp1 and Puf3 in this mechanism. Our results showed that the growth advantage of theMKT189Gallele in cycloheximide and H O wasPBP1-dependent, whereas in 4NQO, the growth advantage was dependent on bothPUF3andPBP1. We compared the mRNA decay kinetics of a set of Puf3 targets in multiple stress environments to understand the allele-specific regulation byMKT1. In oxidative stress, theMKT189Gallele modulated the differential expression of nuclear-encoded mitochondrial genes in aPBP1andPUF3-dependent manner. Additionally,MKT189Gstabilised Puf3 targets, namely,COX17,MRS1, andRDL2,in an allele and stress-specific manner. Our results showed that COX17, MRS1, and RDL2 had a stress-specific response in stress environments, with theMKT189Gallele contributing to better growth; this response was bothPBP1andPUF3-dependent. Our results indicate that the common allele,MKT189G, regulates stress responses by differentially stabilising Puf3-target mitochondrial genes, which allows for the strain’s better growth in stress environments.

TAKE AWAY

MKT1alleles vary stress responses by post-transcriptional modulation of Puf3 targets.PBP1andPUF3influence the regulation of Puf3 target stability under stress.

Nuclear-encoded mitochondrial Puf3 targetsCOX17, MRS1andRDL2,contribute to the growth advantage ofMKT189Gallele in oxidative stress.
An ex vivo human model for safety assessment of immunotoxicity of engineered nanomaterials
Authors: Blersch Josephine , Kurkowsky Birgit , Meyer-Berhorn Anja , Grabowska Agnieszka K. , Feidt Eva , Junglas Ellen , Roth Wera , Stappert Dominik , Kübelbeck Armin , Denner Philip , Fava Eugenio
Published: July 2023

The unique physicochemical properties of nanomaterials (NM) and engineered nanomaterials (ENM) have pushed their use in many applications ranging from medicine to the food industry, textiles, and many more fields. Thus, human exposure to NM and ENM is growing by the day. However, the current toxicity tests do not reflect the special characteristics of ENM and are not developed for ENM risk assessment. Here we propose a high-throughput cell-based assay using human peripheral blood mononuclear cells (PBMCs) that can monitor the effects of NM and ENM on cytotoxicity and innate immunity. The proposed assay is fully automated and miniaturized, with excellent assay performance parameters (Z’-score >0.5), amenable for large screening campaigns in industrial setting. Immunotoxicity data for ENM safety assessment are collected in dose-response format. At different states, multiparametric readouts for cytotoxicity, and innate immunity are conducted in a combinatorial method, avoiding ENM-induced bias by endotoxin contamination. Integrating this high-dimensional data, allows (i) holistic safety assessment of immunotoxicity effects caused by ENM, classifying safe and toxic ENM phenotypes, and (ii) to deconvolve mode of action of the ENM effect on the PBMCs. As added value the data obtained can be used to troubleshoot ENM or for a safe-by-design approach in product development.
Mesenchyme governs hair follicle induction
Authors: Mäkelä Otto J.M. , Mikkola Marja L.
Published: July 2023

Tissue interactions are essential to guide organogenesis. The development of hair follicles is regulated by inductive signalling between the embryonic surface epithelium and the adjacent mesenchyme. Previous studies have established that the mesenchymal component of the hair follicle, the dermal papilla and its precursor dermal condensate, has the capacity for de novo hair follicle induction. However, studies prior to dermal condensate formation have been inconclusive, and therefore the source and the identity of the primary inductive signal have remained unknown. Here, we performed epithelial-mesenchymal tissue recombination experiments using hair-forming back skin and glabrous plantar skin from mouse embryos to unveil that the back skin mesenchyme is inductive even prior to dermal condensate formation. Moreover, the naïve, unpatterned mesenchyme was sufficient to trigger hair follicle formation even in the oral epithelium. Considering the recognized role of Wnt signalling and Bmp activity inhibition in initiation of hair follicle development, we explored the hair-inductive ability of the Wnt agonist R-spondin-1 and a Bmp receptor inhibitor in embryonic skin explants. Although R-spondin-1 instigated precocious placode-specific transcriptional responses, it alone or in combination with the Bmp receptor inhibitor was insufficient for hair follicle induction. Our findings pave the way for identifying the hair follicle-inducing cue.
Electrophysiology of human iPSC-derived vascular smooth muscle cells and cell autonomous consequences of Cantu Syndrome mutations
Authors: Hanson Alex , McClenaghan Conor , Weng Kuo-Chan , Colijn Sarah , Stratman Amber N. , Halabi Carmen M. , Grange Dorothy K. , Silva Jonathan R. , Nichols Colin G.
Published: July 2023

