Biology subjects

Wu, B.

Publications and source records attributed to Wu, B..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Harnessing Protein Language Model for Structure-Based Discovery of Highly Efficient and Robust PET Hydrolases

Plastic waste, particularly polyethylene terephthalate (PET), presents significant environmental challenges, prompting extensive research into enzymatic biodegradation. Existing PET hydrolases are limited to a narrow sequence space and demonstrate insufficient performance for biodegradation. This study introduces a novel discovery pipeline that combines protein language models (PLMs) with a structural representation tree to identify enzymes based on structural similarity. Using the crystal structure of IsPETase as a template, we employed PLMs and a representation tree to efficiently search and cluster target proteins. Screening of candidate proteins was further refined using PLM-based assessments of solubility and thermal stability. Biochemical experiments showed that 14 of 34 candidates exhibited PET degradation activity across a temperature range of 30-60 {degrees}C. Notably, we identified a PET hydrolase -KbPETase, which possesses a melting temperature 32 {degrees}C higher than that of IsPETase and exhibits the highest PET degradation activity within 30-50 {degrees}C compared to other wild-type PETases. KbPETase also shows higher catalytic efficiency than FastPETase. X-ray crystallography and molecular dynamics simulations further revealed that KbPETase has a conserved catalytic domain and enhanced intramolecular interactions. This work develops a novel deep learning approach to discover natural PETases with enhanced functions.

molecular biology↗

bioRxiv2024

Multi-view BLUP: a promising solution for post-omics data integrative prediction

Phenotype prediction is a promising strategy for accelerating molecular plant breeding. Data from multiple sources (called multi-view data) can provide complementary information to characterize a biological object from various aspects. By integrating multi-view information into phenotype prediction, a multi-view best linear unbiased prediction (MVBLUP) method was proposed in this paper. By assigning different weights to measure the importance of different views of data and using a differential evolution algorithm with an early stopping mechanism to adjust the weight vector adaptively, a multi-view kinship matrix was obtained first and then incorporated into the BLUP model for phenotype prediction. To validate the efficiency of MVBLUP, we conducted numerical experiments on four multi-view datasets. Compared to the average performance of the single-view method, the prediction accuracy of the MVBLUP method has improved by a range of 0.038 to 0.201.The results demonstrate that the MVBLUP model is an effective method of integrating multi-view data.

genetics↗

bioRxiv2024

Chemosensation drives divergent social behavior in Drosophila

The social environment can have a considerable impact on animal behavior. However, the molecular signals that drive socially sensitive behaviors are not completely defined. Using the model organism, Drosophila melanogaster, we investigated behavioral responses to housing status. Group housing of male flies induces robust social interactions--composed of chasing and touching--in the Dahomey strain, but not in other commonly used parental lines. Testing mixed-strain groups revealed that strain-specific variation in chemosensation, rather than in the generation of chemosignals, likely underlies the divergent group behaviors. Using locomotor activity as a higher throughput readout for increased social interactions, we found that manipulations that decrease or ablate olfaction--through surgical removal of olfactory organs, silencing of olfactory neurons, or mutations in odorant receptor co-receptor (Orco)--decrease Dahomey social sensitivity. Females of all tested strains, including Dahomey, show no evidence of increased group activity. These results demonstrate that Dahomey social sensitivity is a sexually dimorphic, olfaction-dependent group behavior. The OR43a receptor, as well as signaling through Or43a+ neurons, contributes to Dahomey group hyperactivity. Additional studies also suggest that strain-specific single nucleotide polymorphisms (SNPs) in the Or43a gene are associated with Dahomey social sensitivity. Our studies reveal insights on the mechanisms that regulate sensory recognition and behavioral responses to the social environment, and how divergent strategies may have evolved within the same species.

animal behavior and cognition↗

bioRxiv2024

Reliable prediction of protein-protein binding affinity changes upon mutations with Pythia-PPI

