Biology subjects

Qiang, W.

Publications and source records attributed to Qiang, W..

7 recordsLinked to original sources

bioRxiv2026

Molecular Dynamic simulations of Aβ42 dimers with solid-state NMR restraints capture the key structural motifs in Aβ42 fibrillation pathways

Formation of the {beta}-amyloid (A{beta}) plaques is a pathological hallmark of Alzheimers disease (AD), and is believed to be a primary cause of dementia in elderly individuals. In the present work, we simulated the conformational evolution of A{beta}42 dimers in solution and in membrane-like environment to explore the folding of A{beta}42 along fibrillation. The molecular dynamics (MD) simulation was steered by experimental internuclear distance restraints obtained using solid-state nuclear magnetic resonance (ssNMR) spectroscopy. Our results revealed that several hydrophobic and polar motifs within the A{beta}42 sequence played key roles in the early-stage nucleation process of fibrillation and those motifs are also the stabilizing agents in the mature fibrils judged by the energy contribution. Our results also indicated that the peptide association with membrane bilayers could modulate the structural evolution pathways towards fibrillation. These findings contributed to a better understanding of the molecular level structural polymorphisms inherent to A{beta}42 fibrils. Further, the current work demonstrated that the combination of MD simulations with ssNMR-based experimental restraints provided a reliable method for studying structural changes of A{beta}. HighlightO_LIUsing solid-state NMR restraints guided molecular dynamic simulation, {beta}-amyloid dimers displayed consistent {beta}-strand-prone regions, which are major stabilizing segments for mature fibrils. C_LIO_LI{beta}-amyloid dimers evolved differently with or without interacting with the lipid bilayers. C_LIO_LIExperimental restraints guided simulation provided molecular level insights about early-stage interactions along the progress of {beta}-amyloid fibrillation C_LI

biophysics↗

bioRxiv2024

Isolation and manipulation of meiotic spindles from mouse oocytes reveals migration regulated by pulling force during asymmetric division

Spindles are essential for accurate chromosome segregation in all eukaryotic cells. This study presents a novel approach for isolating fresh mammalian spindles from mouse oocytes, establishing it as a valuable in vitro model system for a wide range of possible studies. Our method enables the investigation of the physical properties and migration force of meiotic spindles in oocytes. We found that the spindle length decreases upon isolation from the oocyte. Combining this observation with direct measurements of spindle mechanics, we examined the forces governing spindle migration during oocyte asymmetric division. Our findings suggest that spindle migration is regulated by a pulling force and a net tensile force of approximately 680 pN is applied to the spindle in vivo during the migration process. This method, unveiling insights into spindle dynamics, holds promise as a robust model for future investigations into spindle formation and chromosome separation. We also found that the same approach could not isolate spindles from somatic cells, indicative of mammalian oocytes having a unique spindle organization amenable to isolation. Significance StatementSpindles are essential for accurate chromosome segregation in all eukaryotic cells, yet studying their mechanical properties in vivo remains challenging. Here, we present a novel method for isolating intact, functional spindles from live mouse oocytes, establishing a powerful in vitro model for dissecting spindle mechanics. Using this system, we reveal that spindle length shortens upon isolation and quantify a net tensile force of approximately 680 pN applied to the spindle during migration, implicating a pulling mechanism in asymmetric division. Notably, this isolation approach does not succeed in somatic cells, highlighting a unique organization of the mammalian oocyte spindle. This platform opens new avenues for understanding spindle dynamics, force generation, and chromosome segregation in meiosis.

cell biology↗

bioRxiv2024

Haploid-phased chromosomal telomere to telomere genome assembly of Uncaria rhynchophylla accelerating gene mining on the biosynthesis of medicinal alkaloids

