bluuebunny/crossref_metadata_2025 huggingface dataset:
2.7 Å cryo-EM structure of ex vivo RML prion fibrils
Authors: Manka Szymon W. , Zhang Wenjuan , Wenborn Adam , Betts Jemma , Joiner Susan , Saibil Helen R. , Collinge John , Wadsworth Jonathan D.F.
Published: December 2021

Mammalian prions are lethal infectious agents that propagate as distinct strains and are composed of multichain assemblies of misfolded host-encoded prion protein (PrP), often referred to as prion rods. The structural features that define infectious prion rods and the molecular determinants of prion strain diversity are poorly understood. Here, we present a near-atomic resolution cryo-EM structure of PrP fibrils present in highly infectious prion rod preparations isolated from the brains of RML prion-infected mice. We found that prion rods comprise single-protofilament helical amyloid fibrils that coexist with twisted pairs of the same protofilaments. Each rung of the protofilament is formed by a single PrP monomer with the ordered core comprising PrP residues 94-225, which folds to create two asymmetric lobes with the N-linked glycans and the glycosylphosphatidylinositol anchor projecting from the C-terminal lobe. The overall architecture is comparable to that of recently reported PrP fibrils isolated from the brain of hamsters infected with the 263K prion strain. However, there are marked conformational variations that could result from differences in PrP primary sequence and/or represent distinguishing features of the distinct prion strains. These conformational changes impact the overall geometry of the fibrils and may also impact fibril pairing, one or both of which may critically influence PrP glycoform selection that occurs during strain-specific prion propagation.
tRForest: a novel random forest-based algorithm for tRNA-derived fragment target prediction
Authors: Parikh Rohan , Wilson Briana , Marrah Laine , Su Zhangli , Saha Shekhar , Kumar Pankaj , Huang Fenix , Dutta Anindya
Published: December 2021

tRNA fragments (tRFs) are small RNAs comparable to the size and function of miRNAs. tRFs are generally Dicer independent, are found associated with Ago, and can repress expression of genes post-transcriptionally. Given that this expands the repertoire of small RNAs capable of post-transcriptional gene expression, it is important to predict tRF targets with confidence. Some attempts have been made to predict tRF targets, but are limited in the scope of tRF classes used in prediction or limited in feature selection. We hypothesized that established miRNA target prediction features applied to tRFs through a random forest machine learning algorithm will immensely improve tRF target prediction. Using this approach, we show significant improvements in tRF target prediction for all classes of tRFs and validate our predictions in two independent cell lines. Finally, Gene Ontology analysis suggests that among the tRFs conserved between mice and humans, the predicted targets are enriched significantly in neuronal function, and we show this specifically for tRF-3009a. These improvements to tRF target prediction further our understanding of tRF function broadly across species and provide avenues for testing novel roles for tRFs in biology. We have created a publicly available website for the targets of tRFs predicted by tRForest.
Glutathione binding to the plant AtAtm3 transporter and implications for the conformational coupling of ABC transporters
Authors: Fan Chengcheng , Rees Douglas C.
Published: December 2021

The ATP Binding Cassette (ABC) transporter of mitochondria (Atm) from Arabidopsis thaliana (AtAtm3) has been implicated in the maturation of cytosolic iron-sulfur proteins and heavy metal detoxification, plausibly by exporting glutathione derivatives. Using single-particle cryo-electron microscopy, we have determined structures of AtAtm3 in multiple conformational states. These structures not only provide a structural framework for defining the alternating access transport cycle, but also highlight an unappreciated feature of the glutathione binding site, namely the paucity of cysteine residues that could potentially form inhibitory mixed disulfides with glutathione. Despite extensive efforts, we were unable to prepare the ternary complex of AtAtm3 with bound GSSG and MgATP. A survey of structurally characterized type IV ABC transporters that includes AtAtm3 establishes that while nucleotides are found associated with all conformational states, they are effectively required to stabilize occluded and outward-facing conformations. In contrast, transport substrates have only been observed associated with inward-facing conformations. The absence of structures containing both nucleotide and transport substrate suggests that this ternary complex exists only transiently during the transport cycle.
ProteinGLUE: A multi-task benchmark suite for self-supervised protein modeling
Authors: Capel Henriette , Weiler Robin , Dijkstra Maurits , Vleugels Reinier , Bloem Peter , Feenstra K. Anton
Published: December 2021

Self-supervised language modeling is a rapidly developing approach for the analysis of protein sequence data. However, work in this area is heterogeneous and diverse, making comparison of models and methods difficult. Moreover, models are often evaluated only on one or two downstream tasks, making it unclear whether the models capture generally useful properties. We introduce the ProteinGLUE benchmark for the evaluation of protein representations: a set of seven tasks for evaluating learned protein representations. We also offer reference code, and we provide two baseline models with hyperparameters specifically trained for these benchmarks.

