bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-wide association study of liking of physical activity in the UK Biobank
Authors: Klimentidis Yann C. , Newell Michelle , van der Zee Matthijs D. , Bland Victoria L. , May-Wilson Sebastian , Menni Cristina , Mangino Massimo , Arora Amit , Raichlen David A. , Alexander Gene E. , Wilson James F. , Boomsma Dorret I. , Hottenga Jouke-Jan , de Geus Eco J.C. , Pirastu Nicola
Published: October 2021

A lack of physical activity (PA) is one of the most pressing health issues facing society today. Our individual propensity for PA is partly influenced by genetic factors. Stated liking of various PA behaviors may capture additional dimensions of PA behavior that are not captured by other measures, and contribute to our understanding of the genetics of PA behavior. Here, in over 157,000 individuals from the UK Biobank, we sought to complement and extend previous findings on the genetics of PA behavior by performing genome-wide association studies of self-reported liking of several PA-related behaviors plus an additional derived trait of overall PA-liking. We identified a total of 19 unique genome-wide significant loci across all traits, only four of which overlap with loci previously identified for PA behavior. The PA-liking traits were genetically correlated with self-reported (rg: 0.38 – 0.80) and accelerometry-derived (rg: 0.26 – 0.49) PA measures, and with a wide range of health-related traits and dietary behaviors. Replication in the Netherlands Twin Register (NTR; n>7,300) and the TwinsUK (n>1,300) study revealed directionally consistent associations. Polygenic risk scores (PRS) were then trained in UKB for each PA-liking trait and for self-reported PA behavior. The PA-liking PRS significantly predicted the same liking trait in NTR. The PRS for liking of going to the gym predicted PA behavior in NTR (r2 = 0.40%) nearly as well as the one constructed based on self-reported PA behavior (r2 = 0.42%). Combining the two PRS into a single model increased the r2 to 0.59%, suggesting that although these PRS correlate with each other, they are also capturing distinct dimensions of PA behavior. In conclusion, we have identified the first loci associated with PA-liking, and extended and refined our understanding of the genetic basis of PA behavior.
Disparities in SARS-CoV-2 exposure: evidence from a citywide seroprevalence study in Holyoke, Massachusetts, USA
Authors: Matias Wilfredo R. , Fulcher Isabel R. , Sauer Sara M. , Nolan Cody P. , Guillaume Yodeline , Zhu Jack , Molano Francisco J. , Uceta Elizabeth , Collins Shannon , Slater Damien M. , Sánchez Vanessa M. , Moheed Serina , Harris Jason B. , Charles Richelle C. , Paxton Ryan M. , Gonsalves Sean F. , Franke Molly F. , Ivers Louise C.
Published: October 2021

Background

Seroprevalence studies are important tools to estimate the prevalence of prior or recent SARS-CoV-2 infections, identifying hotspots and high-risk groups and informing public health responses to the COVID-19 pandemic. We conducted a city-level seroprevalence study in Holyoke, Massachusetts, USA to estimate the seroprevalence of SARS-CoV-2 antibodies and risk factors for seropositivity.

Methods

We invited inhabitants of 2,000 randomly sampled addresses between November 5 and December 31, 2020. Participants completed questionnaires measuring sociodemographic and health characteristics, and COVID-19 exposure history, and provided dried blood spots for measurement of SARS-CoV-2 IgG and IgM antibodies. We calculate total and subgroup seroprevalence estimates based on presence of IgG antibodies using a Bayesian procedure that incorporates uncertainty in antibody test sensitivity and specificity. We account for clustering by household and weighting based on demographic characteristics to ensure estimates represented the city’s population.

Findings

We enrolled 280 households including 472 individuals. 328 underwent antibody testing. The citywide seroprevalence estimate of SARS-CoV-2 IgG was 13.1% (95%CI 6.9-22.3) compared to 9.8% based on publicly reported case counts. Seroprevalence was 16.1% (95%CI 6.2-31.8) among individuals identifying as Hispanic compared to 9.4% (95%CI 4.6-16.4) among those identifying as non-Hispanic white. Seroprevalence was higher among Spanish speaking households (21.9%; 95% CI 8.3-43.9) compared to English speaking households (10.2%; 95% CI 5.2-18.0) and among individuals living in high vulnerability areas (14.4%; 95% CI 7.1-25.5) compared to low vulnerability areas (8.2%; 95% CI 3.1-16.9).

Interpretation

The measured SARS-CoV-2 seroprevalence of IgG antibodies in Holyoke was only 13.1% during the second surge of SARS-CoV-2 in this region, far from accepted thresholds for “herd immunity.” Already vulnerable communities were at highest risk of prior infection. Implementation of local serosurveys in tandem with proactive public health interventions that address disparities in SARS-CoV-2 exposure are crucial to ensure at-risk communities have appropriate educational materials and access to vaccines, testing, and timely treatment.

Funding

The Sullivan Family Foundation, Harvard Data Science Institute Bias2program, the US Centers for Disease Control and Prevention.
Networks of common inputs to motor neurons of the lower limb reveal neural synergies that only partly overlap with muscle innervation
Authors: Hug François , Avrillon Simon , Sarcher Aurélie , Del Vecchio Alessandro , Farina Dario
Published: October 2021

Movements are reportedly controlled through the combination of synergies that generate specific motor outputs by imposing an activation pattern on a group of muscles. To date, the smallest unit of analysis has been the muscle. In this human study, we decoded the spiking activities of spinal motor neurons innervating six lower limb muscles during an isometric multi-joint task. We identified their common low-frequency components, from which networks of common synaptic inputs to the motor neurons were derived. The vast majority of the identified motor neurons shared common inputs with other motor neuron(s). In addition, groups of motor neurons were partly decoupled from their innervated muscle, such that motor neurons innervating the same muscle did not necessarily receive common inputs. Conversely, some motor neurons from different muscles – including distant muscles – received common inputs. Our results provide evidence of a synergistic control of a multi-joint motor task at the spinal motor-neuron level.

