bluuebunny/crossref_metadata_2025 huggingface dataset:
The Regulation of Nucleic Acid Vaccine Responses by the Microbiome
Authors: Johnson Andrew M. F. , Hager Kevin , Alameh Mohamad-Gabriel , Van Phuong , Potchen Nicole , Mayer-Blackwell Koshlan , Fiore-Gartland Andrew , Minot Samuel , Lin Paulo J. C. , Tam Ying K. , Weissman Drew , Kublin James G.
Published: February 2023

Nucleic acid vaccines, including both RNA and DNA platforms, are key technologies that have considerable promise in combating both infectious disease and cancer. However, little is known about the extrinsic factors that regulate nucleic acid vaccine responses and which may determine their effectiveness. The microbiome is recognized as a significant regulator of immune development and response, whose role in regulating some traditional vaccine platforms has recently been discovered. Using germ-free and specific-pathogen-free mouse models in combination with different protein, DNA, and mRNA vaccine regimens, we demonstrate that the microbiome is a significant regulator of nucleic acid vaccine immunogenicity. While the presence of the microbiome enhances CD8+ T cell responses to mRNA lipid nanoparticle (LNP) immunization, the microbiome suppresses immunoglobulin and CD4+ T cell responses to DNA-prime, DNA-protein-boost immunization, indicating contrasting roles for the microbiome in the regulation of these different nucleic acid vaccine platforms. In the case of mRNA-LNP vaccination, germ-free mice display reduced dendritic cell/macrophage activation that may underlie the deficient vaccine response. Our study identifies the microbiome as a relevant determinant of nucleic acid vaccine response with implications for their continued therapeutic development and deployment.
Positive coping supports children’s emotional wellness: Behavioral evidence and neuroendocrine mechanisms
Authors: Tian Ting , Chen Boxuan , Zhao Yuyao , Gao Hongyao , Chen Menglu , He Ying , Xu Jiahua , Jiang Min , Xiong Bingsen , Qin Shaozheng
Published: February 2023

A positive coping style is recognized as a stable disposition to foster emotional wellness and resilience, enabling an adaptive process of assessing and dealing with environmental challenges. Such an adaptive process is believed to rely on a nuanced interplay of the hippocampal system and the primary stress hormone cortisol activity. As a hallmark of diurnal cortisol rhythm, cortisol awakening response (CAR) is sensitive to upcoming stress and subserves the preparation of the hippocampal system for rapid behavioral adaption. Yet, little is known about how the hippocampal system and CAR contribute to the merit of positive coping on emotional wellness. By two studies, we investigate the effects of positive coping on children’s emotional wellness and CAR, as well as longitudinal changes in hippocampal-neocortical functional systems involved in emotional processing. Behaviorally, positive coping predicted better emotional regulation ability, but lower anxiety and lower response caution in emotional decision-making. At the endocrine and neurocognitive level, positive coping was associated with greater CAR, which further predicted higher connectivity of the hippocampus with ventrolateral prefrontal cortex (vlPFC) and stimulus-sensitive neocortex one year later. Furthermore, CAR mediated an indirect association between positive coping and longitudinal increases in hippocampal-neocortical connectivity. Positive coping and CAR together could account for the maturity of vlPFC through longitudinal changes in hippocampal-neocortical connectivity. Overall, our findings suggest a cognitive-neuroendocrinal framework in which positive coping shapes hippocampal-neocortical maturation via stress hormone response to support emotional wellness.

Significance

The role of the hippocampal system in regulating stress response is well recognized, but its contribution to emotional well-being is not yet understood. Here we show that the protective effects of positive coping on emotional well-being are contingent on two factors: the cortisol awakening response (CAR), which is sensitive to upcoming stress, and hippocampal development. We found that positive coping practices promoted emotional wellness, enhanced emotional decision-making and increased CAR in young children. Longitudinal neuroimaging analysis revealed that positive coping-related CAR predicted greater hippocampal connectivity with stimulus-sensitive neocortex one year later. Importantly, CAR acted as a mediator of the promotive influence of positive coping on the longitudinal development of hippocampal-neocortical connectivity, which contributed to the maturity of prefrontal control systems. Our findings emphasize the importance of hippocampal-neocortical development in resilient coping and emotional wellness.
Exploiting heterogeneity in coupled, two plasmid systems for dynamic population adaptation
Authors: Kumar Shalni , Lezia Andrew , Hasty Jeff
Published: February 2023

In synthetic multi-plasmid systems, it is standard to use only plasmids with orthogonal replication mechanisms to avoid phenotypic heterogeneity and ensure plasmid stability. In nature, however, microbial populations actively exploit heterogeneity to survive in fluctuating environments. Here we show that the intentional use of distinct plasmids with identical origins of replication (oris) can help an engineered bacterial population adapt to its environment. We find that copy number coupling between distinct plasmids in such systems allows for copy number buffering of an essential, but high-burden construct through the action of a stably maintained, nonessential plasmid. Plasmid coupling also generates population state memory without additional layers of regulatory control. This work reimagines how we design synthetic populations to survive and adapt by strategically giving control back to the cells.
Priors for natural image statistics inform confidence in perceptual decisions
Authors: West Rebecca K , A-Izzeddin Emily J , Sewell David K , Harrison William J
Published: February 2023