Protein-protein interactions are essential for numerous biological functions, and predicting binding affinity changes caused by mutations is crucial for understanding the impact of genetic variations and advancing protein engineering. Although machine learning-based methods show promise in improving the prediction accuracy, the scarcity of experimental data remains a significant bottleneck. Here, we utilized multi-task learning and self-distillation to overcome the data limitation and improved the accuracy of deep learning-based protein binding affinity prediction. By incorporating a mutation stability prediction task, the model achieved state-of-the-art accuracy on the SKEMPI dataset and was subsequently used to predict binding affinity changes for millions of mutations, generating an expanded dataset for self-distillation. Compared with prevalent methods, Pythia-PPI increased the Pearson correlation between predictions and experimental data from 0.6447 to 0.7850 on the SKEMPI dataset, and from 0.3654 to 0.6051 on the virial-receptor dataset. These findings demonstrated Pythia-PPI to be a valuable tool for analyzing the fitness landscape of protein-protein interactions. We provided a web server at https://pythiappi.wulab.xyz for easy access to Pythia-PPI.

bioinformatics↗

bioRxiv2024

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

BackgroundThe agamid dragon lizard Pogona vitticeps is one of the most popular domesticated reptiles to be kept as pets worldwide. The capacity of breeding in captivity also makes it emerging as a model species for a range of scientific research, especially for the studies of sex chromosome origin and sex determination mechanisms. ResultsBy leveraging the CycloneSEQ and DNBSEQ sequencing technologies, we conducted whole genome and long-range sequencing for a captive-bred ZZ male to construct a chromosome-scale reference genome for P. vitticeps. The new reference genome is [~]1.8 Gb in length, with a contig N50 of 202.5 Mb and all contigs anchored onto 16 chromosomes. Genome annotation assisted by long-read RNA sequencing greatly expanded the P. vitticeps lncRNA catalog. With the chromosome-scale genome, we were able to characterize the whole Z sex chromosome for the first time. We found that over 80% of the Z chromosome remains as pseudo-autosomal region (PAR) where recombination is not suppressed. The sexually differentiated region (SDR) is small and occupied mostly by transposons, yet it aggregates genes involved in male development, such as AMH, AMHR2 and BMPR1A. Finally, by tracking the evolutionary origin and developmental expression of the SDR genes, we proposed a model for the origin of P. vitticeps sex chromosomes which considered the Z-linked AMH as the master sex-determining gene. ConclusionsOur study provides novel insights into the sex chromosome origin and sex determination of this model lizard. The near-complete P. vitticeps reference genome will also benefit future study of amniote evolution and may facilitate genome-assisted breeding.

genomics↗

bioRxiv2024

AI-enabled Alkaline-resistant Evolution of Protein to Apply in Mass Production

Artificial intelligence (AI) models have been used to study the compositional regularities of proteins in nature, enabling it to assist in protein design to improve the efficiency of protein engineering and reduce manufacturing cost. However, in industrial settings, proteins are often required to work in extreme environments where they are relatively scarce or even non-existent in nature. Since such proteins are almost absent in the training datasets, it is uncertain whether AI model possesses the capability of evolving the protein to adapt extreme conditions. Antibodies are crucial components of affinity chromatography, and they are hoped to remain active at the extreme environments where most proteins cannot tolerate. In this study, we applied an advanced large language model (LLM), the Pro-PRIME model, to improve the alkali resistance of a representative antibody, a VHH antibody capable of binding to growth hormone. Through two rounds of design, we ensured that the selected mutant has enhanced functionality, including higher thermal stability, extreme pH resistance and stronger affinity, thereby validating the generalized capability of the LLM in meeting specific demands. To the best of our knowledge, this is the first LLM-designed protein product, which is successfully applied in mass production.

bioinformatics↗

bioRxiv2024

The T-type voltage-gated Ca2+ channel CaV3.1 as a candidate receptor for Pasteurella multocida toxin and contributes to the disruption of respiratory epithelial barrier induced by the toxin

