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1.
Cell ; 184(1): 120-132.e14, 2021 01 07.
Article in English | MEDLINE | ID: mdl-33382968

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic has claimed the lives of over one million people worldwide. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a member of the Coronaviridae family of viruses that can cause respiratory infections of varying severity. The cellular host factors and pathways co-opted during SARS-CoV-2 and related coronavirus life cycles remain ill defined. To address this gap, we performed genome-scale CRISPR knockout screens during infection by SARS-CoV-2 and three seasonal coronaviruses (HCoV-OC43, HCoV-NL63, and HCoV-229E). These screens uncovered host factors and pathways with pan-coronavirus and virus-specific functional roles, including major dependency on glycosaminoglycan biosynthesis, sterol regulatory element-binding protein (SREBP) signaling, bone morphogenetic protein (BMP) signaling, and glycosylphosphatidylinositol biosynthesis, as well as a requirement for several poorly characterized proteins. We identified an absolute requirement for the VMP1, TMEM41, and TMEM64 (VTT) domain-containing protein transmembrane protein 41B (TMEM41B) for infection by SARS-CoV-2 and three seasonal coronaviruses. This human coronavirus host factor compendium represents a rich resource to develop new therapeutic strategies for acute COVID-19 and potential future coronavirus pandemics.


Subject(s)
Coronavirus Infections/genetics , Genome-Wide Association Study , SARS-CoV-2/physiology , A549 Cells , Cell Line , Clustered Regularly Interspaced Short Palindromic Repeats , Coronavirus 229E, Human/physiology , Coronavirus Infections/virology , Coronavirus NL63, Human/physiology , Coronavirus OC43, Human/physiology , Gene Knockout Techniques , HEK293 Cells , Host-Pathogen Interactions/drug effects , Humans , Membrane Proteins/metabolism , Metabolic Networks and Pathways/drug effects , Protein Interaction Mapping
2.
Cell ; 184(1): 133-148.e20, 2021 01 07.
Article in English | MEDLINE | ID: mdl-33338421

ABSTRACT

Flaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection, we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results, we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms present at nearly 20% in East Asian populations reduce flavivirus infection. Based on our mechanistic studies, we propose that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.


Subject(s)
Flavivirus Infections/genetics , Flavivirus/physiology , Membrane Proteins/metabolism , Animals , Asian People/genetics , Autophagy , COVID-19/genetics , COVID-19/metabolism , COVID-19/virology , CRISPR-Cas Systems , Cell Line , Flavivirus Infections/immunology , Flavivirus Infections/metabolism , Flavivirus Infections/virology , Gene Knockout Techniques , Genome-Wide Association Study , Host-Pathogen Interactions , Humans , Immunity, Innate , Membrane Proteins/genetics , Polymorphism, Single Nucleotide , SARS-CoV-2/physiology , Virus Replication , Yellow fever virus/physiology , Zika Virus/physiology
3.
Cell ; 172(3): 423-438.e25, 2018 01 25.
Article in English | MEDLINE | ID: mdl-29249360

ABSTRACT

Stem cells are highly resistant to viral infection compared to their differentiated progeny; however, the mechanism is mysterious. Here, we analyzed gene expression in mammalian stem cells and cells at various stages of differentiation. We find that, conserved across species, stem cells express a subset of genes previously classified as interferon (IFN) stimulated genes (ISGs) but that expression is intrinsic, as stem cells are refractory to interferon. This intrinsic ISG expression varies in a cell-type-specific manner, and many ISGs decrease upon differentiation, at which time cells become IFN responsive, allowing induction of a broad spectrum of ISGs by IFN signaling. Importantly, we show that intrinsically expressed ISGs protect stem cells against viral infection. We demonstrate the in vivo importance of intrinsic ISG expression for protecting stem cells and their differentiation potential during viral infection. These findings have intriguing implications for understanding stem cell biology and the evolution of pathogen resistance.


Subject(s)
Immunity, Innate , Pluripotent Stem Cells/immunology , Virus Diseases/immunology , Animals , Cells, Cultured , Female , HEK293 Cells , Humans , Interferons/metabolism , Male , Mice , Mice, Inbred NOD , Pluripotent Stem Cells/virology , Species Specificity
4.
Cell ; 169(4): 597-609.e11, 2017 May 04.
Article in English | MEDLINE | ID: mdl-28475892

