Biology subjects

Yoon, M.

Publications and source records attributed to Yoon, M..

12 recordsLinked to original sources

bioRxiv2026

Scalable Production of a De Novo SARS-CoV-2 Antiviral miniprotein in Escherichia coli

The rapid emergence of SARS-CoV-2 variants that evade neutralizing antibodies underscores the need for next-generation antiviral biologics that combine molecular precision with scalable, cost-effective manufacturing. Computationally designed miniproteins targeting the receptor-binding domain (RBD) of the spike protein offer a compelling alternative to monoclonal antibodies due to their small size, high thermal stability, and compatibility with microbial expression systems. Here we report the end-to-end development and cGMP production of IPD-52520, a de novo antiviral miniprotein, using an optimized E. coli platform. Two miniprotein candidates, a homotrimeric construct (Trimer is referred to as IPD-52520, 17 kDa) and a tandem fusion (Daisy is referred to as IPD-52521, 25 kDa), were evaluated in parallel through systematic optimization of strain selection, media composition, fed-batch fermentation, inclusion-body solubilization, refolding, and chromatographic purification. The Trimer was downselected as the lead molecule based on superior preclinical efficacy, favorable pharmacokinetic properties, and higher volumetric manufacturing yields. The optimized process delivers approximately 2 g/L of purified protein at greater than 90% purity. Scale-up from 5 L to 50 L under cGMP conditions demonstrated excellent batch-to-batch reproducibility across six independent batches, supporting nonclinical and Phase 1 clinical supply. Comprehensive biophysical characterization confirmed a well-folded, predominantly alpha-helical trimer (Tm = 73.4 {degrees}C; polydispersity = 1.005) with an intact primary structure and strong target-binding affinity (KD < 1 pM). Real-time stability studies indicate that the drug substance is stable at 2-8 {degrees}C for at least 12 months, with ongoing stability studies. These results demonstrate the feasibility of translating computationally designed antiviral miniproteins into manufacturable biologics and provide a platform applicable to rapid-response therapeutics against current and future pandemic threats.

bioengineering↗

bioRxiv2025

Effects of human stress on horse behavior and interaction quality

Human-horse interaction can be influenced by the emotional and physiological state of humans, as horses are highly sensitive to human stress. Understanding these effects is essential for improving outcomes in equine-assisted activities. This study examined how human stress impacts horse behavior and interaction quality. Seven humans and seven horses participated in a crossover design experiment in which participants viewed either stressful or relaxed video stimuli prior to interacting with horses. Electroencephalography (EEG), heart rate variability (HRV), and salivary cortisol was collected to assess human physiological responses, while the Human-Animal Interaction Scale (HAIS) and an ethogram evaluated interaction quality and horse behaviors. Stressful stimuli significantly increased beta and high-beta activity and altered HRV indices, indicated by increased low-frequency power and decreased high-frequency power. HAIS scores were lower under stress conditions, reflecting reduced interaction quality. Horses exhibited more pushing behavior and less lip-licking when handlers were stressed, although task completion time did not differ between conditions. These results demonstrated that human stress negatively influences both physiological states and behavioral outcomes within human-horse interactions. Therefore, managing emotional states and stress levels may enhance interaction quality and effectiveness in equine-assisted programs.

animal behavior and cognition↗

bioRxiv2025

Associations between canine temperament and salivary levels of cortisol and serotonin

Temperament influences canine behavior and helps determine a dogs suitability as a companion or working animal. Although several temperament assessment tools exist, many rely on subjective evaluations, highlighting the need for scientifically validated methods. This study evaluated the validity of the Wesen temperament test by examining its association with physiological biomarkers--salivary cortisol and serotonin. Twenty-four dogs (11 females and 13 males) completed a modified Wesen test comprising seven subtests: Unconscious Confidence, Sociality, Noise Stability, Movement Stability, Desire for Play and Predation, Behavior in Stressful Situations, and Separation. Saliva samples were collected pre- and post-assessment, and cortisol and serotonin levels were measured using ELISA. Hormonal levels and temperament scores were analyzed using correlation, regression, and Kruskal-Wallis tests. Pre-assessment cortisol levels were negatively correlated with total average temperament score and several subtest scores. Post-assessment cortisol levels showed significant negative correlations with total average scores and all subtests. Changes in cortisol levels from pre- to post-assessment were negatively associated with temperament scores. Dogs with higher temperament scores exhibited significantly higher serotonin levels than those with lower scores. These findings support the utility of temperament assessments validated through physiological markers and provide novel evidence linking canine temperament with endocrine function.

