Biology subjects

Yang, J. W.

Publications and source records attributed to Yang, J. W..

10 recordsLinked to original sources

bioRxiv2026

Development of host-mimicking legume-based media for robust induction of sporulation in soybean-associated Cercospora species

Cercospora species associated with soybean cause Cercospora leaf spot and purple seed stain, which are major diseases affecting soybean production worldwide and can lead to significant yield and seed quality losses. However, unstable and poor sporulation under laboratory conditions remains a critical challenge, hindering the recovery of genetically homogeneous isolates and the establishment of standardized experimental protocols. These limitations further restrict our understanding of the biology, epidemiology, and pathogenicity of these pathogens. In this study, we developed specialized legume-based culture media derived from soybean and pea tissues to mimic host-associated environmental conditions. We compared the sporulation efficacy of these media with commonly used artificial media, including potato dextrose agar (PDA) and V8 juice agar. Our results demonstrated that legume-based media consistently supported higher levels of sporulation than PDA and V8 across multiple strains, although conidial yields varied depending on the strain and medium concentration. Transcriptional analysis of sporulation-related genes revealed that while abaA, wetA, and steA did not show significant differential expression among media, velB exhibited distinct medium-dependent expression patterns. Further evaluation using additional field isolates confirmed that legume-based media provide a more reliable method for inducing sporulation than PDA. Overall, legume-based media represent a practical and effective approach for promoting sporulation in soybean-associated Cercospora species under laboratory conditions.

microbiology↗

bioRxiv2025

Ultrasonic Reporter of Kinase Activity

Protein kinases are an essential class of enzymes that regulate cellular signaling pathways, with their dysregulation implicated in pathologies such as cancer and neurodegenerative diseases. Despite the existence of high-performance fluorescent biosensors of kinase activity, it remains challenging to study the function and regulation pathways of kinases in opaque tissues due to the limited tissue penetration of light. To address this limitation, we introduce the first ultrasonic reporter of kinase activity (UReKA), designed to detect protein kinase A (PKA) activity by altering the ultrasound scattering of gas vesicles, a unique class of air-filled protein nanostructures. We engineer a gas vesicle shell protein to respond to PKA, demonstrate the functionality of UReKA both in purified protein format and expressed in mammalian cells, and showcase its capacity to monitor PKA signaling in response to pharmacological stimulation or genetic mutation. This work makes it possible to visualize cellular functional activity in opaque media, with broad potential for future applications in cancer biology, cellular development, and drug discovery.

bioengineering↗

bioRxiv2025

N6-methyladenosine promotes temozolomide resistance through non-canonical regulation of mRNA stability in glioblastoma cells

N6-methyladenosine (m6A) is a critical regulator of mRNA processing and function, impacting nearly every step of the mRNA lifecycle. Changes in m6A status have been implicated in many different types of cancer, including glioblastoma where acquired resistance to temozolomide remains a major clinical challenge. We established glioblastoma cell culture models of acquired temozolomide resistance and analyzed the role of m6A in controlling resistance-associated pathways. We show that m6A stabilizes key genes and pathways promoting temozolomide resistance in glioblastoma, including MGMT, the enzyme that repairs primary temzolomide-induced DNA damage, and PI3K/Akt signaling, a major driver of chemoresistance. Pharmacological inhibition of the m6A methyltransferase METTL3 destabilizes MGMT and other critical mRNAs, restoring temozolomide sensitivity. Collectively, our results suggest that genes associated with temozolomide resistance are stabilized by m6A methylation, even as the majority of the transcriptome remains subject to m6A-mediated mRNA decay. Moreover, these data highlight METTL3 inhibition as a promising therapeutic approach to overcoming temozolomide resistance in glioblastoma.

molecular biology↗

bioRxiv2024

Human Accelerated Regions regulate gene networks implicated in apical-to-basal neural progenitor fate transitions

