Joshua E. Elias
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View article: Cell size-dependent mRNA transcription drives proteome remodeling
Cell size-dependent mRNA transcription drives proteome remodeling Open
Increasing cell size drives proteomic changes that impact cell physiology. However, the molecular basis of size-dependent proteome remodeling has remained unclear. Here, we develop an inducible Cyclin D1 expression system in human cells to…
View article: Replicating without stress: a dengue replicon model reveals distinct host rewiring to accommodate persistence
Replicating without stress: a dengue replicon model reveals distinct host rewiring to accommodate persistence Open
Summary Self-replicating viral RNAs, or replicons, are widely used to study virus-host interactions and screen antiviral compounds, yet their ability to model persistent infection and host adaptation remains poorly understood. Here, we cha…
View article: Characterization of the optical model of the T2K 3D segmented plastic scintillator detector unit cube
Characterization of the optical model of the T2K 3D segmented plastic scintillator detector unit cube Open
The magnetized near detector (ND280) of the T2K long-baseline neutrino oscillation experiment has been recently upgraded aiming to satisfy the requirement of reducing the systematic uncertainty from measuring the neutrino–nucleus interacti…
View article: Parasite and vector circadian clocks mediate efficient malaria transmission
Parasite and vector circadian clocks mediate efficient malaria transmission Open
Malaria transmission begins when Anopheles mosquitos deposit saliva and Plasmodium parasites during a bloodmeal. As Anopheles mosquitos are nocturnal, we investigated whether their salivary glands are under circadian control, anticipating …
View article: Characterization of the optical model of the T2K 3D segmented plastic scintillator detector
Characterization of the optical model of the T2K 3D segmented plastic scintillator detector Open
The magnetised near detector (ND280) of the T2K long-baseline neutrino oscillation experiment has been recently upgraded aiming to satisfy the requirement of reducing the systematic uncertainty from measuring the neutrinonucleus interactio…
View article: BiP/GRP78 is a pro-viral factor for diverse dsDNA viruses that promotes the survival and proliferation of cells upon KSHV infection
BiP/GRP78 is a pro-viral factor for diverse dsDNA viruses that promotes the survival and proliferation of cells upon KSHV infection Open
The Endoplasmic Reticulum (ER)-resident HSP70 chaperone BiP (HSPA5) plays a crucial role in maintaining and restoring protein folding homeostasis in the ER. BiP’s function is often dysregulated in cancer and virus-infected cells, conferrin…
View article: Rapid QC-MS: Interactive Dashboard for Synchronous Mass Spectrometry Data Acquisition Quality Control
Rapid QC-MS: Interactive Dashboard for Synchronous Mass Spectrometry Data Acquisition Quality Control Open
Consistently collecting high-quality liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) data is a time-consuming hurdle for untargeted workflows. Analytical controls such as internal and biological standards are commonly inc…
View article: mTOR activation induces endolysosomal remodeling and nonclassical secretion of IL-32 via exosomes in inflammatory reactive astrocytes
mTOR activation induces endolysosomal remodeling and nonclassical secretion of IL-32 via exosomes in inflammatory reactive astrocytes Open
View article: Circadian rhythms mediate malaria transmission potential
Circadian rhythms mediate malaria transmission potential Open
Malaria transmission begins when infected female Anopheles mosquitos deposit Plasmodium parasites into the mammalian host’s skin during a bloodmeal. The salivary gland-resident sporozoite parasites migrate to the bloodstream, subsequently …
View article: SARS-CoV-2 Nsp1 cooperates with initiation factors EIF1 and 1A to selectively enhance translation of viral RNA
SARS-CoV-2 Nsp1 cooperates with initiation factors EIF1 and 1A to selectively enhance translation of viral RNA Open
A better mechanistic understanding of virus-host dependencies can help reveal vulnerabilities and identify opportunities for therapeutic intervention. Of particular interest are essential interactions that enable production of viral protei…
View article: Rapid QC-MS – Interactive Dashboard for Synchronous Mass Spectrometry Data Acquisition Quality Control
Rapid QC-MS – Interactive Dashboard for Synchronous Mass Spectrometry Data Acquisition Quality Control Open
Consistently collecting high quality liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) data is a time consuming hurdle for untargeted workflows. Analytical controls such as internal and biological standards are commonly inc…
View article: Spatio-temporal analysis of Vaccinia virus infection and host response dynamics using single-cell transcriptomics and proteomics
Spatio-temporal analysis of Vaccinia virus infection and host response dynamics using single-cell transcriptomics and proteomics Open
Poxviruses are a large group of DNA viruses with exclusively cytoplasmic life cycles and complex gene expression programs. A number of systems-level studies have analyzed bulk transcriptome and proteome changes upon poxvirus infection, but…
View article: Global Organelle Profiling Reveals Subcellular Localization and Remodeling at Proteome Scale
Global Organelle Profiling Reveals Subcellular Localization and Remodeling at Proteome Scale Open