Teaser

The generation of movement involves the activation of many spinal motor neurons from multiple muscles. A central and unresolved question is how these motor neurons are controlled to allow flexibility for adaptation to various mechanical constraints. Since the computational load of controlling each motor neuron independently would be extremely large, the central nervous system presumably adopts dimensionality reduction. We identified networks of functional connectivity between spinal motor neurons based on the common synaptic inputs they receive during a multi-joint task. Our findings revealed functional groupings of motor neurons in a low dimensional space. These groups did not necessarily overlap with the muscle anatomy. We provide a new neural framework for a deeper understanding of movement control in health and disease.
Evolutionarily conserved clusters of colon with lung cancer susceptibility loci, linked with most DUSP phosphatase genes, may help to dissect mechanisms of cancer susceptibility
Authors: Quan Lei , Lynch Miranda L. , Demant Peter
Published: October 2021

We show evolutionarily conserved pairwise genetic linkage and clustering of majority of colon and lung cancer susceptibility QTLs in mice, rats and humans. The patterns of susceptibility or resistance to these two cancers in recombinant congenic mouse strains were concordant and the responsible susceptibility loci closely linked, in spite of completely different carcinogens and protocols used for induction of the two tumors. Most DUSP (Dual specificity phosphatase) genes are linked to these clusters. These data suggest that an important part of colon and lung cancer susceptibility is controlled by related and evolutionarily conserved processes.
The Development of Sleep/Wake Disruption and Cataplexy as Hypocretin/Orexin Neurons Degenerate in Male vs. Female Orexin/tTA; TetO-DTA Mice
Authors: Sun Yu , Tisdale Ryan , Park Sunmee , Ma Shun-Chieh , Heu Jasmine , Haire Meghan , Allocca Giancarlo , Yamanaka Akihiro , Morairty Stephen R. , Kilduff Thomas S.
Published: October 2021

Narcolepsy Type 1 (NT1), a sleep disorder with similar prevalence in both sexes, is thought to be due to loss of the hypocretin/orexin (Hcrt) neurons. Several transgenic strains have been created to model this disorder and are increasingly being used for preclinical drug development and basic science studies, yet most studies have solely used male mice. We compared the development of narcoleptic symptomatology in male vs. female orexin-tTA; TetO-DTA mice, a model in which Hcrt neuron degeneration can be initiated by removal of doxycycline (DOX) from the diet. EEG, EMG, body temperature, gross motor activity and video recordings were conducted for 24-h at baseline and 1, 2, 4 and 6 weeks after DOX removal. Female DTA mice exhibited cataplexy, the pathognomonic symptom of NT1, by Week 1 in the DOX(-) condition but cataplexy was not consistently present in males until Week 2. By Week 2, both sexes showed an impaired ability to sustain long wake bouts during the active period, the murine equivalent of excessive daytime sleepiness in NT1. Body temperature appeared to be regulated at lower levels in both sexes as the Hcrt neurons degenerated. During degeneration, both sexes also exhibited the “Delta State”, characterized by sudden cessation of activity, high delta activity in the EEG, maintenance of muscle tone and posture, and the absence of phasic EMG activity. Since the phenotypes of the two sexes were indistinguishable by Week 6, we conclude that both sexes can be safely combined in future studies to reduce cost and animal use.

Statement of Significance

Although narcolepsy is a disorder that affects both men and women with similar frequency, most basic research and preclinical development studies of sleep have utilized male experimental subjects. The identification of the hypocretin/orexin (Hcrt) neuron loss as the likely cause of human narcolepsy has led to the development of transgenic mouse strains that model this disorder. Here, we compare the emergence of narcoleptic symptoms in male vs. female bigenic orexin-tTA; TetO DTA mice, a state-of-the-art narcolepsy model in which degeneration of the Hcrt neurons can be triggered by dietary manipulation. We find that female mice develop the narcoleptic phenotype more rapidly than males but that both sexes are equally symptomatic by the end of the degeneration period.
Beyond Spike: Identification of nine highly prevalent SARS-CoV-2-specific CD8 T-cell epitopes in a large Norwegian cohort
Authors: Meyer Saskia , Blaas Isaac , Bollineni Ravi Chand , Delic-Sarac Marina , Tran Trung T. , Knetter Cathrine , Dai Ke-Zheng , Støve Madssen Torfinn , Vaage John T. , Gustavsen Alice , Yang Weiwen , Nissen-Meyer Lise Sofie Haug , Douvlataniotis Karolos , Laos Maarja , Nielsen Morten Milek , Thiede Bernd , Søraas Arne , Lund-Johansen Fridtjof , Rustad Even H. , Olweus Johanna
Published: October 2021