The evolution of the human cerebral cortex involved modifications in the composition and proliferative potential of the neural stem cell (NSC) niche during brain development. Human Accelerated Regions (HARs) exhibit a significant excess of human-specific sequence changes and have been implicated in human brain evolution. Multiple studies support that HARs include neurodevelopmental enhancers with novel activities in humans, but their biological functions in NSCs have not been empirically assessed at scale. Here we conducted a direct-capture Perturb-seq screen repressing 180 neurodevelopmentally active HARs in human iPSC-derived NSCs with single-cell transcriptional readout. After profiling >188,000 NSCs, we identified a set of HAR perturbations with convergent transcriptional effects on gene networks involved in NSC apicobasal polarity, a cellular process whose precise regulation is critical to the developmental emergence of basal radial glia (bRG), a progenitor population that is expanded in humans. Across multiple HAR perturbations, we found convergent dysregulation of specific apicobasal polarity and adherens junction regulators, including PARD3, ABI2, SETD2, and PCM1. We found that the repression of one candidate from the screen, HAR181, as well as its target gene CADM1, disrupted apical PARD3 localization and NSC rosette formation. Our findings reveal interconnected roles for HARs in NSC biology and cortical development and link specific HARs to processes implicated in human cortical expansion.

neuroscience↗

bioRxiv2024

Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment

Human Accelerated Regions (HARs) are highly conserved across species but exhibit a significant excess of human-specific sequence changes, suggesting they may have gained novel functions in human evolution. HARs include transcriptional enhancers with human-specific activity and have been implicated in the evolution of the human brain. However, our understanding of how HARs contributed to uniquely human features of the brain is hindered by a lack of insight into the genes and pathways that HARs regulate. It is unclear whether HARs acted by altering the expression of gene targets conserved between HARs and their chimpanzee orthologs or by gaining new gene targets in human, a mechanism termed enhancer hijacking. We generated a high-resolution map of chromatin interactions for 1,590 HARs and their orthologs in human and chimpanzee neural stem cells (NSCs) to comprehensively identify gene targets in both species. HARs and their chimpanzee orthologs targeted a conserved set of 2,963 genes enriched for neurodevelopmental processes including neurogenesis and synaptic transmission. Changes in HAR enhancer activity were correlated with changes in conserved gene target expression. Conserved targets were enriched among genes differentially expressed between human and chimpanzee NSCs or between human and non-human primate developing and adult brain. Species-specific HAR gene targets did not converge on known biological functions and were not significantly enriched among differentially expressed genes, suggesting that HARs did not alter gene expression via enhancer hijacking. HAR gene targets, including differentially expressed targets, also showed cell type-specific expression patterns in the developing human brain, including outer radial glia, which are hypothesized to contribute to human cortical expansion. Our findings support that HARs influenced human brain evolution by altering the expression of conserved gene targets and provide the means to functionally link HARs with novel human brain features.

genomics↗

bioRxiv2022

Niche-based deterministic assembly processes strengthen the effects of β-diversity on metacommunity functioning of marine bacterioplankton

Studies at a local community () level have shown that biodiversity positively affects ecosystem functioning due to niche-based deterministic processes like resource partitioning. Extending to a metacommunity ({beta}) level, we hypothesize that {beta} diversity also positively affects metacommunity functioning. We further hypothesize that the {beta} diversity effect is stronger (more positive) when {beta} diversity is increased by deterministic/non-random assembly processes. To test the hypotheses, we collected bacterioplankton along a transect of 6 stations in the southern East China Sea in 14 cruises. All 6 stations within a cruise were regarded as a metacommunity. For any pairs of the 6 stations, the Bray-Curtis index and summed bacterial biomass were calculated to represent {beta} diversity and metacommunity functioning, respectively. We also calculated deviation of observed mean pairwise phylogenetic similarities among species from random to represent the deterministic influences of assembly processes. We found that bacterial {beta} diversity generally positively affects metacommunity functioning; however, the {beta} diversity effect varied among cruises. Cross-cruise comparison indicates that the {beta} diversity effect increased with the deterministic assembly processes selecting for phylogenetically dissimilar species. This study extends the biodiversity-ecosystem functioning research to a metacommunity level, complementing the current framework by considering community assembly in natural environments.

ecology↗

bioRxiv2021

Trade-off between competition ability and invulnerability to predation in marine microbes; protist grazing versus viral lysis effects