Objective

Cantu Syndrome (CS), a multisystem disease with a complex cardiovascular phenotype, is caused by GoF variants in the Kir6.1/SUR2 subunits of ATP-sensitive potassium (KATP) channels, and is characterized by low systemic vascular resistance, as well as tortuous, dilated vessels, and decreased pulse-wave velocity. Thus, CS vascular dysfunction is multifactorial, with distinct hypomyotonic and hyperelastic components. To dissect whether such complexities arise cell-autonomously within vascular smooth muscle cells (VSMCs), or as secondary responses to the pathophysiological milieu, we assessed electrical properties and gene expression in human induced pluripotent stem cell-derived VSMCs (hiPSC-VSMCs), differentiated from control and CS patient-derived hiPSCs, and in native mouse control and CS VSMCs.

Approach and Results

Whole-cell voltage-clamp of isolated aortic and mesenteric VSMCs isolated from wild type (WT) and Kir6.1[V65M] (CS) mice revealed no difference in voltage-gated K+(Kv) or Ca2+currents. Kvand Ca2+currents were also not different between validated hiPSC-VSMCs differentiated from control and CS patient-derived hiPSCs. Pinacidil-sensitive KATPcurrents in control hiPSC-VSMCs were consistent with those in WT mouse VSMCs, and were considerably larger in CS hiPSC-VSMCs. Consistent with lack of any compensatory modulation of other currents, this resulted in membrane hyperpolarization, explaining the hypomyotonic basis of CS vasculopathy. Increased compliance and dilation in isolated CS mouse aortae, was associated with increased elastin mRNA expression. This was consistent with higher levels of elastin mRNA in CS hiPSC-VSMCs, suggesting that the hyperelastic component of CS vasculopathy is a cell-autonomous consequence of vascular KATPGoF.

Conclusions

The results show that hiPSC-VSMCs reiterate expression of the same major ion currents as primary VSMCs, validating the use of these cells to study vascular disease. The results further indicate that both the hypomyotonic and hyperelastic components of CS vasculopathy are cell-autonomous phenomena driven by KATPoveractivity within VSMCs.
Identification of side effects of COVID-19 drug candidates on embryogenesis using an integrated zebrafish screening platform
Authors: Ernst Alexander , Piragyte Indre , Ayisha Marwa MP , Dung Le Ngoc , Grandgirard Denis , Leib Stephen L. , Oates Andrew , Mercader Nadia
Published: July 2023

Drug repurposing is an important strategy in COVID-19 treatment, but many clinically approved compounds have not been extensively studied in the context of embryogenesis, thus limiting their administration during pregnancy. Here we used the zebrafish embryo model organism to test the effects of 162 marketed drugs on cardiovascular development. Among the compounds used in the clinic for COVD-19 treatment, we found that Remdesivir led to reduced body size and heart functionality at clinically relevant doses. Ritonavir and Baricitinib showed reduced heart functionality and Molnupiravir and Baricitinib showed effects on embryo activity. Sabizabulin was highly toxic at concentrations only 5 times higher than Cmax and led to a mean mortality of 20% at Cmax. Furthermore, we tested if zebrafish could be used as a model to study inflammatory response in response to spike protein treatment and found that Remdesivir, Ritonavir, Molnupiravir, Baricitinib as well as Sabizabulin counteracted the inflammatory response related gene expression upon SARS-CoV-2 spike protein treatment. Our results show that the zebrafish allows to study immune-modulating properties of COVID-19 compounds and highlights the need to rule out secondary defects of compound treatment on embryogenesis. All results are available on a user friendly web-interfacehttps://share.streamlit.io/alernst/covasc_dataapp/main/CoVasc_DataApp.pythat provides a comprehensive overview of all observed phenotypic effects and allows personalized search on specific compounds or group of compounds. Furthermore, the presented platform can be expanded for rapid detection of developmental side effects of new compounds for treatment of COVID-19 and further viral infectious diseases.

