Biology subjects

Huang, P.-Y.

Publications and source records attributed to Huang, P.-Y..

12 recordsLinked to original sources

bioRxiv2025

Omnivorous diets of sympatric duck species in a subtropical East Asia wetland unveiled by multi-marker DNA metabarcoding

The East Asian-Australasian Flyway (EAAF) is experiencing notable population decreases in its migratory waterbird species. Our understanding of the foraging ecology of these waterbird species, including ducks, is crucial for monitoring and safeguarding their food sources and wetland habitats. Here, we used a DNA metabarcoding approach to analyze the fecal DNA from duck species to elucidate their dietary composition during the wintering period in a subtropical East Asian wetland. By employing multiple markers (18S, COI, and trnL) targeting different taxonomic groups and levels, we offered a comprehensive dietary analysis for omnivores that consume both plants and animals. We revealed the dietary compositions of common migratory duck species and their intraspecific and interspecific variations. While ducks are generally known to be omnivorous, Anas crecca had a more specialized diet and was primarily herbivorous throughout winter. In contrast, the sympatric Mareca penelope and Spatula clypeata exhibited a more omnivorous foraging behavior. Moreover, A. crecca displayed less dietary variation among individuals, while individuals of M. penelope and S. clypeata were highly variable in their diets. Comparing our results with those of studies conducted in different regions, we found that the dietary compositions of these duck species varied to different degrees across geographic locations. This variation underscores the flexibility of these duck species in their diets and their adaptable foraging strategies. Our findings also indicate that grasslands rich in herbaceous plants and aquatic environments abundant in small aquatic invertebrates are vital foraging habitats for duck species during their winter stay.

ecology↗

bioRxiv2025

CTCF-RNA interactions orchestrate cell-specific chromatin loop organization

CCCTC-binding factor (CTCF) is essential for chromatin organization. CTCF interacts with endogenous RNAs, and deletion of its ZF1 RNA-binding region ({Delta}ZF1) disrupts chromatin loops in mouse embryonic stem cells (ESCs). However, the functional significance of CTCF-ZF1 RNA interactions during cell differentiation is unknown. Using an ESC-to-neural progenitor cell (NPC) differentiation model, we show that CTCF-ZF1 is crucial for maintaining cell-type-specific chromatin loops. Expression of CTCF-{Delta}ZF1 leads to disrupted loops and dysregulation of genes within these loops, particularly those involved in neuronal development and function. We identified NPC-specific, CTCF-ZF1 interacting RNAs. Truncation of two such coding RNAs, Podxl and Grb10, disrupted chromatin loops in cis, similar to the disruption seen in CTCF-{Delta}ZF1 expressing NPCs. These findings underscore the inherent importance of CTCF-ZF1 RNA interactions in preserving cell-specific genome structure and cellular identity. HIGHLIGHTSO_LICTCF loop anchors induced after differentiation are disrupted in the {Delta}ZF1 RNA-binding mutant. C_LIO_LILoop loss in the {Delta}ZF1 mutant is independent of its DNA binding and protein interactions. C_LIO_LIChromatin loop loss is associated with gene dysregulation. C_LIO_LITruncation of cell-specific, CTCF-ZF1-interacting RNAs disrupts chromatin loops in cis. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/643339v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1dad736org.highwire.dtl.DTLVardef@674a5dorg.highwire.dtl.DTLVardef@14345d4org.highwire.dtl.DTLVardef@19d83cb_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Genetic basis and evolution of structural color polymorphism in an Australian songbird

Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaption under differential selection. Some island birds have melanic plumage differing from the color of mainland conspecifics, a trait proposed as an insular adaptation. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure that could produce a blue structural color, suggesting a blue ancestor. An earlier study proposed independent evolution of melanism on the islands based on the history of subspecies divergence. However, the genetic basis of melanism and the origin of color differentiation in this group are still unknown. Here, we used whole-genomes to investigate the genetic basis of melanism by comparing the blue and black M. leucopterus subspecies to identify highly divergent genomic regions. We identified a well-known pigmentation gene ASIP and four candidate genes that may contribute to feather nanostructure development. We also detected signatures of a selective sweep in genomic regions containing ASIP and SCUBE2 not in the black subspecies, as predicted by earlier work, but in the blue subspecies, which possesses many derived SNPs in these regions, suggesting that the mainland subspecies has re-evolved a blue plumage from a black ancestor. This re-evolution was likely driven by a pre-existing female preference. Our findings provide new insight into the evolution of plumage coloration in island versus continental populations, and, importantly, we identify candidate genes that likely play roles in the development and evolution of feather structural coloration.

