Biology subjects

Fang, Q.

Publications and source records attributed to Fang, Q..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Large-scale genome analyses provide insights into Hymenoptera evolution

The order Hymenoptera includes a large number of species with diverse lifestyles and is known for its significant contributions to natural ecosystems. To better understand the evolution of this diverse order, we performed large-scale comparative genomics on 131 species from 13 superfamilies, covering most representative groups. We used these genomes to reveal an overall pattern of genomic change in terms of gene content and evolutionary rate throughout hymenopteran history. We identified genes that possibly contributed to the evolution of several key innovations, such as parasitoidism, wasp-waist, sting, and secondary phytophagy. We also discovered the distinct genomic trajectories between the clade containing major parasitoid wasps (Parasitoida) and stinging species (Aculeata) since their divergence, which are involved in many aspects of genomic change, such as rapidly evolving gene families, gene gain and loss, and metabolic pathway evolution. In addition, we explored the genomic features accompanying the three independent evolution of secondary phytophagy. Our work provides insights for understanding genome evolution and the genomic basis of diversification in Hymenoptera.

genomics↗

bioRxiv2024

The phylogenetic position of the Yunxian cranium elucidates the origin of Dragon Man and the Denisovans

Diverse Middle Pleistocene forms of Homo coexisted in Africa, Europe, and Asia, and its controversial whether these fossil humans represent different species or clades. The [~]1 Ma old Yunxian 2 fossil from China is crucial for understanding the cladogenesis of Homo and the origin of Homo sapiens. Here, we restored and reconstructed the distorted Yunxian 2 cranium using new technology. The results show that this cranium displays mosaic features of plesiomorphy and apomorphy. Geometric-morphometric, phylogenetic and Bayesian tip-dating analyses including the reconstructed Yunxian 2 suggest that it is an early member of the Asian Homo longi clade, which probably includes the Denisovans, and is the sister group to the Homo sapiens clade. Both the H. sapiens and H. longi clades had deep roots extending beyond the Middle Pleistocene, and the basal position of the Yunxian fossil cranium suggests that it represents a population lying close to the last common ancestor of the two clades. One-Sentence SummaryThe newly-reconstructed Yunxian 2 cranium represents a basal member of the Homo longi and Denisovan clade, and probably lies close to the last common ancestor of that clade and the clade of H. sapiens.

evolutionary biology↗

bioRxiv2024

The transcripts of a gastrula-premarked enhancer prime posterior tissue development through cross-talk with morphogen effector

The regulatory mechanisms governing cell fate determination, particularly lineage diversification during mammalian embryonic development, remain poorly understood with in-depth regulatory paradigms yet to be fully elucidated. Here, leveraging the epigenetic landscape of mouse gastrula, we identified p-Enh, a pre-marked enhancer in primitive streak region, as pivotal regulator for posterior tissue development in mouse embryos. Morphological and single-cell transcriptomic analyses confirmed embryonic lethality phenotype with disrupted posterior tissue development trajectories in p-Enh-KO embryos. Molecularly, apart from regulating the neighboring coding-gene Cdx2 in cis, our findings suggest that p-Enh also modulate the global transcriptome and epigenomic landscape, which might through the transient production of eRNA in trans. Further investigation revealed p-Enh participate in the regulatory cascades of TGF-{beta} signaling. Chemical modulation of TGF-{beta} signaling can largely rescue the posterior development deficiency in in vitro gastruloids through a Cdx2-independent mechanism. Thus, we propose a potential model in which the broadly distributed p-Enh transcripts within the nucleus could serve as essential cross-modular coordinators, priming the posterior development of mouse embryo.