Pasteurella multocida toxin (PMT) is an exotoxin produced by several members of the zoonotic respiratory pathogen P. multocida. The role of PMT in disrupting the mammalian respiratory barrier remains to be elucidated. In this study, we discovered that inoculation of recombinantly expressed PMT increased the permeability of the respiratory epithelial barrier in mouse and respiratory cell models. This was evidenced by a decreased expression of tight junctions (ZO-1, occludin) and adherens junctions ({beta}-catenin, E-cadherin), as well as enhanced cytoskeletal rearrangement. In mechanism, we demonstrated that PMT inoculation induced cytoplasmic Ca2+ inflow, leading to an imbalance of cellular Ca2+ homeostasis and endoplasmic reticulum stress. This process further stimulated the RhoA/ROCK signaling, promoting cytoskeletal rearrangement and reducing the expression of tight junctions and adherens junctions. Notably, the T-type voltage-gated Ca2+ channel CaV3.1 was found to participate in PMT-induced cytoplasmic Ca2+ inflow. Knocking out CaV3.1 significantly reduced the cytotoxicity induced by PMT on swine respiratory epithelial cells and mitigated cytoplasmic Ca2+ inflow stimulated by PMT. Further analysis identified Ser (aa92), Glu (aa155), Tyr (aa167), and Leu (aa448) as crucial sites utilized by PMT to interact with CaV3.1. These findings suggest CaV3.1 serves as an important host receptor of PMT and contributes to PMT-induced respiratory epithelial barrier disruption. ImportancePMT is a significant toxin produced by the zoonotic respiratory pathogen P. multocida, yet little is known about its pathogenesis beyond causing progressive atrophic rhinitis in pigs. In our study, we have discovered that PMT has the capacity to disrupt the integrity of the mammalian respiratory epithelial barrier. This disruption involves an imbalance in cellular Ca2+ homeostasis, endoplasmic reticulum stress, and activation of the RhoA/ROCK signaling pathway induced by PMT. Importantly, we have identified CaV3.1 as a pivotal receptor that plays a crucial role in the pathogenic effects of PMT. Our findings highlight the potential of CaV3.1 as a target for intervention strategies aimed at combating the detrimental effects of PMT.

microbiology↗

bioRxiv2024

Modulation of blood-tumor barrier transcriptional programs improves intra-tumoral drug delivery and potentiates chemotherapy in GBM

Glioblastoma (GBM) is the most common malignant primary brain tumor. GBM has an extremely poor prognosis and new treatments are badly needed. Efficient drug delivery to GBM is a major obstacle as the blood-brain barrier (BBB) prevents passage of the majority of cancer drugs into the brain. It is also recognized that the blood-brain tumor barrier (BTB) in the growing tumor represents a challenge. The BTB is heterogeneous and poorly characterized, but similar to the BBB it can prevent therapeutics from reaching effective intra-tumoral doses, dramatically hindering their potential. Here, we identified a 12-gene signature associated with the BTB, with functions related to vasculature development, morphogenesis and cell migration. We identified CDH5 as a core molecule in this set and confirmed its over-expression in GBM vasculature using spatial transcriptomics of GBM patient specimens. We found that the indirubin-derivative, 6-bromoindirubin acetoxime (BIA), could downregulate CDH5 and other BTB signature genes, causing endothelial barrier disruption in endothelial monolayers and BBB 3D spheroids in vitro. Treatment of tumor-bearing mice with BIA enabled increased intra-tumoral accumulation of the BBB non-penetrant chemotherapeutic drug cisplatin and potentiated cisplatin-mediated DNA damage by targeting DNA repair pathways. Finally, using an injectable BIA nanoparticle formulation, PPRX-1701, we significantly improved the efficacy of cisplatin in patient-derived GBM xenografts and prolonged their survival. Overall, our work reveals potential targets at the BTB for improved chemotherapy delivery and the bifunctional properties of BIA as a BTB modulator and potentiator of chemotherapy, supporting its further development.

cancer biology↗

bioRxiv2024

Haplotype-resolved genome assembly of upland switchgrass provides insights into cold tolerance

Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance than lowland ecotype, but the underlying molecular mechanisms remain unclear. Here, we presented a high-quality haplotype-resolved genome of the upland ecotype Jingji31 and conducted multi-omics analysis to understand its cold tolerance. The divergence between upland and lowland ecotypes of switchgrass occurred after the differentiation of the two subgenomes (K and N). Under cold stress, the K subgenome has more differentially expressed genes (DEGs). Transcriptome analysis revealed ecotype-specific differential expressions among members of the cold-responsive (COR) gene families. Specifically, certain members of the AFB1, ATL80, HOS10, and STRS2 gene families exhibited opposite expression changes between the two ecotypes, potentially contributing to their differential cold tolerance. By using haplotype-resolved genome, we identified more cold-induced allele-specific expressions (ASEs) in the upland ecotype, and these ASEs were significantly enriched in the COR gene families. Genome-wide association study detected an association signal on Chr3K related to overwintering rate, which overlapped with a selective sweep region and contained a cytochrome P450 (CYP450) gene highly expressed under cold stress. Heterologous overexpression of CYP450 in rice alleviated leaf wilting and improved cold tolerance. Our study provides a high-quality haplotype-resolved genome of upland switchgrass, to advance conceptual understanding of plant cold tolerance for breeding crops with enhanced cold adaptation.

genomics↗

bioRxiv2024

Bio-macromolecular assembly machine for human limb lengthening

Growth plate (GP) is the critical cartilaginous structure for longitudinal bone growth. Herein, employing high-resolution analytical techniques, we explore the intricate mechanisms that govern the polarized mineralization patterns within GP. The GP-epiphysis interface displays a sharp transition in tissue modulus, acting as a "protective shell" for the underlying GP, whereas the GP-metaphysis interface exhibits a gradual modulus increase, enabling efficient load redistribution to metaphysis. The unique mechanical environments at these two interfaces contribute to polarized CaP mineralization patterns, which are regulated by a complex protein-based molecular machinery. The mineralization inhibitors SPP1 and AHSG enriched at the GP-epiphysis interface could act as a line of defence against mineralization. When these two proteins coexisted with the mineralization-promoting ENPP1 and ALPL at the GP-metaphysis interface, a sequential event of precise nucleation and programmable assembly of CaP minerals occur, forming "mineralization waves" to guide bone elongation. By replicating such specific macromolecular environment at GP-metaphysis interface, a hypertable amorphous calcium phosphate (ACP) phase is well-retained in vitro, demonstrating the possibility for precise and gentle control of ACP-hydroxyapatite (HAp) transformation under physiological conditions. Our study defines a novel concept of "mineralization waves" that govern the velocity and amplitude of GP-guided mineralization process.

bioengineering↗

bioRxiv2024

Low-cost and highly efficient generation of near-complete bacterial pathogen genomes by TELL-Seq

