Biology subjects

Park, H.

Publications and source records attributed to Park, H..

17 recordsLinked to original sources

bioRxiv2026

AnnFlux: object-conditioned neural stochastic differential equations for single-cell perturbation dynamics

Single-cell perturbation profiling measures responses to genetic and chemical interventions, yet most models learn a static map, ignoring how populations move over time and how perturbations combine. AnnFlux, an object-conditioned stochastic differential equation, learns a drift field in latent cell-state space. Conditioning on the perturbing object makes the field queryable one object at a time, yielding per-object drifts comparable across genes and drugs. By learning a drift field tailored to each perturbation context, it interpolates a held-out timepoint in an epithelial-mesenchymal transition time course and predicts unseen perturbations. Beyond point estimates, AnnFlux improves distributional fidelity and predicts responses to held-out perturbation combinations. An IFN-response signature predicted by AnnFlux was associated with TLS proximity in an independent pan-cancer spatial atlas. This framework maps perturbation-driven cell-state evolution as continuous trajectories and represents unseen perturbations using prior-knowledge embeddings.

bioinformatics↗

bioRxiv2018

Cartilaginous and osteochondral tissue formation by human mesenchymal stem cells on three-dimensionally woven scaffolds

The development of mechanically functional cartilage and bone tissue constructs of clinically relevant size, as well as their integration with native tissues, remain important challenges for regenerative medicine. The objective of this study was to assess adult human mesenchymal stem cells (MSC) in large, three dimensionally woven poly({varepsilon}-caprolactone) (PCL) scaffolds in proximity to viable bone, both in a nude rat subcutaneous pouch model and under simulated conditions in vitro. In Study I, various scaffold permutations: PCL alone, PCL-bone, \"point-of- care\" seeded MSC-PCL-bone, and chondrogenically pre-cultured Ch-MSC-PCL-bone constructs were implanted in a dorsal, ectopic pouch in a nude rat. After eight weeks, only cells in the Ch- MSC-PCL constructs exhibited both chondrogenic and osteogenic gene expression profiles. Notably, while both tissue profiles were present, constructs that had been chondrogenically pre- cultured prior to implantation showed a loss of glycosaminoglycan (GAG) as well as the presence of mineralization along with the formation of trabecula-like structures. In Study II of the study, the GAG loss and mineralization observed in Study I in vivo were recapitulated in vitro by the presence of either nearby bone or osteogenic culture medium additives but were prevented by a continued presence of chondrogenic medium additives. These data suggest conditions under which adult human stem cells in combination with polymer scaffolds synthesize functional and phenotypically distinct tissues based on the environmental conditions, and highlight the potential influence that paracrine factors from adjacent bone may have on MSC fate, once implanted in vivo for chondral or osteochondral repair.

bioengineering↗

bioRxiv2018

An efficient genome editing strategy to generate putative null mutants in Caenorhabditis elegans using CRISPR/Cas9

Null mutants are essential for analyzing gene function. Here, we describe a simple and efficient method to generate Caenorhabditis elegans null mutants using CRISPR/Cas9 and short single stranded DNA oligo repair templates to insert a universal 43-nucleotide-long stop knock-in (STOP-IN) cassette into the early exons of target genes. This cassette has stop codons in all three reading frames and leads to frameshifts, which will generate putative null mutations regardless of the reading frame of the insertion position in exons. The STOP-IN cassette also contains an exogenous Cas9 target site that allows further genome editing and provides a unique sequence that simplifies the identification of successful insertion events via PCR. As a proof of concept, we inserted the STOP-IN cassette right at a Cas9 target site in aex-2 to generate new putative null alleles by injecting preassembled Cas9 ribonucleoprotein and a short synthetic single stranded DNA repair template containing the STOP-IN cassette and two 35-nucleotide-long homology arms identical to the sequences flanking the Cas9 cut site. We showed that these new aex-2 alleles phenocopied an existing loss-of-function allele of aex-2. We further showed that the new aex-2 null alleles could be reverted back to the wild-type sequence by targeting exogenous Cas9 cut site included in the STOP-IN cassette and providing a single stranded wild-type DNA repair oligo. We applied our STOP-IN method to generate new putative null mutants for additional 20 genes, including three pharyngeal muscle-specific genes (clik-1, clik-2, and clik-3), and reported a high insertion rate (46%) based on the animals we screened. We showed that null mutations of clik-2 cause recessive lethality with a severe pumping defect and clik-3 null mutants have a mild pumping defect, while clik-1 is dispensable for pumping. We expect that the knock-in method using the STOP-IN cassette will facilitate the generation of new null mutants to understand gene function in C. elegans and other genetic model organisms.\n\nSummaryWe report a simple and efficient CRISPR/Cas9 genome editing strategy to generate putative null C. elegans mutants by inserting a small universal stop knock-in (STOP-IN) cassette with stop codons in three frames and frameshifts. The strategy is cloning-free, with the mixture consisting of preassembled Cas9 ribonucleoprotein and single stranded repair DNA oligos directly injected into gonads of adult C. elegans. The universal STOP-IN cassette also contains a unique sequence that simplifies detection of successful knock-in events via PCR and an exogenous Cas9 target sequence that allows further genome editing.

