Biology subjects

Huang, Y.

Publications and source records attributed to Huang, Y..

At least 289 records · Page 16Linked to original sources

bioRxiv2025

Inconsistent short-term effects of enhanced structural complexity on soil microbial properties across German forests

Structural and biotic homogenization can result from forestry practices that lack promotion of canopy gaps and deadwood. This can lead to biodiversity loss and impaired ecosystem functions. Enhancing structural complexity (ESC) has been proposed to counteract these effects, but its impact on soil properties remains insufficiently understood. Overall, we hypothesize that ESC enhances soil abiotic properties, their spatial variability, and microbial functioning, with effects modulated by environmental context and increasing over time. Data were collected from 148 patches (50 x 50 m) in eight beech forests across Germany. In half of the patches, structural complexity was enhanced by felling 30% of the basal area of living trees through two spatial patterns--aggregated (one large gap) and distributed (small gaps)--combined with leaving or removing deadwood (stumps, logs, and snags). The other half served as controls, representing typically managed, homogeneous production forests. Soil C:N, C%, and N% increased near deadwood. Soil microbial biomass and activity were significantly affected in three of eight forest sites, with effects ranging from -30% to +62%. Higher soil water content was associated with increased microbial biomass, and greater understorey biomass correlated with a lower microbial respiratory quotient. No temporal trends were observed over five years. Although soil properties showed resistance to structural interventions, site-specific effects underline the importance of soil moisture and the understorey vegetation for microbial functioning. Further research building on our results is needed to develop practical forest management strategies to clarify how structural complexity may support soil functioning and ecosystem resilience. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/664741v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@10790f2org.highwire.dtl.DTLVardef@1bd2f95org.highwire.dtl.DTLVardef@17eed6dorg.highwire.dtl.DTLVardef@15a049_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- Deadwood addition increases soil C%, N%, and the soil C:N ratio - Enhanced structural complexity alters soil microbial properties in site-specific ways - Soil water content changes are linked to shifts in microbial biomass - Understorey biomass changes are linked to shifts in the respiratory quotient

ecology↗

bioRxiv2025

Hybrid yak-cattle in situ conservation via interspecies somatic cell nuclear transfer at ultra-high-altitude region

Pien-niu, the hybrid offspring of yak (Bos grunniens) and domestic cattle (Bos taurus), possess exceptional adaptability to ultra-high-altitude environments of the Qinghai-Xizang Plateau. In situ conservation is of special significance for ultra-high-altitude region because the offsprings need to possess the ability to adapt to the unique environment. The present study was to clone Pien-niu in Xizang via interspecies somatic cell nuclear transfer (iSCNT) to practice in situ conservation of large animal at ultra-high-altitude region. Ear fibroblast cells were isolated from Pien-niu at Qushui Experimental Station (3650m above sea level), an animal live conservation farm at Xizang, and used as iSCNT donor cells. The iSCNT blastocysts were transferred into the oviduct of surrogate Pien-niu which are maintained at Qushui Experimental Station. A live cloned Pien-niu calf was born on May 12, 2025 and keeps healthy till now. Results of short tandem repeat analysis revealed that the microsatellite loci of cloned calf were completely matched with that of donor fibroblast cells. The successful cloning of Pien-niu can provide a paradigm for in situ germplasm conservation via iSCNT at ultra-high-altitude region.

zoology↗

bioRxiv2025

Effect of Caenorhabditis elegans U6 Promoters on CRISPR/Cas9-Mediated Gene Editing Efficiency