Pre-training was done on two tasks, masked symbol prediction and next sentence prediction. We show that pre-training yields higher performance on a variety of downstream tasks such as secondary structure and protein interaction interface prediction, compared to no pre-training. However, the larger base model does not outperform the smaller medium. We expect the ProteinGLUE benchmark dataset introduced here, together with the two baseline pre-trained models and their performance evaluations, to be of great value to the field of protein sequence-based property prediction.

Availability

code and datasets from https://github.com/ibivu/protein-glue
A library for fMRI real-time processing systems in python (RTPSpy) with comprehensive online noise reduction, fast and accurate anatomical image processing, and online processing simulation
Authors: Misaki Masaya , Bodurka Jerzy , Paulus Martin P
Published: December 2021

Real-time fMRI (rtfMRI)has enormous potential for both mechanistic brain imaging studies or treatment-oriented neuromodulation. However, the adaption of rtfMRI has been limited due to technical difficulties implement an efficient computational framework. Here, we introduce a python library for real-time fMRI (rtfMRI) data processing systems, Real-Time Processing System in python (RTPSpy), to provide building blocks for a custom rtfMRI application with extensive and advanced functionalities. RTPSpy is a library package including 1) a fast, comprehensive, and flexible online fMRI image processing modules comparable to offline denoising, 2) utilities for fast and accurate anatomical image processing to define an anatomical target region, 3) a simulation system of online fMRI processing to optimize a pipeline and target signal calculation, 4) simple interface to an external application for feedback presentation, and 5) a boilerplate graphical user interface (GUI) integrating operations with RTPSpy library. The fast and accurate anatomical image processing utility wraps external tools, including FastSurfer, ANTs, and AFNI, to make tissue segmentation and region of interest masks. We confirmed that the quality of the output masks was comparable with FreeSurfer, and the anatomical image processing could complete in a few minutes. The modular nature of RTPSpy provides the ability to use it for a simulation analysis to optimize a processing pipeline and target signal calculation. We present a sample script for building a real-time processing pipeline and running a simulation using RTPSpy. The library also offers a simple signal exchange mechanism with an external application using a TCP/IP socket. While the main components of the RTPSpy are the library modules, we also provide a GUI class for easy access to the RTPSpy functions. The boilerplate GUI application provided with the package allows users to develop a customized rtfMRI application with minimum scripting labor. The limitations of the package as it relates to environment-specific implementations are discussed. These library components can be customized and can be used in parts. Taken together, RTPSpy is an efficient and adaptable option for developing rtfMRI applications. The package is available from GitHub (https://github.com/mamisaki/RTPSpy) with GPL3 license.
GiantStarshipelements mobilize accessory genes in fungal genomes
Authors: Gluck-Thaler Emile , Ralston Timothy , Konkel Zachary , Ocampos Cristhian Grabowski , Ganeshan Veena Devi , Dorrance Anne E. , Niblack Terry L. , Wood Corlett W. , Slot Jason C. , Lopez-Nicora Horacio D. , Vogan Aaron A.
Published: December 2021

Accessory genes are variably present among members of a species and are a reservoir of adaptive functions. In bacteria, differences in gene distributions among individuals largely result from mobile elements that acquire and disperse accessory genes as cargo. In contrast, the impact of cargo-carrying elements on eukaryotic evolution remains largely unknown. Here, we show that variation in genome content within multiple fungal species is facilitated byStarships,a novel group of massive mobile elements that are 110 kb long on average, share conserved components, and carry diverse arrays of accessory genes. We identified hundreds ofStarship-like regions across every major class of filamentous Ascomycetes, including 28 distinctStarshipsthat range from 27-393 kb and last shared a common ancestor ca. 400 mya. Using new long-read assemblies of the plant pathogenMacrophomina phaseolina, we characterize 4 additionalStarshipswhose past and ongoing activities contribute to standing variation in genome structure and content. One of these elements,Voyager, inserts into 5S rDNA and contains a candidate virulence factor whose increasing copy number has contrasting associations with pathogenic and saprophytic growth, suggestingVoyager’s activity underlies an ecological trade-off. We propose thatStarshipsare eukaryotic analogs of bacterial integrative and conjugative elements based on parallels between their conserved components and may therefore represent the first known agents of active gene transfer in eukaryotes. Our results suggest thatStarshipshave shaped the content and structure of fungal genomes for millions of years and reveal a new concerted route for evolution throughout an entire eukaryotic phylum.
Single-cell multi-omic velocity infers dynamic and decoupled gene regulation
Authors: Li Chen , Virgilio Maria , Collins Kathleen L. , Welch Joshua D.
Published: December 2021

