Biology subjects

Meng, H.

Publications and source records attributed to Meng, H..

47 records · Page 3Linked to original sources

bioRxiv2022

DeepTracer ID: De Novo Protein Identification from Cryo-EM Maps

The recent revolution in cryo-electron microscopy has made it possible to determine macromolecular structures directly from cell extracts. However, identifying the correct protein from the cryo-EM map is still challenging and often needs additional sequence information from other techniques, such as tandem mass spectrometry and/or bioinformatics. Here, we present DeepTracer-ID, a server-based approach to identify the candidate protein in a user-provided organism de novo from a cryo-EM map, without the need for additional information. Our method first uses DeepTracer to generate a protein backbone model that best represents the cryo-EM map, and this model is then searched against the library of AlphaFold2 predictions for all proteins in the given organism. This method is highly accurate and robust: in all 13 experimental maps tested blindly, DeepTracer-ID identified the correct proteins as the top candidates. Eight of the maps were of known structures, while the other five unpublished maps were validated by prior protein annotation and careful inspection of the model refined into the map. The program also showed promising results for both homomeric and heteromeric protein complexes. This platform is possible because of the recent breakthroughs in large-scale protein 3D structure prediction. Statement of SignificanceWhile it has now become routine for cryo-EM maps of proteins to reach a near-atomic resolution, potentially allowing for reliable atomic models to be built, there are a growing number of instances where the protein identity may not be known. Without knowing the protein sequence, it is impossible to build an atomic model. DeepTracer-ID is a server-based approach to surmount this problem by identifying the proteins in a given organism that are found in the cryo-EM map. A free web service for global academic access is provided.

biophysics↗

bioRxiv2022

Compaction of Drosophila histoblasts in a crowded epidermis is driven by buckling of their apical junctions

The polygonal shape of cells in proliferating epithelia is a result of the tensile forces of the cytoskeletal cortex and packing geometry set by the cell cycle1, 2. In the larval Drosophila epidermis, two cell populations, histoblasts and larval epithelial cells, compete for space as they grow on a limited body surface. They do so in the absence of cell divisions. We report a striking morphological transition of histoblasts during larval development, where they change from a tensed network configuration with straight cell outlines at the level of adherens junctions to a highly folded morphology. The apical surface of histoblasts shrinks while their growing adherens junctions fold, forming deep lobules. Volume increase of growing histoblasts is accommodated basally, compensating for the shrinking apical area. The folded geometry of apical junctions resembles elastic buckling, and we show that the imbalance between the shrinkage of the apical domain of histoblasts and the continuous growth of junctions triggers buckling. Our model is supported by laser dissections and optical tweezer experiments together with computer simulations. Our analysis pinpoints the ability of histoblasts to store mechanical energy to a much greater extent than most other epithelial cell types investigated so far, while retaining the ability to dissipate stress on the hours time scale. Finally, we propose a possible mechanism for size regulation of histoblast apical size through the lateral pressure of the epidermis, driven by the growth of cells on a limited surface. Buckling effectively compacts histoblasts at their apical plane and may serve to avoid physical harm to these adult epidermis precursors during larval life. Our work indicates that in growing non-dividing cells, compressive forces, instead of tension, may drive cell morphology.

developmental biology↗

bioRxiv2022

Adaptive scans allow targeted cell-ablations on curved cell sheets

The mechanical actuation of cells by active forces from the cytoskeleton drives tissue morphogenesis. To understand these forces, multicellular laser dissection has become an essential tool for severing tissue locally and inferring tension from the recoil of surrounding structures. However, conventional laser dissection is limited by 2D steering, which is inadequate for embryos and developing tissues that are intrinsically 3D structures. In this study, we introduce a flexible near-infrared (NIR) fs-pulsed laser dissection system that allows for dissection trajectories to proceed in 3D and adapt to the curved surfaces of cell sheets, which are prominent structures in embryos. Trajectories are computed through an unsupervised search for the surface of interest. Using this technique, we demonstrate sectioning of multicellular domains on curved tissue, which was not possible with regular NIR laser scanning. We apply the developed strategy to map mechanical stresses in the imaginal disc of the developing Drosophila wing. Our targeted, adaptive scans can be used in other non-linear processes, such as two-photon fluorescence imaging or optogenetics. Overall, this new laser dissection system offers an innovative solution for studying complex 3D structures and their mechanical properties.

