Biology subjects

Yoo, R.

Publications and source records attributed to Yoo, R..

12 recordsLinked to original sources

bioRxiv2026

A modular cranial window enabling maintainable widefield optical access in non-human primates

Longitudinal optical imaging of the primate cortex requires stable yet maintainable cortical access, but existing cranial window approaches remain limited by mechanical instability and tissue responses that progressively degrade optical clarity. These challenges are amplified in primates, where large craniotomies and physiological variability complicate chronic experiments. Moving beyond conventional fixed cranial windows, we present the PRIME cranial window (Primate Reconfigurable Interchangeable Modular Enclosure), a modular platform enabling maintainable, long-term, and widefield optical access in awake macaques. Built on a modular architecture, PRIME supports non-invasive adjustment, repeated cortical access, and on-demand maintenance, including tissue removal, without surgical re-entry, while a dual-ring sealing mechanism prevents cerebrospinal fluid leakage and contamination. Combined with optimized viral delivery, implantation, and maintenance strategies, PRIME preserves cortical integrity and optical clarity for long-term optical imaging. PRIME establishes a versatile, re-accessible experimental framework for chronic, large-area optical studies of the primate brain.

neuroscience↗

bioRxiv2025

Structure of endogenous Pfs230:Pfs48/45 in complex with potent malaria transmission-blocking antibodies

The Pfs230:Pfs48/45 complex forms the basis for leading malaria transmission-blocking vaccine candidates, yet li]le is known about its molecular assembly. Here, we used cryogenic electron microscopy to elucidate the structure of the endogenous Pfs230:Pfs48/45 complex bound to six potent transmission-blocking antibodies. Pfs230 consists of multiple domain clusters rigidified by interactions mediated through insertion domains. Membrane-anchored Pfs48/45 forms a disc-like structure and interacts with a short C-terminal peptide on Pfs230 that is critical for Pfs230 membrane-retention in vivo. Interestingly, membrane retention through this interaction is not essential for transmission to mosquitoes, suggesting that complex disruption is not a mode of action for transmission-blocking antibodies. Analyses of Pfs48/45-and Pfs230-targeted antibodies identify conserved epitopes on the Pfs230:Pfs48/45 complex and provides a structural paradigm for complement-dependent activity of Pfs230-targeting antibodies. Altogether, the antibody-bound Pfs230:Pfs48/45 structure presented improves our molecular understanding of this biological complex, informing the development of next-generation Plasmodium falciparum transmission-blocking interventions.

molecular biology↗

bioRxiv2023

Target-agnostic identification of human antibodies to Plasmodium falciparum sexual forms reveals cross stage recognition of glutamate-rich repeats

Circulating sexual stages of Plasmodium falciparum (Pf) can be transmitted from humans to mosquitoes, thereby furthering the spread of malaria in the population. It is well established that antibodies (Abs) can efficiently block parasite transmission. In search for naturally acquired Ab targets on sexual stages, we established an efficient method for target-agnostic single B cell activation followed by high-throughput selection of human monoclonal antibodies (mAbs) reactive to sexual stages of Pf in the form of gamete and gametocyte extract. We isolated mAbs reactive against a range of Pf proteins including well-established targets Pfs48/45 and Pfs230. One mAb, B1E11K, was cross-reactive to various proteins containing glutamate-rich repetitive elements expressed at different stages of the parasite life cycle. A crystal structure of two B1E11K Fab domains in complex with its main antigen, RESA, expressed on asexual blood stages, showed binding of B1E11K to a repeating epitope motif in a head-to-head conformation engaging in affinity-matured homotypic interactions. Thus, this mode of recognition of Pf proteins, previously described only for PfCSP, extends to other repeats expressed across various stages. The findings augment our understanding of immune-pathogen interactions to repeating elements of the Plasmodium parasite proteome and underscore the potential of the novel mAb identification method used to provide new insights into the natural humoral immune response against Pf. Impact StatementA naturally acquired human monoclonal antibody recognizes proteins expressed at different stages of the Plasmodium falciparum lifecycle through affinity-matured homotypic interactions with glutamate-rich repeats

immunology↗

bioRxiv2023

Crystallographic, kinetic, and calorimetric investigation of PKA interactions with L-type calcium channels and Rad GTPase