T-cell epitopes with broad population coverage may form the basis for a new generation of SARS-CoV-2 vaccines. However, published studies on immunoprevalence are limited by small test cohorts, low frequencies of antigen-specific cells and lack of data correlating eluted HLA ligands with T-cell responsiveness. As the protective role of pre-existing cross-reactivity to homologous peptides is unclear, we aimed to identify SARS-CoV-2-specific minimal epitopes recognized by CD8 T-cells among 48 peptides eluted from prevalent HLA alleles, and an additional 84 predicted binders, in a large cohort of convalescents (n=83) and pre-pandemic control samples (n=19). We identified nine conserved SARS-CoV-2-specific epitopes restricted by four of the most prevalent HLA class I alleles in the Norwegian study cohort, to which responding CD8 T cells were detected in 70-100% of convalescents expressing the relevant HLA allele. Only two of these were derived from the Spike protein, included in current vaccines. We found a strong correlation between immunoprevalence and immunodominance. Thus, the CD8 T-cell response to SARS-CoV-2 is more focused than previously believed. Using a new algorithm, we predict that a vaccine including these epitopes could induce a T-cell response in 83% of Caucasians.
A Rapid Bead-Based Assay For Screening Of SARS-CoV-2 Neutralising Antibodies
Authors: Lupitha Santhik Subhasingh , Darvin Pramod , Chandrasekharan Aneesh , Varadarajan Shanakara Narayanan , Divakaran Soumya Jaya , Easwaran Sreekumar , Nelson-Sathi Shijulal , Umasankar Perunthottathu K , Jones Sara , Joseph Iype , Pillai M. Radhakrishna , Santhoshkumar TR
Published: October 2021

Quantitative determination of neutralizing antibodies against Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) is paramount in immunodiagnostics, vaccine efficacy testing, and immune response profiling among the vaccinated population. Cost-effective, rapid, easy-to-perform assays are essential to support the vaccine development process and immunosurveillance studies. Here, we describe a bead-based screening assay for S1-neutralization using recombinant fluorescent proteins of hACE2 and SARS-CoV2-S1, immobilized on solid beads employing nanobodies /metal-affinity tags. Nanobody-mediated capture of SARS-CoV-2 - Spike (S1) on agarose beads served as the trap for soluble recombinant ACE2-GFPSpark, inhibited by neutralizing antibody. The first approach demonstrates single-color fluorescent imaging of ACE2–GFPspark binding to His-tagged S1-Receptor Binding Domain (RBD-His) immobilized beads. The second approach is dual-color imaging of soluble ACE2-GFPSpark to S1-Orange Fluorescent Protein (S1-OFPSpark) beads. Both methods showed a good correlation with the gold standard pseudovirion assay and can be adapted to any fluorescent platforms for screening. Life-time imaging of the ACE2-GFPSpark confirmed the interaction of ACE2 and S1-OFPSpark on beads. The self-renewable source of secreted recombinant proteins from stable cells and its direct use without necessitating purification renders the platform a cost-effective and rapid one than the popular pseudovirion assay and live virus-based assays. Any laboratory with minimum expertise can rapidly perform this bead assay for neutralizing antibody detection using stable engineered cells.
Constitutive nuclear accumulation of endogenous alpha-synuclein in mice causes motor dysfunction and cortical atrophy, independent of protein aggregation
Authors: Geertsma Haley M. , Suk Terry R. , Ricke Konrad M. , Horsthuis Kyra , Parmasad Jean-Louis A. , Fisk Zoe , Callaghan Steve M. , Rousseaux Maxime W.C.
Published: October 2021

Background

A growing body of evidence suggests that nuclear alpha-synuclein (αSyn) plays a role in the pathogenesis of Parkinson’s disease (PD). However, this question has been difficult to address as controlling the localization of αSyn in experimental systems often requires protein overexpression, which affects its aggregation propensity.

Methods

We engineered SncaNLS mice which localize endogenous αSyn to the nucleus. We characterized these mice on a behavioral, histological, and biochemical level to determine whether the increase of nuclear αSyn is sufficient to elicit PD-like phenotypes.

Results

SncaNLS mice exhibit age-dependent motor deficits and altered gastrointestinal function. We found that these phenotypes were not linked to αSyn aggregation or phosphorylation. Through histological analyses, we observed motor cortex atrophy in the absence of midbrain dopaminergic neurodegeneration. We sampled cortical proteomes of SncaNLS mice and controls to determine the molecular underpinnings of these pathologies. Interestingly, we found several dysregulated proteins involved in dopaminergic signaling, namely Darpp-32, which we further confirmed was decreased in cortical samples of the SncaNLS mice compared to controls via immunoblotting.

Conclusions

These results suggest that chronic endogenous nuclear αSyn can elicit toxic phenotypes in mice, independent of its aggregation. This model raises key questions related to the mechanism of αSyn toxicity in PD and provides a new model to study an underappreciated aspect of PD pathogenesis.
Protein degradation analysis by affinity microfluidics
Authors: Brio Lev , Wasserman Danit , Michaely-Barbiro Efrat , Gerber Doron , Tzur Amit
Published: October 2021

Protein degradation mediated by the ubiquitin-proteasome pathway regulates signaling events in all eukaryotic cells, with implications in pathological conditions such as cancer and neurodegenerative diseases. Detection of protein degradation is an elementary need in basic and translational research. In vitro degradation assays, in particular, have been instrumental in the understanding of how cell proliferation and other fundamental cellular processes are regulated. These assays are direct, quantitative and highly informative but also laborious, typically relying on low-throughput polyacrylamide gel-electrophoresis followed by autoradiography or immunoblotting. We present protein degradation on chip (pDOC), a MITOMI-based integrated microfluidic device for discovery and analysis of ubiquitin-mediated proteolysis. The platform accommodates microchambers on which protein degradation is assayed quickly and simultaneously in physiologically relevant environments, using minute amount of reagents. Essentially, pDOC provides a multiplexed, sensitive and colorimetric alternative to the conventional degradation assays, with relevance to biomedical and translational research.
Calcium-independent but voltage-dependent secretion (CiVDS) mediates synaptic transmission in a mammalian central synapse
Authors: Wang Yuan , Huang Rong , Chai Zuying , Wang Changhe , Du Xingyu , Hang Yuqi , Xu Yongxin , Li Jie , Jiang Xiaohan , Wu Xi , Qiao Zhongjun , Li Yinglin , Liu Bing , Zhang Xianying , Cao Peng , Zhu Feipeng , Zhou Zhuan
Published: October 2021

