Biology subjects

Liu, W.

Publications and source records attributed to Liu, W..

At least 379 records · Page 21Linked to original sources

bioRxiv2021

Variation of female pronucleus reveal oocyte or embryo abnormality: An expert experience deep learning of non-dark box analysis

BackgroundPronuclear assessment appears to have the ability to distinguish good and bad embryos in the zygote stage, but paradoxical results were obtained in clinical studies. This situation might be caused by the robust qualitative detection of the development of dynamic pronuclei. Here, we aim to establish a quantitative pronuclear measurement method by applying expert experience deep learning from large annotated datasets. MethodsConvinced handle-annotated 2PN images (13419) were used for deep learning then corresponded errors were recorded through handle check for subsequent parameters adjusting. We used 790 embryos with 52479 PN images from 155 patients for analysis the area of pronuclei and the pre-implantation genetic test results. Establishment of the exponential fitting equation and the key coefficient {beta} 1was extracted from the model for quantitative analysis for pronuclear(PN) annotation and automatic recognition. FindingsBased on the female original PN coefficient {beta}1, the chromosome-normal rate in the blastocyst with biggest PN area is much higher than that of the blastocyst with smallest PN area (58.06% vs. 45.16%, OR=1.68 [1.07-2.64]; P=0.031). After adjusting coefficient {beta}1 by the first three frames which high variance of outlier PN areas was removed, coefficient {beta}1 at 12 hours and at 14 hours post-insemination, similar but stronger evidence was obtained. All these discrepancies resulted from the female propositus in the PGT-SR subgroup and smaller chromosomal errors. Conclusion(s)The results suggest that detailed analysis of the images of embryos could improve our understanding of developmental biology. FundingNone

genetics↗

bioRxiv2021

The dual role of N6-methyladenosine on mouse maternal RNAs and 2-cell specific RNAs revealed by ULI-MeRIP sequencing

N6-methyladenosine (m6A) and its regulatory components play critical roles in various developmental processes in mammals(1-5). However, the landscape and function of m6A in the maternal-to-zygotic transition (MZT) remain unclear due to limited materials. Here, by developing an ultralow-input MeRIP-seq method, we revealed the dynamics of the m6A RNA methylome during the MZT process in mice. We found that more than 1/3 maternal decay and 2/3 zygotic mRNAs were modified by m6A. Moreover, m6As are highly enriched in the RNA of transposable elements MTA and MERVL, which are highly expressed in oocytes and 2-cell embryos, respectively. Notably, maternal depletion of Kiaa1429, a component of the m6A methyltransferase complex, leads to a reduced abundance of m6A-marked maternal RNAs, including both genes and MTA, in GV oocytes, indicating m6A-dependent regulation of RNA stability in oocytes. Interestingly, when the writers were depleted, some m6A-marked 2-cell specific RNAs, including Zscan4 and MERVL, appeared normal at the 2-cell stage but failed to be decayed at later stages, suggesting that m6A regulates the clearance of these transcripts. Together, our study uncovered that m6As function in context-specific manners during MZT, which ensures the transcriptome stability of oocytes and regulates the stage specificity of zygotic transcripts after fertilization. One Sentence Summarym6A RNA methylation stabilizes the maternal RNAs in mouse oocytes and degrades the 2-cell specific RNAs in the cleavage-stage embryos.

developmental biology↗

bioRxiv2021

Fast, live-cell imaging of 15 intracellular compartments by deep learning segmentation of super-resolution data

The number of colors that can be used in fluorescence microscopy to image the live-cell anatomy and organelles interactions is far less than the number of intracellular organelles and compartments. Here, we report that deep convolutional neuronal networks can predict 15 subcellular structures from super-resolution spinning-disk microscopy images using only one dye, one laser excitation, and two detection channels. Comparing to the colocalization images, this method achieves pixel accuracies of over 91.7%, which not only bypasses the fundamental limitation of multi-color imaging but also accelerates the imaging speed by more than one order of magnitude.

