bluuebunny/crossref_metadata_2025 huggingface dataset:
A bivalent EBV vaccine induces neutralizing antibodies that block B and epithelial cell infection and confer immunity in humanized mice
Authors: Wei Chih-Jen , Bu Wei , Nguyen Laura A. , Batchelor Joseph D. , Kim JungHyun , Pittaluga Stefania , Fuller James R. , Nguyen Hanh , Chou Te-Hui , Cohen Jeffrey I. , Nabel Gary J.
Published: January 2022

Epstein Barr virus (EBV) is the major cause of infectious mononucleosis and is associated with several human cancers. Despite its prevalence and major impact on human health, there are currently no specific vaccines or treatments. Four viral glycoproteins, gp 350 and gH/gL/gp42 mediate entry into the major sites of viral replication, B cells and epithelial cells. Here, we designed a nanoparticle vaccine displaying these proteins and show that it elicits potent neutralizing antibodies that protect against infectionin vivo. Based on structural analyses, we designed single chain gH/gL and gH/gL/gp42 proteins that were each fused to bacterial ferritin to form a self-assembling nanoparticles. X-ray crystallographic analysis revealed that single chain gH/gL and gH/gL/gp42 adopted a similar conformation to the wild type proteins, and the protein spikes were observed by electron microscopy. Single chain gH/gL or gH/gL/gp42 nanoparticle vaccines were constructed to ensure product homogeneity needed for clinical development. These vaccines elicited neutralizing antibodies in mice, ferrets, and non-human primates that inhibited EBV entry into both B cells and epithelial cells. When mixed with a previously reported gp350 nanoparticle vaccine, gp350D123, no immune competition was observed. To confirm its efficacy in vivo, humanized mice were challenged with EBV after passive transfer of IgG from mice vaccinated with control, gH/gL/gp42+gp350D123or gH/gL+gp350D123nanoparticles. While all control animals (6/6) were infected, only one mouse in each vaccine group that received immune IgG had transient low level viremia (1/6). Furthermore, no EBV lymphomas were detected in immune animals in contrast to non-immune controls. This bivalent EBV nanoparticle vaccine represents a promising candidate to prevent EBV infection and EBV-related malignancies in humans.

One sentence summary

A bivalent gp350 and gH/gL/gp42 nanoparticle vaccine elicits neutralizing antibodies that protect against EBV infection and EBV lymphomain vivo.
Honey bee flights under ethanol-exposure show changes in body and wing kinematics
Authors: Ahmed Ishriak , Abramson Charles I. , Faruque Imraan A.
Published: January 2022

Flying social insects can provide model systems for inflight interactions in computationally-constrained aerial robot swarms, whose interactions may be chemically modulated under recent measurement advancements provide a capability to simultaneously make precise measurements of insect wing and body motions. This paper presents the first quantitative measurements of ethanol-exposed honey bee flight body and wing kinematic parameters. Four high speed cameras (9000 fps) were used to track the wing and body motions of insects (Apis mellifera). Digitization, consisting of data association, hull reconstruction, and segmentation, achieved the first high speed measurements of ethanol exposed honey bees’ wing and body motions. Kinematic changes induced by exposure to ethanol concentrations from 0% to 5% were studied using statistical analysis tools. Analysis considered trial wide mean and maximum values and gross wingstroke parameters, and tested deviations for statistical significance using Welch’s t-test and Cohen’s d test. The results indicate a decrease in maximal heading and pitch rates of the body, and that roll rate is affected at high concentrations (5%). The wingstroke effects include a stroke frequency decrease, stroke amplitude increase, stroke inclination angle increase, and a more planar wingstroke. These effects due to ethanol exposure are valuable tools to separate from interaction effects.
Pareto-optimal trade-off for phenotypic switching of populations in a stochastic environment
Authors: Dinis L. , Unterberger J. , Lacoste D.
Published: January 2022

Finding optimal survival strategies of living systems embedded in fluctuating environments generally involves a balance between phenotypic diversification and sensing. If we neglect sensing mechanisms, it is known that slow, resp. fast, environmental transitions favor a regime of heterogeneous, resp. homogeneous, phenotypic response.

We focus here on the simplest non-trivial case, i.e. two randomly switching phenotypes subjected to two stochastically switching environments. The optimal asymptotic (long term) growth rate of this model was studied elsewhere; we further expand these results by discussing finite time growth rate fluctuations. An exact asymptotic expression for the variance, alongside with approximations valid in different regimes, are tested numerically in details. Our simulations of the dynamics suggest a close connection between this variance and the extinction probability, understood as risk for the population. Motivated by an earlier trade-off analysis between average capital growth rate and risk in Kelly’s gambling model, we study the trade-off between the average growth rate and the variance in the present model. Despite considerable differences between the two models, we find similar optimal trade-off curves (Pareto fronts), suggesting that our conclusions are robust, and broadly applicable in various fields ranging from biology/ecology to economics.
BrainStat: a toolbox for brain-wide statistics and multimodal feature associations
Authors: de Wael Reinder Vos , Bayrak Şeyma , Benkarim Oualid , Herholz Peer , Larivière Sara , Rodriguez-Cruces Raul , Paquola Casey , Hong Seok-Jun , Misic Bratislav , Evans Alan C. , Valk Sofie L. , Bernhardt Boris C.
Published: January 2022

