bluuebunny/crossref_metadata_2025 huggingface dataset:
T cells expressing multiple co-inhibitory molecules in acute malaria are not exhausted but exert a suppressive function
Authors: Brandi Johannes , Lehmann Cari , Kaminski Lea-Christina , zur Wiesch Julian Schulze , Addo Marylyn , Ramharter Michael , Mackroth Maria , Jacobs Thomas , Riehn Mathias
Published: April 2021

Overwhelming activation of T cells in acute malaria is associated with severe outcomes. Thus, counter-regulation by anti-inflammatory mechanisms is indispensable for an optimal resolution of disease. UsingPlasmodium bergheiANKA (PbA) infection of C57BL/6 mice, we performed a comprehensive analysis of co-inhibitory molecules expressed on CD4+and CD8+T cells using an unbiased cluster analysis approach. We identified similar T cell clusters co-expressing several co-inhibitory molecules like programmed cell death protein 1 (PD-1) and lymphocyte activation gene 3 (LAG-3) in the CD4+and the CD8+T cell compartment. Interestingly, despite expressing co-inhibitory molecules, which are associated with T cell exhaustion in chronic settings, these T cells were more functional compared to activated T cells that were negative for co-inhibitory molecules. However, T cells expressing high levels of PD-1 and LAG-3 also conferred suppressive capacity and thus resembled type I regulatory T cells. To our knowledge, this is the first description of malaria-induced CD8+T cells with suppressive capacity. Importantly, we found an induction of T cells with a similar co-inhibitory rich phenotype inPlasmodium falciparuminfected patients. In conclusion, we demonstrate that malaria-induced T cells expressing co-inhibitory molecules are not exhausted, but acquire additional suppressive capacity, which might represent an immune regulatory pathway to prevent further activation of T cells during acute malaria.
Endothelial SIRPα signaling controls thymic progenitor homing for T cell regeneration and antitumor immunity
Authors: Ren Boyang , Xia Huan , Liao Yijun , Zhou Hang , Wang Zhongnan , Shi Yaoyao , Zhu Mingzhao
Published: April 2021

Thymic homing of hematopoietic progenitor cells (HPCs) is an essential step for the subsequent T cell development. Previously we have identified a subset of specialized thymic portal endothelial cells (TPECs), which is important for thymic HPC homing. However, the underlying molecular mechanism remains still unknown. Here we found that signal regulatory protein alpha (SIRPα) is preferentially expressed on TPECs. Disruption of CD47-SIRPα signaling in mice resulted in reduced number of thymic early T cell progenitors (ETPs) and impaired thymic HPC homing. Mechanistically, SIRPα-deficient ECs and CD47-deficient lymphocytes demonstrated impaired transendothelial migration (TEM). Specifically, SIRPα intracellular ITIM motif-initiated downstream signaling in ECs was found to be required for TEM in a SHP2- and Src-dependent manner. Furthermore, CD47-signaling from migrating cells and SIRPα intracellular signaling were found to be required for VE-cadherin endocytosis in ECs. Functionally, SIRPα signaling is required for T cell regeneration upon sub-lethal total body irradiation (SL-TBI); CD47-SIRPα signaling blockade post SL-TBI diminishes antitumor immunity. Thus, our study reveals a novel role of endothelial SIRPα signaling for thymic HPC homing for T cell regeneration and antitumor immunity.

Graphic abstract

Thymic homing of hematopoietic progenitor cells is fundamental to the T cell-based adaptive immunity, yet the molecular basis of this process is less clear. We discovered that endothelial SIRPα signaling, engaged by migrating cell derived CD47 ligand, regulates thymic homing of hematopoietic progenitor cells for T cell regeneration and antitumor immunity.

SIRPα is preferentially expressed on thymic portal endothelial cells.

Endothelial SIRPα regulates thymic homing of hematopoietic progenitor cells.

CD47-SIRPα downstream signaling induces VE-cadherin endocytosis.

CD47-SIRPα signaling blockade impairs thymic T cell regeneration and antitumor immunity.
Tire abrasion particles negatively affect plant growth even at low concentrations and alter soil biogeochemical cycling
Authors: Leifheit Eva F , Kissener Hanna L , Faltin Erik , Ryo Masahiro , Rillig Matthias C
Published: April 2021

Tire particles (TPs) are a major source of microplastic on land, and considering their chemical composition, they represent a potential hazard for the terrestrial environment. We studied the effects of TPs at environmentally relevant concentrations along a wide concentration gradient (0 – 160 mg g−1) and tested the effects on plant growth, soil pH and the key ecosystem process of litter decomposition and soil respiration. The addition of TPs negatively affected shoot and root growth already at low concentrations. Tea litter decomposition slightly increased with lower additions of TPs but decreased later on. Soil pH increased until a TP concentration of 80 mg kg-1 and leveled off afterwards. Soil respiration clearly increased with increasing concentration of added TPs. Plant growth was likely reduced with starting contamination and stopped when contamination reached a certain level in the soil. The presence of TPs altered a number of biogeochemical soil parameters that can have further effects on plant performance. Considering the quantities of yearly produced TPs, their persistence, and toxic potential, we assume that these particles will eventually have a significant impact on terrestrial ecosystems.
“Thinking out loud”: an open-access EEG-based BCI dataset for inner speech recognition
Authors: Nieto Nicolás , Peterson Victoria , Rufiner Hugo Leonardo , Kamienkoski Juan , Spies Ruben
Published: April 2021