cell biology↗

bioRxiv2021

Structural basis of INTAC-regulated transcription

For the majority of expressed eukaryotic genes, RNA polymerase II (Pol II) forms a paused elongation complex (PEC) and undergoes promoter-proximal pausing downstream of the transcription start site 1-3. The polymerase either proceeds into productive elongation or undergoes promoter-proximal premature transcription termination 4-6. It remains incompletely understood how transcription is regulated at this stage. Here, we determined the structure of PEC bound to INTAC, an Integrator-containing PP2A complex 7, at near-atomic resolution. The structure shows that INTAC partially wraps around PEC through multiple contacts, permitting the memetic nascent RNA to run into substrate-entry tunnel of the endonuclease subunit INTS11 of INTAC for cleavage. Pol II C-terminal domain (CTD) winds over INTAC backbone module through multiple anchors and is suspended above the phosphatase of INTAC for dephosphorylation. Biochemical analysis shows that INTAC-PEC association requires unphosphorylated CTD and could tolerate CTD phosphorylation, suggesting an INTAC-mediated persistent CTD dephosphorylation followed by reinforcement of the INTAC-PEC complex. Our study reveals how INTAC binds PEC and orchestrates RNA cleavage and CTD dephosphorylation, two critical events in generating premature transcription termination.

molecular biology↗

bioRxiv2021

The Flowering Repressor SVP recruits the TOPLESS co-repressor to control flowering in chrysanthemum and Arabidopsis

Plant flowering time is a consequence of the perception of environmental and endogenous signals. The MCM1-AGAMOUSDEFICIENS-SRF-box (MADS-box) gene SHORT VEGETATIVE PHASE (SVP) is a pivotal repressor that negatively regulates the floral transition during the vegetative phase. The transcriptional corepressor TOPLESS (TPL) plays critical roles in many aspects of plant life. An interaction first identified between the second LXLXLX motif (LRLGLP) of CmSVP with CmTPL1-2, which can repress the expression of a key flowering factor CmFTL3 by binding its promotor CArG element in chrysanthemum. Genetic analysis suggested that the CmSVP-CmTPL1-2 transcriptional complex is a prerequisite for SVP to act as a floral repressor, which reduces CmFTL3 transcriptional activity. CmSVP rescued the phenotype of the svp-31 mutant in Arabidopsis, and overexpression of AtSVP or CmSVP in the Arabidopsis dominant negative mutation tpl-1 led to a loss-of-function in late flowering, which confirmed the highly conserved function of SVP in the two completely different species. Thus, we have validated a conserved machinery wherein SVP relies on TPL to inhibit flowering through the direct regulation of FT, which is more meaningful for the evolution of species and could be translated to high-quality cultivation and breeding of crops.

plant biology↗

bioRxiv2021

iEnhancer-CLA: Self-attention-based interpretable model for enhancers and their strength prediction

