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1.
Immunity ; 51(2): 398-410.e5, 2019 08 20.
Article in English | MEDLINE | ID: mdl-31350180

ABSTRACT

Vaccine-induced memory B cell responses to evolving viruses like influenza A involve activation of pre-existing immunity and generation of new responses. To define the contribution of these two types of responses, we analyzed the response to H7N9 vaccination in H7N9-naive adults. We performed comprehensive comparisons at the single-cell level of the kinetics, Ig repertoire, and activation phenotype of established pre-existing memory B cells recognizing conserved epitopes and the newly generated memory B cells directed toward H7 strain-specific epitopes. The recall response to conserved epitopes on H7 HA involved a transient expansion of memory B cells with little observed adaptation. However, the B cell response to newly encountered epitopes was phenotypically distinct and generated a sustained memory population that evolved and affinity matured months after vaccination. These findings establish clear differences between newly generated and pre-existing memory B cells, highlighting the challenges in achieving long-lasting, broad protection against an ever-evolving virus.


Subject(s)
B-Lymphocyte Subsets/immunology , B-Lymphocytes/immunology , Influenza A Virus, H7N9 Subtype/physiology , Influenza Vaccines/immunology , Influenza, Human/immunology , Adult , Antibodies, Viral/metabolism , Antibody Formation , Cells, Cultured , Epitopes/immunology , Female , Hemagglutinin Glycoproteins, Influenza Virus/immunology , Humans , Immunologic Memory , Lymphocyte Activation , Male , Middle Aged , Phenotype , Receptors, Antigen, B-Cell/genetics , Single-Cell Analysis , Vaccination , Young Adult
2.
Genome Res ; 33(5): 729-740, 2023 May.
Article in English | MEDLINE | ID: mdl-37127330

ABSTRACT

Understanding the genetic causes of trait variation is a primary goal of genetic research. One way that individuals can vary genetically is through variable pangenomic genes: genes that are only present in some individuals in a population. The presence or absence of entire genes could have large effects on trait variation. However, variable pangenomic genes can be missed in standard genotyping workflows, owing to reliance on aligning short-read sequencing to reference genomes. A popular method for studying the genetic basis of trait variation is linkage mapping, which identifies quantitative trait loci (QTLs), regions of the genome that harbor causative genetic variants. Large-scale linkage mapping in the budding yeast Saccharomyces cerevisiae has found thousands of QTLs affecting myriad yeast phenotypes. To enable the resolution of QTLs caused by variable pangenomic genes, we used long-read sequencing to generate highly complete de novo genome assemblies of 16 diverse yeast isolates. With these assemblies, we resolved QTLs for growth on maltose, sucrose, raffinose, and oxidative stress to specific genes that are absent from the reference genome but present in the broader yeast population at appreciable frequency. Copies of genes also duplicate onto chromosomes where they are absent in the reference genome, and we found that these copies generate additional QTLs whose resolution requires pangenome characterization. Our findings show the need for highly complete genome assemblies to identify the genetic basis of trait variation.


Subject(s)
Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genetics , Quantitative Trait Loci , Chromosome Mapping , Phenotype , Saccharomyces cerevisiae Proteins/genetics
3.
Nature ; 568(7752): 415-419, 2019 04.
Article in English | MEDLINE | ID: mdl-30971821

ABSTRACT

The HIV-1 envelope glycoprotein (Env) trimer mediates cell entry and is conformationally dynamic1-8. Imaging by single-molecule fluorescence resonance energy transfer (smFRET) has revealed that, on the surface of intact virions, mature pre-fusion Env transitions from a pre-triggered conformation (state 1) through a default intermediate conformation (state 2) to a conformation in which it is bound to three CD4 receptor molecules (state 3)8-10. It is currently unclear how these states relate to known structures. Breakthroughs in the structural characterization of the HIV-1 Env trimer have previously been achieved by generating soluble and proteolytically cleaved trimers of gp140 Env that are stabilized by a disulfide bond, an isoleucine-to-proline substitution at residue 559 and a truncation at residue 664 (SOSIP.664 trimers)5,11-18. Cryo-electron microscopy studies have been performed with C-terminally truncated Env of the HIV-1JR-FL strain in complex with the antibody PGT15119. Both approaches have revealed similar structures for Env. Although these structures have been presumed to represent the pre-triggered state 1 of HIV-1 Env, this hypothesis has never directly been tested. Here we use smFRET to compare the conformational states of Env trimers used for structural studies with native Env on intact virus. We find that the constructs upon which extant high-resolution structures are based predominantly occupy downstream conformations that represent states 2 and 3. Therefore, the structure of the pre-triggered state-1 conformation of viral Env that has been identified by smFRET and that is preferentially stabilized by many broadly neutralizing antibodies-and thus of interest for the design of immunogens-remains unknown.