Abstract

Analysis and interpretation of neuroimaging datasets has become a multidisciplinary endeavor, relying not only on statistical methods, but increasingly on associations with respect to other brain-derived features such as gene expression, histological data, and functional as well as cognitive architectures. Here, we introduce BrainStat - a toolbox for (i) univariate and multivariate linear models in volumetric and surface-based brain imaging datasets, and (ii) multidomain feature association of results with respect to spatial maps of post-mortem gene expression and histology, task-based fMRI meta-analysis, as well as resting-state fMRI motifs across several common surface templates. The combination of statistics and feature associations into a turnkey toolbox streamlines analytical processes and accelerates cross-modal research. The toolbox is implemented in both Python and MATLAB, two widely used programming languages in the neuroimaging and neuroinformatics communities. BrainStat is openly available and complemented by an expandable documentation.
High-resolution map of plastid encoded polymerase binding patterns demonstrates a major role of transcription in chloroplast gene expression
Authors: Palomar V. Miguel , Jaksich Sarah , Fujii Sho , Kuciński Jan , Wierzbicki Andrzej T.
Published: January 2022

Plastids are endosymbiotic organelles containing their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid encoded RNA polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplasts DNA using ptChIP-seq. We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex DNA binding pattern with preferential association at genes encoding rRNA, tRNA, and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with the levels of RNA accumulation, which allowed estimating the quantitative contribution of transcription to RNA accumulation.
An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation
Authors: Seuma Mireia , Lehner Ben , Bolognesi Benedetta
Published: January 2022

Multiplexed assays of variant effects (MAVEs) guide clinical variant interpretation and reveal disease mechanisms. To date, MAVEs have focussed on a single mutation type - amino acid (AA) substitutions - despite the diversity of coding variants that cause disease. Here we use Deep Indel Mutagenesis (DIM) to generate the first comprehensive atlas of diverse variant effects for a disease protein, the amyloid beta (Aß) peptide that aggregates in Alzheimer’s disease (AD) and is mutated in familial AD (fAD). The atlas identifies known fAD mutations and reveals many variants beyond substitutions accelerate Aß aggregation and are likely to be pathogenic. Truncations, substitutions, insertions, single- and internal multi-AA deletions differ in their propensity to enhance or impair aggregation, but likely pathogenic variants from all classes are highly enriched in the polar N-terminus of Aß. This first comparative atlas highlights the importance of including diverse mutation types in MAVEs and provides important mechanistic insights into amyloid nucleation.
Comb-structured mRNA vaccine tethered with short double-stranded RNA adjuvants maximizes cellular immunity for cancer treatment
Authors: Tockary Theofilus A. , Abbasi Saed , Matsui-Masai Miki , Yoshinaga Naoto , Boonstra Eger , Wang Zheng , Fukushima Shigeto , Kataoka Kazunori , Uchida Satoshi
Published: January 2022

Integrating antigen-encoding mRNA and immunostimulatory adjuvant into a single formulation is a promising approach to potentiating the efficacy of mRNA vaccines. Here, we developed a scheme based on RNA engineering to integrate adjuvancy directly into antigen-encoding mRNA strands without hampering the ability to express antigen proteins. Short double-stranded RNA (dsRNA) was designed to target retinoic acid-inducible gene-I (RIG-I), an innate immune receptor, for effective cancer vaccination and then tethered onto mRNA strand via hybridization. Tuning the dsRNA structure and microenvironment by changing its length and sequence enabled the determination of the structure of dsRNA-tethered mRNA efficiently stimulating RIG-I. Eventually, the formulation loaded with dsRNA-tethered mRNA of the optimal structure effectively activated mouse and human dendritic cells and drove them to secrete a broad spectrum of proinflammatory cytokines without increasing the secretion of anti-inflammatory cytokines. Notably, the immunostimulating intensity was tunable by modulating the number of dsRNA along mRNA strand, which prevents excessive immunostimulation. Versatility in the applicable formulation is a practical advantage of the dsRNA-tethered mRNA. Its formulation with three existing systems, i.e., anionic lipoplex, ionizable lipid-based lipid nanoparticles, and polyplex micelles, induced appreciable cellular immunity in the mice model. Of particular interest, dsRNA-tethered mRNA encoding ovalbumin (OVA) formulated in anionic lipoplex used in clinical trials exerted a significant therapeutic effect in the mouse lymphoma (E.G7-OVA) model. In conclusion, the system developed here provides a simple and robust platform to supply the desired intensity of immunostimulation in various formulations of mRNA cancer vaccines.
Loneliness is associated with mentalizing and emotion recognition abilities in schizophrenia, but only in a cluster of patients with social cognitive deficits
Authors: Okruszek Ł. , Jarkiewicz M. , Piejka A. , Chrustowicz M. , Krawczyk M. , Schudy A. , Harvey P.D. , Penn D.L. , Ludwig K. , Green M.F. , Pinkham A.
Published: January 2022

Background

Loneliness is a concern for patients with schizophrenia (SCZ). However, the correlates of loneliness in SCZ are unclear; thus, the aim of the study is to investigate neuro- and social cognitive (SC) mechanisms associated with loneliness in SCZ.

