bluuebunny/crossref_metadata_2025_split huggingface dataset:
N-dihydrogalactochitosan reduces mortality in a lethal mouse model of SARS-CoV-2
Authors: Weiss Christopher M. , Liu Hongwei , Ball Erin E. , Hoover Ashley R. , Wong Talia S. , Wong Chun Fung , Lam Samuel , Hode Tomas , Keel M. Kevin , Levenson Richard M. , Chen Wei R. , Coffey Lark L. 
Published: August 2021

ABSTRACTThe rapid emergence and global dissemination of SARS-CoV-2 that causes COVID-19 continues to cause an unprecedented global health burden resulting in nearly 7 million deaths. While multiple vaccine countermeasures have been approved for emergency use, additional treatments are still needed due to sluggish vaccine rollout, vaccine hesitancy, and inefficient vaccine-mediated protection. Immunoadjuvant compounds delivered intranasally can guide non-specific innate immune responses during the critical early stages of viral replication, reducing morbidity and mortality. N- dihydrogalactochitosan (GC) is a novel mucoadhesive immunostimulatory polymer of β- 0-4-linked N-acetylglucosamine that is solubilized by the conjugation of galactose glycans with current applications as a cancer immunotherapeutic. We tested GC as a potential countermeasure for COVID-19. GC was well-tolerated and did not produce histopathologic lesions in the mouse lung. GC administered intranasally before and after SARS-CoV-2 exposure diminished morbidity and mortality in humanized ACE2 receptor expressing mice by up to 75% and reduced infectious virus levels in the upper airway. Fluorescent labeling of GC shows that it is confined to the lumen or superficial mucosa of the nasal cavity, without involvement of adjacent or deeper tissues. Our findings demonstrate a new application for soluble immunoadjuvants such as GC for preventing disease associated with SARS-CoV-2 and may be particularly attractive to persons who are needle-averse.IMPORTANCEThe ongoing COVID-19 pandemic necessitates new approaches to reduce disease caused by SARS-CoV-2. We tested the immunoadjuvant N-dihydrogalactochitosan (GC), used previously as an immunostimulant for tumor therapy and adjuvant for viral vaccines, as a potential COVID-19 countermeasure. When GC was administered before and after inoculation of a lethal dose of SARS-CoV-2 into the nose of humanized mice expressing an entry receptor for the virus, fewer mice showed weight loss and died compared to mice that received only the vehicle but no GC. GC-treated mice also had lower levels of infectious SARS-CoV-2 in their upper airway. These results suggest that GC may be a candidate to prevent or treat COVID-19.Single Sentence SummaryThe immunoadjuvant N-dihydrogalactochitosan diminishes SARS-CoV-2 disease in humanized ACE2 mice, representing a new countermeasure against COVID-19.
Performance of Core Genome Multilocus Sequence Typing Compared to Capillary-Electrophoresis PCR Ribotyping and SNP Analysis ofClostridioides difficile
Authors: Baktash A , Corver J , Harmanus C , Smits WK , Fawley W , Wilcox MH , Kumar N , Eyre DW , Indra A , Mellmann A , Kuijper EJ 
Published: August 2021

ABSTRACTClostridioides difficileis the most common cause of antibiotic-associated gastrointestinal infections. Capillary-electrophoresis (CE)-PCR ribotyping is currently the gold standard forC. difficiletyping but lacks discriminatory power to study transmission and outbreaks in detail. New molecular methods have the capacity to differentiate better, but backward compatibility with CE-PCR ribotyping must be assessed. Using a well-characterized collection of diverse strains (N=630; 100 unique ribotypes [RTs]), we aimed to investigate PCR ribotyping prediction from core genome multilocus sequence typing (cgMLST). Additionally, we compared the discriminatory power of cgMLST (SeqSphere & EnteroBase) and whole genome MLST (wgMLST) (EnteroBase) with single nucleotide polymorphism (SNP) analysis). A unique cgMLST profile (>6 allele differences) was observed in 82/100 ribotypes, indicating sufficient backward compatibility. Intra-RT allele difference varied per ribotype and MLST clade. Application of cg/wgMLST and SNP analysis in two outbreak settings with ribotypes RT078 and RT181 (known with a low intra-ribotype allele difference) showed no distinction between outbreak- and non-outbreak strains, in contrast to wgMLST and SNP analysis. We conclude that cgMLST has the potential to be an alternative to CE-PCR ribotyping. The method is reproducible, easy to standardize and offers higher discrimination. However, in some ribotype complexes adjusted cut-off thresholds and epidemiological data are necessary to recognize outbreaks. We propose to decrease the current threshold of 6 to 3 alleles to better identify outbreaks.
Defining the pig microglial transcriptome reveals their core signature, regional heterogeneity, and similarity with humans
Authors: Shih Barbara B , Brown Sarah M , Lefevre Lucas , Mabbott Neil A , Priller Josef , Thompson Gerard , Lawrence Alistair B , McColl Barry W 
Published: August 2021

