Biology subjects

Bian, C.

Publications and source records attributed to Bian, C..

14 recordsLinked to original sources

bioRxiv2026

Functional Ultrasound Characterization of Spatiotemporal Cerebral Hemodynamic Responses Evoked by Whisker Stimulation

Functional ultrasound imaging (fUS) measures task-associated changes in cerebral blood volume (CBV) with fine spatial sampling and rapid acquisition, supporting functional mapping and brain-signal decoding. As an indirect measure of neural activity, fUS-CBV signals are shaped by neurovascular coupling and vascular dynamics, which influence the spatial and temporal stimulus information available for decoding. Consequently, the functional distinctions accessible in fUS-CBV signals require characterization under controlled experimental conditions. Here, controlled whisker stimulation in awake, head-fixed mice was used to characterize these decoding-relevant response properties. Whisker identity and number, stimulation duration, and inter-stimulus interval were systematically varied. All-whisker stimulation produced contralaterally dominant responses in the primary somatosensory barrel field and ventral posteromedial thalamic nucleus. Different whisker inputs were associated with distinguishable cortical response distributions, while stimulation involving more whiskers produced broader representative activation patterns. Across durations of 0.5 s to10 s, brief stimulation generated measurable stimulus-associated signals, and response magnitude, persistence, and spatial distribution varied with stimulus duration. For paired 2-s stimuli, trial-level separability was already high at the shortest tested 1-s gap, corresponding to a 3-s onset-to-onset spacing, and reached 100% at gaps of 3 s or longer. Building on the experimentally characterized spatiotemporal response properties of fUS-CBV signals, a proof-of-concept modeling and decoding framework was developed, comprising cross-animal spatial prediction, classification of short versus long stimulation from S1BF {Delta}CBV time courses with known stimulus onset, and modeling of paired-event separability. Together, the results show that fUS-CBV signals retain structured spatial and temporal information about controlled sensory input after neurovascular transformation. These measured response properties characterize the spatiotemporal boundaries within which neural activity can be reliably distinguished using fUS-CBV signals, providing constraints for the development of fUS-based decoding models and the design of stimulation paradigms suitable for reliable fUS decoding.

neuroscience↗

bioRxiv2026

Evolutionary Rewiring of Root Cell-Type Nitrogen Responses

Nitrate induces widespread transcriptional reprogramming in plants, but how transcription factors coordinate these responses across cell types and evolve across species with divergent root patterning remains unclear. Using single-cell transcriptomics in Arabidopsis thaliana and Solanum lycopersicum (tomato) under varying nitrate conditions, we demonstrate that many transcriptional responses are cell type and developmental stage-specific. Arabidopsis NIN-LIKE PROTEIN 7 (NLP7) directly modulates both broadly expressed and cell-type-specific targets, but is not required to establish the cell type specific nature of these patterns. Comparative analysis reveals evolutionary shifts; key nitrogen programs are localized to different cell types in tomato, with the exodermis as a major regulatory hub. Identification of tomato NLP7a and NLP7b direct targets at cellular resolution supports their role in direct modulation of cell type N-transcriptional programs. This is evidenced by NLP7-controlled exodermal cell wall remodeling in low nitrate, highlighting functional conservation despite divergent cellular topographies.

plant biology↗

bioRxiv2025

Genetic and Functional Characterization of AMH Signaling in Zebrafish - Evidence for Roles of Amh-Bmpr2a-Bmpr1bb Pathway in Controlling Gonadal Homeostasis

