Recent Publications by AGS Members
2026-09-02
Published in: Methods in Molecular Biology (clifton, N.j.)
Proteomic studies are highly informative for identifying biological signatures. The data generated from such experiments are highly complex and require substantial computational expertise to analyze appropriately. Rigorous analysis is further confounded by the presence of missing values and multiple sources of technical variance. Here, we present a methodical walkthrough of a workflow for the analysis of Data Independent Acquisition (DIA) proteomics data. The workflow is derived from the...
2026-09-02
Published in: Methods in Molecular Biology (clifton, N.j.)
Post-translational modifications (PTMs) can play vital roles in the protein's structure, function, localization, and interactions, enabling dynamic control of cellular processes. As such, understanding these modifications is essential to elucidate key biological mechanisms. This chapter discusses an unbiased, mass spectrometry-based approach using wildcard (open) searches in the Byonic platform to detect and identify nondisulfide cysteine PTMs. By targeting individual cysteines and scanning for...
2026-09-02
Published in: Methods in Molecular Biology (clifton, N.j.)
The mechano-redox phenomenon-where mechanical forces and redox reactions synergistically regulate protein function-has been demonstrated in several mammalian proteins. Integrins, which mediate cellular adhesion to ligands, are particularly sensitive to redox modulation via thiol-disulfide exchange catalyzed by enzymes such as thiol isomerases. These redox-driven modifications can alter integrin conformation and ligand-binding affinity, ultimately leading to dynamic regulation of cell adhesion...
2026-09-02
Published in: The Journal of Organic Chemistry
A new light-promoted method for the preparation of glycosyl bromides has been developed, exhibiting broad applicability to commonly used substrates. Upon irradiation with purple LEDs, bromine reacts with benzotrifluoride (PhCF3) to generate hydrogen bromide (HBr) in situ, which subsequently transforms the substrate into the glycosyl bromide in excellent yield. Unlike classical methods, the new strategy generates minimal acidic waste and features a simple workup. Notably, its scalability was...
2026-09-02
Published in: Biochemical Society Transactions
Unlike the cornea and tear fluid, glycosylation within the retina remains remarkably underexplored. This review highlights the diverse roles of glycans in retinal development and vision, with a focus on major glycan classes, including glycosphingolipids (GSLs; glycans attached to lipids), N- and O-linked glycans on proteins, glycosaminoglycans (GAGs) on proteoglycans, O-mannosylated proteoglycans, and intracellular O-GlcNAcylation. Together, these components provide a comprehensive framework for...
2026-08-28
Published in: Microbiology Resource Announcements
Campylobacter jejuni and Campylobacter coli are major foodborne pathogens. We announce the deposition of Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) proteomic data sets from PBT2-treated and untreated cultures. These data sets provide a resource for investigating the proteomic response of Campylobacter spp. to the antimicrobial ionophore PBT2.
2026-08-27
Published in: Viruses
Filoviruses cause highly lethal infectious diseases with hemorrhagic symptoms and extremely high fatality rate (up to 90%). Although two vaccines against Ebola virus (EBOV) are licensed for application in endemic areas, vaccines against other filoviruses (SUDV, BDBV, MARV) are still at pre-clinical or clinical stages. The development of vaccines requires protective efficacy studies using animal models of infection. However, animal studies using wild-type filoviruses require maximum biosafety...
2026-08-25
Published in: Proceedings of the National Academy of Sciences of the United States of America
Tumor-associated macrophages (TAMs) are functionally diverse effector cells in the tumor microenvironment (TME). Pro- and anti-inflammatory TAMs are central to cancer progression by shaping inflammation and immune homeostasis, but it remains unknown if polarization-induced remodeling of the TAM glycocalyx critical for cellular communication and interactions occurs within the TME. Taking a systems glycobiology approach, we first used cell surface-focused glycomics and lectin flow cytometry of ex...
2026-08-25
Published in: Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
Caffeine is one of the most consumed stimulants with pharmaceutical benefits; however, its varied pH-dependent solubility (120-500 µg/mL) and moderate stability hinder bioavailability. In this study, a 1:1:1 cocrystal hydrate of caffeine with 4-hydroxybenzoic acid was crystallized and systematically reevaluated. SCXRD and PXRD revealed a triclinic system sustained by O─H···O and C─H···O hydrogen bonds. The Hirshfeld surface showed increased H···O/O···H interactions from 11.0% in caffeine to...