Enhancer is a class of non-coding DNA cis-acting elements that plays a crucial role in the development of eukaryotes for their transcription. Computational methods for predicting enhancers have been developed and achieve satisfactory performance. However, existing computational methods suffer from experience-based feature engineering and lack of interpretability, which not only limit the representation ability of the models to some extent, but also make it difficult to provide interpretable analysis of the model prediction findings.In this paper, we propose a novel deep-learning-based model, iEnhancer-CLA, for identifying enhancers and their strengths. Specifically, iEnhancer-CLA automatically learns sequence 1D features through multiscale convolutional neural networks (CNN), and employs a self-attention mechanism to represent global features formed by multiple elements (multibody effects). In particular, the model can provide an interpretable analysis of the enhancer motifs and key base signals by decoupling CNN modules and generating self-attention weights. To avoid the bias of setting hyperparameters manually, we construct Bayesian optimization methods to obtain model global optimization hyperparameters. The results demonstrate that our method outperforms existing predictors in terms of accuracy for identifying enhancers and their strengths. Importantly, our analyses found that the distribution of bases in enhancers is uneven and the base G contents are more enriched, while the distribution of bases in non-enhancers is relatively even. This result contributes to the improvement of prediction performance and thus facilitates revealing an in-depth understanding of the potential functional mechanisms of enhancers. Author summaryThe enhancers contain many subspecies and the accuracy of existing models is difficult to improve due to the small data set. Motivated by the need for accurate and efficient methods to predict enhancer types, we developed a self-attention deep learning model iEnhancer-CLA, the aim is to be able to distinguish effectively and quickly between subspecies of enhancers and whether they are enhancers or not. The model is able to learn sequence features effectively through the combination of multi-scale CNN blocks, BLSTM layers, and self-attention mechanisms, thus improving the accuracy of the model. Encouragingly, by decoupling the CNN layer it was found that the layer was effective in learning the motif of the sequences, which in combination with the self-attention weights could provide interpretability to the model. We further performed sequence analysis in conjunction with the model-generated weights and discovered differences in enhancer and non-enhancer sequence characteristics. This phenomenon can be a guide for the construction of subsequent models for identifying enhancer sequences.

bioinformatics↗

bioRxiv2021

CyanoHABs: inevitable evolutionary ecological consequence for low nutrient-requiring cyanobacteria in water eutrophication

Cyanobacterial harmful algal blooms (CyanoHABs) arise as cyanobacteria dominate phytoplankton communities when nutrient levels increase from oligotrophic state. From a wholistic perspective, this longstanding altered phytoplankton structure results from two conditions: one sufficient condition that cyanobacteria can grow maximally with elevated nutrients; one necessary condition that co-living algae cannot grow fast or dominate at the same levels. The sufficient condition, the special mechanism of CyanoHABs at the population level, has been established as the synergistic interaction between superior cyanobacterial ecophysiology and elevated nutrients. But it is unknown how these functions arise or whether they are under directed evolution to water eutrophication. The necessary condition, the general mechanism of CyanoHABs at the community level, is little understood: why co-living algae cannot form blooms as cyanobacteria? Literature and bioinformatics analyses show that the superior ecophysiology undergoes no directed positive evolution to worldwide eutrophication in general or any local eutrophic waters in particular; instead, these functions are under strong purifying selection and likely acquired through early adaptive radiation in nutrient-deficient conditions, as functions enabling extant cyanobacteria to occupy other niches. The general mechanism turns out to be quite straightforward: cyanobacteria are simple life forms and thus have lower per capita nutrient demand for growth, compared to co-existing eukaryotic algae in cell size and structure, genome size, size of genome-scale metabolic networks, cell content, nutrient requirement. Lower nutrient demand is proved by existing field nutrient supplementation. Both the special and general mechanisms of CyanoHABs are tentative frameworks awaiting further theoretic improvement and empirical assessment.

evolutionary biology↗

bioRxiv2021

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N=10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase (www.facebase.org, doi.org/10.25550/3-HXMC) and GitHub (https://github.com/jaydevine/MusMorph).

genetics↗

bioRxiv2021

The toll-like receptor 7 agonist imiquimod increases ethanol self-administration and induces expression of toll-like receptor related genes