Anti-Mullerian hormone (AMH), a member of the TGF-{beta} superfamily, plays a crucial role in Mullerian duct regression in mammals. AMH signals through a specific type II receptor (AMHRII) and a type I receptor to activate the downstream Smad1/5/9 signaling pathway. Interestingly, non-mammalian vertebrates, including teleosts, also express AMH despite lacking Mullerian ducts. Accumulating evidence indicates that AMH influences gonadal development and function across vertebrates. Intriguingly, zebrafish, a popular model organism, possesses AMH (Amh/amh) but lacks specific type II receptor (Amhr2). Based on our previous studies and data from others, we propose that Amh may signal through a novel pathway in zebrafish involving the BMP type II receptor Bmpr2a and type I receptor Bmpr1bb. In this study, we provide genetic and functional evidence for the existence of the Amh-Bmpr2a-Bmpr1bb signaling pathway in zebrafish and its role in controlling gonadal homeostasis. Our experimental data excluded the participation of Bmpr2b and Bmpr1ba, paralogues of Bmpr2a and Bmpr1bb respectively, in Amh signaling. Additionally, we also provide genetic evidence that the phenotypes exhibited by amh, bmpr2a, and bmpr1bb mutants, i.e., gonadal hypertrophy, were all dependent on gonadotropin signaling, and that the two gonadotropins (FSH and LH) showed similar potency in driving the development of hypertrophic gonadal growth resulting from dysfunction in the Amh-Bmpr2a-Bmpr1bb signaling pathway. In summary, the present study provides comprehensive evidence for Amh signaling through Bmpr2a-Bmpr1bb pathway and its interplay with gonadotropins in controlling germ cell proliferation and differentiation.

genetics↗

bioRxiv2025

Chromosome-level genome assemblies of five Sinocyclocheilus species

Sinocyclocheilus, a genus of tetraploid fishes, is endemic to the karst regions of Southwest China. All species within this genus are classified as second-class national protected species due to their unique and fragile habitat. However, absence of high-quality genomic resources has hindered various research efforts to elucidate their phylogenetic relationships and the origin of polyploidy. To address these academic challenges, we at first constructed a high-quality genome assembly for the most abundant representative, golden-line barbel (Sinocyclocheilus grahami), by integration of PacBio long-read and Hi-C sequencing technologies. The final scaffold-level genome assembly of S. grahami is 1.6 Gb in length, with a scaffold N50 up to 30.7 Mb. A total of 42,205 protein-coding genes were annotated. Subsequently, 93.1% of the assembled genome sequences (about 1.5 Gb) and 93.8% of the total predicted genes were successfully anchored onto 48 chromosomes. Furthermore, we obtained chromosome-level genome assemblies for four other Sinocyclocheilus species (including S. anophthalmus, S. maitianheensis, S. anshuiensis, and S. rhinocerous) based on homologous comparison. These genomic data we present in this study provide valuable genetic resources for in-depth investigation on cave adaptation and improvement of economic values and conservation of diverse Sinocyclocheilus fishes.

genomics↗

bioRxiv2024

Postharvest partial dehydration of blueberries enhanced blueberry wine aroma via upregulating phenylalanine metabolism and terpene biosynthesis

Postharvest partial dehydration of blueberries can enhance blueberry wine aroma, while the underlying mechanisms remain unclear. In this study, the key odor-active volatiles in blueberry wines fermented from dehydrated blueberries (30% weight loss) were identified via aroma extract dilution analysis. Results showed that increased levels of phenylalanine-derived compounds such as phenylethanol, and terpenes such as linalool and geraniol, primarily led to the enhancement of sweet, floral and fruity aromas of blueberry wines. Postharvest partial dehydration increased the contents of these compounds, which could be linked to the upregulation of VcGOT2 and VcPAR involved in phenylalanine metabolism, and the upregulation of VcDXS, VcHDR and VcTPS involved in terpene biosynthesis. Notably, the upregulated VcTPS encoded a monoterpene synthase responsible for producing linalool. These findings provided insight into the impact of postharvest dehydration on phenylalanine and terpene metabolism in blueberries, offering a reference for improving blueberry wine aroma through postharvest partial dehydration techniques.