ObjectiveThis study investigated the effects of endogenous C. elegans U6 promoters on dpy-10 gene editing efficiency. MethodsWe screened endogenous U6 snRNA genes from the WormBase database and constructed 14 editing plasmids targeting dpy-10 by replacing the U6r07e5.16 promoter in pSX524 (Peft-3::cas9::tbb-2 terminator::U6 r07e5.16::dpy-10 sgRNA) through molecular cloning. Following standardized microinjection protocols, we quantified gene editing efficiency and high-efficiency gene editing index based on dpy-10 mutant phenotypes in F1 progeny. ResultsFifteen U6 snRNA genes (r07e5.16, f35c11.9, t20d3.13, k09b11.15, k09b11.16, w05b2.8, c28a5.7, f54c8.9, k09b11.11, k09b11.12, k09b11.14, t20d3.12, f54c8.8, f54c8.10, k09b11.13) were identified from WormBase database. Comparative analysis revealed four U6 promoters (w05b2.8, c28a5.7, f54c8.9, and k09b11.11) significantly enhanced gene editing compared to other U6 promoters, including commonly used U6r07e5.16 and U6k09b11.12 promoters in C. elegans community. Notably, the gRNAF+E scaffold showed no improvement over the gRNA scaffold when paired with the optimal U6w05b2.8 promoter. ConclusionThis study identifies superior U6 promoters for C. elegans gene editing and demonstrates the critical role of promoter optimization in CRISPR systems, providing novel insights for technical refinement.

molecular biology↗

bioRxiv2025

Assessing large-scale genomic language models in predicting personal gene expression: promises and limitations

Large-scale genomic language models (gLMs) hold promise for modeling gene regulation, yet their ability to predict personal gene expression remains largely unexplored. We developed a framework, gLM2X-Tower, to benchmark gLMs and sequence-to-function (S2F) models on this task with paired personal genome-transcriptome data. With individual-level training, we found that similar to S2F models (e.g., AlphaGenome), gLMs (e.g., Evo2) remain incapable of predicting the inter-person variability on held-out genes. However, such training improves prediction for seen genes in new individuals, particularly by gLMs, highlighting the potential applications in few-shot settings like for rare variants

bioinformatics↗

bioRxiv2025

Influence of the broadly neutralizing antibody VRC01 on HIV breakthrough virus populations in antibody-mediated prevention trials

In the HIV antibody mediated prevention (AMP) trials, the broadly neutralizing antibody VRC01 demonstrated protective efficacy against new diagnoses with susceptible HIV strains. To understand how VRC01 shaped breakthrough infections, we performed deep sequencing on 172 participants in the placebo and treatment arms, generating 63,444 gag-{Delta}pol (2.5 kb) and 53,088 rev-env-{Delta}nef (3 kb) sequences. Sequences were classified into transmitted founder lineages (TFLs), and infections with multiple distinct lineages were determined. Multilineage infections were detected in [~]38% of participants in both the African (HVTN 703/HPTN 081) and Americas/Europe (HVTN 704/HPTN 085) cohorts, regardless of placebo or treatment group, or cohort. The high levels of multilineage infections could be attributed to minor lineages (<5% abundance) identified in 20% of participants. Infection with VRC01 discordant viruses (IC80s >3-fold different) was observed in 40% of multilineage infections, with a trend toward greater intra-host neutralization differences with increasing VRC01 dose (Jonckheere-Terpstra test, p=0.072). In six VRC01 treated participants who acquired both sensitive (IC80<1{micro}g/ml) and resistant viruses (IC80>3{micro}g/ml), the sensitive lineages declined over time. Recombination was pervasive, observed in 63% of multilineage infections at the time of HIV diagnosis. In one treated participant infected with VRC01 discordant lineages, recombinant viruses preferentially inherited the resistance mutation (binomial p=0.004). In conclusion, our in-depth analysis of breakthrough viruses in the AMP trials revealed a high frequency of multilineage infections, including infections with viruses with different VRC01 sensitivities. This analysis also highlights the role of recombination in shaping intra-host viral evolution and facilitating escape from VRC01. SignificanceThis work advances our understanding of the diversity of initial viral infection and evolution and in vivo activity of broadly neutralizing antibodies (bNAbs). Deep sequencing revealed [~]38% of HIV acquisitions with multiple transmitted founder lineages, higher than previous studies. These occurrences were similar in the placebo and VRC01 groups. Viral recombination among post-acquisition variants was common under antibody selection and appeared to favor resistant sequences in the treatment group. These data suggest as with single antiviral therapy, passive and active immunization of bNAbs should be directed at multiple antigen targets of HIV-1.