Decision confidence plays a critical role in humans’ ability to make adaptive decisions in a noisy perceptual world. Despite its importance, there is currently little consensus about the computations underlying confidence judgements in perceptual decisions. In order to better understand these mechanisms, in this study we sought to address the extent to which confidence is informed by a naturalistic prior probability distribution. Contrary to previous research, we did not require participants to internalise the parameters of an arbitrary prior distribution. Instead we used a novel psychophysical paradigm which allowed us to capitalise on probability distributions of low-level image features in natural scenes, which are well-known to influence perception. Participants reported the subjective upright of naturalistic image target patches, and then reported their confidence in their orientation responses. We used computational modelling to relate the statistics of the low-level features in the targets to the distribution of these features across many natural images. As expected, we found that participants used an internalised prior of the regularities of low-level natural image statistics to inform their perceptual judgements. Critically, we also show that the same low-level image statistics predict participants’ confidence judgements. Overall, our study highlights the importance of using naturalistic task designs that capitalise on existing, long-term priors to further our understanding of the computational basis of confidence.
Pressure-driven membrane inflation through nanopores on the cell wall
Authors: Zhong Qi , Wu Chen-Xu , Ma Rui
Published: February 2023

Walled cells, such as plants and fungi, compose an important part of the model systems in biology. The cell wall primarily functions to prevent the cell from over-expansion when exposed to water, and is a porous material distributed with nanosized pores on it. In this paper, we study the deformation of a membrane patch by an osmotic pressure through a nanopore on the cell wall. We find that there exists a critical pore size beyond which the membrane cannot stand against the pressure and would inflate out through the pore. The critical pore size scales exponentially with the membrane tension and the spontaneous curvature, and exhibits a power law dependence on the osmotic pressure. Our results also show that the liquid membrane expansion by pressure is mechanically different from the solid balloon expansion, and predict that the bending rigidity of the membrane in walled cells should be larger than that of the mammalian cells so as to prevent inflation through the pores on the cell wall.
Alternative splicing of its 5’-UTR limits CD20 mRNA translation and enables resistance to CD20-directed immunotherapies
Authors: Ang Zhiwei , Paruzzo Luca , Hayer Katharina E. , Schmidt Carolin , Torres Diz Manuel , Xu Feng , Zankharia Urvi , Zhang Yunlin , Soldan Samantha , Zheng Sisi , Falkenstein Catherine D. , Loftus Joseph P. , Yang Scarlett Y. , Asnani Mukta , King Sainos Patricia , Pillai Vinodh , Chong Emeline , Li Marilyn M. , Tasian Sarah K. , Barash Yoseph , Lieberman Paul M. , Ruella Marco , Schuster Stephen J. , Thomas-Tikhonenko Andrei
Published: February 2023

Aberrant skipping of coding exons in CD19 and CD22 compromises responses to immunotherapy for B-cell malignancies. Here, we show that theMS4A1gene encoding human CD20 also produces several mRNA isoforms with distinct 5’ untranslated regions (5’-UTR). Four variants (V1-4) were detectable by RNA-seq in distinct stages of normal B-cell differentiation and B-lymphoid malignancies, with V1 and V3 being the most abundant by far. During B-cell activation and Epstein-Barr virus infection, redirection of splicing from V1 to V3 coincided with increased CD20 positivity. Similarly, in diffuse large B-cell lymphoma only V3, but not V1, correlated with CD20 protein levels, suggesting that V1 might be translation-deficient. Indeed, the longer V1 isoform was found to contain upstream open reading frames (uORFs) and a stem-loop structure, which cooperatively inhibited polysome recruitment. By modulating CD20 isoforms with splice-switching Morpholino oligomers, we enhanced CD20 expression and anti-CD20 antibody rituximab-mediated cytotoxicity in a panel of B-cell lines. Furthermore, reconstitution of CD20-knockout cells with V3 mRNA led to the recovery of CD20 positivity, while V1-reconstituted cells had undetectable levels of CD20 protein. Surprisingly,in vitroCD20-directed CAR T cells were able to kill both V3- and V1-expressing cells, but the bispecific T cell engager mosunetuzumab was only effective against V3-expressing cells. To determine whether CD20 splicing is involved in immunotherapy resistance, we performed RNA-seq on four post-mosunetuzumab follicular lymphoma relapses and discovered that in two of them downregulation of CD20 was accompanied by the V3-to-V1 shift. Thus, splicing-mediated mechanisms of epitope loss extend to CD20-directed immunotherapies.

Key Points

In normal & malignant human B cells, CD20 mRNA is alternatively spliced into four 5’-UTR isoforms, some of which are translation-deficient.

The balance between translation-deficient and -competent isoforms modulates CD20 protein levels & responses to CD20-directed immunotherapies

Explanation of Novelty

We discovered that in normal and malignant B-cells, CD20 mRNA is alternatively spliced to generate four distinct 5’-UTRs, including the longer translation-deficient V1 variant. Cells predominantly expressing V1 were still sensitive to CD20-targeting chimeric antigen receptor T-cells. However, they were resistant to the bispecific anti-CD3/CD20 antibody mosunetuzumab, and the shift to V1 were observed in CD20-negative post-mosunetuzumab relapses of follicular lymphoma.
A robust Platform for Integrative Spatial Multi-omics Analysis to Map Immune Responses to SARS-CoV-2 infection in Lung Tissues
Authors: Tan Xiao , Grice Laura F. , Tran Minh , Mulay Onkar , Monkman James , Blick Tony , Vo Tuan , Almeida Ana Clara Simões Flórido , Junior Jarbas da Silva Motta , de Moura Karen Fernandes , Machado-Souza Cleber , Souza-Fonseca-Guimaraes Paulo , Baena Cristina Pellegrino , de Noronha Lucia , Guimaraes Fernanda Simoes Fortes , Luu Hung N. , Drennon Tingsheng , Williams Stephen , Stern Jacob , Uytingco Cedric , Pan Liuliu , Nam Andy , Cooper Caroline , Short Kirsty , Belz Gabrielle T. , Souza-Fonseca-Guimaraes Fernando , Kulasinghe Arutha , Nguyen Quan
Published: February 2023