BackgroundThere is growing evidence that immune signaling may be involved in both the causes and consequences of alcohol abuse. Toll-like receptor (TLR) expression is increased by alcohol consumption and is implicated in AUD, and specifically TLR7 may play an important role in ethanol consumption. MethodsWe administered the TLR7-specific agonist imiquimod in male and female Long-Evans rats to determine 1) gene expression changes in brain regions involved in alcohol reinforcement, the nucleus accumbens core and anterior insular cortex, in rats with and without an alcohol history, and 2) whether TLR7 activation could modulate operant alcohol self-administration. ResultsInterferon regulatory factor 7 (IRF7) was dramatically increased in both sexes at both 2 and 24 h post-injection regardless of alcohol history, while TLR3 and 7 gene expression changes were region- and sex-specific. The pro-inflammatory cytokine TNF was increased 24h post-injection in rats with an alcohol self-administration history but this effect did not persist after four injections, suggesting molecular tolerance. In both males and females, ethanol consumption was increased 24 h after imiquimod injections with sex-specific differences: in females this effect emerged following the first injection but in males this increase did not occur until the third injection, suggesting sex differences in adaptation to repeated TLR7 activation. Notably, imiquimod reliably induced weight loss, indicating that sickness behavior persisted across repeated injections. ConclusionThese findings show that TLR7 activation can modulate alcohol drinking in an operant self-administration paradigm, and suggest that TLR7 and IRF7 signaling pathways may be a viable druggable target for treatment of AUD.

neuroscience↗

bioRxiv2021

Remarkable Adsorption Performance of Rutile TiO2 (110) Nanosheet for DNA Nucleobases: A First-Principles Study

The remarkable biocompatibility and supreme physical properties of nanostructured TiO2 have promised itself a strong future for biomedical applications. The present study reported a theoretical study on the adsorption of rutile TiO2 (110) nanosheet for DNA nucleobases using first-principles calculations. The calculations of the binding energy and work function demonstrate that the TiO2 nanosheet has remarkable adsorption strength to the DNA nucleobases, being more than 20 times larger than that of graphene and its derivatives. Further electronic band structure and density of state calculations elucidate the interaction mechanisms, which originate from dramatically reduced energy levels and strong hybridization of the 2p orbital of C, N and/or O with 3d orbital of Ti atoms near the Fermi level. The study directs a promising material at applications in DNA sensors and sequencers.

bioengineering↗

bioRxiv2021

Palaeogenomics reveal a hybrid origin of the world's largest Camelus species

The extinct Camelus knoblochi is known as the largest camel in genus Camelus, but its relationship to modern Camelus species remains unclear. In this study, we reported the first mitochondrial and nuclear analyses of seven Late Pleistocene C. knoblochi samples from Northeastern China. We found that they are inseparable to wild Bactrian camel on the matrilineal side, but belong to a distinct cluster on the biparental nuclear side. Further admixture proportion analyses suggested hybrid ancestry between both the ancestors of the modern wild and domesticated Bactrian camels, with ~65% contribution from the former and ~35% from the later. By calculating the coalescence time for three Camelus species above, we estimated the hybridization event occurred between approximately 0.8 and 0.33 Ma. We also used Bayesian skyline to reconstruct the maternal demographic trajectories for different Camelus to better compare their evolutionary histories. Our results provide molecular insights into C. knoblochi and fill in a vital piece in understanding the genus Camelus.

molecular biology↗

bioRxiv2021

Metabolomic and transcriptomic analyses reveal the effects of grafting on anthocyanin synthesis in grapevine

The grafting has been commonly used in viticulture, which joints the scion from a cultivar with the stem of a rootstock. Grafting has crucial impacts on various phenotypes of the cultivar including berry metabolome and berry coloring, however, the genetics and regulation mechanisms are largely unexplored. In this study, we analyzed the phenotypic, metabolomic and transcriptomic profiles at three stages (45, 75 and105 days after flowering) of the Crimson Seedless (Vitis vinifera, CS) cultivar grafted to four rootstocks (three heterografting: CS/101-14MG, CS/SO4, CS/110R and one self-grafting CS/CS) with an own-rooted grafting-free Crimson Seedless (CS) as a control. All the heterografting plants had a significant influence on berry reddening as early as ~45 days after flowering. The grafting of rootstocks promoted anthocyanin synthesis and accumulation in grape berries. The metabolomic features showed that Cyanidin 3-O-glucoside, Delphinidin 3-O-glucosid, Malvidin 3-O-glucoside, Peonidin 3-O-glucoside and Petunidin 3-O-glucoside were the pigments responsible for the purplish-red color peels. Transcriptomic analyses revealed that the anthocyanins biosynthetic related genes from the upstream (phenylalanine ammonia-lyase) to the downstream (anthocyanidin 3-O-glucosyltransferase and anthocyanidin synthase) were upregulated with the accumulations of anthocyanins in CS/101-14MG, CS/SO4 and CS/110R. At the same time, all these genes were also highly expressed and more anthocyanin was accumulated in CS/CS samples compared to CS samples, suggesting that self-grafting rootstocks might also have promoted berry reddening in grapevine. Our results provide global transcriptomic and metabolomic features in berry coloring regulation under different grafting conditions for improving the berry quality in grapevine production.

