bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultra-deep through-skull mouse brain imaging via the combination of skull optical clearing and three-photon microscopy
Authors: He Mubin , Li Dongyu , Zheng Zheng , Zhang Hequn , Wu Tianxiang , Geng Weihang , Hu Zhengwu , Feng Zhe , Peng Shiyi , Zhu Liang , Xi Wang , Zhu Dan , Qian Jun 
Published: December 2021

AbstractOptical microscopy has enabled in vivo monitoring of brain structures and functions with high spatial resolution. However, the strong optical scattering in turbid brain tissue and skull impedes the observation of microvasculature and neuronal structures at a large depth. Herein, we proposed a strategy to overcome the influence induced by the high scattering effect of both skull and brain tissue via the combination of skull optical clearing (SOC) technique and thee-photon fluorescence microscopy (3PM). The Visible-NIR-II compatible Skull Optical Clearing Agents (VNSOCA) we applied reduced the skull scattering and water absorption in long wavelength by refractive index matching and H2O replacement to D2O respectively. 3PM with the excitation in the 1300-nm window reached 1.5 mm cerebrovascular imaging depth in cranial window. Combining the two advanced technologies together, we achieved so far the largest cerebrovascular imaging depth of 1.0 mm and neuronal imaging depth of >700 μm through intact mouse skull. Dual-channel through-skull imaging of both brain vessels and neurons was also successfully realized, giving an opportunity of non-invasively monitoring the deep brain structures and functions at single-cell level simultaneously.
Isotropic Three-Dimensional Dual-Color Super-Resolution Microscopy with Metal-Induced Energy Transfer
Authors: Thiele Jan Christoph , Jungblut Marvin , Helmerich Dominic A. , Tsukanov Roman , Chizhik Anna , Chizhik Alexey I. , Schnermann Martin , Sauer Markus , Nevskyi Oleksii , Enderlein Jörg 
Published: December 2021

AbstractOver the last two decades, super-resolution microscopy has seen a tremendous development in speed and resolution, but for most of its methods, there exists a remarkable gap between lateral and axial resolution. Similar to conventional optical microscopy, the axial resolution is by a factor three to five worse than the lateral resolution. One recently developed method to close this gap is metal-induced energy transfer (MIET) imaging which achieves an axial resolution down to nanometers. It exploits the distance dependent quenching of fluorescence when a fluorescent molecule is brought close to a metal surface. In the present manuscript, we combine the extreme axial resolution of MIET imaging with the extraordinary lateral resolution of single-molecule localization microscopy, in particular with direct stochastic optical reconstruction microscopy (dSTORM). This combination allows us to achieve isotropic three-dimensional super-resolution imaging of sub-cellular structures. Moreover, we employed spectral demixing for implementing dualcolor MIET-dSTORM that allows us to image and co-localize, in three dimensions, two different cellular structures simultaneously.
Boosting annotation in nutrimetabolomics by Feature-Based Molecular Networking: analytical and computational strategies applied to human urine samples from an untargeted LC-MS/MS based bilberry-blueberry intervention study
Authors: Renai Lapo , Ulaszewska Marynka , Mattivi Fulvio , Bartoletti Riccardo , Bubba Massimo Del , van der Hooft Justin J. J. 
Published: December 2021

AbstractUrine represents a challenging metabolite mixture to decipher. Yet, it contains valuable information on dietary intake patterns as typically investigated using randomized, single-blinded, intervention studies. This research demonstrates how the use of Feature-Based Molecular Networking in combination with public spectral libraries, further expanded with an “In-house” library of metabolite spectra, improved the non-trivial annotation of metabolites occurring in human urine samples following bilberry and blueberry intake. Following this approach, 65 berry-related and human endogenous metabolites were annotated, increasing the annotation coverage by 72% compared to conventional annotation approaches. Furthermore, the structures of 15 additional metabolites were hypothesized by spectral analysis. Then, by leveraging the MzMine quantitative information, several molecular families of phase II (e.g., glucuronidated phenolics) and phase I (e.g., phenylpropionic acid and hydroxybenzoic acid molecular scaffolds) metabolism were identified by correlation analysis of postprandial kinetics, and the dietary impact of endogenous and exogenous metabolites following bilberry-blueberry intake was estimated.
Transcriptome of the synganglion and characterization of the cys-loop ligand-gated ion channel gene family in the tickIxodes ricinus
Authors: Rispe Claude , Hervet Caroline , de la Cotte Nathalie , Daveu Romain , Labadie Karine , Noël Benjamin , Aury Jean-Marc , Thany Steeve , Taillebois Emiliane , Cartereau Alison , Mauff Anaïs Le , Charvet Claude L. , Auger Clément , Neveu Cédric , Plantard Olivier 
Published: December 2021