Summary statement

A zebrafish screening platform assesses side effects on cardiovascular development and behavior of FDA approved drugs used in clinical practice to treat COVID-19 and their immune modulatory effect upon spike protein treatment.
Cellular Substrate of Eligibility Traces
Authors: Caya-Bissonnette Léa , Naud Richard , Béïque Jean-Claude
Published: July 2023

The ability of synapses to undergo associative, activity-dependent weight changes constitutes a linchpin of current cellular models of learning and memory. It is, however, unclear whether canonical forms of Hebbian plasticity, which inherently detect correlations of cellular events occurring over short time scales, can solve the temporal credit assignment problem proper to learning driven by delayed behavioral outcomes. Recent evidence supports the existence of synaptic eligibility traces, a time decaying process that renders synapses momentarily eligible for a weight update by a delayed instructive signal. While eligibility traces offer a means of retrospective credit assignment, their material nature is unknown. Here, we combined whole-cell recordings with two-photon uncaging, calcium imaging and biophysical modeling to address this question. We observed and parameterized a form of behavioral timescale synaptic plasticity (BTSP) in layer 5 pyramidal neurons of mice prefrontal areas wherein the pairing of temporally separated pre- and postsynaptic events (0.5 s – 1 s), irrespective of order, induced synaptic potentiation. By imaging calcium in apical oblique dendrites, we reveal a short-term and associative plasticity of calcium dynamics (STAPCD) whose time-dependence mirrored the induction rules of BTSP. We identified a core set of molecular players that were essential for both STAPCD and BTSP and that, together with computational simulations, support a model wherein the dynamics of intracellular handling of calcium by the endoplasmic reticulum (ER) provides a latent memory trace of neural activity that instantiates synaptic weight updates upon a delayed instructive signal. By satisfying the requirements expected of eligibility traces, this mechanism accounts for how individual neurons can conjunctively bind cellular events that are separated by behaviorally relevant temporal delays, and thus offers a cellular model of reinforced learning.
Sex difference in the facilitation of fear learning by prior fear conditioning
Authors: Cole Kehinde E. , Parsons Ryan G.
Published: July 2023

There is now ample evidence that the strength and underlying mechanisms of memory formation can be drastically altered by prior experience. However, the prior work using rodent models on this topic has used only males as subjects, and as a result, we do know whether or not the effects of prior experience on subsequent learning are similar in both sexes. As a first step towards addressing this shortcoming rats of both sexes were given auditory fear conditioning, or fear conditioning with unsignaled shocks, followed an hour or a day later by a single pairing of light and shock. Fear memory for each experience was assessed by measuring freezing behavior to the auditory cue and fear-potentiated startle to the light. Results showed that males trained with auditory fear conditioning showed facilitated learning to the subsequent visual fear conditioning session when the two training sessions were separated by one hour or one day. Females showed evidence of facilitation in rats given auditory conditioning when they were spaced by an hour, but not when they were spaced by one day. Contextual fear conditioning did not support the facilitation of subsequent learning under any conditions. These results indicate that the mechanism by which prior fear conditioning facilitates subsequent learning differs between sexes, and they set the stage for mechanistic studies to understand the neurobiological basis of this sex difference.
Machine learning reveals the control mechanics of an insect wing hinge
Authors: Melis Johan M. , Siwanowicz Igor , Dickinson Michael H.
Published: July 2023