genetics↗

bioRxiv2018

Human primary motor cortex represents evidence for a perceptual decision before motor response

In perceptual decision making the brain extracts and accumulates decision evidence from a stimulus over time and eventually makes a decision based on the accumulated evidence. Several characteristics of this process have been observed in human electrophysiological experiments, especially an average build-up of motor-related signals supposedly reflecting accumulated evidence, when averaged across trials. A more direct approach to investigate the representation of decision evidence in brain signals is to correlate the trial-to-trial fluctuations of a model-based prediction of evidence with the measured signals. We here report results for an experiment in which we applied this approach to human magnetoencephalographic recordings. These results consolidate a range of previous findings and suggest that decision evidence is processed in three consecutive phases in the human brain: In an early phase around 120 ms after the evidence became visible on the screen, in a transition phase around 180 ms and a plateau phase roughly from 300 to 500 ms. We located sources of evidence representations in these phases in early visual (early), parietal (transition) and motor (plateau) regions of the brain while signals in posterior cingulate cortex represented decision evidence in all three phases. These findings imply that parietal cortex is only transiently involved in the processing of decision evidence, that motor areas represent accumulated evidence throughout decision making and that posterior cingulate cortex may have a central role in processing and maintaining decision evidence.

neuroscience↗

bioRxiv2018

Heterogeneous timing of asexual cycles in Plasmodium falciparum quantified by extended time-lapse microscopy

Malarial fever arises from the synchronous bursting of human red blood cells by the Plasmodium parasite. The released parasites re-infect neighboring red blood cells and undergo another asexual cycle of differentiation and proliferation for 48 hours, before again bursting synchronously. The synchrony of bursting is lost during in vitro culturing of the parasite outside the human body, presumably because the asexual cycle is no longer entrained by host-specific circadian cues. Therefore, most in vitro malaria studies have relied on the artificial synchronization of the parasite population. However, much remains unknown about the degree of timing heterogeneity of asexual cycles and how artificial synchronization may affect this timing. Here, we combined time-lapse fluorescence microscopy and long-term culturing to follow single cells and directly measure the heterogeneous timing of in vitro asexual cycles. We first demonstrate that unsynchronized laboratory cultures are not fully asynchronous and the parasites exhibit a bimodal distribution in their first burst times. We then show that synchronized and unsynchronized cultures had similar asexual cycle periods, which indicates that artificial synchronization does not fundamentally perturb asexual cycle dynamics. Last, we demonstrate that sibling parasites descended from the same schizont exhibited significant variation in asexual cycle period, although smaller than the variation between non-siblings. The additional variance between non-siblings likely arises from the variable environments and/or developmental programs experienced in different host cells.

microbiology↗

bioRxiv2018

Cell adhesion promoted by a unique Shigella IpaA vinculin- and talin-binding site

During Shigella cell invasion, the IpaA effector targets the focal adhesion protein vinculin through three vinculin-binding sites (VBSs). Here, we report that IpaA VBS3 also binds to talin. The 2.5 [A] resolution crystal structure indicates that IpaA VBS3 forms a tightly folded -helical bundle with talin H1-H4, contrasting with bundle unraveling upon vinculin interaction. High-affinity binding of Ipa VBS3 to talin H1-H4 requires a core of hydrophobic residues conserved in vinculin binding and a pair of electrostatic interactions accounting for talin binding specificity. IpaA VBS3 does not bind to talin H1-H5 suggesting the targeting of partially activated stretched talin but not inactive talin. Consistently, IpaA VBS3 labeled filopodial and nascent adhesions and regulated their formation through talin binding. In addition, talin-binding by IpaA VBS3 was required for bacterial capture by filopodia during Shigella invasion and for the stabilization of focal adhesions in infected cells. These findings point to the functional diversity of VBSs and a critical role for talin-binding by Shigella IpaA VBS3 and possibly talin VBSs in the regulation of adhesion structures.