{beta}-adrenergic signalling leads to activation of cAMP-dependent protein kinase (PKA), which can regulate the activity of L-type voltage-gated calcium channels (CaVs) in multiple tissues. In CaV1.2, various sites have been proposed to be involved, including Ser1981 in the C-terminal tail. Its phosphorylation is linked to diabetes progression, synaptic plasticity, and the augmentation of Ca2+ currents in smooth muscle. Its role in augmenting cardiac Ca2+ currents has been heavily scrutinized, with alternative models including the sites Ser1718 and Ser1535. Recently, the GTPase Rad has been identified as a critical PKA target that mediates the augmentation of cardiac CaV1.2 currents upon its phosphorylation. However, it is unclear which of the four potential sites (Ser25, Ser38, Ser272, and Ser300) are favored by PKA. Using quantitative binding experiments and enzyme kinetics, we show that there are two Tiers of target sites, with CaV1.2 residue Ser1981 and Rad residues Ser25 and Ser272 forming Tier 1 substrates for PKA. The other sites form a second Tier, with PKA only showing minimal detectable activity. The Tier 1 substrates share a common feature with two arginine residues that anchor the peptide into the active site of PKA. We report crystal structures of the PKA catalytic subunit (PKAc) with and without a CaV1.2 substrate that represent different successive conformations prior to product turnover. Different target sites utilize different anchoring residues, highlighting the plasticity of PKAc to recognize substrates. SummaryStress signals can alter the electrical properties of excitable cells. cAMP-dependent protein kinase A (PKA) is a key enzyme that is activated upon {beta}-adrenergic stimulation and can alter the function of L-type voltage-gated calcium channels (CaVs) in various tissues. There is a lot of controversy surrounding the exact recognition and specificity of PKA towards CaV1.2, a key calcium channel located in neuronal, cardiac, and smooth muscle tissue, among others. Using a quantitative and unbiased approach, we determined the substrate specificities of PKA towards various sites in CaV1.2 and Rad, an inhibitory protein. Our work highlights two Tiers of substrates, suggesting a potential graded response. Using X-ray crystallography, we determined a high-resolution structure of PKA bound to its strongest target site in CaV1.2, showing how PKA undergoes multiple structural transitions towards binding and how it makes use of a unique anchoring residue.

biochemistry↗

bioRxiv2022

Synapsing with oligodendrocyte precursor cells stop sensory axons regenerating into the spinal cord

Primary sensory axons stop regenerating as they re-enter the spinal cord, resulting in incurable sensory loss. What arrests them has remained unclear. We previously showed that axons stop by forming synaptic contacts with unknown non-neuronal cells. Here, we identified these cells in adult mice as oligodendrocyte precursor cells (OPCs). We also found that only a few axons stop regenerating by forming dystrophic endings, exclusively at the CNS:PNS borderline where OPCs are absent. Most axons stop in contacts with a dense network of OPC processes. Live imaging, immuno-EM and OPC-DRG co-culture additionally suggest that axons are rapidly immobilized by forming synapses with OPCs. Genetic OPC ablation enables many axons to continue regenerating deep into the spinal cord. We propose that sensory axons stop regenerating by encountering OPCs that induce presynaptic differentiation. Our findings identify OPCs as a major regenerative barrier that prevents intraspinal restoration of sensory circuits following spinal root injury.

neuroscience↗

bioRxiv2022

Pan-genomic analysis of transcriptional modules across Salmonella Typhimurium reveals the regulatory landscape of different strains

Salmonella enterica Typhimurium is a serious pathogen that is involved in human nontyphoidal infections. Tackling Typhimurium infections is difficult due to the species dynamic adaptation to its environment, which is dictated by a complex transcriptional regulatory network (TRN). While traditional biomolecular methods provide characterizations of specific regulators, it is laborious to construct the global TRN structure from this bottom-up approach. Here, we used a machine learning technique to understand the transcriptional signatures of S. enterica Typhimurium from the top down, as a whole and in individual strains. Furthermore, we conducted cross-strain comparison of 6 strains in serovar Typhimurium to investigate similarities and differences in their TRNs with pan-genomic analysis. By decomposing all the publicly available RNA-Seq data of Typhimurium with independent component analysis (ICA), we obtained over 400 independently modulated sets of genes, called iModulons. Through analysis of these iModulons, we 1) discover three transport iModulons linked to antibiotic resistance, 2) describe concerted responses to cationic antimicrobial peptides (CAMPs), 3) uncover evidence towards new regulons, and 4) identify two iModulons linked to bile responses in strain ST4/74. We extend this analysis across the pan-genome to show that strain-specific iModulons 5) reveal different genetic signatures in pathogenicity islands that explain phenotypes and 6) capture the activity of different phages in the studied strains. Using all high-quality publicly-available RNA-Seq data to date, we present a comprehensive, data-driven Typhimurium TRN. It is conceivable that with more high-quality datasets from more strains, the approach used in this study will continue to guide our investigation in understanding the pan-transcriptome of Typhimurium. Interactive dashboards for all gene modules in this project are available at https://imodulondb.org/ under the "Salmonella Typhimurium" page to enable browsing for interested researchers.

