bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alkyne modified purines for assessing activation of Plasmodium vivax hypnozoites and growth of pre-erythrocytic and erythrocytic stages in Plasmodium spp
Authors: Botnar Alona , Lawrence Grant , Maher Steven P. , Vantaux Amélie , Witkowski Benoît , Shiau Justine C. , Merino Emilio F. , De Vore David , Yang Christian , Murray Cameron , Cassera Maria B. , Leahy James W. , Kyle Dennis E. 
Published: October 2021

ABSTRACTMalaria is a major global health problem which predominantly afflicts developing countries. Although many antimalarial therapies are currently available, the protozoan parasite causing this disease, Plasmodium spp., continues to evade eradication efforts. One biological phenomenon hampering eradication efforts is the parasite’s ability to arrest development, transform into a drug-insensitive form, and then resume growth post-therapy. Currently, the mechanisms by which the parasite enters arrested development, or dormancy, and later recrudesces or reactivates to continue development, are unknown and the malaria field lacks techniques to study these elusive mechanisms. Since Plasmodium spp. salvage purines for DNA synthesis, we hypothesized that alkyne-containing purine nucleosides could be used to develop a DNA synthesis marker which could be used to investigate mechanisms behind dormancy. Using copper-catalyzed click chemistry methods, we observe incorporation of alkyne modified adenosine, inosine, and hypoxanthine in actively replicating asexual blood stages of P. falciparum and incorporation of modified adenosine in actively replicating liver stage schizonts of P. vivax. Notably, these modified purines were not incorporated in dormant liver stage hypnozoites, suggesting this marker could be used as a tool to differentiate replicating and non-replicating liver forms and, more broadly, a tool for advancing our understanding Plasmodium dormancy mechanisms.
TheLegionellaLqs-LvbR regulatory network controls temperature-dependent growth onset and bacterial cell density
Authors: Hochstrasser Ramon , Hilbi Hubert 
Published: October 2021

AbstractLegionellaspecies are facultative intracellular pathogens, which can cause a life-threatening pneumonia termed Legionnaires’ disease.Legionella pneumophilaemploys theLegionellaquorum sensing (Lqs)-LvbR network to regulate virulence and motility, but its role for growth in media is ill-defined. Compared to the parentalL. pneumophilastrain JR32, a ΔlqsRmutant showed a reduced lag phase at 30°C and reached a higher cell density at 45°C, while the ΔlqsA, ΔlqsSand ΔlqsTmutants exhibited a longer lag phase and reached only a lower cell density. A ΔlvbRmutant resumed growth like the parental strain at 30°C, but exhibited a substantially reduced cell density at 45°C. Thus, LvbR is an important cell density regulator at elevated temperatures. A quantitative analysis of temperature-dependent growth characteristics of environmental and clinical strains revealed thatL. pneumophilastrains grew in AYE medium after distinct lag phases with similar rates at 30°C, reached different cell densities at the optimal growth temperature of 40°C, and no longer grew at 50°C.Legionella longbeachaereached a rather low cell density at 40°C and did not grow at and beyond 45°C. Genes encoding components of the Lqs-LvbR network were present in the genomes of the environmental and clinicalL. pneumophilaisolates, and the PlqsR, PlqsA, PlqsSand PlvbRpromoters from strain JR32 were active in these strains. Taken together, our results indicate that the Lqs-LvbR network governs the temperature-dependent growth onset and cell density of theL. pneumophilareference strain JR32, and possibly also of environmental and clinicalL. pneumophilaisolates.ImportanceEnvironmental bacteria of the genusLegionellaare the causative agents of the severe pneumonia Legionnaires’ disease, the incidence of which is worldwide on the rise.Legionella pneumophilaandLegionella longbeachaeare the clinically most relevant species. The opportunistic pathogens are inhaled through contaminated aerosols and replicate in human lung macrophages with a similar mechanism as in their natural hosts, free-living amoebae. Given their prevalence in natural and technical water systems, an efficient control ofLegionellaspp. by physical, chemical or biological means will reduce the incidence of Legionnaires’ disease. Here we report that theLegionellaquorum sensing (Lqs) system and the pleiotropic transcription factor LvbR govern the temperature-dependent growth onset and cell density of bacterial cultures. Hence, the growth ofL. pneumophilain water systems is not only determined by the temperature and nutrient availability, but also by quorum sensing, i.e., density- and signaling molecule-dependent gene regulation.
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

ABSTRACTA 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

AbstractBackgroundSeroprevalence 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.MethodsWe 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.FindingsWe 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).InterpretationThe 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.FundingThe 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

AbstractMovements 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.TeaserThe 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.
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

AbstractNarcolepsy 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 SignificanceAlthough 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

AbstractT-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

AbstractQuantitative 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

AbstractBackgroundA 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.MethodsWe 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.ResultsSncaNLS 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.ConclusionsThese 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

AbstractProtein 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

AbstractA 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.