Surface electroencephalography is a standard and noninvasive way to measure electrical brain activity. Recent advances in artificial intelligence led to significant improvements in the automatic detection of brain patterns, allowing increasingly faster, more reliable and accessible Brain-Computer Interfaces. Different paradigms have been used to enable the human-machine interaction and the last few years have broad a mark increase in the interest for interpreting and characterizing the “inner voice” phenomenon. This paradigm, called inner speech, raises the possibility of executing an order just by thinking about it, allowing a “natural” way of controlling external devices. Unfortunately, the lack of publicly available electroencephalography datasets, restricts the development of new techniques for inner speech recognition. A ten-subjects dataset acquired under this and two others related paradigms, obtained with an acquisition system of 136 channels, is presented. The main purpose of this work is to provide the scientific community with an open-access multiclass electroencephalography database of inner speech commands that could be used for better understanding of the related brain mechanisms.
Alternative splicing of pericentrin contributes to cell cycle control in cardiomyocytes
Authors: Steinfeldt Jakob , Becker Robert , Vergarajauregui Silvia , Engel Felix B.
Published: April 2021

Induction of cardiomyocyte proliferation is a promising option to regenerate the heart. Thus, it is important to elucidate mechanisms that contribute to the cell cycle arrest of mammalian cardiomyocytes. Here, we assessed the contribution of the pericentrin (Pcnt) S isoform to the cell cycle arrest in postnatal cardiomyocytes. Immunofluorescence staining of Pcnt isoforms combined with siRNA-mediated depletion indicates that Pcnt S preferentially localizes to the nuclear envelope, while the Pcnt B isoform is enriched at centrosomes. This is further supported by the localization of ectopically expressed FLAG-tagged Pcnt S and Pcnt B in postnatal cardiomyocytes. Analysis of centriole configuration upon Pcnt depletion revealed that Pcnt B but not Pcnt S is required for centriole cohesion. Importantly, ectopic expression of Pcnt S induced centriole splitting in a heterologous system, ARPE-19 cells, and was sufficient to impair DNA synthesis in C2C12 myoblasts. Moreover, Pcnt S depletion enhanced serum-induced cell cycle re-entry in postnatal cardiomyocytes. Analysis of mitosis, binucleation rate, and cell number suggests that Pcnt S depletion promotes progression of postnatal cardiomyocytes through the cell cycle resulting in cell division. Collectively, our data indicate that alternative splicing of Pcnt contributes to the establishment of cardiomyocyte cell cycle arrest shortly after birth.
Let’s Do the Time Warp Again: Non-linear time series matching as a tool for sequentially structured data in ecology
Authors: Hegg Jens C. , Kennedy Brian P.
Published: April 2021

Ecological patterns are often fundamentally chronological. However, generalization of data is necessarily accompanied by a loss of detail or resolution. Temporal data in particular contains information not only in data values but in the temporal structure, which is lost when these values are aggregated to provide point estimates. Dynamic Time Warping (DTW) is a time series comparison method that is capable of efficiently comparing series despite temporal offsets that confound other methods. The DTW method is both efficient and remarkably flexible, capable of efficiently matching not only time series but any sequentially structured dataset, which has made it a popular technique in machine learning, artificial intelligence, and big data analytical tasks. DTW is rarely used in ecology despite the ubiquity of temporally structured data. As technological advances have increased the richness of small-scale ecological data, DTW may be an attractive analysis technique because it is able to utilize the additional information contained in the temporal structure of many ecological datasets. In this study we use an example dataset of high-resolution fish movement records obtained from otolith microchemistry to compare traditional analysis techniques with DTW clustering. Our results suggest that DTW is capable of detecting subtle behavioral patterns within otolith datasets which traditional data aggregation techniques cannot. These results provide evidence that the DTW method may be useful across many of the temporal data types commonly collected in ecology, as well other sequentially ordered “pseudo time series” data such as classification of species by shape.

Keywords:classification, cluster analysis, data generalization, DTW, dynamic time warping, otolith chemistry, time series
Ageing via sexual perception is a by-product of male adaptive plasticity inDrosophila melanogaster
Authors: Corbel Quentin , Serra Manuel , García-Roa Roberto , Carazo Pau
Published: April 2021

Sensory perception of environmental cues can dramatically modulate ageing across distant taxa. For example, maleDrosophila melanogasterage faster if they perceive female cues but fail to mate (ageing via sexual perception). This finding has been a breakthrough for our understanding of the mechanisms of ageing, yet we ignore how and why such responses have evolved. Here, we usedD. melanogasterto ask whether ageing via sexual perception may be a by-product of plastic adaptive responses to female cues, and found that while long-term sexual perception leads to reproductive costs, short-term perception increases male lifetime reproductive success in a competitive environment. Simulations under a wide range of socio-sexual and demographic scenario suggest that such plasticity as a response to sexual perception might be a widespread strategy in nature. Finally, we show that sexual perception can significantly magnify sexual selection (15-27% average increase in the opportunity for selection).
Herbivory enhances leaky sex expression in the dioecious herbMercurialis annua
Authors: Villamil Nora , Li Xinji , Seddon Emily , Pannell John R.
Published: April 2021