biochemistry↗

bioRxiv2023

Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits

Nitrogen is an essential element for all life processes in plants. As such, plant roots dynamically respond to nitrogen availability below-ground by executing a signaling and transcriptional cascade resulting in altered plant growth, optimized for nutrient uptake. The NIN-LIKE PROTEIN 7 (NLP7) transcription factor senses nitrogen and along with its closely related paralog NLP6, partially coordinates these transcriptional responses. While post-translational regulation of NLP6/7 is well established, its upstream transcriptional regulation remains understudied in Arabidopsis and other plant species. Here, we dissect a previously identified sub-circuit upstream of NLP6/7 in Arabidopsis and which was predicted to contain multiple multi-node feedforward loops suggestive of an optimized design principle of nitrogen transcriptional regulation. This sub-circuit comprises AUXIN RESPONSE FACTOR 18 (ARF18), ARF9, DEHYDRATION RESPONSE ELEMENT BINDING-PROTEIN 26 (DREB26), A NAC-DOMAIN CONTAINING PROTEIN 32 (ANAC032), NLP6 and NLP7 and their regulation of NITRITE REDUCTASE 1 (NIR1). Conservation and divergence of this circuit and their influence on N-dependent root system architecture are similarly assessed in Solanum lycopersicum. The specific binding sites of these factors within their respective promoters and their putative cis-regulatory architecture are identified. The direct or indirect nature of these interactions are validated in planta. The resulting models were genetically validated in varying concentrations of available nitrate by measuring the transcriptional output of the network revealing rewiring of nitrogen regulation across distinct plant lineages. Significance StatementNitrogen is a critical nutrient for plant growth and yield. While external N has facilitated modern agriculture, over-application of N-containing fertilizers has drastic ecological and environmental consequences. Here, we experimentally validate a six gene regulatory circuit with extensive feedforward loops identified to act upstream of the critical NIN-LIKE PROTEIN 6/7 transcription factors which regulates a nitrogen metabolic enzyme. Our results indicate conservation and divergence in these circuits between Arabidopsis and tomato despite the similar role of NLP7 in N-dependent changes in root system architecture. The resulting network models complement existing knowledge of NLP7 regulation by providing a framework for targeted transcriptional engineering to increase plant nitrogen use efficiency.

plant biology↗

bioRxiv2023

Protein Representation Learning via Knowledge Enhanced Primary Structure Modeling

AO_SCPLOWBSTRACTC_SCPLOWProtein representation learning has primarily benefited from the remarkable development of language models (LMs). Accordingly, pre-trained protein models also suffer from a problem in LMs: a lack of factual knowledge. The recent solution models the relationships between protein and associated knowledge terms as the knowledge encoding objective. However, it fails to explore the relationships at a more granular level, i.e., the token level. To mitigate this, we propose Knowledge-exploited Auto-encoder for Protein (KeAP), which performs tokenlevel knowledge graph exploration for protein representation learning. In practice, non-masked amino acids iteratively query the associated knowledge tokens to extract and integrate helpful information for restoring masked amino acids via attention. We show that KeAP can consistently outperform the previous counterpart on 9 representative downstream applications, sometimes surpassing it by large margins. These results suggest that KeAP provides an alternative yet effective way to perform knowledge enhanced protein representation learning. Code and models are available at https://github.com/RL4M/KeAP.

bioinformatics↗

bioRxiv2021

Verticillium dahliae effector VDAL protects MYB6 from degradation by interacting with PUB25/26 E3 ligases for enhancing Verticillium wilt resistance in Arabidopsis

Verticillium wilt is a severe plant disease that causes massive losses in multiple crops. Increasing the plant resistance to Verticillium wilt is a critical challenge worldwide. Here, we report that the hemibiotrophic Verticillium dahliae (V. dahliae)-secreted Asp f2-like protein VDAL causes leaf wilting when applied to cotton leaves in vitro, but enhances the resistance to V. dahliae when overexpressed in Arabidopsis or cotton without affecting the plant growth and development. VDAL protein interacts with Arabidopsis E3 ligases PUB25 and PUB26 (PUBs) and is ubiquitinated by PUBs in vitro. However, VDAL is not degraded by PUB25 or PUB26 in planta. Besides, the pub25 pub26 double mutant shows higher resistance to V. dahliae than the wild type. PUBs interact with the transcription factor MYB6 in a yeast two-hybrid screen. MYB6 promotes plant resistance to Verticillium wilt while PUBs ubiquitinate MYB6 and mediate its degradation. VDAL competes with MYB6 for binding to PUBs, and the role of VDAL in increasing Verticillium wilt resistance depends on MYB6. Taken together, these results suggest that plants evolute a strategy to utilize the invaded effector protein VDAL to resist the V. dahliae infection without causing a hypersensitive response (HR), Alternatively, in order to take nutrients from host cells, hemibiotrophic pathogens may use some effectors to keep plant cells alive during its infection in order to take nutrients from host cells. This study provides the molecular mechanism for plants increasing disease resistance when overexpressing some effector proteins without inducing HR, and may promote searching for more genes from pathogenic fungi or bacteria to engineer plant disease resistance. One-sentence summaryEctopically expressed VDAL in Arabidopsis alleviates the degradation of a positive disease response factor MYB6 through its interaction with PUB25/26 E3 ligases.