View article: Global organelle profiling reveals subcellular localization and remodeling at proteome scale
Global organelle profiling reveals subcellular localization and remodeling at proteome scale Open
Defining the subcellular distribution of all human proteins and its remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immun…
View article: Cell Size Contributes to Single-Cell Proteome Variation
Cell Size Contributes to Single-Cell Proteome Variation Open
Accurate measurements of the molecular composition of single cells will be necessary for understanding the relationship between gene expression and function in diverse cell types. One of the most important phenotypes that differs between c…
View article: Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells
Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells Open
SUMMARY Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how size influences cell physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, d…
View article: Oral vancomycin treatment suppresses gut trypsin activity and preserves intestinal barrier function during EAE
Oral vancomycin treatment suppresses gut trypsin activity and preserves intestinal barrier function during EAE Open
Studies have reported increased intestinal permeability in multiple sclerosis (MS) patients and its mouse model experimental autoimmune encephalomyelitis (EAE). However, the mechanisms driving increased intestinal permeability that in turn…
View article: metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering
metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering Open
Background The high diversity and complexity of the microbial community make it a formidable challenge to identify and quantify the large number of proteins expressed in the community. Conventional metaproteomics approaches largely rely on…
View article: SARS-CoV-2 Nsp1 regulates translation start site fidelity to promote infection
SARS-CoV-2 Nsp1 regulates translation start site fidelity to promote infection Open
A better mechanistic understanding of virus-host interactions can help reveal vulnerabilities and identify opportunities for therapeutic interventions. Of particular interest are essential interactions that enable production of viral prote…
View article: Extracellular vesicles in systemic juvenile idiopathic arthritis
Extracellular vesicles in systemic juvenile idiopathic arthritis Open
Systemic juvenile idiopathic arthritis is a chronic pediatric inflammatory disease of unknown etiology, characterized by fever, rash, hepatosplenomegaly, serositis, and arthritis. We hypothesized that intercellular communication, mediated …
View article: Additional file 3 of metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering
Additional file 3 of metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering Open
Additional file 3. Table of statistical analysis of significantly changed MCL-clustered protein groups between sample clusters.
View article: Additional file 2 of metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering
Additional file 2 of metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering Open
Additional file 2. Table of statistical analysis of significantly changed consensus peptides between sample clusters.
View article: Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation
Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation Open
View article: Cell size contributes to single-cell proteome variation
Cell size contributes to single-cell proteome variation Open
Accurate measurements of the molecular composition of single cells will be necessary for understanding the relationship between gene expression and function in diverse cell types. One of the most important phenotypes that differs between c…
View article: Delineation of proteome changes driven by cell size and growth rate
Delineation of proteome changes driven by cell size and growth rate Open
Increasing cell size drives changes to the proteome, which affects cell physiology. As cell size increases, some proteins become more concentrated while others are diluted. As a result, the state of the cell changes continuously with incre…
View article: Increasing cell size remodels the proteome and promotes senescence
Increasing cell size remodels the proteome and promotes senescence Open
View article: metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering
metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering Open
Background: The high diversity and complexity of the microbial community make it a formidable challenge to identify and quantify the large number of proteins expressed in the community. Conventional metaproteomics approaches largely rely o…
View article: <scp>ZSCAN1</scp> Autoantibodies Are Associated with Pediatric Paraneoplastic <scp>ROHHAD</scp>
<span>ZSCAN1</span> Autoantibodies Are Associated with Pediatric Paraneoplastic <span>ROHHAD</span> Open
Objective Rapid‐onset Obesity with Hypothalamic Dysfunction, Hypoventilation and Autonomic Dysregulation (ROHHAD), is a severe pediatric disorder of uncertain etiology resulting in hypothalamic dysfunction and frequent sudden death. Freque…
View article: An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease
An efficient urine peptidomics workflow identifies chemically defined dietary gluten peptides from patients with celiac disease Open
View article: Tuning DO:DM Ratios Modulates MHC Class II Immunopeptidomes
Tuning DO:DM Ratios Modulates MHC Class II Immunopeptidomes Open