Biology subjects

Wang, D.

Publications and source records attributed to Wang, D..

At least 397 records · Page 22Linked to original sources

bioRxiv2023

Tissue-specific transfer-learning enables retasking of a general comprehensive model to a specific domain

Machine learning (ML) has proven successful in biological data analysis. However, may require massive training data. To allow broader use of ML in the full spectrum of biology and medicine, including sample-sparse domains, re-directing established models to specific tasks by add-on training via a moderate sample may be promising. Transfer learning (TL), a technique migrating pre-trained models to new tasks, fits in this requirement. Here, by TL, we retasked Enformer, a comprehensive model trained by massive data, tailored to breast cancers using breast-specific data. Its performance has been validated through statistical accuracy of predictions, annotation of genetic variants, and mapping of variants associated with breast cancer. By allowing the flexibility of adding dedicated training data, our TL protocol unlocks future discovery within specific domains with moderate add-on samples by standing on the shoulders of giant models.

bioinformatics↗

bioRxiv2023

Functional connectome through the human life span

The lifespan growth of the functional connectome remains unknown. Here, we assemble task-free functional and structural magnetic resonance imaging data from 33,250 individuals aged 32 postmenstrual weeks to 80 years from 132 global sites. We report critical inflection points in the nonlinear growth curves of the global mean and variance of the connectome, peaking in the late fourth and late third decades of life, respectively. After constructing a fine-grained, lifespan-wide suite of system-level brain atlases, we show distinct maturation timelines for functional segregation within different systems. Lifespan growth of regional connectivity is organized along a primary-to-association cortical axis. These connectome-based normative models reveal substantial individual heterogeneities in functional brain networks in patients with autism spectrum disorder, major depressive disorder, and Alzheimers disease. These findings elucidate the lifespan evolution of the functional connectome and can serve as a normative reference for quantifying individual variation in development, aging, and neuropsychiatric disorders.

neuroscience↗

bioRxiv2023

Elf1 promotes Rad26 interaction with lesion-arrested Pol II for transcription-coupled repair

Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a universal mechanism to recognize a stalled Pol II but interacts more strongly with a lesion-arrested Pol II. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces new interactions between Rad26 and Pol II when the complex is stalled at a lesion. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation.

biophysics↗

bioRxiv2023

Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses

Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Using a meta-transcriptomic approach, we analysed the virome of 2,438 individual mosquitos (79 species), spanning [~]4000 km along latitudes and longitudes in China. From these data we identified 393 core viral species associated with mosquitos, including seven (putative) arbovirus species. We identified potential species and geographic hotspots of viral richness and arbovirus occurrence, and demonstrated that host phylogeny had a strong impact on the composition of individual mosquito viromes. Our data revealed a large number of viruses shared among mosquito species or genera, expanding our knowledge of host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, possibly facilitated by long-distance mosquito migrations. Together, our results greatly expand the known mosquito virome, linked the viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the ecology of viruses of insect vectors.

ecology↗

bioRxiv2023

Preclinical evaluation of the efficacy and safety of AAV1-hOTOF in mice and non-human primates

Pathogenic mutations in the OTOF gene cause autosomal recessive hearing loss 9 (DFNB9), one of the most common forms of auditory neuropathy. There is no biological treatment for DFNB9. Here, we designed an OTOF gene therapy agent by dual AAV1 carrying human OTOF coding sequences with the expression driven by the hair cell-specific promoter Myo15, AAV1-hOTOF. To develop a clinical application of AAV1-hOTOF gene therapy, we evaluated its efficacy and safety in animal models by pharmacodynamics, behavior, and histopathology. AAV1-hOTOF inner ear delivery significantly improved hearing in Otof -/- mice without affecting normal hearing in wild-type mice. AAV1 was predominately distributed to the cochlea although it was detected in other organs such as the central nervous system and the liver, and no obvious toxic effects of AAV1-hOTOF were observed in mice. To further evaluate the safety of Myo15 promoter-driven AAV1-transgene, AAV1-GFP was delivered into the inner ear of Macaca fascicularis via the round window membrane. AAV1-GFP transduced 60-94% of the inner hair cells along the cochlear turns. AAV1-GFP was detected in isolated organs and no significant adverse effects were detected. These results suggest that AAV1-hOTOF is well tolerated and effective in animals, providing critical support for its clinical translation.

