Biology subjects

Du, H.

Publications and source records attributed to Du, H..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Multi-omics analysis reveals the mechanism of BnC07MYB3a is involved in seed coat color in Brassica napus L.

In rapeseed (Brassica napus), yellow-seeded varieties accumulate less flavonoid pigments (anthocyanins/proanthocyanidins) in their seed coats compared with black-seeded varieties. The yellow-seeded trait is associated with greatly improved seed oil yield, quality, and commercial value. Many R2R3 MYB activators have been characterized in rapeseed, but how MYB-type repressors affect pigment biosynthesis is not yet fully understood. In this study, we performed transcriptome sequencing and metabolomic analysis of B. napus varieties with extreme differences in seed coat color, combined with weighted gene co-expression network analysis. This analysis identified an R2R3-MYB-type transcription factor, BnC07MYB3a (BnaC07G0178800ZS), as a candidate regulator of the yellow-seeded trait in B. napus. Overexpressing BnC07MYB3a in Arabidopsis thaliana and B. napus downregulated the expression of flavonoid biosynthetic genes, resulting in significantly lower anthocyanin and proanthocyanidin accumulation than in the wild-type and a lighter seed coat color in transgenic plants. BnC07MYB3a directly binds to the promoter of the TRANSPARENT TESTA (TT) gene BnTT6 and represses its expression. BnC07MYB3a also physically interacts with BnA06bHLH92a and the WD40 transcription factor TRANSPARENT TESTA GLABRA1 (BnTTG1), suggesting that they might form a previously unidentified MYB-bHLH-WD40 transcription factor complex. Our results reveal the molecular mechanism and regulatory network of BnC07MYB3a in determining seed coat color in B. napus and provide a genetic resource for breeding yellow-seeded cultivars of B. napus.

molecular biology↗

bioRxiv2024

PepCleav: a classification method for evaluating the cleavability of peptide fragments presented by MHC class I

Neoantigens, due to their tumor specificity and lack of central tolerance, are promising targets for cancer immunotherapy. Evaluating the cleavability of peptide fragments generated by proteasomes and aminopeptidases is crucial for neoantigen identification, but tools for this purpose are scarce. To address this, we developed PepCleav, a method for evaluating peptide cleavability by classifying the amino acids at the proteasome and aminopeptidase recognition sites of the C- and N-termini. By integrating C- and N-terminal cleavability, PepCleav accurately predicted the overall cleavability of peptide fragments in test datasets, correctly identifying 84-89% of cleavable peptides and 63-92% of non-cleavable peptides. We also found that highly cleavable peptides have a higher likelihood of being effective neoantigens, highlighting PepCleavs potential to improve neoantigen identification. PepCleavs source code is publicly available at https://github.com/Dulab2020/PepCleav.

bioinformatics↗

bioRxiv2024

FLASH radiotherapy using high-energy X-rays: validation of the FLASH effect triggered by a compact single high-energy X-ray source device

PurposeThis preclinical study aimed to verify the FLASH effect of compact single high-energy X-ray source (CHEXs) and to explore whether three irradiations with single-gantry rotation two 30 s pauses can generate FLASH effect in mice. Materials and methodsThe absolute dose and pulsed beam of the CHEXs were measured using an EBTXD radiochromic film and fast current transformer. Healthy C57BL/6J female mice and a subcutaneous tumor model were irradiated under different conditions: sham (control), FLASH-RT (FLASH1: delivering the total dose in 1 fraction; FLASH3: delivering the total dose with two 30 second pauses to simulate a three-field delivery where the gantry rotation is occurring within 30 seconds), and conventional dose rate radiotherapy (CONV-RT). Various total doses were administered to the corresponding normal tissues (whole thorax, 30 Gy; whole abdomen, 12 Gy; and skin, 36 Gy) and tumors (CT26, 16.5 Gy; and LLC, 18 Gy). Survival status, normal tissue damage, and tumor growth suppression were recorded in each group. ResultsThe average dose rate of the CHEXs exceeded 40 Gy/s. For whole-thorax and skin irradiation, both FLASH1 and FLASH3 demonstrated protective effects. For whole-abdomen irradiation, FLASH1 exhibited a superior protective effect. No significant differences in tumor growth responses were observed between the FLASH1, FLASH3, and CONV-RT groups (P>0.05). ConclusionThis study confirmed that the FLASH effect could be triggered using CHEXs FLASH radiotherapy, and demonstrated that three irradiations with single gantry rotation two 30 s pauses can trigger the FLASH effect, indicating the potential benefit of CHEXs 3D conformal radiotherapy. Our findings indicate that further clinical trials on CHEXs are warranted.