2026-08-25
Published in: Nature Communications
Critical illness, including COVID-19 and trauma, induce immune dysregulation associated with morbidity and mortality. Direct comparison is crucial to identify shared pathobiological mechanisms to guide precision therapies. This prospective cohort study undertook a comprehensive, longitudinal comparison of innate immune cell function and plasma protein expression in critically ill patients at days 1, 3, and 5 of intensive care unit admission. We enrolled 26 COVID-19 patients, 20 trauma patients,...
2026-08-19
Published in: Developmental Medicine and Child Neurology
AIM: To identify shared and disorder-specific molecular alterations across encephalitis, Aicardi-Goutières syndrome (AGS), and autism spectrum disorder (ASD) using cerebrospinal fluid (CSF) proteomics.
2026-08-19
Published in: Current Biology : Cb
Fungi transition between cell morphologies to adapt to and colonize environments. For Candida albicans, commensal colonization of humans and virulence depend on a reversible switch between invasive hyphae and disseminating yeast cells. The yeast-to-hyphae transition is well understood, but comparatively little is known about the reverse transition from hyphae back to yeast. By developing an imaging assay to visualize and quantify the hyphae-to-yeast transition, we show that the bacterial natural...
2026-08-18
Published in: Health Science Reports
CONCLUSION: Among U.S. adults, higher TyG-WC was associated with a greater prevalence of self-reported physician-diagnosed gout. TyG-WC showed modest discriminative performance and a numerically higher AUC than other TyG-related indices. Because of the cross-sectional design, these findings should be interpreted as associations and require confirmation in prospective studies.
2026-08-12
Published in: Nature Communications
Immunity to Streptococcus pyogenes infection appears to develop progressively through repeated exposure during early life. However, the intensity or duration of exposure required is unknown, as to why some individuals appear to develop immunity, despite having few or no previously detected infections. Here, drawing on samples from a human model of pharyngeal S. pyogenes infection, we investigate whether symptomatic disease is required for induction of protective immune responses. We show that...
2026-08-11
Published in: The Journal of Infectious Diseases
CONCLUSIONS: The new diagnostic assay detects free and EV-associated Galf-containing glycans enabling urine testing for IA. Further analyses of the design-locked assay are needed for confirmation.
2026-08-04
Published in: Frontiers in Microbiology
Antimicrobial resistance (AMR) has emerged as one of the greatest global health concerns and its threat to effective treatment of infectious diseases is accelerating. Biofilms remain a major contributor to antimicrobial resistance and persistence of infections. Bacterial biofilms are sessile communities of bacteria surrounded by a self-produced extracellular polymeric substance (EPS). Bacterial cells in biofilms are less susceptible to conventional antibiotics and to host immune effector...
2026-08-04
Published in: Carbohydrate Research
Several synthetic strategies for obtaining C-2 functionalized l-idose or l-iduronic acid derivatives were investigated. Synthesis of protected derivatives with a C-2 hydroxy group proceeded smoothly, however, these compounds were prone to competing elimination reactions during subsequent oxidation and HWE steps. Elimination during oxidation could be minimized by replacing benzylidenes with alternative protecting groups, resulting in satisfactory overall yields of the corresponding unsaturated...
2026-07-27
Published in: Singapore Medical Journal
No abstract
2026-07-25
Published in: Journal of the International Aids Society
No abstract
2026-07-25
Published in: Journal of the International Aids Society
CONCLUSIONS: Current evidence from RCTs does not support the use of 4CMenB to prevent gonorrhoea in gay and bisexual men at high risk of acquisition. Results from ongoing RCTs will be critical to determine whether vaccine efficacy varies by population or epidemiological context and to inform future gonorrhoea vaccine policy and development.