Plant reproductive traits are widely understood to be responsive to the selective pressures exerted by pollinators, but there is also increasing evidence for an important role of antagonists such as herbivores in shaping these traits. Many dioecious species show leaky sex expression, with males and females occasionally producing flowers of the opposite sex. Here we show that leaky sex expression in both males and females of the wind-pollinated dioecious herbMercurialis annua(Euphorbiaceae) is enhanced in response to simulated herbivory, increasing the probability and the degree of leakiness in both sexes. We also found that leakiness was greater in larger females but not in larger males. We discuss hypotheses for a possible functional link between herbivory and leaky sex expression, and consider what herbivory-induced leakiness might imply for the evolutionary ecology of plant reproductive systems, especially the breakdown of dioecy and the evolution of hermaphroditism.
Nascent clathrin lattices spontaneously disassemble without sufficient adaptor proteins
Authors: Guo Si-Kao , Sodt Alexander J. , Johnson Margaret E.
Published: April 2021

Clathrin-coated structures must assemble on cell membranes to perform their primary function of receptor internalization. These structures show marked plasticity and instability, but what conditions are necessary to stabilize against disassembly have not been quantified. Recentin vitrofluorescence experiments have measured kinetics of stable clathrin assembly on membranes as controlled by key adaptor proteins like AP-2. Here, we combine this experimental data with microscopic reaction-diffusion simulations and theory to quantify mechanisms of stable vs unstable clathrin assembly on membranes. Both adaptor binding and dimensional reduction on the 2D surface are necessary to reproduce the cooperative kinetics of assembly. By applying our model to more physiologic-like conditions, where the stoichiometry and volume to area ratio are significantly lower thanin vitro, we show that the critical nucleus contains~25 clathrin, remarkably similar to sizes of abortive structures observedin vivo. Stable nucleation requires a stoichiometry of adaptor to clathrin that exceeds 1:1, meaning that AP-2 on its own has too few copies to nucleate lattices. Increasing adaptor concentration increases lattice sizes and nucleation speeds. For curved clathrin cages, we quantify both the cost of bending the membrane and the stabilization required to nucleate cages in solution. We find the energetics are comparable, suggesting that curving the lattice could offset the bending energy cost. Our model predicts how adaptor density controls stabilization of clathrin-coated structures against spontaneous disassembly, and shows remodeling and disassembly does not require ATPases, which is a critical advance towards predicting control of productive vesicle formation.

Significance Statement

Stochastic self-assembly of clathrin-coated structures on the plasma membrane is essential for transport into cells. We show here that even with abundant clathrin available, robust nucleation and growth into stable structures on membranes is not possible without sufficient adaptor proteins. Our results thus provide quantitative justification for why structures observed to formin vivocan still spontaneously disassemble over many seconds. The ATPases that drive clathrin disassembly after productive vesicle formation are therefore not necessary to control remodeling during growth. With parameterization againstin vitrokinetics of assembly on membranes, our reaction-diffusion model provides a powerful and extensible tool for establishing determinants of productive assembly in cells.
Resource Allocation in Annual Plants
Authors: McMorris David , Ledder Glenn
Published: April 2021

The fitness of an annual plant can be thought of as how much fruit is produced by the end of its growing season. Under the assumption that annual plants grow to maximize fitness, we can use techniques from optimal control theory to understand this process. We introduce a model for resource allocation in annual plants which extends classical work by Iwasa and Roughgarden to a case where both carbohydrates and mineral nutrients are allocated to shoots, roots, and fruits in annual plants. We use optimal control theory to determine the optimal resource allocation strategy for the plant throughout its growing season as well as develop a numerical scheme to implement the model in MATLAB. Our results suggest that what is optimal for an individual plant is highly dependent on initial conditions, and optimal growth has the effect of driving a wide range of initial conditions toward common configurations of biomass by the end of a growing season.
Basal forebrain parvalbumin neurons modulate vigilant attention
Authors: Schiffino Felipe L. , McNally James M. , Brown Ritchie E. , Strecker Robert E.
Published: April 2021

Attention is impaired in many neuropsychiatric disorders1and by sleep disruption, leading to decreased workplace productivity and increased risk of accidents2–4. Thus, understanding the underlying neural substrates is important for developing treatments. The basal forebrain (BF) is a brain region which degenerates in dementia5–7and is implicated in the negative effects of sleep disruption on vigilance and cognition8,9. Previous studies demonstrated that the BF controls cortical fast oscillations that underlie attention10–12and revealed the important role of cholinergic neurons13–15. However, the role of other neurochemically defined BF subtypes is unknown. Recent work has shown that one population of BF GABAergic neurons containing the calcium-binding protein parvalbumin (PV) control cortical fast oscillations and arousals from sleep16–19but their role in awake behavior is unclear. Thus, here we test the hypothesis that BF-PV neurons modulate vigilant attention in mice. A lever release version of the rodent psychomotor vigilance test (rPVT) was used to assess vigilant attention as measured by reaction time. Brief and continuous low power optogenetic excitation of BF-PV neurons (1s,473nm@5mW) that preceded the cue light signal by 0.5s improved vigilant attention as indicated by quicker reaction times. In contrast, both sleep deprivation (8h) and optogenetic inhibition of BF-PV neurons (1s,530nm@10mW) slowed reaction times. Importantly, BF-PV excitation rescued the reaction time deficits in sleep deprived mice. These findings reveal for the first time a role for BF-PV neurons in attention.

