Biology subjects

Gao, Y.

Publications and source records attributed to Gao, Y..

At least 361 records · Page 20Linked to original sources

bioRxiv2023

Urinary protein changes during the short-term growth and development of rats

Can the urine proteome reflect short-term changes in the growth and development of animals? Do short-term developmental effects on urinary protein need to be considered when performing urine marker studies using model animals with faster growing periods? In this study, urine samples were collected from 10 Wistar rats aged 6-8 weeks 3 and 6 days apart. The results showed that the urine proteome could sensitively reflect short-term growth and development in rats. For example, comparing the urine proteome of Day 0 and Day 6, 195 differential proteins were identified after screening (FC [≥] 1.5 or [≤] 0.67, P < 0.05), and verified by randomization, the average number of randomly generated differential proteins was 17.99. At least 90.77% of the differential proteins were not randomly generated. This finding demonstrates that the differential proteins identified in the samples collected at different time points were not randomly generated. A large number of biological processes and pathways related to growth and development were enriched, which shows that the urine proteome reflects the short-term growth and development of rats, and provides a means for in-depth and meticulous study of growth and development. Moreover, an interfering factor in animal experiments using 6-to 8-week-old rats to construct models was identified. The results of this study demonstrated that there were differences in the urinary proteome in rats aged 6-8 weeks only 3-6 days apart, which suggests that the sensitivity of urinary proteomics is high and shows the sensitive and precise response of the urinary proteome to body changes.

biochemistry↗

bioRxiv2023

Shortcut barcoding and early pooling for scalable multiplex single-cell reduced-representation CpG methylation sequencing at single nucleotide resolution

DNA methylation is essential for a wide variety of biological processes, yet the development of a highly efficient and robust technology remains a challenge for routine single-cell analysis. We developed a multiplex scalable single-cell reduced representation bisulfite sequencing (msRRBS) technology with off-the-shelf reagents and equipment. It allows cell-specific barcoded DNA fragments of individual cells to be pooled before bisulfite conversion, free of enzymatic modification or physical capture of the DNA ends, and achieves unparalleled read mapping rates of 62.51%, covering 59.95% of CpG islands and 71.62% of promoters in K562 cells on average. Its reproducibility is shown in duplicates of bulk cells with near perfect correlation (R=0.97-99). At a low 1 Mb of clean reads, msRRBS provides consistent coverage of CpG islands and promoters, outperforming the conventional methods with orders of magnitude reduction in cost. Here, we use this method to characterize the distinct methylation patterns and cellular heterogeneity of 6 cell lines, and leukemia and hepatocellular carcinoma models. Taking 4 hours of hands-on time, msRRBS offers a unique, highly efficient approach for dissecting methylation heterogeneity in a variety of multicellular systems.

genomics↗

bioRxiv2023

Cardiomyocyte-specific deletion of PTP1B protects against HFD-induced cardiomyopathy through direct regulation of cardiac metabolic signaling