The SARS-CoV-2 (COVID-19) virus has caused a devastating global pandemic of respiratory illness. To understand viral pathogenesis, methods are available for studying dissociated cells in blood, nasal samples, bronchoalveolar lavage fluid, and similar, but a robust platform for deep tissue characterisation of molecular and cellular responses to virus infection in the lungs is still lacking. We developed an innovative spatial multi-omics platform to investigate COVID-19-infected lung tissues. Five tissue-profiling technologies were combined by a novel computational mapping methodology to comprehensively characterise and compare the transcriptome and targeted proteome of virus infected and uninfected tissues. By integrating spatial transcriptomics data (Visium, GeoMx and RNAScope) and proteomics data (CODEX and PhenoImager HT) at different cellular resolutions across lung tissues, we found strong evidence for macrophage infiltration and defined the broader microenvironment surrounding these cells. By comparing infected and uninfected samples, we found an increase in cytokine signalling and interferon responses at different sites in the lung and showed spatial heterogeneity in the expression level of these pathways. These data demonstrate that integrative spatial multi-omics platforms can be broadly applied to gain a deeper understanding of viral effects on cellular environments at the site of infection and to increase our understanding of the impact of SARS-CoV-2 on the lungs.
DAISIEprep: an R package for the extraction and formatting of data for the island biogeography model DAISIE
Authors: Lambert Joshua W. , Roeble Lizzie , Pannetier Théo , Etienne Rampal S. , Valente Luis
Published: February 2023

Phylogenetic trees are commonly used to answer questions on biogeographical and diversification histories of different groups.

Recently, new approaches have been developed that use community phylogenetic trees requiring a data structure distinct from the single phylogenetic trees that are commonly used, which may be a barrier to the utilisation of these approaches.

DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) is an island biogeography model that can estimate rates of colonisation, speciation and extinction from phylogenetic data across insular communities, as well as simulate islands under those rates.

Here we describe theDAISIEprepR package, a set of pre-processing tools to aid the extraction of data from one or many phylogenetic trees to generate data in a format interpretable by DAISIE for the application of island biogeography inference models. We present examples to illustrate the various data types that can be used.

The package includes simple algorithms to extract data on island colonists and account for bio-geographical, topological and taxonomic uncertainty. It also allows flexible incorporation of either missing species or entire insular lineages when phylogenetic data are not available.

DAISIEprepenables reproducible and user-friendly data extraction and formatting, and will facili-tate addressing questions about island biogeography, diversification and anthropogenic impacts in insular systems.
Multiple forms of neural processing when repeating voluntary thumb flexions
Authors: Kock Ruchella , Ghosh Arko
Published: February 2023

There is considerable trial-to-trial variability in single cortical neurons when performing the same action repeatedly. One possibility is that neural populations are more stable in representing actions; alternatively, they too may be distinctly engaged from trial-to-trial. To address the nature of variability in large neural populations, we captured the EEG signals time-locked to repeated voluntary thumb flexion movements (∼500 repetitions, 23 subjects). By using non-negative matrix factorization on the low-frequency sensorimotor cortical signals, we quantified the trial-to-trial motor-related potentials (MRPs) in terms of prototypical signals (meta-MRPs) and their corresponding prominence at each trial (meta-trials). Clustering the meta-MRPs across the sampled population revealed 5 distinct signal patterns. There were brain-wide correlates of these meta-MRP clusters. Cortical hemispheres were distinctly recruited from trial-to-trial as certain clusters were accompanied by bilateral motor negativity while others were characterized by ipsilateral motor negativity. The sensory feedback too was distinctly processed from trial-to-trial as the central post-movement positivity was present only for certain clusters. A poorly understood pre-motor positivity accompanied all clusters albeit varying in their timing from trial-to-trial. These patterns – including the time-varying positivity preceding the movement – were rendered invisible by the traditional averaging of the signals. We suggest that the variability in EEG signals is not just noise but a consequence of distinct activation patterns deployed by the cortex. We support the idea that the cortex flexibly switches between distinct forms of neural processing to achieve the same behavioral goals.
Peptide ligands for the affinity purification of adeno-associated viruses from HEK 293 cell lysates
Authors: Chu Wenning , Shastry Shriarjun , Barbieri Eduardo , Prodromou Raphael , Greback-Clarke Paul , Smith Will , Moore Brandyn , Kilgore Ryan , Cummings Christopher , Pancorbo Jennifer , Gilleskie Gary , Daniele Michael A. , Menegatti Stefano
Published: February 2023