developmental biology↗

bioRxiv2024

TRIP12 governs DNA Polymerase β involvement in DNA damage response and repair

The multitude of DNA lesion types, and the nuclear dynamic context in which they occur, present a challenge for genome integrity maintenance as this requires the engagement of different DNA repair pathways. Specific repair controllers that facilitate DNA repair pathway crosstalk between double strand break (DSB) repair and base excision repair (BER), and regulate BER protein trafficking at lesion sites, have yet to be identified. We find that DNA polymerase {beta} (Pol{beta}), crucial for BER, is ubiquitylated in a BER complex-dependent manner by TRIP12, an E3 ligase that partners with UBR5 and restrains DSB repair signaling. Here we find that, TRIP12, but not UBR5, controls cellular levels and chromatin loading of Pol{beta}. Required for Pol{beta} foci formation, TRIP12 regulates Pol{beta} involvement after DNA damage. Notably, excessive TRIP12-mediated shuttling of Pol{beta} affects DSB formation and radiation sensitivity, underscoring its precedence for BER. We conclude that the herein discovered trafficking function at the nexus of DNA repair signaling pathways, towards Pol{beta}-directed BER, optimizes DNA repair pathway choice at complex lesion sites. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/588474v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@70c5bdorg.highwire.dtl.DTLVardef@1c60dfborg.highwire.dtl.DTLVardef@1c00ef6org.highwire.dtl.DTLVardef@1677f2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Deep learning modeling of ribosome profiling reveals regulatory underpinnings of translatome and interprets disease variants

Gene expression involves transcription and translation. Despite large datasets and increasingly powerful methods devoted to calculating genetic variants effects on transcription, discrepancy between mRNA and protein levels hinders the systematic interpretation of the regulatory effects of disease-associated variants. Accurate models of the sequence determinants of translation are needed to close this gap and to interpret disease-associated variants that act on translation. Here, we present Translatomer, a multimodal transformer framework that predicts cell-type-specific translation from mRNA expression and gene sequence. We train Translatomer on 33 tissues and cell lines, and show that the inclusion of sequence substantially improves the prediction of ribosome profiling signal, indicating that Translatomer captures sequence-dependent translational regulatory information. Translatomer achieves accuracies of 0.72 to 0.80 for de novo prediction of cell-type-specific ribosome profiling. We develop an in silico mutagenesis tool to estimate mutational effects on translation and demonstrate that variants associated with translation regulation are evolutionarily constrained, both within the human population and across species. Notably, we identify cell-type-specific translational regulatory mechanisms independent of eQTLs for 3,041 non-coding and synonymous variants associated with complex diseases, including Alzheimers disease, schizophrenia, and congenital heart disease. Translatomer accurately models the genetic underpinnings of translation, bridging the gap between mRNA and protein levels, and providing valuable mechanistic insights toward mapping "missing regulation" in disease genetics.

genomics↗

bioRxiv2024

NELF coordinates Pol II transcription termination and DNA replication initiation

Regulation of RNA polymerase II (Pol II) transcription is closely associated with cell proliferation. However, it remains unclear how the Pol II transcription program is altered in cancer to favour cell growth. Here, we find that gene expression of NELFCD, a known negative elongation factor, is up-regulated in colorectal tumours. To dissect the direct role of NELF-C on Pol II transcription in such cancer, we employed an auxin-dependent protein degradation system for NELF-C in combination with nascent transcript sequencing technologies. Strikingly, we demonstrated that the acute loss of NELF-C protein globally perturbs Pol II transcription termination and also increases transcription elongation rate, independently of promoter-proximal Pol II pausing. This results in Pol II transcription into DNA replication initiation zones, and may link to failure of the cell cycle transition into S phase. We anticipate that NELF will be a potential therapeutic target to restrict colorectal cancers by promoting transcription-replication conflict. HIGHLIGHTSO_LIExpression of NELFCD transcript is up-regulated in colorectal tumors C_LIO_LINELF-C protein is mandatory for the transition between G1-S phases during cell cycle C_LIO_LINELF-C loss impairs transcription termination independently of Pol II promoter-proximal pausing C_LIO_LINELF-C loss leads Pol II to invade DNA replication initiation zones C_LI

