Office of Extramural Research

The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past five years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape (https://metaproteomics.org/). We outline the Initiative's organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities.

Surface adhesion is critical to the survival of pathogenic bacteria both in natural niches and during infections, often via forming matrix-embedded communities called biofilms. Vibrio cholerae, the causal agent of pandemic cholera, is capable of forming biofilms adhering to both biotic and abiotic surfaces and the biofilm lifestyle has been implicated in promoting the survival of V. cholerae both in the natural reservoir and during host colonization. Previously, a 57-amino acid loop in the biofilm-specific adhesin Bap1 (Bap1-57aa) has been identified as a key contributor to the adhesion of V. cholerae biofilms to various surfaces including lipid membranes. However, the mechanism underlying its interaction with lipids, as well as its secondary structures, remain unresolved. Here, we combined biophysical, computational, and genetic approaches to elucidate the molecular mechanism of how this adhesive peptide interacts with lipids and lipid-coated surfaces. We found that a central aromatic-rich motif anchors the peptide to lipid bilayers while peripheral pseudo repeats enhance binding through avidity. Surprisingly, the core motif undergoes a lipid-induced conformational transition into a β-hairpin, enabling robust membrane insertion. We confirmed these findings both in vitro and in the biofilm context. Moreover, we demonstrated that the adhesive peptide can adhere to model host surfaces and is sensitive to membrane curvature. Finally, we show that the biofilm-derived peptide is found in several other Vibrio species, and its sequence is well-conserved. Our results provide molecular insight into biofilm adhesion and may lead to new strategies for targeted biofilm removal, as well as the design of bioinspired underwater adhesives.

Commotio retinae (CR) resulting from retinal trauma can lead to focal photoreceptor degeneration and permanent vision loss. Currently no therapies exist for CR-induced retinal degeneration, in part because of the lack of a large-animal model that replicates human injury pathology and allows testing of therapeutics. Severe CR is clinically characterized by subretinal fluid and focal photoreceptor outer nuclear layer thinning. To develop a porcine CR model, we developed a laser-guided projectile apparatus and optimized projectile delivery procedure using porcine cadaveric eyes embedded in a 3D-printed porcine skull. Scleral and corneal impacts resulted in retinal damage consistent with patient injury, but corneal impacts also led to cornea damage and opacification, which precluded follow-up imaging. In live porcine eyes, scleral impacts of 39.5 m/s induced transient blood-retinal barrier breakdown evidenced by subretinal fluid on optical coherence tomography (OCT), leakage observed on fluorescein and indocyanine green angiography, and transient photoreceptor outer segment disruption seen by OCT and multifocal electroretinography. Impacts above 39.5 m/s induced longer-lasting photoreceptor degeneration but only transient blood-retinal barrier breakdown. This porcine model, combined with clinically relevant imaging and diagnostic modalities, will be valuable for testing the safety and efficacy of therapies to restore vision after focal photoreceptor degeneration.

Understanding how drug exposure alters synaptic proteins is essential for uncovering the molecular mechanisms underlying addiction and identifying new therapeutic targets. Synaptoneurosomes (SNs), subcellular fractions enriched in pre- and postsynaptic components, provide a powerful resource for studying synaptic adaptations in the brain. Here, we applied a deep, discovery-based proteomic strategy to profile SNs isolated from the dorsal striatum (DS) of rats 1 h after acute methamphetamine (Meth) administration. To maximize proteome coverage, we combined tandem mass tag (TMT) labeling, offline high-pH fractionation, and low-pH nanoflow liquid chromatography coupled to high-resolution (orbitrap) mass spectrometry (HRMS). This approach enabled identification of ∼6100 cytosolic and membrane proteins from ∼500 ng of SN proteome digest─representing the most comprehensive DS SN proteome reported to date. A comparative analysis between Meth-treated and saline control animals revealed 147 differentially abundant proteins (81 with increased abundance; 66 with decreased abundance) enriched in pathways related to dopamine biosynthesis, synaptic vesicle cycling, mitochondrial energy metabolism, and proteasomal degradation. These findings highlight coordinated molecular remodeling of striatal synapses in response to Meth and demonstrate the utility of deep SN proteomics in addiction research. Deep, low-input SN proteomics nominates vesicle acidification, mitochondrial ATP supply, and proteasome function as testable pathway-level targets in addiction.