microbiology↗

bioRxiv2018

Predictive entrainment of natural speech through two fronto-motor top-down channels

Natural communication between interlocutors is enabled by the ability to predict upcoming speech in a given context. Previously we showed that these predictions rely on a fronto-motor top-down control of low-frequency oscillations in auditory-temporal brain areas that track intelligible speech. However, a comprehensive spatio-temporal characterisation of this effect is still missing. Here, we applied transfer entropy to source-localised MEG data during continuous speech perception. First, at low frequencies (1-4 Hz, brain delta phase to speech delta phase), predictive effects start in left fronto-motor regions and progress to right temporal regions. Second, at higher frequencies (14-18 Hz, brain beta power to speech delta phase), predictive patterns show a transition from left inferior frontal gyrus via left precentral gyrus to left primary auditory areas. Our results suggest a progression of prediction processes from higher-order to early sensory areas in at least two different frequency channels.

neuroscience↗

bioRxiv2018

Graphene-oxide quenching-based molecular beacon imaging of exosome-mediated transfer of neurogenic miR-193a on microfluidic platform

A microRNA (miR-193a) was found to be transferred in the exosomes of differentiated neural progenitors to undifferentiated clones. Graphene-oxide (GO) quenching-based molecular beacon was developed to detect RNAs in living cells and tissues quickly and sensitively. Here, we applied GO quencher-based molecular beacon sensor to visualize neurogenic miR-193a levels delivered via exosome during cell-non-autonomous neurogenesis of neural progenitor cells on microfluidic platform. Fluorescence signals of FAM-labeled peptide nucleic acid (PNA) against miR-193a quenched by GO nanosheets (FAM-PNA193a-GO) were recovered in undifferentiated recipient cells differentiated to the neuronal lineage by exosome-mediated neurogenesis 3 days after co-culture with differentiated donor cells. We propose that molecular beacon imaging using PNA-GO complex can be used to visualize individual cellular expression of mature microRNAs revealing their precise spatial localization and temporal sequences by the intercellular exosome delivery of messages to undergo processes such as cell-non-autonomous neurogenesis.

cell biology↗

bioRxiv2018

Lrfn2-mutant mice display suppressed synaptic plasticity and inhibitory synapse development and abnormal social communication and startle response

SALM1, also known as LRFN2, is a PSD-95-interacting synaptic adhesion molecule implicated in the regulation of NMDA receptor (NMDAR) clustering largely based on in vitro data, although its in vivo functions remain unclear. Here, we found that mice lacking SALM1/LRFN2 (Lrfn2-/- mice) show a normal density of excitatory synapses but altered excitatory synaptic function, including enhanced NMDAR-dependent synaptic transmission but suppressed NMDAR-dependent synaptic plasticity in the hippocampal CA1 region. Unexpectedly, SALM1 expression is detected in both glutamatergic and GABAergic neurons, and Lrfn2-/- CA1 pyramidal neurons show decreases in the density of inhibitory synapses and frequency of spontaneous inhibitory synaptic transmission. Behaviorally, ultrasonic vocalization was suppressed in Lrfn2-/- pups separated from their mothers, and acoustic startle was enhanced, but locomotion, anxiety-like behavior, social interaction, repetitive behaviors, and learning and memory were largely normal in adult Lrfn2-/- mice. These results suggest that SALM1/LRFN2 regulates excitatory synapse function, inhibitory synapse development, and social communication and startle behaviors in mice.\n\nSignificance StatementSynaptic adhesion molecules regulate synapse development and function, which govern neural circuit and brain functions. The SALM/LRFN family of synaptic adhesion proteins consists of five known members whose in vivo functions are largely unknown. Here we characterized mice lacking SALM1/LRFN2 (SALM1 knockout) known to associate with NMDA receptors and found that these mice showed altered NMDA receptor-dependent synaptic transmission and plasticity, as expected, but unexpectedly also exhibited suppressed inhibitory synapse development and synaptic transmission. Behaviorally, SALM1 knockout pups showed suppressed ultrasonic vocalization upon separation from their mothers, and SALM1 knockout adults showed enhanced responses to loud acoustic stimuli. These results suggest that SALM1/LRFN2 regulates excitatory synapse function, inhibitory synapse development, social communication, and acoustic startle behavior.

