Biology subjects

Bae, E.

Publications and source records attributed to Bae, E..

9 recordsLinked to original sources

bioRxiv2025

Structural investigation of QatB and QatC proteins in QatABCD anti-phage defense

QatABCD is a widespread anti-phage defense system in prokaryotes comprising four protein components. QatC, a signature component, is homologous to QueC, an enzyme involved in nucleobase modification during queuosine biosynthesis. QatA and QatD are predicted to function as an ATPase and a nuclease, respectively, while QatB lacks identifiable sequence motifs. Here, we report the structural and functional characterization of QatB and QatC. We determined the structure of QatC bound to the ATP analog AMPPNP and performed structure-guided functional assays. We further found that QatB and QatC form a stable heterodimer and solved the structure of the QatB-QatC complex. In addition to unveiling the structure of QatB, structural analysis suggested that it may serve as a substrate of QatC, implicating a potential regulatory mechanism. These findings provide structural and functional insights into QatB and QatC, laying a foundation for understanding the molecular mechanism of the QatABCD system in phage defense.

biochemistry↗

bioRxiv2025

The gerotherapeutic drugs rapamycin, acarbose, and phenylbutyrate extend lifespan and enhance healthy aging in house crickets.

The house cricket (Acheta domesticus) is a promising preclinical geroscience model due to its short lifespan, low maintenance, age-associated functional decline, and responsiveness to geroprotective drugs. Continuous dosing with rapamycin, acarbose, and phenylbutyrate extends lifespan; whether intermittent dosing offers similar benefits remains unknown. We tested 274 sex-matched crickets given 2-week intermittent dosing of each drug starting at mid-age (8-weeks), followed by behavioral testing at 10-weeks (geriatric stage). Assays included Y-maze olfactory discrimination, open-field exploration, and treadmill performance. Locomotor gaits were identified by velocity-based K-means clustering (silhouette > 0.5). A subset was monitored for post-treatment survival using Kaplan-Meier analysis. Olfactory preference was preserved by all drugs (ds = -1.82 to -1.28, Ps < 0.01), with strongest effects in rapamycin-treated individuals. Rapamycin-treated males matched or exceeded juvenile locomotor activity; phenylbutyrate reduced male activity (d = 1.49, P < 0.05) and acarbose increased walking-to-running ratios (d = -0.75, P < 0.05). Rapamycin increased central exploration and freezing (d = -1.55, P < 0.0001), while acarbose and phenylbutyrate increased peripheral freezing (d = -0.76, P < 0.05). Rapamycin and phenylbutyrate extended maximum running time (ds = -2.30 to -1.32, Ps < 0.0001), with sex-specific jumping gains in rapamycin-treated females and acarbose-treated males. Post-treatment lifespan was prolonged by rapamycin (HR = 0.42, P < 0.001) and reduced by acarbose in females (HRs = 2.92 to 3.03, Ps < 0.05). Intermittent rapamycin preserved survival, cognition, and locomotion, while acarbose and phenylbutyrate produced selective benefits, supporting A. domesticus as a scalable model for geroprotective drug discovery.

pharmacology and toxicology↗

bioRxiv2024

Measuring autofluorescence spectral signatures for detecting antibiotic-resistant bacteria using Bigfoot spectral flow cytometer

Application of flow cytometry to microbiology has been limited due to inadequate availability of bacterial-specific stains, expensive antibody-based fluorophores, ineffective stain cell permeability and challenges in differentiating bacterial cells from cell debris due to their similarity and their small size. In addition, staining cells demands multiple washing steps which limits the sensitivity of detection due to the cell volume that is up to two orders smaller than typical eukaryotic cells. Further, most flow cytometers are not equipped to handle pathogenic organisms. Autofluorescence-based detection of cells can be a useful method for bacterial detection as multiple washing steps can be avoided and it also reduces the time and cost of using stains. Multiple studies have shown that the autofluorescence in bacterial cells are mainly linked to specific proteins, enzymes, or enzyme cofactors such as Flavin Adenine Dinucleotide (FAD) and Nicotinamide Adenine Dinucleotide (NAD) which are involved in bacterial metabolism. In this report, we present a novel method for differentiation between clinically isolated antibiotic resistant and non-resistant bacteria by utilizing their autofluorescence spectral signatures. We utilized a spectral cytometer known as Bigfoot which is equipped with an integrated biosafety cabinet allowing easy handling of pathogenic organisms unlike any other flow cytometers. Bigfoot also has 9 lasers and 54 fluorescence detectors which we utilize to capture the bacterial spectral autofluorescence signatures. As a proof of principle, we initially stressed different types of bacteria (E.coli and Salmonella sp.) using gentamicin antibiotics by collecting spectral autofluorescence over different time points. The spectral signatures were compared with the non-stressed bacteria. We observed that the stressed bacteria showed an increase in autofluorescence at distinct excitation (Ultraviolet, Violet, and blue color) and emission wavelengths whereas the non-stressed did not. The same experiments were repeated to compare the autofluorescence signatures between Methicillin-resistant and methicillin susceptible staphylococcus aureus (MRSA and MSSA) which were stressed with oxacillin antibiotics. MSSA showed an increase in autofluorescence between 4 - 6 h after exposure to oxacillin. MRSA on the other hand showed no increase in autofluorescence and the autofluorescence between stressed and non-stressed MRSA had similar signatures. This demonstrated that the antibiotic resistant or susceptible strain can be detected by observing the change in autofluorescence signature at specific wavelengths in a few hours. This label-free, quantitative, and resistant-specific autofluorescence spectral signatures from the Bigfoot spectral flow cytometer could potentially be utilized for rapid detection of antibioticresistant strain.