As of May 7, 2024, the securities crowdfunding cycle has facilitated the funding of 356 securities, comprising 231 equity securities, 20 debt securities, and 105 sukuk securities. Sukuk experienced an increase in the share of sharia securities funding with a percentage of 30%, up from 22% in 2023. This increase in funding was not accompanied by a specific, legally binding screening standard for sharia securities issuers in the securities offering mechanism. Financial Services Authority or Otoritas Jasa Keuangan (OJK) Regulation Number 35 of 2017 cannot be legally applied as a screening standard for this funding. This research employs a library research methodology with a socio-legal approach to examine this regulatory void. Primary data consists of OJK Regulation No. 35 of 2017 and OJK Regulation No. 57 of 2020, supported by secondary data on offering mechanisms, funding growth, and relevant literature. The study found a lack of specific regulations governing screening standards (core business and financial ratio) for Sharia securities in the SCF cycle. Currently, guidelines are often informally drawn from OJK Regulation No. 35 of 2017, which is legally inappropriate as it is intended for the public-company setting of the Indonesia Stock Exchange. The findings highlight the need for a specific regulation governing screening standards for securities crowdfunding funding. Adopting an economic approach to legal science, this study proposes the development of a specific OJK Regulation (POJK) that provides clear screening criteria and permanent legal consequences for issuers or publishers who violate the Sharia securities criteria.

The mechanisms by which Enterovirus D68 (EV-D68) infection leads to acute flaccid myelitis (AFM), a severe neurological condition characterized by sudden muscle weakness and paralysis, remain poorly understood. To investigate the cellular tropism and infection dynamics of EV-D68, we profiled naive and EV-D68-infected human spinal cord organoids (hSCOs) derived from induced pluripotent stem cells (iPSCs) using single-cell RNA sequencing (scRNA-seq). Examining the cellular composition of healthy hSCOs, we found that hSCOs include diverse cell types, including neurons, astrocytes, oligodendrocyte progenitor cells (OPCs), and multipotent glial progenitor cells (mGPCs). Upon infection with 2 EV-D68 strains, US/IL/14-18952 (a B2 strain) and US/MA/18-23089 (a B3 strain), we observed distinct viral tropism and host transcriptional responses. Notably, US/IL/14-18952 showed a significant preference for neurons, while US/MA/18-23089 exhibited higher rates of infection in cycling astrocytes and OPCs. These findings provide novel insights into the host cell tropism of EV-D68 in the spinal cord, offering insight into the potential mechanisms underlying AFM pathogenesis. Understanding the dynamics of infection at single-cell resolution will inform future therapeutic strategies aimed at mitigating the neurological impact of enterovirus infections.

Zika virus (ZIKV) and dengue virus serotypes 1-4 (DENV1-4) are flaviviruses spread by Aedes mosquitoes. ZIKV infection can cause Guillain-Barré syndrome and microcephaly, while severe dengue can lead to hemorrhagic fever and death. DENV infection of ZIKV-immune individuals is linked to severe clinical outcomes due to antibody-dependent enhancement (ADE) of infection. Thus, the development of broadly protective vaccines is an important objective. We focus on the E dimer epitope (EDE) of ZIKV, which is targeted by broadly neutralizing antibodies that protect against ZIKV and DENV1-4. We engineered ZIKV E dimer variants containing non-native asparagine-linked glycosylation sites to block antibody responses to regions outside the EDE using a structure-based iterative design approach. One candidate, SC30m53, bound EDE mAbs but not other mAbs and induced a potently neutralizing response against ZIKV and moderately cross-neutralizing responses against DENV1-3 in mice. These findings suggest that hyperglycosylation provides a promising approach to focusing the immune response on key epitopes.

Gene-set analysis seeks to identify the biological mechanisms underlying groups of genes with shared functions. Large language models (LLMs) have recently shown promise in generating functional descriptions for input gene sets but may produce factually incorrect statements, commonly referred to as hallucinations in LLMs. Here we present GeneAgent, an LLM-based AI agent for gene-set analysis that reduces hallucinations by autonomously interacting with biological databases to verify its own output. Evaluation of 1,106 gene sets collected from different sources demonstrates that GeneAgent is consistently more accurate than GPT-4 by a significant margin. We further applied GeneAgent to seven novel gene sets derived from mouse B2905 melanoma cell lines. Expert review confirmed that GeneAgent produces more relevant and comprehensive functional descriptions than GPT-4, providing valuable insights into gene functions and expediting knowledge discovery.