bluuebunny/crossref_metadata_2025_split huggingface dataset:
“A novel female-specific circadian clock mechanism regulating metabolism”
Authors: Mekbib Tsedey , Suen Ting-Chung , Rollins-Hairston Aisha , Smith Kiandra , Armstrong Ariel , Gray Cloe , Owino Sharon , Baba Kenkichi , Baggs Julie E. , Ehlen J. Christopher , Tosini Gianluca , DeBruyne Jason P. 
Published: October 2020

AbstractCircadian clocks enable organisms to predict and align their behaviors and physiologies to constant daily day-night environmental cycle. Because the ubiquitin ligase Siah2 has been identified as a potential regulator of circadian clock function in cultured cells, we have used Siah2-deficient mice to examine its functionin vivo. Our experiments demonstrate a striking and unexpected sexually dimorphic effect ofSiah2deficiency on the regulation of rhythmically expressed genes. The absence of Siah2 in females, but not in males, altered the expression of core circadian clock genes and drastically remodeled the rhythmic hepatic transcriptome. Siah2 loss, only in females, increased the expression of 100’s of genes selectively at mid-day, resulting in a >50% increase in the number of rhythmically expressed genes, and shifted the expression of 100’s of other genes from a mid-night peak, to a mid-day peak. The combined result is a near inversion of overall rhythmicity in gene expression selectively in Siah2-deficient females. This dramatic reorganization created a substantial misalignment between rhythmic liver functions and feeding/behavioral rhythms, and consequently disrupted daily patterns of lipid/lipoprotein metabolism and metabolic responses to high-fat diet. Collectively, our results suggest that Siah2 is part of a female-specific circadian mechanism important for maintaining metabolic homeostasis and may play a key role in establishing sexual dimorphisms in metabolism, and broadly reveal that circadian clocks may drive rhythms using novel sex-specific transcriptional pathways.
SunRISE: long-term imaging of individual mRNA molecules in living cells
Authors: Guo Yue , Lee Robin E. C. 
Published: October 2020

AbstractSingle-cell imaging of individual mRNAs has revealed core mechanisms of the central dogma. However, most approaches require cell fixation or have limited sensitivity for live-cell applications. Here, we describe SunRISE (SunTag-based Reporter for Imaging Signal Enriched mRNA), a computationally and experimentally optimized approach for unambiguous single-mRNA detection in living cells. We demonstrate SunRISE with long-term epifluorescence imaging, using translational stress to track mRNA phase separation and recovery from cytosolic droplets.
A genetic variant protective against severe COVID-19 is inherited from Neandertals
Authors: Zeberg Hugo , Pääbo Svante 
Published: October 2020

AbstractIt was recently shown that the major genetic risk factor associated with becoming severely ill with COVID-19 when infected by SARS-CoV-2 is inherited from Neandertals. Thanks to new genetic association studies additional risk factors are now being discovered. Using data from a recent genome-wide associations from the Genetics of Mortality in Critical Care (GenOMICC) consortium, we show that a haplotype at a region associated with requiring intensive care is inherited from Neandertals. It encodes proteins that activate enzymes that are important during infections with RNA viruses. As compared to the previously described Neandertal risk haplotype, this Neandertal haplotype is protective against severe COVID-19, is of more moderate effect, and is found at substantial frequencies in all regions of the world outside Africa.
Membrane transporter dimerization driven by differential lipid solvation energetics of dissociated and associated states
Authors: Chadda Rahul , Bernhardt Nathan , Kelley Elizabeth G. , Teixeira Susana C. M. , Griffith Kacie , Gil-Ley Alejandro , Öztürk Tuğba N. , Hughes Lauren E. , Forsythe Ana , Krishnamani Venkatramanan , Faraldo-Gómez José D. , Robertson Janice L. 
Published: October 2020

