Biology subjects

Huang, Y.-P.

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

5 recordsLinked to original sources

bioRxiv2026

The cap-independent translational regulation of NbRabGAP1 in Nicotiana benthamiana during BaMV infection

While cap-dependent translation is the eukaryotic norm, alternative pathways enable selective protein synthesis during stress. We describe a cap-independent mechanism regulating NbRabGAP1, a host factor essential for bamboo mosaic virus (BaMV) movement in Nicotiana benthamiana. The 5' untranslated region (5' UTR, 553-nt) of NbRabGAP1 contains three upstream open reading frames (uORFs) that typically hinder ribosome scanning. Using bicistronic reporter assays, we identified a functional internal ribosome entry site (IRES) within nucleotides 61-150. This IRES features a predicted stable Y-shaped RNA structure and a purine-rich R-motif. We demonstrate that NbPAB8, a poly(A)-binding protein, specifically binds this R-motif to enhance IRES-mediated translation over 2.5-fold. During BaMV infection, NbPAB8 expression is transiently upregulated, coinciding with maintained NbRabGAP1 levels despite potential repression of global cap-dependent translation. This represents a regulatory switch where viral infection triggers a PAB8-dependent IRES mechanism to sustain the vesicle trafficking machinery required for viral movement. Our findings reveal how viral stress rewires host translational control through specific RNA-protein interactions, ensuring the synthesis of critical host factors via IRES-mediated pathways. HighlightDuring bamboo mosaic virus infection, NbPAB8 binds a purine-rich IRES in the NbRabGAP1 5' UTR, bypassing global translation repression to maintain vesicle trafficking essential for viral movement.

molecular biology↗

bioRxiv2023

Plant-based production of diverse human milk oligosaccharides

Human milk oligosaccharides (HMOs) are a diverse class of carbohydrates that aid in the health and development of infants. The vast health benefits of HMOs have made them a commercial target for microbial production; however, producing the [~]130 structurally diverse HMOs at scale has proven difficult. Here, we produce a vast diversity of HMOs by leveraging the robust carbohydrate anabolism of plants. This diversity includes high value HMOs, such as lacto-N-fucopentaose I, that have not yet been commercially produced using state-of-the-art microbial fermentative processes. HMOs produced in transgenic plants provided strong bifidogenic properties, indicating their ability to serve as a prebiotic supplement. Technoeconomic analyses demonstrate that producing HMOs in plants provides a path to the large-scale production of specific HMOs at lower prices than microbial production platforms. Our work demonstrates the promise in leveraging plants for the cheap and sustainable production of HMOs.

plant biology↗

bioRxiv2020

Transcriptome analysis for the development of cell-type specific labeling to study olfactory circuits

In each sensory system of the brain, mechanisms exist to extract distinct features from stimuli to generate a variety of behavioural repertoires. These often correspond to different cell types at some stage in sensory processing. In the mammalian olfactory system, complex information processing starts in the olfactory bulb, whose output is conveyed by mitral and tufted cells (MCs and TCs). Despite many differences between them, and despite the crucial position they occupy in the information hierarchy, little is known how these two types of projection neurons differ at the mRNA level. Here, we sought to identify genes that are differentially expressed between MCs and TCs, with an ultimate goal to generate a cell-type specific Cre-driver line, starting from a transcriptome analysis using a large and publicly available single-cell RNA-seq dataset (Zeisel et al., 2018). Despite many genes showing differential expressions, we identified only a few that were abundantly and consistently expressed only in MCs. After further validating these putative markers using in-situ hybridization, two genes, namely Pkib and Lbdh2, remained as promising candidates. Using CRISPR/Cas9-mediated gene editing, we generated Cre-driver lines and analysed the resulting recombination patterns. This analysis indicated that our new inducible Cre-driver line, Lbhd2-CreERT2, can be used to genetically label MCs in a tamoxifen dose-dependent manner, as assessed by soma locations, projection patterns and sensory-evoked responses. Hence this line is a promising tool for future investigations of cell-type specific contributions to olfactory processing and demonstrates the power of publicly accessible data in accelerating science.

neuroscience↗

bioRxiv2019

A normative study of modified spatial context memory test in middle and older individuals

In view of the spatial context memory function of hippocampus complex region, we designed a modified spatial context memory test (SCMT) and try to early identify amnesic mild cognitive impairment.\n\nAll participants with non-dementia were recruited and divided 2 age groups (55-65 years and 66-75 years) and 3 education levels (6-9 years, 10-12 years and more than 12 years). The mini-mental state examination, visual associative memory test, visual construction retention test, and logical memory subtest of the Wechsler memory scale-III were used to evaluate the cognition state of the individuals. Spatial-context memory test version I with combination of a spatial memory paradigm and a real-life event included 3 subtests of navigation, scene-event association and people-object association.\n\nA total of 147 individuals were confirmed to be normal in cognition in the assessment of the neuropsychological test battery. Regardless of age or level of education, there was no significance in perseveration errors and the retrieval of learned-well navigation information. In the Scene-Event Association test, the subjects with a low level of education seemed to have relative difficulty to quickly classify new information and establish the effective cues to retrieval. The subjects with a high level of education, the performance of spatial-context memory were negative correlation to the age. In the People-Object association test, the subjects in all six groups made no perseveration errors, but older subjects required more time to retrieval, and this situation was more prominent in the subjects with high level education.\n\nWe establish a normal age- and education-adjusted SCMT score in the middle and elder individuals.

neuroscience↗

bioRxiv2018

An E3 ubiquitin ligase from Nicotiana benthamiana targets the replicase of Bamboo mosaic virus and restricts its replication

One upregulated host gene identified previously was found involved in the infection process of Bamboo mosaic virus (BaMV). The full-length cDNA of this gene was cloned by 5'- and 3'-rapid amplification of cDNA ends and found to encode a polypeptide containing a conserved RING-domain and a transmembrane domain. The gene might function as an E3 ubiquitin ligase. We designated this protein in Nicotiana benthamiana as ubiquitin E3 ligase containing RING-domain 1 (NbUbE3R1). Further characterization by using Tobacco rattle virus-based virus-induced gene silencing revealed an increased BaMV accumulation in both knockdown plants and protoplasts. To further inspect the functional role of NbUbE3R1 in BaMV accumulation, NbUbE3R1 was expressed in N. benthamiana plants. The wild-type NbUbE3R1-orange fluorescent protein (NbUbE3R1-OFP), NbUbE3R1/{bigtriangleup}TM-OFP (removal of the transmembrane domain) and NbUbE3R1/mRING-OFP (mutation at the RING domain, the E2 interaction site) were transiently expressed in plants. NbUbE3R1 and its derivatives all functioned in restricting BaMV accumulation. The common feature of these constructs was the intact substrate-interacting domain. Yeast two-hybrid and co-immunoprecipitation experiments used to determine the possible viral-encoded substrate of NbUbE3R1 revealed the replicase of BaMV as the possible substrate. In conclusion, we identified an upregulated gene, NbUbE3R1, that plays a role in BaMV replication.

microbiology↗