cancer biology↗

bioRxiv2024

TDP-43 mutations-induced defects in miRNA biogenesis and cytotoxicity by differentially obstructing Dicer activity in Drosophila and in vitro

Mutations in the DNA/RNA-binding protein 43 (TDP-43) can cause amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). As an RNA-binding protein, TDP-43 plays a diverse physiological role in RNA processing and is potentially involved in the pathological progression caused by disease mutations. However, the precise mechanisms linking RNA dysregulation and TDP-43 mutations, which propel disease progression, are not yet fully understood. Here, we demonstrate that TDP-43 and its Drosophila homolog, TBPH, whose mutations crucially perturb Dicer presentation, result in dysregulated miRNA profiles. Genetically modulating the expression or pharmacologically activating Dicer implies unique interactions of TDP-43 A315T and M337V with the Dicer protein, suggesting a specific mechanism of C-terminal disease mutations contributes to the pathological process. Unlike TDP-43 A315T, the M337V mutation causes the assembly of aggregates and reorganizes but functionally preserves the Dicer activity in miRNA processing. Mutations in TDP-43 disrupt miRNA biogenesis by hindering its interaction with Dicer, leading to cytotoxicity and providing mechanistic insight into the pathogenic mutations associated with ALS-FTD.

molecular biology↗

bioRxiv2024

Stearoyl coenzyme A desaturase 1 (SCD1) regulates foot-and-mouth disease virus replication by modulating host cell lipid metabolism and 2C-mediated replication complex formation

The life cycle of foot-and-mouth disease virus (FMDV) is tightly regulated by host cell lipid metabolism. In a previous study, we successfully established a BHK-21 cell model (BHK-Op) for persistent FMDV infection by single-cell clone selection and isolated a virus-negative cell line (BHK-VEC cells) from high-passage BHK-Op cells. BHK-VEC cells could be not infected with FMDV. By conforming the transcriptome data of BHK-VEC cells and BHK-21 cells, we identified that the stearoyl coenzyme A desaturase 1 (SCD1), a key enzyme for the fatty acid metabolism, regulates FMDV replication. SCD1 overexpression or exogenous addition of oleic acid (OA), a product of SCD1 enzyme activity, promoted or upregulated FMDV replication in BHK-21 cells or SCD1 knockdown cells, respectively. Interestingly, overexpression of SCD1 or exogenous addition of OA restored the FMDV infection and replication in BHK-VEC cells. Exogenous addition of OA also promoted FMDV replication in BHK-Op. SCD1 recruited the nonstructural FMDV protein 2C to the detergent-resistant membrane located in the perinuclear nucleus to form replication complex. Inhibition of SCD1 enzyme activity resulted in significantly decreased number of FMDV replication complexes with also abnormal morphology. Importantly, inhibition of SCD1 enzyme activity effectively suppressed replication of other positive-sense RNA viruses, such as REO176, PV1 and EV71. Our results demonstrated that, as a key host regulator of RNA virus replication, SCD1 is a potential target for developing novel drugs against positive-sense RNA virus infection.

microbiology↗

bioRxiv2024

Urea amidolyase as the enzyme for urea utilization in algae: functional display in Chlamydomonas reinhardtii and evolution in algae