systems biology↗

bioRxiv2021

NBI-921352, a First-in-Class, Na V 1.6 Selective, Sodium Channel Inhibitor That Prevents Seizures in Scn8a Gain-of- Function Mice, and Wild-Type Mice and Rats

NBI-921352 (formerly XEN901) is a novel sodium channel inhibitor designed to specifically target NaV1.6 channels. Such a molecule provides a precision-medicine approach to target SCN8A-related epilepsy syndromes (SCN8A-RES), where gain-of-function (GoF) mutations lead to excess NaV1.6 sodium current, or other indications where NaV1.6 mediated hyper-excitability contributes to disease (Gardella and Moller, 2019; Johannesen et al., 2019; Veeramah et al., 2012). NBI-921352 is a potent inhibitor of NaV1.6 (IC50 0.051 {micro}M), with exquisite selectivity over other sodium channel isoforms (selectivity ratios of 756X for NaV1.1, 134X for NaV1.2, 276X for NaV1.7, and >583X for NaV1.3, NaV1.4, and NaV1.5). NBI-921352 is a state-dependent inhibitor, preferentially inhibiting activated (inactivated or open) channels. The state dependence leads to potent stabilization of inactivation, inhibiting NaV1.6 currents, including resurgent and persistent NaV1.6 currents, while sparing the closed/rested channels. The isoform-selective profile of NBI-921352 led to a robust inhibition of action-potential firing in glutamatergic excitatory pyramidal neurons, while sparing fast-spiking inhibitory interneurons, where NaV1.1 predominates. Oral administration of NBI-921352 prevented electrically induced seizures in a Scn8a GoF mouse, as well as in wild-type mouse and rat seizure models. NBI-921352 was effective in preventing seizures at lower brain and plasma concentrations than commonly prescribed sodium channel inhibitor antiseizure medicines (ASMs) carbamazepine, phenytoin, and lacosamide. NBI-921352 was well tolerated at higher multiples of the effective plasma and brain concentrations than those ASMs. NBI-921352 is entering phase II proof-of-concept trials for the treatment of SCN8A-developmental epileptic encephalopathy (SCN8A-DEE) and adult focal-onset seizures.

pharmacology and toxicology↗

bioRxiv2021

Machine learning uncovers a data-driven transcriptional regulatory network for the Crenarchaeal thermoacidophile Sulfolobus acidocaldarius

Dynamic cellular responses to environmental constraints are coordinated by the transcriptional regulatory network (TRN), which modulates gene expression. This network controls most fundamental cellular responses, including metabolism, motility, and stress responses. Here, we apply independent component analysis, an unsupervised machine learning approach, to 95 high-quality Sulfolobus acidocaldarius RNA-seq datasets and extract 45 independently modulated gene sets, or iModulons. Together, these iModulons contain 755 genes (32% of the genes identified on the genome) and explain over 70% of the variance in the expression compendium. We show that 5 modules represent the effects of known transcriptional regulators, and hypothesize that most of the remaining modules represent the effects of uncharacterized regulators. Further analysis of these gene sets results in: (1) the prediction of a DNA export system composed of 5 uncharacterized genes, (2) expansion of the LysM regulon, and (3) evidence for an as-yet-undiscovered global regulon. Our approach allows for a mechanistic, systems-level elucidation of an extremophiles responses to biological perturbations, which could inform research on gene-regulator interactions and facilitate regulator discovery in S. acidocaldarius. We also provide the first global TRN for S. acidocaldarius. Collectively, these results provide a roadmap towards regulatory network discovery in archaea.

systems biology↗

bioRxiv2021

Machine learning of all Mycobacterium Tuberculosis H37Rv RNA-seq data reveals complex interplay between metabolism, stress response, and infection