biophysics↗

bioRxiv2022

Core Transcription Programs Controlling Injury-Induced Neurodegeneration of Retinal Ganglion Cells

Neurodegenerative diseases are characterized by neuronal death and regenerative failure. However, gene regulatory programs governing how initial neuronal injuries lead to neuronal death remain poorly understood. In adult mice, optic nerve crush (ONC) injury, which severs all axons of retinal ganglion cells (RGCs), results in massive death of axotomized RGCs and regenerative failure of survivors. We performed an in vivo CRISPR/Cas9-based genome-wide screen of 1893 transcription factors (TFs) to seek repressors of RGC survival and axon regeneration following ONC. In parallel, we profiled the epigenetic and transcriptional landscapes of injured RGCs by ATAC-seq and RNA-seq to identify critical injury responsive TFs and their targets. Remarkably, these independent analyses converged on a set of four ATF/CEBP transcription factors - ATF3, ATF4, C/EBP{gamma} and CHOP (Ddit3) - as critical regulators of survival. Further studies indicate that these TFs contribute to two pro-death transcriptional programs: ATF3/CHOP preferentially regulate pathways activated by cytokines and innate immunity, whereas ATF4/C/EBP{gamma} regulate pathways engaged by intrinsic neuronal stressors. Manipulation of these TFs also protects RGCs in an experimental model of glaucoma, a prevalent disease in which RGCs die. Together, our results reveal core transcription programs that transform an initial axonal insult into a degenerative result and suggest novel strategies for treating neurodegenerative diseases.

neuroscience↗

bioRxiv2021

The Immune Signatures Data Resource: A compendium of systems vaccinology datasets

Vaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems immunology combines traditional immunology with modern omic profiling techniques and computational modeling to promote rapid and transformative advances in vaccinology and vaccine discovery. The NIH/NIAID Human Immunology Project Consortium (HIPC) has leveraged systems immunology approaches to identify molecular signatures associated with the immunogenicity of many vaccines, including those targeting seasonal influenza, yellow fever, and hepatitis B. These data are made available to the broader scientific community through the ImmuneSpace data portal and analysis engine leveraging the NIH/NIAID ImmPort repository1,2. However, a barrier to progress in this area is that comparative analyses have been limited by the distributed nature of some data, potential batch effects across studies, and the absence of multiple relevant studies from non-HIPC groups in ImmPort. To support comparative analyses across different vaccines, we have created the Immune Signatures Data Resource, a compendium of standardized systems vaccinology datasets. This data resource is available through ImmuneSpace, along with code to reproduce the processing and batch normalization starting from the underlying study data in ImmPort and the Gene Expression Omnibus (GEO). The current release comprises 1405 participants from 53 cohorts profiling the response to 24 different vaccines and includes transcriptional profiles and antibody response measurements. This novel systems vaccinology data release represents a valuable resource for comparative and meta-analyses that will accelerate our understanding of mechanisms underlying vaccine responses. [Table 1]

systems biology↗

bioRxiv2020

Genomic Evidence for the Chinese Mountain Cat as a Wildcat Conspecific (Felis silvestris bieti) and Its Introgression to Domestic Cats