A central principle of synaptic transmission is that action potential-induced presynaptic neurotransmitter release occurs exclusively via Ca2+-dependent secretion (CDS). The discovery and mechanistic investigations of Ca2+-independent but voltage-dependent secretion (CiVDS) have demonstrated that the action potential per se is sufficient to trigger neurotransmission in the somata of primary sensory and sympathetic neurons in mammals. One key question remains, however, whether CiVDS contributes to central synaptic transmission. Here we report, in the central transmission from presynaptic (dorsal root ganglion) to postsynaptic (spinal dorsal horn) neurons, (1) excitatory postsynaptic currents (EPSCs) are mediated by glutamate transmission through both CiVDS (up to 87%) and CDS; (2) CiVDS-EPSCs are independent of extracellular and intracellular Ca2+; (3) CiVDS is >100 times faster than CDS in vesicle recycling with much less short-term depression; (4) the fusion machinery of CiVDS includes Cav2.2 (voltage sensor) and SNARE (fusion pore). Together, an essential component of activity-induced EPSCs is mediated by CiVDS in a central synapse.
A linear programming-based strategy to save pipette tips in automated DNA assembly
Authors: Sechkar Kirill , Tuza Zoltan A. , Stan Guy-Bart
Published: October 2021

Laboratory automation and mathematical optimisation are key to improving the efficiency of synthetic biology research. While there are algorithms optimising the construct designs and synthesis strategies for DNA assembly, the optimisation of how DNA assembly reaction mixes are prepared remains largely unexplored. Here, we focus on reducing the pipette tip consumption of a liquid-handling robot as it delivers DNA parts across a multi-well plate where several constructs are being assembled in parallel. We propose a linear programming formulation of this problem based on the capacitated vehicle routing problem, along with an algorithm which applies a linear programming solver to our formulation, hence providing a strategy to prepare a given set of DNA assembly mixes using fewer pipette tips. The algorithm performed well in randomly generated and real-life scenarios concerning several modular DNA assembly standards, proving capable of reducing the pipette tip consumption by up to 61% in large-scale cases. Combining automatic process optimisation and robotic liquid-handling, our strategy promises to greatly improve the efficiency of DNA assembly, either used alone or in combination with other algorithmic methods.
Respiratory and diarrhoeal pathogens in Malawian children hospitalized with diarrhoea and association with short-term growth
Authors: Chisala Mphatso , Nyangulu Wongani , Nyirenda James , Tam Pui-Ying Iroh
Published: October 2021

Background

Pneumonia and diarrhoea are the leading causes of childhood mortality and morbidity worldwide. Recurrence of these common infections are one of the immediate causes of malnutrition, which puts children at risk of further infection. While studies have focused on how gut microbiota is broadly protective against respiratory infection, there has been less attention paid to the reverse relationship, of respiratory microbiota and pathogens influencing the gut, and subsequent association with growth.

Methods

In this sub-study of a prospective cohort study, 27 children (2-24 months) who tested positive forCryptosporidiumwere followed up over 8 weeks. Respiratory and stool pathogens were detected using quantitative molecular methods. Nutritional outcomes were assessed as length-for-age (LAZ), weight-for-length (WLZ) and weight-for-age (WAZ) z-scores. Changes over the study period were compared using repeated analysis of variance and mixed effects model analysis.

Results

In this period,104 sputum and stool samples were collected. All stool samples had at least one pathogen detected, with an average of 5.1 (SD 2.1) stool pathogens, compared to 84% of the sputum samples with an average 3.5 (SD1.8). DiarrhoeagenicE. coliwere the most common stool pathogens (92%), followed byCryptosporidium(52%) andCampylobacterpan (39%). In sputum,S.pneumoniaewas most prevalent (84%), seconded by Rhinovirus (56%) andM. catarrhalis(50%). There was a significant change in WAZ over the follow-up period. Children who had ≥3 GI pathogens had significantly a lower LAZ mean score at enrollment (−1.8 (SD 1.4)) and across the follow-up period. No relationship between respiratory pathogens and short-term growth was observed. Out of 49 sputum samples that had ≥3 pathogens, 42 (85%) simultaneously had ≥3 GI pathogens.

Conclusion

Among young children hospitalized with diarrhoea, multiple gut and respiratory pathogens were prevalent over an 8-week follow-up period. The presence of more GI, but not respiratory, pathogens was significantly associated with reduced short-term growth.