AbstractMicroglia play key roles in brain homeostasis as well as responses to neurodegeneration and neuroinflammatory processes caused by physical disease and psychosocial stress. The pig is a physiologically-relevant model species for studying human neurological disorders, many of which are associated with microglial dysfunction. Furthermore, pigs are an important agricultural species, and there is a need to understand how microglial function affects their welfare. As a basis for improved understanding to enhance biomedical and agricultural research, we sought to characterise pig microglial identity at genome-wide scale and conduct inter-species comparisons.We isolated pig hippocampal tissue and microglia from frontal cortex, hippocampus and cerebellum, as well as alveolar macrophages from the lungs and conducted RNA-sequencing (RNAseq). By comparing the transcriptomic profiles between microglia, macrophages, and hippocampal tissue, we derived a set of 365 highly-enriched genes defining the porcine core microglial signature. We found brain regional heterogeneity based on 215 genes showing significant (adjusted p<0.01) regional variations and that cerebellar microglia were most distinct. We compared normalized gene expression for microglia from human, mice and pigs using microglia signature gene lists derived from each species and demonstrated that a core microglial marker gene signature is conserved across species, but that species-specific expression subsets also exist. Importantly, pig and human microglia shared greater similarity than pig and murine microglia.Our data provide a valuable resource defining the pig microglial transcriptome signature that highlights pigs as a useful large animal species bridging between rodents and humans in which to study the role of microglia during homeostasis and disease.Main Points- Defined a pig microglial transcriptome signature comprising 365 genes.- Demonstrated regional variance in the pig microglial transcriptome across the brain.- Revealed greater similarity between pig and human microglia than mouse.
Decoding gene regulation in the fly brain
Authors: Janssens Jasper , Aibar Sara , Taskiran Ibrahim Ihsan , Ismail Joy N. , Spanier Katina I. , Bravo González-Blas Carmen , Quan Xiao Jiang , Papasokrati Dafni , Hulselmans Gert , Makhzami Samira , Waegeneer Maxime De , Christiaens Valerie , Aerts Stein 
Published: August 2021

SummaryTheDrosophilabrain is a work horse in neuroscience. Single-cell transcriptome analysis1–5,3D morphological classification6, and detailed EM mapping of the connectome7–10have revealed an immense diversity of neuronal and glial cell types that underlie the wide array of functional and behavioral traits in the fruit fly. The identities of these cell types are controlled by – still unknown – gene regulatory networks (GRNs), involving combinations of transcription factors that bind to genomic enhancers to regulate their target genes. To characterize the GRN for each cell type in theDrosophilabrain, we profiled chromatin accessibility of 240,919 single cells spanning nine developmental timepoints, and integrated this data with single-cell transcriptomes. We identify more than 95,000 regulatory regions that are used in different neuronal cell types, of which around 70,000 are linked to specific developmental trajectories, involving neurogenesis, reprogramming and maturation. For 40 cell types, their uniquely accessible regions could be associated with their expressed transcription factors and downstream target genes, through a combination of motif discovery, network inference techniques, and deep learning. We illustrate how these “enhancer-GRNs” can be used to reveal enhancer architectures leading to a better understanding of neuronal regulatory diversity. Finally, our atlas of regulatory elements can be used to design genetic driver lines for specific cell types at specific timepoints, facilitating the characterization of brain cell types and the manipulation of brain function.
Identification and characterization of distinct cell cycle stages in cardiomyocytes using the FUCCI transgenic system
Authors: Baniol Marion , Murganti Francesca , Smialowska Agata , Panula Joni , Lazar Enikö , Brockman Viveka , Giatrellis Sarantis , Derks Wouter , Bergmann Olaf 
Published: August 2021

