Mark Scalf
YOU?
Author Swipe
View article: Interactome screening implicates BAG6 as a suppressor of UBQLN2 misfolding in ALS-dementia
Interactome screening implicates BAG6 as a suppressor of UBQLN2 misfolding in ALS-dementia Open
Ubiquilin-2 (UBQLN2) is a ubiquitin (Ub)-binding shuttle protein that is mutated in X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). ALS/FTD-linked mutations in UBQLN2 disrupt its conformation, incre…
View article: Identifying lncRNA–Protein Interactions in Hematopoietic Progenitor Cells by Hybridization Capture and Mass Spectrometry
Identifying lncRNA–Protein Interactions in Hematopoietic Progenitor Cells by Hybridization Capture and Mass Spectrometry Open
Long noncoding RNAs (lncRNAs) exert regulatory functions in a wide spectrum of biological contexts, and certain regulatory functions involve the formation of RNA-protein complexes. Discovering the structure and function of these complexes …
View article: Dehydroamino acids and their crosslinks in Alzheimer’s disease aggregates
Dehydroamino acids and their crosslinks in Alzheimer’s disease aggregates Open
Alzheimer’s disease (AD) is characterized by the accumulation of protein aggregates, which are thought to be influenced by posttranslational modifications (PTMs). Dehydroamino acids (DHAAs) are rarely observed PTMs that contain an electrop…
View article: DNA-damage dependent isoform switching modulates RIF1 DNA repair complex assembly and phase separation
DNA-damage dependent isoform switching modulates RIF1 DNA repair complex assembly and phase separation Open
How RIF1 (RAP1 interacting factor) fulfills its diverse roles in DNA double-strand break (DSB) repair, DNA replication, and nuclear organization remains elusive. Here we show that alternative splicing (AS) of a cassette exon (Ex32) encodin…
View article: Identification of Host Proteins Involved in Hepatitis B Virus Genome Packaging
Identification of Host Proteins Involved in Hepatitis B Virus Genome Packaging Open
A critical part of the hepatitis B virus (HBV) life cycle is the packaging of the pregenomic RNA (pgRNA) into nucleocapsids. While this process is known to involve several viral elements, much less is known about the identities and roles o…
View article: Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs
Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs Open
Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate differe…
View article: Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs
Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs Open
Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate…
View article: Elucidating the RNA–Protein Interactomes of Target RNAs in Tissue
Elucidating the RNA–Protein Interactomes of Target RNAs in Tissue Open
RNA-protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA-protein …
View article: Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2
Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2 Open
Mutations in the ubiquitin (Ub) chaperone Ubiquilin 2 (UBQLN2 ) cause X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) through unknown mechanisms. Here, we show that aggregation-prone, ALS-associated …
View article: Axon guidance pathways modulate neurotoxicity of ALS-associated UBQLN2
Axon guidance pathways modulate neurotoxicity of ALS-associated UBQLN2 Open
Mutations in the ubiquitin (Ub) chaperone Ubiquilin 2 (UBQLN2) cause X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) through unknown mechanisms. Here we show that aggregation-prone, ALS-associated mu…
View article: Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP
Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP Open
In eukaryotes, splice sites define the introns of pre-mRNAs and must be recognized and excised with nucleotide precision by the spliceosome to make the correct mRNA product. In one of the earliest steps of spliceosome assembly, the U1 smal…
View article: Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1
Discovery of Dehydroamino Acid Residues in the Capsid and Matrix Structural Proteins of HIV-1 Open
Human immunodeficiency virus type 1 (HIV-1) remains a deadly infectious disease despite existing antiretroviral therapies. A comprehensive understanding of the specific mechanisms of viral infectivity remains elusive and currently limits t…
View article: MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses
MetaNetwork Enhances Biological Insights from Quantitative Proteomics Differences by Combining Clustering and Enrichment Analyses Open