Author summary

The gut-lung axis interact in both health and illness, and we aimed to see whether presence of pathogens in the GI and/or respiratory tract is associated with short-term growth. In 104 sputum and stool samples, we observed lower mean short-term growth in participants with higher number of GI, but not respiratory, pathogens.
In vivoimaging of the GnRH pulse generator reveals a temporal order of neuronal activation and synchronization during each pulse
Authors: Moore Aleisha M. , Coolen Lique M. , Lehman Michael N.
Published: October 2021

A hypothalamic pulse generator located in the arcuate nucleus controls episodic release of gonadotropin-releasing hormone (GnRH) and luteinizing hormone (LH) and is essential for reproduction. Recent evidence suggests this generator is comprised of arcuate “KNDy” cells, the abbreviation based on co-expression of kisspeptin, neurokinin B, and dynorphin. However, direct visual evidence of KNDy neuron activity at a single-cell level during a pulse is lacking. Here, we usein vivocalcium imaging in freely moving female mice to show that individual KNDy neurons are synchronously activated in an episodic manner, and these synchronized episodes always precede LH pulses. Furthermore, synchronization among KNDy cells occurs in a temporal order, with some subsets of KNDy cells serving as “leaders” and others as “followers” during each synchronized episode. These results reveal an unsuspected temporal organization of activation and synchronization within the GnRH pulse generator, suggesting that different subsets of KNDy neurons are activated at pulse onset than afterward during maintenance and eventual termination of each pulse. Further studies to distinguish KNDy “leader” from “follower” cells is likely to have important clinical significance, since regulation of pulsatile GnRH secretion is essential for normal reproduction and disrupted in pathological conditions such as polycystic ovary syndrome and hypothalamic amenorrhea.
Injury-induced inflammatory signaling and hematopoiesis in Drosophila
Authors: Evans Cory J. , Liu Ting , Girard Juliet R. , Banerjee Utpal
Published: October 2021

Inflammatory response in Drosophila to sterile (axenic) injury in embryos and adults has received some attention in recent years, and most concentrate on the events at the injury site. Here we focus on the effect sterile injury has on the hematopoietic organ, the lymph gland, and the circulating blood cells in the larva, the developmental stage at which major events of hematopoiesis are evident. In mammals, injury activates Toll-like receptor (TLR)/NFκB signaling in macrophages, which then express and secrete secondary, pro-inflammatory cytokines. In Drosophila larvae, distal puncture injury of the body wall epidermis causes a rapid activation of Toll and Jun kinase (JNK) signaling throughout the hematopoietic system and the differentiation of a unique blood cell type, the lamellocyte. Furthermore, we find that Toll and JNK signaling are coupled in their activation. Secondary to this Toll/JNK response, a cytokine, Upd3, is induced as a Toll pathway transcriptional target, which then promotes JAK/STAT signaling within the blood cells. Toll and JAK/STAT signaling are required for the emergence of the injury-induced lamellocytes. This is akin to the derivation of specialized macrophages in mammalian systems. Upstream, at the injury site, a Duox- and peroxide-dependent signal causes the activation of the proteases Grass and SPE needed for the activation of the Toll-ligand Spz, but microbial sensors or the proteases most closely associated with them during septic injury are not involved in the axenic inflammatory response.
Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry
Authors: Park Young-Jun , De Marco Anna , Starr Tyler N , Liu Zhuoming , Pinto Dora , Walls Alexandra C. , Zatta Fabrizia , Zepeda Samantha K. , Bowen John , Sprouse Kaitlin S , Joshi Anshu , Giurdanella Martina , Guarino Barbara , Noack Julia , Abdelnabi Rana , Foo Shi-Yan Caroline , Lempp Florian A. , Benigni Fabio , Snell Gyorgy , Neyts Johan , Whelan Sean PJ , Virgin Herbert W. , Bloom Jesse D , Corti Davide , Pizzuto Matteo Samuele , Veesler David
Published: October 2021

Understanding broadly neutralizing sarbecovirus antibody responses is key to developing countermeasures effective against SARS-CoV-2 variants and future spillovers of other sarbecoviruses. Here we describe the isolation and characterization of a human monoclonal antibody, designated S2K146, broadly neutralizing viruses belonging to all three sarbecovirus clades known to utilize ACE2 as entry receptor and protecting therapeutically against SARS-CoV-2 beta challenge in hamsters. Structural and functional studies show that most of the S2K146 epitope residues are shared with the ACE2 binding site and that the antibody inhibits receptor attachment competitively. Viral passaging experiments underscore an unusually high barrier for emergence of escape mutants making it an ideal candidate for clinical development. These findings unveil a key site of vulnerability for the development of a next generation of vaccines eliciting broad sarbecovirus immunity.
Novelty and uncertainty interact to regulate the balance between exploration and exploitation in the human brain
Authors: Cockburn Jeffrey , Man Vincent , Cunningham William , O’Doherty John P.
Published: October 2021

Recent evidence suggests that both novelty and uncertainty act as potent features guiding exploration. However, these variables are often conflated with each other experimentally, and an understanding of how these attributes interact to regulate the balance between exploration and exploitation has proved elusive. Using a novel task designed to decouple stimulus novelty and estimation uncertainty, we identify separable behavioral and neural mechanisms by which exploration is colored. We show that uncertainty was avoided except when the information gained through exploration could be reliably exploited in the future. In contrast, and contrary to existing theory, novel options grew increasingly attractive relative to familiar counterparts irrespective of the opportunity to leverage their consequences and despite the uncertainty inherent to novel options. These findings led us to develop a formal computational framework in which uncertainty directed choice adapts to the prospective utility of exploration, while novel stimuli persistently draw favor as a result of inflated reward expectations biasing an exploitative strategy. Crucially, novelty is proposed to actively modulate uncertainty processing, effectively blunting the influence of uncertainty in shaping the subjective utility ascribed to novel stimuli. Both behavioral data and fMRI activity sampled from the ventromedial prefrontal cortex, frontopolar cortex and ventral striatum validate this model, thereby establishing a computational account that can not only explain behavior but also shed light on the functional contribution of these key brain regions to the exploration/exploitation trade-off. Our results point to multiple strategies and neural substrates charged with balancing the explore/exploit dilemma, with each targeting distinct aspects of the decision problem to foster a manageable decomposition of an otherwise intractable task.
Respiratory syncytial virus matrix protein assembles as a lattice with local and extended order that coordinates the position of the fusion glycoprotein
Authors: Sibert Bryan S. , Kim Joseph Y. , Yang Jie E. , Ke Zunlong , Stobart Christopher C. , Moore Martin M. , Wright Elizabeth R.
Published: October 2021