HIGHLIGHTS

Optogenetic methods tested the neural circuitry of vigilant attention in mice

Excitation of basal forebrain parvalbumin neurons quickened reaction times

Sleep deprivation or inhibition of parvalbumin neurons slowed reaction times

Excitation of parvalbumin neurons rescued deficits produced by sleep deprivation
The dynamics of subunit rotation in a eukaryotic ribosome
Authors: Freitas Frederico Campos , Fuchs Gabriele , de Oliveira Ronaldo Junio , Whitford Paul Charles
Published: April 2021

Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ~1MDa) undergoes spontaneous and reversible rotations (~ 8°). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines.
Optogenetic relaxation of actomyosin contractility uncovers mechanistic roles of cortical tension during cytokinesis
Authors: Yamamoto Kei , Miura Haruko , Ishida Motohiko , Sawai Satoshi , Kondo Yohei , Aoki Kazuhiro
Published: April 2021

Actomyosin contractility generated cooperatively by nonmuscle myosin II and actin filaments plays essential roles in a wide range of biological processes, such as cell motility, cytokinesis, and tissue morphogenesis. However, it is still unknown how actomyosin contractility generates force and maintains cellular morphology. Here, we demonstrate an optogenetic method to induce relaxation of actomyosin contractility. The system, named OptoMYPT, combines a catalytic subunit of the type I phosphatase-binding domain of MYPT1 with an optogenetic dimerizer, so that it allows light-dependent recruitment of endogenous PP1c to the plasma membrane. Blue-light illumination was sufficient to induce dephosphorylation of myosin regulatory light chains and decrease in traction force at the subcellular level. The OptoMYPT system was further employed to understand the mechanics of actomyosin-based cortical tension and contractile ring tension during cytokinesis. We found that the relaxation of cortical tension at both poles by OptoMYPT accelerated the furrow ingression rate, revealing that the cortical tension substantially antagonizes constriction of the cleavage furrow. Based on these results, the OptoMYPT system will provide new opportunities to understand cellular and tissue mechanics.
A Multiscale Model of Traumatic Brain Injury Suggests Possible Mechanisms of Post-Traumatic Psychosis
Authors: Sakthivadivel Dalton A R
Published: April 2021

Traumatic brain injury is a devastating injury to the brain that can have permanent or fatal effects, leading to life-long deficits or death. Among these effects is psychosis and schizophrenia, sometimes reported in the population of TBI sufferers. Here we evaluate a possible mechanism of post-traumatic psychosis, shedding light on the anomalous nature of psychosis as over-activity and brain injury as destruction. Using a multiscale model of the brain to relate molecular pathology to connectomic and macroscopic features of the brain, we identify cell lysis and membrane deformation as a possible mechanism for psychosis after injury. We also evaluate the reorganisation of functional networks and cortical activation post-injury, and find the features of a simulated brain under traumatic injury correlate with recorded results on the schizophrenic functional connectome. This provides a possible mechanism for post-traumatic psychosis, as well as a proof-of-principle of advanced multiscale modelling methods in computational psychiatry and neuromedicine. It also elaborates on the relationship between structure and function in the brain, information processing, and the delicate regulation of activity in healthy brains.
Genetic diversity, evolutionary dynamics and pathogenicity of ferret badger rabies virus variants in mainland China, 2008-2018
Authors: Miao Faming , Zhao Jinghui , Li Nan , Liu Ye , Chen Teng , Mi Lijuan , Yang Jinjin , Chen Qi , Zhang Fei , Feng Jie , Li Shunfei , Zhang Shoufeng , Hu Rongliang
Published: April 2021

In contrast to dog associated human rabies cases decline year by year due to the rabies vaccination coverage rates increase in China, ferret badger (FB,Melogale moschata)–associated human rabies cases emerged in the 1990s, and are now an increasingly recognized problem in southeast China. To investigate epidemiology, temporal evolution dynamics, transmission characterization and pathogenicity of FB-associated rabies viruses (RABVs), from 2008 to 2018, we collected 3,622 FB brain samples in Jiangxi and Zhejiang Province, and detected 112 RABV isolates. Four FB-related lineages were identified by phylogenetic analysis (lineages A–D), the estimated Times to Most Recent Common Ancestor were 1941, 1990, 1937 and 1997 for lineages A–D respectively. Furthermore, although no FB-associated human rabies case has been reported there apart from Wuyuan area, FB-RABV isolates are mainly distributed in Jiangxi Province. Pathogenicity of FB-RABVs was assessed using peripheral inoculation in mice and in beagles with masseter muscles, mortality-rates ranging from 20% to 100% in mice and 0 to 20% in beagles in the groups infected with the various isolates. Screening of sera from humans with FB bites and no postexposure prophylaxis to rabies, revealed that 5 of 9 were positive for neutralizing antibodies of RABV. All the results above indicated that FB-RABV variants caused a lesser pathogenicity in mice, beagles and even humans. Vaccination in mice suggests that inactivated vaccine or recombinant subunit vaccine products can be used to control FB- associated rabies, however, oral vaccines for stray dogs and wildlife need to be developed and licensed in China urgently.

