bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circadian regulation of lung repair and regeneration
Authors: Naik Amruta , Forrest Kaitlyn , Issah Yasmine , Valekunja Utham , Reddy Akhilesh B , Hennessy Elizabeth , Brooks Thomas S. , Babu Apoorva , Morley Mike , Grant Gregory R. , FitzGerald Garret A. , Sehgal Amita , Worthen G. Scott , Frank David B. , Morrisey Edward E , Sengupta Shaon 
Published: November 2021

AbstractOptimal lung repair and regeneration is essential for recovery from viral infections such as that induced by influenza A virus (IAV). We have previously demonstrated that lung inflammation induced by IAV is under circadian control. However, it is not known if the circadian clock exerts its influence on lung repair and regenerative processes independent of acute inflammation from IAV. Here, we demonstrate for the first time that lung organoids have a functional clock as they mature and that the absence of an intact circadian clock impairs regenerative capacity. Using several models of circadian disruption, we show that with the absence of an intact clock lung proliferation is disrupted. Further, we find that the circadian clock acts through direct control of the Wnt/β-catenin pathway. We speculate, that adding the circadian dimension to the critical process of lung repair and regeneration will lead to novel therapies and improve outcomes. Finally, we use data from UK Biobank to demonstrate at the population level, the role of poor circadian rhythms in mediating negative outcomes following lung infection.
Organization and dynamics of the SpoVAEa protein, and its surrounding inner membrane lipids upon germination of Bacillus subtilis spores
Authors: Wen Juan , Vischer Norbert O.E. , de Vos Arend L. , Manders Erik. M. M. , Setlow Peter , Brul Stanley 
Published: November 2021

AbstractThe SpoVA proteins make up a channel in the inner membrane (IM) of B. subtilis spore. This channel responds to signals from activated germinant receptors (GRs), and allows release of Ca2+-DPA from the spore core during germination. In the current work, we studied the location and dynamics of SpoVAEa in dormant spores. Notably, the SpoVAEa-SGFP2 proteins were present in a single spot in spores, similar to the complex formed by all GRs. However, while the GRs’ spot remains in one location, the SpoVAEa-SGFP2 spot in the IM moved randomly with high frequency. The dynamics of the SpoVAEa-SGFP2 and its surrounding IM region as stained by fluorescent dyes were also tracked during spore germination, as the dormant spore IM appeared to have an immobile germination related functional microdomain. This microdomain disappeared around the time of appearance of a germinated spore, the loss of fluorescence of the IM by fluorescent dyes, as well as the appearance of SpoVAEa-SGFP2 peak fluorescent intensity occurred in parallel. These observed events were highly related to the rapid phase darkening, which is considered as the Ca2+DPA rapid release. We also tested the response of SpoVAEa and the IM to thermal treatments at 40-80°C. Heat treatment triggered an increase of green autofluorescence, which is speculated to be due to coat protein denaturation, and 80°C treatments induce the appearance of phase-grey-like spores. These spores presumably have a similar intracellular physical state as the phase grey spores detected in the germination but lack the functional proteins for further germination events.
Regnase-1 deficiency restrains Klebsiella pneumoniae infection by regulation of a Type I interferon response
Authors: Trevejo-Nuñez Giraldina , Lin Becky , Fan Li , Aggor Felix E. Y. , Biswas Partha S. , Chen Kong , Gaffen Sarah L. 
Published: November 2021