Respiratory syncytial virus (RSV) is a significant cause of respiratory illness in young children and adults worldwide. There is currently no vaccine or targeted antiviral for RSV. RSV is an enveloped, filamentous, negative-strand RNA virus. Individual virions vary in both diameter and length, with an average diameter of ∼130 nm and ranging from ∼500 nm to over 10 μm in length. The RSV matrix (M) protein is peripherally associated with the interior of the viral membrane. Though the general arrangement of structural proteins within the virion is known, the molecular organization of M and other structural proteins was previously unknown. Here, using whole-cell cryo-electron tomography and sub-tomogram averaging, we show that M is arranged in a packed helical-like lattice of M-dimers ordered at an angle of ∼47° to the viral long axis. Sub-tomogram averages including F and M indicate that the position of F on the viral surface is correlated with the underlying M lattice. Finally, we report that RSV F is frequently observed as pairs, with the F trimers oriented in an anti-parallel conformation to support potential interaction between trimers. These results provide insight into RSV assembly and virion organization and may aid in the identification and development of RSV vaccines and anti-viral targets.
The cyanotoxin 2,4-DAB enhances mortality and causes behavioral and molecular dysfunctions associated with neurodegeneration in larval zebrafish
Authors: Martin Rubia M. , Bereman Michael S. , Marsden Kurt C.
Published: October 2021

Exposure to cyanotoxins has been linked to neurodegenerative diseases, including amyotrophic lateral sclerosis, Alzheimer’s, and Parkinson’s disease. While the cyanotoxin β-methylamino-L-alanine (BMAA) has received much attention, cyanobacteria produce many cyanotoxic compounds, several of which have been detected in nature alongside BMAA including 2,4-diaminobutyric acid (2,4-DAB), and N-(2-aminoethyl)glycine (AEG). Thus, the question of whether DAB and AEG also cause neurotoxic effectsin vivois of great interest, as is the question of whether they interact to enhance toxicity. Here, we evaluate the toxic and neurotoxic effects of these cyanotoxins alone or in combination by measuring zebrafish larval viability and behavior after exposure. 2,4-DAB was the most potent cyanotoxin as it decreased larval viability by approximately 50% at 6 days post fertilization, while BMAA and AEG decreased viability by just 16% and 8%, respectively. Although we only observed minor neurotoxic effects on spontaneous locomotion, BMAA and AEG enhanced acoustic startle sensitivity, and they interacted in an additive manner to exert their effects. 2,4-DAB, however, only modulated the startle kinematics, an indication of motor dysfunction. To investigate the mechanisms of 2,4-DAB’s effects, we analyzed the protein profile of larval zebrafish exposed to 500μM 2,4-DAB at two time points and identified molecular signatures consistent with neurodegeneration, including disruption of metabolic pathways and downregulation of the ALS-associated genes SOD1 and UBQLN4. Together, our data demonstrate that BMAA and its isomers AEG and 2,4-DAB cause neurotoxic effectsin vivo, with 2,4-DAB as the most potent of the three in the zebrafish model.
Rilmenidine mimics caloric restriction via the nischarin I1-imidazoline receptor to extend lifespan inC. elegans
Authors: Bennett Dominic F. , Goyala Anita , Statzer Cyril , Beckett Charles W. , Tyshkovskiy Alexander , Gladyshev Vadim N. , Ewald Collin Y. , de Magalhães João Pedro
Published: October 2021

Caloric restriction increases lifespan across species and has health benefits in humans. Because complying with a low-calorie diet is challenging, here we investigated pharmacological interventions mimicking the benefits of caloric restriction. Searching for compounds that elicit a similar gene expression signature to caloric restriction, we identified rilmenidine, an I1-imidazoline receptor agonist and prescription medication for the treatment of hypertension. We then show that treatingC. eleganswith rilmenidine at young and older ages increases lifespan. We also demonstrate that the stress-resilience, healthspan, and lifespan benefits upon rilmenidine treatment in worms are mediated by the I1-imidazoline receptornish-1, implicating this receptor as a potential longevity target. Furthermore, we show that rilmenidine treatment increased ERK phosphorylation via NISH-1. Consistent with the shared caloric-restriction-mimicking gene signature, supplementing rilmenidine to caloric restrictedC. elegans, genetic reduction of TORC1 function, or rapamycin treatment did not further increase lifespan. The rilmenidine-induced longevity required the transcription factors FOXO/DAF-16 and NRF1,2,3/SKN-1, both important for caloric restriction-mediated longevity. Furthermore, we find that autophagy, but not AMPK signaling, was needed for rilmenidine-induced longevity. Lastly, we find that treating mice with rilmenidine showed transcriptional changes in liver and kidney similar to caloric restriction. Overall, our findings reveal rilmenidine as a caloric restriction mimetic and as a novel geroprotective compound.
Conjugation-based genome engineering in Deinococcus radiodurans
Authors: Brumwell Stephanie L. , Van Belois Katherine D. , Giguere Daniel J. , Edgell David R. , Karas Bogumil J.
Published: October 2021

D. radiodurans has become an attractive microbial platform for the study of extremophile biology and industrial bioproduction. To improve the genomic manipulation and tractability of this species, the development of tools for whole genome engineering and design is necessary. Here, we report the development of a simple and robust conjugation-based transformation system from E. coli to D. radiodurans allowing for the introduction of stable, replicating plasmids expressing antibiotic resistance markers. Using this method with nonreplicating plasmids, we developed a protocol for creating sequential gene deletions in D. radiodurans by targeting re-striction-modification system genes. Importantly, we demonstrated a conjugation-based method for cloning the large (178 kb), high G+C content MP1 megaplasmid from D. radiodurans in E. coli. The conjugation-based tools described here will facilitate the development of D. radiodurans strains with synthetic genomes for biological studies and industrial applications.