ABSTRACTOver two-thirds of integral membrane proteins of known structure assemble into oligomers. Yet, the forces that drive the association of these proteins remain to be delineated, as the lipid bilayer is a solvent environment that is both structurally and chemically complex. In this study we reveal how the lipid solvent defines the dimerization equilibrium of the CLC-ec1 Cl-/H+antiporter. Integrating experimental and computational approaches, we show that monomers associate to avoid a thinned-membrane defect caused by their exposed dimerization interfaces. In this defect, lipids are strongly tilted and less densely packed than in the bulk, with a larger degree of entanglement between opposing leaflets and greater water penetration into the bilayer interior. Dimerization restores the membrane to a near-native state and therefore, appears to be driven by the larger free-energy cost of lipid solvation of the dissociated protomers. Supporting this theory, we demonstrate that addition of short-chain lipids strongly shifts the dimerization equilibrium towards the monomeric state, and show that the cause of this effect is that these lipids preferentially solvate the defect. Importantly, we show that this shift requires only minimal quantities of short-chain lipids, with no measurable impact on either the macroscopic physical state of the membrane or the protein’s biological function. Based on these observations, we posit that free-energy differentials for local lipid solvation define membrane-protein association equilibria. With this, we argue that preferential lipid solvation is a plausible cellular mechanism for lipid regulation of oligomerization processes, as it can occur at low concentrations and does not require global changes in membrane properties.IMPACT STATEMENTDifferences in the lipid solvation energetics of associated and dissociated states is a primary driving force for membrane protein oligomerization, presenting a molecular mechanism for lipid regulation in biology.
Ready-to-use nanopore platform for the detection of any DNA/RNA oligo at attomole range using an Osmium tagged complementary probe
Authors: Kang Albert S. W. , Bernasconi Janette G. , Jack William , Kanavarioti Anastassia 
Published: October 2020

ABSTRACTNanopores can serve as single molecule sensors. We exploited the MinION, a portable nanopore device from Oxford Nanopore Technologies (ONT), and repurposed it to detect any DNA/RNA oligo (target) in a complex mixture by conducting voltage-driven ion-channel measurements. The detection and quantitation of the target is enabled by the use of a unique complementary probe. Using a validated labeling technology, probes are tagged with a bulky Osmium tag (Osmium tetroxide 2,2’-bipyridine), in a way that preserves strong hybridization between probe and target. Intact oligos traverse the MinION’s nanopore relatively quickly compared to the device’s acquisition rate, and exhibit count of events comparable to the baseline. Counts are reported by a publicly available software,OsBp_detect. Due to the presence of the bulky Osmium tag, probes traverse more slowly, produce multiple counts over the baseline, and are even detected at single digit attomole (amole) range. In the presence of the target the probe is “silenced”. Silencing is attributed to a 1:1 double stranded (ds) complex that doesn’t fit and can’t traverse this nanopore. This ready-to-use platform can be tailored as a diagnostic test to meet the requirements for point-of-care cell-free tumor DNA (ctDNA) and microRNA (miRNA) detection and quantitation in body fluids.
Sub-second heat inactivation of coronavirus
Authors: Jiang Yuqian , Zhang Han , Wippold Jose A. , Gupta Jyotsana , Dai Jing , de Figueiredo Paul , Leibowitz Julian L. , Han Arum 
Published: October 2020

ABSTRACTHeat treatment denatures viral proteins that comprise the virion, making virus incapable of infecting a host. Coronavirus (CoV) virions contain single-stranded RNA genomes with a lipid envelope and 4 proteins, 3 of which are associated with the lipid envelope and thus are thought to be easily denatured by heat or surfactant-type chemicals. Prior studies have shown that a temperature of as low as 75 °C and treatment duration of 15 min can effectively inactivate CoV. The applicability of a CoV heat inactivation method greatly depends on the length of time of a heat treatment and the temperature needed to inactivate the virus. With the goal of finding conditions where sub-second heat exposure of CoV can sufficiently inactivate CoV, we designed and developed a simple system that can measure sub-second heat inactivation of CoV. The system is composed of capillary stainless-steel tubing immersed in a temperature-controlled oil bath followed by an ice bath, through which virus solution can be flowed at various speeds. Flowing virus solution at different speeds, along with a real-time temperature monitoring system, allows the virus to be accurately exposed to a desired temperature for various durations of time. Using mouse hepatitis virus (MHV), a beta-coronavirus, as a model system, we identified that 85.2 °C for 0.48 s exposure is sufficient to obtain > 5 Log10reduction in viral titer (starting titer: 5 × 107PFU/mL), and that when exposed to 83.4 °C for 0.95 s, the virus was completely inactivated (zero titer, > 6 Log10reduction).IMPORTANCEThree coronaviruses (CoVs) have now caused global outbreaks within the past 20 years, with the COVID19 pandemic caused by SARS-CoV-2 still ongoing. Methods that can rapidly inactivate viruses, especially CoVs, can play critical roles in ensuring public safety and safeguarding personal health. Heat treatment of viruses to inactive them can be an efficient and inexpensive method, with the potential to be incorporated into various human-occupied spaces. In this work, a simple system that can heat-treat viruses for extremely short period was developed and utilized to show that sub-second exposure of CoV to heat is sufficient to inactivate CoV. This opens up the possibility of developing instruments and methods of disinfecting CoV in diverse settings, including rapid liquid disinfection and airborne virus disinfection. The developed method can also be broadly utilized to assess heat sensitivity of viruses other viral pathogens of interest and develop sub-second rapid heat inactivation approaches.
Can measurements of inflammatory biomarkers be used to spot viral infections?
Authors: Sinha Anirban , Lutter René , Dekker Tamara , Dierdorp Barbara , Sterk Peter J. , Frey Urs , Delgado-Eckert Edgar 
Published: October 2020

