Biology subjects

Hu, Y.

Publications and source records attributed to Hu, Y..

At least 343 records · Page 19Linked to original sources

bioRxiv2023

Dynamics of the epigenetic landscape during development and in response to drought stress in sorghum

Sorghum bicolor is a C4 plant with the characteristics of high stress tolerance, which may be conferred partly by the underlying epigenetic mechanism unique to sorghum. In this study, we revealed some epigenomic features in sorghum that have never been reported before. The long H3K27me3 regions clustered in four areas, which we defined as H3K27me3 islands, were identified in sorghum. H3K36me3 plays some role in inhibiting the deposition of both H3K27me3 and H2A.Z, which may serve as partial motivation for the removal of H3K27me3 and H2A.Z in leaf and root. All the 7 histone marks are involved in the regulation of tissue-specific genes, especially the specific expression of C4 genes in leaf and peroxidase (POD) encoding genes in root, which are involved in the photosynthesis in leaf and lignin synthesis in root, respectively. These marks except H3K36me3 and H3K27me3 also engage in the regulation of stress genes in response to PEG treatment. However, we found that differential enrichment of histone marks on many tissue-specific genes was observed only between leaf and root but hardly in response to PEG treatment, although expression of these genes changed after PEG treatment.

plant biology↗

bioRxiv2023

Liproxstatin-1 alleviates cartilage degradation by inhibiting chondrocyte ferroptosis in temporomandibular joint

Ferroptosis contribute to temporomandibular joint osteoarthritis (TMJOA) lesion development is still poorly understood. In this study, we used different TMJOA animal models to detect whether ferroptosis is related to onset of TMJOA which modelling by monosodium iodoacetate (MIA), IL-1{beta}, occlusion disorder (OD) and unilateral anterior crossbite (UAC). Immunohistochemical staining and Western blot analysis were used to detect ferroptosis proteins and cartilage degradation related protein expression. Our results revealed that lower level of ferroptosis-related proteins GPX4 in cartilage layer, but the level of ACSL4 and P53 increase in that of condyle. Injection of ferroptosis inhibitor liproxstatin-1 (Lip-1) effectively decrease ACSL4, P53 and TRF expression. In vitro, IL-1{beta} induced the reduction of cartilage extracellular matrix expression in mandibular condylar chondrocytes (MCCs). Lip-1 maintain the morphology and function of mitochondria, and inhibited the aggravation of lipid peroxidation and reactive oxygen species (ROS) production which induced by IL-1{beta}. These results suggested that chondrocytes ferroptosis play an important role in the development and progression of TMJOA. Inhibition of condylar chondrocyte ferroptosis could be a promising therapeutic strategy for TMJOA. SUMMARY STATEMENTFerroptosis contributed the development and progression of Temporomandibular Joint Osteoarthritis cartilage degeneration. Lip-1 can effective improvement the cartilage degradation of condyle.

cell biology↗

bioRxiv2023

Toleration of Frameshift Mutations in mRNA Sequences Encoding the N-terminal Peptides of Bacterial Type III Effectors

Gram-negative bacteria deliver effector proteins into eukaryotic host cells through type III and type IV secretion systems, causing infections and diseases. It remains unclear about the signals guiding the specific secretion of the effectors. Here, we adopted an in silico approach to analyze the mRNA sequences encoding the putative peptides essential for effective secretion and translocation of type III and IV effectors. A surprisingly high proportion of type III effectors showed tolerance on frameshift mutations in signal-encoding mRNA sequences, and in contrast, very low percentage of type IV effectors showed the similar frameshift tolerance. The type III effectors with frameshift tolerance of secretion signals were widely distributed in effector or signal families and bacterial species. Natural frameshifts could be identified in type III effector genes, which were often remedied in time by nearby paired insertions or deletions. Frameshift-derived peptide sequences also retained the common properties present in the signal peptides of raw type III effectors. Natural language processing models were adopted to represent the common features in the mRNA sequences encoding N-terminal peptides of type III effectors or C-terminal peptides of type IV effectors, with which transfer learning models could well predict the effectors, especially type IV effectors. The observations in the study would facilitate us understand the nature and evolution of secretion signals of type III and IV effectors. SignificanceIt has been a debate on the nature of signals for translocation of type III secreted effectors for a long time. Meanwhile, there has been no examination on the possibility of mRNA being as translocation signals for type IV or other types of secreted effectors. By computational simulation, the study demonstrated the protein nature of translocation signals for both type IV effectors and most type III effectors. Despite wide frameshift tolerance and atypical common features in mRNA sequences encoding the putative N-terminal signal sequences of type III effectors, more typical common physicochemical and amino acid composition properties between the mutation-derived and raw peptides, and the frequent self-correction phenomenon for naturally happening frameshifts supported the translocation signals at protein level of type III effectors. The common features in mRNA sequences encoding the translocation signal peptides of type III and IV effectors could also be combined in models for better prediction of the effectors respectively.