Insects constitute the most species-rich radiation of metazoa, a success due to the evolution of active flight. Unlike pterosaurs, birds, and bats, the wings of insects did not evolve from legs1, but are novel structures attached to the body via a biomechanically complex hinge that transforms tiny, high-frequency oscillations of specialized power muscles into the sweeping back-and-forth motion of the wings2. The hinge consists of a system of tiny, hardened structures called sclerites that are interconnected to one another via flexible joints and regulated by the activity of specialized control muscles. Here, we imaged the activity of these muscles in a fly using a genetically encoded calcium indicator, while simultaneously tracking the 3D motion of the wings with high-speed cameras. Using machine learning approaches, we created a convolutional neural network3that accurately predicts wing motion from the activity of the steering muscles, and an encoder-decoder4that predicts the role of the individual sclerites on wing motion. By replaying patterns of wing motion on a dynamically scaled robotic fly, we quantified the effects of steering muscle activity on aerodynamic forces. A physics-based simulation that incorporates our model of the hinge generates flight maneuvers that are remarkably similar to those of free flying flies. This integrative, multi-disciplinary approach reveals the mechanical control logic of the insect wing hinge, arguably among the most sophisticated and evolutionarily important skeletal structures in the natural world.
Electron-counting in MicroED
Authors: Hattne Johan , Clabbers Max T. B. , Martynowycz Michael W. , Gonen Tamir
Published: July 2023

The combination of high sensitivity and rapid readout makes it possible for electron-counting detectors to record cryogenic electron microscopy data faster and more accurately without increasing the exposure. This is especially useful for MicroED of macromolecular crystals where the strength of the diffracted signal at high resolution is comparable to the surrounding background. The ability to decrease the exposure also alleviates concerns about radiation damage which limits the information that can be recovered from a diffraction measurement. However, the dynamic range of electron-counting detectors requires careful data collection to avoid errors from coincidence loss. Nevertheless, these detectors are increasingly deployed in cryo-EM facilities, and several have been successfully used for MicroED. Provided coincidence loss can be minimized, electron-counting detectors bring high potential rewards.
Engineering transposon-associated TnpB-ωRNA system for efficient gene editing and disease treatment in mouse
Authors: Li Zhifang , Guo Ruochen , Sun Xiaozhi , Li Guoling , Liu Yuanhua , Huo Xiaona , Yang Rongrong , Shao Zhuang , Zhang Hainan , Zhang Weihong , Zhang Xiaoyin , Ma Shuangyu , Yao Yinan , Liu Xinyu , Yang Hui , Hu Chunyi , Zhou Yingsi , Xu Chunlong
Published: July 2023

Transposon-associated ribonucleoprotein TnpB is known to be the ancestry endonuclease of diverse Cas12 effector proteins from type-V CRISPR system. Given its small size (409 aa), it is of interest to examine whether engineered TnpB could be used for efficient mammalian genome editing. Here, we showed that the gene editing activity of native TnpB in mouse embryos was already higher than previously identified small-sized Cas12f1. Further stepwise engineering of noncoding RNA (ωRNA or reRNA) component of TnpB significantly elevated the nuclease activity of TnpB. Notably, an optimized TnpB-ωRNA system could be efficiently deliveredin vivowith single adeno-associated virus (AAV) and prevented the disease phenotype in a tyrosinaemia mouse model. Thus, the engineered miniature TnpB system represents a new addition to the current genome editing toolbox, with the unique feature of the smallest effector size that facilitate efficient AAV delivery for editing of cells and tissues.
Automated Microbial Classification System based on Deep Convolutional Neural Networks using Images from Colony Picker
Authors: Park Sehyun , Yeoh Jing Wui , Choo Ching Thong , Lim Cheng Kai , Dao Viet Linh , Poh Chueh Loo
Published: July 2023

Colony screening in single and multi-species environments is an essential step for microbiome studies. However, it possesses a high possibility of inaccurately classifying the species of interest and demands a high degree of manpower and time. Thus, automating the classification of microbes is beneficial to minimize the time and inaccuracy in the colony screening/picking step. Here, we developed an automated microbial classification system for five target species, based on deep Convolutional Neural Networks (CNN) using images captured by an automated robotic colony picker. Multiple possible scenarios of colony culture and diverse morphologies of colonies were examined in building the training and test datasets to train and validate the model and performance on real-life implementations. The final model trained using 60,000 training images, with 12,000 images per species and 3-fold cross-validation, achieved a test accuracy of 94.2% and a test loss of 0.154. Upon testing using a deployment dataset of 4,500 images (900 images per species) with different methods of applying cells onto the agar plate, high accuracy of up to 96.6% was obtained. Five evaluation metrics were implemented to evaluate diverse scenarios of the test data to justify the validity of the model in real-life applications. This model forms a foundation for the classification of more species through transfer learning in the future.
Online speech synthesis using a chronically implanted brain-computer interface in an individual with ALS
Authors: Angrick Miguel , Luo Shiyu , Rabbani Qinwan , Candrea Daniel N. , Shah Samyak , Milsap Griffin W. , Anderson William S. , Gordon Chad R. , Rosenblatt Kathryn R. , Clawson Lora , Maragakis Nicholas , Tenore Francesco V. , Fifer Matthew S. , Hermansky Hynek , Ramsey Nick F. , Crone Nathan E.
Published: July 2023