Single-cell multi-omic datasets, in which multiple molecular modalities are profiled within the same cell, provide a unique opportunity to discover the relationships between cellular epigenomic and transcriptomic changes. To realize this potential, we developed MultiVelo, a mechanistic model of gene expression that extends the RNA velocity framework to incorporate epigenomic data. MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of chromatin accessibility and gene expression from single-cell data, providing a quantitative summary of the temporal relationship between epigenomic and transcriptomic changes. Incorporating chromatin accessibility data significantly improves the accuracy of cell fate prediction compared to velocity estimates from RNA only. Fitting MultiVelo on single-cell multi-omic datasets from brain, skin, and blood cells reveals two distinct classes of genes distinguished by whether chromatin closes before or after transcription ceases. Our model also identifies four types of cell states–two states in which epigenome and transcriptome are coupled and two distinct decoupled states. The parameters inferred by MultiVelo quantify the length of time for which genes occupy each of the four states, ranking genes by the degree of coupling between transcriptome and epigenome. Finally, we identify time lags between transcription factor expression and binding site accessibility and between disease-associated SNP accessibility and expression of the linked genes. We provide an open-source Python implementation of MultiVelo on PyPI and GitHub (https://github.com/welch-lab/MultiVelo).
Potential cross-protection against SARS-CoV-2 from previous exposure to bovine coronavirus
Authors: Querne Lana Bazan Peters , Bastos Fernanda Zettel , Beirão Breno Castello Branco
Published: December 2021

Humans have long shared infectious agents with cattle, and the common cold OC-43 CoV is a not-so-distant example of cross-species viral spillover. Human exposure to BCoV is certainly common, as the virus is endemic in cattle-raising regions. This article shows an in silico investigation of shared viral epitopes between BCoV and SARS-CoV-2. HLA recognition and lymphocyte reactivity were assessed using freely-available resources. Several epitopes were shared between BCoV and SARS-CoV-2, both for B and T lymphocytes. These data demonstrate that possible cross-protection is being induced by human exposure to cattle.
Genomic landscape, polymorphism and possible LINE-associated delivery of G-Quadruplex motifs in the bovine genes
Authors: Stefos Georgios C. , Theodorou Georgios , Politis Ioannis
Published: December 2021

G-Quadruplex structures are non-B DNA structures that occur in regions carrying short runs of guanines. They are implicated in several biological processes including transcription, translation, replication and telomere maintenance as well as in several pathological conditions like cancer and thus they have gained the attention of the scientific community. The rise of the –omics era significantly affected the G-quadruplex research and the genome-wide characterization of G-Quadruplexes has been rendered a necessary first step towards applying genomics approaches for their study. While in human and several model organisms there is a considerable number of works studying genome-wide the DNA motifs with potential to form G-quadruplexes (G4-motifs), there is a total absence of any similar studies regarding livestock animals. The objectives of the present study were to provide a detailed characterization of the bovine genic G4-motifs’ distribution and properties and to suggest a possible mechanism for the delivery of G4 motifs in the genes. Our data indicate that the distribution of G4s within bovine genes and the annotation of said genes to Gene Ontology terms are similar to what is already shown for other organisms. By investigating their structural characteristics and polymorphism, it is obvious that the overall stability of the putative quadruplex structures is in line with the current notion in the G4 field. Similarly to human, the bovine G4s are overrepresented in specific LINE repeat elements, the L1_BTs in the case of cattle. We suggest these elements as vehicles for delivery of G4 motifs in the introns of the bovine genes. Lastly, it seems that a basis exists for connecting traits of agricultural importance to the genetic variation of G4 motifs, thus, cattle could become an interesting new model organism for G4-related genetic studies.
Nanoscale details of mitochondrial fission revealed by cryo-electron tomography
Authors: Mageswaran Shrawan Kumar , Grotjahn Danielle Ann , Zeng Xiangrui , Barad Benjamin Asher , Medina Michaela , Hoang My Hanh , Dobro Megan J , Chang Yi-Wei , Xu Min , Yang Wei Yuan , Jensen Grant J.
Published: December 2021

Mitochondrial fission is required for proper segregation during cell division, quality control, and cellular homeostasis (metabolism and energy production). Despite its importance, models of the process remain speculative. Here we apply cryogenic electron tomography to image the nanoscale architecture of mitochondrial fission in mammalian cells. We find that constriction of the inner and outer membranes is coordinated, suggesting that force on both membranes is applied externally. While we observe ER at constriction sites, it did not encircle constrictions. Instead, we find long bundles of both unbranched actin and septin filaments enriched at constrictions. Actin bundles align with the central region of division bridges and septin bundles with the necks on either side. Septin bundles appear to guide microtubules to constriction sites, suggesting, along with autolysosomes observed in the vicinity, a pathway for mitophagy. Together, our results rule out several existing models for mitochondrial fission and provide empirical parameters to inform the development of realistic coarse-grained models in the future.
Determining Risk Factors for Triple Whammy Acute Kidney Injury
Authors: Leete Jessica , Wang Carolyn , López-Hernández Francisco J. , Layton Anita T.
Published: December 2021