Subject(s)
Fluorescence Resonance Energy Transfer , HIV-1/chemistry , Single Molecule Imaging , env Gene Products, Human Immunodeficiency Virus/chemistry , Animals , Antibodies, Neutralizing/immunology , Cattle , Disulfides/chemistry , HEK293 Cells , HIV-1/genetics , HIV-1/immunology , Humans , Models, Molecular , Mutation , Protein Conformation , Protein Multimerization , Protein Stability , env Gene Products, Human Immunodeficiency Virus/genetics , env Gene Products, Human Immunodeficiency Virus/immunology
4.
J Virol ; 97(5): e0160422, 2023 05 31.
Article in English | MEDLINE | ID: mdl-37098956

ABSTRACT

While neutralizing antibodies that target the HIV-1 fusion peptide have been elicited in mice by vaccination, antibodies reported thus far have been from only a single antibody class that could neutralize ~30% of HIV-1 strains. To explore the ability of the murine immune system to generate cross-clade neutralizing antibodies and to investigate how higher breadth and potency might be achieved, we tested 17 prime-boost regimens that utilized diverse fusion peptide-carrier conjugates and HIV-1 envelope trimers with different fusion peptides. We observed priming in mice with fusion peptide-carrier conjugates of variable peptide length to elicit higher neutralizing responses, a result we confirmed in guinea pigs. From vaccinated mice, we isolated 21 antibodies, belonging to 4 distinct classes of fusion peptide-directed antibodies capable of cross-clade neutralization. Top antibodies from each class collectively neutralized over 50% of a 208-strain panel. Structural analyses - both X-ray and cryo-EM - revealed each antibody class to recognize a distinct conformation of fusion peptide and to have a binding pocket capable of accommodating diverse fusion peptides. Murine vaccinations can thus elicit diverse neutralizing antibodies, and altering peptide length during prime can improve the elicitation of cross-clade responses targeting the fusion peptide site of HIV-1 vulnerability. IMPORTANCE The HIV-1 fusion peptide has been identified as a site for elicitation of broadly neutralizing antibodies, with prior studies demonstrating that priming with fusion peptide-based immunogens and boosting with soluble envelope (Env) trimers can elicit cross-clade HIV-1-neutralizing responses. To improve the neutralizing breadth and potency of fusion peptide-directed responses, we evaluated vaccine regimens that incorporated diverse fusion peptide-conjugates and Env trimers with variation in fusion peptide length and sequence. We found that variation in peptide length during prime elicits enhanced neutralizing responses in mice and guinea pigs. We identified vaccine-elicited murine monoclonal antibodies from distinct classes capable of cross-clade neutralization and of diverse fusion peptide recognition. Our findings lend insight into improved immunogens and regimens for HIV-1 vaccine development.


Subject(s)
AIDS Vaccines , HIV Infections , HIV Seropositivity , HIV-1 , Animals , Guinea Pigs , Mice , HIV Antibodies , Immunoglobulin Isotypes , Vaccination , Peptides , Antibodies, Neutralizing , Broadly Neutralizing Antibodies , env Gene Products, Human Immunodeficiency Virus , HIV Infections/prevention & control
5.
Age Ageing ; 51(1)2022 01 06.
Article in English | MEDLINE | ID: mdl-35077553

