Biology subjects

Seo, H.

Publications and source records attributed to Seo, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

mosaicMPI: a framework for modular data integration across cohorts and -omics modalities

Advances in molecular profiling have facilitated generation of large multi-modal datasets that can potentially reveal critical axes of biological variation underlying complex diseases. Distilling biological meaning, however, requires computational strategies that can perform mosaic integration across diverse cohorts and datatypes. Here, we present mosaicMPI, a framework for discovery of low to high-resolution molecular programs representing both cell types and states, and integration within and across datasets into a network representing biological themes. Using existing datasets in glioblastoma, we demonstrate that this approach robustly integrates single cell and bulk programs across multiple platforms. Clinical and molecular annotations from cohorts are statistically propagated onto this network of programs, yielding a richly characterized landscape of biological themes. This enables deep understanding of individual tumor samples, systematic exploration of relationships between modalities, and generation of a reference map onto which new datasets can rapidly be mapped. mosaicMPI is available at https://github.com/MorrissyLab/mosaicMPI.

bioinformatics↗

bioRxiv2023

Engineering a Synthetic Escherichia coli Coculture for Compartmentalized de novo Biosynthesis of Isobutyl Butyrate from Mixed Sugars

Short-chain esters are versatile chemicals with use as flavors, fragrances, solvents, and fuels. The de novo ester biosynthesis consists of diverging and converging pathway submodules, which is challenging to engineer to achieve optimal metabolic fluxes and selective product synthesis. Compartmentalizing the pathway submodules into specialist cells that facilitate pathway modularization and labor division can present a promising solution. Here, we engineered a synthetic Escherichia coli coculture with the compartmentalized sugar utilization and ester biosynthesis pathways to produce isobutyl butyrate from a mixture of glucose and xylose. To compartmentalize the sugar-utilizing pathway submodules, we engineered a xylose-utilizing E. coli specialist that selectively consumes xylose over glucose and bypasses the carbon catabolite repression (CCR) while leveraging the native CCR machinery to activate a glucose-utilizing E. coli specialist. Upon compartmentalizing the isobutyl butyrate pathway submodules into these sugar-utilizing specialist cells, a robust synthetic coculture could be engineered to selectively produce isobutyl butyrate at a level of 392 mg/L, about 31-fold higher than the monoculture.

synthetic biology↗

bioRxiv2023

Hierarchical gradient of timescales in the mammalian forebrain

Many anatomical and physiological features of cortical circuits, ranging from the biophysical properties of synapses to the connectivity patterns among different neuron types, exhibit consistent variation along the hierarchical axis from sensory to association areas. Notably, the scale of temporal correlation of neural activity at rest, known as the intrinsic timescale, increases systematically along this hierarchy in both primates and rodents, analogous to the growing scale and complexity of spatial receptive fields. However, how the timescales for task-related activity vary across brain regions and whether their hierarchical organization appears consistently across different mammalian species remain unexplored. Here, we show that both the intrinsic timescale and the timescales of task-related activity follow a similar hierarchical gradient in the cortices of monkeys, rats, and mice. We also found that these timescales covary similarly in both the cortex and basal ganglia, whereas the timescales of thalamic activity are shorter than cortical timescales and do not conform to the hierarchical order predicted by their cortical projections. These results suggest that the hierarchical gradient of cortical timescales might be a universal feature of intra-cortical circuits in the mammalian brain. Significance StatementA gradual increase in the intrinsic timescales of cortical activity along the anatomical hierarchy reflects the functional specialization of cortical circuits. However, it is unknown whether this gradient of timescales is a common feature across distinct mammalian species in both intrinsic and task-related timescales and whether it is also observed in subcortical areas. This study reveals that the hierarchical gradient of multiple cortical timescales is conserved across multiple mammalian species. By contrast, thalamic timescales were shorter than cortical timescales and did not follow the hierarchical order inferred from their cortical projections. These findings imply a crucial role of intra-cortical connections in structuring distinct temporal dynamics observed across the cortex.

neuroscience↗

bioRxiv2023

Consolidated Bioprocessing of Lignocellulosic Biomass Poplar to Produce Short-Chain Esters by Clostridium thermocellum