Concurrent use of a diuretic, a renin-angiotensin system (RAS) inhibitor, and a non-steroidal anti-inflammatory drug (NSAID) significantly increases the risk of acute kidney injury (AKI). This phenomenon is known as “triple whammy”. Diuretics and RAS inhibitors, such as an angiotensin converting enzyme inhibitor or angiotensin receptor blocker, are often prescribed in tandem for the treatment of hypertension, whereas some NSAIDs, such as ibuprofen, are available over the counter. As such, concurrent treatment with all three drugs is common. The goals of this study are to better understand the mechanisms underlying the development of triple whammy AKI and to identify physiological factors that may increase an individual’s susceptibility. To accomplish these goals, we utilize computational models of long-term blood pressure regulation. These models include variables describing the heart and circulation, kidney function, sodium and water reabsorption in the nephron and the RAS and are parameterized separately for men and women. Hypertension is modeled as overactive renal sympathetic nervous activity. Model simulations suggest that individual variations in water intake, the myogenic response, and drug sensitivity may predispose patients with hypertension to develop triple whammy-induced AKI.
Chemical-induced Gene Expression Ranking and its Application to Pancreatic Cancer Drug Repurposing
Authors: Pham Thai-Hoang , Qiu Yue , Liu Jiahui , Zimmer Steven , O’Neill Eric , Xie Lei , Zhang Ping
Published: December 2021

Chemical-induced gene expression profiles provide critical information on the mode of action, off-target effect, and cellar heterogeneity of chemical actions in a biological system, thus offer new opportunities for drug discovery, system pharmacology, and precision medicine. Despite their successful applications in drug repurposing, large-scale analysis that leverages these profiles is limited by sparseness and low throughput of the data. Several methods have been proposed to predict missing values in gene expression data. However, most of them focused on imputation and classification settings which have limited applications to real-world scenarios of drug discovery. Therefore, a new deep learning framework named chemical-induced gene expression ranking (CIGER) is proposed to target a more realistic but more challenging setting in which the model predicts the rankings of genes in the whole gene expression profiles induced byde novochemicals. The experimental results show that CIGER significantly outperforms existing methods in both ranking and classification metrics for this prediction task. Furthermore, a new drug screening pipeline based on CIGER is proposed to select approved or investigational drugs for the potential treatments of pancreatic cancer. Our predictions have been validated by experiments, thereby showing the effectiveness of CIGER for phenotypic compound screening of precision drug discovery in practice.
GREPore-seq: A Robust Workflow to Detect Changes after Gene Editing through Long-range PCR and Nanopore Sequencing
Authors: Quan Zi-Jun , Li Si-Ang , Yang Zhi-Xue , Zhao Juan-Juan , Li Guo-Hua , Zhang Feng , Wen Wei , Cheng Tao , Zhang Xiao-Bing
Published: December 2021

To achieve the enormous potential of gene-editing technology in clinical therapies, both the on-target and unintended editing consequences need to be thoroughly evaluated. However, there is a lack of a comprehensive, pipelined, large-scale and economical workflow for detecting genome editing outcomes, in particular insertion or deletion of a large fragment. Here, we describe an approach for efficient and accurate detection of multiple genetic changes after CRISPR-Cas9 editing by pooled nanopore sequencing of barcoded long-range PCR products. To overcome the high error rates and indels of nanopore sequencing, we developed a pipeline to capture the barcoded sequences by grepping reads of nanopore amplicon sequencing (GREPore-seq). GREPore-seq can detect NHEJ-mediated double-stranded oligodeoxynucleotide (dsODN) insertions with comparable accuracy to Illumina next-generation sequencing (NGS). GREPore-seq also identifies HDR-mediated large gene knock-in, which excellently correlates with FACS analysis data. Low-level plasmid backbone insertion after HDR editing was also detected. We have established a practical workflow to identify genetic changes, including quantifying dsODN insertions, knock-ins, plasmid backbone insertions, and large fragment deletions after CRISPR editing. This toolkit for nanopore sequencing of pooled long amplicons should have broad applications in assessing on-target HDR editing and inadvertent large indels of over 1 kb. GREPore-seq is freely available at GitHub (https://github.com/lisiang/GREPore-seq).
SBP-SITA: A sequence-based prediction tool for S-itaconation
Authors: Zhang Laizhi , Wang Xuanwen , Zhang Lin , Meng Yanzheng , Wang Ziyu , Chen Yu , Li Lei
Published: December 2021

As a recently-reported post-translational modification, S-itaconation plays an important role in inflammation suppression. In order to understand its regulatory mechanism in many life activities, the essential step is the recognition of S-itaconation. However, it is difficult to identify S-itaconation in the proteome for the high cost, which limits further investigation. In this study, we constructed an ensemble algorithm based on Soft Voting Classifier. The area under the ROC curve (AUC) value 0.73 for ensemble model. Accordingly, we constructed the on-line prediction tool dubbed SBP-SITA for easily identifying Cystine sites. SBP-SITA is available at http://www.bioinfogo.org/sbp-sita.
Simulated colonic fluid replicates the in vivo growth capabilities of Citrobacter rodentium mutants and highlights a critical role for the Cpx envelope stress response in mediating stressors encountered in the gastrointestinal tract
Authors: Gilliland Ashley , Gavino Christina , Gruenheid Samantha , Raivio Tracy
Published: December 2021

