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The Journal of Infectious Diseases Mar 2020The natural history of cytomegalovirus (CMV) infection is complex. Individuals may experience primary infection, reactivation of latent infection, or reinfection with a...
The natural history of cytomegalovirus (CMV) infection is complex. Individuals may experience primary infection, reactivation of latent infection, or reinfection with a new strain despite natural immunity. The ability of this virus to continue to replicate despite substantial immune responses is attributable to the many immune evasion genes encoded within its genome. Given this complex natural history and immunology, the design of clinical trials of CMV vaccines may require components not usually found in trials of vaccines designed to protect against viruses that cause only acute infections. In this article, we focus on specific aspects of clinical trial design that could be adopted to address the complexities of CMV infections. We consider women of childbearing age, toddlers, recipients of solid organ transplantation, and stem cell transplant patients, emphasizing the parallels between women and solid organ transplantation that could allow vaccines to be developed in parallel in both these patient groups. We emphasize the potential for studies of passive immunity to inform the selection of immunogens as candidates for active immunization and vice versa. We also illustrate how application of whole-genomic sequencing could document whether vaccines protect against reactivation or reinfection of CMV or both.
Topics: Age Factors; Clinical Decision-Making; Cytomegalovirus; Cytomegalovirus Infections; Cytomegalovirus Vaccines; Disease Management; Female; Hematopoietic Stem Cell Transplantation; Humans; Infant, Newborn; Infectious Disease Transmission, Vertical; Male; Organ Transplantation; Population Surveillance; Pregnancy; Pregnancy Complications, Infectious; Sex Factors; Vaccination
PubMed: 32134487
DOI: 10.1093/infdis/jiz537 -
RNA (New York, N.Y.) Sep 2020Polyriboadenylic [poly(rA)] strands of sufficient length form parallel double helices in acidic and/or ammonium-containing conditions. Poly(rA) duplexes in acidic...
Polyriboadenylic [poly(rA)] strands of sufficient length form parallel double helices in acidic and/or ammonium-containing conditions. Poly(rA) duplexes in acidic conditions are held together by A-A base-pairing also involving base interactions with the phosphate backbone. Traditional UV-melting studies of parallel poly(A) duplexes have typically examined homo-duplex formation of a single nucleic acid species in solution. We have adapted a technique utilizing a DNA nanoswitch that detects interaction of two different strands either with similar or differing lengths or modifications. Our method detected parallel duplex formation as a function of length, chemical modifications, and pH, and at a sensitivity that required over 100-fold less concentration of sample than prior UV-melting methods. While parallel polyriboadenylic acid and poly-2'-O-methyl-adenylic acid homo-duplexes formed, we did not detect homo-duplexes of polydeoxyriboadenylic acid strands or poly-locked nucleic acid (LNA)-adenylic strands. Importantly however, a poly-locked nucleic acid (LNA)-adenylic strand, as well as a poly-2'-O-methyl-adenylic strand, formed a hetero-duplex with a polyriboadenylic strand. Overall, our work validates a new tool for studying parallel duplexes and reveals fundamental properties of poly(A) parallel duplex formation. Parallel duplexes may find use in DNA nanotechnology and in molecular biology applications such as a potential poly(rA) tail capture tool as an alternative to traditional oligo(dT) based purification.
Topics: Base Pairing; DNA; Nucleic Acid Conformation; Oligonucleotides; Poly A
PubMed: 32414856
DOI: 10.1261/rna.075408.120 -
Molecular Biology and Evolution Sep 2020Understanding the genetic basis of similar phenotypes shared between lineages is a long-lasting research interest. Even though animal evolution offers many examples of...
Understanding the genetic basis of similar phenotypes shared between lineages is a long-lasting research interest. Even though animal evolution offers many examples of parallelism, for many phenotypes little is known about the underlying genes and mutations. We here use a combination of whole-genome sequencing, expression analyses, and comparative genomics to study the parallel genetic origin of ptilopody (Pti) in chicken. Ptilopody (or foot feathering) is a polygenic trait that can be observed in domesticated and wild avian species and is characterized by the partial or complete development of feathers on the ankle and feet. In domesticated birds, ptilopody is easily selected to fixation, though extensive variation in the type and level of feather development is often observed. By means of a genome-wide association analysis, we identified two genomic regions associated with ptilopody. At one of the loci, we identified a 17-kb deletion affecting PITX1 expression, a gene known to encode a transcription regulator of hindlimb identity and development. Similarly to pigeon, at the second loci, we observed ectopic expression of TBX5, a gene involved in forelimb identity and a key determinant of foot feather development. We also observed that the trait evolved only once as foot-feathered birds share the same haplotype upstream TBX5. Our findings indicate that in chicken and pigeon ptilopody is determined by the same set of genes that affect similar molecular pathways. Our study confirms that ptilopody has evolved through parallel evolution in chicken and pigeon.