ABSTRACT

Antibodies to Zika virus (ZIKV) can be protective. To examine the antibody response in individuals who develop high titers of anti-ZIKV antibodies, we screened cohorts in Brazil and Mexico for ZIKV envelope domain III (ZEDIII) binding and neutralization. We find that serologic reactivity to dengue 1 virus (DENV1) EDIII before ZIKV exposure is associated with increased ZIKV neutralizing titers after exposure. Antibody cloning shows that donors with high ZIKV neutralizing antibody titers have expanded clones of memory B cells that express the same immunoglobulin VH3-23/VK1-5 genes. These recurring antibodies cross-react with DENV1, but not other flaviviruses, neutralize both DENV1 and ZIKV, and protect mice against ZIKV challenge. Structural analyses reveal the mechanism of recognition of the ZEDIII lateral ridge by VH3-23/VK1-5 antibodies. Serologic testing shows that antibodies to this region correlate with serum neutralizing activity to ZIKV. Thus, high neutralizing responses to ZIKV are associated with pre-existing reactivity to DENV1 in humans.


Subject(s)
Antibodies, Neutralizing/chemistry , Antibodies, Viral/chemistry , Zika Virus Infection/immunology , Animals , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Antibodies, Viral/blood , Antibodies, Viral/immunology , B-Lymphocytes/immunology , Brazil , Female , Humans , Immunologic Memory , Leukocytes, Mononuclear/immunology , Male , Mexico , Mice , Zika Virus Infection/blood
5.
Nature ; 618(7963): 102-109, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37225985

ABSTRACT

Parasitic nematodes are a major threat to global food security, particularly as the world amasses 10 billion people amid limited arable land1-4. Most traditional nematicides have been banned owing to poor nematode selectivity, leaving farmers with inadequate means of pest control4-12. Here we use the model nematode Caenorhabditis elegans to identify a family of selective imidazothiazole nematicides, called selectivins, that undergo cytochrome-p450-mediated bioactivation in nematodes. At low parts-per-million concentrations, selectivins perform comparably well with commercial nematicides to control root infection by Meloidogyne incognita, a highly destructive plant-parasitic nematode. Tests against numerous phylogenetically diverse non-target systems demonstrate that selectivins are more nematode-selective than most marketed nematicides. Selectivins are first-in-class bioactivated nematode controls that provide efficacy and nematode selectivity.


Subject(s)
Antinematodal Agents , Tylenchoidea , Animals , Humans , Antinematodal Agents/chemistry , Antinematodal Agents/metabolism , Antinematodal Agents/pharmacology , Caenorhabditis elegans/drug effects , Caenorhabditis elegans/metabolism , Tylenchoidea/drug effects , Tylenchoidea/metabolism , Thiazoles/chemistry , Thiazoles/metabolism , Thiazoles/pharmacology , Cytochrome P-450 Enzyme System/drug effects , Plant Roots/drug effects , Plant Roots/parasitology , Plant Diseases , Species Specificity , Substrate Specificity
6.
Proc Natl Acad Sci U S A ; 120(51): e2317367120, 2023 Dec 19.
Article in English | MEDLINE | ID: mdl-38096415

ABSTRACT

Vaccination will likely be a key component of strategies to curtail or prevent future sarbecovirus pandemics and to reduce the prevalence of infection and disease by future SARS-CoV-2 variants. A "pan-sarbecovirus" vaccine, that provides maximum possible mitigation of human disease, should elicit neutralizing antibodies with maximum possible breadth. By positioning multiple different receptor binding domain (RBD) antigens in close proximity on a single immunogen, it is postulated that cross-reactive B cell receptors might be selectively engaged. Heteromultimeric vaccines could therefore elicit individual antibodies that neutralize a broad range of viral species. Here, we use model systems to investigate the ability of multimeric sarbecovirus RBD immunogens to expand cross-reactive B cells and elicit broadly reactive antibodies. Homomultimeric RBD immunogens generated higher serum neutralizing antibody titers than the equivalent monomeric immunogens, while heteromultimeric RBD immunogens generated neutralizing antibodies recognizing each RBD component. Moreover, RBD heterodimers elicited a greater fraction of cross-reactive germinal center B cells and cross-reactive RBD binding antibodies than did homodimers. However, when serum antibodies from RBD heterodimer-immunized mice were depleted using one RBD component, neutralization activity against the homologous viral pseudotype was removed, but neutralization activity against pseudotypes corresponding to the other RBD component was unaffected. Overall, simply combining divergent RBDs in a single immunogen generates largely separate sets of individual RBD-specific neutralizing serum antibodies that are mostly incapable of neutralizing viruses that diverge from the immunogen components.