genetics↗

bioRxiv2023

Cell free expression in proteinosomes prepared from native protein-PNIPAAm conjugates

Towards the goal of building synthetic cells from the bottom-up, the establishment of micrometer-sized compartments that contain and support cell free transcription and translation that couple cellular structure to function is of critical importance. Proteinosomes, formed from crosslinked cationized protein-polymer conjugates offer a promising solution to membrane-bound compartmentalisation with an open, semi-permeable membrane. Critically, to date, there have been no demonstration of cell free transcription and translation within water-in-water proteinosomes. Herein, we present a novel approach to the fabrication of proteinosomes directly from native protein-polymer (BSA-PNIPAAm) conjugates. We show that these native proteinosomes offer an excellent alternative as artificial cell chassis. Significantly, the native proteinosomes are stable under high salt conditions and can consequently support cell free transcription and translation. The native proteinosomes offer enhanced protein expression compared to proteinosomes prepared from traditional methodologies. Furthermore, we demonstrate the integration of proteinosomes into higher order cellular architectures with membrane free compartments and liposomes. The integration of bioinspired architectural elements with the central dogma is an essential building block for realizing minimal synthetic cells and is key for exploiting artificial cells in real-world applications.

synthetic biology↗

bioRxiv2023

S-PLM: Structure-aware Protein Language Model via Contrastive Learning between Sequence and Structure

Proteins play an essential role in various biological and engineering processes. Large protein language models (PLMs) present excellent potential to reshape protein research by accelerating the determination of protein function and the design of proteins with the desired functions. The prediction and design capacity of PLMs relies on the representation gained from the protein sequences. However, the lack of crucial 3D structure information in most PLMs restricts the prediction capacity of PLMs in various applications, especially those heavily dependent on 3D structures. To address this issue, we introduce S-PLM, a 3D structure-aware PLM that utilizes multi-view contrastive learning to align the sequence and 3D structure of a protein in a coordinated latent space. S-PLM applies Swin-Transformer on AlphaFold-predicted protein structures to embed the structural information and fuses it into sequence-based embedding from ESM2. Additionally, we provide a library of lightweight tuning tools to adapt S-PLM for diverse protein property prediction tasks. Our results demonstrate S-PLMs superior performance over sequence-only PLMs on all protein clustering and classification tasks, achieving competitiveness comparable to state-of-the-art methods requiring both sequence and structure inputs. S-PLM and its lightweight tuning tools are available at https://github.com/duolinwang/S-PLM/.

bioinformatics↗

bioRxiv2023

Migrasome formation is initiated preferentially in tubular junctions by alternations of membrane tension or intracellular pressure

Migrasomes, the transient vesicle-like cellular organelles, arise on the retraction fibers (RFs), the branched tubular extensions of the plasma membrane generated during cell migration. Migrasomes form in two steps: a local RF swelling is followed by a protein-dependent stabilization of the emerging spherical bulge. Here we approached experimentally and theoretically the previously unaddressed mechanism of the initial RF swelling. We hypothesized that the swelling can be driven by alterations of the generic mechanical factors, the RFs luminal pressure and membrane tension. To examine the effects of pressure, we exposed migrating RF-producing cells to a hypotonic medium and observed the formation of migrasome-like bulges with a preferential location in the RF branching sites. To test the results of tension variations, we developed a biomimetic system of three membrane tubules connected by a junction and subjected to controlled membrane tension. An abrupt increase of tension resulted in a migrasome-like bulge formation in the junction and in the tubular regions. Following the formation, the tubules bulges moved toward and merged with the junctional bulge. To understand the physical forces behind the observations, we considered theoretically the mechanical energy of a membrane system consisting of a three-way tubular junction with emerging tubular arms connected to a membrane reservoir. The energy minimization predicted the membrane bulging, preferably, in the junction site as a result of both an increase in the luminal pressure and an abrupt rise of the membrane tension. We discuss the common physical background of the two phenomena.

biophysics↗

bioRxiv2023

Differential substrate affinity and catabolite repression enable preferential use of urea by ammonia-oxidizing bacteria