Citrobacter rodentium is an attaching and effacing (A/E) pathogen used as a model for enteropathogenic and enterohemorrhagic Escherichia coli infections in mice. While in the host, C. rodentium must adapt to stresses in the gastrointestinal tract such as antimicrobial peptides, pH changes, and bile salts. The Cpx envelope stress response (ESR) is a two-component system used by some bacteria to remediate stress by modulating gene expression and is necessary for C. rodentium pathogenesis in mice. To investigate genes in the Cpx regulon that may contribute to C. rodentium pathogenesis, RNA-Seq, SILAC, and microarray data from previous research was mined and the genes yebE, ygiB, bssR, and htpX were confirmed to be strongly upregulated by the presence of CpxRA using lux reporter constructs. To determine the function of these genes in vivo, knockout mutants were tested in C57Bl/6J and C3H/HeJ mice. Although none of the mutants exhibited marked virulence phenotypes, the ΔcpxRA mutant had reduced colonization and attenuated virulence, as previously determined. We also found that the absence of the Cpx ESR resulted in higher expression of the LEE master regulator, ler. In addition, we determined that the ΔcpxRA mutant had a growth defect in medium simulating the colon, as did several of the mutants bearing deletions in Cpx-upregulated genes. Overall, these results indicate that the ΔcpxRA virulence defect is not due to any single Cpx regulon gene examined. Instead, attenuation may be the result of defective growth in the colonic environment resulting from the collective impact of multiple Cpx-regulated genes.
SARS-CoV-2 Omicron: evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern
Authors: Aggarwal Anupriya , Stella Alberto Ospina , Walker Gregory , Akerman Anouschka , Milogiannakis Vanessa , Brilot Fabienne , Amatayakul-Chantler Supavadee , Roth Nathan , Coppola Germano , Schofield Peter , Jackson Jennifer , Henry Jake Y. , Mazigi Ohan , Langley David , Lu Yonghui , Forster Charles , McAllery Samantha , Mathivanan Vennila , Fichter Christina , Hoppe Alexandra Carey , Munier Mee Ling , Jack Hans-Martin , Cromer Deborah , Darley David , Matthews Gail , Christ Daniel , Khoury David , Davenport Miles , Rawlinson William , Kelleher Anthony D. , Turville Stuart
Published: December 2021

Genetically distinct viral variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recorded since January 2020. Over this time global vaccine programs have been introduced, contributing to lowered COVID-19 hospitalisation and mortality rates, particularly in the first world. In late 2021, the Omicron (B.1.1.529) virus variant emerged, with significant genetic differences and clinical effects from other variants of concern (VOC). This variant demonstrated higher numbers of polymorphisms in the gene encoding the Spike (S) protein, and there has been displacement of the dominant Delta variant. We assessed the impact of Omicron infection on the ability of: serum from vaccinated and / or previously infected individuals; concentrated human IgG from plasma donors, and licensed monoclonal antibody therapies to neutralise virus in vitro. There was a 17 to 22-fold reduction in neutralisation titres across all donors who had a detectable neutralising antibody titre to the Omicron variant. Concentrated pooled human IgG from convalescent and vaccinated donors had greater breadth of neutralisation, although the potency was still reduced 16-fold. Of all therapeutic antibodies tested, significant neutralisation of the Omicron variant was only observed for Sotrovimab, with other monoclonal antibodies unable to neutralise Omicron in vitro. These results have implications for ongoing therapy of individuals infected with the Omicron variant.
Rehydration of freeze substituted brain tissue for pre-embedding immunoelectron microscopy
Authors: Pérez-Garza Janeth , Parrish-Mulliken Emily , Deane Zachary , Ostroff Linnaea E.
Published: December 2021

Electron microscopy (EM) volume reconstruction is a powerful tool for investigating the fundamental structure of brain circuits, but the full potential of this technique is limited by the difficulty of integrating molecular information. High quality ultrastructural preservation is necessary for EM reconstruction, and intact, highly contrasted cell membranes are essential for following small neuronal processes through serial sections. Unfortunately, the antibody labeling methods used to identify most endogenous molecules result in compromised morphology, especially of membranes. Cryofixation can produce superior morphological preservation and has the additional advantage of allowing indefinite storage of valuable samples. We have developed a method based on cryofixation that allows sensitive immunolabeling of endogenous molecules, preserves excellent ultrastructure, and is compatible with high-contrast staining for serial EM reconstruction.
Nested calcium dynamics support daily cell unity and diversity in the suprachiasmatic nuclei of free-behaving mice
Authors: Cheikh Hussein Lama El , Fontanaud Pierre , Mollard Patrice , Bonnefont Xavier
Published: December 2021