Subject(s)
Antibodies, Neutralizing , Severe acute respiratory syndrome-related coronavirus , Animals , Mice , Humans , Antibodies, Viral , Neutralization Tests , Vaccination , Spike Glycoprotein, Coronavirus/chemistry
7.
Amino Acids ; 56(1): 4, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38300362

ABSTRACT

This study investigated the effect of high-intensity interval exercise on total and individual amino acid concentrations in red blood cells (RBCs) and plasma. Seven males (31 ± 13 yr) provided venous blood samples at rest, immediately and 15 min and 30 min following an 8-min high-intensity exercise bout. The exercise bout was 16 × 15 s cycle efforts at 0.4N/kg of body mass and 90 rpm, interspersed with 15 s passive recovery. Total and individual amino acid concentrations of RBC and plasma and blood cell parameters were analysed. No significant differences for total amino acid concentrations between RBC and plasma were found. Individual amino acid analyses showed significant interaction effects for alanine and α-aminoadipic acid (P < 0.05), with plasma alanine significantly increased from baseline across the recovery period (P < 0.001). Blood fraction (group) effects showed greater concentrations of glycine, serine, asparagine, aspartic acid, glutamic acid, α-aminoadipic acid and ornithine in RBC, while greater concentrations of alanine, α-aminobutyric acid, valine, leucine, isoleucine, threonine, proline, phenylalanine, glutamine, tryptophan and cystine were found in plasma (P < 0.05). Comparable levels of histidine, lysine and tyrosine were observed between blood fractions. Significant differences in the variation of total amino acids in RBC were reported with higher variance at rest compared to following exercise (P = 0.01). Haemoglobin, pack cell volume and white blood cell count significantly increased immediately following exercise (P < 0.05) but returned to baseline after 15 min recovery. These results support the notion of individualised amino acid transportation roles for RBC and plasma during exercise.


Subject(s)
Amino Acids , Erythrocytes , Male , Humans , Plasma , Alanine , Glutamic Acid
8.
J Allergy Clin Immunol ; 151(1): 147-158, 2023 01.
Article in English | MEDLINE | ID: mdl-36191689

ABSTRACT

BACKGROUND: Atopic dermatitis (AD, eczema) is driven by a combination of skin barrier defects, immune dysregulation, and extrinsic stimuli such as allergens, irritants, and microbes. The role of environmental allergens (aeroallergens) in triggering AD remains unclear. OBJECTIVE: We systematically synthesized evidence regarding the benefits and harms of allergen immunotherapy (AIT) for AD. METHODS: As part of the 2022 American Academy of Allergy, Asthma & Immunology/American College of Allergy, Asthma and Immunology Joint Task Force on Practice Parameters AD Guideline update, we searched the MEDLINE, EMBASE, CENTRAL, CINAHL, LILACS, Global Resource for Eczema Trials, and Web of Science databases from inception to December 2021 for randomized controlled trials comparing subcutaneous immunotherapy (SCIT), sublingual immunotherapy (SLIT), and/or no AIT (placebo or standard care) for guideline panel-defined patient-important outcomes: AD severity, itch, AD-related quality of life (QoL), flares, and adverse events. Raters independently screened, extracted data, and assessed risk of bias in duplicate. We synthesized intervention effects using frequentist and Bayesian random-effects models. The GRADE approach determined the quality of evidence. RESULTS: Twenty-three randomized controlled trials including 1957 adult and pediatric patients sensitized primarily to house dust mite showed that add-on SCIT and SLIT have similar relative and absolute effects and likely result in important improvements in AD severity, defined as a 50% reduction in SCORing Atopic Dermatitis (risk ratio [95% confidence interval] 1.53 [1.31-1.78]; 26% vs 40%, absolute difference 14%) and QoL, defined as an improvement in Dermatology Life Quality Index by 4 points or more (risk ratio [95% confidence interval] 1.44 [1.03-2.01]; 39% vs 56%, absolute difference 17%; both outcomes moderate certainty). Both routes of AIT increased adverse events (risk ratio [95% confidence interval] 1.61 [1.44-1.79]; 66% with SCIT vs 41% with placebo; 13% with SLIT vs 8% with placebo; high certainty). AIT's effect on sleep disturbance and eczema flares was very uncertain. Subgroup and sensitivity analyses were consistent with the main findings. CONCLUSIONS: SCIT and SLIT to aeroallergens, particularly house dust mite, can similarly and importantly improve AD severity and QoL. SCIT increases adverse effects more than SLIT. These findings support a multidisciplinary and shared decision-making approach to optimally managing AD.