Consolidated bioprocessing (CBP) of lignocellulosic biomass using cellulolytic microorganisms presents a promising sustainable and economical biomanufacturing platform where enzyme production, biomass hydrolysis, and fermentation to produce biofuels, biochemicals, and biomaterials occur in a single step. However, understanding and redirecting metabolism of microorganisms to be compatible with CBP to produce non-native metabolites are limited. In this study, we metabolically engineered a cellulolytic thermophile Clostridium thermocellum and demonstrated its compatibility with CBP integrated with a mild Co-solvent Enhanced Lignocellulosic Fractionation (CELF) pretreatment for conversion of hardwood poplar into short-chain esters (i.e., ethyl acetate, ethyl isobutyrate, isobutyl acetate, isobutyl isobutyrate) with broad use as solvents, flavors, fragrances, and biofuels. A recombinant C. thermocellum engineered with deletion of carbohydrate esterases and stable overexpression of a thermostable alcohol acetyltransferase improved the target esters production without compromised deacetylation activities. We discovered these esterases exhibited promiscuous thioesterase activities and their deletion improved ester production by increasing isobutanol flux and rerouting the native electron and carbon fermentative metabolism besides their known major function of ester degradation. The total ester production could be further enhanced up to 80-fold and the composition of short-chain esters could be modified by deleting lactate biosynthesis and/or CELF-pretreated poplar under different pretreatment conditions.

bioengineering↗

bioRxiv2023

Unrecognized Potent Activities of Colistin Against Clinically Important mcr+ Enterobacteriaceae Revealed in Synergy with Host Immunity

Colistin (COL) is a cationic cyclic peptide that disrupts negatively-charged bacterial cell membranes and frequently serves as an antibiotic of last resort to combat multidrug-resistant Gram-negative bacterial infections. Emergence of the horizontally transferable plasmid-borne mobilized colistin resistance (mcr) determinant and its spread to Gram-negative strains harboring extended-spectrum {beta}-lactamase and carbapenemase resistance genes threatens futility of our chemotherapeutic arsenal. COL is widely regarded to have zero activity against mcr+ patients based on standard antimicrobial susceptibility testing (AST) performed in enriched bacteriological growth media; consequently, the drug is withheld from patients with mcr+ infections. However, these standard testing media poorly mimic in vivo physiology and omit host immune factors. Here we report previously unrecognized bactericidal activities of COL against mcr-1+ isolates of Escherichia coli (EC), Klebsiella pneumoniae (KP), and Salmonella enterica (SE) in standard tissue culture media containing the physiological buffer bicarbonate. Moreover, COL promoted serum complement deposition on the mcr-1+ Gram-negative bacterial surface and synergized potently with active human serum in pathogen killing. At COL concentrations readily achievable with standard dosing, the peptide antibiotic killed mcr-1+ EC, KP, and SE in freshly isolated human blood proved effective as monotherapy in a murine model of mcr-1+ EC bacteremia. Our results suggest that COL, currently ignored as a treatment option based on traditional AST, may in fact benefit patients with mcr-1+ Gram negative infections based on evaluations performed in a more physiologic context. These concepts warrant careful consideration in the clinical microbiology laboratory and for future clinical investigation of their merits in high risk patients with limited therapeutic options.

microbiology↗

bioRxiv2022

Balance-directed protein engineering of IsPETase enhances both PET hydrolysis activity and thermostability

A mesophilic PETase from Ideonella sakaiensis (IsPETase) has been shown to exhibit high PET hydrolysis activity, but its low thermostability limits its industrial applications. We herein developed an engineering strategy for IsPETase to enhance PET hydrolysis activity, thermostability, and protein folding of the enzyme. Balance-directed Z1-PETase variant outperforms the stability-directed Z2-PETase variant under both mesophilic and thermophilic conditions, although Z2-PETase exhibits higher thermostability than Z1-PETase. The Z1-PETase is also superior to Fast-PETase, Dura-PETase, and LC-CICCG in terms of depolymerization rate regardless of temperature conditions we tested. Thus, maintaining a balance between PET hydrolysis activity and thermostability is essential for the development of high-performance PET hydrolases. In a pH-stat bioreactor, Z1-PETase depolymerized >90% of both transparent and colored post-consumer PET powders within 24 and 8 hours at 40{degrees}C and 55{degrees}C, respectively, demonstrating that the balance-directed IsPETase variant produced herein may be applicable in the bio-recycling of PET.