microbiology↗

bioRxiv2023

Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements

Cis-regulatory elements control gene expression and are dynamic in their structure, reflecting changes to the composition of diverse effector proteins over time1-3. Here we sought to connect the structural changes at cis-regulatory elements to alterations in cellular fate and function. To do this we developed PRINT, a computational method that uses deep learning to correct sequence bias in chromatin accessibility data and identifies multi-scale footprints of DNA-protein interactions. We find that multi-scale footprints enable more accurate inference of TF and nucleosome binding. Using PRINT with single-cell multi-omics, we discover wide-spread changes to the structure and function of candidate cis-regulatory elements (cCREs) across hematopoiesis, wherein nucleosomes slide, expose DNA for TF binding, and promote gene expression. Activity segmentation using the co-variance across cell states identifies "sub-cCREs" as modular cCRE subunits of regulatory DNA. We apply this single-cell and PRINT approach to characterize the age-associated alterations to cCREs within hematopoietic stem cells (HSCs). Remarkably, we find a spectrum of aging alterations among HSCs corresponding to a global gain of sub-cCRE activity while preserving cCRE accessibility. Collectively, we reveal the functional importance of cCRE structure across cell states, highlighting changes to gene regulation at single-cell and single-base-pair resolution.

genomics↗

bioRxiv2023

Cell-type specific EWAS identifies genes involved in HIV pathogenesis andoncogenesis among people with chronic HIV infection

Epigenome-wide association studies (EWAS) of heterogenous blood cells have identified CpG sites associated with chronic HIV infection, which offer limited knowledge of cell-type specific methylation patterns associated with HIV infection. Applying a computational deconvolution method validated by capture bisulfite DNA methylation sequencing, we conducted a cell type-based EWAS and identified differentially methylated CpG sites specific for chronic HIV infection among five immune cell types in blood: CD4+ T-cells, CD8+ T-cells, B cells, Natural Killer (NK) cells, and monocytes in two independent cohorts (Ntotal=1,134). Differentially methylated CpG sites for HIV-infection were highly concordant between the two cohorts. Cell-type level meta-EWAS revealed distinct patterns of HIV-associated differential CpG methylation, where 67% of CpG sites were unique to individual cell types (false discovery rate, FDR <0.05). CD4+ T-cells had the largest number of HIV-associated CpG sites (N=1,472) compared to any other cell type. Genes harboring statistically significant CpG sites are involved in immunity and HIV pathogenesis (e.g. CX3CR1 in CD4+ T-cells, CCR7 in B cells, IL12R in NK cells, LCK in monocytes). More importantly, HIV-associated CpG sites were overrepresented for hallmark genes involved in cancer pathology (FDR<0.05) (e.g. BCL family, PRDM16, PDCD1LGD, ESR1, DNMT3A, NOTCH2). HIV-associated CpG sites were enriched among genes involved in HIV pathogenesis and oncogenesis such as Kras-signaling, interferon- and -{gamma}, TNF-, inflammatory, and apoptotic pathways. Our findings are novel, uncovering cell-type specific modifications in the host epigenome for people with HIV that contribute to the growing body of evidence regarding pathogen-induced epigenetic oncogenicity, specifically on HIV and its comorbidity with cancers.

cancer biology↗

bioRxiv2023

Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China

Sharing among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 E. coli and S. enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using novel data-mining methods. Most isolates within same hosts possessed same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Machine learning revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials and primarily associated with resistance in Escherichia coli and susceptibility in Salmonella enterica. Many of these genes were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.

genomics↗

bioRxiv2023

Single-Soma Deep RNA sequencing of Human DRG Neurons Reveals Novel Molecular and Cellular Mechanisms Underlying Somatosensation