IMPORTANCE

In recent years FB-associated rabies virus has been identified as a major life-threatening pathogen in some districts in China. To understand the risk to public health and the contemporary dynamics, the present study conducted extensive investigations on FB rabies, distribution, virus isolation, phylogeny analysis, pathogenicity determination of various FB rabies virus strains, besides, serologic epidemiology survey to those whom bit by FB was also collected. The results show that the majority of FBs dwell in southeast China, like Jiangxi and Zhejiang Province, Phylogenetic analysis indicates that all isolated FB RABVs evolved from dogs, and the FB RABV can separate into 4 distinct lineages distributed relatively independent in different areas. The isolate strains differ in pathogenicity, although they have relatively lower pathogenicity compared to dog rabies virus according to our study, the need for further study to licensed oral vaccines and FB RABV pathogenesis is emphasized in order to control rabies.
Prevalence of severe adverse events in health professionals after receiving the first dose of the COVID-19 vaccination in Togo, March 2021
Authors: Konu Yao Rodion , Gbeasor-Komlanvi Fifonsi Adjidossi , Yerima Mouhoudine , Sadio Arnold , Tchankoni Martin Kouame , Zida-Compaore Wendpouire Ida Carine , Nayo-Apetsianyi Josée , Afanvi Kossivi Agbélénbko , Agoro Sibabe , Salou Mounerou , Landoh Dadja Essoya , Nyansa Atany B. , Boko Essohanam , Mijiyawa Moustafa , Ekouevi Didier Koumavi
Published: April 2021

Introduction

Covid-19 vaccines can cause adverse events (AE) that can lead to increased hesitation or fear of vaccination. This study aims at estimating the prevalence of severe adverse events (SAEs) and their associated factors among health professionals (HPs) vaccinated with COVISHIELD™ vaccine in Togo.

Methods

A cross-sectional study was conducted from March 13th to 19th, 2021 in Togo among HPs who received the first dose of vaccine. An online self-administered questionnaire was used to collect data on sociodemographic characteristics and vaccination. SAEs were defined as one resulting in hospitalization, medical consultation, or inability to work the day following the administration of the vaccine. Regression analysis were performed to assess factors associated with SAEs.

Results

A total of 1,639 HP (70.2% male) with a median age [IQR] of 32 years [27-40] participated. At least one AE was reported among 71.6% (95%CI= [69.3-73.8]). The most commonly reported AEs were pain at the injection site (91.0%), asthenia (74.3%), headache (68.7%), soreness (55.0%), and fever (47.5%). An increased libido was also reported in 3.0% of HP. Among HP who experienced AEs, 18.2% were unable to go to work the day after vaccination, 10.5% consulted a medical doctor, and 1.0% were hospitalized. The SAE prevalence was 23.8% (95%CI= [21.8-25.9]). Being <30 years (aOR=5.54; p<0.001), or 30-49 years (aOR=3.62; p<0.001) and being female (aOR=1.97; p<0.001) were associated with SAEs.

Conclusion

Despite the occurrence of SAEs, current data collected in Togo about adverse events are reassuring with COVISHIELD™ vaccine and how they could be managed.

Key points

The prevalence of severe adverse events (SAEs) after COVID-19 vaccination was high among health professionals in Togo, especially in the youths (under 30years).

Despite the occurrence of SAEs, current data collected in Togo about adverse events are reassuring with COVISHIELD(TM) vaccine and provide information about how the could be managed.
mRNA COVID-19 vaccine elicits potent adaptive immune response without the persistent inflammation seen in SARS-CoV-2 infection
Authors: Ivanova Ellie N. , Shwetar Jasmine , Devlin Joseph C. , Buus Terkild B. , Gray-Gaillard Sophie , Koide Akiko , Cornelius Amber , Samanovic Marie I. , Herrera Alberto , Mimitou Eleni P. , Zhang Chenzhen , Karmacharya Trishala , Desvignes Ludovic , Ødum Niels , Smibert Peter , Ulrich Robert J. , Mulligan Mark J. , Koide Shohei , Ruggles Kelly V. , Herati Ramin S. , Koralov Sergei B.
Published: April 2021

SARS-CoV-2 infection and vaccination elicit potent immune responses. Our study presents a comprehensive multimodal single-cell dataset of peripheral blood of patients with acute COVID-19 and of healthy volunteers before and after receiving the SARS-CoV-2 mRNA vaccine and booster. We compared host immune responses to the virus and vaccine using transcriptional profiling, coupled with B/T cell receptor repertoire reconstruction. COVID-19 patients displayed an enhanced interferon signature and cytotoxic gene upregulation, absent in vaccine recipients. These findings were validated in an independent dataset. Analysis of B and T cell repertoires revealed that, while the majority of clonal lymphocytes in COVID-19 patients were effector cells, clonal expansion was more evident among circulating memory cells in vaccine recipients. Furthermore, while clonal αβ T cell responses were observed in both COVID-19 patients and vaccine recipients, dramatic expansion of clonal γδT cells was found only in infected individuals. Our dataset enables comparative analyses of immune responses to infection versus vaccination, including clonal B and T cell responses. Integrating our data with publicly available datasets allowed us to validate our findings in larger cohorts. To our knowledge, this is the first dataset to include comprehensive profiling of longitudinal samples from healthy volunteers pre/post SARS-CoV-2 vaccine and booster.
A novel strain of lumpy skin disease virus causes clinical disease in cattle in Hong Kong
Authors: Flannery John , Shih Barbara , Haga Ismar R. , Ashby Martin , Corla Amanda , King Simon , Freimanis Graham , Polo Noemi , Tse Anne Ching-Nga , Brackman Christopher J. , Chan Jason , Pun Patrick , Ferguson Andrew D. , Law Andy , Lycett Samantha , Batten Carrie , Beard Philippa M.
Published: April 2021