Abstract Figure
Gasotransmitter H2S accelerates seed germination via activating AOX mediated cyanide-resistant respiration pathway
Authors: Fang Huihui , Liu Ruihan , Yu Zhenyuan , Wu Gang , Pei Yanxi
Published: October 2021

Hydrogen sulfide (H2S) has been witnessed as a crucial gasotransmitter involving in various physiological processes in plants. H2S signaling has been reported to involve in regulating seed germination, but the underlying mechanism remains poorly understood. Here, we found that endogenous H2S production was activated in germinating Arabidopsis seeds, correlating with upregulated both the transcription and the activity of enzymes (LCD and DES1) responsible for H2S production. Moreover, NaHS (the H2S donor) fumigation significantly accelerated seed germination, while H2S-generation defective (lcd/des1) seeds exhibited decreased germination speed. Further results indicated that the alternative oxidase (AOX), a cyanide-insensitive terminal oxidase, can be stimulated by imbibition, and the expression of AOX genes was provoked lag behind H2S production during germination. Additionally, exogenous H2S fumigation significantly reinforced imbibition induced enhancement of AOX1A expression, and mediated post-translational modification to keep AOX in its reduced and active state, which mainly involved H2S induced increase of the GSH/GSSG ratio and the cell reducing power. Consequently, H2S signaling acts as a trigger to induce AOX mediated cyanide-resistant respiration to accelerate seed germination. Our study correlates H2S signaling to cyanide metabolism, which also participates in endogenous H2S generation, providing evidence for more extensive studies of H2S signaling.

Highlight

Gasotransmitter H2S provokes AOX mediated cyanide-resistant respiration, mainly through both long-term (up-regulating AOX1A expression) and short-term (inducing post-translational activation of AOX) regulatory modes, to accelerate seed germination.
Inhibiting ACSL1 related ferroptosis restrains MHV-A59 infection
Authors: Xia Huawei , Zhang Zeming , You Fuping
Published: October 2021

Murine hepatitis virus strain A59 (MHV-A59) belongs to the β -coronavirus and is considered as a representative model for studying coronavirus infection. MHV-A59 was shown to induce pyroptosis, apoptosis and necroptosis of infected cells, especially the murine macrophages. However, whether ferroptosis, a recently identified form of lytic cell death, was involved in the pathogenicity of MHV-A59, is unknown. Here, we demonstrate inhibiting ferroptosis suppresses MHV-A59 infection. MHV-A59 infection upregulates the expression of Acsl1, a novel ferroptosis inducer. MHV-A59 upregulates Acsl1 expression depending on the NF-kB activation, which is TLR4-independent. Ferroptosis inhibitor inhibits viral propagation, inflammatory cytokines release and MHV-A59 infection induced cell syncytia formation. ACSL1 inhibitor Triacsin C suppresses MHV-A59 infection induced syncytia formation and viral propagation. In vivo administration of liproxstatin-1 ameliorates lung inflammation and tissue injuries caused by MHV-A59 infection. Collectively, these results indicate that ferroptosis inhibition protects hosts from MHV-A59 infection. Targeting ferroptosis may serves as a potential treatment approach for dealing with hyper-inflammation induced by coronavirus infection.
Local and global crosstalk among heterochromatin marks drives epigenome patterning in Arabidopsis
Authors: To Taiko Kim , Yamasaki Chikae , Oda Shoko , Tominaga Sayaka , Kobayashi Akie , Tarutani Yoshiaki , Kakutani Tetsuji
Published: October 2021

Transposable elements (TEs) are robustly silenced by targeting of multiple epigenetic marks, but dynamics of crosstalk among these marks remains enigmatic. In Arabidopsis, TEs are silenced by cytosine methylation in both CpG and non-CpG contexts (mCG and mCH) and histone H3 lysine 9 methylation (H3K9me). While mCH and H3K9me are mutually dependent for their maintenance, mCG and mCH/H3K9me are independently maintained. Here we show that establishment, rather than maintenance, of mCH depends on mCG, accounting for the synergistic colocalization of these silent marks in TEs. When mCG is lost, establishment of mCH is abolished in TEs. mCG also guides mCH in active genes, although genic mCH/H3K9me is removed there. Unexpectedly, the targeting efficiency of mCH depends on relative, rather than absolute, levels of mCG, suggesting underlying global negative controls. We propose that the local positive feedback in heterochromatin dynamics, together with global negative feedback, drive robust and balanced epigenome patterning.
A more complex basal complex: novel components mapped to theToxoplasma gondiicytokinesis machinery portray an expanded hierarchy of its assembly and function
Authors: Engelberg Klemens , Bechtel Tyler , Michaud Cynthia , Weerapana Eranthie , Gubbels Marc-Jan
Published: October 2021

