Biology subjects

Phan, K.

Publications and source records attributed to Phan, K..

6 recordsLinked to original sources

bioRxiv2026

Chromosome segregation synchrony in S. pombe is noise-limited and arises without positive feedback

Anaphase is a key cell cycle transition that ensures faithful genome inheritance. At anaphase onset, sister chromatids separate abruptly and synchronously upon activation of the protease separase. Major cell cycle transitions often involve positive feedback, which contributes to their abruptness and irreversibility; however, whether such feedback is required for anaphase remains unclear. Here, we analyze sister chromatid separation dynamics in fission yeast using high-resolution live-cell imaging and computational modeling. We find that anaphase synchrony relies on fast degradation of the separase inhibitor securin, but does not require separase-mediated positive feedback. Hence, sister chromatid separation, being inherently irreversible, may be one of the few major cell cycle transitions that can proceed without positive feedback. A stochastic model fitted to the data revealed that separation synchrony is limited by stochasticity resulting from small-number effects. Together, these results support a feedback-independent mechanism for anaphase onset and identify molecular noise as a fundamental constraint on its temporal precision.

cell biology↗

bioRxiv2025

In vivo human embryonic spinal cord atlas validates stem cell-derived human dorsal interneurons and reveals ASD spinal signatures

Restoring somatosensory function after spinal cord injury (SCI) faces fundamental challenges: neuronal subtypes must match both axial position and circuit identity, yet the developmental patterning of human dorsal spinal interneurons (dIs) remains incompletely defined. Here, we integrate six single-cell transcriptomics datasets derived from human embryonic spinal cord tissue spanning gestational weeks 4-25 to generate a reference atlas of early human somatosensory circuit development. The atlas reveals molecular signatures underlying expansion and specialization of dI4 and dI5 interneuron populations associated with mechanosensory and nociceptive processing. Guided by this resource, we established a neuromesodermal progenitor-based differentiation approach that generates dorsal interneurons spanning anterior-posterior identities. Comparison of in vivo and in vitro dI4/dI5 subclasses identified conserved gene networks associated with sensory modalities and revealed enrichment of autism spectrum disorder-associated genes within mechanosensory interneuron populations. Together, these findings clarify how human dorsal spinal interneuron diversity is established.

neuroscience↗

bioRxiv2023

Spontaneous Mutation in 2310061I04Rik Results in Reduced Expression of Mitochondrial Genes and Impaired Brain Myelination

Here, we describe a spontaneous mouse mutant with a deletion in a predicted gene 2310061I04Rik (Rik) of unknown function located on chromosome 17. A 59 base pair long deletion occurred in the first intron of the Rik gene and disrupted its expression. Riknull mice were born healthy and appeared anatomically normal up to two weeks of age. After that, these mice showed inhibited growth, ataxic gait, and died shortly after postnatal day 24 (P24). Transcriptome analysis at P14 and P23 revealed significantly reduced expression of mitochondrial genes in Riknull brains compared to wild type controls including mt-Nd4, mt-Cytb, mt-Nd2, mt-Co1, mt-Atp6, and others. Similarly, genes specific for myelinating oligodendrocytes also showed reduced expression in P23 Riknull brains compared to controls. Histological examination of anterior thalamic nuclei demonstrated decreased myelination of anteroventral nuclei but not of anterodorsal nuclei in P23 Riknull mice. Myelination of the anterior commissure was also impaired and displayed extensive vacuolation. Consistent with these findings, immunohistochemistry showed reduced expression of Opalin, a glycoprotein expressed in differentiated oligodendrocytes. Taken together, these results suggest that RIK is important for oligodendrocyte maturation, and myelination in the developing brain.

neuroscience↗

bioRxiv2022

Isolation and Characterization of Endocardial Endothelial Cells from the Left Ventricular Wall and Outflow Tract of the Porcine Heart

