bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-pathogenic virus induced immunity against TBEV protects mice from disease but not from virus entry into the CNS
Authors: Petry Monique , Palus Martin , Leitzen Eva , Mitterreiter Johanna Gracia , Huang Bei , Kröger Andrea , Verjans Georges M.G.M , Baumgärtner Wolfgang , Rimmelzwaan Guus F. , Růžek Daniel , Osterhaus Albert , Prajeeth Chittappen Kandiyil 
Published: January 2021

AbstractTick-borne encephalitis virus (TBEV) is a leading cause of vector-borne viral encephalitis with expanding endemic regions across Europe. Although currently used inactivated whole virus vaccines are effective, vaccination breakthroughs have been reported for which the reasons are unclear. In this study we tested in mice the efficacy of pre-infection with a closely related low-virulent flavivirus, Langat virus (LGTV strain TP21), or a naturally avirulent TBEV strain (TBEV-280) in providing protection against lethal infection with the highly virulent TBEV strain TBEV-Hypr (referred to as TBEV-Hypr). LGTV has been evaluated as an experimental live vaccine against TBE, but further development was abandoned due to too high residual pathogenicity of a LGTV-based vaccine. Here we show that prior infection with TP21 or TBEV-280 is efficient in protecting mice from lethal TBEV-Hypr challenge. Histopathological analysis of brains from non-immunized control mice revealed neuronal TBEV infection and necrosis. Neuroinflammation, gliosis and neuronal necrosis was however also observed in some of the TP21 and TBEV-280 pre-infected mice although at reduced frequency as compared to the non-immunized TBEV-Hypr infected control mice. Interestingly, qPCR detected the presence of viral RNA in the brains and spinal cord of both TP21 and TBEV-280 immunized mice after TBEV-Hypr challenge, but significantly reduced compared to mock-immunized mice. Our results indicate that although TBEV-Hypr infection is effectively controlled in the periphery upon immunization with low-virulent LGTV or naturally avirulent TBEV-280, it may still enter the CNS of these animals. These findings improve our understanding of potential causes for vaccine failure in individuals vaccinated with TBE vaccines.
Niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle ofSalmonella enterica
Authors: Powers TuShun R. , Haeberle Amanda L. , Hammarlöf Disa L. , Cundiff Jennifer A. , Predeus Alexander V. , Hokamp Karsten , Hinton Jay C.D. , Knodler Leigh A. 
Published: January 2021

AbstractSalmonella entericaserovar Typhimurium (S. Typhimurium) is a zoonotic pathogen that causes diarrheal disease in humans and animals. During salmonellosis,S. Typhimurium colonizes epithelial cells lining the gastrointestinal tract.S. Typhimurium has an unusual lifestyle in epithelial cells that begins within an endocytic-derivedSalmonella-containing vacuole (SCV), followed by escape into the cytosol, epithelial cell lysis and bacterial release. The cytosol is a more permissive environment than the SCV and supports rapid bacterial growth. The physicochemical conditions encountered byS.Typhimurium within the cytosol, and the bacterial genes required for cytosolic colonization, remain unknown. Here we have exploited the parallel colonization strategies ofS. Typhimurium in epithelial cells to decipher the two niche-specific bacterial virulence programs. By combining a population-based RNA-seq approach with single-cell microscopic analysis, we identified bacterial genes/sRNAs with cytosol-specific or vacuole-specific expression signatures. Using these genes/sRNAs as environmental biosensors, we defined thatSalmonellais exposed to iron and manganese deprivation and oxidative stress in the cytosol and zinc and magnesium deprivation in the SCV. Furthermore, iron availability was critical for optimalS. Typhimurium replication in the cytosol, as well asentC,fepB,soxSandsitA-mntH. Virulence genes that are typically associated with extracellular bacteria, namelySalmonellapathogenicity island 1 (SPI1) and SPI4, had a cytosolic-specific expression profile. Our study reveals that the cytosolic and vacuolarS. Typhimurium virulence gene programs are unique to, and tailored for, residence within distinct intracellular compartments. Therefore, this archetypical vacuole-adapted pathogen requires extensive transcriptional reprogramming to successfully colonize the mammalian cytosol.Author SummaryIntracellular pathogens reside either within a membrane-bound vacuole or are free-living in the cytosol and their virulence programs are tailored towards survival within a particular intracellular compartment. Some bacterial pathogens (such asSalmonella enterica) can successfully colonize both intracellular niches, but how they do so is unclear. Here we have exploited the parallel intracellular lifestyles ofS. entericain epithelial cells to identify the niche-specific bacterial expression profiles and environmental cues encountered byS. enterica. We have also discovered bacterial genes that are required for colonization of the cytosol, but not the vacuole. Our results advance our understanding of pathogen-adaptation to alternative replication niches and highlight an emerging concept in the field of bacteria-host cell interactions.
Characterization of 475 novel, putative small RNAs (sRNAs) in Carbon-starvedSalmonella entericaserovar typhimurium
Authors: Houserova Dominika , Dahmer Donavon J. , Amin Shivam V. , Crucello Aline , King Valeria M. , Barnhill Emmaline C. , Huang Yulong , Zambrano Mike E. , Dean Meghan A. , Aria Kevin M. , Spector Michael P. , Borchert Glen M. 
Published: January 2021