The basal complex (BC) ofToxoplasma gondiihas an essential role in cell division but details on the mechanism are lacking. To promote insights in this process, reciprocal proximity based biotinylation was used to map the basal complex proteome. An assembled protein map was interrogated by spatiotemporal characterization of critical components as well as functionally by disrupting the expression of the components. Spatially, this revealed four proteins sub-complexes with distinct sub-structural BC localization. Temporally, several patterns were differentiated based on their first appearance and/or disappearance from the BC corresponding with different steps in BC development (initiation, expansion, constriction, maturation). We also identified a protein pre-ceding BC formation (BCC0) laid out in a 5-fold symmetry. This symmetry marks the apical annuli and site of alveolar suture formation. From here, it was determined that the apical cap is assembled in the apical direction, whereas the rest of the IMC expands in the basal direction, inspiring a new bi-directional daughter budding process. Furthermore, we discovered BCC4, an essential protein exclusively localizing to the BC during cell division. Although depletion of BCC4 did not prevent BC formation, it led to BC fragmentation at the mid-point of cell division. Based on these data, a model is presented wherein BCC4 and MORN1 stabilize each other and form a rubber band that implies an essential role for the BC in preventing the fraying of the basal end of the assembling daughter cytoskeleton scaffolds. Furthermore, one new component of the Myosin J and Centrin2 cluster was BCC1, a hypothetical protein whose depletion prevents the non-essential last step of BC constriction. Overall, the BC is a highly dynamic, multi-functional structure that is critical to the hierarchical assembly of the daughter parasites.
Regulation of Liver Regeneration by hepatocyte O-GlcNAcylation in mice
Authors: Robarts Dakota R. , McGreal Steven R. , Umbaugh David S. , Parkes Wendena S. , Kotulkar Manasi , Abernathy Sarah , Lee Norman , Jaeschke Hartmut , Gunewardena Sumedha , Whelan Stephen A. , Hanover John A. , Zachara Natasha E. , Slawson Chad , Apte Udayan
Published: October 2021

The liver has a unique capacity to regenerate after injury in a highly orchestrated and regulated manner. Here we report that O-GlcNAcylation, an intracellular post-translational modification (PTM) regulated by two enzymes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), is a critical termination signal for liver regeneration (LR) following partial hepatectomy (PHX). We studied liver regeneration after PHX on hepatocyte specific OGT and OGA knockout mice (OGT-KO and OGA-KO), which caused a significant decrease (OGT-KO) and increase (OGA-KO) in hepatic O-GlcNAcylation, respectively. OGA-KO mice had normal regeneration, but the OGT-KO mice exhibited substantial defects in termination of liver regeneration with increased liver injury, sustained cell proliferation resulting in significant hepatomegaly, hepatic dysplasia and appearance of small nodules at 28 days after PHX. This was accompanied by a sustained increase in expression of cyclins along with significant induction in pro-inflammatory and pro-fibrotic gene expression in the OGT-KO livers. RNA-Seq studies revealed inactivation of hepatocyte nuclear 4 alpha (HNF4α), the master regulator of hepatic differentiation and a known termination signal, in OGT-KO mice at 28 days after PHX, which was confirmed by both Western blot and IHC analysis. Furthermore, a significant decrease in HNFα target genes was observed in OGT-KO mice, indicating a lack of hepatocyte differentiation following decreased hepatic O-GlcNAcylation. Immunoprecipitation experiments revealed HNF4α is O-GlcNAcylated in normal differentiated hepatocytes. These studies show that O-GlcNAcylation plays a critical role in the termination of LR via regulation of HNF4α in hepatocytes.

Layman summary

O-GlcNAcylation is a protein modification that plays a critical role in various biological processes including cell proliferation, differentiation, and disease progression. These studies show that O-GlcNAcylation in hepatocytes is essential for proper liver regeneration. Without O-GlcNAcylation, hepatocytes keep on proliferating eventually forming liver tumors.
Recurrent Duplication and Diversification of Acrosomal Fertilization Proteins in Abalone
Authors: Carlisle J. A. , Glenski M. A. , Swanson W. J.
Published: October 2021

Reproductive proteins mediating fertilization commonly exhibit rapid sequence diversification driven by positive selection. This pattern has been observed among nearly all taxonomic groups, including mammals, invertebrates, and plants, and is remarkable given the essential nature of the molecular interactions mediating fertilization. Gene duplication is another iimportant mechanism that facilitates the generation of molecular novelty. Following duplication, paralogs may parse ancestral gene function (subfunctionalization) or acquire new roles (neofunctionalization). However, the contributions of duplication followed by sequence diversification to the molecular diversity of gamete recognition genes has been understudied in many models of fertilization. The marine gastropod mollusk abalone is a classic model for fertilization. Its two acrosomal proteins (lysin and sp18) are ancient gene duplicates with unique gamete recognition functions. Through detailed genomic and bioinformatic analyses we show how duplication events followed by sequence diversification has played an ongoing role in the evolution of abalone acrosomal proteins. The common ancestor of abalone had four members of its acrosomal protein family in a tandem gene array that repeatedly experienced positive selection. We find that both sp18 paralogs contain positively selected sites located in different regions of the paralogs, consistent with a subfunctionalization model where selection acted upon distinct binding interfaces in each paralog. Further, a more recent species-specific duplication of both lysin and sp18 in the European abalone H. tuberculata is described. Despite clade-specific acrosomal protein paralogs, there are no concomitant duplications of egg coat proteins in H. tuberculata, indicating that duplication of egg proteins per se is not responsible for retention of duplicated acrosomal proteins. We hypothesize that, in a manner analogous to host/pathogen evolution, sperm proteins are selected for increased diversity through extensive sequence divergence and recurrent duplication driven by conflict mechanisms.