Recent studies have shown that speech can be reconstructed and synthesized using only brain activity recorded with intracranial electrodes, but until now this has only been done using retrospective analyses of recordings from able-bodied patients temporarily implanted with electrodes for epilepsy surgery. Here, we report online synthesis of intelligible words using a chronically implanted brain-computer interface (BCI) in a clinical trial participant (ClinicalTrials.gov,NCT03567213) with dysarthria due to amyotrophic lateral sclerosis (ALS). We demonstrate a reliable BCI that synthesizes commands freely chosen and spoken by the user from a vocabulary of 6 keywords originally designed to allow intuitive selection of items on a communication board. Our results show for the first time that a speech-impaired individual with ALS can use a chronically implanted BCI to reliably produce synthesized words that are intelligible to human listeners while preserving the participants voice profile.
In vivocharacterization of the optical and hemodynamic properties of the human sternocleidomastoid muscle through ultrasound-guided hybrid near-infrared spectroscopies
Authors: Cortese Lorenzo , Fernández Esteberena Pablo , Zanoletti Marta , Lo Presti Giuseppe , Aranda Velazquez Gloria , Ruiz Janer Sabina , Buttafava Mauro , Renna Marco , Di Sieno Laura , Tosi Alberto , Dalla Mora Alberto , Wojtkiewicz Stanislaw , Dehghani Hamid , de Fraguier Sixte , Nguyen-Dinh An , Rosinski Bogdan , Weigel Udo M. , Mesquida Jaume , Squarcia Mattia , Hanzu Felicia A. , Contini Davide , Mora Porta Mireia , Durduran Turgut
Published: July 2023

The non-invasive monitoring of the hemodynamics and metabolism of the sternocleidomastoid muscle (SCM) during respiration became a topic of increased interest partially due to the increased use of mechanical ventilation during the COVID-19 pandemic. Near-infrared diffuse optical spectroscopies were proposed as potential practical monitors of increased recruitment of SCM during respiratory distress. They can provide clinically relevant information on the degree of the patient’s respiratory effort that is needed to maintain an optimal minute ventilation, with potential clinical application ranging from evaluating chronic pulmonary diseases to more acute settings, such as acute respiratory failure, or to determine the readiness to wean from invasive mechanical ventilation.

In this paper, we present a detailed characterization of the optical properties (wave-length dependent absorption and reduced scattering coefficients) and hemodynamic properties (oxy-, deoxy- and total hemoglobin concentrations, blood flow, blood oxygen saturation and metabolic rate of oxygen extraction) of the human SCM, obtained by measuring sixty-five subjects through ultrasound-guided near-infrared time-resolved and diffuse correlation spectroscopies.

We provide detailed tables of the results related to SCM baseline (i.e. muscle at rest) properties, and reveal significant differences on the measured parameters due to variables such as side of the neck, sex, age, body mass index and thickness of the overlaying tissues, allowing future clinical studies to take into account such dependencies.
The successor representation subserves hierarchical abstraction for goal-directed behavior
Authors: Wientjes Sven , Holroyd Clay B.
Published: July 2023