2026-07-17
Published in: Acute Medicine & Surgery
No abstract
2026-07-17
Published in: Biorxiv : the Preprint Server for Biology
Controlling protein glycosylation as a critical quality attribute of biopharmaceuticals remains challenging when glycosylation is coupled to cellular production systems. Here, we present a proof-of-concept glycosyltransferase immobilised enzyme reactor (IMER) housed within a 3D-printed column that enables directed post-production glycan modification of purified glycoproteins. Using β-1,4-galactosyltransferase (β4GalT1-IMER) and α-2,6-sialyltransferase (ST6Gal1-IMER) immobilised on Ni-NTA resin,...
2026-07-15
Published in: Science Advances
Macrophages are key drivers of inflammatory and fibrotic diseases, and their activation is shaped by interactions in their tissue microenvironment. However, dissecting the processes that drive immunopathology has proved challenging, as traditional two-dimensional (2D) culture methods fail to capture the complex molecular environment that macrophages inhabit in vivo. To address this, we generated a 3D in vitro model to better mimic the in vivo biophysical microenvironment. We show that the...
2026-07-15
Published in: Nature Communications
The emergence of mobile colistin resistance (mcr) genes threatens the efficacy of polymyxins as last-resort antibiotics for treating multidrug-resistant bacterial infections. Here, we identify a novel environmental mcr gene, mcr-12, discovered in Pigmentiphaga litoralis from Australian sediment, and evaluate its potential role in the intersection between environmental resistance reservoirs and clinically relevant bacteria. Gene mcr-12 was located within a metal-resistance gene cluster on plasmid...
2026-07-13
Published in: Chemical Science
Bacterial catabolism of 2,3-dihydroxypropanesulfonate (DHPS) links algal production to marine degradation and connects sulfosugar metabolism to sulfide production in the gut. In surface seawater, DHPS occurs as a dilute, mixed R/S pool, whereas in the anaerobic gut it is produced predominantly as S-DHPS through bacterial sulfoglycolysis pathways. Uptake is achieved via tripartite ATP-independent periplasmic (TRAP) transporters that employ periplasmic substrate-binding proteins (HpsK), but the...
2026-07-11
Published in: Small (weinheim an Der Bergstrasse, Germany)
Stimuli-responsive delivery systems, particularly thermoresponsive platforms, are becoming increasingly important for physiological applications, but their development has been limited by poor biocompatibility, slow response, and non-scalable fabrication methods. Liposomes offer a biocompatible and adaptable foundation for this need, but no scalable approach exists to produce uniform thermosensitive liposomes that activate above 37°C. Here, we present the first scalable strategy for generating...
2026-07-08
Published in: The New England Journal of Medicine
CONCLUSIONS: 4CMenB did not result in a lower incidence of N. gonorrhoeae infection than placebo among MSM who were at high risk for gonorrhea. (Funded by the Australian National Health and Medical Research Council and GSK; GoGoVax ClinicalTrials.gov number, NCT04415424.).
2026-07-03
Published in: Annals of Noninvasive Electrocardiology : the Official Journal of the International Society for Holter and Noninvasive Electrocardiology, Inc
No abstract
2026-07-01
Published in: Journal of Medicinal Chemistry
Clostridioides difficile (C. difficile) is the leading cause of hospital-acquired life-threatening diarrhea. C. difficile toxins TcdA and TcdB contain a glucosyltransferase domain (GTD) that glucosylates and inactivates host GTPases, disrupting the actin cytoskeleton and compromising epithelial integrity. TcdB, the most potent virulence factor, drives disease progression and is a high-priority target forC. difficiletreatment and prevention. The iminosugar isofagomine has been shown to inhibit...
2026-06-30
Published in: Analytical Chemistry
On-bead single-pot solid-phase enhanced sample preparation, SP3, also known as protein aggregation capture (PAC), is a robust, high-throughput, and widely utilized approach for proteomic sample preparation. Recent studies have highlighted PAC/SP3 as an ideal platform for chemoproteomics, allowing chemical labeling while minimizing sample loss and improving recovery of derivatized peptides. In this work, we establish an on-bead PAC/SP3 protein-level amine and carboxyl derivatization approach to...
2026-06-29
Published in: Nature Genetics
Maize primary metabolism drives complex agronomic traits, yet its genetic regulation remains difficult to resolve. Here we integrated genomic, transcriptomic and metabolomic data from 1,404 maize progenies derived from 24 diverse founders to dissect the genetic architecture of primary metabolism. We constructed a high-confidence regulatory network that resolved causal genes underlying metabolic quantitative trait loci and successfully identified targets for improving maize nutritional quality....