Four distinct lineages of ammonia-oxidizing microorganisms (AOM) collectively contribute to one of the largest nitrogen fluxes in the global nitrogen budget. AOM possess widely different specific affinities for ammonia, thought to determine their niche differentiation. Nevertheless, ammonia-oxidizing archaea and bacteria (AOA, AOB), and complete ammonia oxidizers (comammox) co-occur in soils, freshwater sediments, and aquifers, suggesting that other factors must drive their coexistence. Here, we show that representatives of four AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct competition for either substrate. The tested AOA and comammox species preferentially used ammonia over urea, while beta-proteobacterial AOB favored urea utilization, repressed ammonia transport in the presence of urea, and showed higher affinity for urea than ammonia, whereas gamma-proteobacterial AOB co-utilized both substrates. Stable isotope tracing, kinetics, and transcriptomics experiments revealed that both assimilation and oxidation of ammonia are transport-dependent. These results reveal novel mechanisms of nitrogen metabolism regulation and transporter-based affinity underlying the contrasting niche adaptation and coexistence patterns among the major AOM lineages.

microbiology↗

bioRxiv2023

Oligo-PROTAC strategy for cell-selective and targeted degradation of activated STAT3

Decoy-oligodeoxynucleotides (D-ODNs) can target undruggable transcription factors, such as STAT3. However, challenges in D-ODN delivery and potency hampered their translation. To overcome these limitations, we conjugated STAT3-specific D-ODN to thalidomide (Tha), a known ligand to cereblon (CRBN, a component of E3 ubiquitin ligase) to generate a proteolysis-targeting chimera (STAT3DPROTAC). STAT3DPROTAC downregulated STAT3, but not STAT1 or STAT5, in target cells. Computational modeling of the STAT3DPROTAC ternary complex predicted two surface lysines on STAT3, K601 and K626 as potential ubiquitination sites for the PROTAC bound E3 ligase. Accordingly, K601/K626 point mutations in STAT3, as well as proteasome inhibitors, and CRBN deletion alleviated STAT3DPROTAC effect. Next, we conjugated STAT3DPROTAC to a CpG ligand targeting Toll-like receptor 9 (TLR9) to generate myeloid/B-cell-selective C-STAT3DPROTAC conjugate. Naked C-STAT3DPROTAC was spontaneously internalized by TLR9+ myeloid cells, B cells as well as human Ly18 and mouse A20 lymphoma cells, but not by T cells. C-STAT3DPROTAC decreased STAT3 levels to 50% at 250 nM and over 85% at 2 {micro}M dosing in myeloid cells. We also observed significantly improved downregulation of STAT3 target genes involved in lymphoma cell proliferation and/or survival (BCL2L1, CCND2, MYC). Finally, we assessed the antitumor efficacy of C-STAT3DPROTAC compared to C-STAT3D or scrambled control (C-SCR) against human lymphoma xenotransplants. Local C-STAT3DPROTAC administration triggered lymphoma regression while control treatments had limited effects. Our results underscore feasibility of using PROTAC strategy for cell-selective, decoy oligonucleotide-based targeting of STAT3 and potentially other tumorigenic transcription factors for cancer therapy.

cancer biology↗

bioRxiv2023

Dynamic simulations of feeding and respiration of the early Cambrian periderm-bearing cnidarian polyps