Humans have the ability to craft abstract, temporally extended and hierarchically organized plans. For instance, when considering how to make spaghetti for dinner, we typically concern ourselves with useful “subgoals” in the task, such as cutting onions, boiling pasta, and cooking a sauce, rather than particulars such as how many cuts to make to the onion, or exactly which muscles to contract. A core question is how such decomposition of a more abstract task into logical subtasks happens in the first place. Previous research has shown that humans are sensitive to a form of higher-order statistical learning named “community structure”. Community structure is a common feature of abstract tasks characterized by a logical ordering of subtasks. This structure can be captured by a model where humans learn predictions of upcoming events multiple steps into the future, discounting predictions of events further away in time. One such model is the “successor representation”, which has been argued to be useful for hierarchical abstraction. As of yet, no study has convincingly shown that this hierarchical abstraction can be put to use for goal-directed behavior. Here, we investigate whether participants utilize learned community structure to craft hierarchically informed action plans for goal-directed behavior. Participants were asked to search for paintings in a virtual museum, where the paintings were grouped together in “wings” representing community structure in the museum. We find that participants’ choices accord with the hierarchical structure of the museum and that their response times are best predicted by a successor representation. The degree to which the response times reflect the community structure of the museum correlates with several measures of performance, including the ability to craft temporally abstract action plans. These results suggest that successor representation learning subserves hierarchical abstractions relevant for goal-directed behavior.

AUTHOR SUMMARY

Humans have the ability to achieve a diverse range of goals in a highly complex world. Classic theories of decision making focus on simple tasks involving single goals. In the current study, we test a recent theoretical proposal that aims to address the flexibility of human decision making. By learning to predict the upcoming events, humans can acquire a ‘model’ of the world which they can then leverage to plan their behavior. However, given the complexity of the world, planning directly over all possible events can be overwhelming. We show that, by leveraging this predictive model, humans group similar events together into simpler “hierarchical” representations, which makes planning over these hierarchical representations markedly more efficient. Interestingly, humans seem to learn and remember both the complex predictive model and the simplified hierarchical model, using them for distinct purposes.
Post-exposure intranasal IFNα suppresses replication and neuroinvasion of Venezuelan Equine Encephalitis virus within olfactory sensory neurons
Authors: Cain Matthew D. , Rubin Klein N. , Jiang Xiaoping , Klein Robyn S.
Published: July 2023

Venezuelan Equine Encephalitis virus(VEEV) may enter the central nervous system (CNS) within olfactory sensory neurons (OSN) that originate in the nasal cavity after intranasal exposure. While it is known that VEEV has evolved several mechanisms to inhibit type I interferon (IFN) signaling within infected cells, whether this inhibits virologic control during neuroinvasion along OSN has not been studied. Here, we utilized an established murine model of intranasal infection with VEEV to assess the cellular targets and IFN signaling responses after VEEV exposure. We found that immature OSN, which express higher levels of the VEEV receptor LDLRAD3 than mature OSN, are the first cells infected by VEEV. Despite rapid VEEV neuroinvasion after intranasal exposure, olfactory neuroepithelium (ONE) and olfactory bulb (OB) IFN responses, as assessed by evaluation of expression of interferon signaling genes (ISG), are delayed for up to 48 hours during VEEV neuroinvasion, representing a potential therapeutic window. Indeed, a single intranasal dose of recombinant IFNα triggers early ISG expression in both the nasal cavity and OB. When administered at the time of or early after infection, IFNα treatment delayed onset of sequelae associated with encephalitis and extended survival by several days. VEEV replication after IFN treatment was also transiently suppressed in the ONE, which inhibited subsequent invasion into the CNS. Our results demonstrate a critical and promising first evaluation of intranasal IFNα for the treatment of human encephalitic alphavirus exposures.

AUTHOR SUMMARY

Venezuelan Equine Encephalitis virus (VEEV) may enter the brain through the nasal cavity upon intranasal exposure. The nasal cavity normally displays brisk antiviral immune responses, thus it is unclear why this type of exposure leads to fatal VEEV infection. Using an established murine model of intranasal infection with VEEV we identified the initial targets of infection within the nasal cavity and found that antiviral immune responses to virus at this site and during brain infection are delayed for up to 48 hours. Thus, administration of a single intranasal dose of recombinant IFNα at the time of or early after infection improved early antiviral immune responses and suppressed viral replication, which delayed onset of brain infection and extended survival by several days. VEEV replication after IFN treatment was also transiently suppressed in the nasal cavity, which inhibited subsequent invasion into the CNS. Our results demonstrate a critical and promising first evaluation of intranasal IFNα for the treatment of human VEEV exposures.
Bridges instead of boats? The Mla system of diderm FirmicuteVeillonella parvulareveals an ancestral transenvelope core of phospholipid trafficking
Authors: Grasekamp Kyrie P. , Beaud Basile , Taib Najwa , Audrain Bianca , Bardiaux Benjamin , Rossez Yannick , Izadi-Pruneyre Nadia , Lejeune Maylis , Trivelli Xavier , Chouit Zina , Guerardel Yann , Ghigo Jean-Marc , Gribaldo Simonetta , Beloin Christophe
Published: July 2023