2026-06-23
Published in: Nature Communications
Most bacteria have evolved mechanisms to compete with other bacteria, often through the specialised secretion of proteinaceous toxins. However, mycobacteria have not previously been reported to engage in this form of competition. The thick and unusual mycobacterial cell wall, comprised of peptidoglycan, arabinogalactan and mycolic acids, is generally thought to be highly protective to these bacteria. Here, we show that some mycobacteria can use endo-D-arabinanases of the GH183 family for...
2026-06-23
Published in: Molecular Systems Biology
Protein-protein interactions (PPIs) are dynamic and critical to adaptive homeostasis. While there have been massive efforts to catalogue proteome-wide PPIs, global quantification of changes remains a challenge. Here, we integrate dynamic protein correlation profiling - mass spectrometry (PCP-MS) and quantitative cross linking-mass spectrometry (qXL-MS) using multiplexed stable isotope labelling to characterise global PPI remodelling following the development of chronic skeletal muscle insulin...
2026-06-17
Published in: Talanta
Porous graphitized carbon (PGC) LC-MS/MS-based detection of glycans ranging from approximately 3-15 saccharide residues is a gold standard in glycomics; however, robust glycoprofiling workflows that also cover mono- and disaccharide glycans (e.g. Tn, T, sialyl Tn O-glycans) are less mature. Given the growing appreciation that short glycans are biologically and clinically important, we here address this analytical shortcoming by testing the glycoprofiling performance of a new Supel Carbon PGC...
2026-06-15
Published in: Mbio
Helicobacter pylori colonizes the gastric mucosa of around half of the world's population and is a major cause of chronic gastritis, peptic ulcer disease, and gastric cancer. Current therapies are becoming increasingly ineffective due to the rapid spread of antibiotic resistance, creating an urgent need for new treatment options with distinct mechanisms of action. Drug repurposing offers a practical and cost-effective approach to address this gap. PBT2 is an 8-hydroxyquinoline derivative...
2026-06-14
Published in: Chemistry, an Asian Journal
A C-2 functionalized l-IdoA derivative was designed as a potential pharmacological chaperone for MPS II, and several routes to its synthesis were investigated. Successful synthesis proceeded via an oxidation/Horner-Wadsworth-Emmons sequence, overcoming significant challenges with competing elimination reactions to give alkene derivatives in good overall yields. Catalytic hydrogenation of the double bonds proceeded stereoselectively in high yield to give the desired L-ido-configured products,...
2026-06-12
Published in: Research Square
Mycobacteriophages, viruses that infect mycobacteria, hold promise as therapeutics against antibiotic-resistant mycobacterial infections. Although thousands of mycobacteriophages have been isolated, high-resolution baseplate structures have been reported for only two, revealing a knowledge gap in understanding phage-host interactions. Most mycobacteriophages are siphophages, possessing four structural components: capsid, connector, non-contractile tail and baseplate. The baseplate plays a...
2026-06-09
Published in: Applied and Environmental Microbiology
Inducible gene expression is pivotal to dissect bacterial physiology and virulence mechanisms. Across the Burkholderia genus, a limited range of inducible systems currently exist that allow tight regulation. In this study, we engineer a set of cumate inducible vectors for use in Burkholderia cenocepacia that offer minimal basal expression and the ability to control B. cenocepacia gene expression in eukaryotic cells. Through mutagenesis-based studies of cumate circuits and the cumate regulator...
2026-06-08
Published in: Jci Insight
It remains unclear why vaccines targeting prominent microbial virulence factors often fail in clinical trials. Because microbial virulence depends on interaction with the host immune system, we investigated how changes in host immune function alter vaccine efficacy. Using a vaccine against Staphylococcus aureus α-toxin (Hla), which targets host metalloprotease ADAM10 on myeloid cells, we show that Hla virulence is reduced in aged mice due to diminished ADAM10 activity and impaired myeloid cell...