molecular biology↗

bioRxiv2024

Genomic signatures of the evolution of loss of egg yolk in parasitoid wasps

Trait regression and loss have occurred repeatedly in numerous lineages throughout evolutionary history in response to changing environments. In parasitoid wasps, a mega-diverse group of hymenopteran insects, loss or reduction of yolk in the egg has been reported in many species. This phenotypic change likely evolved as a response to the shift from ectoparasitism to endoparasitism. However, the genetic basis of this trait and the impact of its loss on genome evolution remain poorly understood. Here, we performed a comparative genomic analysis of 64 hymenopteran insects. The conserved insect yolk protein gene vitellogenin (Vg) underwent five independent loss events in four families, involving 23 of the analyzed endoparasitoid species. Whole-genome alignment suggested that Vg loss occurred during genome rearrangement events. Analysis of Vg receptor gene (VgR) loss, selection, and structural variation in lineages lacking Vg demonstrated functional biases in the patterns of gene loss. The ectoparasitism to endoparasitism transition did not appear to be the primary driver of Vg loss or the subsequent VgR evolution. A number of parallel and convergent genomic changes were observed between Vg-loss lineages, including gene family evolution and selection of genes related to transport, development, and metabolism. These changes may have facilitated embryonic development without the yolk in these lineages. Together, these findings reveal the genomic basis underlying a unique trait loss in parasitoid wasps. More broadly, this study enhances our understanding of yolk loss evolution outside the class Mammalia, highlighting a potential evolutionary trend arising from the availability of an alternative nutrient source for embryonic development.

evolutionary biology↗

bioRxiv2023

Wide-field Intensity Fluctuation Imaging

The temporal intensity fluctuations contain important information about the light source and light-medium interaction and are typically characterized by the intensity autocorrelation function, g2({tau}). The measurement of g2({tau}) is a central topic in many optical sensing applications, ranging from stellar intensity interferometer in astrophysics, to fluorescence correlation spectroscopy in biomedical sciences and blood flow measurement with dynamic light scattering. Currently, g2({tau}) at a single point is readily accessible through high-frequency sampling of the intensity signal. However, two-dimensional widefield measurement of g2({tau}) is still limited by camera frame rates. We propose and demonstrate a 2-pulse within-exposure modulation approach to break through the camera frame rate limit and obtain the quasi g2({tau}) map in wide field with cameras of only ordinary frame rates. HighlightsO_LIThe quasi intensity autocorrelation function can be measured at almost arbitrary time lags C_LIO_LICameras of ordinary frame rates are sufficient for the measurement C_LIO_LIIllumination within the camera exposure is modulated by an acoustic optical modulator using two short pulses C_LI

bioengineering↗

bioRxiv2023

A parasitoid serpin gene that disrupts host immunity shows adaptive evolution of alternative splicing

Alternative splicing (AS) is a major source of protein diversity in eukaryotes, but less is known about its evolution compared to gene duplication (GD). How AS and GD interact is also largely understudied. By constructing the evolutionary trajectory of a serpin gene PpSerpin-1 (Pteromalus puparum serpin 1) in parasitoids and other insects, we found that both AS and GD jointly contribute to serpin protein diversity. These two processes are negatively correlated and show divergent features in both protein and regulatory sequences. Furthermore, parasitoid wasps exhibit higher numbers of serpin protein/domains than nonparasitoids, resulting from more GD but less AS in parasitoids. Nevertheless, PpSerpin-1 shows an exon expansion of AS compared to other parasitoids. We find that several isoforms of PpSerpin-1 are involved in the wasp immune response, have been recruited to both wasp venom and larval saliva, and suppress host immunity. In summary, we report the differential features of AS and GD in the evolution of insect serpins and their associations with the parasitic life strategy, and we provide an example of how a parasitoid serpin gene adapts to parasitism through AS.