Interpreting proteomics data remains challenging due to the large number of proteins that are quantified by modern mass spectrometry methods. Weighted gene correlation network analysis (WGCNA) can identify groups of biologically related pr…
View article: Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules
Towards an Ideal In Cell Hybridization-Based Strategy to Discover Protein Interactomes of Selected RNA Molecules Open
RNA-binding proteins are crucial to the function of coding and non-coding RNAs. The disruption of RNA–protein interactions is involved in many different pathological states. Several computational and experimental strategies have been devel…
View article: Fused in sarcoma regulates DNA replication timing and kinetics
Fused in sarcoma regulates DNA replication timing and kinetics Open
Fused in sarcoma (FUS) encodes an RNA-binding protein with diverse roles in transcriptional activation and RNA splicing. While oncogenic fusions of FUS and transcription factor DNA-binding domains are associated with soft tissue sarcomas, …
View article: Multi-Factor Authentication of Potential 5’ Splice Sites by the <i>Saccharomyces cerevisiae</i> U1 snRNP
Multi-Factor Authentication of Potential 5’ Splice Sites by the <i>Saccharomyces cerevisiae</i> U1 snRNP Open
In eukaryotes, splice sites define the introns of pre-mRNAs and must be recognized and excised with nucleotide precision by the spliceosome to make the correct mRNA product. In one of the earliest steps of spliceosome assembly, the U1 smal…
View article: Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics
Mesh Fragmentation Improves Dissociation Efficiency in Top-down Proteomics Open
Top-down proteomics is a key mass spectrometry-based technology for comprehensive analysis of proteoforms. Proteoforms exhibit multiple high charge states and isotopic forms in full MS scans. The dissociation behavior of proteoforms in dif…
View article: Identification of host proteins differentially associated with HIV-1 RNA splice variants
Identification of host proteins differentially associated with HIV-1 RNA splice variants Open
HIV-1 generates unspliced (US), partially spliced (PS), and completely spliced (CS) classes of RNAs, each playing distinct roles in viral replication. Elucidating their host protein ‘interactomes’ is crucial to understanding virus-host int…
View article: Identifying HIV-1 RNA splice variant protein interactomes using HyPR-MS<sub>SV</sub>
Identifying HIV-1 RNA splice variant protein interactomes using HyPR-MS<sub>SV</sub> Open
HIV-1 generates unspliced (US), partially spliced (PS), and completely spliced (CS) classes of RNAs; each playing distinct roles in viral replication. Elucidating their host protein “interactomes” is crucial to understanding virus-host int…
View article: Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data
Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data Open
Cellular functions are performed by a vast and diverse set of proteoforms. Proteoforms are the specific forms of proteins produced as a result of genetic variations, RNA splicing, and post-translational modifications (PTMs). Top-down mass …
View article: Fused in sarcoma regulates DNA replication timing and progression
Fused in sarcoma regulates DNA replication timing and progression Open
Fused in sarcoma (FUS ) encodes a low complexity RNA-binding protein with diverse roles in transcriptional activation and RNA processing. While oncogenic fusions of FUS and transcription factor DNA-binding domains are associated with soft …
View article: A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics
A Bayesian Null Interval Hypothesis Test Controls False Discovery Rates and Improves Sensitivity in Label-Free Quantitative Proteomics Open
Statistical significance tests are a common feature in quantitative proteomics workflows. The Student's t-test is widely used to compute the statistical significance of a protein's change between two groups of samples. However, the t-test'…
View article: Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis
Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis Open
The 26S proteasome is an essential protease that selectively eliminates dysfunctional and short-lived regulatory proteins in eukaryotes. To define the composition of this proteolytic machine in plants, we tagged either the core protease (C…
View article: Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database
Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database Open
Complex human biomolecular processes are made possible by the diversity of human proteoforms. Constructing proteoform families, groups of proteoforms derived from the same gene, is one way to represent this diversity. Comprehensive, high-c…