Despite extensive characterisation of envelope biogenesis systems in diderm bacteria, glycerophospholipid (GPL) trafficking remains poorly understood, and has only been studied in a handful of model species. Within the Proteobacteria, the maintenance of lipid asymmetry (Mla) system facilitates retrograde GPL trafficking via six proteins, MlaA-F. GPLs are extracted from the outer leaflet of the outer membrane by the lipoprotein MlaA which associates with porin trimers, then shipped through the periplasmic space by the chaperone MlaC, which finally delivers GPLs to the inner membrane complex formed by MlaBDEF. Here, we investigate GPL trafficking inVeillonella parvula, a diderm member of the Firmicutes which encodes an Mla system devoid of MlaA and MlaC.V. parvulaΔmlamutants display phenotypes characteristic of disrupted lipid asymmetry such as hypervesiculation and detergent hypersensitivity, and lipid content analysis from outer membrane vesicles reveals an enrichment for the major lipid component phosphatidylethanolamine. Interestingly, suppressor analysis identifies mutations intamBthat rescue detergent hypersensitivity and hypervesiculation of Δmlastrains, supporting the involvement of these two systems in antagonistic GPL trafficking functions across diverse bacterial lineages. A combination of structural modeling and subcellular localisation assays shows that MlaDVpis longer than in classical diderm models and forms a transenvelope bridge, encoding both an inner membrane-localised MCE domain and an outer membrane ß-barrel. These results strongly suggest thatV. parvulapossesses a minimal Mla system for GPL trafficking, replacing the need for chaperones and outer membrane lipoproteins by directly connecting the two membranes. Finally, phylogenomic analysis indicates that this MlaEFD self-contained architecture is widely distributed in diderm bacteria and most likely represents the ancestral functional core of the Mla system, which subsequently increased in complexity in Proteobacteria and closely related phyla following the emergence of MlaABC. Our work broadens the diversity of current models of GPL trafficking in diderm bacteria, challenging the paradigm set by classical models and shedding light on the evolution of a crucial system in the biogenesis and maintenance of the bacterial outer membrane.
How Myosin VI Traps its Off-State, is Activated and Dimerizes
Authors: Canon Louise , Kikuti Carlos , Planelles-Herrero Vicente J. , Lin Tianming , Mayeux Franck , Sirkia Helena , Lee Young il , Heidsieck Leila , Velikovsky Léonid , David Amandine , Liu Xiaoyan , Moussaoui Dihia , Forest Emma , Höök Peter , Petersen Karl J. , Di Cicco Aurélie , Sires-Campos Julia , Lévy Daniel , Delevoye Cédric , Sweeney H. Lee , Houdusse Anne
Published: July 2023

Myosin VI (Myo6) is the only minus-end directed nanomotor on actin, allowing it to uniquely contribute to numerous cellular functions. As for other nanomotors, proper functioning of Myo6 relies on precise spatio-temporal control of motor activity via a poorly defined off-state and interactions with partners. Our structural, functional, and cellular studies reveal key features of myosin regulation and indicate that not all partners can activate Myo6. TOM1 and Dab2 cannot bind the off-state while, GIPC1 binds Myo6, releases its auto-inhibition and triggers proximal dimerization. Myo6 partners thus differentially recruit Myo6. We solved a crystal structure of the proximal dimerization domain, and show that its disruption compromises endocytosis in HeLa cells, emphasizing the importance of Myo6 dimerization. Finally, we show that the L926Q deafness mutation disrupts Myo6 auto-inhibition and indirectly impairs proximal dimerization. Our study thus demonstrates the importance of partners in the control of Myo6 auto-inhibition, localization, and activation.
BiodecomposingSpirulina platensisby ade novodesignedBacillus subtilis-based method to develop a medium for the high cell-density cultivation ofEscherichia coliin batch mode
Authors: Li Xiaowen , Wei Zhengqi , Ge Jingyi , Pan Yingying , Chu Xiang , Huang Baolin , Zhao Jiawei , Li Yanzhao , Zhou Yizhuang
Published: July 2023