Methods

Data for the study were pooled from two cross-national samples (Poland/USA) and included 147 SCZ and 103 healthy controls (HC) overall. Data from clinical, neurocognitive, and SC assessments were examined as potential predictors of loneliness in HC and SCZ samples pooled across two sites. Furthermore, Latent Class Analysis (LCA) was used to cluster patients based on SC capacity. Next, the relationship between SC and loneliness was explored in each cluster of SCZ.

Results

SCZ reported higher levels of loneliness than HC. Loneliness was linked to increased negative and affective symptoms in patients. A negative association between loneliness and mentalizing and emotion recognition abilities was found in the patients with social-cognitive impairments, but not in those who performed at normative levels.

Conclusions

We have elucidated a novel mechanism which may explain previous inconsistent findings regarding the correlates of loneliness in SCZ. As decreased SC capacity may be linked with loneliness only in patients with observable SC impairments, SC heterogeneity in SCZ needs to be recognized while planning psychosocial interventions targeting loneliness in this group.
Controlled adhesion, membrane pinning and vesicle transport by Janus particles
Authors: Ewins Eleanor J. , Han Koohee , Bharti Bhuvnesh , Robinson Tom , Velev Orlin D. , Dimova Rumiana
Published: January 2022

The interactions between biomembranes and particles are key to many applications, but the lack of controllable model systems to study them limits the progress in their research. Here, we describe how Janus polystyrene microparticles, half coated with iron, can be partially engulfed by artificial cells, namely giant vesicles, with the goals to control and investigate their adhesion and degree of encapsulation. The interaction between the Janus particles and these model cell membrane systems is mediated by electrostatic charge, offering a further mode of modulation in addition to the iron patches. The ferromagnetic particle coatings also enable the ability to manipulate and transport the vesicles by magnetic fields.
Dynamics and structural changes of calmodulin upon interaction with its potent antagonist calmidazolium
Authors: Léger Corentin , Pitard Irène , Sadi Mirko , Carvalho Nicolas , Brier Sébastien , Mechaly Ariel , Raoux-Barbot Dorothée , Davi Maryline , Hoos Sylviane , Weber Patrick , Vachette Patrice , Durand Dominique , Haouz Ahmed , Guijarro J. Iñaki , Ladant Daniel , Chenal Alexandre
Published: January 2022

Calmodulin (CaM) is a eukaryotic multifunctional, calcium-modulated protein that regulates the activity of numerous effector proteins involved in a variety of physiological processes. Calmidazolium (CDZ) is a potent small molecule antagonist of CaM and one the most widely used inhibitors of CaM in cell biology. Here, we report the structural characterization of CaM:CDZ complexes using combined SAXS, X-ray crystallography, HDX-MS and NMR approaches. Our results provide molecular insights into the CDZ-induced dynamics and structural changes of CaM leading to its inhibition. CDZ-binding induces an open-to-closed conformational change of CaM and results in a strong stabilization of its structural elements associated with a reduction of protein dynamics over a large time range. These CDZ-triggered CaM changes mimic those induced by CaM-binding peptides derived from protein targets, despite their distant chemical nature. CaM residues in close contact with CDZ and involved in the stabilization of the CaM:CDZ complex have been identified. These results open the way to rationally design new CaM-selective drugs.

Figure and text for the Table of Contents (ToC)

Calmidazolium is a potent and widely used inhibitor of calmodulin, a major mediator of calcium-signaling in eukaryotic cells. Structural characterization of calmidazolium-binding to calmodulin reveals that it triggers open-to-closed conformational changes similar to those induced by calmodulin-binding peptides derived from enzyme targets. These results open the way to rationally design new and more selective inhibitors of calmodulin.
Nulliparity affects the expression of a limited number of genes and pathways in Day 8 equine embryos
Authors: Derisoud E. , Jouneau L. , Archilla C. , Jaszczyszyn Y. , Legendre R. , Daniel N. , Peynot N. , Dahirel M. , Auclair-Ronzaud J. , Duranthon V. , Chavatte-Palmer P.
Published: January 2022

Nulliparous mares produce lighter and smaller foals compared to mares having previously foaled, with effects observed at least until 4 months of age. The need for a first gestation priming for the uterus to reach its full capacity has been proposed to explain this observation. Embryo developmental defects could be hypothesized but effects of maternal parity on the embryo have only been described once, in old mares, thus combining effects of parity and old age. The aim of this study was to determine effects of mare parity on embryo gene expression. Day-8 post ovulation blastocysts were collected from young (5/6 years old) nulliparous (YN, N=6) or multiparous (YM, N=4) non-nursing Saddlebred mares, inseminated with the semen of one stallion. Pure (TE_part) or inner-cell-mass-enriched (ICMandTE) trophoblast were obtained by embryo bisection for RNA sequencing (paired end, non-oriented, Illumina, NextSeq500). Deconvolution was performed on the ICMandTE dataset. Differential expression, with embryo sex and diameter as cofactors and gene set enrichment analysis (GO BP, KEGG, REACTOME databases) were performed using a false discovery rate <0.05 cutoff. Only a few genes were altered (ICM: n=18; TE: n=6) but several gene sets were perturbed (ICM: n=62; TE: n=50) by maternal parity. In YM, only pathways related to transcription, RNA processing and vesicle transport functions were enriched in the ICM whereas only pathways related to RNA localization were enriched in TE. In YN, while only gene sets related to ribosomes and extracellular matrix were enriched in the ICM, functions related to energy and lipid metabolism, lipid transport and interleukin-1 signaling were enriched in the TE. In conclusion, several genes and pathways are affected in embryos collected from nulliparous mares, with different effects on TE and ICM. Embryo development is altered in nulliparous mares, which could partially explain the term phenotype. Whether differences in gene expression result/induce poor embryo-maternal communication remains to be determined.
Context-Dependent Enhancer Function Revealed by Targeted Inter-TAD Relocation
Authors: Bolt Christopher Chase , Lopez-Delisle Lucille , Hintermann Aurélie , Mascrez Bénédicte , Rauseo Antonella , Andrey Guillaume , Duboule Denis
Published: January 2022