evolutionary biology↗

bioRxiv2023

Characterizing Mineral Ellipsoids in New Bone Formation at the Interface of Ti6Al4V Porous Implants

The hierarchy of newly formed bone contains elements of disorder within an ordered multiscale structure, spanning from the macroscale to below the nanoscale. With mineralized structures presenting in the shape of ellipsoids in mature and mineralizing tissue, this work characterizes the heterogeneity in mineral ellipsoid packing at the interface of porous titanium implants. The characterization of mineral at the bone-implant interface offers insight into the osseointegration of titanium implants and the mechanical properties of the interfacial bone tissue. Using scanning transmission electron microscopy and plasma focused ion beam - scanning electron microscopy, mineral ellipsoids are characterized at the implant interface in both 2D and 3D. Heterogeneous in their size and shape within the newly formed bone tissue, ellipsoids are observed with alternating orientations corresponding to unique lamellar packets within 2-3 m of the titanium implant interface - although this motif is not universal, and a mineral-dense zone can also appear at the implant interface. Short-order ellipsoid orientation shifts are also present in the 3D probe of the implant interface, where an approximate 90{degrees} misorientation angle between neighbouring packets of mineral ellipsoid resolves with increasing distance from the titanium, possibly providing a strengthening mechanism to prevent crack propagation in the peri-implant bone. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/524810v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@3c34a1org.highwire.dtl.DTLVardef@a3437borg.highwire.dtl.DTLVardef@a374e1org.highwire.dtl.DTLVardef@14e9572_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Osseointegration of functionally-graded Ti6Al4V porous implants: Histology of the pore network

The additive manufacturing of titanium into porous geometries offers a means to generate low-stiffness endosseous implants with a greater surface area to improve osseointegration. In order to optimize pore size in the scaffolds, it is important to first understand the timeline of osseointegration in pre-clinical models. In this work, selective laser melting was used to produce gyroid-based scaffolds with a uniform pore size of 300 m or functionally-graded pore size from 600 m to 300 m before implantation in New Zealand white rabbit tibiae for 4 and 12 weeks. Initial in vitro assessment with Saos-2 cells showed favourable cell proliferation at pore sizes of 300 and 600 m. At four weeks, histological observations indicated some residual inflammation alongside neovessel infiltration into the scaffold interior and some early apposition of mineralized bone tissue. At twelve weeks, both scaffolds were filled with a mixture of adipocyte-rich marrow, micro-capillaries, and mineralized bone tissue. X-ray microcomputed tomography showed a higher bone volume fraction (BV/TV) and percentage of bone-implant contact (BIC) in the implants with 300 m pores than in the functionally-graded specimens, indicating that these smaller pore sizes may be favourable for osseointegration in leporine bone. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/521963v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@2e319aorg.highwire.dtl.DTLVardef@baa9deorg.highwire.dtl.DTLVardef@e66075org.highwire.dtl.DTLVardef@c6c8c4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

A compact breast shape acquisition system for improving diffuse optical tomography image reconstructions

Diffuse optical tomography (DOT) has been investigated for diagnosing malignant breast lesions but its accuracy relies on model-based image reconstructions which in turn depends on the accuracy of breast shape acquisition. In this work, we have developed a dual-camera structured light imaging (SLI) breast shape acquisition system tailored for a mammography-like compression setting. Illumination pattern intensity is dynamically adjusted to account for skin tone differences while thickness-informed pattern masking reduces artifacts due to specular reflections. This compact system is affixed to a rigid mount that can be installed into existing mammography or parallel-plate DOT systems without the need for camera-projector re-calibration. Our SLI system produces sub-millimeter resolution with a mean surface error of 0.26 mm. This breast shape acquisition system results in more accurate surface recovery, with an average 1.6-fold reduction in surface estimation errors over a reference method via contour extrusion. Such improvement translates to 25% to 50% reduction in mean squared error in the recovered absorption coefficient for a series of simulated tumors 1-2 cm below the skin.