molecular biology↗

bioRxiv2025

Epigenetic Programming of Estrogen Receptor in Adipose Tissue by High Fat Diet Regulates Obesity-Induced Inflammation

Adipose inflammation plays a key role in obesity-induced metabolic abnormalities. Epigenetic regulation, including DNA methylation, is a molecular link between environmental factors and complex diseases. Here we found that high fat diet (HFD) feeding induced a dynamic change of DNA methylome in mouse white adipose tissue (WAT) analyzed by reduced representative bisulfite sequencing. Interestingly, DNA methylation at the promoter of estrogen receptor (Esr1) was significantly increased by HFD, concomitant with a down-regulation of Esr1 expression. HFD feeding in mice increased the expression of DNA methyltransferase 1 (Dnmt1) and Dnmt3a, and binding of DNMT1 and DNMT3a to Esr1 promoter in WAT. Mice with adipocyte-specific Dnmt1 deficiency displayed increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity upon HFD challenge; while mice with adipocyte-specific Dnmt3a deficiency showed a mild metabolic phenotype. Using a modified CRISPR/RNA-guided system to specifically target DNA methylation at the Esr1 promoter in WAT, we found that reducing DNA methylation at Esr1 promoter increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity in HFD-challenged mice. Our study demonstrates that DNA methylation at Esr1 promoter plays an important role in regulating adipose inflammation, which may contribute to obesity-induced insulin resistance.

physiology↗

bioRxiv2025

Time-series modeling with neural flow maps

Constructing mathematical models from data is fundamental for understanding complex systems across scientific disciplines. However, real-world data often pose challenges such as irregular sampling, sparsity, and noise, that hinder the development of accurate, mechanistic models. In this work, we present a deep learning framework that directly reconstruct flow maps from data, assuming only that the observed patterns arise from an autonomous dynamical system. We demonstrate that our method accurately captures system dynamics across diverse settings, even with limited and irregularly sampled training data. When applied to the circadian transcriptomic time series data, it generates biologically valid predictions by integrating information across multiple organs. By parameterizing the full dynamical system, our proposed approach enables efficient computation of time derivatives and Jacobians directly from data, offering a powerful tool for analyzing and interpreting high-dimensional biological systems.

systems biology↗

bioRxiv2025

Nanopore Sequencing Unveils Somatic Structural Variations as Biomarkers in Laryngeal squamous cell carcinoma Genomes

Laryngeal squamous cell carcinoma (LSCC) is an aggressive cancer with poor quality of life, largely due to the absence of reliable molecular biomarkers for early diagnosis and prognosis. While somatic structural variations (SVs) have been documented in LSCC, conventional short-read sequencing approaches are inherently limited in detecting of large-scale somatic SVs, which are critical to understanding tumorigenesis. Here, we presented SomaGauss-SV, a somatic SVs detection workflow leveraging nanopore long-read sequencing data. Benchmarking against five paired tumor cell line datasets showed SomaGauss-SV consistently achieves a balanced high precision and recall. SomaGauss-SV applied to 15 paired LSCC tumor-blood samples uncovered a comprehensive SVs landscape and a significant positive correlation between somatic deletion burden and smoking intensity. Furthermore, a high-frequency somatic simple repeat expansion was identified in 20/27 (74.1%) of LSCC patients, upregulating the expression of genes TP53BP2 and FBXO28 through spatial proximity. These findings underscore the potential of long-read sequencing and SomaGauss-SV in uncovering previously unexplored genomic rearrangements in LSCC, providing valuable resources for biomarker discovery.

bioinformatics↗

bioRxiv2025

Deepening imaging-based spatial proteomics at high spatial resolution through controlled tissue resizing and in-situ bottom-up mass spectrometry