The expression of genes with a key function during development is frequently controlled by large regulatory landscapes containing multiple enhancer elements. These landscapes often match Topologically Associating Domains (TADs) and sometimes integrate range of similar enhancers, thus leading to TADs having a global regulatory specificity. To assess the relative functional importance of enhancer sequences versus the regulatory domain they are included in, we set out to transfer one particular enhancer sequence from its native domain into a TAD with a closely related, yet different functional specificity. We used Hoxd genes and their biphasic regulation during limb development as a paradigm, since they are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced at the time when the neighboring TAD starts to activate its enhancers in distal limb cells. We introduced a strong distal limb enhancer into the ‘proximal limb TAD’ and found that its new context strongly suppresses its distal specificity, even though it continues to be bound by HOX13 transcription factors, which normally are responsible for this activity. Using local genetic alterations and chromatin conformation measurements, we see that the enhancer is capable of interacting with target genes, with a pattern comparable to its adoptive neighborhood of enhancers. Its activity in distal limb cells can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the local chromatin context, which can exert a dominant control over its activity.
Phase separation driven by interchangeable properties in the intrinsically disordered regions of protein paralogs
Authors: Chiu Shih-Hui , Ho Wen-Lin , Sun Yung-Chen , Kuo Jean-Cheng , Huang Jie-rong
Published: January 2022

Paralogs, arising from gene duplications, increase the functional diversity of proteins. Protein functions in paralog families have been extensively studied, but little is known about the roles of intrinsically disordered regions (IDRs), even though more than half of eukaryotic proteins have them. Using the RNA-binding protein Musashi family as an example, we applied multiple structural techniques and phylogenetic analysis to show how members in a paralog family have evolved their IDRs to different physicochemical properties but converge to the same function. In this example, the lower prion-like tendency of Musashi-1’s IDRs, rather than Musashi-2s’, is compensated by its higher α-helical propensity to assist their assembly. Without a folded structure to restraint, IDRs’ sequences mutate faster along with evolution. No matter how fast they change, our work suggests that IDRs evolve different traits to a converged function, such as liquid-liquid phase separation.
Excessive self-grooming, gene dysregulation and imbalance between the striosome and matrix compartments in the striatum ofShank3mutant mice
Authors: Allain-Thibeault Ferhat , Elisabeth Verpy , Anne Biton , Benoît Forget , de Chaumont Fabrice , Florian Mueller , Anne-Marie Le Sourd , Sabrina Coqueran , Julien Schmitt , Christelle Rochefort , Laure Rondi-Reig , Aziliz Leboucher , Anne Boland , Bertrand Fin , François Deleuze Jean , Boeckers Tobias M. , Elodie Ey , Thomas Bourgeron
Published: January 2022

Autism is characterised by atypical social communication and stereotyped behaviours. Mutations in the gene encoding the synaptic scaffolding protein SHANK3 are detected in 1-2% of patients with autism and intellectual disability (ID), but the mechanisms underpinning the symptoms remain largely unknown. Here, we characterised the behaviour ofShank3Δ11/Δ11mice from three to twelve months of age. We observed decreased locomotor activity, increased stereotyped self-grooming and modification of socio-sexual interaction compared to wild-type littermates. We then used RNAseq on four brain regions of the same animals to identify differentially expressed genes (DEG). DEGs were identified mainly in the striatum and were associated with synaptic transmission (e.g.Grm2, Dlgap1), G-protein-signalling pathways (e.g.Gnal, Prkcg1, and Camk2g), as well as excitation/inhibition balance (e.g.Gad2). Downregulated and upregulated genes were enriched in the gene clusters of medium-sized spiny neurons expressing the dopamine 1 (D1-MSN) and the dopamine 2 receptor (D2-MSN), respectively. Several DEGs (Cnr1, Gnal1, Gad2, and Drd4) were reported as striosome markers. By studying the distribution of the glutamate decarboxylase GAD65, encoded byGad2, we showed that the striosome compartment ofShank3Δ11/Δ11mice was enlarged and displayed much higher expression of GAD65 compared to wild-type mice. Altogether, these results indicate altered gene expression in the striatum of SHANK3-deficient mice and strongly suggest, for the first time, that the impairment in behaviour of these mice are related to an imbalance striosomes/matrix.
Biochemistry and nanomechanical properties of human colon cells upon simvastatin, lovastatin and mevastatin supplementations – Raman imaging and AFM studies
Authors: Beton K. , Brożek-Płuska B.
Published: January 2022