The versatility of somatosensation arises from heterogeneous dorsal root ganglion (DRG) neurons. However, soma transcriptomes of individual human DRG (hDRG) neurons - critical information to decipher their functions - are lacking due to technical difficulties. Here, we developed a novel approach to isolate individual hDRG neuron somas for deep RNA sequencing (RNA-seq). On average, >9,000 unique genes per neuron were detected, and 16 neuronal types were identified. Cross-species analyses revealed remarkable divergence among pain-sensing neurons and the existence of human-specific nociceptor types. Our deep RNA-seq dataset was especially powerful for providing insight into the molecular mechanisms underlying human somatosensation and identifying high potential novel drug targets. Our dataset also guided the selection of molecular markers to visualize different types of human afferents and the discovery of novel functional properties using single-cell in vivo electrophysiological recordings. In summary, by employing a novel soma sequencing method, we generated an unprecedented hDRG neuron atlas, providing new insights into human somatosensation, establishing a critical foundation for translational work, and clarifying human species-specific properties.

neuroscience↗

bioRxiv2023

Cysteine: an ancestral Cu binding ligand in green algae?

Growth of Chlamydomonas reinhardtii in zinc (Zn) limited medium leads to disruption of copper (Cu) homeostasis, resulting in up to 40-fold Cu over-accumulation relative to its typical Cu quota. We show that Chlamydomonas controls its Cu quota by balancing Cu import and export, which is disrupted in a Zn deficient cell, thus establishing a mechanistic connection between Cu and Zn homeostasis. Transcriptomics, proteomics and elemental profiling revealed that Zn-limited Chlamydomonas cells up-regulate a subset of genes encoding "first responder" proteins involved in sulfur (S) assimilation and consequently accumulate more intracellular S, which is incorporated into L-cysteine, {gamma}-glutamylcysteine and homocysteine. Most prominently, in the absence of Zn, free L-cysteine is increased ~80-fold, corresponding to ~ 2.8 x 109 molecules/cell. Interestingly, classic S-containing metal binding ligands like glutathione and phytochelatins do not increase. X-ray fluorescence microscopy showed foci of S accumulation in Zn-limited cells that co-localize with Cu, phosphorus and calcium, consistent with Cu-thiol complexes in the acidocalcisome, the site of Cu(I) accumulation. Notably, cells that have been previously starved for Cu do not accumulate S or Cys, causally connecting cysteine synthesis with Cu accumulation. We suggest that cysteine is an in vivo Cu(I) ligand, perhaps ancestral, that buffers cytosolic Cu.

biochemistry↗

bioRxiv2023

RNA Sensing and Innate Immunity Constitutes a Barrier for Interspecies Chimerism

Interspecies chimera formation with human pluripotent stem cells (PSCs) holds great promise to generate humanized animal models and provide donor organs for transplant. However, the approach is currently limited by low levels of human cells ultimately represented in chimeric embryos. Different strategies have been developed to improve chimerism by genetically editing donor human PSCs. To date, however, it remains unexplored if human chimerism can be enhanced in animals through modifying the host embryos. Leveraging the interspecies PSC competition model, here we discovered retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) signaling, an RNA sensor, in "winner" cells plays an important role in the competitive interactions between co-cultured mouse and human PSCs. We found that genetic inactivation of Ddx58/Ifih1-Mavs-Irf7 axis compromised the "winner" status of mouse PSCs and their ability to outcompete PSCs from evolutionarily distant species during co-culture. Furthermore, by using Mavs-deficient mouse embryos we substantially improved unmodified donor human cell survival. Comparative transcriptome analyses based on species-specific sequences suggest contact-dependent human-to-mouse transfer of RNAs likely plays a part in mediating the cross-species interactions. Taken together, these findings establish a previously unrecognized role of RNA sensing and innate immunity in "winner" cells during cell competition and provides a proof-of-concept for modifying host embryos, rather than donor PSCs, to enhance interspecies chimerism.