AbstractAn increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression when bacteria faces various environmental stressors.Salmonella enterica, a well-studied foodborne pathogen, is known for its ability to survive in and adapt to various environmental challenges, making it a difficult pathogen to eliminate, as well as an important model for examining ncRNA contributions to cellular stress survival. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers ofSalmonellastress response. Generally thought to be 50-500 nucleotides in length and to occur mainly in intergenic regions, sRNAs regulate protein expression through base pairing with mRNA targets. Through employing a refined definition of sRNAs that allows for shorter sequences and for sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during Carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs. Additionally, our computational analyses find the majority to be highly conserved and structurally-related to known sRNAs. Importantly, we show that deletion of one of the dynamic sRNAs, sRNA4130247, significantly impairs theSalmonellaC-starvation response (CSR), confirming its involvement (and suggesting the involvements of many other sRNAs identified in this work) in theSalmonellaCSR. Strikingly, the 475 novel sRNAs identified in this study more than double the number ofSalmonella entericaserovar Typhimurium SL1344 sRNAs described to date, increasing the total number of annotatedSalmonellasRNAs from 396 to 871. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs inSalmonella, experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and strongly suggests that sRNA loci likely outnumber those of protein-coding genes inSalmonella.
Voxel-wise and spatial modelling of binary lesion masks: Comparison of methods with a realistic simulation framework
Authors: Kindalova Petya , Kosmidis Ioannis , Nichols Thomas E. 
Published: January 2021

AbstractObjectivesWhite matter lesions are a very common finding on MRI in older adults and their presence increases the risk of stroke and dementia. Accurate and computationally efficient modelling methods are necessary to map the association of lesion incidence with risk factors, such as hypertension. However, there is no consensus in the brain mapping literature whether a voxel-wise modelling approach is better for binary lesion data than a more computationally intensive spatial modelling approach that accounts for voxel dependence.MethodsWe review three regression approaches for modelling binary lesion masks including massunivariate probit regression modelling with either maximum likelihood estimates, or mean bias-reduced estimates, and spatial Bayesian modelling, where the regression coefficients have a conditional autoregressive model prior to account for local spatial dependence. We design a novel simulation framework of artificial lesion maps to compare the three alternative lesion mapping methods. The age effect on lesion probability estimated from a reference data set (13,680 individuals from the UK Biobank) is used to simulate a realistic voxel-wise distribution of lesions across age. To mimic the real features of lesion masks, we propose matching brain lesion summaries (total lesion volume, average lesion size and lesion count) across the reference data set and the simulated data sets. Thus, we allow for a fair comparison between the modelling approaches, under a realistic simulation setting.ResultsOur findings suggest that bias-reduced estimates for voxel-wise binary-response generalized linear models (GLMs) overcome the drawbacks of infinite and biased maximum likelihood estimates and scale well for large data sets because voxel-wise estimation can be performed in parallel across voxels. Contrary to the assumption of spatial dependence being key in lesion mapping, our results show that voxel-wise bias-reduction and spatial modelling result in largely similar estimates.ConclusionBias-reduced estimates for voxel-wise GLMs are not only accurate but also computationally efficient, which will become increasingly important as more biobank-scale neuroimaging data sets become available.
Cell cortex microtubules contribute to division plane positioning during telophase in maize
Authors: Bellinger Marschal A. , Uyehara Aimee N. , Martinez Pablo , McCarthy Michael C. , Rasmussen Carolyn G. 
Published: January 2021

AbstractThe phragmoplast is a plant-specific microtubule and microfilament structure that forms during telophase to direct new cell wall formation. The phragmoplast expands towards a specific location at the cell cortex called the division site. How the phragmoplast accurately reaches the division site is currently unknown. We show that a previously uncharacterized microtubule arrays accumulated at the cell cortex. These microtubules were organized by transient interactions with division-site localized proteins and were then incorporated into the phragmoplast to guide it towards the division site. A phragmoplast-guidance defective mutant,tangled1, had aberrant cortical-telophase microtubule accumulation that correlated with phragmoplast positioning defects. Division-site localized proteins may promote proper division plane positioning by organizing the cortical-telophase microtubule array to guide the phragmoplast to the division site during plant cell division.One Sentence SummaryMicrotubules accumulate at the cell cortex and interact with the plant division machinery to direct its movement towards the division site.
Deficiency of intellectual disability-related geneBrpf1reduced inhibitory neurotransmission andMap2k7expression in GABAergic interneurons
Authors: Cao Jingli , Xian Weiwei , Palihati Maierdan , Zhu Yu , Wang Guoxiang , Xie Yunli , Zhou Guomin , You Linya 
Published: January 2021