plant biology↗

bioRxiv2021

Single-cell RNA-seq analysis reveals aberrant CSF1 expression in disease-causing synovial fibroblasts of pigmented villonodular synovitis

ObjectivesAlthough the role of the CSF1/CSF1R axis in pigmented villonodular synovitis (PVNS) has been confirmed, the cells that express CSF1 and CSF1R and the underlying mechanism remain unclear. Single-cell RNA sequencing (scRNA-seq) of PVNS obtained through biopsies depicted the cellular diversity of PVNS, revealed specific CSF1/CSF1R-expressing cells and further identified novel gene expression that is associated with the development of PVNS. MethodsscRNA-seq was performed on tissues obtained from the 6 biopsies of 3 patients with PVNS. Flow cytometry, immunofluorescence and western blot validated the transcriptional results, while co-culture systems revealed the cross talk between fibroblasts and macrophages. Results8 subsets of fibroblasts and 5 subsets of macrophages were identified from the synovium of patients with PVNS and were found to be related to distinct signaling pathways. The cellular components of localized and diffuse PVNS are overall similar. Moreover, the synovium and nodule of PVNS share similar composition. The specific cells expressing CSF1/CSF1R were also identified. Other than that, unique CXCL12+CSF1+ fibroblasts were revealed to attract macrophages as disease-causing synovial fibroblasts, leading to the formation of masses in PVNS. ConclusionsPVNS consists of macrophages, fibroblasts, T cells, endothelial cells and mast cells. Among them, the CSF1-expressing fibroblasts appeared to be tumor-like cells that attract macrophages, subsequently forming tumor-like mass in PVNS. This paves the path for novel treatments of PVNS by targeting CXCL12+CSF1+ fibroblasts and the CXCL12-CXCR4 axis.

molecular biology↗

bioRxiv2021

Inhibition of Kallikrein-related peptidases 7 restrains pancreatic tumor growth through induction of ferroptosis

Pancreatic cancer is one of the most aggressive and lethal malignancies with extremely poor prognosis, and KLK7 was considered as a potential therapeutic target. In this study, we analyzed the expression of KLK7 in TCGA and GTEx databases and found that KLK7 had a negative correlation to long-term survival rate (>1.5 years) of pancreatic cancer patients. Compound 42 is a coumarinic derivative, a suicide substrate inhibitor of KLK7, which has been proved to inhibit the proliferation of PANC-1 cells in vitro effectively in our previous study. In this study, we further investigated the inhibition ability of Compound 42 in tumor formation and development in CDX and PDX tumor models of pancreatic cancer subsequently. Besides, we studied the inhibitory mechanism of Compound 42 and the result showed that Compound 42 arrested the pancreatic cancer cell cycle in G0/G1 phase and induced ferroptosis through down-regulation of GPX4 protein level and accumulation of iron ion. Thus, these experiments demonstrate that Compound 42, suppressing pancreatic cancer in vivo, is expected to become a novel drug for pancreatic cancer treatment.

molecular biology↗

bioRxiv2021

Crotamiton derivative JM03 extends lifespan and improves oxidative and hypertonic stress resistance in Caenorhabditis elegans via inhibiting OSM-9