plant biology↗

bioRxiv2020

Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patients immunological status, and found dramatic changes in the IGH within the patients immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones during 2-3 weeks of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34 and IGHV4-39 in COVID-19 patients were more abundant than that of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.

immunology↗

bioRxiv2020

Rapid Neural Reorganization during Retrieval Practice Predicts Subsequent Long-term Retention and False Memory

Active retrieval can induce changes to the strength and content of a memory, yielding enhanced or distorted subsequent recall. But how consolidation influences these retrieval-induced seemingly contradictory outcomes remains unknown. Here we show rapid neural reorganization over eight runs of retrieval practice predicted subsequent recall. Behaviorally, retrieval practice boosted memory following a 24-hour (long-term) but not a 30-minute delay, and increased false memory at both delays. Long-term retention gains were predicted by multi-voxel representation distinctiveness in the posterior parietal cortex that increased progressively over retrieval practice. False memory was predicted by unstable representation distinctiveness in the medial temporal lobe during retrieval practice. Memory-related neural networks gradually reconfigured over retrieval practice, with the ventrolateral and medial prefrontal cortex acting as hubs for functional connections that predicted long-term retention gains and false memory outcomes respectively. Our findings demonstrate dynamic neural reorganization during retrieval practice, through which memories are arranged into discrete yet malleable representations for subsequent consolidation.

neuroscience↗

bioRxiv2019

Genome-wide association analyses of multiple traits in Duroc pigs using low-coverage whole-genome sequencing strategy

High-density markers discovered in large size samples are essential for mapping complex traits at the gene-level resolution for agricultural livestock and crops. However, the unavailability of large reference panels and array designs for a target population of agricultural species limits the improvement of array-based genotype imputation. Recent studies showed very low coverage sequencing (LCS) of a large number of individuals is a cost-effective approach to discover variations in much greater detail in association studies. Here, we performed cohort-wide whole-genome sequencing at an average depth of 0.73x and identified more than 11.3 M SNPs. We also evaluated the data set and performed genome-wide association analysis (GWAS) in 2885 Duroc boars. We compared two different pipelines and selected a proper method (BaseVar/STITCH) for LCS analyses and determined that sequencing of 1000 individuals with 0.2x depth is enough for identifying SNPs with high accuracy in this population. Of the seven association signals derived from the genome-wide association analysis of the LCS variants, which were associated with four economic traits, we found two QTLs with narrow intervals were possibly responsible for the teat number and back fat thickness traits and identified 7 missense variants in a single sequencing step. This strategy (BaseVar/STITCH) is generally applicable to any populations and any species which have no suitable reference panels. These findings show that the LCS strategy is a proper approach for the construction of new genetic resources to facilitate genome-wide association studies, fine mapping of QTLs, and genomic selection, and implicate that it can be widely used for agricultural animal breeding in the future.

genetics↗

bioRxiv2019

Identification of \"Missing Link\" Families of Small DNA Tumor Viruses

Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA (dsDNA) viruses. This supports the inference that at least some polintons are viruses that remain capable of cell-to-cell spread. At present, there are no polinton-associated capsid protein genes annotated in public sequence databases. To rectify this deficiency, we used a data-mining approach to investigate the distribution and gene content of polinton-like elements and related DNA viruses in animal genomic and metagenomic sequence datasets. The results define a discrete family-like clade of animal-specific viruses with two genus-level divisions. We suggest the family name Adintoviridae, connoting similarities to adenovirus virion proteins and the presence of a retrovirus-like integrase gene. Although adintovirus-class PolB sequences were detected in datasets for fungi and various unicellular eukaryotes, sequences resembling adintovirus virion proteins and accessory genes appear to be restricted to animals. Degraded adintovirus sequences are endogenized into the germlines of a wide range of animals, including humans.

microbiology↗

bioRxiv2018

Mapping and Analysis of QTL for Early Maturity Trait in Tetraploid Potato (Solanum tuberosum L.)