The enigmatic Chinese mountain cat, endemic to the Qinghai-Tibet Plateau, has a controversial taxonomic status, whether a true species or conspecific with the wildcat (Felis silvestris) and whether it may have contributed to the domestication of cats (F. s. catus) in Asia. Here, we sampled 270 domestic and wild cats across China, sequenced 51 nuclear genomes, 55 mitogenomes, and multi-locus regions from modern and museum specimens. Genome-wide phylogenies supported taxonomic classification of the Chinese mountain cat as wildcat subspecies, F. s. bieti. No involvement of F. s. bieti in cat domestication in East Asia was detected, confirming that domestic cats shared a single origin from the African wildcat (F. s. lybica). A complex hybridization scenario including ancient introgression from the Asiatic wildcat (F. s. ornata) to F. s. bieti, and contemporary gene flow between F. s. bieti and sympatric domestic cats in the Tibetan region, raises the prospect of disrupting the genetic integrity of F. s. bieti, an issue with profound conservation implications.

evolutionary biology↗

bioRxiv2020

Sex dependent compensatory mechanisms to preserve blood pressure homeostasis in PGI2 receptor deficient mice

Inhibitors of microsomal prostaglandin E synthase-1 (mPges-1) are in the early phase of clinical development. Deletion of mPges-1 confers analgesia, restrains atherogenesis and fails to accelerate thrombogenesis, while suppressing prostaglandin (PG) E2, but increasing biosynthesis of prostacyclin (PGI2). In hyperlipidemic mice, this last effect represents the dominant mechanism by which mPges-1 deletion restrains thrombogenesis, while suppression of PGE2 accounts for its anti-atherogenic effect. However, the impact of mPges-1 depletion on blood pressure (BP) in this setting remains unknown. To address how differential effects on PGE2 and PGI2 might modulate salt-evoked BP responses in the absence of mPges-1, we generated mice lacking the I prostanoid (Ipr) receptor or mPges-1 on a hyperlipidemic background caused by deletion of the low density lipoprotein receptor (Ldlr KOs). Here, mPges-1 depletion significantly increased the BP response to salt loading in male Ldlr KO mice, whereas, despite the direct vasodilator properties of PGI2, Ipr deletion suppressed it. Furthermore, combined deletion of the Ipr abrogated the exaggerated BP response in male mPges-1 KO mice. Suppression of PGE2 biosynthesis was enough to explain the exaggerated BP response to salt loading by either mPges-1/Ldlr depletion or by an MPGES-1 inhibitor in mice expressing human mPGES-1. However, the lack of a hypertensive response to salt in Ipr-deficient mice was attributable to reactive activation of the atrial natriuretic peptide pathway. Interestingly, these unexpected BP phenotypes were not observed in female mice fed a high salt diet. This is attributable to the protective effect of estrogen in Ldlr KO mice and in Ipr /Ldlr DKOs. Thus, estrogen compensates for a deficiency in PGI2 to maintain BP homeostasis in response to high salt in hyperlipidemic female mice. In males, by contrast, augmented formation of ANP plays a similar compensatory role, restraining hypertension and oxidant stress in the setting of Ipr depletion. Hyperlipidemic males on a high salt diet might be at risk of a hypertensive response to mPGES-1 inhibitors.

pharmacology and toxicology↗

bioRxiv2019

Seasonal Variability and Shared Molecular Signatures of Inactivated Influenza Vaccination in Young and Older Adults

The seasonal influenza vaccine is an important public health tool but is only effective in a subset of individuals. The identification of molecular signatures provides a mechanism to understand the drivers of vaccine-induced immunity. Most previously reported molecular signatures of influenza vaccination were derived from a single age group or season, ignoring the effects of immunosenescence or vaccine composition. Thus, it remains unclear how immune signatures of vaccine response change with age across multiple seasons. Here we profile the transcriptional landscape of young and older adults over five consecutive vaccination seasons to identify shared signatures of vaccine response as well as marked seasonal differences. Along with substantial variability in vaccine-induced signatures across seasons, we uncovered a common transcriptional signature 28 days post-vaccination in both young and older adults. However, gene expression patterns associated with vaccine-induced antibody responses were distinct in young and older adults; for example, increased expression of Killer Cell Lectin Like Receptor B1 (KLRB1; CD161) 28 days post-vaccination positively and negatively predicted vaccine-induced antibody responses in young and older adults, respectively. These findings contribute new insights for developing more effective influenza vaccines, particularly in older adults.