bioengineering↗

bioRxiv2023

Variant-specific Mendelian Risk Prediction Model

Many pathogenic sequence variants (PSVs) have been associated with increased risk of cancers. Mendelian risk prediction models use Mendelian laws of inheritance to predict the probability of having a PSV based on family history, as well as specified PSV frequency and penetrance (agespecific probability of developing cancer given genotype). Most existing models assume penetrance is the same for any PSVs in a certain gene. However, for some genes (for example, BRCA1/2), cancer risk does vary by PSV. We propose an extension of Mendelian risk prediction models to relax the assumption that risk is the same for any PSVs in a certain gene by incorporating variant-specific penetrances and illustrating these extensions on two existing Mendelian risk prediction models, BRCAPRO and PanelPRO. Our proposed BRCAPRO-variant and PanelPRO-variant models incorporate variant-specific BRCA1/2 PSVs through the region classifications. Due to the sparsity of the variant information we classify BRCA1/2 PSVs into three regions; the breast cancer clustering region (BCCR), the ovarian cancer clustering region (OCCR), and an other region. Simulations were conducted to evaluate the performance of the proposed BRCAPRO-variant model compared to the existing BRCAPRO model which assumes the penetrance is the same for any PSVs in BRCA1 (and respectively BRCA2). Simulation results showed that the BRCAPRO-variant model was well calibrated to predict region-specific BRCA1/2 carrier status with high discrimination and accuracy on the region-specific level. In addition, we showed that the BRCAPRO-variant model achieved performance gains over the existing risk prediction models in terms of calibration without loss in discrimination and accuracy. We also evaluated the performance of the two proposed models, BRCAPRO-variant and PanelPRO-variant, on a cohort of 1,961 families from the Cancer Genetics Network (CGN). We showed that our proposed models provide region-specific PSV carrier probabilities with high accuracy, while the calibration, discrimination and accuracy of gene-specific PSV carrier probabilities were comparable to the existing gene-specific models. As more variant-specific PSV penetrances become available, we have shown that Mendelian risk prediction models can be extended to integrate the additional information, providing precise variant or region-specific PSV carrier probabilities and improving future cancer risk predictions.

genetics↗

bioRxiv2022

The first fossil replete ant worker establishes living food storage in the Eocene

Worker specialization extends the behavioral and ecological repertoire of ant colonies. Specialization may relate to colony defense, brood care, foraging, and, in some taxa, storage. Replete workers swell the crop and gaster to store liquid food, which can be accessed by other colony members through trophallaxis. This storage ability, known as repletism, has independently evolved across several ant lineages, but the temporal history of this trait has not yet been investigated. Here, we describe the first fossil replete in the extinct species Leptomyrmex neotropicus Baroni Urbani, 1980 preserved in Miocene-age Dominican amber. Together with new evidence of repletism in L. neotropicus extant sister species, L. relictus Boudinot et al., 2016, we reconstruct the pattern of acquisition and descent in this storage-linked trait. Our ancestral state reconstruction suggests that Leptomyrmex acquired replete workers in the Eocene and may therefore represent the earliest instance of so-called "honeypot" ants among all known ants, both living and extinct.