Recent evidences suggest that de novo genome assembly can provide additional insights into genomic variation landscape beyond short-read NGS analyses. Despite the advent of longread sequencing technologies, generating high-quality bacterial genome assemblies remains expensive and requires high-quality and large quantities of DNA. TELL-Seq, an emerging linked-read technology, has been reported as a low-cost alternative for producing nearcomplete genome assembly in certain bacterial species. However, a systematic assessment of its performance and characteristics in de novo bacterial genome assembly has not yet been conducted. To address this, we benchmarked TELL-Seq using a set of clinical and standard bacterial pathogens with a wide range of genome size (2.0 6.4 Mbp), GC-content (32% - 68%), genome complexity (mappability from 0.15 to 0.60) and Gram types. Our findings indicate that, with 1/6 cost and 1/15,000 of DNA compared to PacBio HiFi, TELL-Seq could generate as high quality near-complete bacterial genome assemblies. The optimal depth for assembly is around 200x, as increased depth improves contiguity and completeness, though quality plateaus at 250x. In general, genome complexity was significantly correlated with assembly quality, but GC-content was not. Nevertheless, genomes with extreme GC-content may require higher depths for accurate assembly. Our study suggests that TELL-Seq could be a scalable method for large-scale bacterial genomic surveys. The data generated from this study could serve as a benchmark dataset for further algorithm development. Impact StatementAn increasing body of literature have shown that de novo genome assembles could provide additional insights into genomic variation beyond standard short-read technologies. Its particularly useful in clinical and epidemiological studies of bacteria, due to high variable nature of their genomes. Although great advances have been made in long-read sequencing technology, its still expensive with high requirement over sample DNAs quality and quantity, limiting its adoption in large-scale studies or surveys. Linked-read technology is an inexpensive alternative which used single molecule barcoding to mark origin of reads for better scaffolding of contigs assembled from normal short reads. TELL-Seq, as one of these promising technologies, was reported to be able to inexpensively and efficiently generate near-complete bacterial de novo genomic assemblies with low DNA inputs. Theres not yet a systematic benchmarking of this technology in bacterial pathogens. In this study, a set of clinically important bacterial pathogens with a wide spectrum of GC-content, genome size, genome complexity, and Gram Type were used to investigate the performance of TELL-Seq technology in de novo genome assembly. We found that, with about 1/6 of cost and 1/15000 of DNA quantity, it could generate comparable de novo assemblies compared to standard reference genomes or PacBio HiFi assemblies, while beating conventional short-read assemblies. We found several key factors, such as genome complexity, and sequencing depth, which would impact the quality of the assembly. Our study suggests that a sequencing depth of 200x is sufficient to achieve satisfactory results. Our study has revealed characteristics of this technology in bacterial genome assembly and paved the way for its large-scale application in clinical or epidemiological surveys. Data SummaryO_LIRaw sequencing data for all isolates have been deposited to SRA, accessible through these NCBI BioProject PRJNA1133244. C_LIO_LIA full list of SRA BioSample accession numbers are available in Tab S5. C_LIO_LIAssemblies and analyses companion this paper is available at: https://github.com/x-lab/tellseq_bacteria C_LI

bioinformatics↗

bioRxiv2024

High accuracy methylation identification tools on single molecular level for PacBio HiFi data

PacBios Circular Consensus Sequencing (CCS) allows us to obtain highly accurate bases and simultaneously determine the methylation states of individual molecules. However, existing CCS-based methods for 5mC detection have low accuracy (<90% on most datasets) at the single-molecule level and can produce inaccurate methylation patterns. These methods rely on the information from 21 bp contexts surrounding the target CpGs and have over 29% low-confidence (<75% accuracy) calls at CpGs with less distinguishable signals. We hypothesize that incorporating CpG methylation correlation information at the single-molecule level could improve the methylation calls on low-confidence CpGs. Here, we present a novel deep graph convolutional network (hifimeth) that uses 400 bp context in CCS-based 5mC calling and show that its improved performance is mainly due to the inclusion of more neighboring CpGs in contexts. Hifimeth achieves an average single-molecule accuracy of 94.7% and an average F1 score of 94.2%, 5.5% and 5.9% higher than the previous state-of-the-art method, respectively. Hifimeth-based methylation frequency quantification by read counting outperforms previous methods on all human and zebrafish datasets tested. The results also show that hifimeths high-accuracy calls can reveal complex single-molecule methylation patterns, either related to haplotypes or repeat regions, with up to single-motif resolution.