evolutionary biology↗

bioRxiv2023

Novel Chromatin Insulating Activities Uncovered upon Eliminating KnownInsulators in vivo

Partitioning of repressive from actively transcribed chromatin in mammalian cells fosters cell-type specific gene expression patterns. While this partitioning is reconstructed during differentiation, the chromatin occupancy of the key insulator, CTCF, is unchanged at the developmentally important Hox clusters. Thus, dynamic changes in chromatin boundaries must entail other activities. Given its requirement for chromatin loop formation, we examined cohesin-based chromatin occupancy without known insulators, CTCF and MAZ, and identified a family of zinc finger proteins (ZNFs), some of which exhibit tissue-specific expression. Two such ZNFs foster chromatin boundaries at the Hox clusters that are distinct from each other and from MAZ. PATZ1 was critical to the thoracolumbar boundary in differentiating motor neurons and mouse skeleton, while ZNF263 contributed to cervicothoracic boundaries. We propose that these insulating activities act with cohesin, alone or combinatorially, with or without CTCF, to implement precise positional identity and cell fate during development.

genetics↗

bioRxiv2021

Impact of Glycosylation on SARS-CoV-2 Infection and Broadly Protective Vaccine Design

A major challenge to end the pandemic caused by SARS-CoV-2 is to develop a broadly protective vaccine. As the key immunogen, the spike protein is frequently mutated with conserved epitopes shielded by glycans. Here, we reveal that spike glycosylation has site-differential effects on viral infectivity and lung epithelial cells generate spike with more infective glycoforms. Compared to the fully glycosylated spike, immunization of spike protein with N-glycans trimmed to the monoglycosylated state (Smg) elicits stronger immune responses and better protection for hACE2 transgenic mice against variants of concern. In addition, a broadly neutralizing monoclonal antibody was identified from the Smg immunized mice, demonstrating that removal of glycan shields to better expose the conserved sequences is an effective and simple approach to broad-spectrum vaccine development. One-Sentence SummaryRemoving glycan shields to expose conserved epitopes is an effective approach to develop a broad-spectrum SARS-CoV-2 vaccine.

microbiology↗

bioRxiv2021

Sex-biased response to and brain cell infection by SARS-CoV-2 in a highly susceptible human ACE2 transgenic model

The COVID-19 pandemic is caused by SARS-CoV-2 infection. Human angiotensin-converting enzyme II (hACE2) has been identified as the receptor enabling SARS-CoV-2 host entry. To establish a mouse model for COVID-19, we generated transgenic mouse lines using the (HS4)2-pCAG-hACE2-HA-(HS4)2 transgene cassette, which expresses HA-tagged hACE2 under control of the CAG promoter and is flanked by HS4 insulators. Expression levels of the hACE2 transgene are respectively higher in lung, brain and kidney of our CAG-hACE2 transgenic mice and relatively lower in duodenum, heart and liver. The CAG-hACE2 mice are highly susceptibility to SARS-CoV-2 infection, with 100 PFU of SARS-CoV-2 being sufficient to induce 87.5% mortality at 9 days post-infection and resulting in a sole (female) survivor. Mortality was 100% at the higher titer of 1000 PFU. At lower viral titers, we also found that female mice exposed to SARS-CoV-2 infection suffered much less weight loss than male mice, implying sex-biased responses to SARS-CoV-2 infection. We subjected neuronal cultures to SARS-CoV-2 pseudovirus infection to ascertain the susceptibilities of neurons and astrocytes. Moreover, we observed that expression of SARS-CoV-2 Spike protein alters the synaptic responses of cultured neurons. Our transgenic mice may serve as a model for severe COVID-19 and sex-biased responses to SARS-CoV-2 infection, aiding in the development of vaccines and therapeutic treatments for this disease.