While screening our in-house 1,072 marketed drugs for their ability to extend the lifespan using Caenorhabditis elegans (C. elegans) as an animal model, crotamiton (N-ethyl-o-crotonotoluidide) showed anti-aging activity and was selected for further structural optimization. After replacing the ortho-methyl of crotamiton with ortho-fluoro, crotamiton derivative JM03 was obtained and showed better activity in terms of lifespan-extension and stress resistance than crotamiton. It was further explored that JM03 extended the lifespan of C. elegans through osmotic avoidance abnormal-9 (OSM-9). Besides, JM03 improves the ability of nematode to resist oxidative stress and hypertonic stress through OSM-9, but not osm-9/capsaicin receptor related-2 (OCR-2). Then the inhibition of OSM-9 by JM03 reduces the aggregation of Q35 in C. elegans via upregulating the genes associated with proteostasis. SKN-1 signaling was also found to be activated after JM03 treatment, which might contribute to proteostasis, stress resistance and lifespan extension. In summary, this study explored a new small molecule derived from crotamiton, which has efficient anti-oxidative, anti-hypertonic and anti-aging effects, and could further lead to promising application prospects.

cell biology↗

bioRxiv2021

Ancient genomes redate the extinction of Sussemionus, a subgenus of Equus, to late Holocene

The exceptionally-rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses and zebras represent three extant subgenus of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in Pleistocene. We sequenced 26 archaeological specimens from northern China in Holocene showing morphological features reminiscent of Equus ovodovi, a species representative of Sussemionus, and further confirmed them as this species by genetic analyses. Thus, we present the first high-quality complete genome of the Sussemionus that we sequenced to 12.0x depth-of-coverage and demonstrate that it survived until [~]3,500 years ago, despite the continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree, and found Sussemionus diverged from the ancestor of non-caballine equids [~]2.3-2.7 Million years ago and admixture events could have taken place between them. Our works suggest the small genetic diversity but not the enhanced inbreeding mainly limited the chances of survival of the species, and illustrates how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.

genomics↗

bioRxiv2021

Azacytidine targeting SARS-CoV-2 viral RNA as a potential treatment for COVID-19

The COVID-19 pandemic is a global health disaster. Moreover, emerging mutated virus strains present an even greater challenge for existing vaccines and medications. One possible solution is to design drugs based on the properties of virus epigenome, which are more common among coronaviruses. Here, we reported an FDA-approved drug for myelodysplastic syndrome, azacytidine (5Aza), limited virus infection and protected mice against SARS-CoV-2. We demonstrated that this antiviral effect is related to 5Aza incorporation into viral RNA, which disrupt m5C RNA methylation modification profile. This work suggests that targeting viral epigenomes is a viable therapeutic strategy, potentially opening new pathways for treating COVID-19.

microbiology↗

bioRxiv2021

DNA as a Recyclable Natural Polymer

Nature has the ability of circularly re-using its components to produce molecules and materials it needs. An example is the ability of most living organisms of digesting proteins they feed off into amino acids and then using such amino acids in the ribosomal synthesis of new proteins. Recently, we have shown that such recycling of proteins can be reproduced outside living organisms. The key proteins feature that allows for this type of recycling is their being sequence-defined polymers. Arguably, Natures most famous sequence-defined polymer is DNA. Here we show that it is possible starting from sheared calf-DNA to obtain all the four nucleotides as monophosphate-nucleotides (dNMPs). These dNMPs were phosphorylated in a one-pot, multi-enzymes, phosphorylation reaction to generate triphosphate-nucleotides (dNTPs). Finally, we used the dNTPs so achieved (with a global yield of [~]60%) as reagents for PCR (polymerase chain reaction) to produce target DNA strands, and for the diagnose of targeted DNA by quantitative PCR (qPCR). This approach is an efficient, convenient, and environmentally friendly way to produce dNTPs and DNA through recycling according to the paradigm of circular economy.

biochemistry↗