bioengineering↗

bioRxiv2022

Ketamine selectively changes outcome valuation in a biased matching pennies task

The discovery of rapid-acting antidepressant, ketamine has opened a pathway to a new generation of treatments for depression, and inspired neuroscientific investigation based on a new perspective that non-adaptive changes in the intrinsic excitatory and inhibitory circuitry might underlie the pathophysiology of depression. Nevertheless, it still remains largely unknown how the hypothesized molecular and synaptic levels of changes in the circuitry might mediate behavioral and neuropsychological changes underlying depression, and how ketamine might restore adaptive behavior. Here, we used computational models to analyze behavioral changes induced by therapeutic doses of ketamine, while rhesus macaques were iteratively making decisions based on gains and losses of tokens. When administered intramuscularly or intranasally, ketamine reduced the aversiveness of undesirable outcomes such as losses of tokens without significantly affecting the evaluation of gains, behavioral perseveration, motivation and other cognitive aspects of learning such as temporal credit assignment and time scales of choice and outcome memory. Ketamines potentially-antidepressant effect was separable from other side effects such as fixation errors, which unlike outcome evaluation, was readily countered with strong motivation to avoid errors. We discuss how the acute effect of ketamine to reduce the initial impact of negative events could potentially mediate longer-term antidepressant effects through mitigating the cumulative effect of those events produced by slowly decaying memory, and how the disruption-resistant affective memory might pose challenges in treating depression. Our study also invites future investigations on ketamines antidepressant action over diverse mood states and with affective events exerting their impacts at diverse time scales.

neuroscience↗

bioRxiv2022

Proteome reallocation enables the selective de novo biosynthesis of non-linear, branched-chain acetate esters

The one-carbon recursive ketoacid elongation pathway is responsible for making various branched-chain amino acids, aldehydes, alcohols, and acetate esters in living cells. Controlling selective microbial biosynthesis of these target molecules at high efficiency is challenging due to enzyme promiscuity, regulation, and metabolic burden. In this study, we present a systematic modular design approach to control proteome reallocation for selective microbial biosynthesis of branched-chain acetate esters. Through pathway modularization, we partitioned the branched-chain ester pathways into four submodules including keto-isovalerate submodule for converting pyruvate to keto-isovalerate, ketoacid elongation submodule for producing longer carbon-chain keto-acids, ketoacid decarboxylase submodule for converting ketoacids to alcohols, and alcohol acyltransferase submodule for producing branched-chain acetate esters by condensing alcohols and acetyl-CoA. By systematic manipulation of pathway gene replication and transcription, enzyme specificity of the first committed steps of these submodules, and downstream competing pathways, we demonstrated selective microbial production of isoamyl acetate over isobutyl acetate. We found that the optimized isoamyl acetate pathway globally redistributed the amino acid fractions in the proteomes and required up to 23-31% proteome reallocation at the expense of other cellular resources, such as those required to generate precursor metabolites and energy for growth and amino acid biosynthesis. The engineered strains produced isoamyl acetate at a titer of 8.8 g/L (> 0.25 g/L toxicity limit), a yield of 0.17 g/g (47% of maximal theoretical value), and 86% selectivity, achieving the highest titers, yields and selectivity of isoamyl acetate reported to date.

synthetic biology↗

bioRxiv2022

Existence of blood circulating immune-cell clusters (CICs) comprising antigen-presenting cells and B cells