Subject(s)
Asthma , Dermatitis, Atopic , Eczema , Hypersensitivity , Sublingual Immunotherapy , Adult , Animals , Humans , Child , Dermatitis, Atopic/drug therapy , Quality of Life , Bayes Theorem , Desensitization, Immunologic/adverse effects , Pyroglyphidae , Hypersensitivity/etiology , Asthma/drug therapy , Allergens/therapeutic use , Sublingual Immunotherapy/adverse effects , Dermatophagoides pteronyssinus
9.
J Allergy Clin Immunol ; 152(6): 1493-1519, 2023 12.
Article in English | MEDLINE | ID: mdl-37678572

ABSTRACT

BACKGROUND: Atopic dermatitis (AD) is a common skin condition with multiple topical treatment options, but uncertain comparative effects. OBJECTIVE: We sought to systematically synthesize the benefits and harms of AD prescription topical treatments. METHODS: For the 2023 American Academy of Allergy, Asthma & Immunology and American College of Allergy, Asthma, and Immunology Joint Task Force on Practice Parameters AD guidelines, we searched MEDLINE, EMBASE, CENTRAL, CINAHL, LILACS, ICTRP, and GREAT databases to September 5, 2022, for randomized trials addressing AD topical treatments. Paired reviewers independently screened records, extracted data, and assessed risk of bias. Random-effects network meta-analyses addressed AD severity, itch, sleep, AD-related quality of life, flares, and harms. The Grading of Recommendations Assessment, Development and Evaluation approach informed certainty of evidence ratings. We classified topical corticosteroids (TCS) using 7 groups-group 1 being most potent. This review is registered in the Open Science Framework (https://osf.io/q5m6s). RESULTS: The 219 included trials (43,123 patients) evaluated 68 interventions. With high-certainty evidence, pimecrolimus improved 6 of 7 outcomes-among the best for 2; high-dose tacrolimus (0.1%) improved 5-among the best for 2; low-dose tacrolimus (0.03%) improved 5-among the best for 1. With moderate- to high-certainty evidence, group 5 TCS improved 6-among the best for 3; group 4 TCS and delgocitinib improved 4-among the best for 2; ruxolitinib improved 4-among the best for 1; group 1 TCS improved 3-among the best for 2. These interventions did not increase harm. Crisaborole and difamilast were intermediately effective, but with uncertain harm. Topical antibiotics alone or in combination may be among the least effective. To maintain AD control, group 5 TCS were among the most effective, followed by tacrolimus and pimecrolimus. CONCLUSIONS: For individuals with AD, pimecrolimus, tacrolimus, and moderate-potency TCS are among the most effective in improving and maintaining multiple AD outcomes. Topical antibiotics may be among the least effective.


Subject(s)
Asthma , Dermatitis, Atopic , Dermatologic Agents , Eczema , Humans , Dermatitis, Atopic/drug therapy , Tacrolimus/therapeutic use , Network Meta-Analysis , Quality of Life , Randomized Controlled Trials as Topic , Dermatologic Agents/therapeutic use , Asthma/drug therapy , Anti-Bacterial Agents/therapeutic use
10.
J Virol ; 96(7): e0151621, 2022 04 13.
Article in English | MEDLINE | ID: mdl-35297669

ABSTRACT

ADP-ribosylation is a highly dynamic posttranslational modification frequently studied in stress response pathways with recent attention given to its role in response to viral infection. Notably, the alphaviruses encode catalytically active macrodomains capable of ADP-ribosylhydrolase (ARH) activities, implying a role in remodeling the cellular ADP-ribosylome. This report decouples mono- and poly-ARH contributions to macrodomain function using a newly engineered Sindbis virus (SINV) mutant with attenuated poly-ARH activity. Our findings indicate that viral poly-ARH activity is uniquely required for high titer replication in mammalian systems. Despite translating incoming genomic RNA as efficiently as WT virus, mutant viruses have a reduced capacity to establish productive infection, offering a more complete understanding of the kinetics and role of the alphavirus macrodomain with important implications for broader ADP-ribosyltransferase biology. IMPORTANCE Viral macrodomains have drawn attention in recent years due to their high degree of conservation in several virus families (e.g., coronaviruses and alphaviruses) and their potential druggability. These domains erase mono- or poly-ADP-ribose, posttranslational modifications written by host poly-ADP-ribose polymerase (PARP) proteins, from undetermined host or viral proteins to enhance replication. Prior work determined that efficient alphavirus replication requires catalytically active macrodomains; however, which form of the modification requires removal and from which protein(s) had not been determined. Here, we present evidence for the specific requirement of poly-ARH activity to ensure efficient productive infection and virus replication.