Adeno-associated viruses (AAVs) are the vector of choice for delivering gene therapies that can cure inherited and acquired diseases. Clinical research on various AAV serotypes significantly increased in recent years alongside regulatory approvals of AAV-based therapies. The current AAV purification platform hinges on the capture step, for which several affinity resins are commercially available. These adsorbents rely on protein ligands – typically camelid antibodies – that provide high binding capacity and selectivity, but suffer from low biochemical stability and high cost, and impose harsh elution conditions (pH < 3) that can harm the transduction activity of recovered AAVs. Addressing these challenges, this study introduces peptide ligands that selectively capture AAVs and release them under mild conditions (pH 6.0). The peptide sequences were identified by screening a focused library and modeledin silicoagainst AAV serotypes 2 and 9 (AAV2 and AAV9) to select candidate ligands that target homologous sites at the interface of the VP1-VP2 and VP2-VP3 virion proteins with mild binding strength (KD∼ 10-5-10-6M). Selected peptides were conjugated to Toyopearl resin and evaluated via binding studies against AAV2 and AAV9, demonstrating the ability to target both serotypes with values of dynamic binding capacity (DBC10%> 1013vp per mL of resin) and product yields (∼50-80%) on par with commercial adsorbents. The peptide-based adsorbents were finally utilized to purify AAV2 from a HEK 293 cell lysate, affording high recovery (50-80%), 80-to-400-fold reduction of host cell proteins (HCPs), and high transduction activity (up to 80%) of the purified viruses.
Distinct mobility patterns of BRCA2 molecules at DNA damage sites
Authors: Paul Maarten W. , Aaron Jesse , Wait Eric , Van Genderen Romano M. , Tyagi Arti , Kabbech Hélène , Smal Ihor , Chew Teng-Leong , Kanaar Roland , Wyman Claire
Published: February 2023

BRCA2 is an essential tumor suppressor protein involved in promoting faithful repair of DNA lesions. The activity of BRCA2 needs to be tuned precisely to be active when and where it is needed. Here, we quantified the spatio-temporal dynamics of BRCA2 in living cells using aberration-corrected multifocal microscopy (acMFM). Using multicolor imaging to identify DNA damage sites, we were able to quantify its dynamic motion patterns in the nucleus and at DNA damage sites. While a large fraction of BRCA2 molecules localized near DNA damage sites appear immobile, an additional fraction of molecules exhibits subdiffusive motion, providing a potential mechanism to retain an increased number of molecules at DNA lesions. Super-resolution microscopy revealed inhomogeneous localization of BRCA2 relative to other DNA repair factors at sites of DNA damage. This suggests the presence of multiple nanoscale compartments in the chromatin surrounding the DNA lesion, which could play an important role in the contribution of BRCA2 to the regulation of the repair process.
Selective targeting of α4β7/MAdCAM-1 axis suppresses liver fibrosis by reducing proinflammatory T cell recruitment to the liver
Authors: Gupta Biki , Rai Ravi Prakash , Pal Pabitra B. , Chaudhary Sudrishti , Chiaro Anna , Seaman Shannon , Singhi Aatur D. , Monga Satdarshan P. , Iyer Smita S. , Raeman Reben
Published: February 2023

Integrin α4β7+ T cells perpetuate tissue injury in chronic inflammatory diseases, yet their role in hepatic fibrosis progression remains poorly understood. Here we report increased accumulation of α4β7+ T cells in the liver of people with cirrhosis relative to disease controls. Similarly, hepatic fibrosis in the established mouse model of CCl4-induced liver fibrosis was associated with enrichment of intrahepatic α4β7+ CD4 and CD8 T cells. Monoclonal antibody (mAb)-mediated blockade of α4β7or its ligand mucosal addressin cell adhesion molecule (MAdCAM)-1 attenuated hepatic inflammation and prevented fibrosis progression in CCl4treated mice. Improvement in liver fibrosis was associated with a significant decrease in the infiltration of α4β7+ CD4 and CD8 T cells suggesting that α4β7/MAdCAM-1 axis regulates both CD4 and CD8 T cell recruitment to the fibrotic liver, and α4β7+ T cells promote hepatic fibrosis progression. Analysis of hepatic α4β7+ and α4β7-CD4 T cells revealed that α4β7+ CD4 T cells enriched for markers of activation and proliferation demonstrating an effector phenotype. Notably, blockade of α4β7or MAdCAM-1 did not affect the recruitment of Foxp3+ regulatory T cells, demonstrating the specificity of α4β7/MAdCAM-1 axis in regulating effector T cell recruitment to the liver. The findings suggest that α4β7+ T cells play a critical role in promoting hepatic fibrosis progression, and mAb-mediated blockade of α4β7or MAdCAM-1 represents a promising therapeutic strategy for slowing hepatic fibrosis progression in chronic liver diseases.
Human Arm Redundancy - A New Approach for the Inverse Kinematics Problem
Authors: Barliya Avi , Krausz Nili , Naaman Hila , Chiovetto Enrico , Giese Martin , Flash Tamar
Published: February 2023