The heart contains six different types of endothelial cells, each with a unique function. We sought to characterize the endocardial endothelial cells (EECs), which line the chambers of the heart. EECs are relatively understudied, yet their dysregulation can lead to various cardiac pathologies. Due to the lack of commercial availability of this cell line, we developed a protocol for isolating EECs from porcine hearts and detailed our methodology for establishing populations of EECs through cell sorting. Additionally, we compared the EEC phenotype and fundamental behaviors to a well-studied endothelial cell line, human umbilical vein endothelial cells (HUVECs). The EECs were slightly smaller than HUVECs, and they stained positively for classic endothelial phenotypic markers such as CD31, von Willebrand Factor, and vascular endothelial (VE) cadherin. The EECs proliferated more quickly than HUVECs, yet migrated more slowly to cover a scratch wound assay. Finally, the EECs maintained their robust endothelial phenotype (expression of CD31) through more than a dozen passages. In contrast, the HUVECs showed significantly reduced CD31 expression in later passages. These important phenotypic differences between EECs and HUVECs highlight the need for researchers to utilize the most relevant cell lines when studying or modeling a disease of interest. Impact statementMany researchers model cardiovascular disease via tissue engineering to determine disease etiology on the cellular and molecular level. However, researchers usually rely on commercially-available cell lines, which can result in utilizing cells that are not specific to the region of the heart being modeled and could lead to incorrect conclusions. By providing a detailed protocol for isolating and purifying endocardial endothelial cells, we are enabling other researchers to access this cell line and model cardiovascular disease states more accurately.

pathology↗

bioRxiv2021

Amikacin potentiator activity of zinc complexed to a pyrithione derivative with enhanced solubility

Resistance to amikacin in Gram-negatives is usually mediated by the 6'-N-acetyltransferase type Ib [AAC(6')-Ib], which catalyzes the transfer of an acetyl group from acetyl CoA to the 6' position of the antibiotic molecule. A path to continue the effective use of amikacin against resistant infections is to combine it with inhibitors of the inactivating reaction. We have recently observed that addition of Zn2+ to in-vitro enzymatic reactions, obliterates acetylation of the acceptor antibiotic. Furthermore, when added to amikacin-containing culture medium in complex to ionophores such as pyrithione (ZnPT), it prevents the growth of resistant strains. An undesired property of ZnPT is its poor water-solubility, a problem that currently affects a large percentage of newly designed drugs. Water-solubility helps drugs to dissolve in body fluids and be transported to the target location. We tested a pyrithione derivative described previously (Magda et al. Cancer Res. 2008, 68:5318-5325) that contains the amphoteric group di(ethyleneglycol)-methyl ether at position 5 (compound 5002), a modification that enhances the solubility. Compound 5002 in complex with zinc (Zn5002) was tested to assess growth inhibition of amikacin-resistant Acinetobacter baumannii and Klebsiella pneumoniae strains in the presence of the antibiotic. Zn5002 complexes in combination with amikacin at different concentrations completely inhibited growth of the tested strains. However, the concentrations needed to achieve growth inhibition were higher than those required to achieve the same results using ZnPT. Time-kill assays showed that the effect of the combination amikacin/Zn5002 was bactericidal. These results indicate that derivatives of pyrithione with enhanced water-solubility, a property that would make them drugs with better bioavailability and absorption, are a viable option for designing inhibitors of the resistance to amikacin mediated by AAC(6')-Ib, an enzyme commonly found in the clinics.

microbiology↗

bioRxiv2019

Apcdd1 is a dual BMP/Wnt inhibitor in the developing nervous system and skin

Animal development and homeostasis depend on precise temporal and spatial intercellular signaling. Components shared between signaling pathways, generally thought to decrease specificity, paradoxically can also provide a solution to pathway coordination. Here we show that the Bone Morphogenetic Protein (BMP) and Wnt signaling pathways share Apcdd1 as a common inhibitor and that Apcdd1 is a taxon-restricted gene with novel domains and signaling functions. Previously, we showed that Apcdd1 inhibits Wnt signaling, here we find that Apcdd1 potently inhibits BMP signaling in body axis formation and neural differentiation in chicken, frog, zebrafish, and humans. Our results from experiments and modeling suggest that Apcdd1 may coordinate the outputs of two signaling pathways central to animal development and human disease. Significance StatementApcdd1 is a taxon-restricted gene that inhibits both BMP and Wnt intercellular signaling pathways in multiple organisms including mice, frog, zebrafish, and chicken. It encodes a bi-functional protein with a novel protein domain that can bind to Wnt and BMP receptors and block downstream signaling.

systems biology↗