Subject(s)
Coronavirus , Hydrolases , RNA, Viral , Sindbis Virus , Animals , Coronavirus/genetics , Hydrolases/metabolism , Mammals/genetics , Poly Adenosine Diphosphate Ribose/metabolism , RNA, Viral/genetics , Sindbis Virus/enzymology , Sindbis Virus/genetics , Virus Replication
11.
Proc Natl Acad Sci U S A ; 117(18): 9865-9875, 2020 05 05.
Article in English | MEDLINE | ID: mdl-32321830

ABSTRACT

Recent epidemics demonstrate the global threat of Zika virus (ZIKV), a flavivirus transmitted by mosquitoes. Although infection is usually asymptomatic or mild, newborns of infected mothers can display severe symptoms, including neurodevelopmental abnormalities and microcephaly. Given the large-scale spread, symptom severity, and lack of treatment or prophylaxis, a safe and effective ZIKV vaccine is urgently needed. However, vaccine design is complicated by concern that elicited antibodies (Abs) may cross-react with other flaviviruses that share a similar envelope protein, such as dengue virus, West Nile virus, and yellow fever virus. This cross-reactivity may worsen symptoms of a subsequent infection through Ab-dependent enhancement. To better understand the neutralizing Ab response and risk of Ab-dependent enhancement, further information on germline Ab binding to ZIKV and the maturation process that gives rise to potently neutralizing Abs is needed. Here we use binding and structural studies to compare mature and inferred-germline Ab binding to envelope protein domain III of ZIKV and other flaviviruses. We show that affinity maturation of the light-chain variable domain is important for strong binding of the recurrent VH3-23/VK1-5 neutralizing Abs to ZIKV envelope protein domain III, and identify interacting residues that contribute to weak, cross-reactive binding to West Nile virus. These findings provide insight into the affinity maturation process and potential cross-reactivity of VH3-23/VK1-5 neutralizing Abs, informing precautions for protein-based vaccines designed to elicit germline versions of neutralizing Abs.


Subject(s)
Antibodies, Neutralizing/isolation & purification , Antibodies, Viral/immunology , Viral Envelope Proteins/immunology , Zika Virus Infection/immunology , Zika Virus/immunology , Animals , Antibodies, Monoclonal/immunology , Antibodies, Neutralizing/immunology , Dengue Virus/immunology , Dengue Virus/pathogenicity , Epitopes/immunology , Germ Cells/immunology , Humans , Infant, Newborn , Protein Domains/immunology , Viral Vaccines/immunology , West Nile virus/immunology , West Nile virus/pathogenicity , Yellow fever virus/immunology , Yellow fever virus/pathogenicity , Zika Virus/isolation & purification , Zika Virus Infection/diagnosis , Zika Virus Infection/virology
12.
Proc Natl Acad Sci U S A ; 117(14): 7981-7989, 2020 04 07.
Article in English | MEDLINE | ID: mdl-32209664

ABSTRACT

Human infection by Zika virus (ZIKV) during pregnancy can lead to vertical transmission and fetal aberrations, including microcephaly. Prophylactic administration of antibodies can diminish or prevent ZIKV infection in animal models, but whether passive immunization can protect nonhuman primates and their fetuses during pregnancy has not been determined. Z004 and Z021 are neutralizing monoclonal antibodies to domain III of the envelope (EDIII) of ZIKV. Together the two antibodies protect nonpregnant macaques against infection even after Fc modifications to prevent antibody-dependent enhancement (ADE) in vitro and extend their half-lives. Here we report on prophylactic coadministration of the Fc-modified antibodies to pregnant rhesus macaques challenged three times with ZIKV during first and second trimester. The two antibodies did not entirely eliminate maternal viremia but limited vertical transmission, protecting the fetus from neurologic damage. Thus, maternal passive immunization with two antibodies to EDIII can shield primate fetuses from the harmful effects of ZIKV.


Subject(s)
Antibodies, Monoclonal/administration & dosage , Infectious Disease Transmission, Vertical/prevention & control , Pregnancy Complications, Infectious/prevention & control , Zika Virus Infection/prevention & control , Zika Virus/immunology , Animals , Animals, Newborn , Antibodies, Monoclonal/genetics , Antibodies, Monoclonal/immunology , Antibodies, Neutralizing/administration & dosage , Antibodies, Neutralizing/genetics , Antibodies, Neutralizing/immunology , Disease Models, Animal , Drug Therapy, Combination , Female , Fetus/immunology , Fetus/virology , HEK293 Cells , Humans , Immunoglobulin Fc Fragments/administration & dosage , Immunoglobulin Fc Fragments/genetics , Immunoglobulin Fc Fragments/immunology , Immunoglobulin G/administration & dosage , Immunoglobulin G/genetics , Immunoglobulin G/immunology , Pregnancy , Pregnancy Complications, Infectious/immunology , Pregnancy Complications, Infectious/virology , Protein Engineering , RNA, Viral/isolation & purification , Recombinant Proteins/administration & dosage , Recombinant Proteins/genetics , Recombinant Proteins/immunology , Zika Virus/genetics , Zika Virus/pathogenicity , Zika Virus Infection/immunology , Zika Virus Infection/transmission , Zika Virus Infection/virology
13.
PLoS Pathog ; 16(9): e1008927, 2020 09.
Article in English | MEDLINE | ID: mdl-32997711