The suprachiasmatic nuclei (SCN) of the anterior hypothalamus host the circadian pacemaker that synchronizes mammalian rhythms with the day-night cycle. SCN neurons are intrinsically rhythmic, thanks to a conserved cell-autonomous clock mechanism. In addition, circuit-level emergent properties confer a unique degree of precision and robustness to SCN neuronal rhythmicity. However, the multicellular functional organization of the SCN is not yet fully understood. Although SCN neurons are well coordinated, experimental evidences indicate that some neurons oscillate out of phase in SCN explants, and possibly to a larger extentin vivo. Here, we used microendoscopic Ca2+iimaging to investigate SCN rhythmicity at a single cell resolution in free-behaving mice. We found that SCN neuronsin vivoexhibited fast Ca2+ispikes superimposed upon slow changes in baseline Ca2+ilevels. Both spikes and baseline followed a time-of-day modulation in many neurons, but independently from each other. Daily rhythms in basal Ca2+iwere well coordinated, while spike activity from the same neurons peaked at multiple times of the light cycle, and unveiled clock-independent interactions at the multicellular level. Hence, fast Ca2+ispikes and slow changes in baseline Ca2+ilevels highlighted how diverse activity patterns could articulate within the temporal network unity of the SCNin vivo, and provided support for a multiplex neuronal code in the circadian pacemaker.
Innate heuristics and fast learning support escape route selection in mice
Authors: Claudi Federico , Campagner Dario , Branco Tiago
Published: December 2021

When faced with imminent danger, animals must rapidly take defensive actions to reach safety. Mice can react to innately threatening stimuli in less than 250 milliseconds [1] and, in simple environments, use spatial memory to quickly escape to shelter [2,3]. Natural habitats, however, often offer multiple routes to safety which animals must rapidly identify and choose from to maximize the chances of survival [4]. This is challenging because while rodents can learn to navigate complex mazes to obtain rewards [5,6], learning the value of different routes through trial-and-error during escape from threat would likely be deadly. Here we have investigated how mice learn to choose between different escape routes to shelter. By using environments with paths to shelter of varying length and geometry we find that mice prefer options that minimize both path distance and path angle relative to the shelter. This choice strategy is already present during the first threat encounter and after only ~10 minutes of exploration in a novel environment, indicating that route selection does not require experience of escaping. Instead, an innate heuristic is used to assign threat survival value to alternative paths after rapidly learning the spatial environment. This route selection process is flexible and allows quick adaptation to arenas with dynamic geometries. Computational modelling of different classes of reinforcement learning agents shows that the observed behavior can be replicated by model-based agents acting in an environment where the shelter location is rewarding during exploration. These results show that mice combine fast spatial learning with innate heuristics to choose escape routes with the highest survival value. They further suggest that integrating priors acquired through evolution with knowledge learned from experience supports adaptation to changing environments while minimizing the need for trial-and-error when the errors are very costly.
Structural dissection of the first events following membrane binding of the islet amyloid polypeptide
Authors: Khemtemourian Lucie , Fatafta Hebah , Davion Benoit , Lecomte Sophie , Castano Sabine , Strodel Birgit
Published: December 2021

Amyloid forming proteins are involved in many pathologies and often belong to the class of intrinsically disordered proteins. One of these proteins is the islet amyloid polypeptide (IAPP), which is the main constituent of the amyloid fibrils found in the pancreas of type 2 diabetes patients. The molecular mechanism of IAPP-induced cell death is not yet understood, however it is known that cell membrane plays a dual role, being a catalyst of IAPP aggregation and the target of IAPP toxicity. Using FTIR spectroscopy, transmission electron microscopy, and molecular dynamics simulations we investigate the very first molecular steps following IAPP binding to a lipid membrane. In particular, we assess the combined effects of the charge state of amino-acid residue 18 and the IAPP-membrane interactions on the structures of monomeric and aggregated IAPP. Both our experiments and simulations reveal distinct IAPP-membrane interaction modes for the various IAPP variants. Membrane binding causes IAPP to fold into an amphipathic helix, which in the case of H18K- and H18R-IAPP can easily insert into the membrane. For all IAPP variants but H18E-IAPP, the membrane-bound α-helical structure is an intermediate on the way to IAPP amyloid aggregation, while H18E-IAPP remains in a stable helical conformation. The fibrillar aggregates of wild-type IAPP and H18K-IAPP are dominated by an antiparallel β-sheet conformation, while H18R- and H18A-IAPP exhibit both antiparallel and parallel β-sheets as well as amorphous aggregates. In summary, our results emphasize the importance of residue 18 for the structure and membrane interaction of IAPP. This residue is thus a good target for destabilizing amyloid fibrils of IAPP and inhibit its toxic actions by possible therapeutic molecules.
1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives
Authors: Dubini Romeo C. A. , Korytiaková Eva , Schinkel Thea , Heinrichs Pia , Carell Thomas , Rovó Petra
Published: December 2021

5-carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and baseexcision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ~10-20 kJ mol−1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the μs time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark.
A calibrated cell-based functional assay to aide classification of MLH1 DNA mismatch repair gene variants
Authors: Rath Abhijit , Radecki Alexander A. , Rahman Kaussar , Gilmore Rachel B. , Hudson Jonathan R. , Cenci Matthew , Tavtigian Sean V. , Grady James P. , Heinen Christopher D.
Published: December 2021

PURPOSE

Functional assays provide important evidence for classifying the disease significance of germline variants in the DNA mismatch repair genes. We sought to develop a cell-based approach for testing the function of variants of uncertain significance (VUS) in the MLH1 gene.