ABSTRACT

BACKGROUND: Mobility is defined as the ability to independently move around the environment and is a key contributor to quality of life, especially in older age. The aim of this study was to evaluate the use of mobility as a decisive outcome for the marketing authorisation of drugs by the European Medicines Agency (EMA). METHODS: Fifteen therapeutic areas which commonly lead to relevant mobility impairments and alter the quantity and/or the quality of walking were selected: two systemic neurological diseases, four conditions primarily affecting exercise capacity, seven musculoskeletal diseases and two conditions representing sensory impairments. European Public Assessment Reports (EPARs) published by the EMA until September 2020 were examined for mobility endpoints included in their 'main studies'. Clinical study registries and primary scientific publications for these studies were also reviewed. RESULTS: Four hundred and eighty-four EPARs yielded 186 relevant documents with 402 'main studies'. The EPARs reported 153 primary and 584 secondary endpoints which considered mobility; 70 different assessment tools (38 patient-reported outcomes, 13 clinician-reported outcomes, 8 performance outcomes and 13 composite endpoints) were used. Only 15.7% of those tools distinctly informed on patients' mobility status. Out of 402, 105 (26.1%) of the 'main studies' did not have any mobility assessment. Furthermore, none of these studies included a digital mobility outcome. CONCLUSIONS: For conditions with a high impact on mobility, mobility assessment was given little consideration in the marketing authorisation of drugs by the EMA. Where mobility impairment was considered to be a relevant outcome, questionnaires or composite scores susceptible to reporting biases were predominantly used.


Subject(s)
Drug Approval , Pharmaceutical Preparations , Aged , Humans , Marketing , Quality of Life
6.
Proc Natl Acad Sci U S A ; 116(27): 13474-13479, 2019 07 02.
Article in English | MEDLINE | ID: mdl-31213541

ABSTRACT

A major obstacle to vaccination against antigenically variable viruses is skewing of antibody responses to variable immunodominant epitopes. For influenza virus hemagglutinin (HA), the immunodominance of the variable head impairs responses to the highly conserved stem. Here, we show that head immunodominance depends on the physical attachment of head to stem. Stem immunogenicity is enhanced by immunizing with stem-only constructs or by increasing local HA concentration in the draining lymph node. Surprisingly, coimmunization of full-length HA and stem alters stem-antibody class switching. Our findings delineate strategies for overcoming immunodominance, with important implications for human vaccination.


Subject(s)
Antibodies, Neutralizing/immunology , Epitopes/immunology , Hemagglutinins/immunology , Immunodominant Epitopes/immunology , Influenza A virus/immunology , Influenza Vaccines/immunology , Animals , Antibodies, Viral/immunology , B-Lymphocytes/immunology , Female , Mice , Mice, Inbred C57BL , Orthomyxoviridae Infections/immunology , Orthomyxoviridae Infections/prevention & control , Stem Cells/immunology
7.
J Virol ; 94(13)2020 06 16.
Article in English | MEDLINE | ID: mdl-32295908

ABSTRACT

HIV-1 envelope (Env) trimers, stabilized in a prefusion-closed conformation, can elicit humoral responses capable of neutralizing HIV-1 strains closely matched in sequence to the immunizing strain. One strategy to increase elicited neutralization breadth involves vaccine priming of immune responses against a target site of vulnerability, followed by vaccine boosting of these responses with prefusion-closed Env trimers. This strategy has succeeded at the fusion peptide (FP) site of vulnerability in eliciting cross-clade neutralizing responses in standard vaccine-test animals. However, the breadth and potency of the elicited responses have been less than optimal. Here, we identify three mutations (3mut), Met302, Leu320, and Pro329, that stabilize the apex of the Env trimer in a prefusion-closed conformation and show antigenically, structurally, and immunogenically that combining 3mut with other approaches (e.g., repair and stabilize and glycine-helix breaking) yields well-behaved clade C-Env trimers capable of boosting the breadth of FP-directed responses. Crystal structures of these trimers confirmed prefusion-closed apexes stabilized by hydrophobic patches contributed by Met302 and Leu320, with Pro329 assuming canonically restricted dihedral angles. We substituted the N-terminal eight residues of FP (FP8, residues 512 to 519) of these trimers with the second most prevalent FP8 sequence (FP8v2, AVGLGAVF) and observed a 3mut-stabilized consensus clade C-Env trimer with FP8v2 to boost the breadth elicited in guinea pigs of FP-directed responses induced by immunogens containing the most prevalent FP8 sequence (FP8v1, AVGIGAVF). Overall, 3mut can stabilize the Env trimer apex, and the resultant apex-stabilized Env trimers can be used to expand the neutralization breadth elicited against the FP site of vulnerability.IMPORTANCE A major hurdle to the development of an effective HIV-1 vaccine is the elicitation of serum responses capable of neutralizing circulating strains of HIV, which are extraordinarily diverse in sequence and often highly neutralization resistant. Recently, we showed how sera with 20 to 30% neutralization breadth could, nevertheless, be elicited in standard vaccine test animals by priming with the most prevalent N-terminal 8 residues of the HIV-1 fusion peptide (FP8), followed by boosting with a stabilized BG505-envelope (Env) trimer. Here, we show that subsequent boosting with a 3mut-apex-stabilized consensus C-Env trimer, modified to have the second most prevalent FP8 sequence, elicits higher neutralization breadth than that induced by continued boosting with the stabilized BG505-Env trimer. With increased neutralizing breadth elicited by boosting with a heterologous trimer containing the second most prevalent FP8 sequence, the fusion peptide-directed immune-focusing approach moves a step closer toward realizing an effective HIV-1 vaccine regimen.