cell biology↗

bioRxiv2023

Distinct activation mechanisms of β-arrestin 1 revealed by 19F NMR spectroscopy

{beta}-Arrestins ({beta}arrs) are functionally versatile proteins that play critical roles in the G-protein-coupled receptor (GPCR) signaling pathways. While the classical theory of GPCR-mediated {beta}arr activation centers around the formation of a stable complex between {beta}arr and the phosphorylated receptor tail, emerging evidences highlight the indispensable contribution from membrane lipids for many receptors. Due to the intrinsic complexity of {beta}arr conformational dynamics, detailed molecular mechanisms of its activation by different binding partners remain elusive. Herein we present a comprehensive study of the structural changes of {beta}arr1 in critical structural regions during activation using 19F NMR method. We demonstrate that phosphopeptides derived from different classes of GPCRs show distinct abilities in inducing {beta}arr1 activation. We further show that the membrane phosphoinositide PIP2 independently modulates {beta}arr1 conformational dynamics without displacing its autoinhibitory carboxyl tail, leading to a distinct partially activated state. Our results delineate two activation mechanisms of {beta}arr1 by different binding partners, uncovering a highly multifaceted conformational energy landscape for this protein family.

biochemistry↗

bioRxiv2023

Atomic resolution structure of a DNA-binding histone protein from the bacterium Bdellovibrio bacteriovorus

Histones are essential for genome compaction and transcription regulation in eukaryotes, where they assemble into octamers to form the nucleosome core. In contrast, archaeal histones assemble into dimers that form hypernucleosomes upon DNA binding. Although histone homologs have been identified in bacteria recently, their DNA-binding characteristics remain largely unexplored. Our study reveals that the bacterial histone HBb (Bd0055) is indispensable for the survival of Bdellovibrio bacteriovorus, suggesting critical roles in DNA organization and gene regulation. By determining crystal structures of free and DNA-bound HBb, we unveil its distinctive dimeric assembly, diverging from those of eukaryotic and archaeal histones, while also elucidating how it binds and bends DNA through interaction interfaces reminiscent of eukaryotic and archaeal histones. Building on this, by employing various biophysical and biochemical approaches, we further substantiated the ability of HBb to bind and compact DNA by bending in a sequence-independent manner. Finally, using DNA affinity purification and sequencing, we reveal that HBb binds along the entire genomic DNA of B. bacteriovorus without sequence specificity. These distinct DNA-binding properties of bacterial histones, showcasing remarkable similarities yet significant differences from their archaeal and eukaryotic counterparts, highlight the diverse roles histones play in DNA organization across all domains of life. SummaryHistones, traditionally known for organizing and regulating DNA in eukaryotes and archaea, have recently been discovered in bacteria, opening up a new frontier in our understanding of genome organization across the domains of life. Our study investigates the largely unexplored DNA-binding properties of bacterial histones, focusing on HBb in Bdellovibrio bacteriovorus. We reveal that HBb is essential for bacterial survival and exhibits DNA-binding properties similar to archaeal and eukaryotic histones. However, unlike eukaryotic and archaeal histones, which wrap DNA, HBb bends DNA without sequence specificity. This work not only broadens our understanding of DNA organization across different life forms but also suggests that bacterial histones may have diverse roles in genome organization.

molecular biology↗

bioRxiv2023

The scale-invariant covariance spectrum of brain-wide activity

Understanding neural activity organization is vital for deciphering brain function. By recording whole-brain calcium activity in larval zebrafish during hunting and spontaneous behaviors, we find that the shape of the neural activity space, described by the neural covariance spectrum, is scale-invariant: a smaller, randomly sampled cell assembly resembles the entire brain. This phenomenon can be explained by Euclidean Random Matrix theory, where neurons are reorganized from anatomical to functional positions based on their correlations. Three factors contribute to the observed scale invariance: slow neural correlation decay, higher functional space dimension, and neural activity heterogeneity. In addition to matching data from zebrafish and mice, our theory and analysis demonstrate how the geometry of neural activity space evolves with population sizes and sampling methods, thus revealing an organizing principle of brain-wide activity.

neuroscience↗

bioRxiv2023

Lower shear stress exacerbates atherosclerosis by inducing the generation of neutrophil extracellular traps via Piezo1-mediated mechanosensation