AbstractIntellectual disability is closely related to impaired GABA neurotransmission.Brpf1was specifically expressed in medial ganglionic eminence (MGE), a developmental niche of GABAergic interneurons, and patients withBRPF1mutations were mentally retarded. To test its role in development and function of MGE-derived GABAergic interneurons, we performed immunofluorescence staining, whole-cell patch-clamp, MGE transplantation and mRNA-Seq to understand its effect on neuronal differentiation, dendritic morphology, electrophysiology, migration and gene regulation, using mouse MGE-derived GABAergic interneurons infected with AAV-shBrpf1. We found a decreasing trend on parvalbumin+interneuron differentiation. Moreover, increased firing threshold, decreased number of evoked APs, and a reduced amplitude of mIPSCs were observed before any significant change of MAP2+dendritic morphology andin vivomigration appeared. Finally, mRNA-Seq analysis revealed that genes related to neurodevelopment and synaptic transmission such asMap2k7were dysregulated. Our results demonstrated a key role ofBrpf1in inhibitory neurotransmission and related gene expression of GABAergic interneurons.
Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases
Authors: Korsunsky Ilya , Wei Kevin , Pohin Mathilde , Kim Edy Y. , Barone Francesca , Kang Joyce B. , Friedrich Matthias , Turner Jason , Nayar Saba , Fisher Benjamin A. , Raza Karim , Marshall Jennifer L. , Croft Adam P. , Sholl Lynette M. , Vivero Marina , Rosas Ivan O. , Bowman Simon J. , Coles Mark , Frei Andreas P. , Lassen Kara , Filer Andrew , Powrie Fiona , Buckley Christopher D. , Brenner Michael B. , Raychaudhuri Soumya 
Published: January 2021

SummaryPro-inflammatory fibroblasts are critical to pathogenesis in rheumatoid arthritis, inflammatory bowel disease, interstitial lung disease, and Sjögren’s syndrome, and represent a novel therapeutic target for chronic inflammatory disease. However, the heterogeneity of fibroblast phenotypes, exacerbated by the lack of a common cross-tissue taxonomy, has limited the understanding of which pathways are shared by multiple diseases. To investigate, we profiled patient-derived fibroblasts from inflamed and non-inflamed synovium, intestine, lung, and salivary glands with single-cell RNA-sequencing. We integrated all fibroblasts into a multi-tissue atlas to characterize shared and tissue-specific phenotypes. Two shared clusters, CXCL10+CCL19+immune-interacting and SPARC+COL3A1+vascular-interacting fibroblasts were expanded in all inflamed tissues and additionally mapped to dermal analogues in a public atopic dermatitis atlas. We further confirmed these human pro-inflammatory fibroblasts in animal models of lung, joint, and intestinal inflammation. This work represents the first cross-tissue, single-cell fibroblast atlas revealing shared pathogenic activation states across four chronic inflammatory diseases.
Synthesis, Characterization, and Nanodisc formation of Non-ionic Polymers
Authors: Ravula Thirupathi , Ramamoorthy Ayyalusamy 
Published: January 2021

AbstractDespite lipid-nanodiscs are increasingly used in the structural studies of membrane proteins, drug delivery and other applications, the interaction between the nanodisc-belt and the protein to be reconstituted is a major limitation. To overcome this limitation and to further broaden the scope of nanodiscs, a family of non-ionic amphiphilic polymers synthesized by hydrophobic functionalization of fructo-oligosaccharides/inulin is reported. We show the stability of lipid-nanodiscs formed by these polymers against pH and divalent metal ions, and their magnetic-alignment properties. The reported results also demonstrate that the non-ionic polymers extract membrane proteins with unprecedented efficiency.
Cryo-EM Structures of the N501Y SARS-CoV-2 Spike Protein in Complex with ACE2 and Two Potent Neutralizing Antibodies
Authors: Zhu Xing , Mannar Dhiraj , Srivastava Shanti S. , Berezuk Alison M. , Demers Jean-Philippe , Saville James W , Leopold Karoline , Li Wei , Dimitrov Dimiter S. , Tuttle Katharine S. , Zhou Steven , Chittori Sagar , Subramaniam Sriram 
Published: January 2021