The inverse kinematics problem deals with the question of how the nervous system coordinates movement to resolve redundancy, such as in the case of arm reaching movements where more degrees of freedom are available at the joint versus hand level. In particular, this work focuses on determining which coordinate frames can best represent human movements, allowing the motor system to solve the inverse kinematics problem in the presence of kinematic redundancies. In particular, in this work we used a multi-dimensional sparse source separation method called FADA to derive sets of basis functions (here called sources) for both the task and joint spaces, with joint space being represented in terms of either the absolute or anatomical joint angles. We assessed the similarities between the joint and task sources in each of these joint representations. We found that the time-dependent profiles of the absolute reference frame’s sources show greater similarity to those of the corresponding sources in the task space. This result was found to be statistically significant. Hence, our analysis suggests that the nervous system represents multi-joint arm movements using a limited number of basis functions, to allow for simple transformations between task and joint spaces. Importantly, joint space seems to be represented in terms of an absolute reference frame to achieve successful performance and simplify inverse kinematics transformations in the face of the existing kinematic redundancies. Further studies will be needed to determine the generalizability of this finding and its implications for neural control of movement.
The cytidine deaminase APOBEC3A is required for large ribosomal subunit biogenesis
Authors: McCool Mason A. , Bryant Carson J. , Abriola Laura , Surovtseva Yulia V. , Baserga Susan J.
Published: February 2023

Cancer initiates as a consequence of genomic mutations, and its subsequent progression relies on increased production of ribosomes to maintain high levels of protein synthesis for unchecked cell growth. Recently, cytidine deaminases have been uncovered as sources of mutagenesis in cancer. To form more established connections between these two cancer driving processes, we interrogated the cytidine deaminase family of proteins for potential roles in human ribosome biogenesis. We identified and validated APOBEC3A and APOBEC4 as novel ribosome biogenesis factors through our laboratory’s established screening platform for the discovery of regulators of nucleolar function in MCF10A cells. We show that APOBEC3A is required for cell cycle progression and global protein synthesis. More specifically, we highlight APOBEC3A’s role within the processing and maturation steps that form the large subunit 5.8S and 28S ribosomal (r)RNAs. Through an innovative nuclear RNA sequencing methodology, we identify candidate APOBEC3A C-to-U editing sites on the pre-rRNA and pre-mRNAs for the first time. Our work reveals the exciting possibility that the pre-rRNA can be edited during its maturation. More broadly, we found an additional function of APOBEC3A in cancer pathology, expanding its relevance as a target for cancer therapeutics.
Modernizing the original influenza vaccine to enhance protective antibody responses against neuraminidase antigens
Authors: Martinez Mira Rakic , Gao Jin , Wan Hongquan , Kang Hyeog , Klenow Laura , Daniels Robert
Published: February 2023

Most seasonal influenza vaccines are produced using hemagglutinin (HA) surface antigens from inactivated virions. However, virions are thought to be a suboptimal source for the less abundant NA surface antigen, which is also protective against severe disease. Here, we demonstrate that inactivated influenza virions are compatible with two modern approaches for improving protective NA antibody responses. Using a DBA/2J mouse model, we confirmed that the strong infection-induced NA inhibitory (NAI) antibody responses are only achieved by high dose immunizations of inactivated virions, likely due to low viral NA content. Based on this observation, we first produced virions with higher NA content by using reverse genetics to exchange the viral internal gene segments. Single immunizations with these inactivated virions enhanced NAI antibody responses, improved NA-based protection from a lethal viral challenge and allowed the development of natural immunity to the heterotypic challenge virus HA. Second, we combined inactivated virions with recombinant NA proteins. These mixtures increased NA-based protection following viral challenge and elicited stronger NA antibody responses than either component alone, especially when the NAs were homologous. Together, these results indicate that viral- and protein-based vaccines can be combined in a single syringe to improve protective antibody responses to influenza antigens.
Direct optical nanoscopy unveils signatures of cytokine-induced β-cell structural and functional stress
Authors: Pugliese Licia Anna , De Lorenzi Valentina , Bernardi Mario , Ghignoli Samuele , Tesi Marta , Marchetti Piero , Cardarelli Francesco , Pesce Luca
Published: February 2023

Here we exploit a combination of advanced optical-microscopy tools and fluorescently-labeled molecular targets in rat Insulinoma 1E β-cells exposed to proinflammatory cytokines. Expansion microscopy (ExM) is used to achieve the spatial resolution (~50 nm) needed to analyze the structural features of key subcellular targets, i.e. insulin secretory granules (ISGs), microtubules, actin filaments, and mitochondria; time-lapse live-cell microscopy, on the other hand, provides complementary information on key dynamic and metabolic subcellular parameters. It is found that 24-hours exposure to proinflammatory cytokines induces a neat decrease in the number of ISGs and alteration in the dynamics of the residual pool, marked depolymerization of microtubules, change in mitochondrial morphology and metabolic activity, and decreased cell responsiveness to glucose stimulation. This is accompanied by clear signatures of the production of reactive oxygen species. Reported results provide direct evidence that proinflammatory cytokines act as potent stimulators of insulin secretion and, concomitantly, as cell stressors.
Integrated analysis and annotation for T-cell receptor sequences using TCRosetta
Authors: Yue Tao , Chen Si-Yi , Shen Wen-Kang , Cheng Liming , Guo An-Yuan
Published: February 2023

Background

T cells and T cell receptors (TCRs) are essential components of the adaptive immune system. TCRs, on the surface of T cells, are responsible for recognizing and binding antigen peptide-MHC complex and play vital roles in T-cell immunology. Characterization of TCR repertoire offers a promising and high informative source for understanding the functions of T cells in immune responses and immunotherapies. Many researchers are now interested in TCR repertoire study; however, there are rare online servers for TCR analysis, especially no servers for TCR annotation and advanced analyses.