microbiology↗

bioRxiv2020

A CRISPR Screen Identifies Myc-associated Zinc Finger Protein (MAZ) as an Insulator Functioning at CTCF boundaries in Hox Clusters

The essential CCCTC-binding factor (CTCF) is critical to three-dimensional (3D) genome organization. CTCF binding insulates active and repressed genes within the Hox clusters upon differentiation, but such binding does not participate in boundary formation in all cell types, such as embryonic stem cells. We conducted a genome-wide CRISPR knockout screen to identify genes required for CTCF boundary activity at the HoxA cluster, complemented by novel biochemical approaches. This screen identified Myc-associated zinc finger protein (MAZ) as a CTCF insulator co-factor, among other candidates listed herein. MAZ depletion or specific deletion of MAZ motifs within the Hox clusters led to de-repression of posterior Hox genes immediately after CTCF boundaries upon differentiation, which phenocopied deletion of the proximal CTCF motifs. Similar to CTCF, MAZ interacted with the cohesin subunit, RAD21. Upon loss of MAZ, local contacts within topologically associated domains (TADs) were disrupted, as evidenced by HiC analysis. Thus, MAZ is a novel factor sharing insulation properties with CTCF and contributing to the genomic architectural organization. One Sentence SummaryMAZ is identified as an insulator functioning at CTCF boundaries delimiting active and repressed genes at Hox clusters

biochemistry↗

bioRxiv2019

Enhancer regulation for induced WNT3A expression during neuronal regeneration

The treatment of traumatic brain injury (TBI) is limited by a lack of knowledge about the mechanisms underlying neuronal regeneration. WNT family members have been implicated in neurogenesis and aberrant WNT signaling has been associated with neurodegenerative diseases. The current study compared the expression of WNT genes during regeneration of injured cortical neurons. Recombinant WNT3A showed positive effect in promoting neuronal regeneration via in vitro and in vivo TBI models. Intranasal administration of WNT3A protein to TBI mice increased NeuN+ cells compared to control mice as well as retained motor function based on behavior analysis. Since TBI is known to reprogram the epigenome, chromatin immunoprecipitation-sequencing of histone H3K27ac and H3K4me3 was performed to address the transcriptional regulation of WNT3A during neuronal regeneration. We predicted, characterized and proposed that a histone H3K4me1-marked enhancer may undergo topological transformation to regulate the WNT3A gene expression.

molecular biology↗

bioRxiv2018

Small Data Challenge: Structural Analysis and Optimization of Convolutional Neural Networks with a Small Sample Size

Deep neural networks have gained immense popularity in the Big Data problem; however, the availability of training samples can be relatively limited in certain application domains, particularly medical imaging, and consequently leading to overfitting problems. This \"Small Data\" challenge may need a mindset that is entirely different from the existing Big Data paradigm. Here, under the small data setting, we examined whether the network structure has a substantial influence on the performance and whether the optimal structure is predominantly determined by sample size or data nature. To this end, we listed all possible combinations of layers given an upper bound of the VC-dimension to study how structural hyperparameters affected the performance. Our results showed that structural optimization improved accuracy by 27.99%, 16.44%, and 13.11% over random selection for a sample size of 100, 500, and 1,000 in the MNIST dataset, respectively, suggesting that the importance of the network structure increases as the sample size becomes smaller. Furthermore, the optimal network structure was mostly determined by the data nature (photographic, calligraphic, or medical images), and less affected by the sample size, suggesting that the optimal network structure is data-driven, not sample size driven. After network structure optimization, the conventional convolutional neural network could achieve 91.13% in accuracy with only 500 samples, 93.66% in accuracy with only 1000 samples for the MNIST dataset and 94.10% in accuracy with only 3300 samples for the Mitosis (microscopic) dataset. These results indicate the primary importance of the network structure and the nature of the data in facing the Small Data challenge.