AbstractUnderstanding the regulatory mechanism by which cardiomyocyte proliferation transitions to endoreplication and cell cycle arrest during the neonatal period is crucial for identifying proproliferative factors and developing regenerative therapies.We used a transgenic mouse model based on the fluorescent ubiquitination-based cell cycle indicator (FUCCI) system to isolate and characterize cycling cardiomyocytes at different cell cycle stages at a single-cell resolution. Single-cell transcriptome analysis of cycling and noncycling cardiomyocytes was performed at postnatal days 0 (P0) and 7 (P7).The FUCCI system proved to be efficient for the identification of cycling cardiomyocytes with the highest mitotic activity at birth, followed by a gradual decline in the number of cycling and mitotic cardiomyocytes during the neonatal period. Cardiomyocytes showed premature cell cycle exit at G1/S shortly after birth and delayed G1/S progression during endoreplication at P7. Single-cell RNA-seq confirmed previously described signaling pathways involved in cardiomyocyte proliferation (Erbb2 and Hippo/YAP), cardiomyocyte motility, and maturation-related transcriptional changes during postnatal development, including the metabolic switch from glycolysis to fatty acid oxidation in cardiomyocytes. Additionally, we generated transcriptional profiles specific to cell division and endoreplication in cardiomyocytes.Deciphering transcriptional changes at different developmental stages and in a cell cycle-specific manner may facilitate the identification of genes important for adult cardiomyocyte proliferation and heart regeneration.Main findingsFUCCI reliably identifies cycling cardiomyocytes at distinct cell cycle stages in neonatal, juvenile, and adult hearts.Cell cycle activity decreases as the metabolic switch transitions from glycolysis to fatty acid metabolism in postnatal cardiomyocytes.Cell cycle arrest at G1/S is linked to the DNA damage response in postnatal cardiomyocytes. Distinct gene expression patterns are linked to different cell cycle phases in dividing and endoreplicating postnatal cardiomyocytes.
Early neutrophilia marked by aerobic glycolysis sustains host metabolism and delays cancer cachexia
Authors: Petruzzelli Michele , Ferrer Miriam , Schuijs Martijn , Hall Zoe , Perera David , Raghunathan Shwethaa , Vacca Michele , Gaude Edoardo , Lukey Michael J. , Jodrell Duncan I. , Frezza Christian , Wagner Erwin F. , Janowitz Tobias , Halim Timotheus Y.F. , Venkitaraman Ashok R. 
Published: August 2021

ABSTRACTAn elevated neutrophil-to-lymphocyte ratio negatively predicts the outcome of patients with cancer and is associated with cachexia, the terminal wasting syndrome. Here, we show using murine model systems of colorectal and pancreatic cancer that neutrophilia in the circulation and multiple organs, accompanied by extramedullary hematopoiesis, is an early event during cancer progression. Transcriptomic and metabolic assessment reveals that neutrophils in tumor-bearing animals utilize aerobic glycolysis, alike to cancer cells. Although pharmacological inhibition of aerobic glycolysis slows down tumor growth in C26 tumor-bearing mice, it precipitates cachexia, thereby shortening overall survival. This negative effect may be explained by our observation that acute depletion of neutrophils in pre-cachectic mice impairs systemic glucose homeostasis secondary to altered hepatic lipid processing. Thus, changes in neutrophil number, distribution and metabolism play an adaptive role in host metabolic homeostasis during cancer progression. Our findings provide insight into early events during cancer progression to cachexia, with implications for therapy.
Altered sleep intensity upon DBS to hypothalamic sleep-wake centers in rats
Authors: Masneuf S. , Imbach L.L. , Büchele F. , Colacicco G. , Penner M. , Moreira C.G. , Ineichen C. , Jahanshahi A. , Temel Y. , Baumann C.R. , Noain D. 
Published: August 2021