BackgroundHeart failure is the number one cause of death worldwide and mortality is directly correlated with the high incidence of obesity and diabetes. Indeed, the epidemic phenomenon of obesity was projected to reach 50% in the US by the year 2030. However, the mechanisms linking metabolic dysfunction with heart disease are not clear. Protein Tyrosine Phosphatase 1B (PTP1B), a negative regulator of insulin signaling, is considered to be an emerging therapeutic target against the development of obesity, insulin resistance, and diabetes. Increased PTP1B levels and activity have been observed in brain, muscle and adipose tissues isolated from obese and/or diabetic animals, as well as in human obese human patients. Its role, however, and the mechanisms by which it modulates metabolic processes in the heart remain unknown. Method and ResultsWe generated cardiomyocyte (CM)-specific PTP1B knock-out (PTP1Bfl/fl::MHCCre/+) mice to investigate the cardiomyocyte-specific role of PTP1B in response to high fat diet (HFD)-induced cardiac dysfunction. While we did not observe any physiological or functional cardiac differences at baseline, in response to HFD, we found that PTP1Bfl/fl::MHCCre/+ mice were protected against development of cardiac hypertrophy, mitochondrial dysfunction, and diminished cardiac steatosis. Metabolomics data revealed that hearts with CM-specific deletion of PTP1B had increased fatty acid oxidation and NAD+ metabolism, but reduced glucose metabolism; we further validated these findings by real-time qPCR analysis. Mechanistically, we identified a novel PTP1B PKM2-AMPK axis in the heart, which acts as a molecular switch to promote fatty acid oxidation. In this regard, we identified that hearts from PTP1Bfl/fl::MHCCre/+ mice had upregulated levels of nicotinamide adenine dinucleotide (NAD+) and NAD phosphate (NADPH), leading to higher levels of nicotinamide phosphoribosyl transferase (NAMPT), the rate-limiting step of the NAD+ salvage pathway and an enzyme associated with obesity and diabetes. ConclusionsTogether, these results suggest that CM-specific deletion of PTP1B mediates a substrate switch from glucose to fatty acid metabolism, protecting hearts against development of HFD-induced cardiac hypertrophy and dysfunction through mechanisms involving a novel PTP1B/PKM2/AMPK axis that is critical for the regulation of NAMPT and NAD+ biosynthesis.

molecular biology↗

bioRxiv2023

Transcriptome mining of RNA viruses (family Totiviridae) in Eimeria necatrix and Eimeria stiedai

Coccidian protozoa from the genus Eimeria are widespread parasites of vertebrates, causing serious disease (coccidiosis) and economic loss most notably in poultry. Several species of Eimeria are themselves infected with small RNA viruses assigned to the family Totiviridae. In this study, the sequences of two such viruses were newly determined, one of which represents the first complete protein-coding sequence of a virus from E. necatrix, an important pathogen of chickens, and the other of which is from E. stiedai, an important pathogen of rabbits. Sequence features of the newly identified viruses, compared with those of ones reported previously, provide several insights. Phylogenetic analyses suggest that these eimerian viruses constitute a well-demarcated clade, probably deserving of recognition as a distinct genus.

microbiology↗

bioRxiv2023

CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli

Hydrogen sulfide (H2S), mainly produced from L-cysteine (Cys), renders bacteria highly resistant to oxidative stress. This mitigation of oxidative stress was suggested to be an important survival mechanism to achieve antimicrobial resistance (AMR) in many pathogenic bacteria. CyuR (known as DecR or YbaO) is a recently characterized Cys-dependent transcription regulator, responsible for the activation of the cyuAP operon and generation of hydrogen sulfide from Cys. Despite its potential importance, the regulatory network of CyuR remains poorly understood. In this study, we investigated the roles of the CyuR regulon in a Cys-dependent AMR mechanism in E. coli strains. We found: 1) Cys metabolism has a significant role in AMR and its effect is conserved in many E. coli strains, including clinical isolates; 2) CyuR negatively controls the expression of mdlAB encoding a transporter that exports antibiotics such as cefazolin and vancomycin; 3) CyuR binds to a DNA sequence motif GAAwAAATTGTxGxxATTTsyCC in the absence of Cys, confirmed by an in vitro binding assay; and 4) CyuR may regulate 25 additional genes as suggested by in silico motif scanning and transcriptome sequencing. Collectively, our findings expanded the understanding of the biological roles of CyuR relevant to antibiotic resistance associated with Cys.

systems biology↗

bioRxiv2023

Bacterial Cytochrome P450-catalyzed Post-translational Macrocyclization

Bacterial cytochrome P450s represent an emerging enzyme family that can modify ribosomally synthesized peptides to generate structurally complex macrocyclic skeletons. However, the functional sequence space of this type of enzyme is largely unexplored. In this study, we conduct a systematic genome mining of small ribosomal peptide-tailoring P450s from genomes of actinobacteria via a precursor-centric, primary sequence-, and structure-guided strategy. We uncovered 1,957 putative P450s, prioritized two representative families for functional study, and characterized two P450 enzymes that can respectively catalyze Tyrosine-to-Tryptophan and Tryptophan-to-Tryptophan crosslinks to form 3-mer or 4-mer macrocycle. These two P450 enzymes exhibit broad substrate selectivity, suggesting a promising starting template for engineering unnatural cyclic peptide construction. Our work expanded the enzymatic catalysis of P450s and could inspire the community to discover hidden peptide-modifying enzymes.