Lumpy skin disease virus (LSDV) is an emerging poxviral pathogen of cattle that is currently spreading throughout Asia. The disease situation is of high importance for farmers and policy makers in Asia. In October 2020, feral cattle in Hong Kong developed multifocal cutaneous nodules consistent with lumpy skin disease (LSD). Gross and histological pathology further supported the diagnosis and samples were sent to the OIE Reference Laboratory at The Pirbright Institute for confirmatory testing. LSDV was detected using quantitative polymerase chain reaction (qPCR) and additional molecular analyses. This is the first report of LSD in Hong Kong. Whole genome sequencing (WGS) of the strain LSDV/HongKong/2020 and phylogenetic analysis were carried out in order to identify connections to previous outbreaks of LSD, and better understand the drivers of LSDV emergence. Analysis of the 90 core poxvirus genes revealed LSDV/HongKong/2020 was a novel strain most closely related to the live-attenuated Neethling vaccine strains of LSDV and more distantly related to wildtype LSDV isolates from Africa, the Middle East and Europe. Analysis of the more variable regions located towards the termini of the poxvirus genome revealed genes in LSDV/HongKong/2020 with different patterns of grouping when compared to previously published wildtype and vaccine strains of LSDV. This work reveals that the LSD outbreak in Hong Kong in 2020 was caused by a different strain of LSDV than the LSD epidemic in the Middle East and Europe in 2015-2018. The use of WGS is highly recommended when investigating LSDV disease outbreaks.
Global profiling of human blood ILC subtypes reveals that NK cells produce homeostatic cytokine amphiregulin and sheds light on HIV-1 pathogenesis
Authors: Wang Yetao , Lifshitz Lawrence , Silverstein Noah J. , Mintzer Esther , Luk Kevin , St. Louis Pam , Brehm Michael A , Wolfe Scot A. , Deeks Steven G. , Luban Jeremy
Published: April 2021

The interrelatedness of human blood innate lymphoid cell (ILC) subsets, and how they are perturbed by HIV-1, remains unclear. Transcriptional and chromatin profiling separated blood ILCs into ILC2s, ILCPs, one cluster that included CD56dimand CD56−NK cells, and CD56hiNK cells that have features of both CD56dim/–NK cells and ILCs. In contrast to mice, human NK cells expressed tissue repair protein amphiregulin (AREG), with greater production by CD56hiNK cells than by ILCs. AREG was induced by TCF7/WNT signaling, IL-2, or IL-15, but not by inflammatory cytokines, and was inhibited by TGFB1, a cytokine elevated in people living with HIV-1. NK cell knockout of the TGFB1-stimulated WNT antagonist RUNX3 increased AREG production. In people living with HIV-1, AREG+NK cell percentage correlated with numbers of ILCs and CD4+T cells, and correlated inversely with inflammatory cytokine IL-6. RNA-Seq showed increased antiviral gene expression in all ILC subsets from people who were HIV-1 viremic, and increased expression of anti-inflammatory gene MYDGF in CD56hiNK cells from elite controllers. Functionally-defective CD56−NK cells were increased in people living with HIV-1 in inverse correlation with CD56dimNK cells, ILCs, and CD4+T cells. Experiments with human PBMCsex vivoand in humanized mice revealed that CD4+T cells and their production of IL-2 prevented CD56dimtransition to CD56−NK cells by activating mTOR, and, in people living with HIV-1, plasma IL-2 correlated with CD4+T cell number but not with CD8+T cells. These studies clarify how ILC subsets are interrelated and provide insight into how HIV-1 infection disrupts NK cells, including homeostatic functions of NK cells discovered here.

Graphical Abstract
Molecular coevolution of nuclear and nucleolar localization signals inside basic domain of HIV-1 Tat
Authors: Kurnaeva Margarita A. , Zalevsky Arthur O. , Arifulin Eugene A. , Lisitsyna Olga M. , Tvorogova Anna V. , Shubina Maria Y. , Bourenkov Gleb P. , Tikhomirova Maria A. , Potashnikova Daria M. , Kachalova Anastasia I. , Musinova Yana R. , Golovin Andrey V. , Vassetzky Yegor S. , Sheval Eugene V.
Published: April 2021