Subject(s)
AIDS Vaccines/immunology , env Gene Products, Human Immunodeficiency Virus/genetics , env Gene Products, Human Immunodeficiency Virus/immunology , Animals , Antibodies, Neutralizing/immunology , Female , Guinea Pigs , HEK293 Cells , HIV Antibodies/immunology , HIV Seropositivity , HIV-1/immunology , Humans , Immunization, Secondary , Peptides , Vaccines, Subunit
8.
J Vet Pharmacol Ther ; 44(3): 406-410, 2021 May.
Article in English | MEDLINE | ID: mdl-33686699

ABSTRACT

Injectable vitamin B12 (cobalamin) is traditionally used to prevent or treat vitamin B12 deficiencies in ruminants. Sheep and human studies have demonstrated the superiority of a single dose of hydroxocobalamin (OHB12) over cyanocobalamin (CNB12) in maintaining high levels of cobalamin in plasma and liver. However, limited data are available for cattle. The purpose of this study was to compare the pharmacokinetics of two forms of cobalamin-OHB12 and CNB12-as a single subcutaneous injection of 28 µg/kg BW at the same time of a trace mineral injection in six non-cobalt/B12 -deficient Holstein-Friesian steers. Plasma and liver samples were obtained to determine cobalamin concentration after treatment. Cyanocobalamin had lower retention in plasma and liver than OHB12 (p < .05). Cobalamin levels peaked in plasma by 8 h after treatment in both groups. However, OHB12 reached a higher peak compared to CNB12. Levels of cobalamin in plasma dropped closer to baseline levels 24 h after CNB12 treatment while OHB12 maintained higher concentrations. Hydroxocobalamin increased significantly hepatic concentration of cobalamin 28 days after treatment, while CNB12 did not increase liver levels relative to pre-treatment (p < .05). These results confirm that a single subcutaneous OHB12 injection increases the level of cobalamin in the blood in the first 24 hours, and this increase is maintained in the liver for at least 28 days.


Subject(s)
Hydroxocobalamin , Trace Elements , Animals , Cattle , Injections/veterinary , Pilot Projects , Sheep , Vitamin B 12
9.
J Virol ; 91(10)2017 05 15.
Article in English | MEDLINE | ID: mdl-28275193