biochemistry↗

bioRxiv2023

Dynamic cell differentiation in multicellularity with specialized cell types

The specialization of cells is a hallmark of complex multicellularity. Cell differentiation enables the emergence of specialized cell types that carry out separate functions previously executed by a multifunctional ancestor cell. One view is that initial cell differentiation occurred randomly, especially for genetically identical cells, exposed to the same life history environment. How such a change in differentiation probabilities can affect the evolution of differentiation patterns is still unclear. We develop a theoretical model to investigate the effect of stage-dependent cell differentiation - cells change their developmental trajectories during a single round of development via cell divisions - on the evolution of optimal differentiation patterns. We found that irreversible differentiation - a cell type gradually losing its differentiation capability to produce other cell types - is more favored under stage-dependent than stage-independent cell differentiation in relatively small organisms with limited differentiation probability variations. Furthermore, we discovered that irreversible differentiation of germ cells, which is the gradual loss of germ cells ability to differentiate, is a prominent pattern among irreversible differentiation patterns under stage-dependent cell differentiation. In addition, large variations in differentiation probabilities prohibit irreversible differentiation from being the optimal differentiation pattern. Author summaryThe differentiation of cells into different branches is a characteristic feature of multicellular organisms. To understand its origin, the mechanism of division of labour was proposed, where cells are specialized at distinct tasks. In previous models, a cell type is usually assumed to produce another cell type with a fixed probability which is referred to as stage-independent differentiation. However, it has been argued that cell differentiation is a dynamic process in which cells possess changing differentiation capabilities during the different stages of an organisms development. Stage-dependent differentiation exhibits more diverse patterns of development than differentiation with fixed probabilities, thus it can lead to novel targets of selection. How does stage-dependent differentiation impact the evolution of optimal differentiation patterns compared with stage-independent one? To address this question, we built a stage-dependent cell differentiation model and classified differentiation patterns based on the cells differentiation capability in their last cell division. We investigate how stage-dependent differentiation probabilities impact the evolution of the optimal differentiation pattern, which acts on the fitness of an organism. As we take the growth rate as a proxy of an organisms fitness, we seek the "optimal strategy" that leads to the fastest growth. Our numerical results show that irreversible differentiation which gradually loses its differentiation capability, is favored over stage-independent differentiation in small organisms. Meanwhile, irreversible differentiation wont be optimal when there are no constraints on the changes of stage-dependent differentiation probabilities between successive cell divisions.

evolutionary biology↗

bioRxiv2023

Abnormal homeostasis of P53 gene knockout mice can be reflected in urinary proteome

In this experiment, the urinary proteome analysis of p53 knockout mice at four relatively early time points before death was performed from three dimensions. One was to compare the differential proteins screened by homozygote and heterozygote at the same time point; the other was to compare the differential proteins screened by homozygote and wild-type as well as heterozygote and wild-type at the same time point; the third was to compare the differential proteins screened by homozygote and heterozygote before and after each time point, and to screen the differential proteins of three mice by self-control analysis and screening. Later, enrichment analysis of the differential proteins was performed mainly by Metascape and String, and disease association analysis of gene or variant genotype-phenotype with the help of DisGeNET and Monarch. We found that the biological pathways mainly related to metabolism were most abundant, and at the same time abnormal homeostasis, cancer and tumor, cardiovascular diseases, and neurodegenerative diseases appeared. However, under the analysis of Monarch, homozygotes or heterozygotes contained abnormal homeostasis at all time points, and most of them ranked the first or at least the top, while all timepoints in the growth and development of each normal rat were not enriched to abnormal homeostasis and other disease pathways.