Cell-to-cell physical interactions are involved in almost every physiological processes in multicellular organisms. Although the dynamics of these interactions could be highly diverse and complex in many circumstances, certain cell-to-cell interactions among immune cells have been well studied due importance in understanding disease pathogenesis and immune therapy development1. Dendritic cells (DCs) and B cells are directly involved in adaptive immune response against pathogens. Interaction mechanism between these two celltypes is well-known to occur in germinal centers either indirectly via helper T (Th) cells or directly via cell contact. However, there are animal in vitro and in vivo evidence that such direct DC-to-B cell contact can occur outside germinal centers like in peripheral blood or collagen matrix and display antiviral immune-related activity2,3. Here, we provide evidence that certain types of antigen presenting cells (APCs) can form robust cell clusters with B cells and circulate in blood. From healthy human blood immune single cell RNA-seq datasets, we detected APC subpopulations (0.34{+/-}0.19% of total PBMCs) that were also enriched with well-known naive B cell markers. We visually observed DC:B doublets and multiplets ([~]0.69% of total live PBMCs) in wildtype mouse blood using flow cytometry and microscopic imaging, thus proving the existence of circulating immune-cell clusters (CICs) composed of APCs and B cells. BCR repertoire of these healthy mouse CICs were similar to circulating B cells. Noticeably, frequency of these APC:B CICs were higher COVID-19 patients than healthy donors and their B cell subtype composition (e.g. naive, plasmablast, IgM+, IgG+) varied with disease severity.

immunology↗

bioRxiv2022

PSGL-1 directs early TCR signaling to repress metabolism and promote T cell exhaustion by modulating the TCF-1/TOX axis in CD8+ T cells.

Summary/AbstractWe previously identified the adhesion molecule PSGL-1 as a T cell intrinsic immune checkpoint regulator of T cell exhaustion. Here we show that the ability of PSGL-1 to restrain TCR sginaling correlates with decreased expression of the Zap70 inhibitor Ubash3b (Sts-1) in PSGL-1-deficient T cells. PSGL-1-deficency in T cells supports antitumor responses to a PD-1 blockade resistant melanoma wherein tumor-specific CD8+ T cells sustain an enhanced metabolic state, with an elevated metabolic gene signature that promotes increased glycolysis and glucose uptake to support effector functions. In models of chronic virus infection and cancer, this outcome was associated with CD8+ T cell stemness, as PSGL-1 deficient CD8+ T cells displayed increased TCF-1 and decreased TOX expression, a phenotype shown to be crucial for responsiveness to checkpoint inhibition. Further, we demonstrate that PSGL-1 signaling promotes development of exhaustion in human CD8+ T cells. Finally, pharmacologic blockade of PSGL-1 was sufficient to curtail T cell exhaustion and enhance functionality both with melanoma tumors and chronic LCMV infection, demonstrating that PSGL-1 represents a therapeutic target for immunotherapy for PD-1/PD-L1 resistant tumors.

immunology↗

bioRxiv2021

Functionalizing lipid sponge droplets with DNA

Nucleic acids are among the most versatile molecules for the construction of biomimetic systems because they can serve as information carriers and programmable construction materials. How nucleic acids interact with membranous coacervate compartments such as lipid sponge droplets is not known. Here we systematically characterize the potential of DNA to functionalize lipid sponge droplets and demonstrate a strong size dependence for sequestration into the sponge phase. Double stranded DNA molecules of more than 300 bp are excluded and form a corona on the surface of droplets they are targeted to. Shorter DNA molecules partition efficiently into the lipid sponge phase and can direct DNA-templated reactions to droplets. We demonstrate repeated capture and release of labeled DNA strands by dynamic hybridization and strand displacement reactions that occur inside droplets. Our system opens new opportunities for DNA-encoded functions in lipid sponge droplets such as cargo control and signaling.

synthetic biology↗

bioRxiv2021

Key Factors in the Cortical Response to Transcranial Electrical Stimulations--A Multi-Scale Modeling Study