METHODS

Using CRISPR gene editing, we knocked-in MLH1 VUS into the endogenous MLH1 loci in human embryonic stem cells. We examined their impact at the RNA and protein level, including their ability to maintain stability of microsatellite sequences and instigate a DNA damage response. We calibrated these assays by testing well-established pathogenic and benign control variants.

RESULTS

Five VUS resulted in functionally abnormal protein, 15 VUS resulted in functionally normal protein, and one VUS showed mixed results. Furthermore, we converted the functional outputs into a single odds in favor of pathogenicity score for each VUS.

CONCLUSION

Our CRISPR-based functional assay successfully models phenotypes observed in patients in a cellular context. Using this approach, we generated evidence for or against pathogenicity for utilization by variant classification expert panels. Ultimately, this information will assist in proper diagnosis and disease management for suspected Lynch syndrome patients.
Preterm birth alters the maturation of the GABAergic system in the human prefrontal cortex
Authors: Lacaille Helene , Vacher Claire-Marie , Penn Anna A.
Published: December 2021

Developmental changes in GABAergic and glutamatergic systems during frontal lobe development have been hypothesized to play a key role in neurodevelopmental disorders seen in children born very preterm or low birth weight, but the associated cellular changes have not yet been identified. Here we studied the molecular development of the GABAergic system specifically in the dorsolateral prefrontal cortex, a region that that has been implicated in neurodevelopmental and psychiatric disorders. The maturation state of the GABAergic system in this region was assessed in human post-mortem brain samples, from term infants ranging in age from 0 to 8 months (n=17 male, 9 female). Gene expression was measured for 47 GABAergic genes and used to calculate a maturation index. This maturation index was significantly more dynamic in male than female infants. To evaluate the impact of premature birth on the GABAergic system development, samples from one-month-old term (n=9 male, 4 female) and one-month corrected-age (n=8 male, 6 female) very preterm infants, were compared using the same gene list and methodology. The maturation index for the GABAergic system was significantly lower (–50% p<0.05) in male preterm infants, with major alterations in genes linked to GABAergic function in astrocytes, suggesting astrocytic GABAergic developmental changes as a new cellular mechanism underlying preterm brain injury.
Evidence for a mouse origin of the SARS-CoV-2 Omicron variant
Authors: Wei Changshuo , Shan Ke-Jia , Wang Weiguang , Zhang Shuya , Huan Qing , Qian Wenfeng
Published: December 2021

The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting the possibility of host-jumping. The molecular spectrum (i.e., the relative frequency of the twelve types of base substitutions) of mutations acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients, but was highly consistent with spectra associated with evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host, then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak.
Cdc42 GTPase activating proteins Rga4 and Rga6 coordinate septum synthesis and membrane trafficking at the division plane during cytokinesis
Authors: Campbell Bethany F. , Hercyk Brian S. , Williams Ashlei R. , Miguel Ema San , Young Haylee G. , Das Maitreyi E.
Published: December 2021

Fission yeast cytokinesis is driven by simultaneous septum synthesis, membrane furrowing and actomyosin ring constriction. The septum consists of a primary septum flanked by secondary septa. First, delivery of the glucan synthase Bgs1 and membrane vesicles initiate primary septum synthesis and furrowing. Next, Bgs4 is delivered for secondary septum formation. It is unclear how septum synthesis is coordinated with membrane furrowing. Cdc42 promotes delivery of Bgs1 but not Bgs4. We find that after primary septum initiation, Cdc42 inactivators Rga4 and Rga6 localize to the division site. In rga4Δrga6Δ mutants Cdc42 activity is enhanced during late cytokinesis and cells take longer to separate. Electron micrographs of the division site in these mutants exhibit malformed septum with irregular membrane structures. These mutants have a larger division plane with enhanced Bgs1 delivery but fail to enhance accumulation of Bgs4 and several exocytic proteins. Additionally, these mutants show endocytic defects at the division site. This suggests that Cdc42 regulates only specific membrane trafficking events. Our data indicate that while active Cdc42 promotes primary septum synthesis, as cytokinesis progresses Rga4 and Rga6 localize to the division site to decrease Cdc42 activity. This couples specific membrane trafficking events with septum formation to allow proper septum morphology.