Results

We developed TCRosetta, a comprehensive online server integrating the analytical methods for TCR repertoire/sequences analysis and visualization. TCRosetta combines general features analysis, large-scale sequence clustering, network construction, TCR-peptide binding prediction, generation probability calculation, and k-mer motif analysis for robust TCR sequence analysis, making TCR data analysis as simple as possible and allowing users to concentrate on research rather than coding. In addition, TCRosetta could annotate disease information for TRB CDR3 sequences by batch searching similar sequences in manually curated disease-related TCR database. The TCRosetta server accepts multiple input data formats and can analyze ∼20000 TCR sequences in less than three minutes.

Conclusions

TCRosetta is the most comprehensive web server to date for TCR sequences/repertoires analysis and it is freely available athttp://bioinfo.life.hust.edu.cn/TCRosetta/. It can be applied to help discover novel biomarkers for disease diagnosis and identify cancer-associated TCR sequences.

WHAT IS ALERADY KNOWN ON THIS TOPIC

T cell receptor repertoires are largely untapped resource than can be used for predicting immune responses to different exposures including viral infections and tumor neoantigens. The downstream analysis of TCR repertoire is often performed by different tools requiring diverse operating environments and expertise. There is no webserver for comprehensive TCR repertoire analysis including general and advanced analysis.

WHAT THIS STUDY ADDS

We developed TCRosetta, a comprehensive platform for analyzing T-cell repertoire which combines nearly all TCR analysis methods. It supports different kinds of the format of input including most mainstream TCR extraction tools or amino acid sequences. It could analyze the features of TCR repertoire and display them in interactive graphs and is the first platform with a batch search and TCR annotation function.

HOW THIS STUDY MIGHT AFFECT RESEARCH, PACTICE OR POLICY

TCRosetta can be applied to discover novel biomarkers to predict response in immunotherapy such TCR repertoire diversity and clonality. It also can identify cancer-associated TCR sequences by clustering biochemically similar CDR3 sequences. It can make TCR repertoire analysis as effortless as possible and help users focus on research instead of coding.
Birds are easier to trick: an effect of magnetic field manipulation on migratory orientation of Nathusius’ pipistrelle in the circular release box
Authors: Cellarius Fyodor , Utvenko Gleb , Markovets Mikhail , Pakhomov Alexander
Published: February 2023

Bats, like birds, are capable of long annual migrations; however, a very limited number of studies are devoted to the role of the Earth’s magnetic field in bat navigation. We aimed to perform a series of experiments on Nathusius’ pipistrelle (Pipistrellus nathusii) to ensure that they are able to use the geomagnetic field for orientation. Bats were tested under two different conditions: in the geomagnetic field and the field, rotated 120° CW. To determine the takeoff direction and analyse behaviour in different magnetic conditions, we used the modified circular release box (CRBox) and a mini camera with IR LEDs. Helmholtz magnetic coils were used to manipulate the magnetic field. Bats were captured during migration through the Curonian spit (Kaliningrad region, Russia). Totally 53 bats were tested during August and September 2021-2022. During the second year, we recorded post-release bats’ behaviour using a thermal camera. Although results from 2021 are ambiguous, data obtained in 2022 suggests that under given conditions bats, unlike birds, could prefer local audible landmarks and wind direction prior to global cues. However, the recordings of released bats clearly show that they have some specific directional preferences, which correspond to their migratory orientation.
Antibody-mediated cell entry of SARS-CoV-2
Authors: Kibria Md Golam , Lavine Christy L. , Tang Weichun , Wang Shaowei , Gao Hailong , Shi Wei , Zhu Haisun , Voyer Jewel , Rits-Volloch Sophia , Keerti  , Bi Caihong , Peng Hanqin , Wesemann Duane R. , Lu Jianming , Xie Hang , Seaman Michael S. , Chen Bing
Published: February 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells by first engaging its cellular receptor angiotensin converting enzyme 2 (ACE2) to induce conformational changes in the virus-encoded spike protein and fusion between the viral and target cell membranes. We report here that certain monoclonal neutralizing antibodies against distinct epitopic regions of the receptor-binding domain of the spike can replace ACE2 to serve as a receptor and efficiently support membrane fusion and viral infectivity. These receptor-like antibodies can function in the form of a complex of their soluble immunoglobulin G with Fc-gamma receptor I, a chimera of their antigen-binding fragment with the transmembrane domain of ACE2 or a membrane-bound B cell receptor, indicating that ACE2 and its specific interactions with the spike protein are dispensable for SARS-CoV-2 entry. These results suggest that antibody responses against SARS-CoV-2 may expand the viral tropism to otherwise nonpermissive cell types; they have important implications for viral transmission and pathogenesis.
A standardized and reproducible workflow for membrane glass slides in routine histology and spatial proteomics
Authors: Nordmann Thierry M. , Schweizer Lisa , Metousis Andreas , Thielert Marvin , Rodriguez Edwin , Rahbek-Gjerdrum Lise Mette , Stadler Pia-Charlotte , Bzorek Michael , Mund Andreas , Rosenberger Florian A. , Mann Matthias
Published: February 2023