Urea is a crucial nitrogen nutrient source for algae with the potential to stimulate harmful algal blooms, but the molecular machinery underpinning urea uptake and assimilation by algae is not fully understood. Urease (URE) is commonly regarded as the responsible enzyme, but the urea amidolyase (UAD) system, albeit known to exist, has hardly been studied. Here, the phylogenetic distribution, expression patterns, and functional roles of UAD system are examined, which comprises subunits DUR1, DUR2, and DUR3. We find a widespread occurrence of UAD, spanning four major phytoplankton lineages, and potentially independent evolution of URE and lineage-specific loss. Besides, a stronger regulation of UAD by environmental nitrogen concentrations compared to URE is uncovered in both global ocean and local dinoflagellate-dominant bloom events. CRISPR-based mutation in Chlamydomonas reinhardtii shows that subunit DUR2 is essential for urea utilization. DUR2 inactivation led to completely growth restriction and upregulation of DUR1 and DUR3A, suggesting its functional interaction with them. In contrast, DUR3B inactivation only partially halted urea uptake and cell growth but significantly reduced gene expression across the entire UAD system. These findings not only reveal the crucial role of DUR2 in urea utilization in C. reinhardtii and potentially in many other algae, but also suggest DUR2 to be a more suitable indicator of urea utilization than urease, and underscore the importance to consider both URE and UAD enzyme systems when urea utilization by algae is assessed.

ecology↗

bioRxiv2024

Mechanism Study on the Effect of Kidney Tonifying and Liver Soothing Methods on Mouse Oocyte Quality by Regulating OSFs and Smads Pathways

Objective: To observe the effects of kidney tonifying and liver soothing methods on the secretion of factor BMP-6, related receptors ALK-2/6, and downstream Smads pathway Smad1/5/844 in oocytes, and to explore the targeted mechanisms of their effects on mouse oocyte quality; Method: Healthy female mice aged 6-7 weeks were randomly divided into 6 groups, namely high and low dose kidney tonifying groups; High - and low-dose liver soothing groups; Control group and normal group. The high-dose and low-dose groups of tonifying the kidney were given oral solution of tonifying the kidney and regulating the meridian at 5.4g/ml and 2.7g/ml, respectively. The high-dose and low-dose groups of soothing the liver were given suspension of Xiaoyao Pill at 0.6g/ml and 0.3g/ml, respectively. The control group and normal group were given distilled water by gavage. Immunohistochemistry and Western blot were used to detect the expression of BMP-6, ALK-2/6, and Smad1/5/8/4 proteins in oocytes, while PCR was used to detect the mRNA expression of these indicators in oocytes; Result: Both methods can increase the expression of BMP-6 in oocytes of mice in the treatment group, activate ALK-2/6, and phosphorylate Smad1/5/8 to bind with Smad4, initiating signal transduction; The high-dose group of kidney tonifying is superior to other groups in regulating BMP-6, ALK-2/6, and Smad1/5/4. Conclusion: Kidney tonifying and liver soothing methods can regulate BMP-6 and its Smads pathway through different mechanisms to improve mouse oocyte quality.

synthetic biology↗

bioRxiv2024

A general platform for targeting MHC-II antigens via a single loop

Class-II major histocompatibility complexes (MHC-IIs) are central to the communications between CD4+ T cells and antigen presenting cells (APCs), but intrinsic structural features associated with MHC-II make it difficult to develop a general targeting system with high affinity and antigen specificity. Here, we introduce a protein platform, Targeted Recognition of Antigen-MHC Complex Reporter for MHC-II (TRACeR-II), to enable the rapid development of peptide-specific MHC-II binders. TRACeR-II has a small helical bundle scaffold and uses an unconventional mechanism to recognize antigens via a single loop. This unique antigen-recognition mechanism renders this platform highly versatile and amenable to direct structural modeling of the interactions with the antigen. We demonstrate that TRACeR-II binders can be rapidly evolved across multiple alleles, while computational protein design can produce specific binding sequences for a SARS-CoV-2 peptide of unknown complex structure. TRACeR-II sheds light on a simple and straightforward approach to address the MHC peptide targeting challenge, without relying on combinatorial selection on complementarity determining region (CDR) loops. It presents a promising basis for further exploration in immune response modulation as well as a broad range of theragnostic applications.