ABSTRACT

Viruses cleave cellular proteins to remodel the host proteome. The study of these cleavages has revealed mechanisms of immune evasion, resource exploitation, and pathogenesis. However, the full extent of virus-induced proteolysis in infected cells is unknown, mainly because until recently the technology for a global view of proteolysis within cells was lacking. Here, we report the first comprehensive catalog of proteins cleaved upon enterovirus infection and identify the sites within proteins where the cleavages occur. We employed multiple strategies to confirm protein cleavages and assigned them to one of the two enteroviral proteases. Detailed characterization of one substrate, LSM14A, a p body protein with a role in antiviral immunity, showed that cleavage of this protein disrupts its antiviral function. This study yields a new depth of information about the host interface with a group of viruses that are both important biological tools and significant agents of disease.


Subject(s)
Cysteine Endopeptidases/metabolism , Enterovirus Infections/virology , Enterovirus/pathogenicity , Virus Replication/physiology , Antiviral Agents/metabolism , Enterovirus/metabolism , Host-Pathogen Interactions/physiology , Humans , Proteolysis , Viral Proteins/metabolism
14.
Proc Natl Acad Sci U S A ; 116(48): 24303-24309, 2019 11 26.
Article in English | MEDLINE | ID: mdl-31719195

ABSTRACT

Infection of animal cells by numerous viruses is detected and countered by a variety of means, including recognition of nonself nucleic acids. The zinc finger antiviral protein (ZAP) depletes cytoplasmic RNA that is recognized as foreign in mammalian cells by virtue of its elevated CG dinucleotide content compared with endogenous mRNAs. Here, we determined a crystal structure of a protein-RNA complex containing the N-terminal, 4-zinc finger human (h) ZAP RNA-binding domain (RBD) and a CG dinucleotide-containing RNA target. The structure reveals in molecular detail how hZAP is able to bind selectively to CG-rich RNA. Specifically, the 4 zinc fingers create a basic patch on the hZAP RBD surface. The highly basic second zinc finger contains a pocket that selectively accommodates CG dinucleotide bases. Structure guided mutagenesis, cross-linking immunoprecipitation sequencing assays, and RNA affinity assays show that the structurally defined CG-binding pocket is not required for RNA binding per se in human cells. However, the pocket is a crucial determinant of high-affinity, specific binding to CG dinucleotide-containing RNA. Moreover, variations in RNA-binding specificity among a panel of CG-binding pocket mutants quantitatively predict their selective antiviral activity against a CG-enriched HIV-1 strain. Overall, the hZAP RBD RNA structure provides an atomic-level explanation for how ZAP selectively targets foreign, CG-rich RNA.


Subject(s)
GC Rich Sequence , RNA, Viral/metabolism , RNA-Binding Proteins/chemistry , RNA-Binding Proteins/metabolism , Repressor Proteins/chemistry , Repressor Proteins/metabolism , Binding Sites , Crystallography, X-Ray , Fluorescence Polarization , HEK293 Cells , HIV-1/genetics , Humans , Models, Molecular , Mutagenesis , Mutation , Protein Domains , RNA, Viral/chemistry , RNA-Binding Proteins/genetics , Repressor Proteins/genetics , Zinc Fingers
15.
Aust Educ Res ; 49(3): 547-569, 2022.
Article in English | MEDLINE | ID: mdl-35702374

ABSTRACT

This duoethnography, informed by the new materialist turn, explores how educational work is materially reconfigured within university-community collaborations. Through our co-facilitation of two community-based Master of Education programs we, as White settlers, endeavoured to journey with Indigenous colleagues, community members, and students to respond to calls for transformative reconciliation. It is within these complex relational fields that we explore the shifting nature of our work as educators within a Canadian university. When educational work resides within community, it becomes a living relationship among people and place, requiring a new type of faculty expertise that disrupts the usual boundaries between disciplinary knowledge and the academic triad, and exceeds professional responsibilities. Through our MEd programs, we are coming to understand our work as educators as always a collaborative act in the making, and as a form of scholarly activism.