One of the most important areas of medical science is oncology, which is responsible for both the diagnostics and treatment of cancer diseases. Over the years, there has been an intensive development of cancer diagnostics and treatment. This paper shows the comparison of normal (CCD-18Co) and cancerous (CaCo-2) cell lines of the human gastrointestinal tract on the basis of nanomechanical and biochemical properties in order to obtain information on the cancer biomarkers useful in oncological diagnostics. The research techniques used were: Atomic Force Microscopy and Raman spectroscopy and imaging. In addition, the studies included also the effect of the statins compounds: mevastatin, lovastatin and simvastatin and their influence on nanomechanical and biochemical changes of properties of cells tracking using AFM and Raman imaging techniques. The cytotoxicity of mevastatin and lovastatin was determined by using XTT tests.
Targeting SARS-CoV-2 infection through CAR-T like bispecific T cell engagers incorporating ACE2
Authors: Dogan Mikail , Kozhaya Lina , Placek Lindsey , Karabacak Fatih , Yigit Mesut , Unutmaz Derya
Published: January 2022

Despite advances in antibody treatments and vaccines, COVID-19 caused by SARS-CoV-2 infection remains a major health problem resulting in excessive morbidity and mortality and the emergence of new variants has reduced the effectiveness of current vaccines. Here, as a proof-of-concept we engineered primary CD8 T cells to express SARS-CoV-2 Spike protein-specific CARs, using extracellular region of ACE2, and demonstrated their highly specific and potent cytotoxicity towards Spike-expressing target cells. To improve on this concept as a potential therapeutic, we developed a bispecific T cell engager combining ACE2 with an anti-CD3 scFv (ACE2-Bite) to target infected cells and the virus. Similar to CAR-T cell approach, ACE2-Bite endowed cytotoxic cells to selectively kill Spike-expressing targets. Furthermore, ACE2-Bite neutralized the pseudoviruses of SARS-CoV, SARS-CoV-2 wild-type and variants including Delta and Omicron, as a decoy protein. Remarkably, ACE2-Bite molecule showed a higher binding and neutralization affinity to Delta and Omicron variants compared to SARS-CoV-2 wild-type Spike proteins, suggesting the potential of this approach as a variant-proof, therapeutic strategy for future SARS-CoV-2 variants, employing both humoral and cellular arms of the adaptive immune response.
Distinctive mechanisms of epilepsy-causing mutants discovered by measuring S4 movement in KCNQ2 channels
Authors: Edmond Michaela A. , Hinojo-Perez Andy , Wu Xiaoan , Perez Rodriguez Marta E. , Barro-Soria Rene
Published: January 2022

Neuronal KCNQ channels mediate the muscarine-regulated M-current, a key regulator of membrane excitability in the central and peripheral nervous systems. Mutations in KCNQ2 channels cause severe neurodevelopmental disorders, including epileptic encephalopathies. However, the impact that mutations have on channel function remain poorly defined, largely because of our limited understanding of the voltage sensing mechanisms that trigger channel gating. Here, we present measurements of voltage sensor movements in wt-KCNQ2 and channels bearing epilepsy-causing mutations using mutagenesis, cysteine accessibility, and voltage clamp fluorometry (VCF). Cysteine modification reveals that a stretch of 8-9 amino acids in the S4 become exposed upon opening of KCNQ2 channels. VCF shows that the voltage dependence and kinetics of S4 movement and channel opening/closing closely correlate, suggesting an activation scheme in which channel opening does not require multiple voltage-sensor movements. VCF and kinetic modeling reveal different mechanisms by which epilepsy-causing mutations affect KCNQ2 channel voltage-dependent gating. This study provides insight into KCNQ2 channel function, which will aid in uncovering the mechanisms underlying channelopathies.
Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion
Authors: Barth Roman , Shaban Haitham A.
Published: January 2022

Gene transcription by RNA polymerase II (RNAP II) is a tightly regulated process in the genomic, temporal, and spatial context. Transcriptionally active genes often spatially cluster at RNA Pol II foci, called transcription factories, causing long-range interactions between distal sites of the genome. Recently, we have shown that chromatin exhibits spatially long-range coherently moving regions over the entire nucleus, and transcription enhances this long-range correlated DNA movement. Yet, it remains unclear how the mobility of RNA Pol II molecules is affected by transcription regulation and whether this response depends on the coordinated chromatin movement. We applied our Dense Flow reConstruction and Correlation method to analyze nucleus-wide coherent movements of RNA Pol II in living human cancer cells. We quantify the spatial correlation length of RNA Pol II in the context of DNA motion. We observe a spatially coherent movement of RNA Pol II molecules over ~1 μm, considerably less than for DNA, suggesting that spatially coherent RNA Pol II motion does not solely result from the DNA motion. In contrast to DNA, inducing transcription in quiescent cells decreased the coherent motion of RNA Pol II, while the inhibition of transcription elongation by using DRB slightly increased coherent RNA Pol II motion. The spatially coherent movement of RNA Pol II domains is affected by the transcriptional state and largely independent of the underlying chromatin domains. Our study reveals the nucleus-wide interplay between chromatin and RNA Pol II in the dynamic regulation of chromatin organization.
An ancient role for the Hippo pathway in axis formation and morphogenesis
Authors: Brooun Maria , Salvenmoser Willi , Dana Catherine , Sudol Marius , Steele Robert , Hobmayer Bert , McNeill Helen
Published: January 2022