neuroscience↗

bioRxiv2018

Audio-tactile and peripersonal space processing around the trunk in human parietal and temporal cortex: an intracranial EEG study

Interactions with the environment happen by the medium of the body within ones peripersonal space (PPS) - the space surrounding the body. Studies in monkey and humans have highlighted a multisensory distributed cortical network representing the PPS. However, electrophysiological evidence for a multisensory encoding of PPS in humans is lacking. Here, we recorded for the first time intracranial electroencephalography (iEEG) in humans while administering tactile stimulation (T) on the trunk, approaching auditory stimuli (A), and the combination of the two (AT). To map PPS, in AT trials, tactile stimulation was delivered when the sound was far, at an intermediate location, or close to the body. We first identified electrodes showing AT multisensory integration (i.e., AT vs. A+T): 19% of the recording electrodes. Among those electrodes, we identified those showing a PPS effect (30% of the AT electrodes), i.e., a modulation of the evoked response to AT stimulation as a function of the distance between the sound and body. For most sites, AT multisensory integration and PPS effects had similar spatiotemporal characteristics, with an early response (~50ms) in the insular cortex, and later responses (~200ms) in pre- and post-central gyri. Superior temporal cortex showed a different response pattern with AT multisensory integration at ~100ms without PPS effect. These results, representing the first iEEG delineation of PPS processing in humans, show that PPS processing happens at neural sites where also multisensory integration occurs and at similar time periods, suggesting that PPS representation (around the trunk) is based on a spatial modulation of multisensory integration.

neuroscience↗

bioRxiv2017

Potent and Selective Antitumor Activity of a T-Cell Engaging Bispecific Antibody Targeting a Membrane-Proximal Epitope of ROR1

T-cell engaging bispecific antibodies present a promising strategy for cancer immunotherapy and numerous bispecific formats have been developed for retargeting cytolytic T cells toward tumor cells. To explore the therapeutic utility of T-cell engaging bispecific antibodies targeting the receptor tyrosine kinase ROR1, which is expressed by tumor cells of various hematologic and solid malignancies, we used a bispecific ROR1 x CD3 scFv-Fc format based on a heterodimeric and aglycosylated Fc domain designed for extended circulatory half-life and diminished systemic T-cell activation. A diverse panel of ROR1-targeting scFv derived from immune and naive rabbit antibody repertoires was compared in this bispecific format for target-dependent T-cell recruitment and activation. A ROR1-targeting scFv with a membrane-proximal epitope, R11, revealed potent and selective antitumor activity in vitro and in vivo and emerged as a prime candidate for further preclinical and clinical studies. To elucidate the precise location and engagement of this membrane-proximal epitope, which is conserved between human and mouse ROR1, the three-dimensional structure of scFv R11 in complex with the kringle domain of ROR1 was determined by X-ray crystallography at 1.6-[A] resolution.

immunology↗

bioRxiv2017

Entrained audiovisual speech integration implemented by two independent computational mechanisms: Redundancy in left posterior superior temporal gyrus and Synergy in left motor cortex

Information integration is fundamental to many aspects of human behavior, and yet its neural mechanism remains to be understood. For example, during face-to-face communication we know that the brain integrates the auditory and visual inputs but we do not yet understand where and how such integration mechanisms support speech comprehension. Here we show that two independent mechanisms forge audiovisual representations for speech comprehension in different brain regions. With a novel information theoretic measure, we found that theta (3-7 Hz) oscillations in the posterior superior temporal gyrus/sulcus (pSTG/S) code speech information that is common (i.e. redundant) to the auditory and visual inputs whereas the same oscillations in left motor and inferior temporal cortex code synergistic information between the same inputs. Importantly, redundant coding in the left pSTG/S and synergistic coding in the left motor cortex predict behavior - i.e. speech comprehension performance. Our findings therefore demonstrate that processes classically described as integration effectively reflect independent mechanisms that occur in different brain regions to support audiovisual speech comprehension.

neuroscience↗

bioRxiv2017

A Dynamic Bayesian Observer Model Reveals Origins of Bias in Visual Path Integration