Abstract Figure

Synopsis

The GTPase Cdc42 regulates cytokinesis in cell-walled fission yeast. Active Cdc42 promotes the initiation of septum (new cell wall) synthesis to physically divide daughter cells. Here we show that Cdc42 activity must be decreased at the later stages of cytokinesis to enable proper septum formation. Mutants lacking Cdc42 inactivators, Rga4 and Rga6, lead to membrane trafficking defects and malformed septa consequently delaying cell separation.
pop-1/TCF, ref-2/ZIC and T-box factors regulate the development of anterior cells in the C. elegans embryo
Authors: Rumley Jonathan D. , Preston Elicia A. , Cook Dylan , Peng Felicia L. , Zacharias Amanda L. , Wu Lucy , Jileaeva Ilona , Murray John Isaac
Published: December 2021

Patterning of the anterior-posterior axis is fundamental to animal development. The Wnt pathway plays a major role in this process by activating the expression of posterior genes in animals from worms to humans. This observation raises the question of whether the Wnt pathway or other regulators control the expression of the many anterior-expressed genes. We found that the expression of five anterior-specific genes in Caenorhabditis elegans embryos depends on the Wnt pathway effectors pop-1/TCF and sys-1/β-catenin. We focused further on one of these anterior genes, ref-2/ZIC, a conserved transcription factor expressed in multiple anterior lineages. Live imaging of ref-2 mutant embryos identified defects in cell division timing and position in anterior lineages. Cis-regulatory dissection identified three ref-2 transcriptional enhancers, one of which is necessary and sufficient for anterior-specific expression. This enhancer is activated by the T-box transcription factors TBX-37 and TBX-38, and surprisingly, concatemerized TBX-37/38 binding sites are sufficient to drive anterior-biased expression alone, despite the broad expression of TBX-37 and TBX-38. Taken together, our results highlight the diverse mechanisms used to regulate anterior expression patterns in the embryo.
Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization
Authors: Doria-Rose Nicole A. , Shen Xiaoying , Schmidt Stephen D , O’Dell Sijy , McDanal Charlene , Feng Wenhong , Tong Jin , Eaton Amanda , Maglinao Maha , Tang Haili , Manning Kelly E. , Edara Venkata-Viswanadh , Lai Lilin , Ellis Madison , Moore Kathryn , Floyd Katharine , Foster Stephanie L. , Atmar Robert L. , Lyke Kirsten E. , Zhou Tongqing , Wang Lingshu , Zhang Yi , Gaudinski Martin R , Black Walker P , Gordon Ingelise , Guech Mercy , Ledgerwood Julie E , Misasi John N , Widge Alicia , Roberts Paul C. , Beigel John , Korber Bette , Pajon Rolando , Mascola John R. , Suthar Mehul S. , Montefiori David C.
Published: December 2021

The Omicron variant of SARS-CoV-2 is raising concerns because of its increased transmissibility and potential for reduced susceptibility to antibody neutralization. To assess the potential risk of this variant to existing vaccines, serum samples from mRNA-1273 vaccine recipients were tested for neutralizing activity against Omicron and compared to neutralization titers against D614G and Beta in live virus and pseudovirus assays. Omicron was 41-84-fold less sensitive to neutralization than D614G and 5.3-7.4-fold less sensitive than Beta when assayed with serum samples obtained 4 weeks after 2 standard inoculations with 100 µg mRNA-1273. A 50 µg boost increased Omicron neutralization titers and may substantially reduce the risk of symptomatic vaccine breakthrough infections.
Acute decrease in plasma membrane tension induces macropinocytosis via
PLD2 activation
Authors: Loh Julie , Joseph Jophin , Chuang Mei-Chun , Lin Shan-Shan , Chang Yu-Chen , Su You-An , Liu Allen P. , Liu Ya-Wen
Published: December 2021

Internalization of macromolecules and membrane into cells through
endocytosis is critical for cellular growth, signaling, and membrane tension
homeostasis. Although endocytosis is responsive to both biochemical and physical
stimuli, how physical cues modulate endocytic pathways is less understood. In
contrary to the accumulating discoveries on effects of increased membrane
tension on endocytosis, little is known about how a drop of tension impacts
membrane trafficking. Here we reveal that acute reduction of plasma membrane
tension results in phosphatidic acid, F-actin and dynamin 2-enriched dorsal
membrane ruffling and subsequent macropinocytosis in myoblast. The membrane
flaccidity-induced local phosphatidic acid production depends on phospholipase
D2 (PLD2) that is activated via lipid raft
disruption. Furthermore, the “membrane flaccidity-PLD2-macropinocytosis” pathway
is dominant in myotube, reflecting a potential mechanism of membrane tension
homeostasis upon intensive muscle stretching and relaxation. Together, we
identify a new mechanotransduction pathway which converts acute tension drop
into PA production and subsequently initiates macropinocytosis
via actin and dynamin activities.

We reveal a mechanical induction of macropinocytosis that is elicited by
acute decrease of plasma membrane tension, followed by lipid raft
destabilization, PLD2 activation and PA production.