How did cells of early metazoan organisms first organize themselves to form a body axis? The canonical Wnt pathway has been shown to be sufficient for induction of axis in Cnidaria, a sister group to Bilateria, and is important in bilaterian axis formation. Here, we provide experimental evidence that in cnidarian Hydra the Hippo pathway regulates the formation of a new axis during budding upstream of the Wnt pathway. The target of Hippo pathway, the transcriptional co-activator YAP, inhibits the initiation of budding in Hydra, and is regulated by Hydra LATS. In addition, we show functions of Hippo pathway in regulation of actin organization and cell proliferation in Hydra. We hypothesize that Hippo pathway served as a link between continuous cell division, cell density and axis formation early in metazoan evolution.
A single, improbable B cell receptor mutation confers potent neutralization against cytomegalovirus
Authors: Jenks Jennifer A. , Amin Sharmi , Kumar Amit , Sponholtz Madeline R. , Wrapp Daniel , Venkatayogi Sravani , Tu Joshua , McLellan Jason S. , Wiehe Kevin , Permar Sallie R.
Published: January 2022

Cytomegalovirus (CMV) is a leading cause of infant hearing loss and neurodevelopmental delay, but vaccine candidates have faced challenges eliciting neutralizing antibodies. One of the most well-studied targets for CMV vaccines is the viral fusogen glycoprotein B (gB), which is required for viral entry into host cells. Within gB, antigenic domain 2 site 1 (AD-2S1) is a target of potently neutralizing antibodies, but gB-based candidate vaccines have yet to elicit robust responses against this region. We mapped the genealogy of B cells encoding potently neutralizing anti-gB AD-2S1 antibodies from their inferred unmutated common ancestor (UCA) and characterized the binding and function of early lineage ancestors. Remarkably, we found that the single amino acid heavy chain mutation A33N, an improbable mutation rarely generated by somatic hypermutation machinery, conferred broad CMV neutralization to the UCA antibody. Structural studies revealed that this mutation mediated key contacts with the gB AD-2S1 epitope. Collectively, these results provide insight into potently neutralizing gB-directed antibody evolution and a foundation for designing next-generation CMV vaccines.

One-sentence summary

This manuscript identifies an early B cell lineage mutation that confers neutralizing function to antibodies targeting CMV fusogen gB.
A genetically-defined population in the lateral and ventrolateral periaqueductal gray selectively promotes flight to safety
Authors: La-Vu Mimi , Sethi Ekayana , Maesta-Pereira Sandra , Schuette Peter J , Tobias Brooke C , Reis Fernando MCV , Wang Weisheng , Leonard Saskia J , Lin Lilly , Adhikari Avishek
Published: January 2022

When encountering external threats, survival depends on the engagement of appropriate defensive reactions to minimize harm. There are major clinical implications for identifying the neural circuitry and activation patterns that produce such defensive reactions, as maladaptive overactivation of these circuits underlies pathological human anxiety and fear responses. A compelling body of work has linked activation of large glutamatergic neuronal populations in the midbrain periaqueductal gray (PAG) to defensive reactions such as freezing, flight and threat-induced analgesia. These pioneering data have firmly established that the overarching functional organization axis of the PAG is along anatomically-defined columnar boundaries. Accordingly, broad activation of the dorsolateral column induces flight, while activation of the lateral or ventrolateral (l and vl) columns induces freezing. However, the PAG contains a diverse arrangement of cell types that vary in neurochemical profile and location. How these cell types contribute to defensive responses remains largely unknown, indicating that targeting sparse, genetically-defined populations can lead to a deeper understanding of how the PAG generates a wide array of behaviors. Though several prior works showed that broad excitation of the lPAG or vlPAG causes freezing, we found that activation of lateral and ventrolateral PAG (l/vlPAG) cholecystokinin-expressing (cck) cells selectively causes flight to safer regions within an environment. Furthermore, inhibition of l/vlPAG-cck cells reduces avoidance of a predatory threat without altering other defensive behaviors like freezing. Lastly, l/vlPAG-cck activity increases away from threat and during movements towards safer locations. In contrast, activating l/vlPAG cells pan-neuronally promoted freezing and these cells were activated near threat. These data underscore the importance of investigating genetically-identified PAG cells. Using this approach, we found a sparse population of cck-expressing l/vlPAG cells that have distinct and opposing function and neural activation motifs compared to the broader local ensemble defined solely by columnar anatomical boundaries. Thus, in addition to the anatomical columnar architecture of the APG, the molecular identity of PAG cells may confer an additional axis of functional organization, revealing unexplored functional heterogeneity.
The Intrinsically Disordered Region of Coronins Fine-tunes Oligomerization and Actin Polymerization
Authors: Han Xiao , Hu Zixin , Surya Wahyu , Ma Qianqian , Zhou Feng , Nordenskiöld Lars , Torres Jaume , Lu Lanyuan , Miao Yansong
Published: January 2022