Although fossil evidence suggests the existence of an early muscular system in the ancient cnidarian jellyfish from the early Cambrian Kuanchuanpu biota (ca. 535 Ma), south China, the mechanisms underlying the feeding and respiration of the early jellyfish are conjectural. Recently, the polyp inside the periderm of olivooids was demonstrated to be a calyx-like structure, most likely bearing short tentacles and bundles of coronal muscles at the edge of the calyx, thus presumably contributing to feeding and respiration. Here, we simulate the contraction and expansion of the microscopic periderm-bearing olivooid Quadrapyrgites via the fluid-structure interaction computational fluid dynamics (CFD) method to investigate their feeding and respiratory activities. The simulations show that the rate of water inhalation by the polyp subumbrella is positively correlated with the rate of contraction and expansion of the coronal muscles, consistent with the previous feeding and respiration hypothesis. The dynamic simulations also show that the frequent inhalation/exhalation of water through the periderm polyp expansion/contraction conducted by the muscular system of Quadrapyrgites most likely represents the ancestral feeding and respiration patterns of Cambrian sedentary medusozoans that predated the rhythmic jet-propelled swimming of the modern jellyfish. Most importantly for these Cambrian microscopic sedentary medusozoans, the increase of body size and stronger capacity of muscle contraction may have been indispensable in the stepwise evolution of active feeding and subsequent swimming in a higher flow (or higher Reynolds number) environment. Impact statementTo the best of our knowledge, our study is the first to simulate the feeding and respiration patterns of Quadrapyrgites by introducing a dynamic fluid-structure coupling method, revealing the relationship between the ancient medusozoans and modern jellyfish.

evolutionary biology↗

bioRxiv2023

Characterization of covalent inhibitors that disrupt the interaction between the tandem SH2 domains of SYK and FCER1G phospho-ITAM

RNA sequencing and genetic data support spleen tyrosine kinase (SYK) and high affinity immunoglobulin epsilon receptor subunit gamma (FCER1G) as putative targets to be modulated for Alzheimers disease (AD) therapy. FCER1G is a component of Fc receptor complexes that contain an immunoreceptor tyrosine-based activation motif (ITAM). SYK interacts with the Fc receptor by binding to doubly phosphorylated ITAM (p-ITAM) via its two tandem SH2 domains (SYK-tSH2). Interaction of the FCER1G p-ITAM with SYK-tSH2 enables SYK activation via phosphorylation. Since SYK activation is reported to exacerbate AD pathology, we hypothesized that disruption of this interaction would be beneficial for AD patients. Herein, we developed biochemical and biophysical assays to enable the discovery of small molecules that perturb the interaction between the FCER1G p-ITAM and SYK-tSH2. We identified two distinct chemotypes using a high-throughput screen (HTS) and orthogonally assessed their binding. Both chemotypes covalently modify SYK-tSH2 and inhibit its interaction with FCER1G p-ITAM.

neuroscience↗

bioRxiv2023

Gradient-based implementation of linear model outperforms deep learning models

Deep learning has been widely considered more effective than traditional statistical models in modeling biological complex data such as single-cell omics. Here we show the devil is hidden in details: by adapting a modern gradient solver to a traditional linear mixed model, we showed that conventional models can outperform deep models in terms of both speed and accuracy. This work reveals the potential of re-implementing traditional models with modern solvers.

bioinformatics↗

bioRxiv2023

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

AbstractThe Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

genomics↗

bioRxiv2023

3 Directional Inception-ResUNet: deep spatial feature learning for multichannel singing voice separation with distortion

Singing voice separation on robots faces the problem of interpreting ambiguous auditory signals. The acoustic signal, which the humanoid robot perceives through its onboard microphones, is a mixture of singing voice, music, and noise, with distortion, attenuation, and reverberation. In this paper, we used the 3 directional Inception-Resnet structure in the U-shaped encoding and decoding network to improve the utilization of the spatial and spectral information of the spectrograms. Multi-objectives were used to train the model: magnitude consistency loss, phase consistency loss, and magnitude correlation consistency loss. We recorded the singing voice and accompaniment derived from the MIR-1k datasets with NAO robots and synthesized the 10-channel datasets for training the model. The experimental results show that the proposed model trained by multi-objective reaches an average NSDR of 11.55db on the test datasets, which outperforms the comparison model. Author summaryThe mixture in the real singing voice separation is always mixed with noise and distortion. In this paper, the acoustic signals with distortion and noise perceived by the robot are used to study the separation of singing voices in real scenes. This paper described how to synthesize the training datasets, proposed a 3 directional Inception-ResUNet structure for multichannel singing voice separation, and adopted multi-objectives including magnitude correlation consistency loss to train the model. The experimental results showed that the magnitude correlation consistency loss reduces distortions, the proposed model achieves better performance than the compared models.