Topics: Animals; Biological Evolution; Chickens; Columbidae; Feathers; Foot; Haplotypes; Multifactorial Inheritance; Paired Box Transcription Factors; T-Box Domain Proteins; Whole Genome Sequencing
PubMed: 32344429
DOI: 10.1093/molbev/msaa092 -
Aging Cell Aug 2023"Lipid raft aging" in nerve cells represents an early event in the development of aging-related neurodegenerative diseases, such as Alzheimer's disease. Lipid rafts are...
"Lipid raft aging" in nerve cells represents an early event in the development of aging-related neurodegenerative diseases, such as Alzheimer's disease. Lipid rafts are key elements in synaptic plasticity, and their modification with aging alters interactions and distribution of signaling molecules, such as glutamate receptors and ion channels involved in memory formation, eventually leading to cognitive decline. In the present study, we have analyzed, in vivo, the effects of dietary supplementation of n-3 LCPUFA on the lipid structure, membrane microviscosity, domain organization, and partitioning of ionotropic and metabotropic glutamate receptors in hippocampal lipid raffs in female mice. The results revealed several lipid signatures of "lipid rafts aging" in old mice fed control diets, consisting in depletion of n-3 LCPUFA, membrane unsaturation, along with increased levels of saturates, plasmalogens, and sterol esters, as well as altered lipid relevant indexes. These changes were paralleled by increased microviscosity and changes in the raft/non-raft (R/NR) distribution of AMPA-R and mGluR5. Administration of the n-3 LCPUFA diet caused the partial reversion of fatty acid alterations found in aged mice and returned membrane microviscosity to values found in young animals. Paralleling these findings, lipid rafts accumulated mGluR5, NMDA-R, and ASIC2, and increased their R/NR proportions, which collectively indicate changes in synaptic plasticity. Unexpectedly, this diet also modified the lipidome and dimension of lipid rafts, as well as the domain redistribution of glutamate receptors and acid-sensing ion channels involved in hippocampal synaptic plasticity, likely modulating functionality of lipid rafts in memory formation and reluctance to age-associated cognitive decline.
Topics: Female; Mice; Animals; Fatty Acids; Fatty Acids, Unsaturated; Hippocampus; Membrane Microdomains; Diet
PubMed: 37254617
DOI: 10.1111/acel.13867 -
Atherosclerosis Apr 2022Scavenger receptors form a superfamily of membrane-bound receptors that bind and internalize different types of ligands, including pro-atherogenic oxidized low-density...
BACKGROUND AND AIMS
Scavenger receptors form a superfamily of membrane-bound receptors that bind and internalize different types of ligands, including pro-atherogenic oxidized low-density lipoproteins (oxLDLs). In vitro studies have indicated a role for the liver sinusoidal endothelial cell receptors stabilin 1 (stab1) and 2 (stab2) in oxLDL clearance. In this study, we evaluated the potential role of stab1 and stab2 in lipoprotein uptake in zebrafish, an upcoming model for studying cholesterol metabolism and atherosclerosis.
METHODS
Lipoproteins were injected in the duct of Cuvier of wild-type (ABTL) or stab1 and stab2 mutant (stab1stab2) zebrafish larvae at 3 days post-fertilization. To examine the effect of stabilin deficiency on lipoprotein and cholesterol metabolism, zebrafish larvae were challenged with a high cholesterol diet (HCD; 4% w/w) for 10 days.
RESULTS
Lipoprotein injections showed impaired uptake of both LDL and oxLDL into the vessel wall of caudal veins of stab1stab2 zebrafish, which was paralleled by redistribution to tissue macrophages. Total body cholesterol levels did not differ between HCD-fed stab1stab2 and ABTL zebrafish. However, stab1stab2 larvae exhibited 1.4-fold higher mRNA expression levels of ldlra involved in (modified) LDL uptake, whereas the expression levels of scavenger receptors scarb1 and cd36 were significantly decreased.
CONCLUSIONS
We have shown that stabilins 1 and 2 have an important scavenging function for apolipoprotein B-containing lipoproteins in zebrafish and that combined deficiency of these two proteins strongly upregulates the clearance of lipoproteins by macrophages within the caudal vein. Our current study highlights the use of zebrafish as model to study lipoprotein metabolism and liver sinusoidal endothelial cell function.
Topics: Animals; Apolipoproteins B; Atherosclerosis; CD36 Antigens; Cholesterol; Lipoproteins, LDL; Receptors, Scavenger; Zebrafish
PubMed: 35247629
DOI: 10.1016/j.atherosclerosis.2022.02.018 -
Journal of Virology Sep 2019Congenital human cytomegalovirus (HCMV) infection causes a broad spectrum of central and peripheral nervous system disorders, ranging from microcephaly to hearing loss....