Mycobacterium tuberculosis is one of the most consequential human bacterial pathogens, posing a serious challenge to 21st century medicine. A key feature of its pathogenicity is its ability to adapt its transcriptional response to environmental stresses through its transcriptional regulatory network (TRN). While many studies have sought to characterize specific portions of the M. tuberculosis TRN, a systems level characterization and analysis of interactions among the controlling transcription factors remains to be achieved. Here, we applied an unsupervised machine learning method to modularize the M. tuberculosis transcriptome and describe the role of transcription factors (TFs) in the TRN. By applying Independent Component Analysis (ICA) to over 650 transcriptomic samples, we obtained 80 independently modulated gene sets known as "iModulons," many of which correspond to known regulons. These iModulons explain 61% of the variance in the organisms transcriptional response. We show that iModulons: 1) reveal the function of previously unknown regulons, 2) describe the transcriptional shifts that occur during environmental changes such as shifting carbon sources, oxidative stress, and virulence events, and 3) identify intrinsic clusters of transcriptional regulons that link several important metabolic systems, including lipid, cholesterol, and sulfur metabolism. This transcriptome-wide analysis of the M. tuberculosis TRN informs future research on effective ways to study and manipulate its transcriptional regulation, and presents a knowledge-enhanced database of all published high-quality RNA-seq data for this organism to date.

systems biology↗

bioRxiv2021

Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks

We are firmly in the era of biological big data. Millions of omics datasets are publicly accessible and can be employed to support scientific research or build a holistic view of an organism. Here, we introduce a workflow that converts all public gene expression data for a microbe into a dynamic representation of the organisms transcriptional regulatory network. This five-step process walks researchers through the mining, processing, curation, analysis, and characterization of all available expression data, using Bacillus subtilis as an example. The resulting reconstruction of the B. subtilis regulatory network can be leveraged to predict new regulons and analyze datasets in the context of all published data. The results are hosted at https://imodulondb.org/, and additional analyses can be performed using the PyModulon Python package. As the number of publicly available datasets increases, this pipeline will be applicable to a wide range of microbial pathogens and cell factories.

bioinformatics↗

bioRxiv2020

Co-targeting myelin inhibitors and CSPGs enhances sensory axon regeneration within, but not into, the spinal cord

A major barrier to intraspinal regeneration after dorsal root (DR) injury is the DR entry zone (DREZ), the CNS/PNS interface. DR axons stop regenerating at the DREZ, even if regenerative capacity is increased by a nerve conditioning lesion. This potent blockade has long been attributed to myelin-associated inhibitors and CSPGs, but incomplete lesions and conflicting reports have prevented conclusive agreement. Here we evaluated DR regeneration in mice, using novel strategies to facilitate complete lesions and analyses, selective tracing of proprioceptive and mechanoreceptive axons, and the first simultaneous targeting of Nogo/Reticulon-4, MAG, OMgp, CSPGs and GDNF. Co-eliminating myelin inhibitors and CSPGs elicited regeneration of only a few conditioning-lesioned DR axons across the DREZ. Their absence, however, markedly and synergistically enhanced regeneration of GDNF-stimulated axons, highlighting the importance of sufficiently elevating intrinsic growth capacity. We also conclude that myelin inhibitors and CSPGs are not the primary mechanism stopping axons at the DREZ.

neuroscience↗

bioRxiv2020

Synthesis of the novel transporter YdhC, is regulated by the YdhB transcription factor controlling adenosine and adenine uptake.

The YdhB transcriptional factor, re-named here AdnB, homologous to the allantoin regulator, AllS, was shown to regulate ydhC gene expression in Escherichia coli, which is divergently transcribed from adnB, and this gene arrangement is conserved in many Protreobacteria. The predicted consensus DNA binding sequence for YdhB is also conserved in Entrobacterial genomes. RNA-seq data confirmed the activation predicted due to the binding of AdnB as shown by Chip-Exo results. Fluorescent polarization experiments revealed binding of YdhB to the predicted binding site upstream of ydhC in the presence of 0.35 mM adenine, but not in its absence. The E. coli MG1655, strain lacking the ydhB gene, showed a lower level of ydhC mRNA in cells grown in M9-glucose supplemented with 2 mM adenosine. Adenosine and adenine are products of purine metabolism and provide sources of ammonium for many organisms. They are utilized under nitrogen starvation conditions as single nitrogen sources. Deletion of either the ydhC or the ydhB gene leads to a substantially decreased growth rate for E. coli in minimal M9 medium with glycerol as the carbon source and adenosine or adenine as the single nitrogen source. The ydhC mutant showed increased resistance to Paromomycine, Sulfathiazole and Sulfamethohazole using Biolog plates. We provide evidence that YdhB, (a novel LysR family regulator) activates expression of the ydhC gene, encoding a novel adenosine/adenine transporter in E. coli. The YdhB binding consensus for different groups of Enterobacteria was predicted.

microbiology↗