physiology↗

bioRxiv2024

Impact of exogenous aminoacyl-tRNA synthetase and tRNA on temperature sensitivity in Escherichia coli: towards a genetic code-expanded biological logic gate

Genetic code expansion (GCE) is a powerful strategy that expands the genetic code of an organism for incorporating non-canonical amino acids (ncAAs) into proteins using engineered tRNAs and aminoacyl-tRNA synthetases (aaRSs). While GCE has opened up new possibilities for synthetic biology, little is known about the potential side effects of exogenous aaRS/tRNA pairs. In this study, we investigated the impact of exogenous aaRS and amber suppressor tRNA on gene expression in Escherichia coli. We discovered that in DH10{beta} {Delta}cyaA, transformed with the F1RP/F2P two-hybrid system, high consumption rate of cellular ATP by exogenous aaRS/tRNA at elevated temperatures induces temperature sensitivity in the expression of genes regulated by the catabolite activator protein. We harnessed this temperature sensitivity to create a novel biological AND gate in E. coli, responsive to both p-benzoylphenylalanine (BzF) and low temperature, using a BzF-dependent variant of E. coli chorismate mutase and split subunits of Bordetella pertussis adenylate cyclase. Our study provides new insights into the unexpected effects of exogenous aaRS/tRNA pairs and offers a new approach for constructing a biological logic gate.

synthetic biology↗

bioRxiv2023

NbPTR1 confers resistance against Pseudomonas syringae pv. actinidiae in kiwifruit

Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) causes a devastating canker disease in yellow-fleshed kiwifruit (Actinidia chinensis). The effector HopZ5, which is present in all isolates of Psa3 causing global outbreaks of pandemic kiwifruit canker disease, triggers immunity in Nicotiana benthamiana and is not recognised in susceptible A. chinensis cultivars. In a search for N. benthamiana non-host resistance genes against HopZ5, we found that the nucleotide-binding leucine-rich repeat receptor NbPTR1 recognised HopZ5. RPM1-interacting protein 4 (RIN4) orthologues from multiple plants, including kiwifruit, were associated with NbPTR1-mediated autoimmunity suppression and recognition of HopZ5. No functional orthologues of NbPTR1 were found in A. chinensis. NbPTR1 transformed into Psa3-susceptible A. chinensis var. chinensis Hort16A plants introduced HopZ5-specific resistance against Psa3. Altogether, this study suggested that expressing NbPTR1 in Psa3-susceptible kiwifruit is a viable approach to acquiring resistance to Psa3 and it provides valuable information for engineering resistance in otherwise susceptible kiwifruit genotypes.

plant biology↗

bioRxiv2022

Contrasting effector profiles between bacterial colonisers of kiwifruit reveal redundant roles and interplay converging on PTI-suppression and RIN4

O_LITesting effector-knockout strains of the Pseudomonas syringae pv. actinidiae biovar 3 (Psa3) for reduced in planta growth in their native kiwifruit host revealed a number of non- redundant effectors that contribute to Psa3 pathogenicity. Conversely, complementation in the weak kiwifruit pathogen P. syringae pv. actinidifoliorum (Pfm) for increased growth identified redundant Psa3 effectors. C_LIO_LIPsa3 effectors hopAZ1a and HopS2b and the entire exchangeable effector locus ({Delta}EEL; 10 effectors) were significant contributors to bacterial colonisation of the host and were additive in their effects on pathogenicity. Four of the EEL effectors (HopD1a, AvrB2b, HopAW1a, and HopD2a) redundantly contribute to pathogenicity through suppression of pattern-triggered immunity (PTI). C_LIO_LIImportant Psa3 effectors include several redundantly required effectors early in the infection process (HopZ5a, HopH1a, AvrPto1b, AvrRpm1a, and HopF1e). These largely target the plant immunity hub, RIN4. C_LIO_LIThis comprehensive effector profiling revealed that Psa3 carries robust effector redundancy for a large portion of its effectors, covering a few functions critical to disease. C_LI

plant biology↗

bioRxiv2021

A conserved glutamate residue in RPM1-interacting protein4 is ADP-ribosylated by Pseudomonas effector AvrRpm2 to activate RPM1-mediated response