16.
Prospects (Paris) ; 51(4): 627-641, 2022.
Article in English | MEDLINE | ID: mdl-33487759

ABSTRACT

The government's rapid response to the spread of Covid-19 in British Columbia has resulted in drastic and unprecedented changes to the delivery of K-12 education. Using qualitative research methods, including remote in-depth interviews, this article addresses the question: What is the educational impact of the Covid-19 rapid response on teachers, students, and families in the Lower Mainland of British Columbia, Canada? Six themes are discussed, including teacher and family responses to change, vulnerability, transitions, work/home life balance, holistic teaching practices and communication. The article ends with recommendations relating to the communication and implementation of health, care, and educational practices that better attend to vulnerable populations and address social emotional wellness.

17.
PLoS Pathog ; 15(5): e1007798, 2019 05.
Article in English | MEDLINE | ID: mdl-31116799

ABSTRACT

Cellular antiviral programs encode molecules capable of targeting multiple steps in the virus lifecycle. Zinc-finger antiviral protein (ZAP) is a central and general regulator of antiviral activity that targets pathogen mRNA stability and translation. ZAP is diffusely cytoplasmic, but upon infection ZAP is targeted to particular cytoplasmic structures, termed stress granules (SGs). However, it remains unclear if ZAP's antiviral activity correlates with SG localization, and what molecular cues are required to induce this localization event. Here, we use Sindbis virus (SINV) as a model infection and find that ZAP's localization to SGs can be transient. Sometimes no apparent viral infection follows ZAP SG localization but ZAP SG localization always precedes accumulation of SINV non-structural protein, suggesting virus replication processes trigger SG formation and ZAP recruitment. Data from single-molecule RNA FISH corroborates this finding as the majority of cells with ZAP localization in SGs contain low levels of viral RNA. Furthermore, ZAP recruitment to SGs occurred in ZAP-expressing cells when co-cultured with cells replicating full-length SINV, but not when co-cultured with cells replicating a SINV replicon. ZAP recruitment to SGs is functionally important as a panel of alanine ZAP mutants indicate that the anti-SINV activity is correlated with ZAP's ability to localize to SGs. As ZAP is a central component of the cellular antiviral programs, these data provide further evidence that SGs are an important cytoplasmic antiviral hub. These findings provide insight into how antiviral components are regulated upon virus infection to inhibit virus spread.


Subject(s)
Alphavirus Infections/prevention & control , Antiviral Agents/pharmacology , Cytoplasmic Granules/metabolism , RNA-Binding Proteins/pharmacology , Sindbis Virus/pathogenicity , Stress, Physiological , Virus Replication/drug effects , Alphavirus Infections/metabolism , Alphavirus Infections/virology , Antiviral Agents/metabolism , Bone Neoplasms/drug therapy , Bone Neoplasms/metabolism , Bone Neoplasms/virology , Humans , Osteosarcoma/drug therapy , Osteosarcoma/metabolism , Osteosarcoma/virology , Protein Transport , RNA Interference , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA-Binding Proteins/metabolism , Tumor Cells, Cultured
18.
J Virol ; 93(18)2019 09 15.
Article in English | MEDLINE | ID: mdl-31118263

ABSTRACT

Given the unprecedented scale of the recent Ebola and Zika viral epidemics, it is crucial to understand the biology of host factors with broad antiviral action in order to develop novel therapeutic approaches. Here, we look into one such factor: zinc finger antiviral protein (ZAP) inhibits a variety of RNA and DNA viruses. Alternative splicing results in two isoforms that differ at their C termini: ZAPL (long) encodes a poly(ADP-ribose) polymerase (PARP)-like domain that is missing in ZAPS (short). Previously, it has been shown that ZAPL is more antiviral than ZAPS, while the latter is more induced by interferon (IFN). In this study, we discovered and confirmed the expression of two additional splice variants of human ZAP: ZAPXL (extralong) and ZAPM (medium). We also found two haplotypes of human ZAP. Since ZAPL and ZAPS have differential activities, we hypothesize that all four ZAP isoforms have evolved to mediate distinct antiviral and/or cellular functions. By taking a gene-knockout-and-reconstitution approach, we have characterized the antiviral, translational inhibition, and IFN activation activities of individual ZAP isoforms. Our work demonstrates that ZAPL and ZAPXL are more active against alphaviruses and hepatitis B virus (HBV) than ZAPS and ZAPM and elucidates the effects of splice variants on the action of a broad-spectrum antiviral factor.IMPORTANCE ZAP is an IFN-induced host factor that can inhibit a wide range of viruses, and there is great interest in fully characterizing its antiviral mechanism. This is the first study that defines the antiviral capacities of individual ZAP isoforms in the absence of endogenous ZAP expression and, hence, cross talk with other isoforms. Our data demonstrate that ZAP is expressed as four different forms: ZAPS, ZAPM, ZAPL, and ZAPXL. The longer ZAP isoforms better inhibit alphaviruses and HBV, while all isoforms equally inhibit Ebola virus transcription and replication. In addition, there is no difference in the abilities of ZAP isoforms to enhance the induction of type I IFN expression. Our results show that the full spectrum of ZAP activities can change depending on the virus target and the relative levels of basal expression and induction by IFN or infection.