AbstractTicks represent a major health issue for humans and domesticated animals. Assessing the expression patterns of the tick’s central nervous system, known as the synganglion, is an important step in understanding tick physiology and in managing tick-borne diseases. Neuron-specific genes like the cys-loop ligand-gated ion channels (cys-loop LGICs) are important pharmacological targets of acaricides. Here, we carried out the sequencing of transcriptomes of theI. ricinussynganglion, for adult ticks in different conditions (unfed males, unfed females, and partially-fed females). Thede novoassembly of these transcriptomes allowed us to obtain a large collection of cys-loop LGICs sequences. A reference meta-transcriptome based on synganglion and whole body transcriptomes was then produced, showing high completeness and allowing differential expression analyses between synganglion and whole body. Many of the genes upregulated in the synganglion were related to biological processes or functions associated with neurotransmission and located in neurones or the synaptic membrane, including most of the cys-loop LGICs. As a first step of a functional study of cysLGICs, we cloned the predicted sequence of the resistance to dieldrin (RDL) subunit homologue, and functionally reconstituted the first GABA-gated receptor ofIxodes ricinususing a hetrologous expression approach. A phylogenetic study was performed for the nicotinic acetylcholine receptors (nAChRs) and for other cys-loop LGICs respectively, showing tick-specific expansions of some types of receptors (Histamine-gated, GluCls).
GPR55 in B cells limits atherosclerosis development and regulates plasma cell maturation
Authors: Guillamat-Prats Raquel , Hering Daniel , Rami Martina , Härdtner Carmen , Santovito Donato , Rinne Petteri , Bindila Laura , Hristov Michael , Pagano Sabrina , Vuilleumier Nicolas , Schmid Sofie , Janjic Aleksandar , Enard Wolfgang , Weber Christian , Maegdefessel Lars , Faussner Alexander , Hilgendorf Ingo , Steffens Sabine 
Published: December 2021

AbstractIdentifying novel pathways regulating the adaptive immune response in chronic inflammatory diseases such as atherosclerosis is of particular interest in view of developing new therapeutic drugs. Here we report that the lipid receptor GPR55 is highly expressed by splenic B cells and inversely correlates with atheroma plaque size in mice. In human carotid endarterectomy specimen, GPR55 transcript levels were significantly lower in unstable compared to stable carotid plaques. To study the impact of GPR55 deficiency in atherosclerosis, we crossedGpr55knockout mice with apolipoprotein E (ApoE) knockout mice and subjected the mice to Western diet for 4 to 16 weeks. Compared toApoE-/-controls,ApoE-/-Gpr55-/-mice developed larger plaques with increased necrotic core size, associated with elevated circulating and aortic leukocyte counts. Flow cytometry, immunofluorescence and RNA-sequencing analysis of splenic B cells in these mice revealed a hyperactivated B cell phenotype with disturbed plasma cell maturation and immunoglobulin (Ig)G antibody overproduction. The specific contribution of B cell GPR55 in atherosclerosis was further studied in mixedGpr55-/-/µMTbone marrow chimeras on low density receptor deficiency (Ldlr-/-) background, revealing that B-cell specific depletion ofGpr55was sufficient to promote plaque development. Conversely, adoptive transfer of wildtype B cells intoApoE-/-Gpr55-/-mice blunted the proatherogenic phenotype.In vitrostimulation of splenocytes with the endogenous GPR55 ligand LPI promoted plasma cell proliferation and enhanced B cell activation marker expression, which was inhibited by the GPR55 antagonist CID16020046. Collectively, these discoveries provide new evidence for GPR55 as key modulator of the adaptive immune response in atherosclerosis. Targeting GPR55 could be useful to limit inflammation and plaque progression in patients suffering from atherosclerosis.
A deep dive into VDAC1 conformational diversity using all-atom simulations provides new insights into the structural origin of the closed states
Authors: Preto Jordane , Gorny Hubert , Krimm Isabelle 
Published: December 2021