Congenital human cytomegalovirus (HCMV) infection causes a broad spectrum of central and peripheral nervous system disorders, ranging from microcephaly to hearing loss. These ramifications mandate the study of virus-host interactions in neural cells. Neural progenitor cells are permissive for lytic infection. We infected two induced pluripotent stem cell (iPSC) lines and found these more primitive cells to be susceptible to infection but not permissive. Differentiation of infected iPSCs induced expression of viral antigens. iPSCs can be cultured in three dimensions to generate cerebral organoids, closely mimicking development. Mock- or HCMV-infected iPSCs were subjected to a cerebral organoid generation protocol. HCMV IE1 protein was detected in virus-infected organoids at 52 days postinfection. Absent a significant effect on organoid size, infection induced regions of necrosis and the presence of large vacuoles and cysts. Perhaps more in parallel with the subtler manifestations of HCMV-induced birth defects, infection dramatically altered neurological development of organoids, decreasing the number of developing and fully formed cortical structure sites, with associated changes in the architectural organization and depth of lamination within these structures, and manifesting aberrant expression of the neural marker β-tubulin III. Our observations parallel published descriptions of infected clinical samples, which often contain only sparse antigen-positive foci yet display areas of focal necrosis and cellular loss, delayed maturation, and abnormal cortical lamination. The parallels between pathologies present in clinical specimens and the highly tractable three-dimensional (3D) organoid system demonstrate the utility of this system in modeling host-virus interactions and HCMV-induced birth defects. Human cytomegalovirus (HCMV) is a leading cause of central nervous system birth defects, ranging from microcephaly to hearing impairment. Recent literature has provided descriptions of delayed and abnormal maturation of developing cortical tissue in infected clinical specimens. We have found that infected induced pluripotent stem cells can be differentiated into three-dimensional, viral protein-expressing cerebral organoids. Virus-infected organoids displayed dramatic alterations in development compared to those of mock-infected controls. Development in these organoids closely paralleled observations in HCMV-infected clinical samples. Infection induced regions of necrosis, the presence of larger vacuoles and cysts, changes in the architectural organization of cortical structures, aberrant expression of the neural marker β-tubulin III, and an overall reduction in numbers of cortical structure sites. We found clear parallels between the pathologies of clinical specimens and virus-infected organoids, demonstrating the utility of this highly tractable system for future investigations of HCMV-induced birth defects.
Topics: Cell Differentiation; Cell Line; Coculture Techniques; Cytomegalovirus; Cytomegalovirus Infections; Humans; Immediate-Early Proteins; Induced Pluripotent Stem Cells; Models, Biological; Neural Stem Cells; Organ Culture Techniques; Organoids; Tubulin
PubMed: 31217239
DOI: 10.1128/JVI.00957-19 -
Archives of Gerontology and Geriatrics May 2023This study protocol describes the conceptual framework, design, and methods being employed to evaluate the implementation of the Transitional Care Model (TCM) as part of...
This study protocol describes the conceptual framework, design, and methods being employed to evaluate the implementation of the Transitional Care Model (TCM) as part of a randomized controlled trial. The trial, designed to examine the health and cost outcomes of at-risk hospitalized older adults, is being conducted in the context of the COVID-19 pandemic. This parallel study is guided by the Practical, Robust, Implementation and Sustainability Model (PRISM) and uses a fixed, mixed methods convergent parallel design to identify challenges encountered by participating hospitals and post-acute and community-based providers that impact the implementation of the TCM with fidelity, strategies implemented to address those challenges and the relationships between challenges, strategies, and rates of fidelity to TCM's core components over time. Prior to the study's launch and throughout its implementation, qualitative and quantitative data related to COVID and non-COVID challenges are being collected via surveys and meetings with healthcare system staff. Strategies implemented to address challenges and fidelity to TCM's core components are also being assessed. Analyses of quantitative (established metrics to evaluate TCM's core components) and qualitative data (barriers and facilitators to implementation) are being conducted independently. These datasets are then merged and interpreted together. General linear and mixed effects modeling using all merged data and patients' socio-demographic and social determinants of health characteristics, will be used to examine relationships between key variables and fidelity rates. Implications of study findings in the context of COVID-19 and future research opportunities are suggested. Trial registration: ClinicalTrials.gov Identifier: NCT04212962.
Topics: Humans; Aged; COVID-19; Transitional Care; Pandemics; Delivery of Health Care; Randomized Controlled Trials as Topic
PubMed: 36709563
DOI: 10.1016/j.archger.2023.104944 -
Frontiers in Network Physiology 2022Whole brain network models are now an established tool in scientific and clinical research, however their use in a larger workflow still adds significant informatics...