AbstractExcessive inflammatory responses can cause collateral tissue damage or autoimmune inflammation, sometimes with severe morbidity or mortality. During host defense responses, numerous negative feedback mechanisms are established to prevent excessive unchecked inflammation. However, this restraint can sometimes come at the cost of suboptimal infection control, and we do not fully understand how this balance is maintained during different infection settings. The endoribonuclease Regnase-1 (Reg1, Zc3h12a, MCPIP1) is an RNA binding protein (RBP) that binds and degrades many target mRNA transcripts. Reg1 is a potent feedback regulator of IL-17 and LPS signal transduction, among other stimuli. Consequently, Reg1 deficiency exacerbates autoimmune inflammation in multiple mouse models, but on the other hand, reduced Reg1 improves immunity to fungal infection. To date, the role of Reg1 in bacterial immunity is poorly defined. Here, we show that mice deficient in Reg1 are more resistant to pulmonary Klebsiella pneumoniae (KP) infection. Unexpectedly, effects of Reg1 deficiency were not due to accelerated eradication of bacteria or increased pro-inflammatory cytokine expression. Rather, alveolar macrophages from Reg1-deficient mice showed enrichment of Type I IFN-related genes upon KP infection, accompanied by increased Ifnb1 expression. Surprisingly, the stability of Ifnb1 mRNA was not altered by Reg1-deficiency; rather, mRNA encoding its upstream regulator IRF7 appeared to be a more prominent target. Blockade of IFNR during KP infection reversed disease improvement. Thus, impaired Reg1 induces Type I IFN and enhances resistance to KP, raising the possibility that Reg1 could be a potential clinical target in acute bacterial infections.Graphical abstract
The Contributions of Eye Gaze Fixations and Target-Lure Similarity to Behavioral and fMRI Indices of Pattern Separation and Pattern Completion
Authors: Bjornn Daniel K. , Van Julie , Brock Kirwan C. 
Published: November 2021

AbstractPattern separation and pattern completion are generally studied in humans using mnemonic discrimination tasks such as the Mnemonic Similarity Task (MST) where participants identify similar lures and repeated items from a series of images. Failures to correctly discriminate lures are thought to reflect a failure of pattern separation and a propensity toward pattern completion. Recent research has challenged this perspective, suggesting that poor encoding rather than pattern completion accounts for the occurrence of false alarm responses to similar lures. In two experiments, participants completed a continuous recognition task version of the MST while eye movement (Experiments 1 and 2) and fMRI data (Experiment 2) were collected. In Experiment 1, we replicated the result that fixation counts at study predicted accuracy on lure trials (consistent with poor encoding predicting mnemonic discrimination performance), but this effect was not observed in our fMRI task. In both experiments we found that target-lure similarity was a strong predictor of accuracy on lure trials. Further, we found that fMRI activation changes in the hippocampus were significantly correlated with the number of fixations at study for correct but not incorrect mnemonic discrimination judgments when controlling for target-lure similarity. Our findings indicate that while eye movements during encoding predict subsequent hippocampal activation changes for correct mnemonic discriminations, the predictive power of eye movements for activation changes for incorrect mnemonic discrimination trials was modest at best.
Artificial Intelligence uncovers carcinogenic human metabolites
Authors: Mittal Aayushi , Mohanty Sanjay Kumar , Gautam Vishakha , Arora Sakshi , Saproo Sheetanshu , Gupta Ria , S Roshan , Garg Prakriti , Aggarwal Anmol , R Padmasini , Dixit Nilesh Kumar , Pal Singh Vijay , Mehta Anurag , Tayal Juhi , Naidu Srivatsava , Sengupta Debarka , Ahuja Gaurav 
Published: November 2021

ABSTRACTThe genome of a eukaryotic cell is often vulnerable to both intrinsic and extrinsic threats due to its constant exposure to a myriad of heterogeneous compounds. Despite the availability of innate DNA damage response pathways, some genomic lesions trigger cells for malignant transformation. Accurate prediction of carcinogens is an ever-challenging task due to the limited information aboutbona fide(non)carcinogens. We developed Metabokiller, an ensemble classifier that accurately recognizes carcinogens by quantitatively assessing their electrophilicity as well as their potential to induce proliferation, oxidative stress, genomic instability, alterations in the epigenome, and anti-apoptotic response. Concomitant with the carcinogenicity prediction, Metabokiller is fully interpretable since it reveals the contribution of the aforementioned biochemical properties in imparting carcinogenicity. Metabokiller outperforms existing best-practice methods for carcinogenicity prediction. We used Metabokiller to unravel cells’ endogenous metabolic threats by screening a large pool of human metabolites and predicted a subset of these metabolites that could potentially trigger malignancy in normal cells. To cross-validate Metabokiller predictions, we performed a range of functional assays usingSaccharomyces cerevisiaeand human cells with two Metabokiller-flagged human metabolites namely 4-Nitrocatechol and 3,4-Dihydroxyphenylacetic acid and observed high synergy between Metabokiller predictions and experimental validations.
Determining international spread of novel B.1.1.523 SARS-CoV-2 lineage
Authors: Zemaitis Lukas , Alzbutas Gediminas , Gecys Dovydas , Komissarov Andrey , Pautienius Arnoldas , Ugenskiene Rasa , Sukys Marius , Lesauskaite Vaiva 
Published: November 2021