Understanding the spatial organization of proteins in tissues is essential for elucidating biological function, but current proteomic imaging methods face limitations in resolution, sensitivity, and multiplexing capability. Here, we present IMPACT (Imaging Mass Spectrometry for Proteome Analysis on Compressed Tissue), a hydrogel-based workflow that integrates controlled vertical tissue compression following expansion to enhance protein detection while improving spatial resolution in mass spectrometry imaging (MSI). Through a 6-fold lateral expansion and 100-fold thickness reduction, analytes were concentrated at the surface to improve detection and enable analysis of thick specimen. Coupled with optimized in-gel digestion using hybrid enzymes, IMPACT increased protein identifications 3-fold compared to conventional MSI while maintaining spatial fidelity. We demonstrate IMPACTs utility in mapping low-abundance proteins and resolving fine anatomical structures. Orthogonal validation with immunofluorescence and integration with spatial transcriptomics further reveal protein-RNA distribution discrepancies, highlighting the need for direct proteomic imaging. IMPACT bridges critical gaps in spatial proteomics by enabling high-resolution, high-sensitivity, and multiplexed untargeted protein imaging, opening new avenues for tissue biology and biomarker discovery.

biophysics↗

bioRxiv2025

Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae

Orchidaceae (orchids) is commonly known as one of the largest families of seed plants, and grow in an extensive range of habitats worldwide. In the present study, we generated chromosome-level reference genomes for two orchids using a combination of PacBio, Illumina, and Hi-C sequencing, Cypripedium singchii has the largest genome and chromosomes among the sequenced species so far, with a genome size of 43.19 Gb (1C) with ten chromosomes, and Apostasia fujianica has the smallest known genome and chromosomes in Orchidaceae, with a genome size of 340.90 Mb (1C) with 35 chromosomes. We predicted a total of 32,412 and 21,724 protein-coding genes for C. singchii and A. fujianica, respectively. The overall BUSCO score was 85.01% for C. singchii and 91.80% in A. fujianica. Based on protein-coding sequences from 55 conserved single-copy families across 21 plant species, we constructed a high-confidence phylogenetic tree and estimated the divergence times. The high-quality genomes of super-giga and tiny orchids offer key insight for future evolutionary researches.

genomics↗

bioRxiv2025

Maternal exercise rescues fetal akinesia-impaired joint and bone development

Fetal movements exert mechanical forces that shape the developing skeleton. Conditions that impair fetal movements can cause skeletal defects, but interventions are limited. Here, we show that maternal wheel running exercise regulates fetal skeletal development in mice. In wild-type fetuses, maternal exercise stimulated joint and bone morphogenesis. We reasoned that these effects occurred through either indirect maternofetal communication or direct mechanical stimulation of the fetus. Maternal exercise did not alter placental measures of nutrient transport. However, in the Splotch-delayed (Spd) mouse model of fetal akinesia, which features intact maternofetal communication but lacks fetal movements, maternal exercise substantially rescued fetal akinesia-impaired joint and bone development and prevented disuse-induced resorption of the deltoid tuberosity. Further, direct mechanical stimulation of Spd limbs explanted from systemic factors similarly stimulated joint morphogenesis. Together, these findings identify maternal exercise as a regulator of fetal skeletal development, providing a platform for studying skeletal developmental mechanobiology and suggesting potential therapeutic applications for fetuses with impaired movement.

developmental biology↗

bioRxiv2025

DCPS modulates TDP-43 mediated neurodegeneration through P-body regulation

The proteinopathy of the RNA-binding protein TDP-43, characterized by nuclear clearance and cytoplasmic inclusion, is a hallmark of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimers disease (AD). Through CRISPR interference (CRISPRi) screening in human neurons, we identified the decapping enzyme scavenger (DCPS) as a novel genetic modifier of TDP-43 loss-of-function (LOF)-mediated neurotoxicity. Our findings reveal that TDP-43 LOF leads to aberrant mRNA degradation, via disrupting the properties and function of processing bodies (P-bodies). TDP-43 interacts with P-body component proteins, potentially influencing their dynamic equilibrium and assembly into ribonucleoprotein (RNP) granules. Reducing DCPS restores P-body integrity and RNA turnover, ultimately improving neuronal survival. Overall, this study highlights a novel role of TDP-43 in RNA processing through P-body regulation and identifies DCPS as a potential therapeutic target for TDP-43 proteinopathy-related neurodegenerative diseases.

neuroscience↗

bioRxiv2025

Local optogenetic control of genome editing and tumorigenesis in vivo using wireless implantable optoelectronics