Maturity is one of the important traits of potato. In order to get the genetic segment of potato early maturity trait, a tetraploid potato maturity segregation population of Zhongshu 19 x Zhongshu 3 was used for genetic analysis through the combination of high throughput simplified genome sequencing (2b-RAD) and bulked segregation analysis (BSA). A genetic segment related to the early maturity trait at the 3.7~4.2 Mb locus on the short arm of chromosome 5 was obtained and eight markers were developed based on this segment, while five of them were closely linked to the early maturity trait loci. Moreover, 42 SSR markers were developed based on the reference sequence of DM. Finally, a genetic map of chromosome 5 contained 50 markers was constructed using the Tetraploidmap software. The total map length was 172 cM with an average genetic distance of 3.44 cM. Combining with phenotypic data of the segregation population, we mapped the early maturity trait QTL with the contribution of 33.55% on the short arm of chromosome 5, located at 84cM between the flanking markers SSR5-85-1 and SCAR5-8 with the physical interval of 471kb. Gene annotation showed that there exist 34 genes in this region, 12 of them are unknown function. Among the other 22 annotated genes, E3 ubiquitin ligase gene PUB14 may be related to maturity and regulate tuber formation. Our fine mapping of the early maturity QTL made a solid foundation for cloning of the early maturity controlled gene or genes.\n\nKey messageEarly maturity site was mapped using a tetraploid potato segregation population derived from cv. Zhongshu 19 and Zhongshu 3. One major QTL with 33.55% contribution to early maturity was fine mapped in physical interval of 471kb on chromosome 5.

genetics↗

bioRxiv2018

Adomaviruses: an emerging virus family provides insights into DNA virus evolution

Adenoviruses, papillomaviruses, and polyomaviruses are collectively known as small DNA tumor viruses. Although it has long been recognized that small DNA tumor virus oncoproteins and capsid proteins show a variety of structural and functional similarities, it is unclear whether these similarities reflect descent from a common ancestor, convergent evolution, horizontal gene transfer among virus lineages, or acquisition of genes from host cells. Here, we report the discovery of a dozen new members of an emerging virus family, the Adomaviridae, that unite a papillomavirus/polyomavirus-like replicase gene with an adenovirus-like virion maturational protease. Adomaviruses were initially discovered in a lethal disease outbreak among endangered Japanese eels. New adomavirus genomes were found in additional commercially important fish species, such as tilapia, as well as in reptiles. The search for adomavirus sequences also revealed an additional candidate virus family, which we refer to as xenomaviruses, in mollusk datasets. Analysis of native adomavirus virions and expression of recombinant proteins showed that the virion structural proteins of adomaviruses are homologous to those of both adenoviruses and another emerging animal virus family called adintoviruses. The results pave the way toward development of vaccines against adomaviruses and suggest a framework that ties small DNA tumor viruses into a shared evolutionary history. Author SummaryIn contrast to cellular organisms, viruses do not encode any universally conserved genes. Even within a given family of viruses, the amino acid sequences encoded by homologous genes can diverge to the point of unrecognizability. Although members of an emerging virus family, the Adomaviridae, encode replicative DNA helicase proteins that are recognizably similar to those of polyomaviruses and papillomaviruses, the functions of other adomavirus genes have been difficult to identify. Using a combination of laboratory and bioinformatic approaches, we identify the adomavirus virion structural proteins. The results link adomavirus virion protein operons to those of other midsize non-enveloped DNA viruses, including adenoviruses and adintoviruses.

microbiology↗