Coronins are highly conserved actin-binding proteins (ABPs) in the eukaryotic kingdom for polymerizing actin cytoskeleton. The biochemical activity of coronins is primarily mediated by the structural N-terminal β-propeller and the C-terminal helical coiled-coil (CC) domains, but less is known about the function of a middle nonconserved region, the “unique region (UR)”. The coronin UR is an intrinsically disordered region (IDR). Herein, we demonstrate that the low complexity of the UR is a conserved signature of the coronin protein family, and the UR/IDR exhibits a striking evolutionary correlated pattern associated with sequence length. By analyzing the role of the IDR in coronins via coarse-grained simulations, we reveal that evolutionary selection of IDR length is coupled with the oligomerization of IDR-containing proteins (IDPs) to provide optimal functional output. By integrating biochemical and cell biology experiments and protein engineering, we found that the IDR regulates Crn1 biochemical activity, both in vivo and in vitro, by fine-tuning CC domain oligomerization and maintaining Crn1 in a tetrameric state. The IDR-guided optimization of Crn1 oligomerization is critical for Arp2/3-mediated actin polymerization.
Genomic databanks and targeted assays help characterise domestic mosquito incursions
Authors: Schmidt Thomas L. , Endersby-Harshman Nancy , Kurucz Nina , Pettit William , Krause Vicki L , Ehlers Gerhard , Muzari Mutizwa Odwell , Currie Bart J , Hoffmann Ary A
Published: January 2022

Biosecurity strategies that aim to restrict the spread of invasive pests can benefit from knowing where new incursions have come from. This knowledge can be acquired using genomic databanks, by comparing genetic variation in incursion samples against reference samples. Here we use genomic databanks to investigate domestic incursions of two mosquito species in Australia, and assess the performance of genomic tracing methods when databank samples were collected some time ago or are genetically similar. We used a deep learning method to trace a 2021 invasion of Aedes aegypti in Tennant Creek, Northern Territory, to Townsville, Queensland, and to trace two years of Ae. albopictus incursions to two specific islands in the Torres Strait. We observed high precision of tracing despite 30-70 generations separating incursion and reference samples. Targeted assays also provided additional information on the origin of the Tennant Creek Ae. aegypti, in this case by comparing Wolbachia infection data and mitochondrial DNA variation. Patterns of relatedness and inbreeding indicated that Tennant Creek was likely invaded by one family of Ae. aegypti, whereas Torres Strait incursions involved distinct kinship groups. Our results highlight the value of genomic databanks that remain informative over years and for a range of biological conditions, and demonstrate how additional targeted assays (e.g. Wolbachia) can improve inferences.

Key Message

Genomic tracing can provide valuable information on pest incursions and new invasions.

Evolution will lead to increasing differences between databanks and extant populations.

We tested how well genomic databanks could trace incursions sampled 30-70 generations later and where genetic differentiation was low.

We show that tracing methods are robust for a wide range of conditions, and report specific incursion origins for two Aedes species.

Our results suggest that genomic databanks will remain informative over years and for a range of invasive systems.
Intra-granuloma accumulation and inflammatory differentiation of neutrophils underlie mycobacterial ESX-1-mediated immunopathology
Authors: Lienard Julia , Munke Kristina , Wulff Line , Da Silva Clément , Vandamme Julien , Laschanzky Katie , Joeris Thorsten , Agace William , Carlsson Fredric
Published: January 2022

The conserved ESX-1 type VII secretion system is a major virulence determinant of pathogenic mycobacteria, including Mycobacterium tuberculosis and Mycobacterium marinum. ESX-1 is known to interact with infected macrophages, but its potential roles in regulating other host cells and immunopathology have remained largely unexplored. Using a murine M. marinum infection model we identify neutrophils and Ly6C+MHCII+ monocytes as the main cellular reservoirs for the bacteria. We show that ESX-1 promotes intra-granuloma accumulation of neutrophils and that neutrophils have a previously unrecognized required role in executing ESX-1-mediated pathology. To explore if ESX-1 also regulates the function of recruited neutrophils we performed single cell RNA-seq analysis indicating that ESX-1 drives newly recruited uninfected neutrophils into an inflammatory phenotype via an extrinsic mechanism. In contrast, monocytes restricted the accumulation of neutrophils and immunopathology, demonstrating a major host-protective function for monocytes specifically by suppressing ESX-1-mediated neutrophilic inflammation. iNOS activity was required for the suppressive mechanism and we identified Ly6C+MHCII+ monocytes as the main iNOS-expressing cell type in the infected tissue. These results suggest that ESX-1 mediates immunopathology by driving neutrophil accumulation and phenotypic differentiation in the infected tissue, and they demonstrate an antagonistic interplay between monocytes and neutrophils by which monocytes suppress host-detrimental neutrophilic inflammation.

Author Summary

The ESX-1 type VII secretion system is required for virulence of pathogenic mycobacteria, including Mycobacterium tuberculosis. ESX-1 interacts with infected macrophages, but its potential roles in regulating other host cells and immunopathology have remained largely unexplored. We demonstrate that ESX-1 promotes immunopathology by driving intra-granuloma accumulation of neutrophils, which upon arrival adopt an inflammatory phenotype in an ESX-1-dependent manner. In contrast, monocytes limited the accumulation of neutrophils and neutrophil-mediated pathology via an iNOS-dependent mechanism, suggesting a major host-protective function for monocytes specifically by restricting ESX-1-mediated neutrophilic inflammation. These findings provide insight into how ESX-1 promotes disease, and they reveal an antagonistic functional relationship between monocytes and neutrophils that may regulate immunopathology not only in mycobacterial infection, but also in other infections as well as in inflammatory conditions and cancer.
Safety and immunogenicity of Pfizer/BioNTech SARS-CoV-2 mRNA third booster vaccine against SARS-CoV-2 Omicron variant in Japanese healthcare workers
Authors: Seki Yohei , Yoshihara Yasuo , Nojima Kiyoko , Momose Haruka , Fukushi Shuetsu , Moriyama Saya , Wagatsuma Ayumi , Numata Narumi , Sasaki Kyohei , Kuzuoka Tomoyo , Yato Yoshiyuki , Takahashi Yoshimasa , Maeda Ken , Suzuki Tadaki , Mizukami Takuo , Hamaguchi Isao
Published: January 2022