BACKGROUNDAtherosclerosis is a chronic lipid-driven inflammatory disease, largely influenced by hemodynamics. Neutrophil extracellular traps (NETs)-mediated inflammation plays an important role in atherosclerosis. However, little is known about the mechanism of the generation of NETs under different shear stress and subsequent damage to endothelial cells. We sought to identify a novel mechanical signal provokes NETs generation and to investigate its potential role in atherosclerosis. METHODSApoE-/- mice were fed with high-fat diet (HFD) to induce atherosclerosis. The model of lower shear stress (LSS) with a partial ligation of the left carotid artery was established to assess the role of LSS in NETs generation and atherosclerotic lesions development. Furthermore, the underlying mechanism of LSS promoting NETs generation and injuring endothelial cells was deciphered in neutrophil-like human promyelocytic leukemia (HL-60) cells in parallel-plate flow chamber. RESULTSWe found that LSS correlated spatially with both NETs and atherosclerosis, while inhibition of NETosis could significantly reduce plaque formation in ApoE-/- mice. In vitro, LSS could promote NETs generation directly through down-regulation of Piezo1, a mechanosensitive ion channel. downexpression of Piezol could activate neutrophils and promote NETosis in static. Conversely, Yoda1-evoked activation of Piezo1 attenuated LSS-induced NETosis. Mechanistically, the downexpression of Piezo1 resulted in decreased Ca2+ influx and increased histone deacetylase 2 (HDAC2), which increase reactive oxygen species levels, then led to NETosis. LSS-induced NETs generation promoted the apoptosis and adherence of endothelial cells. CONCLUSIONSLSS directly promotes NETosis through piezo1-HDAC2 axis in atherosclerosis progression. This study uncovers the essential role of Piezo1-mediated mechanical signaling in NETs generation and plaque formation, which provides a promising therapeutic strategy for atherosclerosis. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/529165v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@583911org.highwire.dtl.DTLVardef@aa3e2org.highwire.dtl.DTLVardef@8d83e5org.highwire.dtl.DTLVardef@ce55a0_HPS_FORMAT_FIGEXP M_FIG C_FIG Proposed mechanism for lower shear stress LSS exacerbating atherosclerosis. LSS stimuli decrease Piezo1 expression in the neutrophils, resulting in decreased intracellular Ca2+ concentration, as well as the higher expression level of HDAC2, which could activate oxidative stress and promote intracellular reactive oxygen species formation, and ultimately lead to NETs generation. NETs could aggravate endothelial cells injury and exasperate atherosclerosis. Highlights{blacksquare} Lower shear stress (LSS) promotes Neutrophil extracellular traps (NETs) formation, which is critical for lipid deposits and plaque formation in Atherosclerosis. {blacksquare}Atherosclerotic plaque formation was significantly reduced in the aorta of high fat diet fed ApoE-/- mice intraperitoneal injected with NETs inhibitor, GSK484, especially in the lower shear stress regions. {blacksquare}Piezo1 is a key molecule in the process of neutrophils sense lower shear stress. {blacksquare}lower shear stress inhibits the activation of Piezo1 and promotes NETosis through piezo1-HDAC2 axis. {blacksquare}LSS-induced NETs promote the apoptosis and adhesion of endothelial cells.

cell biology↗

bioRxiv2023

PANGEA: A New Gene Set Enrichment Tool for Drosophila and Common Research Organisms

Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an omics study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualisations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for Drosophila and other major model organisms based on high-quality annotated information available for these species.

bioinformatics↗

bioRxiv2023

Protective effect of plasma neutralization from prior SARS-CoV-2 Omicron infection against BA.5 subvariant symptomatic reinfection

From December 2022 to January 2023, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections caused by BA.5 and BF.7 subvariants of B.1.1.529 (Omicron) swept across mainland China. It is crucial to estimate the protective effect of the neutralizing antibodies generated by such mass infections against the next potential SARS-CoV-2 reinfection wave, especially if driven by CH.1.1 or XBB.1.5. Previously, we recruited and continuously followed a cohort of individuals that experienced Omicron BA.1, BA.2, and BA.5 breakthrough infections, as well as a control cohort with no history of SARS-CoV-2 infection. In the previously uninfected cohort, the total symptomatic infection rate surveyed during the outbreak was 91.6%, while the symptomatic reinfection rate was 32.9%, 10.5%, and 2.8% among individuals with prior Omicron BA.1, BA.2 and BA.5 infection, respectively, with median intervals between infections of 335, 225 and 94 days. Pseudovirus neutralization assays were performed in plasma samples collected from previously Omicron BA.1-infected individuals approximately 3 months before the outbreak. Results indicate a robust correlation between the plasma neutralizing antibody titers and the protective effect against symptomatic reinfection. The geometric mean of the 50% neutralizing titers (NT50) against D614G, BA.5, and BF.7 were 2.0, 2.5, and 2.3-fold higher in individuals without symptomatic reinfection than in those with symptomatic reinfection (p < 0.01). Low plasma neutralizing antibody titer (below the geometric mean of NT50) was associated with an enhanced cumulative risk of symptomatic reinfection, with a hazard ratio (HR) of 23.55 (95% CI: 9.23-60.06) against BF.7 subvariant. Importantly, neutralizing antibodies titers post one month after BF.7/BA.5 breakthrough infections against CH.1.1 and XBB.1.5 are similar to that against BF.7 from individuals with prior BA.1 infection while not experiencing a symptomatic BF.7/BA.5 reinfection (plasma collected 3 months before the outbreak), suggesting that the humoral immunity generated by the current BF.7/BA.5 breakthrough infection may provide protection against CH.1.1 and XBB.1.5 symptomatic reinfection wave for 4 months. Of note, the higher hACE2 binding of XBB.1.5 may reduce the protection period since the potential increase of infectivity.