Path integration is a navigation strategy by which animals track their position by integrating their self-motion velocity over time. To identify the computational origins of bias in visual path integration, we asked human subjects to navigate in a virtual environment using optic flow, and found that they generally travelled beyond the goal location. Such a behaviour could stem from leaky integration of unbiased self-motion velocity estimates, or from a prior expectation favouring slower speeds that causes underestimation of velocity. We tested both alternatives using a probabilistic framework that maximizes expected reward, and found that subjects biases were better explained by a slow-speed prior than imperfect integration. When subjects integrate paths over long periods, this framework intriguingly predicts a distance-dependent bias reversal due to build-up of uncertainty, which we also confirmed experimentally. These results suggest that visual path integration performance is limited largely by biases in processing optic flow rather than by suboptimal signal integration.

neuroscience↗

bioRxiv2017

The Rosetta all-atom energy function for macromolecular modeling and design

Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosettas success is the energy function: amodel parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, beta_nov15. Applying these concepts,we explain how to use Rosetta energies to identify and analyze the features of biomolecular models.Finally, we discuss the latest advances in the energy function that extend capabilities from soluble proteins to also include membrane proteins, peptides containing non-canonical amino acids, carbohydrates, nucleic acids, and other macromolecules.

biophysics↗

bioRxiv2016

Generating in vivo somatic mouse mosaics with locus-specific, stably-integrated transgenic elements

Viral vectors and electroporation (EP)-mediated gene transfers are efficient means of inducing somatic mosaicism in mice, but they lack the exquisite control over transgene copy number, gene zygosity, and genomic-locus specificity that genetically engineered mouse models (GEMMs) provide. Here, we develop and demonstrate a simple and generalizable in vivo method, mosaic analysis by dual recombinase-mediated cassette exchange (MADR). MADR allows for stable labeling of mutant cells express transgenic elements from a precisely-defined chromosomal locus. To test our method, we generated reporter-labeled lineages from stem and progenitor cells in a well-defined Rosa26mTmG mouse. We demonstrate the power and versatility of MADR by creating novel glioma models with mixed, reporter-defined zygosity or with \"personalized\" driver mutations from pediatric glioma--each manipulation altering the profile of resulting tumors. Thus, MADR provides a high-throughput genetic platform for the dissection of development and disease, and this rapid method can be applied to the thousands of existing gene-trap mice.

neuroscience↗

bioRxiv2016

Melittin-induced alterations in morphology and deformability of human red blood cells using quantitative phase imaging techniques

Here, the actions of melittin, the active molecule of apitoxin or bee venom, were investigated on human red blood cells (RBCs) using quantitative phase imaging techniques. High-resolution realtime 3-D refractive index (RI) measurements and dynamic 2-D phase images of individual melittin-bound RBCs enabled in-depth examination of melittin-induced biophysical alterations of the cells. From the measurements, morphological, biochemical, and mechanical alterations of the RBCs were analyzed quantitatively. Furthermore, leakage of haemoglobin (Hb) inside the RBCs at high melittin concentration was also investigated.

biophysics↗

bioRxiv2016

Refractive index tomograms and dynamic membrane fluctuations of red blood cells from patients with diabetes mellitus

In this paper we present the optical characterisations of diabetic red blood cells (RBCs) in a non-invasive manner employing three-dimensional (3-D) quantitative phase imaging. By measuring 3-D refractive index tomograms and 2-D time-series phase images, the morphological (volume, surface area and sphericity), biochemical (haemoglobin concentration and content) and mechanical (membrane fluctuation) parameters were quantitatively retrieved at the individual cell level. With simultaneous measurements of individual cell properties, systematic correlative analyses on retrieved RBC parameters were also performed. Our measurements show that diabetic patients had RBCs of reduced cell sphericity and elevated intracellular haemoglobin concentration and content compared to healthy (non-diabetic) subjects. Furthermore, membrane deformability of diabetic RBCs is significantly lower than that of healthy, non-diabetic RBCs. Interestingly, non-diabetic RBCs exhibit strong correlations between the elevated glycated haemoglobin in RBC cytoplasm and decreased cell deformability, whereas diabetic RBCs do not show correlations. Our observations strongly support the idea that slow and irreversible glycation of haemoglobin and membrane proteins of RBCs by hyperglycaemia significantly compromises RBC deformability in diabetic patients.

biophysics↗