AbstractDeep brain stimulation (DBS) has been scarcely investigated in the field of sleep research. We hypothesize that DBS onto hypothalamic sleep- and wake-promoting centers will produce significant neuromodulatory effects, and potentially become a therapeutic strategy for patients suffering severe, drug-refractory sleep-wake disturbances. We aimed to investigate whether continuous electrical high-frequency DBS, such as that often implemented in clinical practice, in the ventrolateral preoptic nucleus (VLPO) or the perifornical area of the posterior lateral hypothalamus (PeFLH), significantly modulates sleep-wake characteristics and behavior. We implanted healthy rats with electroencephalographic/electromyographic electrodes and recorded vigilance states in parallel to bilateral bipolar stimulation of VLPO and PeFLH at 125 Hz at 90 μA over 24 h to test the modulating effects of DBS on sleep-wake proportions, stability and spectral power in relation to baseline. We unexpectedly found that VLPO DBS at 125 Hz deepens slow-wave sleep as measured by increased delta power, while sleep proportions and fragmentation remain unaffected. Thus, the intensity, but not the amount of sleep or its stability, is modulated. Similarly, the proportion and stability of vigilance states remained altogether unaltered upon PeFLH DBS but, in contrast to VLPO, 125 Hz stimulation unexpectedly weakened SWS, evidenced by reduced delta power. This study provides novel insights into non-acute functional outputs of major sleep-wake centers in the rat brain in response to electrical high-frequency stimulation, a paradigm frequently used in human DBS. In the conditions assayed, while exerting no major effects on sleep-wake architecture, hypothalamic high-frequency stimulation arises as a provocative sleep intensity-modulating approach.
The light chain of the L9 antibody is critical for binding circumsporozoite protein minor repeats and preventing malaria
Authors: Wang Lawrence T. , Hurlburt Nicholas K. , Schön Arne , Flynn Barbara J. , Pereira Lais S. , Dillon Marlon , Flores-Garcia Yevel , Bonilla Brian , Zavala Fidel , Idris Azza H. , Francica Joseph R. , Pancera Marie , Seder Robert A. 
Published: August 2021

ABSTRACTL9 is a potent human monoclonal antibody (mAb) that preferentially binds two adjacent NVDP minor repeats and cross-reacts with NANP major repeats of thePlasmodium falciparumcircumsporozoite protein (PfCSP) on malaria-infective sporozoites. Understanding this mAb’s ontogeny and mechanisms of binding PfCSP to neutralize sporozoites will facilitate vaccine development. Here, we isolated mAbs clonally related to L9 and showed that this B-cell lineage has baseline NVDP affinity and evolves to acquire NANP reactivity. Pairing the L9 kappa light chain (L9κ) with clonally-related heavy chains resulted in chimeric mAbs that cross-linked two NVDP, cross-reacted with NANP, and more potently neutralized sporozoites compared to their original light chain. Structural analyses revealed that chimeric mAbs bound the minor repeat motif in a type-1 β-turn seen in other repeat-specific antibodies. These data highlight the importance of L9κ in binding NVDP on PfCSP to neutralize SPZ and suggest that PfCSP-based immunogens might be improved by presenting ≥2 NVDP.
Analysis of combinatorial chemokine receptor expression dynamics using multi-receptor reporter mice
Authors: Medina-Ruiz Laura , Bartolini Robin , Dyer Douglas P , Vidler Francesca , Hughes Catherine E , Schuette Fabian , Love Samantha , Fu Jun , Stewart A. Francis , Graham Gerard J 
Published: August 2021

SummaryInflammatory chemokines and their receptors are central to the development of inflammatory/immune pathologies. The apparent complexity of this system, coupled with lack of appropriate in vivo models, has limited our understanding of how chemokines orchestrate inflammatory responses and has hampered attempts at targeting this system in inflammatory disease. Novel approaches are therefore needed to provide crucial biological, and therapeutic, insights into the chemokine-chemokine receptor family. Here, we report the generation of transgenic multi-chemokine receptor reporter mice in which spectrally-distinct fluorescent reporters mark expression of CCRs 1, 2, 3 and 5, key receptors for myeloid cell recruitment in inflammation. Analysis of these animals has allowed us to define, for the first time, individual and combinatorial receptor expression patterns on myeloid cells in resting and inflamed conditions. Our results demonstrate that chemokine receptor expression is highly specific, and more selective than previously anticipated.
Dynamic Spatial-Temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals
Authors: Qian Sheng Hu , Xiong Yu-Li , Chen Lu , Geng Ying-Jie , Tang Xiao-Man , Chen Zhen-Xia 
Published: August 2021