biochemistry↗

bioRxiv2023

Spatiotemporal transcriptome atlas of human embryos after gastrulation

The spatial and temporal atlas of gene expression in the human embryo at early gestation is critical in understanding embryo development, organogenesis, and disease origins. We obtained the spatiotemporal transcriptome from 90 sagittal sections of 16 whole human embryos from 3 to 8 post-conception weeks by Stereo-seq with high resolution and ultra-large field, establishing the development trajectory/regulatory profiling of 49 organs. We uncovered the organ-specific regulons as potential lineage-determining factors and identified the new regulatory networks during heart and brain development. The atlas refines the key organs/cell types vulnerable to virus infection and genetic disorders, and, reveals the dynamics of allelic gene expression in specific organs at different stages. These results present the first comprehensive delineation of the spatiotemporal transcriptomic dynamics of human organogenesis. One Sentence SummaryThe spatiotemporal transcriptome atlas presents a comprehensive delineation of human embryogenesis after gastrulation.

developmental biology↗

bioRxiv2023

Reply to: The pitfalls of negative data bias for the T-cell epitope specificity challenge

Predicting and identifying TCR-antigen pairings accurately presents a significant computational challenge within the field of immunology. The negative sampling issue is important T-cell specificity modeling and it is known clearly by the community that different negative data sampling strategy will influence the prediction results. Therefore, proper negative data sampling strategy should be carefully selected, and this is exactly what PanPep has noticed, emphasized and performed. Now we would like to clarify this point further by formulating this problem as a PU learning. Our findings suggest that the reshuffling strategy may generate potential false negative samples, which can adversely affect model training and result in biased model testing for PanPep. Furthermore, a proper comparison between different negative sampling strategies should be performed in a consistent way to make a proper conclusion. Finally, future updating to explore more possible and suitable negative sampling strategy is expected.

bioinformatics↗

bioRxiv2023

Sterile Soil as Prebiotics Mitigate Intergenerational Loss of Gut Microbial Diversity and Anxiety-Like Behavior Induced by Antibiotics in mice

The decline in gut microbial diversity of modern human is closely associated with the rising prevalence of various diseases. It is imperative to investigate the underlying causes of gut microbial loss and the rescue measures. Although the impact of non-perinatal antibiotic use on gut microbiota has been recognized, its intergenerational effects remain unexplored. Our previous research has highlighted soil in the farm environment as a key prebiotic for gut microbiome health by restoring gut microbial diversity and balance. In this study, we investigated the intergenerational consequences of antibiotic exposure and the therapeutic potential of soil prebiotics. We treated mice with vancomycin and streptomycin for 2 weeks continuously, followed by 4-8 weeks of withdrawal period before breeding. The process was repeated across 3 generations. Half of the mice in each generation received an oral soil prebiotic intervention. We assessed gut microbial diversity, anxiety behavior, microglia reactivity, and gut barrier integrity across generations. The antibiotics exposure led to a decrease in gut microbial diversity over generations, along with aggravated anxiety behavior, microglia abnormalityies, and altered intestinal tight junction protein expression. Notably, the third generation of male mice exhibited impaired reproductive capacity. Oral sterile soil intervention restored gut microbial diversity in adult mice across generations, concomitantly rescuing abnormalities in behavior, microglia activity, and intestinal barrier integrity. In conclusion, this study simulated an important process of the progressive loss gut microbiota diversity in modern human and demonstrated the potential of sterile soil as a prebiotic to reverse this process. The study provides a theoretical and experimental basis for the research and therapeutic interventions targeting multiple modern chronic diseases related to intestinal microorganisms.

microbiology↗

bioRxiv2023

Interspecies blastocyst complementation generates functional rat cell-derived forebrain tissues in mice