Trade-offs between competition ability and invulnerability to predation are important mechanisms explaining how predation promotes bacterial diversity. However, existence of these trade-offs has apparently not been investigated in natural marine bacterial communities. Here, we address this question with growth-based measurements for each marine bacterial taxon by conducting on-board dilution experiments to manipulate predation pressure and using high-throughput sequencing to assess the response of bacterial communities. We determined that bacterial taxa with a higher predation-free growth rate were accompanied with higher predation-caused mortality, supporting existence of competitiveness-invulnerability trade-off. This trade-off was stronger and more consistent under viral lysis than protist grazing. In addition, predation generally flattened out the rank-abundance distribution and increased the evenness and richness of the bacterial community. These findings supported the "Kill-the-Winner" hypothesis. All experiments supported a significant competitiveness-invulnerability trade-off, but there was substantial variation among bacterial communities in response to predation across experiments conducted in various sites and seasons. Therefore, we inferred that the Kill-the-Winner hypothesis is important but likely not the only deterministic mechanism explaining how predation shapes bacterial assemblages in natural marine systems.

ecology↗

bioRxiv2021

The middle lipin (M-Lip) domain is a new dimeric protein fold that binds membranes

Phospholipid synthesis and fat storage as triglycerides is regulated by lipin phosphatidic acid phosphatases (PAPs), whose enzymatic PAP function requires association with cellular membranes. Using hydrogen deuterium exchange mass spectrometry, we find mouse lipin 1 binds membranes through an N-terminal amphipathic helix and a middle lipin (M-Lip) domain that is conserved in mammalian and mammalian-like lipins. Crystal structures of the M-Lip domain reveal a previously unrecognized and novel protein fold that dimerizes. The isolated M-Lip domain binds membranes both in vitro and in cells through conserved basic and hydrophobic residues. Deletion of the M-Lip domain in full-length lipin 1 influences PAP activity, membrane binding, subcellular localization, oligomerization, and adipocyte differentiation, but does not affect transcriptional co-activation. This establishes the M-Lip domain as a new dimeric protein fold that binds membranes and is critical for full functionality of mammalian lipins.

biochemistry↗

bioRxiv2019

Computationally guided high-throughput design of self-assembling drug nanoparticles

Nanoformulations are transforming our capacity to effectively deliver and treat a myriad of conditions. However, many nanoformulation approaches still suffer from high production complexity and low drug loading. One potential solution relies on harnessing co-assembly of drugs and small molecular excipients to facilitate nanoparticle formation through solvent exchange without the need for chemical synthesis, generating nanoparticles with up to 95% drug loading. However, there is currently no understanding which of the millions of possible combinations of small molecules can result in the formation of these nanoparticles. Here we report the development of a high-throughput screening platform coupled to machine learning to enable the rapid evaluation of such nanoformulations. Our platform identified 101 novel self-assembling drug nanoparticles from 2.1 million pairings derived from 788 candidate drugs with one of 2686 excipients, spanning treatments for multiple diseases and often harnessing well-known food additives, vitamins, or approved drugs as carrier materials - with potential for accelerated approval and translation. Given their long-term stability and potential for clinical impact, we further characterize novel sorafenib-glycyrrhizin and terbinafine-taurocholic acid nanoparticles ex vivo and in vivo. We anticipate that this platform could accelerate the development of safer and more efficacious nanoformulations with high drug loadings for a wide range of therapeutics.

bioengineering↗

bioRxiv2019

Single cell ATAC-seq identifies broad changes in neuronal abundance and chromatin accessibility in Down Syndrome

Down Syndrome (DS) is caused by triplication of chr21 and is associated with cognitive impairment, Alzheimers Disease, and other developmental alterations. The Ts65Dn mouse model for DS has triplication of sequences syntenic with human chr21, and traits resembling those seen in humans with DS. We performed single-cell combinatorial indexing assay for transposase accessible chromatin using sequencing (sci-ATAC-seq) on cortices of adult Ts65Dn mice and control littermates. Analyses of 13,766 cells revealed 26 classes of cells. The most abundant class of excitatory neurons was reduced by 17% in Ts65Dn mice, and three of the four most common classes of interneurons were increased by 50%. Ts65Dn mice display changes in accessibility at binding motifs for transcription factors that are determinants of neuronal lineage, and others encoded within triplicated regions. These studies define previously uncharacterized cellular and molecular features of DS, and potential mechanisms underlying the condition.

genomics↗