Recorded traditionary medicinal plants contain important resources, including many natural medicinal alkaloids, for new medicine discovery and development. Uncaria genus is such a woody plant, with a high medicinal value in alkaloids, e.g. (iso)rhynchophylline. Natural alkaloids contents usually vary between germplasms and are affected by the growth environment, which requires a genomics solution to understand the genetic and environmental factors that influence alkaloid production in more detail. Here, we have dissected the haploid-resolved chromosomal T2T genome assembly of Uncaria rhynchophylla with a size of [~]634 Mb and contig N50 of 26 Mb using PacBio HiFi long-reads and Hi-C and anchored the contigs on 22 pairs of confirmed chromosomes. This genome contains 56% repeat sequences and [~]2,9000 protein-encoding genes. U. rhynchophylla diverged from a common ancestor shared with Coffea around 20 million years ago and contains expanded and contracted gene families associated with secondary metabolites and plant-associated defenses. We constructed the pathway for (iso)rhynchophylline biosynthesis with genes mined from the genome and comparative transcriptomes. 53 alkaloids out of 2,578 metabolites were identified in (iso)rhynchophylline biosynthesis, where eight differentially expressed genes were the key for regulating the catalytic steps leading to alkaloid abundance difference between tissues. The chromosome-level genome and pathways of (iso)rhynchophylline constructed in this study provide a genetic basis and guidance for further breeding improvements and the development of pharmaceutical alkaloids.

genomics↗

bioRxiv2024

Cell-cycle and Age-Related Modulations in Mouse Chromosome Stiffness

Chromosome structure is complex, and many aspects of chromosome organization are still not understood. Measuring the stiffness of chromosomes offers valuable insight into their structural properties. In this study, we analyzed the stiffness of chromosomes from metaphase I (MI) and metaphase II (MII) oocytes. Our results revealed a ten-fold increase in stiffness (Youngs modulus) of MI chromosomes compared to somatic chromosomes. Furthermore, the stiffness of MII chromosomes was found to be lower than that of MI chromosomes. We examined the role of meiosis-specific cohesin complexes in regulating chromosome stiffness. Surprisingly, the stiffness of chromosomes from three meiosis-specific cohesin mutants did not significantly differ from that of wild-type chromosomes, indicating that these cohesins may not be primary determinants of chromosome stiffness. Additionally, our findings revealed an age-related increase of chromosome stiffness for MI oocytes. Since aging is associated with elevated levels of DNA damage, we investigated the impact of etoposide-induced DNA damage on chromosome stiffness and found that it led to a reduction in stiffness in MI oocytes. Overall, our study underscores the dynamic and cyclical nature of chromosome stiffness, modulated by both the cell cycle, and by age-related factors.

biophysics↗

bioRxiv2022

Reconstitution and Expression of mcy Gene Cluster in The Model Cyanobacterium Synechococcus 7942 Reveals a Roll of MC-LR in Cell Division

Cyanobacterial blooms pose a serious threat to public health due to the presence of cyanotoxins. The most common cyanotoxins, microcystins (MCs), can cause acute poisoning at high concentrations and hepatocellular carcinoma following chronic exposure. Among all MC variants, MC-LR produced by Microcystis aeruginosa PCC 7806 is the most common toxic MC. Although the biosynthetic pathway for MC-LR has been proposed, experimental support of this pathway is lacking. In an effort to experimentally validate this pathway, we expressed the 55 kb microcystin biosynthetic gene cluster (mcy cluster) (mcyA-J) and produced MC-LR in the model cyanobacterium Synechococcus 7942. We designed and constructed the strong bidirectional promoter biPpsbA2 between mcyA and mcyD, reassembled the mcy cluster in yeast by transformation-associated recombination (TAR cloning), transformed the gene cluster into the NSII site of Synechococcus 7942, and successfully expressed MC-LR at a level of 0.006-0.018 fg cell-1 day-1. The expression of MC-LR led to abnormal cell division and the filamentation of Synechococcus 7942 cells, further analysis proved a role of MC-LR in functional assembly of the cell division protein FtsZ, by competing its GTP binding site. These results represent the first synthetic biological expression of the mcy cluster and the autotrophic production of MC-LR in a photosynthetic model organism, which lays the foundation for resolving the MC biosynthesis pathway. The suggested role of MC-LR in cell division reveals a mechanism of how blooming cyanobacteria gain a competitive edge over their non-blooming counterparts. HighlightsO_LIWe expressed the 55 kb mcy cluster and produced MC-LR in the model cyanobacterium Synechococcus 7942. C_LIO_LIThis is the first realized production of MC in the model non-toxin-production cyanobacteria from CO2 by photosynthesis. C_LIO_LICompared with the self-replicating plasmid, the recombination of the mcy cluster into the genome of Synechococcus 7942 is more suitable for the heterologous production of microcystin. C_LIO_LIMC-LR inhibits cell division by irreversibly competing the GTP binding domain of the cell division protein FtsZ. C_LIO_LIThe newly discovered effect of MC-LR on cell division reveals a mechanism of how blooming cyanobacteria gain competitive edge over their non-blooming counterparts. C_LI