AbstractIn the evolutionary model of dosage compensation, per-allele expression level of the X chromosome was proposed to have two-fold upregulation, compensating for its dose reduction in males (XY) compared to females (XX). However, the upregulation of X chromosome is still in dispute, and comprehensive evaluations are still lacking. By integrating multi-omics datasets in mammals, we investigated the expression ratios and underlying pattern of X to autosomes (X:AA ratio) and X to orthologs (X:XXratio) at the transcriptome, translatome, and proteome layers. The results indicated a dynamic spatial-temporal X:AA ratio during development in human and mouse. Meanwhile, by tracing the evolution of orthologous gene expressions in chicken, platypus, and opossum, we found a constant expression ratio between X-linked genes in human and their autosomal orthologs in other species (X:XX~1) across tissues and developmental stages, demonstrating stable dosage compensation in mammals. We also revealed that different epigenetic regulations could shape the higher tissue- and stage-specificity of X-linked gene expression, and affect X:AA ratios. We conclude that the dynamics of X:AA ratios are attributed to the different gene contents and expression preferences of the X chromosome, instead of the stable dosage compensation.
Essential Loop Dynamics Modulates Catalytic Activity in α-Chymotrypsin
Authors: Biswas Pritam , Pal Uttam , Adhikari Aniruddha , Mondal Susmita , Ghosh Ria , Mukherjee Dipanjan , Saha-Dasgupta Tanusri , Choudhury Sudeshna Shyam , Das Ranjan , Pal Samir Kumar 
Published: August 2021

AbstractConformational dynamics of macromolecules including enzymes are essential for their function. The present work reports the role of essential dynamics in alpha-chymotrypsin (CHT) which correlates with its catalytic activity. Detailed optical spectroscopy and classical molecular dynamics (MD) simulation were used to study thermal stability, catalytic activity and dynamical flexibility of the enzyme. The study of the enzyme kinetics reveals an optimum catalytic efficiency at 308K. Polarization gated fluorescence anisotropy with 8-anilino-1-napthelene sulfonate (ANS) have indicated increasing flexibility of the enzyme with an increase in temperature. Examination of the structure of CHT reveal the presence of five loop regions (LRs) around the catalytic S1 pocket. MD simulations have indicated that flexibility increases concurrently with temperature which decreases beyond optimum temperature. Principal component analysis (PCA) of the eigenvectors manifests essential dynamics and gatekeeping role of the five LRs surrounding the catalytic pocket which controls the enzyme activity.
Sub-3 Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly
Authors: Liu Di , Thélot François A. , Piccirilli Joseph A. , Liao Maofu , Yin Peng 
Published: August 2021

AbstractMany functional RNAs fold into intricate and precise 3D architectures, and high-resolution structures are required to understand their underlying mechanistic principles. However, RNA structural determination is difficult. Herein, we present a nanoarchitectural strategy to enable the efficient single-particle cryogenic electron microscopy (cryo-EM) analysis of RNA-only structures. This strategy, termedRNAoligomerization-enabledcryo-EM via installingkissing-loops (ROCK), involves the engineering of target RNAs by installing kissing-loop sequences onto functionally nonessential stems for the assembly into closed homomeric nanoarchitectures. Assembly with geometric restraints leads to (1) molecular weight multiplication and (2) structural flexibility mitigation, both beneficial for cryo-EM analysis. Together with construct optimization and symmetry-expansion reconstruction, ROCK yields the cryo-EM reconstruction of theTetrahymenagroup I intron at an overall resolution of 2.98 Å (2.85 Å resolution for the core domains), enabling the de novo model building of the complete intron RNA including previously unknown peripheral domains. When applied to smaller RNAs, ROCK readily produces modest-resolution maps, revealing the conformational rearrangement of theAzoarcusgroup I intron and the bound ligand in the FMN riboswitch. Our work unleashes the largely unexplored potential of cryo-EM in RNA structural studies.