bioengineering↗

bioRxiv2024

Single-cell transcriptomics reveals colonic immune perturbations during amyloid-β driven Alzheimer's disease in mice

The "gut-brain axis" is emerging as an important target in Alzheimers disease (AD). However, immunological mechanisms underlying this axis remain poorly understood. Using single-cell RNA sequencing of the colon immune compartment in the 5XFAD amyloid-{beta} (A{beta}) mouse model, we uncovered AD-associated changes in ribosomal activity, oxidative stress, and BCR/plasma cell activity. Strikingly, levels of colon CXCR4+ antibody secreting cells (ASCs) were significantly reduced. This corresponded with accumulating CXCR4+ B cells and gut-specific IgA+ cells in the brain and dura mater, respectively. Consistently, a chemokine ligand for CXCR4, CXCL12, was expressed at higher levels in 5XFAD glial cells and in in silico analyzed human brain studies, supporting altered neuroimmune trafficking. An inulin prebiotic fiber diet attenuated AD markers including A{beta} plaques and overall frailty. These changes corresponded to an expansion of gut IgA+ cells and rescued peripheral Tregs levels. Our study points to a key glia-gut axis and potential targets against AD. Study HighlightsO_LIAD is associated with altered immune parameters in the gut of 5XFAD mice. C_LIO_LI5XFAD colon has reduced ASCs, including CXCR4+ cells with a migratory gene signature. C_LIO_LI5XFAD brain gliosis includes increased CXCL12 expression. C_LIO_LICXCR4+ B cells and gut-specific IgA+ ASCs accumulate in the 5XFAD brain and/or dura mater. C_LIO_LIInulin diet attenuates AD disease parameters while boosting IgA+ cell and Treg levels. C_LI

immunology↗

bioRxiv2023

Loss of TMEM106B exacerbates Tau pathology and neurodegeneration in PS19 mice

TMEM106B, a gene encoding a lysosome membrane protein, is tightly associated with brain aging, hypomyelinating leukodystrophy, and multiple neurodegenerative diseases, including frontotemporal lobar degeneration with TDP-43 aggregates (FTLD-TDP). Recently, TMEM106B polymorphisms have been associated with tauopathy in chronic traumatic encephalopathy (CTE) and FTLD-TDP patients. However, how TMEM106B influences Tau pathology and its associated neurodegeneration, is unclear. Here we show that loss of TMEM106B enhances the accumulation of pathological Tau, especially in the neuronal soma in the hippocampus, resulting in severe neuronal loss in the PS19 Tau transgenic mice. Moreover, Tmem106b-/- PS19 mice develop significantly increased disruption of the neuronal cytoskeleton, autophagy-lysosomal function, and lysosomal trafficking along the axon as well as enhanced gliosis compared with PS19 and Tmem106b-/- mice. Together, our findings demonstrate that loss of TMEM106B drastically exacerbates Tau pathology and its associated disease phenotypes, and provide new insights into the roles of TMEM106B in neurodegenerative diseases.

neuroscience↗

bioRxiv2023

Study on the preparation of bovine milk exosomes and the stability of lyophilized powder

Bovune milk exosomes (MK-exo) have bioactive effects on the health of consumers and can also serve as excellent drug delivery vehicles. However, long-term preservation and transportation remain major challenges at present. In this report, high-quality MK-exo are prepared on a large scale. We then developed a lyophilization method belonging to MK-exo, and performed acceleration and long-term stability experiments on the lyophilized MK-exo to evaluate the effect of lyophilization. The results showed that the lyophilized MK-exo can be stored at room temperature for at least 3 months and 2-8{degrees}C for 15 months. These findings provide data support for further understanding of the properties and applications of MK-exo.