bioinformatics↗

bioRxiv2024

Mechanistic basis of lineage restriction

Lineage restriction is the biological phenomenon where cells lose developmental potency during differentiation for all except their adopted lineages. Lineage restriction is foundational to multicellularity as it secures the functional identities of the myriad cell types in the body. As yet, the mechanisms of lineage restriction remain enigmatic. By developing Potency-Seq to systematically map transcriptional potency of genes across the genome, we uncovered a link between the restriction of developmental potency of cells and the occlusion of transcriptional potency of their genomes. We further showed that, strikingly, genes can undergo irreversible occlusion of their transcriptional potency simply by chromatinization into the nucleosomal form with unmodified histones. These findings led to a comprehensive mechanistic account of lineage restriction as driven by gene occlusion. Specifically, naive pluripotent stem cells at the onset of development possess the unique capacity to erase occlusion globally to reset full transcriptional potency of the genome, which in turn establishes full developmental potency of the cells. Such deocclusion capacity is abolished when cells progress from naive to primed pluripotency. From this stage onward, lineage-inappropriate genes can undergo nucleosome-mediated occlusion in an irreversible manner when their cognate transcription factors (TFs) and/or placeholder factors (PFs) no longer exist in cells to protect them. Consequently, the transcriptionally potent portion of the genome shrinks progressively and irreversibly during differentiation, thus permanently restricting the developmental potency of differentiating cells. ONE-SENTENCE SUMMARYDevelopmental potency of cells is linked to transcriptional potency of their genomes

developmental biology↗

bioRxiv2024

Potent LILRB1 D1D2-containing antibodies inhibit RIFIN-mediated immune evasions

The spread of drug-resistant malaria parasites presents a major challenge to global efforts in malaria control, increasing the urgency for new treatments and vaccines. A promising approach involves developing antibodies that can counteract the parasites immune evasion mechanisms. In this study, we designed a receptor-containing antibody, targeting the D1D2 domain of the LILRB1 receptor, using a structure-based rational approach. We began with the MDB1 antibody as a scaffold and replaced the LILRB1-D3D4 insertion domain with D1D2.v, a high-affinity variant optimized through yeast surface display. The modified D1D2.v-IgG efficiently blocked the interaction between RIFIN#1 (from PF3D7_1254800) and LILRB1, thereby reversing the inhibition of NK cell activity caused by RIFIN#1. To further enhance this effect, we developed NK-biAb, a bispecific antibody based on D1D2.v-IgG that targets both RIFIN#1 and NKG2D receptors. NK-biAb exhibited superior biological performance compared to D1D2.v-IgG alone. These findings provide a clear framework for designing antibodies that target immune evasion in malaria, potentially guiding the development of more effective treatments and vaccines.

biochemistry↗

bioRxiv2024

A Tough Biointerface in Human Knee Empowered by Dynamic Phase-transforming Minerals in Collagenous Matrix

Joining heterogeneous materials in engineered structures remains a daunting challenge because of stress concentration, often resulting in unexpected failures1,2. Studying the structures in organisms that evolved for centuries provides valuable insights that can be instrumental in addressing this mechanical challenge3-5. The human meniscus root-bone interface is a remarkable example known for its exceptional fatigue resistance, toughness and interfacial adhesion properties throughout its lifespan6-8. We studied the multiscale graded mineralization structure designs within the 30-micron soft-hard interface at the root-bone junction and examined its toughening mechanisms. This graded interface with interdigitated structures and exponential modulus increase exhibits a phase transition from amorphous calcium phosphate (ACP) to gradually matured hydroxyapatite (HAP) crystals, mediated by location-specific distributed biomolecules. In coordination with collagen fibril deformation and reorientation, ACP particles debond with collagen and slide to new positions which enable frictional energy dissipation, and HAP particles arrest cracks. The mineral in transforming phases work synergistically to provide interfacial toughening. The presented biointerface model exemplifies human musculoskeletal systems adaptations to mechanical requirements, offering a blueprint for developing tough interfaces in broad applications.

bioengineering↗

bioRxiv2024

Efficient generation of CAR NK cells from human umbilical cord blood CD34+ stem and progenitors for democratizing affordable immunotherapy