AbstractThe voltage-dependent anion channel 1 (VDAC1) is a crucial mitochondrial transporter which controls the flow of ions and respiratory metabolites entering or exiting mitochondria. As a voltage-gated channel, VDAC1 can switch between a high conducting “open” state and low conducting “closed” states emerging at high transmembrane potential. Although cell homeostasis depends on channel gating to regulate the transport of ions and metabolites, structural hallmarks characterizing the closed states remain unknown. Here we performed microsecond accelerated molecular dynamics to highlight a vast region of VDAC1 conformational landscape accessible at typical voltage known to promote closure. Conformers exhibiting stable subconducting properties inherent to closed states were identified. In all cases, the low conductance was due to the particular positioning of an unfolded part of the N-terminus which obstructed the channel pore. While the N-terminal tail was found to be sensitive to voltage orientation, our low-conducting models suggest that closed states predominantly take place from disordered events and do not result from the displacement of a voltage sensor or a significant change in the pore. In addition, our results were consistent with conductance jumps observed in experiments and corroborates a recent study describing entropy as a key factor for VDAC gating.
Explore synergistic and competitive miRNA regulation mechanisms in the miRNA-mRNA regulatory network from the information decomposition perspective
Authors: Pan Chu , Jiang Jing , Jing Limei , Chen Wangqing , Yang Yi , Liu Ying , Luo Jiawei , Zeng Xiangxiang 
Published: December 2021

ABSTRACTSince multiple microRNAs can target 3’ untranslated regions of the same mRNA transcript, it is likely that these endogenous microRNAs may form synergistic alliances, or compete for the same mRNA harbouring overlapping binding site matches. Synergistic and competitive microRNA regulation is an intriguing yet poorly elucidated mechanism. We here introduce a computational method based on the multivariate information measurement to quantify such implicit interaction effects between microRNAs. Our informatics method of integrating sequence and expression data is designed to establish the functional correlation between microRNAs. To demonstrate our method, we exploited TargetScan and The Cancer Genome Atlas data. As a result, we indeed observed that the microRNA pair with neighbouring binding site(s) on the mRNA is likely to trigger synergistic events, while the microRNA pair with overlapping binding site(s) on the mRNA is likely to cause competitive events, provided that the pair of microRNAs has a high functional similarity and the corresponding triplet presents a positive/negative ‘synergy-redundancy’ score.
Leveraging TOPMed Imputation Server and Constructing a Cohort-Specific Imputation Reference Panel to Enhance Genotype Imputation among Cystic Fibrosis Patients
Authors: Sun Quan , Liu Weifang , Rosen Jonathan D. , Huang Le , Pace Rhonda G. , Dang Hong , Gallins Paul J. , Blue Elizabeth E. , Ling Hua , Corvol Harriet , Strug Lisa J. , Bamshad Michael J. , Gibson Ronald L. , Pugh Elizabeth W. , Blackman Scott M. , Cutting Garry R. , O’Neal Wanda K. , Zhou Yi-Hui , Wright Fred A. , Knowles Michael R. , Wen Jia , Li Yun 
Published: December 2021