Subject(s)
RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , A549 Cells , Alphavirus/genetics , Alternative Splicing , Cell Line , HEK293 Cells , Haplotypes , HeLa Cells , Hepatitis B virus/genetics , Humans , Protein Isoforms , RNA Splicing/genetics , RNA, Viral/genetics , Virus Replication/drug effects , Zinc Fingers
19.
Plant Dis ; 104(11): 2979-2985, 2020 Nov.
Article in English | MEDLINE | ID: mdl-32924874

ABSTRACT

Chia (Salvia hispanica L.) seeds are used for food, drinks, oil, and animal feed, and all plant parts are employed in traditional medicine. The growing demand for the seed has created a need for improved disease management. Plant-parasitic nematodes have been found on other Salvia spp., but none have been reported from S. hispanica. Chia has also not been tested for production of compounds active against these nematodes. Therefore, aqueous extracts from shoots and roots of six chia lines, Brad's Organic, Cono, E2, G3, G5, and W13.1, were tested in laboratory assays. Some concentrations of all extracts were nematotoxic, killing about one-third of Meloidogyne incognita (Kofoid & White) Chitwood second-stage juveniles (J2s) in shoot extracts and up to nearly half of J2s in root extracts. Hatch was generally not affected by the extracts. In greenhouse trials, all six chia lines were hosts of M. incognita. Chia line G3 had approximately two times or more eggs per gram of root than Brad's Organic or Cono. When cucumber seedlings were transplanted into soil amended with chopped chia shoots (2.3 or 2.5% weight of fresh shoots/weight of dry soil), galling and egg production on cucumber roots were not suppressed. To our knowledge, this is the first report that chia is a host to M. incognita (or any phytoparasitic nematode) and that chia shoots and roots produce compounds active against a nematode.


Subject(s)
Cucumis sativus , Tylenchida , Tylenchoidea , Animals , Plant Extracts/pharmacology , Seeds
20.
J Nematol ; 52: 1-16, 2020.
Article in English | MEDLINE | ID: mdl-32722901

ABSTRACT

Festulolium hybrids are forage grasses used worldwide in temperate climates. They are associated with the fungal endophyte Epichloë uncinata, which aids in nutrient uptake, drought tolerance, and production of metabolites that protect against parasites and herbivores. Epichloë uncinata produces loline alkaloids, which can deter insect pests. Festulolium has not been widely studied for susceptibility to plant-parasitic nematodes, so Festulolium lines, with and without fungal endophytes, were tested in the greenhouse for host status to the root-knot nematode Meloidogyne incognita. All were poor hosts, regardless of line or endophyte status. Pepper seedlings planted into soil following removal of the Festulolium plants were infected by nematodes, likely because of surviving nematodes from the original inoculation combined with some reproduction on Festulolium. Lolines were found in shoots and roots of all endophyte-associated lines, and some types of lolines in roots increased after nematode infection. Methanolic extracts from roots and shoots of a tested Festulolium line did not inhibit egg hatch, but killed nearly a third of second-stage juveniles whether an endophyte was present or not. Further studies would indicate whether these Festulolium lines aid in suppressing field populations of M. incognita.Festulolium hybrids are forage grasses used worldwide in temperate climates. They are associated with the fungal endophyte Epichloë uncinata, which aids in nutrient uptake, drought tolerance, and production of metabolites that protect against parasites and herbivores. Epichloë uncinata produces loline alkaloids, which can deter insect pests. Festulolium has not been widely studied for susceptibility to plant-parasitic nematodes, so Festulolium lines, with and without fungal endophytes, were tested in the greenhouse for host status to the root-knot nematode Meloidogyne incognita. All were poor hosts, regardless of line or endophyte status. Pepper seedlings planted into soil following removal of the Festulolium plants were infected by nematodes, likely because of surviving nematodes from the original inoculation combined with some reproduction on Festulolium. Lolines were found in shoots and roots of all endophyte-associated lines, and some types of lolines in roots increased after nematode infection. Methanolic extracts from roots and shoots of a tested Festulolium line did not inhibit egg hatch, but killed nearly a third of second-stage juveniles whether an endophyte was present or not. Further studies would indicate whether these Festulolium lines aid in suppressing field populations of M. incognita.

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