Interspecies organogenesis via blastocyst complementation provides a unique platform to study development in an evolutionarily context and holds potential to overcome world-wide organ shortages1. By using this technique, rat pancreas, thymus, heart, and eye tissues have been generated in mice2-4. To date, however, xeno-generation of brain tissues has not been achieved through blastocyst complementation. Here, we developed an optimized one-step blastocyst complementation strategy based on C-CRISPR5, which facilitated rapid screening of candidate genes to support blastocyst complementation. Among the seven WNT pathway-related genes selected for targeting, only Dkk1 or Hesx1 deficiency supported forebrain complementation by blastocyst injection of mouse embryonic stem cells (mESCs). Further, injecting rat ESCs (rESCs) into mouse blastocysts deficient for Hesx1 but not Dkk1 supported the development of adult chimeric forebrains comprised a large proportion of rat cells that were structurally and functionally similar to the mouse forebrains. Our analysis revealed that the rESC-derived forebrains developed along the spatial-temporal trajectory with the mouse forebrains rather than rat forebrains, but gene expression profiles of rESC-derived nerve cells surprisingly maintained the characteristics of the rat cells. We noted that the chimeric rate gradually decreased as development progressed, suggesting xenogeneic barriers during mid-to-late prenatal development. Interspecies forebrain complementation opens the door for studying evolutionarily conserved and divergent mechanisms underlying brain development and cognitive function. The C-CRIPSR based IBC strategy developed here holds great potential to broaden the study and application of interspecies organogenesis.

developmental biology↗

bioRxiv2023

Chemo-phosphoproteomic profiling with ATR inhibitors berzosertib and gartisertib uncovers new biomarkers and DNA damage response regulators

The ATR kinase protects cells against DNA damage and replication stress and represents a promising anti-cancer drug target. The ATR inhibitors (ATRi) berzosertib and gartisertib are in clinical trials for treatment of advanced solid tumours as monotherapy or in combination with genotoxic agents. However, the pharmacodynamic ATR biomarker phospho-CHK1 has shown limited sensitivity in for quantitative assessment of ATR activity in clinical trials. Therefore, better biomarkers are needed, and with this in mind we carried out quantitative phospho-proteomic screening for ATR biomarkers that are highly sensitive to berzosertib and gartisertib. Screening identified novel ATR-dependent targets in three broad classes: i) targets whose phosphorylation is highly sensitive to ATRi; ii) novel targets with known genome maintenance roles; iii) novel targets whose cellular roles are unclear, including SCAF1. We show that SCAF1 interacts with RNAPII in a phospho-dependent manner and suppresses homologous recombination in cells lacking the BRCA1 tumour suppressor. Taken together these data reveal potential new ATR biomarkers and new genome maintenance factors.

biochemistry↗

bioRxiv2023

Early microbial intervention reduces diarrhea while improves later milk production in newborn calves

The rumen of neonatal calves is not well-developed and exhibits limited functionality. Therefore, the establishment of intestinal microbiota may play an instrumental role in their health and performance, but it has been rarely explored. Thus, we aim to explore the temporal colonization of the gut microbiome and the potential benefits of early microbial intervention in newborn calves. We followed up on the temporal dynamics of the gut microbiome and plasma metabolome in 36 newborn calves during the first two months of life and established their relationships with their health status and performance. We also evaluated whether microbiota transplantation (MT) could influence their phenotypes by modulating metabolism and its impact on later milk production performance.We showed that the composition and ecological interactions of the gut microbiome are likely to reach maturity one month after birth. Temporal changes in the gut microbiome of newborn calves are widely associated with changes in their physiological statuses, such as growth and fiber digestion. Importantly, we observed that MT reshapes the gut microbiome of newborns by altering the abundance and interaction of Bacteroides species, as well as amino acid pathways, such as arginine biosynthesis. Two-year follow-up of those calves further showed that MT improves their later milk production. Notably, MT improves fiber digestion, antioxidant capacity of newborns while reducing diarrhea. MT also contributes to significant changes in the metabolomic landscape, and with putative causal mediation analysis, we suggest that altered gut microbial composition in newborns may influence physiological status through microbial-derived metabolites. The data from the study may help develop strategies to manipulate the gut microbiota during early life, which may be significantly relevant to the health and production of newborn calves. HIGHLIGHTSO_LIThe gut microbial composition and ecological interaction in newborn calves reach maturity one month after birth C_LIO_LITemporal shifts in the gut microbiome of newborn calves are associated with phenotypic changes, including growth, digestion, and antioxidative capacity C_LIO_LIEarly microbial intervention in newborn calves reduces diarrhea while improving later milk production C_LIO_LIThe gut microbial impact on newborn calves is mediated by plasma metabolites C_LI

microbiology↗

bioRxiv2023

Bayesian Inference for Brain Source Imaging with Joint Estimation of Structured Low-rank Noise