Background

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in Japan in November 2021. This variant contains up to 36 mutations in the spike protein, the target of neutralizing antibodies, and can escape vaccine-induced immunity. The third booster vaccination campaign began with healthcare workers and high-risk groups. The safety and immunogenicity of third booster vaccination against Omicrons remain unknown.

Methods

In total, 272 healthcare workers were evaluated for their long-term safety and immunogenicity. Here, we established vaccine panels to evaluate the safety and immunogenicity against variants of concern (VOCs), including the Omicron variant, using a live virus microneutralization assay.

Findings

Two-dose vaccination induced robust anti-spike antibodies and neutralization titers (NTs) against the ancestral strain WK-521, whereas NTs in VOCs were significantly decreased. Within 93–247 days of the second vaccine dose, NTs against Omicron were completely abolished in up to 80% of individuals among the vaccine panels. The third booster vaccination induced a robust increase in anti-spike antibodies and NTs against the WK-521, Delta, and Omicron variants. The breadth of humoral immunity and cross-reactivity with Omicron increased. The cytokine signature and adverse event rate remained unchanged after three-dose vaccination.

Conclusions

The third vaccination dose is safe and effective against Omicron infection.

Funding

This study was supported by grants from AMED (Grant Number JP21fk0108104 and JP21mk0102146).
Genomic and transcriptomic characterization of Delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)
Authors: Kotwa Jonathon D. , Lobb Briallen , Massé Ariane , Gagnier Marianne , Aftanas Patryk , Banerjee Arinjay , Banete Andra , Blais-Savoie Juliette , Bowman Jeff , Buchanan Tore , Chee Hsien-Yao , Kruczkiewicz Peter , Maguire Finlay , McGeer Allison J. , Nirmalarajah Kuganya , Soos Catherine , Yip Lily , Lindsay L. Robbin , Doxey Andrew C. , Lung Oliver , Pickering Bradley , Mubareka Samira
Published: January 2022

White-tailed deer are susceptible to SARS-CoV-2 and represent a highly important species for surveillance. Nasal swabs and retropharyngeal lymph nodes from white-tailed deer (n=258) collected in November 2021 from Québec, Canada were analyzed for SARS-CoV-2 RNA. We employed viral genomics and transcriptomics to further characterize infection and investigate host response to infection. We detected Delta SARS-CoV-2 (AY.44) in deer from the Estrie region; sequences clustered with human sequences from GISAID collected in October 2021 from Vermont, USA, which borders this region. Mutations in the S-gene and a deletion in ORF8 encoding a truncated protein were detected. Host expression patterns in SARS-CoV-2 infected deer were associated with the innate immune response, including signalling pathways related to anti-viral, pro- and anti-inflammatory signalling, and host damage. Our findings provide preliminary insights of host response to SARS-CoV-2 infection in deer and underscores the importance of ongoing surveillance of key wildlife species for SARS-CoV-2.
Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells
Authors: Zhao Lili , Zhao Qun , An Yuxin , Gao Hang , Zhang Weijie , Gong Zhou , Liu Xiaolong , Zhao Baofeng , Liang Zhen , Tang Chun , Zhang Lihua , Zhang Yukui
Published: January 2022

The protein structures and interactions that maintain and regulate cellular processes in different subcellular organelles are heterogeneous and dynamic. However, it remains challenging to characterize the subcellular specificity and translocation of protein complexes in terms of conformation and interactions. Herein, we developed a spatially resolved protein complex profiling approach by biocompatible chemical cross-linking in living cells (SPACX) to monitor the dynamics of protein conformation, interactions and translocation. The advancement of fast capturing protein complexes in the physiological state, coupled with efficient enrichment of the cross-linked peptides, ensured deep-coverage analysis of the protein interactome in living cells. By ensemble structure refinement with cross-linking restraints, subcellular-specific conformation heterogeneity was identified for PTEN. PTEN displayed a broader range of dynamic conformation changes on the dual specificity domains in the nucleus than in the cytoplasm. Moreover, based on conformational differences, different interacting assemblies involving 25 cytoplasm-exclusively and 18 nucleus-exclusively PTEN-interacting proteins were found to account for diverse biological functions. Upon ubiquitin-proteasome system (UPS) stress, the assembly of PTEN and its interacting partners changed obviously during translocation. We newly identified 36 PTEN-interacting proteins, which were found to be highly enriched in functional pathways closely related to cell apoptosis. Inspiringly, the interactions among PTEN isoforms and their interacting proteins were accessible by the determination of sequence-unique cross-linking interfaces for direct interactions. All these results indicate the promise of SPACX to elucidate the functional heterogeneity of proteins in individual subcellular sociology.