immunology↗

bioRxiv2023

Impact of experimental bias on compositional analysis of microbiome data

Microbiome data are subject to experimental bias that is caused by DNA extraction, PCR amplification among other sources, but this important feature is often ignored when developing statistical methods for analyzing microbiome data. McLaren, Willis and Callahan (2019) proposed a model for how such bias affects the observed taxonomic profiles, which assumes main effects of bias without taxon-taxon interactions. Our newly developed method, LOCOM (logistic regression for compositional analysis) for testing differential abundance of taxa, is the first method that accounted for experimental bias and is robust to the main effect biases. However, there is also evidence for taxon-taxon interactions. In this report, we formulated a model for interaction biases and used simulations based on this model to evaluate the impact of interaction biases on the performance of LOCOM as well as other available compositional analysis methods. Our simulation results indicated that LOCOM remained robust to a reasonable range of interaction biases. The other methods tended to have inflated FDR even when there were only main effect biases. LOCOM maintained the highest sensitivity even when the other methods cannot control the FDR. We thus conclude that LOCOM outperforms the other methods for compositional analysis of microbiome data considered here.

bioinformatics↗

bioRxiv2023

Omics Analysis Unveils the Pathway Involved in the Purple Coloration in Tomato Seedling and Fruits

The purple tomato variety Indigo Rose(InR) is favored due to its bright appearance and abundant anthocyanins. SlHY5 is associated with anthocyanin biosynthesis in Indigo Rose plants. However, residual anthocyanins still present in Slhy5 seedlings and fruit peel indicated there was an anthocyanin induction pathway that is independent of HY5 in plants. The molecular mechanism of color formation in Indigo Rose and Slhy5 mutants is unclear. In this study, we performed omics analysis to clarify the regulatory network underlying coloration in seedling and fruit peel of Indigo Rose and Slhy5 mutant. Results showed that the total amount of anthocyanins in both seedling and fruit of InR were significantly higher than those in Slhy5 mutant and most genes associated with anthocyanin biosynthesis exhibited higher expression levels in InR, suggesting that SlHY5 play pivotal roles in flavonoid biosynthesis both in tomato seedlings and fruit. Yeast two-hybrid (Y2H) results revealed that SlBBX24 physically interacts with SlAN2-like and SlAN2, while SlWRKY44 could interact with SlAN11 protein. Unexpectedly, both SlPIF1 and SlPIF3 were found to interact with SlBBX24, SlAN1 and SlJAF13 by yeast two-hybrid assay. Suppression of SlBBX24 by virus-induced gene silencing (VIGS) retarded the purple coloration of the fruit peel, indicating an important role of SlBBX24 in the regulation of anthocyanin accumulation. These results deepen the understanding of purple color formation in tomato seedling and fruits in an HY5-dependent or independent manner via excavating the genes involved in anthocyanin biosynthesis based on omics analysis.

molecular biology↗

bioRxiv2023

Unraveling codon usage of Escherichia coli using machine learning

Machine learning is used to investigate the codon usage of protein-encoding genes, which is one of the fundamental questions of molecular biology. The presentation, parameter learning, and decoding of the conditional random field (CRF) model are implemented and then utilized to analyze the codon usage of the genes of Escherichia coli and its phages. Most genes of E. coli use codons conforming to the weights of the model determined by all E. coli genes. Phages use the codons like their host E. coli. Finally, the study evaluates the codon usage of several example genes in the context of the model. These results help to understand the codon usage in E. coli.

systems biology↗