ABSTRACT

The HIV-1 envelope (Env) trimer is a target for vaccine design as well as a conformational machine that facilitates virus entry by transitioning between prefusion-closed, CD4-bound, and coreceptor-bound conformations by transitioning into a postfusion state. Vaccine designers have sought to restrict the conformation of the HIV-1 Env trimer to its prefusion-closed state as this state is recognized by most broadly neutralizing, but not nonneutralizing, antibodies. We previously identified a disulfide bond, I201C-A433C (DS), which stabilizes Env in the vaccine-desired prefusion-closed state. When placed into the context of BG505 SOSIP.664, a soluble Env trimer mimic developed by Sanders, Moore, and colleagues, the engineered DS-SOSIP trimer showed reduced conformational triggering by CD4. Here, we further stabilize DS-SOSIP through a combination of structure-based design and 96-well-based expression and antigenic assessment. From 103 designs, we identified one, named DS-SOSIP.4mut, with four additional mutations at the interface of potentially mobile domains of the prefusion-closed structure. We also determined the crystal structures of DS-SOSIP.4mut at 4.1-Å resolution and of an additional DS-SOSIP.6mut variant at 4.3-Å resolution, and these confirmed the formation of engineered disulfide bonds. Notably, DS-SOSIP.4mut elicited a higher ratio of tier 2 autologous titers versus tier 1 V3-sensitive titers than BG505 SOSIP.664. DS-SOSIP.4mut also showed reduced recognition of CD4 and increased thermostability. The improved antigenicity, thermostability, and immunogenicity of DS-SOSIP.4mut suggest utility as an immunogen or a serologic probe; moreover, the specific four alterations identified here, M154, M300, M302, and L320 (4mut), can also be transferred to other HIV-1 Env trimers of interest to improve their properties.IMPORTANCE One approach to elicit broadly neutralizing antibodies against HIV-1 is to stabilize the structurally flexible HIV-1 envelope (Env) trimer in a conformation that displays predominantly broadly neutralizing epitopes and few to no nonneutralizing epitopes. The prefusion-closed conformation of HIV-1 Env has been identified as one such preferred conformation, and a current leading vaccine candidate is the BG505 DS-SOSIP variant, comprising two disulfides and an Ile-to-Pro mutation of Env from strain BG505. Here, we introduced additional mutations to further stabilize BG505 DS-SOSIP in the vaccine-preferred prefusion-closed conformation. In guinea pigs, our best mutant, DS-SOSIP.4mut, elicited a significantly higher ratio of autologous versus V3-directed neutralizing antibody responses than the SOSIP-stabilized form. We also observed an improvement in thermostability and a reduction in CD4 affinity. With improved antigenicity, stability, and immunogenicity, DS-SOSIP.4mut-stabilized trimers may have utility as HIV-1 immunogens or in other antigen-specific contexts, such as with B-cell probes.


Subject(s)
CD4 Antigens/immunology , CD4 Antigens/metabolism , HIV Antigens/immunology , HIV-1/immunology , env Gene Products, Human Immunodeficiency Virus/chemistry , env Gene Products, Human Immunodeficiency Virus/immunology , AIDS Vaccines/chemistry , AIDS Vaccines/immunology , Animals , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Guinea Pigs , HIV Antibodies/blood , HIV Antibodies/immunology , HIV Antigens/chemistry , HIV Antigens/metabolism , HIV-1/genetics , Humans , Protein Multimerization , Protein Stability , env Gene Products, Human Immunodeficiency Virus/metabolism
10.
BMC Genomics ; 18(1): 215, 2017 02 28.
Article in English | MEDLINE | ID: mdl-28245789

ABSTRACT

BACKGROUND: The transcriptional corepressor Groucho (Gro) is required for the function of many developmentally regulated DNA binding repressors, thus helping to define the gene expression profile of each cell during development. The ability of Gro to repress transcription at a distance together with its ability to oligomerize and bind to histones has led to the suggestion that Gro may spread along chromatin. However, much is unknown about the mechanism of Gro-mediated repression and about the dynamics of Gro targeting. RESULTS: Our chromatin immunoprecipitation sequencing analysis of temporally staged Drosophila embryos shows that Gro binds in a highly dynamic manner primarily to clusters of discrete (<1 kb) segments. Consistent with the idea that Gro may facilitate communication between silencers and promoters, Gro binding is enriched at both cis-regulatory modules, as well as within the promotors of potential target genes. While this Gro-recruitment is required for repression, our data show that it is not sufficient for repression. Integration of Gro binding data with transcriptomic analysis suggests that, contrary to what has been observed for another Gro family member, Drosophila Gro is probably a dedicated repressor. This analysis also allows us to define a set of high confidence Gro repression targets. Using publically available data regarding the physical and genetic interactions between these targets, we are able to place them in the regulatory network controlling development. Through analysis of chromatin associated pre-mRNA levels at these targets, we find that genes regulated by Gro in the embryo are enriched for characteristics of promoter proximal paused RNA polymerase II. CONCLUSIONS: Our findings are inconsistent with a one-dimensional spreading model for long-range repression and suggest that Gro-mediated repression must be regulated at a post-recruitment step. They also show that Gro is likely a dedicated repressor that sits at a prominent highly interconnected regulatory hub in the developmental network. Furthermore, our findings suggest a role for RNA polymerase II pausing in Gro-mediated repression.