bioinformatics↗

bioRxiv2023

Biophysical principles predict fitness of SARS-CoV-2 variants

SARS-CoV-2 employs its spike proteins receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our understanding of how RBDs biophysical properties contribute to SARS-CoV-2s epidemiological fitness remains largely incomplete. Through a comprehensive approach, comprising large-scale sequence analysis of SARS-CoV-2 variants and the discovery of a fitness function based on binding thermodynamics, we unravel the relationship between the biophysical properties of RBD variants and their contribution to viral fitness. We developed a biophysical model that uses statistical mechanics to map the molecular phenotype space, characterized by binding constants of RBD to ACE2, LY-CoV016, LY-CoV555, REGN10987, and S309, onto a epistatic fitness landscape. We validate our findings through experimentally measured and machine learning (ML) estimated binding affinities, coupled with infectivity data derived from population-level sequencing. Our analysis reveals that this model effectively predicts the fitness of novel RBD variants and can account for the epistatic interactions among mutations, including explaining the later reversal of Q493R. Our study sheds light on the impact of specific mutations on viral fitness and delivers a tool for predicting the future epidemiological trajectory of previously unseen or emerging low frequency variants. These insights offer not only greater understanding of viral evolution but also potentially aid in guiding public health decisions in the battle against COVID-19 and future pandemics. Significance StatementThis research presents a biophysical model that maps the molecular properties of SARS-CoV-2s receptor binding domain into an epistatic fitness landscape. By linking the binding affinities of the virus to its epidemic fitness, we offer a powerful tool for understanding and predicting the emergence and success of new viral variants. Our model, validated with real-world data and informed by theoretical insights, provides a foundation for interpreting the evolutionary trajectory of past pandemics and predicting those of the future. The adaptability of this biophysical model extends to the key proteins of other viruses as well, signifying its potential in guiding public health interventions, and advancing our understanding of viral evolution.

biophysics↗

bioRxiv2023

De novo progesterone synthesis in plants

The essential roles of progesterone and other C21 steroids in animals are well-documented. Progesterone is an essential hormone for females to maintain a regular menstrual cycle and pregnancy, while also exhibiting anti-inflammatory and antitumor effects. While the biosynthesis pathway of C21 steroids is comprehensively understood in animals, the synthesis mechanisms of progesterone in plants remain unclear. To our best knowledge, this is the first study to elucidate the complete pathway for progesterone biosynthesis in the plant Marsdenia tenacissima, involving the two sterol side chain cleaving cytochrome P450 enzymes (P450scc) Mt108 or Mt150, as well as the {Delta}5-3{beta}-hydroxysteroid dehydrogenase/{Delta}5-{Delta}4 ketosteroid isomerase MtHSD5. This critical discovery paves the way for the sustainable synthesis of steroid hormone drugs using either plants or microbial host cells.

plant biology↗

bioRxiv2023

Analysis of Drosophila and mouse mutants reveals that Peroxidasin is required for tissue mechanics and full viability

Basement membranes are thin strong sheets of extracellular matrix. They provide mechanical and biochemical support to epithelia, muscles, nerves, and blood vessels, among other tissues. The mechanical properties of basement membranes are conferred in part by Collagen IV (Col4), an abundant protein of basement membrane that forms an extensive two-dimensional network through head-to-head and tail-to-tail interactions. After the Col4 network is assembled into a basement membrane, it is crosslinked by the matrix-resident enzyme Peroxidasin to form a large covalent polymer. Peroxidasin and Col4 crosslinking are highly conserved, indicating they are essential, but homozygous mutant mice have mild phenotypes. To explore the role of Peroxidasin, we analyzed mutants in Drosophila, including a newly generated catalytic null, and found that homozygotes were mostly lethal with 13% viable escapers. A Mendelian analysis of mouse mutants shows a similar pattern, with homozygotes displaying [~]50% lethality and [~]50% escapers. Despite the strong mutations, the homozygous escapers had low but detectable levels of Col4 crosslinking, indicating that inefficient alternative mechanisms exist and that are probably responsible for the viable escapers. Further, fly mutants have phenotypes consistent with a decrease in stiffness. Interestingly, we found that even after adult basement membranes are assembled and crosslinked, Peroxidasin is still required to maintain stiffness. These results suggest that Peroxidasin crosslinking may be more important than previously appreciated.

cell biology↗