Defining the molecular phenotype of single cellsin-situis essential for understanding tissue heterogeneity in health and disease. Powerful imaging technologies have recently been joined by spatial omics technologies, promising unparalleled insights into the molecular landscape of biological samples. One approach involves laser microdissection in combination with membrane glass slides for the isolation of single cells from specific anatomical regions for further analysis by spatial omics. However, so far this is not fully compatible with automated staining platforms and routine histology procedures such as heat-induced epitope retrieval, limiting reproducibility, throughput and integration of advanced staining procedures. This study describes a robust workflow for routine use of glass membrane slides, allowing precise extraction of tissue in combination with automated and multicolor immunofluorescence staining. The key advance is the addition of glycerol to standard heat-induced epitope retrieval protocol, preventing membrane distortion while preserving antigen retrieval properties. Importantly, we show that glycerol is fully compatible with mass-spectrometry based proteomics and does not affect proteome depth or quality. Further, we enable single focal plane imaging by removing remaining trapped air pockets with an incision. We demonstrate our workflow using the recently introduced Deep Visual Proteomics technology on the single-cell type analysis of adjacent suprabasal and basal keratinocytes of human skin. Our protocol extends the utility of membrane glass slides and enables much more robust integration with routine histology procedures, high-throughput multiplexed imaging and sophisticated downstream spatial omics technologies.
Cysteine-Rich Intestinal Protein 1 is a Novel Surface Marker for Myometrial Stem/Progenitor Cells
Authors: Paul Emmanuel N. , Carpenter Tyler J. , Fitch Sarah , Sheridan Rachael , Lau Kin H. , Arora Ripla , Teixeira Jose M.
Published: February 2023

Myometrial stem/progenitor cells (MyoSPCs) have been proposed as the cells of origin for uterine fibroids, which are benign tumors that develop in the myometrium of most reproductive age women, but the identity of the MyoSPC has not been well established. We previously identified SUSD2 as a possible MyoSPC marker, but the relatively poor enrichment in stem cell characteristics of SUSD2+ over SUSD2- cells compelled us to find better discerning markers for more rigorous downstream analyses. We combined bulk RNA-seq of SUSD2+/- cells with single cell RNA-seq to identify markers capable of further enriching for MyoSPCs. We observed seven distinct cell clusters within the myometrium, with the vascular myocyte cluster most highly enriched for MyoSPC characteristics and markers, includingSUSD2. CRIP1expression was found highly upregulated in both techniques and was used as a marker to sort CRIP1+/PECAM1- cells that were both enriched for colony forming potential and able to differentiate into mesenchymal lineages, suggesting that CRIP1+/PECAM1- cells could be used to better study the etiology of uterine fibroids.
Recruitment of the SNX17-Retriever recycling pathway regulates synaptic function and plasticity
Authors: Rivero-Ríos Pilar , Tsukahara Takao , Uygun Tunahan , Chen Alex , Chavis Garrett D. , Giridharan Sai Srinivas Panapakkam , Iwase Shigeki , Sutton Michael A. , Weisman Lois S.
Published: February 2023

Trafficking of cell-surface proteins from endosomes to the plasma membrane is a key mechanism to regulate synaptic function. In non-neuronal cells, proteins recycle to the plasma membrane either via the SNX27-Retromer-WASH pathway, or via the recently discovered SNX17-Retriever-CCC-WASH pathway. While SNX27 is responsible for the recycling of key neuronal receptors, the roles of SNX17 in neurons are less understood. Here, using cultured hippocampal neurons, we demonstrate that the SNX17 pathway regulates synaptic function and plasticity. Disruption of this pathway results in a loss of excitatory synapses and prevents structural plasticity during chemical long-term potentiation (cLTP). cLTP drives SNX17 recruitment to synapses, where its roles are in part mediated by regulating surface expression of β1-integrin. SNX17 recruitment relies on NMDAR activation, CamKII signaling, and requires binding to the Retriever and PI(3)P. Together, these findings provide molecular insights into the regulation of SNX17 at synapses, and define key roles for SNX17 in synaptic maintenance and in regulating enduring forms of synaptic plasticity.
Complex petal spot formation in the Beetle Daisy (Gorteria diffusa) relies on spot-specific accumulation of malonylated anthocyanin regulated by paralogous GdMYBSG6 transcription factors
Authors: Fattorini Róisín , Khojayori Farahnoz , Mellers Gregory , Moyroud Edwige , Serrano Eva Herrero , Kellenberger Roman T , Walker Rachel , Wang Qi , Hill Lionel , Glover Beverley J
Published: February 2023

Gorteria diffusahas elaborate petal spots that attract male bee-fly pollinators through sexual deception but the genetic basis ofG. diffusapetal spot development is currently unknown. Here we investigate the regulation of pigmentation during spot formation.

We used UHPLC-MS/MS to determine the anthocyanin composition of spots and background pigmentation inG. diffusa. Combining gene expression analysis with protein interaction assays we characterised three R2R3-MYB genes regulating anthocyanin production inG. diffusaspots.

We found that cyanidin 3-glucoside pigmentsG. diffusaray floret petals. Unlike other petal regions, spots contain a high proportion of malonylated anthocyanin. We identified three paralogous subgroup 6 R2R3-MYB transcription factors that activate the production of petal spot pigmentation. The corresponding genes are upregulated in developing spots and induce ectopic anthocyanin production upon heterologous expression in tobacco. EMSAs and dual luciferase assays suggest that these transcription factors regulate genes encoding three anthocyanin synthesis enzymes: anthocyanidin synthase (GdANS), dihydroflavonol reductase (GdDFR) and malonyl transferase (GdMAT1), accounting for the spot-specific production of malonylated pigments.