AbstractAccurate detection of human respiratory viral infections is highly topical. We investigated how strongly inflammatory biomarkers (FeNO, eosinophils, neutrophils, and cytokines in nasal lavage fluid) and lung function parameters change upon rhinovirus-16 infection, in order to explore their potential use for infection detection. To this end, within a longitudinal cohort study, healthy and mildly asthmatic volunteers were experimentally inoculated with rhinovirus-16 and time series of these parameters/biomarkers were systematically recorded and compared between the pre- and post-infection phases of the study, which lasted 2 and 1 month/s, respectively. We found that the parameters’/biomarkers’ ability to discriminate between the infected and the uninfected state varied over the observation time period. Consistently over time, the concentration of cytokines in nasal lavage fluid showed moderate to very good discrimination performance, thereby qualifying for disease progression monitoring. On the other hand, lung function and FeNO, while quickly and non-invasively measurable using cheap portable devices (e.g., at airports), performed poorly.
Recapitulating the frataxin activation mechanism in an engineered bacterial cysteine desulfurase supports the architectural switch model
Authors: Patra Shachin , Lin Cheng-Wei , Ghosh Manas K. , Havens Steven M. , Cory Seth A. , Russell David H. , Barondeau David P. 
Published: October 2020

ABSTRACTIron-sulfur (Fe-S) clusters have a key role in many biochemical processes and are essential for most life forms. Despite recent mechanistic advances in understanding the Fe-S cluster biosynthetic pathway, critical questions remain unresolved. Although human NFS1 andE. coliIscS share ∼60% sequence identity, NFS1 exhibits low activity and requires activation by the Friedreich’s ataxia protein frataxin (FXN) forin vivofunction. Surprisingly, structures of the human complex reveal three distinct quaternary structures with one form exhibiting the same subunit interactions as IscS. An architectural switch model has been proposed in which evolutionarily lost interactions between NFS1 subunits results in the formation of low-activity architectures; FXN binding compensates for these lost interactions and facilitates a subunit rearrangement to activate the complex. Here, we used a structure and evolution-guided approach to identify three conserved residues proposed to weaken interactions between NFS1 subunits and transplanted these amino acids into IscS. Compared to native IscS, the engineered variant had a 4000-fold weaker dimer interface and diminished activity that correlated with the absence of the second catalytic subunit. Remarkably, the addition of the FXN homolog to the engineered variant stimulated the decay of the Cys-quinonoid pyridoxal 5’-phosphate intermediate, shifted IscS from the monomeric to dimeric form, and increased the cysteine desulfurase activity, reproducing results from the human system and supporting the architectural switch model. Overall, these studies indicate a weakening of the homodimeric interface was a key development during the evolution of the eukaryotic system and provide new insights into the role of FXN.
Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection
Authors: Flynn Ryan A. , Belk Julia A. , Qi Yanyan , Yasumoto Yuki , Schmitz Cameron O. , Mumbach Maxwell R. , Limaye Aditi , Wei Jin , Alfajaro Mia Madel , Parker Kevin R. , Chang Howard Y. , Horvath Tamas L. , Carette Jan E. , Bertozzi Carolyn , Wilen Craig B. , Satpathy Ansuman T. 
Published: October 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a pandemic with growing global mortality. There is an urgent need to understand the molecular pathways required for host infection and anti-viral immunity. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with viral ChIRP-MS data from three other positive-sense RNA viruses defined pan-viral and SARS-CoV-2-specific host interactions. Functional interrogation of these factors with a genome-wide CRISPR screen revealed that the vast majority of viral RNA-binding proteins protect the host from virus-induced cell death, and we identified known and novel anti-viral proteins that regulate SARS-CoV-2 pathogenicity. Finally, our RNA-centric approach demonstrated a physical connection between SARS-CoV-2 RNA and host mitochondria, which we validated with functional and electron microscopy data, providing new insights into a more general virus-specific protein logic for mitochondrial interactions. Altogether, these data provide a comprehensive catalogue of SARS-CoV-2 RNA-host protein interactions, which may inform future studies to understand the mechanisms of viral pathogenesis, as well as nominate host pathways that could be targeted for therapeutic benefit.Highlights· ChIRP-MS of SARS-CoV-2 RNA identifies a comprehensive viral RNA-host protein interaction network during infection across two species· Comparison to RNA-protein interaction networks with Zika virus, dengue virus, and rhinovirus identify SARS-CoV-2-specific and pan-viral RNA protein complexes and highlights distinct intracellular trafficking pathways· Intersection of ChIRP-MS and genome-wide CRISPR screens identify novel SARS-CoV-2-binding proteins with pro- and anti-viral function· Viral RNA-RNA and RNA-protein interactions reveal specific SARS-CoV-2-mediated mitochondrial dysfunction during infection
GNS561 exhibits potentin vitroantiviral activity against SARS-CoV-2 through autophagy inhibition
Authors: Halfon Philippe , Bestion Eloïne , Zandi Keivan , Andreani Julien , Baudoin Jean-Pierre , La Scola Bernard , Mege Jean-Louis , Mezouar Soraya , Schinazi Raymond F. 
Published: October 2020