immunology↗

bioRxiv2019

Landscape and regulation of m6A and m6Am methylome across human and mouse tissues

N6-methyladenosine (m6A), the most abundant internal mRNA modification, and N6,2-O-dimethyladenosine (m6Am), found at the first-transcribed nucleotide, are two examples of dynamic and reversible epitranscriptomic marks. However, the profiles and distribution patterns of m6A and m6Am across different human and mouse tissues are poorly characterized. Here we report the m6A and m6Am methylome through an extensive profiling of 42 human tissues and 16 mouse tissue samples. Globally, the m6A and m6Am peaks in non-brain tissues demonstrates mild tissue-specificity but are correlated in general, whereas the m6A and m6Am methylomes of brain tissues are clearly resolved from the non-brain tissues. Nevertheless, we identified a small subset of tissue-specific m6A peaks that can readily classify the tissue types. The number of m6A and m6Am peaks are partially correlated with the expression levels of their writers and erasers. In addition, the m6A- and m6Am-containing regions are enriched for single nucleotide polymorphisms. Furthermore, cross-species analysis of m6A and m6Am methylomes revealed that species, rather than tissue types, is the primary determinant of methylation. Collectively, our study provides an in-depth resource for dissecting the landscape and regulation of the m6A and m6Am epitranscriptomic marks across mammalian tissues.

molecular biology↗

bioRxiv2019

12h-clock control of central dogma information flow by XBP1s

Our group recently discovered a cell-autonomous mammalian 12h-clock regulating physiological unfolded protein response. Xbp1s ablation impairs 12h-transcript oscillations in vitro, and we now show liver-specific deletion of XBP1s globally impaired murine 12h-transcriptome, but not the circadian rhythms in vivo. XBP1s-dependent 12h-transcriptome is enriched for transcription, mRNA processing, ribosome biogenesis, translation, and protein ER-Golgi processing/sorting in a temporal order consistent with the progressive molecular processing sequence described by the central dogma information flow (CEDIF). The 12h-rhythms of CEDIF are cell-autonomous and evolutionarily conserved in circatidal marine animals. Mechanistically, we found the motif stringency of promoter XBP1s binding sites, but not necessarily XBP1s expression, dictates its ability to drive 12h-rhythms of transcription and further identified GABP as putative novel transcriptional regulator of 12h-clock. We hypothesize the 12h-rhythms of CEDIF allows rush hours gene expression and processing, with the particular genes processed at each rush hour regulated by circadian and/or tissue specific pathways.

systems biology↗

bioRxiv2018

Whole-tree heartwood inducing technique for Dalbergia odorifera

The dried heartwood of Dalbergia odorifera is a very important traditional Chinese medicine. In nature, D. odorifera heartwood forms slowly over several decades, and excessive harvesting has caused large-scale reductions of its wild populations. To date, there have been no studies on artificial methods to induce heartwood formation in trees that have not already begun producing heartwood. We have published a patent for a whole-tree heartwood inducing technique for D. odorifera (the \"Dodor-Wit\" method); here, we describe and analyze its efficacy. Trees in four plantations in China were treated using this method. After two years, in 2016 and 2017, they were harvested and analyzed. Average heartwood yield per tree was 3,161.95 g. Heartwood induction rate (dry heartwood weight to total dry trunk weight after peeling) was 21.60%. Average volatile oil content per tree was 1.42%. Alcohol-soluble extract of the induced heartwood was 15.77%, exceeding the Chinese Pharmacopoeia standard. This is the first report on the Dodor-Wit method and heartwood induction in D. odorifera trees aged 5-8 years. The heartwood induced by Dodor-Wit satisfies the requirements of the Chinese Pharmacopoeia. The Dodor-Wit method has an important role in solving the extreme scarcity of Chinese medicinal herbs.

plant biology↗