ABSTRACTHere we report the emergence of variant lineage B.1.1.523 that contains a set of mutations including 156_158del, E484K and S494P in Spike protein. E484K and S494P are known to significantly reduce SARS-CoV-2 neutralization by convalescent and vaccinee sera and are considered as mutations of concern. Lineage B.1.1.523 has presumably originated in Russian Federation and spread across European countries with the peak of transmission in April – May 2021. The B.1.1.523 lineage has now been reported from 27 countries.
Re-evaluating the actin-dependence of spectraplakin functions during axon growth and maintenance
Authors: Qu Yue , Alves-Silva Juliana , Gupta Kriti , Hahn Ines , Parkin Jill , Sánchez-Soriano Natalia , Prokop Andreas 
Published: November 2021

AbstractAxons are the long and slender processes of neurons constituting the biological cables that wire the nervous system. The growth and maintenance of axons require bundles of microtubules that extend through their entire length. Understanding microtubule regulation is therefore an essential aspect of axon biology. Key regulators of neuronal microtubules are the spectraplakins, a well-conserved family of cytoskeletal cross-linkers that underlie neuropathies in mouse and humans. Spectraplakin deficiency in mouse orDrosophilacauses severe decay of microtubule bundles and axon growth inhibition. The underlying mechanisms are best understood forDrosophilaShort stop (Shot) and believed to involve cytoskeletal cross-linkage: the N-terminal calponin homology (CH) domains bind to F-actin, and the C-terminus to microtubules and Eb1. Here we have gained new understanding by showing that the F-actin interaction must be finely balanced: altering the properties of F-actin networks or deleting/exchanging Shot’s CH domains induces changes in Shot function - with a Lifeact-containing Shot variant causing remarkable remodelling of neuronal microtubules. In addition to actin-MT cross-linkage, we find strong indications that Shot executes redundant MT bundle-promoting roles that are F-actin-independent. We argue that these likely involve the neuronal Shot-PH isoform, which is characterised by a large, unexplored central plakin repeat region (PRR). Work on PRRs might therefore pave the way towards important new mechanisms of axon biology and architecture that might similarly apply to central PRRs in mammalian spectraplakins.
Vibrio cholerae El Tor strains linked to global cholera are homogeneous by pulsed-field gel electrophoresis
Authors: Johura Fatema-Tuz , Biswas Sahitya Ranjan , Rashed Shah M , Islam Mohammad Tarequl , Islam Saiful , Sultana Marzia , Huq Anwar , Thomson Nicholas R , Colwell Rita R. , Watanabe Haruo , Alam Munirul 
Published: November 2021