During evolution, viruses had to adapt to an increasingly complex environment of eukaryotic cells. Viral proteins that need to enter the cell nucleus or associate with nucleoli possess nuclear localization signals (NLSs) and nucleolar localization signals (NoLSs) for nuclear and nucleolar accumulation, respectively. As viral proteins are relatively small, acquisition of novel sequences seems to be a more complicated task for viruses than for eukaryotes. Here, we carried out a comprehensive analysis of the basic domain (BD) of HIV-1 Tat to show how viral proteins might evolve with NLSs and NoLSs without an increase in protein size. The HIV-1 Tat BD is involved in several functions, the most important being the transactivation of viral transcription. The BD also functions as an NLS, although it is substantially longer than a typical NLS. It seems that different regions in the BD could function as NLSs due to its enrichment with positively charged amino acids. Additionally, the high positive net charge inevitably causes the BD to function as an NoLS through a charge-specific mechanism. The integration of NLSs and NoLSs into functional domains enriched with positively charged amino acids might be a mechanism that allows the condensation of different functional sequences in small protein regions and, as a result, to reduce protein size, influencing the origin and evolution of NLSs and NoLSs in viruses.
Detection of precisely edited CRISPR/Cas9 alleles through co-introduced restriction-fragment length polymorphisms
Authors: Tsai-Morris Chon-Hwa , Hertafeld Sydney , Rosario Yvonne , Iben James , Chang Eric , Yi Ling , Coon Steven L. , Kaler Stephen G. , Dale Ryan , Feldman Benjamin
Published: April 2021

CRISPR/Cas9 is a powerful tool for producing genomicinsertions anddeletions (indels) to interrogate gene function. Modified CRISPR/Cas9 protocols can produce targeted genetic changes that are more precise than indels, but founder recovery is less efficient. Focusing on producing missense mutations in zebrafish usingsingle-strandedoligodeoxynucleotide (ssODN) donor templates, we pioneered a strategy of adding synonymous changes to create novelrestriction-enzyme (RE) sites, allowing detection of rare precise edits in a modified fluorescent-PCR fragment assay. We have named this process TIARS (test forincorporation ofaddedrecognitionsites). Aided by TIARS, we induced two distinct amino-acid substitutions (T979I and P1387S) in theatp7agene among somatic tissues of CRISPR-Cas9-treated F0zebrafish. One of these F0stransmitted the allele toatp7aT979I/+F1progeny, and trans-heterozygosity of this allele against a nullatp7aallele causes hypopigmentation, consistent with more severe pigment deficits in zebrafish or humans carrying only null mutations inatp7a/ATP7A. Design of ssODNs with novel RE recognition sites is labor-intensive, so we developed anin silicotool, TIARS Designer, and performed bioinformatic validation indicating that TIARS should be generalizable to other genes and experimental systems that employ donor template DNA.
A billion years arms-race between viruses, virophages and eukaryotes
Authors: Nino Barreat Jose Gabriel , Katzourakis Aris
Published: April 2021

Bamfordviruses are arguably the most diverse group of viruses infecting eukaryotes. They include the Nucleocytoplasmic Large DNA viruses (NCLDVs), virophages, adenoviruses,Mavericksand Polinton-like viruses. Two main hypotheses for their origins have been proposed: the “nuclear-escape” and “virophage-first” hypotheses. The “nuclear-escape” hypothesis proposes an endogenous,Maverick-like ancestor which escaped from the nucleus and gave rise to adenoviruses and NCLDVs. In contrast, the “virophage-first” hypothesis proposes that NCLDVs coevolved with protovirophages;Mavericksthen evolved from virophages that became endogenous, with adenoviruses escaping from the nucleus at a later stage. Here, we test the predictions made by both models and consider alternative evolutionary scenarios. We use a data set of the four core virion proteins sampled across the diversity of the lineage, together with Bayesian and maximum-likelihood hypothesis-testing methods, and estimate rooted phylogenies. We find strong evidence that adenoviruses and NCLDVs are not sister groups, and thatMavericksand Mavirus acquired the rve-integrase independently. We also found strong support for a monophyletic group of virophages (familyLavidaviridae) and a most likely root placed between virophages and the other lineages. Our observations support alternatives to the nuclear-escape scenario and a billion years evolutionary arms-race between virophages and NCLDVs.
CRISPR/Cas9 modifiedAn. gambiaecarrying kdr mutation L1014F functionally validate its contribution in insecticide resistance and interaction with metabolic enzymes
Authors: Grigoraki Linda , Cowlishaw Ruth , Nolan Tony , Donnelly Martin , Lycett Gareth , Ranson Hilary
Published: April 2021

Insecticide resistance inAnophelesmosquitoes is a major obstacle in maintaining the momentum in reducing the malaria burden; mitigating strategies require improved understanding of the underlying mechanisms. Mutations in the target site of insecticides (the voltage gated sodium channel for the most widely used pyrethroid class) and over-expression of detoxification enzymes are commonly reported, but their relative contribution to phenotypic resistance remain poorly understood. Here we present a genome editing pipeline to introduce single nucleotide polymorphisms inAn. gambiaewhich we have used to study the effect of the classical kdr mutation L1014F (L995F based onAn. gambiaenumbering), one of the most widely distributed resistance alleles. Introduction of 1014F in an otherwise fully susceptible genetic background increased levels of resistance to all tested pyrethroids and DDT ranging from 9.9-fold for permethrin to >24-fold for DDT. The introduction of the 1014F allele was sufficient to reduce mortality of mosquitoes after exposure to deltamethrin treated bednets, even as the only resistance mechanism present. When 1014F was combined with over-expression of glutathione transferase Gste2, resistance to permethrin increased further demonstrating the critical combined effect between target site resistance and detoxification enzymesin vivo. We also show that mosquitoes carrying the 1014F allele in homozygosity showed fitness disadvantages including increased mortality at the larval stage and a reduction in fecundity and adult longevity, which can have consequences for the strength of selection that will apply to this allele in the field.