AbstractCystic fibrosis (CF) is a severe genetic disorder that can cause multiple comorbidities affecting the lungs, the pancreas, the luminal digestive system and beyond. In our previous genome-wide association studies (GWAS), we genotyped ∼8,000 CF samples using a mixture of different genotyping platforms. More recently, the Cystic Fibrosis Genome Project (CFGP) performed deep (∼30x) whole genome sequencing (WGS) of 5,095 samples to better understand the genetic mechanisms underlying clinical heterogeneity among CF patients. For mixtures of GWAS array and WGS data, genotype imputation has proven effective in increasing effective sample size. Therefore, we first performed imputation for the ∼8,000 CF samples with GWAS array genotype using the TOPMed freeze 8 reference panel. Our results demonstrate that TOPMed can provide high-quality imputation for CF patients, boosting genomic coverage from ∼0.3 - 4.2 million genotyped markers to ∼11 - 43 million well-imputed markers, and significantly improving Polygenic Risk Score (PRS) prediction accuracy. Furthermore, we built a CF-specific CFGP reference panel based on WGS data of CF patients. We demonstrate that despite having ∼3% the sample size of TOPMed, our CFGP reference panel can still outperform TOPMed when imputing some CF disease-causing variants, likely due to allele and haplotype differences between CF patients and general populations. We anticipate our imputed data for 4,656 samples without WGS data will benefit our subsequent genetic association studies, and the CFGP reference panel built from CF WGS samples will benefit other investigators studying CF.
Long-lasting germinal center responses to a priming immunization with continuous proliferation and somatic mutation
Authors: Lee Jeong Hyun , Sutton Henry , Cottrell Christopher A. , Phung Ivy , Ozorowski Gabriel , Sewall Leigh M. , Nedellec Rebecca , Nakao Catherine , Silva Murillo , Richey Sara T. , Torres Jonathan L. , Lee Wen-Hsin , Georgeson Erik , Kubitz Michael , Hodges Sam , Mullen Tina-Marie , Adachi Yumiko , Cirelli Kimberly M. , Kaur Amitinder , Allers-Hernandez Carolina , Fahlberg Marissa , Grasperge Brooke F. , Dufour Jason P. , Schiro Faith , Aye Pyone P. , Carnathan Diane G. , Silvestri Guido , Shen Xiaoying , Montefiori David C. , Veazey Ronald S. , Ward Andrew B. , Hangartner Lars , Burton Dennis R. , Irvine Darrell J. , Schief William R. , Crotty Shane 
Published: December 2021

SummaryGerminal centers (GCs) are the engines of antibody evolution. Using HIV Env protein immunogen priming in rhesus monkeys (RM) followed by a long period without further immunization, we demonstrate GC B cells (BGC) lasted at least 6 months (29 weeks), all the while maintaining rapid proliferation. A 186-fold BGC cell increase was present by week 10 compared to a conventional immunization. Single cell transcriptional profiling revealed that both light zone and dark zone GC states were sustained throughout the 6 months. Antibody somatic hypermutation (SHM) of BGC cells continued to accumulate throughout the 29 week priming period, with evidence of selective pressure. Additionally, Env-binding BGC cells were still 49-fold above baseline 29 weeks after immunization, suggesting that they could be active for significantly longer periods of time. High titers of HIV neutralizing antibodies were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing significant immunodominance challenges for B cells, among other difficulties. Memory B cells (BMem) generated under these long priming conditions had higher levels of SHM, and both BMem cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous BGC cell lineage phylogenies spanning the >6-month GC period were identified, demonstrating continuous GC activity and selection for at least 191 days, with no additional antigen exposure. A long prime, adjuvanted, slow delivery (12-day) immunization approach holds promise for difficult vaccine targets, and suggests that patience can have great value for tuning GCs to maximize antibody responses.
Engraftment, fate, and function of HoxB8-conditional neutrophil progenitors in the unconditioned murine host
Authors: Cohen Joshua T. , Danise Michael , Hinman Kristina D. , Neumann Brittany M. , Johnson Renita , Wilson Zachary S. , Chorzalska Anna , Dubielecka Patrycja M. , Lefort Craig T. 
Published: December 2021

AbstractThe development and use of murine myeloid progenitor cell lines that are conditionally immortalized through expression of HoxB8 has provided a valuable tool for studies of neutrophil biology. Recent work has extended the utility of HoxB8-conditional progenitors to thein vivosetting via their transplantation into irradiated mice. Here, we describe the isolation of HoxB8-conditional progenitor cell lines that are unique in their ability to engraft in the naïve host in the absence of conditioning of the hematopoietic niche. Our results indicate that HoxB8-conditional progenitors engraft in a β1 integrin-dependent manner and transiently generate donor-derived mature neutrophils. Furthermore, we show that neutrophils derivedin vivofrom transplanted HoxB8-conditional progenitors are mobilized to the periphery and recruited to sites of inflammation in a manner that depends on the C-X-C chemokine receptor 2 and β2 integrins, the same mechanisms that have been described for recruitment of endogenous primary neutrophils. Together, our studies advance the understanding of HoxB8-conditional neutrophil progenitors and describe an innovative tool that, by virtue of its ability to engraft in the naïve host, will facilitate mechanisticin vivoexperimentation on neutrophils.
Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3 information
Authors: Heather James M. , Spindler Matthew J. , Alonso Marta Herrero , Shui Yifang Ivana , Millar David G. , Johnson David S. , Cobbold Mark , Hata Aaron N. 
Published: December 2021