Subject(s)
Basic Helix-Loop-Helix Transcription Factors/metabolism , Gene Expression Regulation, Developmental , Genomics , Repressor Proteins/metabolism , Animals , Chromatin/metabolism , Drosophila melanogaster/embryology , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , Embryo, Nonmammalian/metabolism , Protein Binding
11.
J Biol Chem ; 290(50): 30119-30, 2015 Dec 11.
Article in English | MEDLINE | ID: mdl-26483546

ABSTRACT

Groucho (Gro) is a Drosophila co-repressor that regulates the expression of a large number of genes, many of which are involved in developmental control. Previous studies have shown that its central region is essential for function even though its three domains are poorly conserved and intrinsically disordered. Using these disordered domains as affinity reagents, we have now identified multiple embryonic Gro-interacting proteins. The interactors include protein complexes involved in chromosome organization, mRNA processing, and signaling. Further investigation of the interacting proteins using a reporter assay showed that many of them modulate Gro-mediated repression either positively or negatively. The positive regulators include components of the spliceosomal subcomplex U1 small nuclear ribonucleoprotein (U1 snRNP). A co-immunoprecipitation experiment confirms this finding and suggests that a sizable fraction of nuclear U1 snRNP is associated with Gro. The use of RNA-seq to analyze the gene expression profile of cells subjected to knockdown of Gro or snRNP-U1-C (a component of U1 snRNP) showed a significant overlap between genes regulated by these two factors. Furthermore, comparison of our RNA-seq data with Gro and RNA polymerase II ChIP data led to a number of insights, including the finding that Gro-repressed genes are enriched for promoter-proximal RNA polymerase II. We conclude that the Gro central domains mediate multiple interactions required for repression, thus functioning as a regulatory hub. Furthermore, interactions with the spliceosome may contribute to repression by Gro.


Subject(s)
Basic Helix-Loop-Helix Transcription Factors/physiology , Gene Expression Regulation , Repressor Proteins/physiology , Animals , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Drosophila , Gene Knockdown Techniques , Repressor Proteins/genetics , Repressor Proteins/metabolism , Ribonucleoprotein, U1 Small Nuclear/metabolism , Spliceosomes , Transcription, Genetic
12.
bioRxiv ; 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38903081

ABSTRACT

Evolutionary arms races can arise at the contact surfaces between host and viral proteins, producing dynamic spaces in which genetic variants are continually pursued. However, the sampling of genetic variation must be balanced with the need to maintain protein function. A striking case is given by protein kinase R (PKR), a member of the mammalian innate immune system. PKR detects viral replication within the host cell and halts protein synthesis to prevent viral replication by phosphorylating eIF2α, a component of the translation initiation machinery. PKR is targeted by many viral antagonists, including poxvirus pseudosubstrate antagonists that inhibit PKR by interacting with the same binding surface as eIF2α. Remarkably, PKR has several rapidly evolving residues at this interface, suggesting it is engaging in an evolutionary arms race, despite the surface's critical role in phosphorylating eIF2α. To systematically explore the evolutionary opportunities available at this dynamic interface, we generated and characterized a library of 426 SNP-accessible nonsynonymous variants of human PKR for their ability to escape inhibition by the model pseudosubstrate inhibitor K3 from vaccinia virus. We identified key sites in the PKR kinase domain that harbor K3-resistant variants, as well as critical sites where variation leads to loss of function. We find K3-resistant variants are readily available throughout the interface and are enriched at sites under positive selection. Moreover, variants beneficial against K3 were also beneficial against an enhanced variant of K3, indicating resilience to viral adaptation. Overall, we find that the eIF2α-binding surface of PKR is highly malleable, potentiating its evolutionary ability to combat viral inhibition.