bioengineering↗

bioRxiv2023

Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures

BackgroundThe duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a type of complex genomic rearrangement (CGR) hypothesized to result from replicative repair of DNA due to replication fork collapse. It is often mediated by a pair of inverted low-copy repeats (LCR) followed by iterative template switches resulting in at least two breakpoint junctions in cis. Although it has been identified as an important mutation signature of pathogenicity for genomic disorders and cancer genomes, its architecture remains unresolved and is predicted to display at least four structural variation (SV) haplotypes. ResultsHere we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the genomic DNA of 24 patients with neurodevelopmental disorders identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted SV haplotypes. Using a combination of short-read genome sequencing (GS), long- read GS, optical genome mapping and StrandSeq the haplotype structure was resolved in 18 samples. This approach refined the point of template switching between inverted LCRs in 4 samples revealing a DNA segment of [~]2.2-5.5 kb of 100% nucleotide similarity. A prediction model was developed to infer the LCR used to mediate the non-allelic homology repair. ConclusionsThese data provide experimental evidence supporting the hypothesis that inverted LCRs act as a recombinant substrate in replication-based repair mechanisms. Such inverted repeats are particularly relevant for formation of copy-number associated inversions, including the DUP-TRP/INV-DUP structures. Moreover, this type of CGR can result in multiple conformers which contributes to generate diverse SV haplotypes in susceptible loci.

genetics↗

bioRxiv2023

Guided Diffusion for molecular generation with interaction prompt

Molecular generative models have demonstrated their potential in designing molecules from scratch with high binding affinities in a pre-determined protein pocket and could be combined with traditional structural based drug design strategy. However, the generative processes of such models are random and the atomic interaction information between ligand and protein are ignored. On the other hand, the ligand has high propensity to bind with residues called hotspots. Hotspot residues contribute to the majority of the binding free energies and have been recognized as appealing targets for designed molecules. In this work, we develop an interaction prompt guided diffusion model-InterDiff to deal with the challenges. Four kinds of atomic interactions are involved in our model and represented as learnable vector embeddings. These embeddings serve as conditions for each residue to guide the molecular generative process. Comprehensive in-silico experiments evince that our model could generate molecules with desired ligand-protein interactions in a guidable way. Furthermore, we validate InterDiff on two realistic protein-based therapeutic agents. Results show that InterDiff could generate molecules with better or similar binding mode compared to known targeted drugs.

bioinformatics↗

bioRxiv2023

Genome-wide Perturbation Analysis Screening System for Exosomes-Related Genes Based on the CRISPR/Cas9 Platform

As reported previously, exosomes have significant impacts on the physiological and pathological state in vivo. Exosomes have been extensively studied as a drug delivery carrier and some exosomes drugs have been undergoing clinical research. The mechanisms of exosome production, transport, and secretion remain to be studied in depth. Thus, here, we developed a novel CRISPR-UMI-based gene screening system, with which we can reveal the exosomes biogenesis, transport, and uptake mechanisms on a genome-wide scale. This system consists of two parts: one is a gene knockout component; the other part is a unique molecular identifiers (UMI) labeling component that can label the exosomes produced by the knockout cells, in which each sgRNA corresponds to a specific UMI. In this way, by detecting the UMI loaded in the exosomes, we can trace the knockout gene. In this study, we first verified the function of each component using plasmids and lentiviruses respectively. Next, we simulated the infection of cells with lentiviral libraries using a single lentivirus to validate the functionality of the screening system. Finally, we constructed a CRISPR-UMI-based library targeting 15 genes (genes with clear effects on exosomes biogenesis) to further validate the reliability of the screening system. The development of this screening system is of indispensable importance for the in-depth study of the mechanisms of exosome production and secretion, as well as for the improvement of exosomes production and the advancement of exosomes industrialization.

bioengineering↗

bioRxiv2023

Comprehensive catalogs for microbial genes and metagenome-assembled genomes of the swine lower respiratory tract microbiome identify the relationship of microbial species with lung lesions