AbstractVibrio cholerae O1 El Tor, causative agent of the ongoing seventh cholera pandemic, is native to the aquatic environment of the Ganges Delta, Bay of Bengal (GDBB). Recent studies traced pandemic strains to the GDBB and proposed global spread of cholera had occurred via intercontinental transmission. In the research presented here, NotI-digested genomic DNA extracted from V. cholerae O1 clinical and environmental strains isolated in Bangladesh during 2004 – 2014 was analyzed by pulsed-field gel electrophoresis (PFGE). Results of cluster analysis showed 94.67% of the V. cholerae isolates belonged to clade A and included the majority of clinical isolates of spatio-temporal origin and representing different cholera endemic foci. The rest of the strains were estuarine, all environmental isolates from Mathbaria, Bangladesh, and occurred as singletons, clustered in clades B and C, or in the small clades D and E. Cluster analysis of the Bangladeshi strains and including 157 El Tor strains from thirteen countries in Asia, Africa, and the Americas revealed 85% of the total set of isolates belonged to clade A, indicating all were related, yet did not form an homogeneous cluster. Overall, 15% of the global strains comprised multiple small clades or segregated as singletons. Three sub-clades could be discerned within the major clade A, reflecting distinct lineages of V. cholerae El Tor associated with cholera in Asia, Africa, and the Americas. The presence in Asia and the Americas of non-pandemic V. cholerae El Tor populations differing by PFGE and from strains associated with cholera globally suggests different ecotypes are resident in distant geographies.Author SummaryCholera is a major health threat, especially in the Ganges Delta, Bay of Bengal (GDBB). Vibrio cholerae, causative agent of cholera, is native to the GDBB aquatic environment. Recent genomic studies suggest GDBB is the cholera hotspot where the disease spreads globally via human activity. Pulsed-field gel electrophoresis (PFGE) of NotI-digested genomic DNA from V. cholerae El Tor endemic cholera strains was done, including Bangladesh aquatic environment and clinical strains from distant geographical regions representing three cholera-prone continents. Results showed the majority of pandemic strains belonged to a major cluster, suggesting clonal relatedness. Ecotypes were detected, indicating geographically specific lineages. It is concluded that epidemic strains in Bangladesh and thirteen countries of Asia, Africa, and the Americas are geographically adapted, with independent evolution of the bacterium in respective geographical regions.
SmdA is a novel cell morphology determinant in Staphylococcus aureus
Authors: Myrbråten Ine Storaker , Stamsås Gro Anita , Chan Helena , Angeles Danae Morales , Knutsen Tiril Mathiesen , Salehian Zhian , Shapaval Volha , Straume Daniel , Kjos Morten 
Published: November 2021

AbstractCell division and cell wall synthesis in staphylococci need to be precisely coordinated and controlled to allow the cell to multiply while maintaining their nearly spherical shape. The mechanisms ensuring correct placement of the division plane and synthesis of new cell wall have been studied intensively, however, hitherto unknown factors and proteins are likely to play key roles in this complex interplay. We here identified and investigated a protein with major influence on cell morphology in Staphylococcus aureus. The protein, named SmdA (for staphylococcal morphology determinant A), is a membrane-protein with septum-enriched localization. By CRISPRi knockdown and overexpression combined with different microscopy techniques, we demonstrate that proper levels of SmdA is necessary for cell division, including septum formation and cell splitting. We also identified conserved residues in SmdA that are critical for its functionality. Pulldown- and bacterial two-hybrid interaction experiments showed that SmdA interacts with several known cell division- and cell wall synthesis proteins, including penicillin binding proteins (PBPs) and EzrA. Notably, SmdA also affects susceptibility to cell wall targeting antibiotics, particularly in methicillin-resistant S. aureus (MRSA). Together, our results show that S. aureus is dependent on balanced amounts of membrane-attached SmdA in order to carry out proper cell division.ImportanceStaphylococcus aureus is an important human and animal pathogen. Antibiotic resistance is a major problem in treatment of staphylococcal infections, and cell division and cell wall synthesis factors have previously been shown to modulate susceptibility to antibiotics in this species. In the current work we investigated the function of an essential protein named SmdA, which was identified based on its septal localization and knockdown phenotype resulting in defective cellular morphologies. We demonstrate that this protein is critical for normal cell division in S. aureus. Depletion of SmdA sensitize resistant staphylococci to β-lactam antibiotics. This work thus reveals a new staphylococcal cell division factor and a potential future target for narrow spectrum antimicrobials or compounds to resensitize antibiotic resistant staphylococcal strains.
KEEPING IN TOUCH WITH OUR HIDDEN SIDE
Authors: Mathieu Benjamin , Abillama Antonin , Martinez Malvina , Mouchnino Laurence , Blouin Jean 
Published: November 2021