bioengineering↗

bioRxiv2018

Small effect size leads to reproducibility failure in resting-state fMRI studies

Thousands of papers using resting-state functional magnetic resonance imaging (RS-fMRI) have been published on brain disorders. Results in each paper may have survived correction for multiple comparison. However, since there have been no robust results from large scale meta-analysis, we do not know how many of published results are truly positives. The present meta-analytic work included 60 original studies, with 57 studies (4 datasets, 2266 participants) that used a between-group design and 3 studies (1 dataset, 107 participants) that employed a within-group design. To evaluate the effect size of brain disorders, a very large neuroimaging dataset ranging from neurological to psychiatric isorders together with healthy individuals have been analyzed. Parkinsons disease off levodopa (PD-off) included 687 participants from 15 studies. PD on levodopa (PD-on) included 261 participants from 9 studies. Autism spectrum disorder (ASD) included 958 participants from 27 studies. The meta-analyses of a metric named amplitude of low frequency fluctuation (ALFF) showed that the effect size (Hedges g) was 0.19 - 0.39 for the 4 datasets using between-group design and 0.46 for the dataset using within-group design. The effect size of PD-off, PD-on and ASD were 0.23, 0.39, and 0.19, respectively. Using the meta-analysis results as the robust results, the between-group design results of each study showed high false negative rates (median 99%), high false discovery rates (median 86%), and low accuracy (median 1%), regardless of whether stringent or liberal multiple comparison correction was used. The findings were similar for 4 RS-fMRI metrics including ALFF, regional homogeneity, and degree centrality, as well as for another widely used RS-fMRI metric namely seed-based functional connectivity. These observations suggest that multiple comparison correction does not control for false discoveries across multiple studies when the effect sizes are relatively small. Meta-analysis on un-thresholded t-maps is critical for the recovery of ground truth. We recommend that to achieve high reproducibility through meta-analysis, the neuroimaging research field should share raw data or, at minimum, provide un-thresholded statistical images.

neuroscience↗

bioRxiv2017

NINJA-Associated ERF19 Negatively Regulates Arabidopsis Pattern-Triggered Immunity

Recognition of microbe-associated molecular patterns (MAMPs) derived from invading pathogens by plant pattern recognition receptors (PRRs) initiates defense responses known as pattern-triggered immunity (PTI). Transcription factors (TFs) orchestrate the onset of PTI through complex signaling networks. Here, we characterize the function of ERF19, a member of the Arabidopsis thaliana ethylene response factor (ERF) family. ERF19 was found to act as a negative regulator of PTI against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 (Pst). Notably, overexpression of ERF19 increased plant susceptibility to these pathogens and repressed MAMP-induced PTI outputs. In contrast, expression of the chimeric dominant repressor ERF19-SRDX boosted PTI activation, conferred increased resistance to B. cinerea, and enhanced elf18-triggered immunity against Pst. Consistent with a negative role of ERF19 in PTI, MAMP-mediated growth inhibition was respectively weakened or augmented in lines overexpressing ERF19 or expressing ERF19-SRDX. Moreover, we demonstrate that the transcriptional repressor Novel INteractor of JAZ (NINJA) associates with and represses the function of ERF19. Our work reveals ERF19 as a key player in a buffering mechanism to avoid defects imposed by over-activation of PTI and a potential role for NINJA in fine-tuning ERF19-mediated regulation.

plant biology↗

bioRxiv2017

Toward D-Peptide Biosynthesis: Elongation Factor P Enables Ribosomal Incorporation Of Consecutive D-Amino Acids

To maintain stereospecific biochemistry in cells, living organisms have evolved mechanisms to exclude D-amino acids (DAA) in their protein synthesis machinery, which also limits our exploration of the realm of mirror-image molecules. Here, we show that high affinity between EF-Tu and aminoacyl-tRNA promotes D-amino acid incorporation. More strikingly, Elongation Factor P efficiently resolves peptidyl transferase stalling between two consecutive D-amino acids, and hence enables the translation of D-peptides.

biochemistry↗