The inverse problem in brain source imaging is the reconstruction of brain activity from non-invasive recordings of electroencephalography (EEG) and magnetoencephalography (MEG). One key challenge is the efficient recovery of sparse brain activity when the data is corrupted by structured noise that is low-rank noise. This is often the case when there are a few active sources of environmental noise and the MEG/EEG sensor noise is highly correlated. In this paper, we propose a novel robust empirical Bayesian framework which provides us a tractable algorithm for jointly estimating a low-rank noise covariance and brain source activity. Specifically, we use a factor analysis model for the structured noise, and infer a sparse set of variance parameters for source activity, while performing Variational Bayesian inference for the noise. One key aspect of this algorithm is that it does not require any additional baseline measurements to estimate the noise covariance from the sensor data. We perform exhaustive experiments on both simulated and real datasets. Our algorithm achieves superior performance as compared to several existing benchmark algorithms.

bioengineering↗

bioRxiv2023

Time-resolved cryo-EM of G protein activation by a GPCR

G protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by stimulating the exchange of guanine nucleotide in the G subunit. To visualize this mechanism, we developed a time-resolved cryo-EM approach that examines the progression of ensembles of pre-steady-state intermediates of a GPCR-G protein complex. Using variability analysis to monitor the transitions of the stimulatory Gs protein in complex with the {beta}2-adrenergic receptor ({beta}2AR) at short sequential time points after GTP addition, we identified the conformational trajectory underlying G protein activation and functional dissociation from the receptor. Twenty transition structures generated from sequential overlapping particle subsets along this trajectory, compared to control structures, provide a high-resolution description of the order of events driving G protein activation upon GTP binding. Structural changes propagate from the nucleotide-binding pocket and extend through the GTPase domain, enacting alterations to G Switch regions and the 5 helix that weaken the G protein-receptor interface. Molecular dynamics (MD) simulations with late structures in the cryo-EM trajectory support that enhanced ordering of GTP upon closure of the alpha-helical domain (AHD) against the nucleotide-bound Ras-homology domain (RHD) correlates with irreversible 5 helix destabilization and eventual dissociation of the G protein from the GPCR. These findings also highlight the potential of time-resolved cryo-EM as a tool for mechanistic dissection of GPCR signaling events.

physiology↗

bioRxiv2023

A laser capture microdissection transcriptome of M. truncatula roots responding to rhizobia reveals spatiotemporal tissue expression patterns of genes involved in nodule signaling and organogenesis

We report a public resource for examining the spatiotemporal RNA expression of 54,893 M. truncatula genes during the first 72 hours of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of over 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response data set generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of ACC synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division.

plant biology↗

bioRxiv2023

Urine proteomic characterization of active and recovered COVID-19 patients

BackgroundThe molecular changes in COVID-19 patients have been reported in many studies. However, there were limited attention has been given to the disease sequelae in the recovered COVID-19 patients. MethodsHere, we profiled the urine proteome of a cohort of 29 COVID-19 patients in their disease onset and recovery period, including mild, severe, and fatal patients and survivors who recovered from mild or severe symptoms. ResultsThe molecular changes in the COVID-19 onset period suggest that viral infections, immune response changes, multiple organ damage, cell injury, coagulation system changes and metabolic changes are associated with COVID-19 progression. The patients who recovered from COVID-19 still exhibited an innate immune response, coagulation system changes and central nervous system changes. We also proposed four potential biomarkers to monitor the whole progression period of COVID-19. ConclusionsOur findings provide valuable knowledge about the potential molecular pathological changes and biomarkers that can be used to monitor the whole period of COVID-19.

biochemistry↗