AbstractPrevious studies have shown that the sensory modality used to identify the position of proprioceptive targets hidden from sight, but frequently viewed, influences the type of the body representation employed for reaching them with the finger. The question then arises as to whether this observation also applies to proprioceptive targets which are hidden from sight, and rarely, if ever, viewed. We used an established technique for pinpointing the type of body representation used for the spatial encoding of targets which consisted of assessing the effect of peripheral gaze fixation on the pointing accuracy. More precisely, an exteroceptive, visually dependent, body representation is thought to be used if gaze deviation induces a deviation of the pointing movement. Three light-emitting diodes (LEDs) were positioned at the participants’ eye level at −25 deg, 0 deg and +25 deg with respect to the cyclopean eye. Without moving the head, the participant fixated the lit LED before the experimenter indicated one of the three target head positions: topmost point of the head (vertex) and two other points located at the front and back of the head. These targets were either verbal-cued or tactile-cued. The goal of the subjects (n=27) was to reach the target with their index finger. We analysed the accuracy of the movements directed to the topmost point of the head, which is a well-defined, yet out of view anatomical point. Based on the possibility of the brain to create visual representations of the body areas that remain out of view, we hypothesized that the position of the vertex is encoded using an exteroceptive body representation, both when verbally or tactile-cued. Results revealed that the pointing errors were biased in the opposite direction of gaze fixation for both verbal-cued and tactile-cued targets, suggesting the use of a vision-dependent exteroceptive body representation. The enhancement of the visual body representations by sensorimotor processes was suggested by the greater pointing accuracy when the vertex was identified by tactile stimulation compared to verbal instruction. Moreover, we found in a control condition that participants were more accurate in indicating the position of their own vertex than the vertex of other people. This result supports the idea that sensorimotor experiences increase the spatial resolution of the exteroceptive body representation. Together, our results suggest that the position of rarely viewed body parts are spatially encoded by an exteroceptive body representation and that non-visual sensorimotor processes are involved in the constructing of this representation.
Using light-sheet microscopy to study spontaneous activity in the developing lateral-line system
Authors: Zhang Qiuxiang , Kindt Katie 
Published: November 2021

AbstractHair cells are the sensory receptors in the auditory and vestibular systems of all vertebrates, and in the lateral-line system of aquatic vertebrates. During development, spontaneous activity in hair cells shapes the formation of these sensory systems. In auditory hair cells of mice, coordinated waves of spontaneous activity can be triggered by concomitant activity in nearby supporting cells. But in mammals, developing auditory and vestibular hair cells can also autonomously generate spontaneous events independent of supporting cell activity. To date, significant progress has been made studying spontaneous activity in the auditory and vestibular systems of mammals, in isolated cultures. The purpose of this work is to explore the zebrafish lateral-line system as a model to study and understand spontaneous activity in vivo. Our work applies genetically encoded calcium indicators along with light-sheet fluorescence microscopy to visualize spontaneous calcium activity in the developing lateral-line system. Consistent with our previous work, we show that spontaneous calcium activity is present in developing lateral-line hair cells. We now show that supporting cells that surround hair cells, and cholinergic efferent terminals that directly contact hair cells are also spontaneously active. Using two-color functional imaging we demonstrate that spontaneous activity in hair cells does not correlate with activity in either supporting cells or cholinergic terminals. We find that during lateral-line development, hair cells autonomously generate spontaneous events. Using localized calcium indicators, we show that within hair cells, spontaneous calcium activity occurs in two distinct domains–the mechanosensory bundle and the presynapse. Further, spontaneous activity in the mechanosensory bundle ultimately drives spontaneous calcium influx at the presynapse. Comprehensively, our results indicate that in developing lateral-line hair cells, autonomously generated spontaneous activity originates with spontaneous mechanosensory events. Overall, with robust spontaneous activity three different cell types, the developing lateral line is a rich model to study these activities in an intact sensory organ. Future work studying this model may further our understanding of these activities and their role in sensory system formation, function and regeneration.