13.
Digit Biomark ; 8(1): 30-39, 2024.
Article in English | MEDLINE | ID: mdl-38510264

ABSTRACT

Background: Fatigue is a prominent symptom in many diseases and is strongly associated with impaired daily function. The measurement of daily function is currently almost always done with questionnaires, which are subjective and imprecise. With the recent advances of digital wearable technologies, novel approaches to evaluate daily function quantitatively and objectively in real-life conditions are increasingly possible. This also creates new possibilities to measure fatigue-related changes of daily function using such technologies. Summary: This review examines which digitally assessable parameters in immune-mediated inflammatory and neurodegenerative diseases may have the greatest potential to reflect fatigue-related changes of daily function. Key Messages: Results of a standardized analysis of the literature reporting about perception-, capacity-, and performance-evaluating assessment tools indicate that changes of the following parameters: physical activity, independence of daily living, social participation, working life, mental status, cognitive and aerobic capacity, and supervised and unsupervised mobility performance have the highest potential to reflect fatigue-related changes of daily function. These parameters thus hold the greatest potential for quantitatively measuring fatigue in representative diseases in real-life conditions, e.g., with digital wearable technologies. Furthermore, to the best of our knowledge, this is a new approach to analysing evidence for the design of performance-based digital assessment protocols in human research, which may stimulate further systematic research in this area.

14.
bioRxiv ; 2023 Nov 22.
Article in English | MEDLINE | ID: mdl-38076952

ABSTRACT

The interfaces between host and viral proteins can be dynamic spaces in which genetic variants are continually pursued, giving rise to evolutionary arms races. One such scenario is found between the mammalian innate immunity protein PKR (protein kinase R) and the poxvirus antagonist K3. Once activated, PKR phosphorylates the natural substrate eIF2α, which halts protein synthesis within the cell and prevents viral replication. K3 acts as a pseudosubstrate antagonist against PKR by directly antagonizing this halt in protein synthesis, enabling poxviruses to replicate in the cell. Exploring the impact of genetic variants in both PKR and K3 is necessary not only to highlight residues of evolutionary constraint and opportunity but also to elucidate the mechanism by which human PKR is able to subvert a rapidly evolving viral antagonist. To systematically explore this dynamic interface, we have generated a combinatorial library of PKR and K3 missense variants to be co-expressed and characterized in a high-throughput yeast selection assay. This assay allows us to characterize hundreds of thousands of unique PKR-K3 genetic combinations in a single pooled experiment. Our results highlight specific missense variants available to PKR that subvert the K3 antagonist. We find that improved PKR variants are readily available at sites under positive selection, with limited opportunity at sites interfacing with K3 and eIF2α. Additionally, we find many variants that improve and disable K3 antagonism, suggesting a pliable interface. We reason that this approach can be leveraged to explore the evolutionary plasticity of many other host-virus interfaces.

15.
Animals (Basel) ; 13(1)2023 Jan 03.
Article in English | MEDLINE | ID: mdl-36611786

ABSTRACT

This study was conducted on five commercial farms across Victoria, Australia, between September 2018 and November 2019, where the TM status of ewes was within normal ranges before joining. Mix breed ewes (n = 1484) were randomly allocated to receive either nil treatment (Control) or two injections of an ITM product containing zinc (40 mg/mL), manganese (10 mg/mL), selenium (3 mg/mL), and copper (10 mg/mL); 0.2 mL per 10 kg BW (Multimin® plus Copper for Sheep, Virbac (Australia) Pty Ltd., Milperra, NSW, Australia) 30 days before the start of joining and 30 days before the start of lambing. Approximately 90 days after joining, pregnancy status and conception rate were determined by ultrasound. The marking rate was determined approximately four weeks after the end of lambing, and lamb weights were determined at weaning (12 weeks after the end of lambing). In all farms, ITM treatment did not affect the conception rate. The average conception rate was 156 ± 11.0% (p > 0.05). The marking rate of ITM ewes was 9% higher than control ewes (95% Confidence Interval 3−21%). Lambs born to ITM ewes were 2.31 kg heavier at weaning than lambs born to control ewes (p < 0.001). Although not significant, ewe mortality across farms was 1.3% lower in the ITM group than in the control group. On average, ewes treated with ITM pre-joining and pre-lambing produced more and heavier lambs that represent an extra AU$ 2338 per 100 ewes net benefit for the producer. These results help to understand strategic TM supplementation for animal health, performance and farm profitability beyond the treatment of clinical deficiencies.