Gram-negative bacterial plant pathogens directly inject effectors into their hosts to hijack and manipulate metabolism, eluding the frontier surveillance at the cell surface. The effector AvrRpm1Pma from Pseudomonas syringae pv. maculicola functions as an ADP-ribosyl transferase, modifying RPM1-interacting protein4 (RIN4), leading to the activation of Arabidopsis resistance protein RPM1. We identified the ADP-ribosyl transferase activity of another bacterial effector AvrRpm2Psa from Pseudomonas syringae pv. actinidiae via infection using a Pseudomonas syringae pv. tomato strain following Agrobacterium-mediated transient expression of RIN4 in N. benthamiana. We conducted mutational analysis in combination with mass spectrometry to genetically locate the modified residue. We show that a conserved glutamate residue (E156) of AtRIN4 is the target site for AvrRpm2Psa by demonstrating the modified AtRIN4 with E156A substitution is no longer ADP-ribosylated. Accordingly, naturally occurring soybean and snap bean RIN4 homologs with no glutamate at the positions corresponding to the E156 of AtRIN4 are not ADP-ribosylated by AvrRpm2Psa. In contrast with another effector AvrB, modifications of potential phosphorylation sites including T166 in AtRIN4 affected neither ADP-ribosylation nor RPM1 activation by AvrRpm2Psa. This study suggests that separate biochemical reactions by different pathogen effectors may trigger the activation of the same resistance protein through distinct modifications of RIN4. One sentence summaryA conserved glutamate residue (E156) in the C-NOI domain of RPM1-interacting protein4 is ADP-ribosylated by Pseudomonas effector AvrRpm2 to activate RPM1-mediated defence response, independently of phosphorylation at T166.

plant biology↗

bioRxiv2020

Potent in vitro anti-SARS-CoV-2 activity by gallinamide A and analogues via inhibition of cathepsin L

The emergence of SARS-CoV-2 in late 2019, and the subsequent COVID-19 pandemic, has led to substantial mortality, together with mass global disruption. There is an urgent need for novel antiviral drugs for therapeutic or prophylactic application. Cathepsin L is a key host cysteine protease utilized by coronaviruses for cell entry and is recognized as a promising drug target. The marine natural product, gallinamide A and several synthetic analogues, were identified as potent inhibitors of cathepsin L activity with IC50 values in the picomolar range. Lead molecules possessed selectivity over cathepsin B and other related human cathepsin proteases and did not exhibit inhibitory activity against viral proteases Mpro and PLpro. We demonstrate that gallinamide A and two lead analogues potently inhibit SARS-CoV-2 infection in vitro, with EC50 values in the nanomolar range, thus further highlighting the potential of cathepsin L as a COVID-19 antiviral drug target.

biochemistry↗

bioRxiv2020

AvrE1 and HopR1 from Pseudomonas syringae pv. actinidiae are additively required for full virulence on kiwifruit

Pseudomonas syringae pv. actinidiae ICMP 18884 biovar 3 (Psa3) produces necrotic lesions during infection of its kiwifruit host. Bacterial growth in planta and lesion formation are dependent upon a functional type III secretion system (T3S), which translocates multiple effector proteins into host cells. Associated with the T3S locus is the conserved effector locus (CEL), which has been characterised and shown to be essential for the full virulence in other P. syringae pathovars. Two effectors at the CEL, hopM1 and avrE1, as well as an avrE1-related non-CEL effector, hopR1, have been shown to be redundant in the model pathogen P. syringae pv. tomato DC3000 (Pto), a close relative of Psa. However, it is not known whether CEL-related effectors are required for Psa pathogenicity. The Psa3 allele of hopM1, and its associated chaperone, shcM, have diverged significantly from their orthologs in Pto. Furthermore, the CEL effector hopAA1-1, as well as a related non-CEL effector, hopAA1-2, have both been pseudogenised. We have shown that HopM1 does not contribute to Psa3 virulence due to a truncation in shcM, a truncation conserved in the Psa lineage, likely due to the need to evade HopM1-triggered immunity in kiwifruit. We characterised the virulence contribution of CEL and related effectors in Psa3 and found that only avrE1 and hopR1, additively, are required for in planta growth and lesion production. This is unlike the redundancy described for these effectors in Pto and indicates that these two Psa3 genes are key determinants essential for kiwifruit bacterial canker disease.