bioengineering↗

bioRxiv2022

Simultaneous transcriptome and proteome profiling in a single mouse oocyte with a deep single-cell multi-omics approach

Nowadays, although single-cell multi-omics technologies are undergoing rapid development, simultaneous transcriptome and proteome analysis of a single-cell individual still faces great challenges. Here, we developed a single-cell simultaneous transcriptome and proteome (scSTAP) analysis platform based on microfluidics, high-throughput sequencing and mass spectrometry technology, to achieve deep and joint quantitative analysis of transcriptome and proteome at the single-cell level for the first time. This platform was applied to analyze single mouse oocytes at different meiotic maturation stages, reaching an average quantification depth of 19948 genes and 2663 protein groups in single mouse oocytes. This reliable quantitative two-omics dataset of single cells provided an important resource for understanding the relationship between the transcriptome and the proteome in cells. Based on the correlation analysis of RNAs and proteins in the same single cell, we demonstrated the expressive heterogeneity of transcriptome and proteome during the cellular biological process. Specially, we analyzed the meiosis regulatory network during oocyte maturation with an unprecedented depth at the single-cell level, and identified 30 transcript-protein pairs as specific oocyte maturational signatures, providing crucial insights into the regulatory features of transcription and translation during oocyte meiotic maturation.

cell biology↗

bioRxiv2022

Evolution of the Growth Hormone Gene Duplication in Passerine Birds

Birds of the order Passeriformes represent the most speciose radiation of land vertebrates, yet the cause or causes of their elevated species richness have not been satisfactorily explained. One potential key adaptation is their sole lineage-specific gene, a duplicate copy of growth hormone (GH), present in all major lineages of passerines, but in no other group of birds. Growth hormone genes plausibly influence extreme life history traits that passerines exhibit, including the shortest embryo-to-fledging developmental period of any avian order. To unravel the implications of this GH duplication, we investigated the molecular evolution of the ancestral avian GH gene (GH or GH1) and the novel passerine GH paralog (GH2), using 497 gene sequences extracted from 342 genomes. Passerine GH1 and GH2 are reciprocally monophyletic, consistent with a single duplication event from a microchromosome onto a macrochromosome in a common ancestor of extant passerines. Additional chromosomal rearrangements have changed the syntenic and potential regulatory context of these genes. Both passerine GH1 and GH2 paralogs display substantially higher rates of nonsynonymous codon change than non-passerine avian GH, suggesting positive selection following duplication. A site involved in signal peptide cleavage is under selection in both paralogs. Other sites under positive selection differ between the two paralogs, but many are clustered in one region of a 3D model of the protein. Both paralogs retain key functional features and are actively but differentially expressed in two major passerine suborders. These phenomena suggest that growth hormone genes may be evolving novel adaptive roles in passerine birds.

molecular biology↗

bioRxiv2022

Interpreting ICT: from Blood Flow to Vascular Network

The inverse correlation time (ICT) is a key quantity in laser speckle contrast imaging (LSCI) measurements. Traditionally, ICT is regarded as a metric of blood flow, such as speed or perfusion. However, we highlight that ICT not only contains important information about blood flow, but also reflects the underlying structure of the vascular network. In the past, ICT has been found to be correlated with vessel diameter. Here, we further report that ICT exhibits a different sensitivity to blood flow depending on vessel orientation. Specifically, ICT is more sensitive to blood flow speed changes in vessels descending from or arising to the tissue surface, compared with those laying parallel to the surface. Those findings shift our understanding of ICT from purely blood flow to a combination of blood flow and vascular network structure. We also develop theories to facilitate the study of vascular networks impact on ICT.

bioengineering↗

bioRxiv2022

Pick-up Single-Cell Proteomic Analysis for Quantifying up to 3000 Proteins in a Tumor Cell