Precise spatial regulation of site-specific DNA recombination (SSR) in vivo remains a challenge due to limited tunability of current platforms. Here, we present an optogenetic approach that overcome these limitations by employing engineered light-regulated recombinase E-LightR-Cre and tunable wireless implantable optoelectronic devices. E-LightR-Cre meets the key criteria for spatial regulation of SSR in vivo, showing no detectable activity in the dark, while demonstrating robust activation upon blue-light illumination. To achieve local E-LightR-Cre activation in murine lungs, we developed wireless, fully-implantable optoelectronic devices enabling focal illumination with no discernible organ damage. By modulating illumination intensity and duration, we can control the size of the activated area. Local expression of oncogenic KRas-G12D in a photoactivated subpopulation of cells in vitro revealed rapid reprogramming of the mutant expressing cells and their non-activated neighbors. Light-guided activation of E-LightR-Cre in mouse lungs resulted in focal expression of a reporter gene and allowed us to induce local formation of oncogenic lesions in vivo.

bioengineering↗

bioRxiv2025

Ultra-wide-field, deep, adaptive two-photon microscopy

Observing the activity patterns of large neural populations throughout the brain is essential for understanding brain function. However, capturing neural interactions across widely distributed brain regions from both superficial and deep cortical layers remains challenging with existing microscopy technologies. Here, we introduce a state-of-the-art two-photon microscopy system, ULTRA, capable of single-cell resolution imaging across an ultra-large field of view (FOV) exceeding 50 mm{superscript 2}, enabling deep and very wide field in vivo imaging. To demonstrate its capabilities, we conducted a series of experiments under multiple imaging conditions, successfully visualizing brain structures and neuronal activities spanning a spatial range of over 7 mm from superficial layers to depths of up to 900 m, while covering a volume of 45.24 mm3 in the mouse brain. This versatile imaging platform overcomes traditional spatial constraints, providing a powerful tool for comprehensive exploration of neuronal circuitry over extensive spatial scales with cellular resolution.

neuroscience↗

bioRxiv2025

Development of a Novel Benzodiazepine to Delineate Peripheral GABA-A Signaling Mechanisms in Visceral Pain Syndromes

Background and AimsVisceral pain is a cardinal symptom of many disorders affecting the gut. Modulators of gamma-aminobutyric acid (GABA) such as benzodiazepines may attenuate colonic pain but the specific contribution of peripheral GABAA receptors remains unclear as these agents have prominent central effects. MethodsUsing medicinal chemistry optimization of the benzodiazepine scaffold, we developed a novel and potent benzodiazepine-based positive allosteric modulator (PAM) of GABAA receptors, Li633, with no significant central nervous system (CNS) penetration. ResultsThe locomotor activity of rats placed in an open field was unchanged with Li633 at doses up to 30 mg/kg, confirming its lack of a CNS effect. LI-633 produced robust potentiation of GABA-induced inward current, with EC50 values ranging from 8 nM (5{beta}2{gamma}2) to 128 nM (3{beta}2{gamma}2). In vitro electrophysiological studies confirmed its ability to reduce excitability of human dorsal root ganglion (DRG) neurons. LI-633 potentiated muscimol-induced GABAergic currents in rat DRG neurons in a dose-dependent manner, with an EC50 of 70.4 nM. In vivo, LI-633 significantly attenuated visceral hypersensitivity and pain behavior in a rat model of irritable bowel syndrome (IBS) and functional dyspepsia (FD). In the IBS model, administration of the drug also resulted in decreased excitability of colon-specific DRG neurons and significantly reduced the colonic afferent response to balloon distention as measured by recordings of neural activity in dorsal ganglia rootlets. ConclusionsThese findings highlight the potential of targeting peripheral GABAA receptors for pain management in IBS and other disorders associated with visceral hypersensitivity.

neuroscience↗

bioRxiv2025

piR-bmo-796514 Facilitates the Proliferation of Exogenous DNA Virus (Baculovirus) by Targeting the Host E3 Ubiquitin Ligase RNF181