2026-06-04
Published in: Arteriosclerosis, Thrombosis, and Vascular Biology
CONCLUSIONS: This study provides genetic and pharmacological evidence that FUT8-mediated core fucosylation of platelet receptors promotes platelet activation and thrombus formation. Our results suggest that FUT8 in platelets may be a therapeutic target for thrombosis-related cardiovascular diseases.
2026-06-04
Published in: Current Opinion in Structural Biology
Glycosylation can be critical for determining the structure and functions of proteins, but it is often neglected, leading to significant knowledge gaps in our understanding of biology. The inherent heterogeneity of glycans presents technical challenges to glycoprotein characterisation and impedes the representation of intact glycoprotein structures. Here we discuss how glycan heterogeneity constitutes a fundamental property of glycoproteins and acts as a remarkably powerful strategy for...
2026-06-03
Published in: The Journal of Antimicrobial Chemotherapy
CONCLUSIONS: These results highlight the potential of IP-antibiotic 12 as a novel therapeutic against multidrug-resistant gram-positive bacteria and provide a foundation for the development of next-generation IP-antibiotics with enhanced in vivo therapeutic efficacy.
2026-06-01
Published in: Clinical and Translational Medicine
No abstract
2026-05-28
Published in: Journal of Proteome Research
Burkholderia cenocepacia is an opportunistic pathogen associated with severe cystic fibrosis (CF) lung infections, where macrophages serve as both a crucial reservoir and a key mediator of intense inflammation. Currently, there is a paucity of insight into how B. cenocepacia infection impacts both the host and the B. cenocepacia proteomes. A key limitation for understanding the proteomic changes during intracellular replication of B. cenocepacia is its low infectivity, which results in in vitro...
2026-05-26
Published in: Journal of Virology
Human noroviruses are a leading cause of acute gastroenteritis, yet no licensed vaccine or antiviral is currently available. The extensive genetic diversity of noroviruses and the limited cross-protective immunity between genotypes complicate the development of broadly effective interventions. To systematically characterize norovirus-specific B cell responses from healthy individuals, we applied linking B cell receptor to antigen specificity through sequencing (LIBRA-seq) to peripheral blood...
2026-05-20
Published in: Nature Communications
Measurements of glycans modifying glycoproteins are hampered by the lack of standards that reflect the wide diversity in structure typically observed. To this end we exploit a large library of N-glycan standards comprised of a unique collection of 226 N-glycans including oligomannose, hybrid, and complex-type and apply a method employing porous graphitised carbon (PGC) and liquid chromatography mass spectrometry (PGC-LC-MS) to provide a high-resolution separation and characterisation of...
2026-05-18
Published in: Acs Omega
Heparan sulfate (HS) can act as an attachment receptor for many different animal viruses. Virus binding to HS occurs through electrostatic interactions between the negatively charged sulfate and carboxyl groups of HS and positively charged amino acids present in viral proteins. Soluble heparin, a glycosaminoglycan related to HS, can inhibit infection by many viruses, but the clinical use of heparin is limited by its anticoagulant activity. Synthetic HS mimetics that lack anticoagulant activity...
2026-05-18
Published in: Microbiology Resource Announcements
Neisseria meningitidis is a primary cause of bacterial meningitis and septicemia, which is a significant global public health concern. Here, we report Oxford Nanopore Technologies RNA sequencing for N. meningitidis serogroup B strain M0579. This strain encodes the phase-variable DNA methyltransferase ModD1, an epigenetic regulator associated with hyperinvasive meningococcal B lineages.
2026-05-18
Published in: Acs Chemical Biology
Growth factor signaling governs essential cellular processes, and its precision relies on interactions with heparan sulfate on the cell surface. The sulfation pattern of heparan sulfate dictates its capacity to bind specific growth factors and their receptors, thereby controlling the signaling strength and specificity. Extracellular endosulfatases, including sulfatase 1 and sulfatase 2, further modulate these interactions by selectively removing sulfate groups from defined regions of heparan...
2026-05-11
Published in: International Journal of Cardiology. Heart & Vasculature
CONCLUSIONS: Although serum syndecan-1 and endocan levels decreased in peripheral blood over time post-MI on guideline-directed therapy, this study identified only modest relationships between syndecan-1 (and not endocan) and OCT compositional characteristics of lipid-rich, rupture-prone plaque.