evolutionary biology↗

bioRxiv2022

BOSS: Beta-mixture Unsupervised Oligodendrocytes Segmentation System

To develop reparative therapies for multiple sclerosis (MS), we need to better understand the physiology of loss and replacement of oligodendrocytes, the cells that make myelin and the target of damage in MS. In vivo two-photon fluorescence microscopy allows direct visualization of oligodendrocytes in transgenic mouse models, and promises a deeper understanding of the longitudinal dynamics of replacing oligodendrocytes after damage. However, the task of tracking oligodendrocytes requires extensive human effort and is especially challenging in three-dimensional images. While several models exist for automatically annotating cells in two-dimensional images, few models exist to annotate cells in three-dimensional images and even fewer are designed for tracking cells in longitudinal imaging. Furthermore, the complexity of processes and myelin formed by individual oligodendrocytes can result in the failure of algorithms that are specifically designed for tracking cell bodies alone. Here, we propose a novel beta-mixture unsupervised oligodendrocyte segmentation system (BOSS) that can segment and track oligodendrocytes in three-dimensional images over time that requires minimal human input. We evaluated the performance of the BOSS model on a set of eight images obtained longitudinally. We showed that the BOSS model can segment and track oligodendrocytes similarly to a blinded human observer. Our method offers many advantages, as it does not require fully curated data, reduces computational time, and most importantly recapitulates cell dynamic patterns observed by manually tracking oligodendrocytes. Although BOSS was developed to apply to our studies on oligodendrocytes, we anticipate that it can be modified to study four-dimensional in vivo data of any brain cell.

neuroscience↗

bioRxiv2021

SIRT5 is the desuccinylase of LDHA as novel cancer metastatic stimulator in aggressive prostate cancer

Prostate cancer (PCa) is the most commonly diagnosed genital cancer in men worldwide. Among patients who developed advanced PCa, 80% suffered from bone metastasis, with a sharp drop in the survival rate. Despite great efforts, the details of the mechanisms underlying castration-resistant PCa (CRPC) remains unclear. SIRT5, an NAD+-dependent desuccinylase, is hypothesized to be a key regulator of various cancers. However, compared to other SIRTs, the role of SIRT5 in cancer has not been extensively studied. Here, we showed significantly decreased SIRT5 levels in aggressive PCa cells relative to the PCa stages. The correlation between the decrease in the SIRT5 level and the patients survival rate was also confirmed. Using quantitative global succinylome analysis, we characterized a significant increase of lysine 118 succinylation (K118su) of lactate dehydrogenase A (LDHA), which plays a role in increasing LDH activity. As a substrate of SIRT5, LDHA-K118su significantly increased the migration and invasion of PCa cells and LDH activity in PCa patients. This study investigated the reduction of SIRT5 and LDHA-K118su as a novel mechanism involved in PCa progression. It can also be proposed as a new target that can prevent castration-resistant PCa progression, which is key to PCa treatment.

cancer biology↗

bioRxiv2019

SMAD3 Determines Conventional versus Plasmacytoid Dendritic Cell Fates

Transforming growth factor (TGF)-{beta} plays crucial roles in differentiation of dendritic cells (DC). However, molecular mechanisms how TGF-{beta} regulates DC differentiation remain largely unknown. Here, we show that selective repression of one of the TGF-{beta} receptor-regulated SMADs (R-SMADs), SMAD3 directs conventional DC (cDC) differentiation, whereas maintenance of SMAD3 is indispensable for plasmacytoid DC (pDC) differentiation. Expression of SMAD3 was specifically downregulated in CD115+ common DC progenitor (CDP), pre-cDCs and cDCs. SMAD3 deficient mice showed a significant reduction in pre-pDCs and pDCs with increased CDP, pre-cDCs and cDCs. SMAD3 upregulated the pDC-related genes: SPI-B, E2-2 and IKAROS, while it repressed FLT3 and the cDC-related genes: IRF4 and ID2. STAT3 and a SMAD transcriptional co-repressor, c-SKI repressed SMAD3 for cDC differentiation, whereas canonical SMAD-mediated TGF-{beta} signalling maintained SMAD3 for pDC differentiation. Thus, SMAD3 is the pivotal determinant to bifurcate cDC and pDC differentiation in the steady-state condition.

immunology↗

bioRxiv2017

Authentic Enzyme Intermediates Captured "on-the-fly" by Mix-and-Inject Serial Crystallography

Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. Here, we demonstrate a general method for capturing enzyme catalysis in-action by mix-and-inject serial crystallography. Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis -lactamase with the 3rd generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation on the millisecond to second time scales including the crossover from transition state kinetics to steady-state kinetics.\n\nSynopsisAn enzymatically catalyzed reaction is initiated by diffusion based mixing of substrate and followed at runtime by time-resolved serial crystallography using a free electron laser.

biophysics↗