PIWI-interacting RNAs (piRNAs), a class of 23-31 nucleotide non-coding RNAs, are known for silencing transposons and endogenous retroviruses that reside in animal genomes. However, the mechanisms by which host piRNAs affect exogenous viral infections, particularly those by DNA viruses, remain poorly understood. Here, we demonstrate that infection by Bombyx mori nucleopolyhedrovirus (BmNPV), a large DNA virus, induces significant upregulation of silkworm host piR-bmo-796514, which facilitates viral proliferation by suppressing the expression of E3 ubiquitin ligase RNF181. We further reveal that RNF181 exerts antiviral activity through ubiquitin-mediated degradation of Integrin 2b-like, a cellular membrane protein that interacts with viral GP64 protein to mediate BmNPV entry. This study unveils a previously unrecognized regulatory axis connecting host derived piRNAs with exogenous DNA virus infection, providing further mechanistic insights into the modulation of exogenous viral pathogenesis through the reprogramming of the piRNA pathway. Our findings not only advance the understanding of the immune escape mechanism of exogenous viruses but also provide new insights for the development of oligonucleotide antiviral drugs that target proviral piRNAs.

immunology↗

bioRxiv2025

Impact of trait measurement error on quantitative genetic analysis of computer vision derived traits

BackgroundQuantitative genetic analysis of image- or video-derived phenotypes is increasingly being performed for a wide range of traits. Pig body weight values estimated by a conventional approach or a computer vision system can be considered as two different measurements of the same trait, but with different sources of phenotyping error. Previous studies have shown that trait measurement error, defined as the difference between manually collected phenotypes and image-derived phenotypes, can be influenced by genetics, suggesting that the error is systematic rather than random and is more likely to lead to misleading quantitative genetic analysis results. Therefore, we investigated the effect of trait measurement error on genetic analysis of pig body weight (BW). ResultsCalibrated scale-based and image-based BW showed high coefficients of determination and goodness of fit. Genomic heritability estimates for scale-based and image-based BW were mostly identical across growth periods. Genomic heritability estimates for trait measurement error were consistently negligible, regardless of the choice of computer vision algorithm. In addition, genome-wide association analysis revealed no overlap between the top markers identified for scale-based BW and those associated with trait measurement error. Overall, the deep learning-based regressions outperformed the adaptive thresholding segmentation methods. ConclusionsThis study showed that manually measured scale-based and image-based BW phenotypes yielded the same quantitative genetic results. We found no evidence that BW trait measurement error could be influenced, at least in part, by genetic factors. This suggests that trait measurement error in pig BW does not contain systematic errors that could bias downstream genetic analysis.

genetics↗

bioRxiv2025

Single-cell spatial map of cis-regulatory elements for disease-related genes in the macaque cortex

Single-cell spatial transcriptomes have demonstrated molecular and cellular diversity in the brain1, 2, 3, 4, 5, 6, 7, 8, but gene regulatory mechanisms underlying transcriptomic profiles and disease pathogenesis remain largely unknown in primates. Here we performed single-nucleus Assay for Transposase-Accessible Chromatin followed by sequencing (snATAC-seq) for [~]1.6 million cells from 142 cortical regions of two male cynomolgus monkeys (Macaca fascicularis), and identified distinct chromatin accessibility profiles of cis-regulatory elements (CREs) for various cell types. By integrative analysis with large-scale spatial transcriptome data, we found that these CREs showed laminar and regional preferences, with their regional accessibility exhibiting striking dependence on the regions hierarchical level. Cross-species comparison of snATAC-seq data revealed human/macaque-enriched layer-4 glutamatergic neurons and LAMP5/LHX6-expressing GABAergic neurons as well as human/macaque-biased CREs for genes related to neurodevelopment and psychiatric diseases. Importantly, risk single-nucleotide polymorphisms for many brain disorders strongly associated with human/macaque-biased CREs in glutamatergic neuronal types and those for Alzhemers disease strongly associated with CREs exclusively in microglia. Our results provided the basis for understanding the spatial gene regulatory mechanisms underlying cellular diversity and disease pathogenesis in the primate cortex.

neuroscience↗