pathology↗

bioRxiv2020

Sensitivity of radio-photoluminescence glass dosimeters to accumulated doses

BackgroundThis study investigated the effect of accumulated doses on radio-photoluminescence glass dosimeters (RPLGDs) from measurements involving mega-voltage photons. MethodsForty-five commercially available RPLGDs were irradiated to estimate their dose responses. Photon beams of 6, 10, and 15 MV were irradiated onto the RPLGDs inside a phantom, which were divided into five groups with different doses and energies. Groups 1 and 2 were irradiated at 1, 5, 10, 50, and 100 Gy in a sequential manner; Group 3 was irradiated 10 times with a dose of 10 Gy; and Groups 4 and 5 followed the same method as that of Group 3, but with doses of 50 Gy and 100 Gy, respectively. ResultsFor the annealed Group 1, RPLGD exhibited a linearity response with variance within 5%. For the non-annealed Group 2, readings demonstrated hyperlinearity at 6 MV and 10 MV, and linearity at 15 MV. Following the 100 Gy irradiation, the readings for Group 2 were 118.7 {+/-} 1.9%, 112.2 {+/-} 2.7%, and 101.5 {+/-} 2.3% at 6, 10, and 15 MV, respectively. For Groups 3, 4, and 5, the responsiveness of the RPLGDs gradually decreased as the number of repeated irradiations increased. The percentage readings for the 10th beam irradiation with respect to the readings for the primary beam irradiation were 84.6 {+/-} 1.9%, 87.5 {+/-} 2.4%, and 93.0 {+/-} 3.0% at 6 MV, 10 MV, and 15 MV, respectively. ConclusionsThe non-annealed RPLGD response to dose was hyperlinear for the 6 MV and 10 MV photon beams but not for the 15 MV photon beam. Additionally, the annealed RPLGD exhibited a fading phenomenon when the measurement was repeated several times and demonstrated a relatively large fading effect at low energies than at high energies.

cancer biology↗

bioRxiv2020

Variation at the common polysaccharide antigen locus drives lipopolysaccharide diversity within the P. syringae species complex

The common polysaccharide antigen (CPA) from the lipopolysaccharide (LPS) component of cell walls from the species complex Pseudomonas syringae is highly variable both in structure and immunological specificity, but the genetic basis for this is not well understood. We have characterised the CPA locus from P. syringae pv. actinidiae (Psa). This locus has a modular structure with genes for both L- and D- rhamnose (Rha) biosynthesis and that of an unknown sugar. It also contains an operon coding for ABC transporter subunits, a bifunctional glycosyltransferase and an O-methyltransferase. This operon is predicted to have a role in transport, elongation and termination of the Rha backbone of the CPA oligosaccharide and is referred to as the TET operon. This is the first report of the identification of this operon in P. syringae. Two alleles of the TET operon were present amongst the different biovars of Psa and lineages of the closely related pathovar P. syringae pv. actinidifoliorum. This allelic variation was reflected in the electrophoretic properties of purified LPS from the different isolates. Gene knockout of the TET operon allele from biovar 1 and replacement with that from biovar 3, demonstrated the link between the genetic locus and the electrophoretic and immunogenic properties of the LPS molecules in Psa. Sequence analysis of the TET operon from a wide range of P. syringae and P. viridiflava isolates displayed a phylogenetic history which is incongruent with core gene phylogeny, but correlates with previously reported tailocin sensitivity, suggesting a functional relationship between LPS structure and tailocin susceptibility.

microbiology↗

bioRxiv2018

Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis

The earliest developmental origins of dysmorphologies are poorly understood in many congenital diseases. They often remain elusive because the first signs of genetic misregulation may initiate as subtle changes in gene expression, which can be obscured later in development due to secondary phenotypic effects. We here develop a method to trace back the origins of phenotypic abnormalities by accurately quantifying the 3D spatial distribution of gene expression domains in developing organs. By applying geometric morphometrics to 3D gene expression data obtained by Optical Projection Tomography, our approach is sensitive enough to find regulatory abnormalities never previously detected. We identified subtle but significant differences in gene expression of a downstream target of the Fgfr2 mutation associated with Apert syndrome. Challenging previous reports, we demonstrate that Apert syndrome mouse models can further our understanding of limb defects in the human condition. Our method can be applied to other organ systems and models to investigate the etiology of malformations.

developmental biology↗