AbstractThe recently reported “UK variant” of SARS-CoV-2 is thought to be more infectious than previously circulating strains as a result of several changes, including the N501Y mutation. We present a 2.9-Å resolution cryo-EM structure of the complex between the ACE2 receptor and N501Y spike protein ectodomains that shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2. The additional interactions result in increased affinity of ACE2 for the N501Y mutant, accounting for its increased infectivity. However, this mutation does not result in large structural changes, enabling important neutralization epitopes to be retained in the spike receptor binding domain. We confirmed this through biophysical assays and by determining cryo-EM structures of spike protein ectodomains bound to two representative potent neutralizing antibody fragments.Short summaryThe N501Y mutation found in the coronavirus UK variant increases infectivity but some neutralizing antibodies can still bind.
Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in white-tailed deer (Odocoileus virginianus)
Authors: Minich David , Madden Christopher , Evans Morgan V. , Ballash Gregory A. , Barr Daniel J. , Poulsen Keith P. , Dennis Patricia M. , Hale Vanessa L. 
Published: January 2021

AbstractChronic wasting disease (CWD) is a fatal, contagious, neurodegenerative prion disease affecting both free-ranging and captive cervid species. CWD is spread via direct or indirect contact or oral ingestion of prions. In the gastrointestinal tract, prions enter the body through microfold cells (M-cells), and the abundance of these cells can be influenced by the gut microbiota. To explore potential links between the gut microbiota and CWD, we collected fecal samples from farmed and free-ranging white-tailed deer (Odocoileus virginianus) around the Midwest. Farmed deer orignated from farms that were depopulated due to CWD. Free-ranging deer were sampled during annual deer harvests. All farmed deer were tested for CWD via ELISA and IHC, and we used 16S rRNA gene sequencing to characterize the gut microbiota. We report significant differences in gut microbiota by provenance (Farm 1, Farm 2, Free-ranging), sex, and CWD status. CWD-positive deer from Farm 1 and 2 had increased abundances ofAkkermansia,LachnospireaceaUCG-010, and RF39 taxa. Overall, differences by provenance and sex appear to be driven by diet, while differences by CWD status may be linked to CWD pathogenesis.
Screening by deep sequencing reveals mediators of microRNA tailing inC. elegans
Authors: Vieux Karl-Frédéric , Prothro Katherine , Kelley Leanne H. , Maine Eleanor M. , Veksler-Lublinsky Isana , McJunkin Katherine 
Published: January 2021

AbstractmicroRNAs are frequently modified by addition of untemplated nucleotides to the 3’ end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailingin vivo, usingC. elegans.MicroRNA tailing inC. elegansconsists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. Through a targeted RNAi screen, we discover that the TUT4/TUT7 gene family member CID-1/CDE-1/PUP-1 is required for uridylation, whereas the GLD2 gene family member F31C3.2 – here namedGLD-2-related2(GLDR-2) – is required for adenylation. Thus, the TUT4/TUT7 and GLD2 gene families have broadly conserved roles in miRNA modification. We specifically examine the role of tailing in microRNA turnover. We determine half-lives of microRNAs after acute inactivation of microRNA biogenesis, revealing that half-lives are generally long (median=20.7h), as observed in other systems. Although we observe that the proportion of tailed species increases over time after biogenesis, disrupting tailing does not alter microRNA decay. Thus, tailing is not a global regulator of decay inC. elegans. Nonetheless, by identifying the responsible enzymes, this study lays the groundwork to explore whether tailing plays more specialized context- or miRNA-specific regulatory roles.
Quantitative analysis of signaling responses during mouse primordial germ cell specification
Authors: Morgani Sophie M. , Hadjantonakis Anna-Katerina 
Published: January 2021

AbstractDuring early mammalian development, the pluripotent cells of the embryo are exposed to a combination of signals that drive exit from pluripotency and germ layer differentiation. At the same time, a small population of pluripotent cells give rise to the primordial germ cells (PGCs), the precursors of the sperm and egg, which pass on heritable genetic information to the next generation. Despite the importance of PGCs, it remains unclear how they are first segregated from the soma, and if this involves distinct responses to their signaling environment. To investigate this question, we mapped BMP, MAPK and WNT signaling responses over time in PGCs and their surrounding nichein vitroandin vivoat single-cell resolution. We showed that, in the mouse embryo, early PGCs exhibit lower BMP and MAPK responses compared to neighboring extraembryonic mesoderm cells, suggesting the emergence of distinct signaling regulatory mechanisms in the germline versus soma. In contrast, PGCs and somatic cells responded comparably to WNT, indicating that this signal alone is not sufficient to promote somatic differentiation. Finally, we investigated the requirement of a BMP response for these cell fate decisions. We found that cell lines with a mutation in the BMP receptor (Bmpr1a−/−), which exhibit an impaired BMP signaling response, can efficiently generate PGC-like cells revealing that canonical BMP signaling is not cell autonomously required to direct PGC-like differentiation.