AbstractSince December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/2019-nCoV) has spread quickly worldwide, with more than 29 million cases and 920,000 deaths. Interestingly, coronaviruses were found to subvert and hijack the autophagic process to allow their viral replication. One of the spotlights had been focused on the autophagy inhibitors as a target mechanism effective in the inhibition of SARS-CoV-2 infection. Consequently, chloroquine (CQ) and hydroxychloroquine (HCQ), a derivative of CQ, was suggested as the first potentially be therapeutic strategies as they are known to be autophagy inhibitors. Then, they were used as therapeutics in SARS-CoV-2 infection along with remdesivir, for which the FDA approved emergency use authorization. Here, we investigated the antiviral activity and associated mechanism of GNS561, a small basic lipophilic molecule inhibitor of late-stage autophagy, against SARS-CoV-2. Our data indicated that GNS561 showed the highest antiviral effect for two SARS-CoV-2 strains compared to CQ and remdesivir. Focusing on the autophagy mechanism, we showed that GNS561, located in LAMP2-positive lysosomes, together with SARS-CoV-2, blocked autophagy by increasing the size of LC3-II spots and the accumulation of autophagic vacuoles in the cytoplasm with the presence of multilamellar bodies characteristic of a complexed autophagy. Finally, our study revealed that the combination of GNS561 and remdesivir was associated with a strong synergistic antiviral effect against SARS-CoV-2. Overall, our study highlights GNS561 as a powerful drug in SARS-CoV-2 infection and supports that the hypothesis that autophagy inhibitors could be an alternative strategy for SARS-CoV-2 infection.
Cytoplasmic short linear motifs in ACE2 and integrin β3 link SARS-CoV-2 host cell receptors to endocytosis and autophagy
Authors: Kliche Johanna , Ali Muhammad , Ivarsson Ylva 
Published: October 2020