AbstractThe study and manipulation of T cell receptors (TCRs) is central to multiple fields across basic and translational immunology research. Produced by V(D)J recombination, TCRs are often only recorded in the literature and data repositories as a combination of their V and J gene symbols, plus their hypervariable CDR3 amino acid sequence. However, numerous applications require full-length coding nucleotide sequences. Here we present Stitchr, a software tool developed to specifically address this limitation. Given minimal V/J/CDR3 information, Stitchr produces complete coding sequences representing a fully spliced TCR cDNA. Due to its modular design, Stitchr can be used for TCR engineering using either published germline or novel/modified variable and constant region sequences. Sequences produced by Stitchr were validated by synthesizing and transducing TCR sequences into Jurkat cells, recapitulating the expected antigen specificity of the parental TCR. Using a companion script, Thimble, we demonstrate that Stitchr can process a million TCRs in under ten minutes using a standard desktop personal computer. By systemizing the production and modification of TCR sequences, we propose that Stitchr will increase the speed, repeatability, and reproducibility of TCR research. Stitchr is available on GitHub.
MERS-CoV endoribonuclease and accessory proteins jointly evade host innate immunity during infection of lung and nasal epithelial cells
Authors: Comar Courtney E. , Otter Clayton J. , Pfannenstiel Jessica , Doerger Ethan , Renner David M. , Tan Li Hui , Perlman Stanley , Cohen Noam A. , Fehr Anthony R. , Weiss Susan R. 
Published: December 2021

AbstractMiddle East respiratory syndrome coronavirus (MERS-CoV) emerged into humans in 2012, causing highly lethal respiratory disease. The severity of disease may be in part because MERS-CoV is adept at antagonizing early innate immune pathways – interferon (IFN) production and signaling, protein kinase R (PKR), and oligoadenylate synthetase ribonuclease L (OAS/RNase L) – generated in response to viral double-stranded (ds)RNA generated during genome replication. This is in contrast to SARS-CoV-2, which we recently reported activates PKR and RNase L and to some extent, IFN signaling. We previously found that MERS-CoV accessory proteins NS4a (dsRNA binding protein) and NS4b (phosphodiesterase) could weakly suppress these pathways, but ablation of each had minimal effect on virus replication. Here we investigated the antagonist effects of the conserved coronavirus endoribonuclease (EndoU), in combination with NS4a or NS4b. Inactivation of EndoU catalytic activity alone in a recombinant MERS-CoV caused little if any effect on activation of the innate immune pathways during infection. However, infection with recombinant viruses containing combined mutations with inactivation of EndoU and deletion of NS4a or inactivation of the NS4b phosphodiesterase promoted robust activation of the dsRNA-induced innate immune pathways. This resulted in ten-fold attenuation of replication in human lung derived A549 and primary nasal cells. Furthermore, replication of these recombinant viruses could be rescued to the level of WT MERS-CoV by knockout of host immune mediators MAVS, PKR, or RNase L. Thus, EndoU and accessory proteins NS4a and NS4b together suppress dsRNA-induced innate immunity during MERS-CoV infection in order to optimize viral replication.ImportanceMiddle East Respiratory Syndrome Coronavirus (MERS-CoV) causes highly lethal respiratory disease. MERS-CoV encodes several innate immune antagonists, accessory proteins NS4a and NS4b unique to the merbeco lineage and the nsp15 protein endoribonuclease (EndoU), conserved among all coronaviruses. While mutation of each antagonist protein alone has little effect on innate immunity, infections with recombinant MERS-CoVs with mutations of EndoU in combination with either NS4a or NS4b, activate innate signaling pathways and are attenuated for replication. Our data indicate that EndoU and accessory proteins NS4a and NS4b together suppress innate immunity during MERS-CoV infection, to optimize viral replication. This is in contrast to SARS-CoV-2 which activates these pathways and consistent with greater mortality observed during MERS-CoV infection compared to SARS-CoV-2.