Transcranial electrode stimulation (tES), one of the techniques used to apply non-invasive brain stimulation (NIBS), modulates cortical activities by delivering weak electric currents through scalp-attached electrodes. This emerging technique has gained increasing attention recently; however, the results of tES vary greatly depending upon subjects and the stimulation paradigm, and its cellular mechanism remains uncertain. In particular, there is a controversy over the factors that determine the cortical response to tES. Some studies have reported that the electric fields (EF) orientation is the determining factor, while others have demonstrated that the EF magnitude itself is the crucial factor. In this work, we conducted an in-depth investigation of cortical activity in two types of electrode montages used widely--the conventional (C)-tES and high-definition (HD)-tES--as well as two stimulation waveforms--direct current (DC) and alternating current (AC). To do so, we constructed a multi-scale model by coupling an anatomically realistic human head model and morphologically realistic multi-compartmental models of three types of cortical neurons (layer 2/3 pyramidal neuron, layer 4 basket cell, layer 5 pyramidal neuron). Then, we quantified the neuronal response to the C-/HD-tDCS/tACS and explored the relation between the electric field (EF) and the radial fields (RF: radial component of EF) magnitude and the cortical neurons threshold. The EF tES induced depended upon the electrode montage, and the neuronal responses were correlated with the EF rather than the RFs magnitude. The electrode montages and stimulation waveforms caused a small difference in threshold, but the higher correlation between the EFs magnitude and the threshold was consistent. Further, we observed that the neurons morphological features affected the degree of the correlation highly. Thus, the EF magnitude was a key factor in the responses of neurons with arborized axons. Our results demonstrate that the crucial factor in neuronal excitability depends upon the neuron models morphological and biophysical properties. Hence, to predict the cellular targets of NIBS precisely, it is necessary to adopt more advanced neuron models that mimic realistic morphological and biophysical features of actual human cells.

neuroscience↗

bioRxiv2021

Probing Specificities of Alcohol Acyltransferases for Designer Ester Biosynthesis with a High-Throughput Microbial Screening Platform

Alcohol acyltransferases (AATs) enables microbial biosynthesis of a large space of esters by condensing an alcohol and an acyl CoA. However, substrate promiscuity of AATs prevents microbial biosynthesis of designer esters with high selectivity. Here, we developed a high-throughput microbial screening platform that facilitates rapid identification of AATs for designer ester biosynthesis. First, we established a microplate-based culturing technique with in situ fermentation and extraction of esters. We validated its capability in rapid profiling of the alcohol substrate specificity of 20 chloramphenicol acetyltransferase variants derived from Staphylococcus aureus (CATSa) for microbial biosynthesis of acetate esters with various exogeneous alcohol supply. By coupling the microplate-based culturing technique with a previously established colorimetric assay, we developed a high-throughput microbial screening platform for AATs. We demonstrated that this platform could not only confirm CATSa F97W with enhanced isobutyl acetate synthesis but also identify three ATF1Sc (P348M, P348A, and P348S) variants, derived from Saccharomyces cerevisiaes AAT and engineered by model-guided protein design, for enhanced butyl acetate production. We anticipate the high-throughput microbial screening platform is a useful tool to identify novel AATs that have important roles in nature and industrial biocatalysis for designer bioester production.

bioengineering↗

bioRxiv2020

Transient neuronal suppression for exploitation of new sensory evidence

In noisy but stationary environments, decisions should be based on the temporal integration of sequentially sampled evidence. This strategy has been supported by many behavioral studies and is qualitatively consistent with neural activity in multiple brain areas. By contrast, decision-making in the face of non-stationary sensory evidence remains poorly understood. Here, we trained monkeys to identify the dominant color of a dynamically refreshed bicolor patch that becomes informative after a variable delay. Animals' behavioral responses were briefly suppressed after evidence changes, and many neurons in the frontal eye field displayed a corresponding dip in activity at this time, similar to that frequently observed after stimulus onset. Generalized drift-diffusion models revealed consistency of behavior and neural activity with brief suppression of motor output, but not with pausing or resetting of evidence accumulation. These results suggest that momentary arrest of motor preparation is an important component of dynamic perceptual decision making.

neuroscience↗

bioRxiv2020

Repurposing chloramphenicol acetyltransferase for a robust and efficient designer ester biosynthesis platform