synthetic biology↗

bioRxiv2018

Pancreatic adenocarcinoma human organoids share structural and genetic features with primary tumors

Patient-derived pancreatic ductal adenocarcinoma (PDAC) organoid systems show great promise for understanding the biological underpinnings of disease and advancing therapeutic precision medicine. Despite the increased use of organoids, the fidelity of molecular features, genetic heterogeneity, and drug response to the tumor of origin remain important unanswered questions limiting their utility. To address this gap in knowledge, we created primary tumor- and PDX-derived organoids, and 2D cultures for in-depth genomic and histopathological comparisons to the primary tumor. Histopathological features and PDAC representative protein markers showed strong concordance. DNA and RNA sequencing of single organoids revealed patient-specific genomic and transcriptomic consistency. Single-cell RNAseq demonstrated that organoids are primarily a clonal population. In drug response assays, organoids displayed patient-specific sensitivities. Additionally, we examined the in vivo PDX response to FOLFIRINOX and Gemcitabine/Abraxane treatments, which was recapitulated in vitro by organoids. The patient-specific molecular and histopathological fidelity of organoids indicate that they can be used to understand the etiology of the patients tumor and the differential response to therapies and suggests utility for predicting drug responses.

cancer biology↗

bioRxiv2017

Influence Of Drought Stress On Alfalfa Yields And Nutritional Composition

It is predicted that climate change may increase the risk of local droughts, with severe consequences for agricultural practices. Here we report the influence of drought on alfalfa yields and its nutritional composition, based on artificially induced drought conditions during two field experiments. Two types of alfalfa cultivars were compared, Gold Queen and Suntory. The severity and timing of a drought period was varied, and the crop was harvested either early during flowering stage, or late at full bloom. The obtained dry mass yields of Gold Queen were higher than Suntory, and the first was also more resistant to drought. Early harvest resulted in higher yields. Decreases in yields due to water shortage were observed with both cultivars, and the fraction of crude protein (CP) decreased as a result of drought stress; this fraction was higher in Gold Queen than in Suntory and higher in early harvest compared to late harvest. Severe drought late in spring had the highest effect on CP content. The fraction of fibre, split up into neutral detergent fibre (NDF) and acid detergent fibre (ADF) increased as a result of drought and was lower in early harvested plants compared to late harvest. Suntory alfalfa produced higher fibre fractions than Gold Queen. The fraction of water-soluble carbohydrates (WSC) was least affected by drought. It was consistently higher in Gold Queen compared to Suntory alfalfa, and late harvest resulted in higher WSC content. In combination, these results suggest that the nutritive value of alfalfa will likely decrease after a period of drought. These effects can be partly overcome by choosing the Gold Queen cultivar over Suntory, by targeted irrigation, in particular in late spring, and by harvesting at an earlier time.

plant biology↗