Alma L. Burlingame

Optimization of Search and Acquisition Strategies for DSSO Crosslinking Mass Spectrometry using Protein Prospector and Touchstone.

The paper evaluates DSSO crosslinking strategies using Protein Prospector and Touchstone, finding that DSSO's advantage comes from backbone fragmentation, not diagnostic ions, and that MS3 is better for proteome-scale samples.

Paralemmin 2 is a shared, alternatively-spliced regulator of axon initial segments and paranodal junctions in oligodendrocytes

This study identifies Paralemmin 2 as a lipid raft-associated protein that regulates axon initial segments and paranodal junctions through cell type-specific splicing.

Calcium-dependent synaptic proteomics reveals EGFR signaling at active synapses

The paper develops a method to profile synaptic proteomes under physiological conditions and identifies EGFR signaling as a key activity-dependent process at synapses.

Synaptic vesicles that store monoamines and glutamate differ in protein composition.

This study compares synaptic vesicle protein composition between dopamine and glutamate release sites, identifying differences in abundance and function that affect recycling kinetics.

Myelin basic protein is an RNA chaperone in microglial nuclear retro-transport

The paper identifies myelin basic protein (MBP) as an RNA chaperone that facilitates microglial nuclear import of myelin RNA, with implications for multiple sclerosis pathology.

AlphaFold2-Guided Functional Screens Reveal a Conserved Antioxidant Protein at ER Membranes

The paper identifies ERGU-1 as a conserved antioxidant protein at ER membranes using AlphaFold2 and functional screens in C. elegans, showing its role in H2O2 detoxification and antioxidant defense.

Diverse and Location-Specific Roles of PlexinA2, PlexinA4, and NCAM in Developing Hippocampal Mossy Fibers

This study investigates the roles of PlexinA2, PlexinA4, and NCAM in the development of mossy fibers in the hippocampus, revealing distinct and overlapping functions in axon bundling and targeting.

COUNTERING AGE-ASSOCIATED ALTERATIONS IN OLIGODENDROCYTE-DERIVED EXTRACELLULAR MATRIX REJUVENATES COGNITION

The paper shows that reversing age-related changes in oligodendrocyte-derived extracellular matrix improves cognition in aged mice.

Acetylation of Axonal G3BP1 through ELP3 Accelerates Axon Regeneration

This study shows that acetylation of G3BP1 by ELP3 promotes axon regeneration and neuronal recovery after injury.

Liver CYP4A autophagic-lysosomal degradation (ALD): A major role for the autophagic receptor SQSTM1/p62 through an uncommon target interaction site

The paper identifies SQSTM1/p62 as a key autophagic receptor for CYP4A degradation, showing its role in preventing proinflammatory metabolite production and insoluble aggregates in liver cells.

An intrinsically disordered region of histone demethylase KDM5A activates catalysis through interactions with the nucleosomal acidic patch and DNA

This study identifies an intrinsically disordered region in KDM5A that binds the nucleosome's acidic patch and DNA, enabling catalytic activity through multivalent interactions.

Assessing Heterogeneity in the N-Telopeptides of Type I Collagen by Mass Spectrometry

The paper develops a method to identify N-terminal cross-linked peptides from collagen I in Achilles tendon using mass spectrometry, revealing differences in cross-links in bovine pulmonary hypertension.

Identification and Characterization of PCAHIT, a Novel Long Non-Coding RNA Associated with Poor Outcomes in Prostate Cancer

This study identifies PCAHIT, a lncRNA linked to poor outcomes in prostate cancer, showing it promotes aggressive phenotypes by affecting steroid biosynthesis and immune response.

Reversible histone deacetylase activity catalyzes lysine acylation

The paper shows class I HDACs can catalyze beta-hydroxybutyrylation of lysine, a reversible modification, expanding the role of HDACs beyond traditional deacetylation.

Functional screen for mediators of onco-mRNA translation specificity

The paper identifies RBM42 as a key regulator of MYC translation in PDAC, showing its role in oncogenic transcript regulation and tumor growth.

The VGCC auxiliary subunit α2δ1 is an extracellular GluA1 interactor and regulates LTP, spatial memory, and seizure susceptibility

This study identifies α2δ1 as an extracellular GluA1 interactor that regulates LTP, spatial memory, and seizure susceptibility through its role in AMPAR trafficking.

TAOK2 Drives Opposing Cilia Length Deficits in 16p11.2 Deletion and Duplication Carriers

The paper identifies TAOK2 as a regulator of primary cilium length in 16p11.2 CNV carriers, showing opposing effects in deletion and duplication cases.

RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages

RAPIDASH enriches ribosome-associated proteins from diverse samples, revealing their roles in neurodevelopment and immune response.

NEK1 modulates neurite outgrowth in motor neurons through coordinating retromer formation

This study identifies NEK1's role in motor neuron neurite outgrowth by coordinating retromer formation through interactions with SMC3.

Antibody-directed extracellular proximity biotinylation reveals Contactin-1 regulates axo-axonic innervation of axon initial segments.

The paper identifies Contactin-1 as an AIS cell surface protein that regulates axo-axonic innervation by interacting with Neurofascin and NrCAM.

PTBP1 Regulates Injury Responses and Sensory Pathways in Adult Peripheral Neurons

This study shows PTBP1 is expressed in adult sensory and motor neurons, with increased axonal levels after injury, affecting axon outgrowth and sensation.

Contrasting synaptic roles of MDGA1 and MDGA2

The paper investigates the distinct synaptic roles of MDGA1 and MDGA2, showing MDGA1 modulates excitatory synapses while MDGA2 affects inhibitory synapses.

Targeted high throughput mutagenesis of the human spliceosome reveals its in vivo operating principles

This study uses CRISPR-Cas9 base editing to target the human spliceosome and identifies functional sites and resistance substitutions, revealing SUGP1's role in spliceosome disassembly.

A new monoclonal antibody enables BAR analysis of subcellular importin β1 interactomes

This paper develops a novel anti-KPNB1 monoclonal antibody for BAR analysis, revealing new importin β1 interactors and expanding its known functions beyond nucleocytoplasmic transport.

Capturing the Hierarchically Assorted Modules of Protein Interaction in the Organized Nucleome

The paper introduces a pipeline called CHAMPION that uses qXL-MS and MONET modulomics to identify nuclear protein interactions and modules, revealing novel interactors and hormone-specific variants.

Intra-axonal translation of Khsrp mRNA slows axon regeneration by destabilizing localized mRNAs

This study identifies KHSRP as an axonal RNA-binding protein whose mRNA is locally translated after nerve injury, leading to mRNA destabilization and slowed axon regeneration.

Molecular characterization of AMPA receptor trafficking vesicles

The paper isolates and characterizes AMPA receptor trafficking vesicles from mouse brains, identifying known and novel proteins involved in their composition and function in synaptic plasticity.

Ankyrin-R regulates fast-spiking interneuron excitability through perineuronal nets and Kv3.1b K+ channels

This study identifies AnkR's role in regulating fast-spiking interneuron excitability through perineuronal nets and Kv3.1b K+ channels in mouse and human.

A dose-sensitive OGT-TET3 complex is necessary for normal Xist RNA distribution and function

The paper identifies an OGT-TET3 complex that regulates 5mC and 5hmC levels and XCI in female mouse embryonic stem cells.

Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions

This study identifies AtACINUS as an O-GlcNAcylated and O-fucosylated protein that regulates transcription and alternative splicing of reproductive regulators in Arabidopsis.