Whole brain network models are now an established tool in scientific and clinical research, however their use in a larger workflow still adds significant informatics complexity. We propose a tool, RateML, that enables users to generate such models from a succinct declarative description, in which the mathematics of the model are described without specifying how their simulation should be implemented. RateML builds on NeuroML's Low Entropy Model Specification (LEMS), an XML based language for specifying models of dynamical systems, allowing descriptions of neural mass and discretized neural field models, as implemented by the Virtual Brain (TVB) simulator: the end user describes their model's mathematics once and generates and runs code for different languages, targeting both CPUs for fast single simulations and GPUs for parallel ensemble simulations. High performance parallel simulations are crucial for tuning many parameters of a model to empirical data such as functional magnetic resonance imaging (fMRI), with reasonable execution times on small or modest hardware resources. Specifically, while RateML can generate Python model code, it enables generation of Compute Unified Device Architecture C++ code for NVIDIA GPUs. When a CUDA implementation of a model is generated, a tailored model driver class is produced, enabling the user to tweak the driver by hand and perform the parameter sweep. The model and driver can be executed on any compute capable NVIDIA GPU with a high degree of parallelization, either locally or in a compute cluster environment. The results reported in this manuscript show that with the CUDA code generated by RateML, it is possible to explore thousands of parameter combinations with a single Graphics Processing Unit for different models, substantially reducing parameter exploration times and resource usage for the brain network models, in turn accelerating the research workflow itself. This provides a new tool to create efficient and broader parameter fitting workflows, support studies on larger cohorts, and derive more robust and statistically relevant conclusions about brain dynamics.
PubMed: 36926112
DOI: 10.3389/fnetp.2022.826345 -
Journal of Burn Care & Research :... Mar 2021Coronavirus disease 2019 obliged many countries to apply lockdown policies to contain the spread of infection. The restrictions in Israel included limitations on...
Coronavirus disease 2019 obliged many countries to apply lockdown policies to contain the spread of infection. The restrictions in Israel included limitations on movement, reduction of working capacity, and closure of the educational system. The present study focused on patients treated at a referral center for burns in northern Israel. Their goal was to investigate temporal variations in burn injuries during this period. Data were retrospectively extracted from the medical records of burn patients treated at our hospital between March 14, 2020 and April 20, 2020 (ie, the period of aggravated lockdown). Data from this period were compared with that from paralleling periods between 2017 and 2019. During the lockdown and paralleling periods, 178 patients were treated for burn injuries, of whom 44% were under 18. Although no restrictions were enforced during the virus outbreak period with regard to seeking medical care, we noticed a decrease in the number of patients admitted to the emergency room for all reasons. Of particular interest was a 66% decrease in the number of adult burn patients (P < .0001). Meanwhile, among the pediatric population, no significant decrease was observed. Nonetheless, subgroups with higher susceptibility to burn injuries included children aged 2 to 5 years (56.3% vs 23.8%, P = .016) and female patients from all pediatric age groups (57.1% vs 25%, P = .027). These findings may be explained by the presumably busier kitchen and dining areas during the lockdown. Overall, the study results can assist with building a stronger understanding of varying burn injuries and with developing educational and preventive strategies.
Topics: Adolescent; Adult; Burn Units; Burns; COVID-19; Child; Child, Preschool; Emergency Service, Hospital; Female; Forecasting; Humans; Infant; Intensive Care Units; Israel; Length of Stay; Male; Retrospective Studies; Treatment Outcome
PubMed: 32914186
DOI: 10.1093/jbcr/iraa154 -
Journal of Applied Statistics 2021The logit binomial logistic dose response model is commonly used in applied research to model binary outcomes as a function of the dose or concentration of a substance....
The logit binomial logistic dose response model is commonly used in applied research to model binary outcomes as a function of the dose or concentration of a substance. This model is easily tailored to assess the relative potency of two substances. Consequently, in instances where two such dose response curves are parallel so one substance can be viewed as a dilution of the other, the degree of that dilution is captured in the relative potency model parameter. It is incumbent that experimental researchers working in fields including biomedicine, environmental science, toxicology and applied sciences choose efficient experimental designs to run their studies to both fit their dose response curves and to garner important information regarding drug or substance potency. This article provides far-reaching practical design strategies for dose response model fitting and estimation of relative potency using key illustrations. These results are subsequently extended here to handle situations where the assessment of parallelism and the proper dose-scale are also of interest. Conclusions and recommended strategies are supported by both theoretical and simulation results.
PubMed: 35707079
DOI: 10.1080/02664763.2021.1880556