16.
Article in English | MEDLINE | ID: mdl-37416339

ABSTRACT

The Australian paralysis tick Ixodes holocyclus continues to be a serious threat to companion animals along Australia's east coast. The tick produces a potent neurotoxin which causes a rapidly ascending flaccid paralysis, which if left untreated, can result in the death of the animal. There is currently only a limited number of products registered in Australia for the treatment and control of paralysis ticks in cats. Felpreva® is an effective spot-on combination containing emodepside, praziquantel and tigolaner. To investigate the therapeutic and long-term persistent efficacy of Felpreva® (2.04% w/v emodepside, 8.14% w/v praziquantel and 9.79% w/v tigolaner) against experimental infestation with I. holocyclus in cats, two studies were undertaken. Fifty cats were included in the studies on study Day -17. These cats were immunized against paralysis tick holocyclotoxin prior to the study commencing. Immunity to holocyclotoxin was confirmed with a tick carrying capacity (TCC) test conducted prior to treatment. Cats were treated once on Day 0. Group 1 cats were treated with the placebo formulation and Group 2 cats were treated with Felpreva®. Cats were infested on Days -14 (tick carrying capacity test), 0, 28, 56, 70, 84 and 91 (weeks 4, 8, 10, 12 and 13). Ticks were counted on cats 24 h, 48 h and 72 â€‹h post-treatment and infestation, except during the tick carrying capacity test when they were counted approximately 72 â€‹h post-infestation only. The 24-h and 48-h assessments were conducted without removing the ticks. The ticks were assessed, removed and discarded at the 72-h assessment time-points. Significant differences in total live tick counts at ∼24 h, ∼48 h and ∼72 â€‹h post-infestation were observed between the treatment and control group. Differences were significant (P â€‹< â€‹0.05 to â€‹< â€‹0.001) in all instances. Treatment efficacies of 98.1-100% were observed ∼72 â€‹h post-infestation through to 13 weeks (94 days) post-treatment. These results show that a single application of Felpreva® provides effective treatment and control against induced infestation with paralysis ticks for 13 weeks.

18.
Value Health ; 15(6): 804-11, 2012.
Article in English | MEDLINE | ID: mdl-22999129

ABSTRACT

The appropriate development of a model begins with understanding the problem that is being represented. The aim of this article was to provide a series of consensus-based best practices regarding the process of model conceptualization. For the purpose of this series of articles, we consider the development of models whose purpose is to inform medical decisions and health-related resource allocation questions. We specifically divide the conceptualization process into two distinct components: the conceptualization of the problem, which converts knowledge of the health care process or decision into a representation of the problem, followed by the conceptualization of the model itself, which matches the attributes and characteristics of a particular modeling type with the needs of the problem being represented. Recommendations are made regarding the structure of the modeling team, agreement on the statement of the problem, the structure, perspective, and target population of the model, and the interventions and outcomes represented. Best practices relating to the specific characteristics of model structure and which characteristics of the problem might be most easily represented in a specific modeling method are presented. Each section contains a number of recommendations that were iterated among the authors, as well as among the wider modeling taskforce, jointly set up by the International Society for Pharmacoeconomics and Outcomes Research and the Society for Medical Decision Making.


Subject(s)
Advisory Committees , Comparative Effectiveness Research/standards , Concept Formation , Models, Theoretical , Consensus , Decision Support Systems, Clinical , Evidence-Based Practice
20.
Int J Gen Med ; 15: 7879-7884, 2022.
Article in English | MEDLINE | ID: mdl-36325498

ABSTRACT

How does budget impact and affordability in healthcare work? In this episode of the Value Insider podcast, host Mike Chambers speaks with Prof. Sean Sullivan about affordability and budget impact for the "payers" of healthcare interventions. Prof. Sullivan is Dean of the University of Washington School of Pharmacy. He is past president of the International Society for Pharmacoeconomics and Outcomes Research (ISPOR) and served as chair of the health technology assessment (HTA) committee of US Health Insurer Premera Blue Cross, was part of the US Governmental Medicare coverage evidence committee and led the ISPOR Task Force on Methods for Conducting and Reporting Budget Impact Assessments. Prof. Sullivan explains how budget impact and affordability are intertwined and how this plays a role in decisions in the US, but also the rest of the world.

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