Here we provide the first molecular characterisation ofG. diffusaspot development, showing that the elaboration of complex spots begins with accumulation of malonylated pigments at the base of ray floret petals, positively regulated by three subgroup 6 R2R3-MYB transcription factors.
A discrete choice experiment on oral and injection treatment preferences among moderate‐to‐severe psoriasis patients in Japan
Authors: Komine Mayumi , Kim Hyunchung , Yi Jingbo , Zhong Yichen , Sakai Yoko , Crawford Bruce , Habiro Katsuyoshi , Hikichi Yusuke , Feldman Steven R.
Published: February 2023

Long‐term psoriasis (PsO) management remains challenging. With growing variation in treatment efficacy, cost, and modes of administration, patient preferences for different treatment characteristics are not well understood. A discrete choice experiment (DCE), informed by qualitative patient interviews, was conducted to assess patient preferences for different attributes of PsO treatments; 222 adult patients with moderate‐to‐severe PsO receiving systemic therapy participated in the DCE web survey. Better long‐term efficacy and lower cost were preferred (preference weights p < 0.05). Long‐term efficacy had the highest relative importance (RI) and mode of administration was as important as the outcome attributes (efficacy and safety). Patients also preferred oral to injectable administration. In subgroup analyses by disease severity, residence, psoriatic arthritis as a comorbidity, and gender, the trends for each subgroup were the same as the overall population although the extent of RI for administration mode varied. Mode of administration was more important for patients with moderate versus severe disease, or rural versus urban residence. This DCE utilized attributes related to both oral and injectable treatment as well as a broad study population of systemic treatment users. Preferences were further stratified by patient characteristics to explore trends in different subgroups. Understanding the RI of treatment attributes and the attribute trade‐offs acceptable to patients helps inform moderate‐to‐severe PsO systemic treatments decisions.
Strain‐specific quorum‐sensing responses determine virulence properties in Vibrio anguillarum
Authors: Mauritzen Jesper Juel , Søndberg Emilie , Kalatzis Panos G. , Roager Line , Gram Lone , Svenningsen Sine Lo , Middelboe Mathias
Published: February 2023

Bacterial populations communicate using quorum‐sensing (QS) molecules and switch on QS regulation to engage in coordinated behaviour such as biofilm formation or virulence. The marine fish pathogen Vibrio anguillarum harbours several QS systems, and our understanding of its QS regulation is still fragmentary. Here, we identify the VanT‐QS regulon and explore the diversity and trajectory of traits under QS regulation in Vibrio anguillarum through comparative transcriptomics of two wildtype strains and their corresponding mutants artificially locked in QS‐on (ΔvanO) or QS‐off (ΔvanT) states. Intriguingly, the two wildtype populations showed different QS responses to cell density changes and operated primarily in the QS‐on and QS‐off spectrum, respectively. Examining 27 V. anguillarum strains revealed that ~11% were QS‐negative, and GFP‐reporter measurements of nine QS‐positive strains revealed a highly strain‐specific nature of the QS responses. We showed that QS controls a plethora of genes involved in processes such as central metabolism, biofilm formation, competence, T6SS, and virulence properties in V. anguillarum, with large strain‐specific differences. Moreover, we demonstrated that the QS state is an important driver of virulence towards fish larvae in one of two V. anguillarum strains. We speculate that infections by mixed‐strain communities spanning diverse QS strategies optimize the infection efficiency of the pathogen.
Parental satisfaction with programmes provided for children with learning difficulties in Oman
Authors: Al‐Qaryouti Ibrahim , Al‐Salmi Laila , Al‐Aiasare Amur , Adul‐Hadi Amani
Published: February 2023

This study aimed to explore parental satisfaction with programmes provided for children with learning difficulties (LD) in Oman. A sample was collected from 299 parents who filled out an electronic self‐reporting questionnaire during the second semester of 2021. The researchers designed a 19‐item questionnaire that was distributed over two domains: 14 items on parent satisfaction and five items on parent co‐operation. The results revealed that parents' overall satisfaction with the effectiveness of the LD programmes in which their children were enrolled was high. The results also indicated statistically significant differences among the mean scores on parents' satisfaction over the age variable groups, in favor of the younger group, followed by the middle group, and lastly the older group. There were also statistically significant differences among the mean scores on parents' satisfaction according to the province locations, in favor of the capital city of Oman, Muscat, and its peripheral provinces, followed by the western provinces, and lastly, the eastern provinces. The study recommends conducting similar studies to investigate the satisfaction of school principals, specialists, teachers and children with LD to determine the effectiveness of Oman's LD programmes.
Using iPads for the social communication and emotional regulation of autistic pupils: an exploration of key stakeholders' perspectives and practices
Authors: Achtypi Alexia , Guldberg Karen K. , Papoudi Despina
Published: February 2023

Little research has focused on the implementation of iPad practices in real contexts and the identification of relevant challenges and enablers. This work explored practices relating to using iPads for autistic pupils' social communication (SC) and emotional regulation (ER) based on key stakeholders' perspectives. It employed two case studies undertaken in two primary schools located in the United Kingdom's West Midlands. The data were gathered by interviewing practitioners and parents and analyzing the schools' computing policies. The outcomes varied from iPads being used as multimodal learning tools, to teachers focusing on SC and ER, and parents mainly on recreation and ER. The findings were evaluated using Abbott's concept of e‐inclusion (2007), considering the impact of the relationship between technology, individuals and context on iPad use in situ. Issues are highlighted around pedagogy and teaching methods, offering insights into what drives teachers to make decisions regarding technology use.