Robust and efficient enzymes are essential modules for metabolic engineering and synthetic biology strategies across biological systems to engineer whole-cell biocatalysts. By condensing an acyl-CoA and an alcohol, alcohol acyltransferases (AATs) can serve as an interchangeable metabolic module for microbial biosynthesis of a diverse class of ester molecules with broad applications as flavors, fragrances, solvents, and drop-in biofuels. However, the current lack of robust and efficient AATs significantly limits their compatibility with heterologous precursor pathways and microbial hosts. Through bioprospecting and rational protein engineering, we identified and repurposed chloramphenicol acetyltransferases (CATs) from mesophilic prokaryotes to function as robust and efficient AATs compatible with at least 21 alcohol and 8 acyl-CoA substrates for microbial biosynthesis of linear, branched, saturated, unsaturated and/or aromatic esters. By plugging the best engineered CAT (CATec3 Y20F) into the gram-negative mesophilic bacterium Escherichia coli, we demonstrated that the recombinant strain could effectively convert various alcohols into desirable esters, for instance, achieving a titer of 13.9 g/L isoamyl acetate with 95% conversion by fed-batch fermentation. The recombinant E. coli was also capable of simulating the ester profile of roses with high conversion (> 97%) and titer (> 1 g/L) from fermentable sugars at 37{degrees}C. Likewise, a recombinant gram-positive, cellulolytic, thermophilic bacterium Clostridium thermocellum harboring CATec3 Y20F could produce many of these esters from recalcitrant cellulosic biomass at elevated temperatures (>50{degrees}C) due to the engineered enzymes remarkable thermostability. Overall, the engineered CATs can serve as a robust and efficient platform for designer ester biosynthesis from renewable and sustainable feedstocks.

synthetic biology↗

bioRxiv2020

Broad-spectrum, patient-adaptable inhaled niclosamide-lysozyme particles are efficacious against coronaviruses in lethal murine infection models

Niclosamide (NIC) has demonstrated promising in vitro antiviral efficacy against SARS-CoV-2, the causative agent of the COVID-19 pandemic. Though NIC is already FDA-approved, the oral formulation produces systemic drug levels that are too low to inhibit SARS-CoV-2. As an alternative, direct delivery of NIC to the respiratory tract as an aerosol could target the primary site of for SARS-CoV-2 acquisition and spread. We have developed a niclosamide powder suitable for delivery via dry powder inhaler, nebulizer, and nasal spray through the incorporation of human lysozyme (hLYS) as a carrier molecule. This novel formulation exhibits potent in vitro and in vivo activity against MERS-CoV and SARS-CoV-2 and may protect against methicillin-resistance staphylococcus aureus pneumonia and inflammatory lung damage occurring secondary to CoV infections. The suitability of the formulation for all stages of the disease and low-cost development approach will ensure wide-spread utilization

pharmacology and toxicology↗

bioRxiv2020

Multiple timescales of neural dynamics and integration of task-relevant signals across cortex

Recent studies have proposed the orderly progression in the time constants of neural dynamics as an organizational principle of cortical computations. However, relationships between these timescales and their dependence on response properties of individual neurons are unknown. We developed a comprehensive method to simultaneously estimate multiple timescales in neuronal dynamics and integration of task-relevant signals along with selectivity to those signals. We found that most neurons exhibited multiple timescales in their response, which consistently increased from parietal to prefrontal to cingulate cortex. While predicting rates of behavioral adjustments, these timescales were not correlated across individual neurons in any cortical area, resulting in independent parallel hierarchies of timescales. Additionally, none of these timescales depended on selectivity to task-relevant signals. Our results not only suggest multiple canonical mechanisms for increasing timescales of neural dynamics across cortex but also point to additional mechanisms that allow decorrelation of these timescales to enable more flexibility.

neuroscience↗

bioRxiv2019

Confluence of timing and reward biases in perceptual decision-making dynamics

Although the decisions of our daily lives often occur in the context of temporal and reward structures, the impact of such regularities on decision-making strategy is poorly understood. Here, to explore how temporal and reward context modulate strategy, we trained rhesus monkeys to perform a novel perceptual decision-making task with asymmetric rewards and time-varying evidence reliability. To model the choice and response time patterns, we developed a computational framework for fitting generalized drift-diffusion models (GDDMs) which flexibly accommodates diverse evidence accumulation strategies. We found that a dynamic urgency signal and leaky integration, in combination with two independent forms of reward biases, best capture behavior. We also tested how temporal structure influences urgency by systematically manipulating the temporal structure of sensory evidence, and found that the time course of urgency was affected by temporal context. Overall, our approach identified key components of cognitive mechanisms for incorporating temporal and reward structure into decisions.

neuroscience↗