High cell-density cultivation (HCDC) is fundamental to basic research and industrial applications, especially in batch mode. However, limited media are available for batch culture of HCDC, because the media for batch culture must contain extremely sufficient nutrients on the one hand and few or even no substrates to generate detrimental metabolite on the other hand to attain HCDC.Spirulina platensis(SP), a new media material, is considered ideal for the development of such media. Here, we develop a biolysis method for SP degradation based on the cultivation supernatant ofBacillus subtilisand extensively demonstrate its higher degradation (indicated by the production of more small peptides and free amino acids) and cultivation effectiveness with three other methods. Based on its SP hydrolysates, a modified SP-based broth (MSP) is then formulated. Tests onEscherichia coliK-12 show that MSP achieves HCDC with several benefits: (i) its maximum optical density at 600 nm is ∼16.67, significantly higher than that of Luria-Bertani (LB) broth (only ∼6.30); (ii) MSP requires only 36 h to reach peak growth, much faster than that of LB (48 h); (iii) its maximum growth (1.12 ± 0.01 h−1) is significantly higher than that of LB (0.20 ± 0.00 h−1); (v) MSP initiates growth immediately after inoculation (lag time <0), comparable to LB; (iv) the number of viable cells in MSP is high (∼2.16 × 1011ml-1), ∼10.19 times the amount in LB. Consequently, we envision MSP will become the first choice forE. coliHCDC batch culture in the future.

Importance

So far, it is the first time to develop a high-efficiency method for transformingSpirulina platensis(SP) into medium ingredients. Based on its SP hydrolysates, a high cell-density cultivation (HCDC) medium for the batch culture ofEscherichia coliis formulated for the first time, which is greatly beneficial for both basic research and industrial applications. In addition to HCDC, the SP hydrolysates can be extended to a wide range of applications, due to their rich nutrient content. Besides, this study demonstrates for the first time that SP is an ideal material to develop HCDC media. Furthermore, this study demonstrates that medium development and modification for batch culture can attain HCDC, without the development of new culture technologies. Therefore, this study highlights the importance of the rebirth of medium development and modification and supports the shift from developing new culture technologies to medium development and modification for HCDC in batch mode.
Interaction between PSD 95 and TRPV4 through PDZ domain controls TRPV4’s localization and activity
Authors: Lee Eun Jeoung , Kim Kiwol , Davaadorj Otgonnamjil , Shin Sung Hwa , Kang Sang Sun
Published: July 2023

The TRPV4 cation channel, is expressed in a broad range of tissues where it participates in generation of Ca2+signal and/or depolarization of membrane potential. Here, we identified post synaptic density protein 95 (PSD95) as an interacting protein of this epithelial Ca2+channel using confocal microscopy analysis and immunological assay. Using co-immunoprecipitation assays, we demonstrated that PSD95 was part of the TRPV4 protein complex. PSD95 protein was specifically associated with the C-terminal tail of TRPV4 to form a complex. A TRPV4 tail deletion mutant (ΔDAPL871: 4d) exhibited a diminished capacity to bind PSD95. Confocal microscopy analysis suggested that apical localization of TRPV4 required PSD95–TRPV4 interaction. Our data clearly suggest that formation of a complex between TRPV4 and PSD95 can regulate TRPV4 membrane localization. Both TRPV4 Ca2+channel and its autophagy activity of 4d were reduced by more than 80% compared to those of the TRPV4 wild type. Our observation suggests that PSD95–TRPV4 complex plays crucial roles in routing TRPV4 to the apical plasma membrane and maintaining its authentic Ca2+channel and biological function.

Capsule

Background

TRPV4 contain putative PDZ tail motif (DAPL871).

Results

Deletion of TRPV4 tail PDZ motif fails to interact with PSD95 PDZ III domain.

Conclusion

TRPV4 tail is an authentic PDZ motif to interact with PSD95.

Significance

Interaction between TRPV4 and PSD95 requires for its proper biological functions.