The shotgun proteomic analysis is currently the most promising single-cell protein sequencing technology, however its identification level of [~]1000 proteins per cell is still insufficient for practical applications. Here, we develop a pick-up single-cell proteomic analysis (PiSPA) workflow to achieve a deep identification capable of quantifying up to 3000 protein groups in a tumor cell using the label-free quantitative method. The PiSPA workflow is specially established for single-cell samples mainly based on a nanoliter-scale microfluidic liquid handling robot, capable of achieving single-cell capture, pretreatment and injection under the pick-up operation strategy. Using this customized workflow with remarkable improvement in protein identification, 1804-3349, 1778-3049 and 1074-2487 protein groups are quantified in single A549 cells (n = 37), HeLa cells (n = 44) and U2OS cells (n = 27), respectively. Benefiting from the flexible cell picking-up ability, we study tumor cell migration at the single cell proteome level, demonstrating the potential in practical biological research from single-cell insight.

cancer biology↗

bioRxiv2022

Multifaceted role of RIMBP2 in promoting hearing in murine cochlear hair cells

In peripheral, the mammalian cochlea is a remarkable sensory apparatus, owning to its outer and inner hair cells (OHCs and IHCs) that amplify and transmit auditory signals to the brain, respectively. Rab3-interacting molecular (RIM) binding protein 2 (RIMBP2) is widely expressed in receptor cells and neurons, specifically in the active zones for exocytosis of synaptic vesicles (SVs), but its exact functions in the cochlea are not very well understood. We therefore generated a Rimbp2 knockout mouse model (Rimbp2-/-), which exhibited severely impaired hearing with not only elevated hearing thresholds but also increased latencies and reduced amplitudes in the Wave I of their auditory brainstem responses (ABRs). Consistent with the threshold elevation, we found significant loss of OHCs, likely through apoptosis, in the Rimbp2-/- cochlea. Consistent with changes observed in the ABR Wave I, we found greatly reduced exocytosis, both spontaneously and upon stimulation, in Rimbp2-/- IHCs. Specifically, our patch-clamp analysis on IHCs and postsynaptic spiral ganglion neurons (SGNs) revealed not only reduced readily releasable pool (RRP) of SVs but also reduced sustained release rate, along with complete blockade of fast endocytosis, in Rimbp2-/- IHCs. Lastly, with immunostaining of whole-mounted cochleae, we found that while the number of ribbon synapses in Rimbp2-/- IHCs was unchanged, their localization moved subtly but significantly towards the basal pole of IHCs. Taken together, we uncovered an unexpected role of RIMBP2 for OHC survival and a more extensive role in promoting IHC exocytosis than previously believed.

neuroscience↗

bioRxiv2022

A genetic model for in vivo proximity labeling of the mammalian secretome

Organ functions are highly specialized and interdependent. Secreted factors regulate organ development and mediate homeostasis through serum trafficking and inter-organ communication. Enzyme-catalyzed proximity labeling enables the identification of proteins within a specific cellular compartment. Here, we report a BirA*G3 mouse strain that enables CRE-dependent promiscuous biotinylation of proteins trafficking through the endoplasmic reticulum. When broadly activated throughout the mouse, widespread labeling of proteins was observed within the secretory pathway. Streptavidin affinity purification and peptide mapping by quantitative mass spectrometry (MS) proteomics revealed organ-specific secretory profiles and serum trafficking. As expected, secretory proteomes were highly enriched for signal peptide-containing proteins, highlighting both conventional and non-conventional secretory processes, and ectodomain shedding. Lower-abundance proteins with hormone-like properties were recovered and validated using orthogonal approaches. Hepatocyte-specific activation of BirA*G3 highlighted liver-specific biotinylated secretome profiles. The BirA*G3 mouse model demonstrates enhanced labeling efficiency and tissue specificity over viral transduction approaches and will facilitate a deeper understanding of secretory protein interplay in development, and healthy and diseased adult states.

cell biology↗