Author Summary

Escalation of pyrethroid resistance inAnophelesmosquitoes threatens to reduce the effectiveness of our most important tools in malaria control. Studying the mechanisms underlying insecticide resistance is critical to design mitigation strategies. Here, using genome modified mosquitoes, we functionally characterize the most prevalent mutation in resistant mosquitoes, showing that it confers substantial levels of resistance to all tested pyrethroids and undermines the performance of pyrethroid-treated nets. Furthermore, we show that combining this mutation with elevated levels of a detoxification enzyme further increases resistance. The pipeline we have developed provides a robust approach to quantifying the contribution of different combinations of resistance mechanisms to the overall phenotype, providing the missing link between resistance monitoring and predictions of resistance impact.
Outer membrane vesicles produced by pathogenic strains ofEscherichia coliblock autophagic flux and exacerbate inflammasome activation
Authors: David Laure , Taieb Frédéric , Pénary Marie , Bordignon Pierre-Jean , Planès Rémi , Bagayoko Salimata , Duplan-Eche Valérie , Meunier Etienne , Oswald Eric
Published: April 2021

Escherichia colistrains are responsible for a majority of human extra-intestinal infections, resulting in huge direct medical and social costs. We had previously shown that HlyF encoded by a large virulence plasmid harbored by pathogenicE. coliis not a hemolysin but a cytoplasmic enzyme leading to the overproduction of outer membrane vesicles (OMVs). Here, we show that these specific OMVs inhibit the autophagic flux by impairing the autophagosome – lysosome fusion, thus preventing the formation of acidic autophagolysosome and autophagosome clearance. Furthermore, HlyF-associated OMVs are more prone to activate the non-canonical inflammasome pathway. Since autophagy and inflammation are crucial in the host’s response to infection especially during sepsis, our findings reveal an unsuspected role of OMVs in the crosstalk between bacteria and their host, highlighting the fact that these extracellular vesicles have exacerbated pathogenic properties.
Enrichment analyses identify shared associations for 25 quantitative traits in over 600,000 individuals from seven diverse ancestries
Authors: Smith Samuel Pattillo , Shahamatdar Sahar , Cheng Wei , Zhang Selena , Paik Joseph , Graff Misa , Haiman Christopher , Matise T.C. , North Kari E , Peters Ulrike , Kenny Eimear , Gignoux Chris , Wojcik Genevieve , Crawford Lorin , Ramachandran Sohini
Published: April 2021

Since 2005, genome-wide association (GWA) datasets have been largely biased toward sampling European ancestry individuals, and recent studies have shown that GWA results estimated from self-identified European individuals are not transferable to non-European individuals due to various confounding challenges. Here, we demonstrate that enrichment analyses which aggregate SNP-level association statistics at multiple genomic scales—from genes to genomic regions and pathways—have been underutilized in the GWA era and can generate biologically interpretable hypotheses regarding the genetic basis of complex trait architecture. We illustrate examples of the robust associations generated by enrichment analyses while studying 25 continuous traits assayed in 566,786 individuals from seven diverse self-identified human ancestries in the UK Biobank and the Biobank Japan, as well as 44,348 admixed individuals from the PAGE consortium including cohorts of African-American, Hispanic and Latin American, Native Hawaiian, and American Indian/Alaska Native individuals. We identify 1,000 gene-level associations that are genome-wide significant in at least two ancestry cohorts across these 25 traits, as well as highly conserved pathway associations with triglyceride levels in European, East Asian, and Native Hawaiian cohorts.
Behavioral interactions between bacterivorous nematodes and predatory bacteria in a synthetic community
Authors: Mayrhofer Nicola , Velicer Gregory J. , Schaal Kaitlin A. , Vasse Marie
Published: April 2021

Theory and empirical studies in metazoans predict that apex predators should shape the behavior and ecology of mesopredators and prey at lower trophic levels. Despite the ecological importance of microbial communities, few studies of predatory microbes examine such behavioral responses and the multiplicity of trophic interactions. Here, we sought to assemble a three-level microbial food chain and to test for behavioral interactions between the predatory nematodeCaenorhabditis elegansand the predatory social bacteriumMyxococcus xanthuswhen cultured together with two basal prey bacteria that both predators can eat -Escherichia coliandFlavobacterium johnsoniae. We find that >90% ofC. elegansworms failed to interact withM. xanthuseven when it was the only potential prey species available, whereas most worms were attracted to pure patches ofE. coliandF. johnsoniae. In addition,M. xanthusaltered nematode predatory behavior on basal prey, repellingC. elegansfrom two-species patches that would be attractive withoutM. xanthus, an effect similar to that ofC. eleganspathogens. The nematode also influenced the behavior of the bacterial predator:M. xanthusincreased its predatory swarming rate in response toC. elegansin a manner dependent both on basal-prey identity and on worm density. Our results suggest thatM. xanthusis an unattractive prey for some soil nematodes and is actively avoided when more lucrative prey are available. Most broadly, we find that nematode and bacterial predators mutually influence one another’s predatory behavior, with likely consequences for coevolution within complex microbial food webs.