Chimeric antigen receptor (CAR) natural killer cells (CAR NK) cells, leveraging safety and not requiring HLA match in adoptive infusion, have emerged as promising alternative cells to CAR-T cells for immunotherapies. High and multiple doses of CAR NK cell infusions are essential to maintain therapeutic efficacy in clinical trials. This requires efficient methods for generating large-scale CAR NK cells and significantly reducing CAR engineering costs. In this study, we develop a three-step strategy to generate highly high yields of induced NK (iNK) and CAR iNK cells from human umbilical cord blood CD34+ hematopoietic stem and progenitor cells (CD34+ HSPCs). Starting from a single umbilical cord blood CD34+ HSPC, our reliable method efficiently produces 14-83 million mature iNK cells or 7-32 million CAR iNK cells with high expression levels of CD16 and zero T cell contaminations. Introducing CAR expression elements at the HSPC level reduces the quantities of CAR pseudoviruses to 1 / 140.000 - 1 / 600,000 compared to engineering CARs in mature NK cells. The iNK and CAR iNK cells, including fresh cells and thawed cells from cryopreserved conditions, demonstrate remarkable tumoricidal activities against various human cancer cells and significantly prolong the survival of human tumor-bearing animals. The high yields of CAR NK cells and negligible costs of CAR engineering of our method support the broad applications of CAR NK cells for treating cancer patients.

cell biology↗

bioRxiv2024

TCMNP: a data processing and visualization database and R package for traditional Chinese medicine network pharmacology

BackgroundNetwork pharmacology is pivotal for the study of the mechanism of action of traditional Chinese medicine (TCM). However, there are currently some challenges in data processing and visualization for traditional Chinese medicine network pharmacology (TCMNP). We develop the R-environment-based software database and package TCMNP. MethodsTCMNP is designed for the analysis and visualization of compositions in TCM compounds, herbs, ingredients, corresponding targets and pathway enrichment. Data analysis and visualization in R using "dplyr", "clusterProfiler", "ggplot2", and "circlize" packages, as well as functions of our own making. ResultsTCMNP is designed for the analysis and visualization of compositions in TCM compounds, herbs, ingredients, corresponding targets and pathway. The TCMNP database contains 571 kinds of TCM herbs, 17,118 ingredients, 10,013 diseases, and 15,956 targets. TCMNP simplifies the data analysis process and realizes a complete set of process operations from Chinese herbal compound composition, component and target automatic screening, enrichment analysis visualization, protein interaction and TF and target gene screening. Its built-in functions of various types provide a tidy interface for the visualization of TCM network pharmacology. TCMNP database is freely available at https://tcmlab.top/tcmr. TCMNP package is freely available at https://github.com/tcmlab/TCMNP. ConclusionThe TCMNP database and package provide a comprehensive overview of the interconnections between components of a TCM compound and its potential effects on disease treatment. TCMNP database is available for free at https://tcmlab.top/tcmr/. TCMNP package is available for free at https://github.com/tcmlab/TCMNP. We anticipate that TCMNP will help to explore the mechanism of TCM to treat diseases.

bioinformatics↗

bioRxiv2024

Origin and stepwise improvement of vertebrate lungs

Lungs, essential for terrestrial vertebrates and present in bony fishes but absent in cartilaginous fishes, provide an ideal model for studying organ origination. Our study analyzed single-cell RNA sequencing data from mature and developing vertebrate lungs, revealing substantial similarities in cell composition, developmental trajectories and gene expression pattern across species. Notably, most lung-related genes are also present in cartilaginous fishes, indicating that gene presence alone does not guarantee lung development. We identified thousands of lung regulatory elements specific to bony fishes, with higher concentrations around genes such as tbx4 and the hoxb gene cluster. These regulatory changes might contribute to lung emergence as well as the unique co-expression patterns in lung epithelial cells, such as those related to pulmonary surfactants and cell morphology. Our research also revealed that AT1 cells are specific to mammals, and we identified a mammal-specific gene, sfta2. Knockout experiments demonstrated that sfta2 deletion causes severe respiratory defects in mice, underscoring its critical role in specialized mammalian lungs. In conclusion, our results demonstrate that the origin and evolution of lungs are driven by a complex interplay of regulatory network modifications and the emergence of new genes, underscoring the multifaceted nature of organ evolution.

evolutionary biology↗