AbstractThe spike protein of the SARS-CoV-2 interacts with angiotensin converting enzyme 2 (ACE2) and enters the host cell by receptor-mediated endocytosis. Concomitantly, evidence is pointing to the involvement of additional host cell receptors, such as integrins. The cytoplasmic tails of ACE2 and integrin β3 contain a plethora of predicted binding motifs. Here, we confirm the functionality of some of these motifs through affinity measurements. The class I PDZ binding motif in the ACE2 cytoplasmic tail binds the first PDZ domain of the scaffold protein NHERF3. The clathrin-adaptor subunit AP2 μ2 interacts with an endocytic motif in the ACE2 with low affinity and the interaction is abolished by phosphorylation of Tyr781. Furthermore, the C-terminal region of integrin b3 contains a LC3-interacting region, and its interaction with ATG8 domains is enhanced by phosphorylation. Together, our data provides possible molecular links between host cell receptors and endocytosis and autophagy.One sentence summaryAffinity measurements confirmed binding of short linear motifs in the cytoplasmic tails of ACE2 and integrin β3, thereby linking the receptors to endocytosis and autophagy.
SARS-CoV-2 infection damages airway motile cilia and impairs mucociliary clearance
Authors: Robinot Rémy , Hubert Mathieu , de Melo Guilherme Dias , Lazarini Françoise , Bruel Timothée , Smith Nikaïa , Levallois Sylvain , Larrous Florence , Fernandes Julien , Gellenoncourt Stacy , Rigaud Stéphane , Gorgette Olivier , Thouvenot Catherine , Trébeau Céline , Mallet Adeline , Duménil Guillaume , Gobaa Samy , Etournay Raphaël , Lledo Pierre-Marie , Lecuit Marc , Bourhy Hervé , Duffy Darragh , Michel Vincent , Schwartz Olivier , Chakrabarti Lisa A. 
Published: October 2020

ABSTRACTUnderstanding how SARS-CoV-2 spreads within the respiratory tract is important to define the parameters controlling the severity of COVID-19. We examined the functional and structural consequences of SARS-CoV-2 infection in a reconstituted human bronchial epithelium model. SARS-CoV-2 replication caused a transient decrease in epithelial barrier function and disruption of tight junctions, though viral particle crossing remained limited. Rather, SARS-CoV-2 replication led to a rapid loss of the ciliary layer, characterized at the ultrastructural level by axoneme loss and misorientation of remaining basal bodies. The motile cilia function was compromised, as measured in a mucociliary clearance assay. Epithelial defense mechanisms, including basal cell mobilization and interferon-lambda induction, ramped up only after the initiation of cilia damage. Analysis of SARS-CoV-2 infection in Syrian hamsters further demonstrated the loss of motile ciliain vivo. This study identifies cilia damage as a pathogenic mechanism that could facilitate SARS-CoV-2 spread to the deeper lung parenchyma.
Ascertaining service quality and medical practitioners' sensitivity towards surgical instruments using SERVQUAL
Authors: MM Sulphey , Jasim K. Mohamed 
Published: October 2020

PurposeService quality (SQ) has become an essential and indispensable component in healthcare and many other industries. SQ can deliver guaranteed stakeholder value and consequent consumer delight in the healthcare sector. The purpose of this study is to identify the relationships of various SERVQUAL elements with respect to the SQ of surgical instrument suppliers among surgeons.Design/methodology/approachData were collected from a sample of 112 surgeons working in the USA using the “snowball sampling” technique. A few standardised questionnaires, including SERQUAL, were used to collect the data. R-programming was used to perform structural equation modelling (SEM) analysis on the collected data.FindingsThe research study identified that service delivery factors and the SQ of surgical instruments contribute significantly towards medical practitioner sensitivity in the US healthcare industry. Word of mouth (WOM) did not have any significant impact on the medical practitioners' sensitivity.Originality/valueA review of related literature revealed that studies that examine the surgeon's perspectives of SQ are scarce. Thus, the present study is directed towards this gap in literature. The findings of the study are significant in nature and have made a substantial contribution to management literature.
An attribute-based framework for students' motivation to join an HEI: a self-determination theory perspective
Authors: Mishra Abhishek , Yousaf Anish , Amin Insha 
Published: October 2020

PurposeThe current work explores the attributes that serve as motivation regulations for students' selection of a higher education institute (HEI).Design/methodology/approachWith a self-determination theory (SDT) perspective, the current study used a mixed-method approach to develop a scale to measure HEI attribute-based motivation regulations.FindingsA total of eight regulations were proposed: academic/extracurricular activities, infrastructure, faculty research expertise, teaching and learning quality, placement opportunities, marketing and promotion, education cost and social influence. The first four were autonomous motivations and the remaining were controlled motivations.Research limitations/implicationsThe study leverages the SDT motivation continuum into a structured HEI attribute-based student motivation framework.Practical implicationsThe study guides HEI managers with specific attributes to position the institute appropriately.Originality/valueThis is one of the few works in the higher education utilizing the complete SDT framework.