Understanding the community structure and functional capacity of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about it owing to the difficulty in obtaining microbial samples from the lower respiratory tract. Here we collected 745 microbial samples from the porcine lower respiratory tract by harvesting 675 pigs, and constructed a gene catalog containing 10,337,194 nonredundant genes, of which only 30% could be annotated taxonomically. We obtained 397 metagenome-assembled genomes (MAGs) including 111 MAGs with high-quality. These 397 MAGs were further clustered into 292 species-level genome bins (SGBs), among which 56% SGBs are unknown with current databases. Combining with the lung lesion phenotype, we found that Mycoplasma hyopneumoniae strains and the adhesion-related virulence factors harboring in their genomes were significantly associated with porcine lung lesions, implying the role of adhesion and overgrowth of pathogenic M. hyopneumoniae in host lung diseases. This study provided important resources for the study of porcine lower respiratory tract microbiome and lung health.

microbiology↗

bioRxiv2023

Histone deacetylase 3 plays a critical role in hypertension-induced kidney inflammation and fibrosis

Objective: Hypertension is a major cause of chronic kidney disease. The molecular mechanisms how hypertension causes kidney disease are not fully understood. In this study, we examined the functional role of histone deacetylase 3 (HDAC3) in the pathogenesis of hypertensive kidney disease. Approach and Results: Myeloid HDAC3 knockout mice were generated by crossing HDAC3f/f mice with LysM-Cre+/- mice. Both LysM-Cre-/-HDAC3f/f (HDAC3CON) mice and LysM-Cre+/+HDAC3f/f (HDAC3MKO) mice were subjected to uninephrectomy and treated with angiotensin II at 1.5 ug/kg/min or vehicle for 28 days. Blood pressure increased comparably in both HDAC3CON and HDAC3MKO mice following angiotensin II treatment. Compared with HDAC3CON mice, HDAC3MKO mice were protected from angiotensin II-induced kidney dysfunction and pathological injury and developed less proteinuria. Myeloid HDAC3 deficiency markedly attenuated the protein levels of fibronectin, collagen I, and ?-SMA in the kidney following angiotensin II treatment. Furthermore, HDAC3MKO mice accumulated significantly fewer myeloid fibroblasts and macrophages in the kidney after angiotensin II treatment. Myeloid HDAC3 deficiency significantly reduced the mRNA expression of proinflammatory molecules in the kidney following angiotensin II treatment. In cultured macrophages, knockdown of HDAC3 with shRNA suppressed proinflammatory molecule expression. Furthermore, knockdown of HDAC3 inhibited NF-kB p65 enrichment to IL-6 promoter. Conclusion: Our study identifies a critical role of myeloid HDAC3 in the regulation of hypertension-induced kidney inflammation and fibrosis. Targeting HDAC3 may represent a novel therapeutic strategy for hypertensive kidney disease.

pathology↗

bioRxiv2023

OmicVerse: A single pipeline for exploring the entire transcriptome universe

Single-cell sequencing is frequently marred by "interruptions" due to limitations in sequencing throughput, yet bulk RNA-seq may harbor these ostensibly "interrupted" cells. In response, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping community. This approach proficiently interpolates and restores the continuity of "interrupted" cells within single-cell RNA sequencing dataset. Furthermore, OmicVerse provides an extensive toolkit for bulk and single cell RNA-seq analysis, offering uniform access to diverse methodologies, streamlining computational processes, fostering exquisite data visualization, and facilitating the extraction of novel biological insights to advance scientific research.

bioinformatics↗

bioRxiv2023

Whole genome sequencing reveals autooctoploidy in the Chinese sturgeon and its evolutionary trajectories

The Order Acipenseriformes, which include sturgeons and paddlefishes, represent "living fossils" with complex genomes that are good models for understanding whole genome duplication (WGD) and ploidy evolution in fishes. Here we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis (Chinese sturgeon), a critically endangered species that also represents a poorly understood ploidy group in Acipenseriformes. Our results show that A. sinensis is a complex autooctoploid species containing four kinds of octovalents (8 n), a hexavalent (6 n), two tetravalents (4 n), and a divalent (2 n). We propose based on an analysis taking into account delayed rediploidization that its octoploid genome composition results from two rounds of homologous whole genome duplications (WGDs), and further provide insight into the timing of its ploidy evolution. This study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy composition and evolutionary trajectories of polyploidy fishes.

genomics↗