Biology subjects

Ye, K.

Publications and source records attributed to Ye, K..

68 records · Page 4Linked to original sources

bioRxiv2020

A Fast Lysine Cross-linker DOPA Enables Mass Spectrometry Analyses of Protein Unfolding and Weak Protein-protein Interactions

Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) has become a widely used method for protein structure analysis. Central to this technology are chemical cross-linkers. The most popular cross-linkers are N-hydroxysuccinimide (NHS) esters, which react with protein amino groups relatively slowly over 10 minutes or more while in competition with the hydrolysis reaction of NHS esters. To improve the speed of cross-linking, we developed a new class of amine-selective and non-hydrolyzable di-ortho-phthalaldehyde (DOPA) cross-linkers. DOPA can cross-link proteins in 10 seconds under near physiological conditions, which is 60 times faster than the NHS ester cross-linker DSS. DOPA also works at low pH, low temperature, or in the presence of high concentrations of denaturants such as 8 M urea or 6 M guanidine hydrochloride. Further, DOPA-mediated pulse cross-linking captured the dynamic conformational changes associated with RNase A unfolding. Lastly, DOPA outperformed DSS at capturing weak but specific protein-protein interactions.

biochemistry↗

bioRxiv2020

Human cerebrospinal fluids have no microbiome but can contain potential pathogens

Cerebrospinal fluids circulating human central nervous system have long been considered aseptic in healthy individuals, because normally the blood-brain barrier protects against microbial invasions. However, this dogma has been questioned by several reports that microbes were identified in human brains, raising the question whether a microbial community is present in cerebrospinal fluids of healthy individuals without neurological diseases. Here, we collected and analyzed metagenomic and metatranscriptomic sequencing data of cerebrospinal fluid specimens from a cohort of 23 pregnant women aged between 23 and 40 and one-to-one matched contamination controls. From data analysis of 116 specimens of eight different types, we detected 619 nonredundant microbial taxa which were dominated by bacteria (75%) and viruses (24%). In cerebrospinal fluids metagenomic samples, a total of 76 redundant species were detected including four (one nonredundant) eukaryota taxa, eleven (four nonredundant) bacteria, and 61 (21 nonredundant) viruses that were mostly bacteriophages. Metagenomic data analysis found no significant difference between cerebrospinal fluid specimens and negative controls in terms of microbial species diversity. In addition, no active or viable microbiome were present in the cerebrospinal fluid samples after subtracting microbes detected in contamination controls. In conclusion, we found no strong evidence that colonized microbial community exist in the cerebrospinal fluids of healthy individuals. IMPORTANCEMicrobiome are prevalent throughout human bodies with profound health implications. However, it remains unclear whether a microbiome is present and active in human cerebrospinal fluids that are long considered aseptic given the blood-brain barrier. Here, we applied unbiased metagenomic and metatranscriptomic sequencing to detect microbiome in cerebrospinal fluids collected from a cohort of 23 pregnant women with matched controls. By analyzing 116 specimens of eight types, no strong evidence was found to support a presence of colonized microbiome in the cerebrospinal fluids. Our findings have profound implications to human immunity against neurological infections and disorders, providing a guide for disease diagnostics, prevention and therapeutics in clinical settings.

microbiology↗

bioRxiv2020

Cryo-EM structure of yeast 90S preribosome at 3.4 Angstrom resolution

Previously, we determined a cryo-EM structure of Saccharomyces cerevisiae 90S preribosome obtained after depletion of the RNA helicase Mtr4 at 4.5 [A] resolution (Sun et al., 2017). The 90S preribosome is an early assembly intermediate of small ribosomal subunit. Here, the structure was improved to 3.4 [A] resolution and reveals many previously unresolved structures and interactions, in particular around the central domain of 18S rRNA. The central domain adopts a closed conformation in our structure, in contrast to an open conformation in another high-resolution structure of S. cerevisiae 90S. The new model of 90S would serve as a better reference for investigation of the assembly mechanism of small ribosomal subunit.

biophysics↗

bioRxiv2020

Proto-sex locus in large yellow croaker provides insights into early evolution of the sex chromosome

Autosomal origins of heterogametic sex chromosomes have been inferred frequently from suppressed recombination and gene degeneration manifested in incompletely differentiated sex chromosomes. However, the initial transition of an autosome region to a proto-sex locus has been not explored in depth. By assembling and analyzing a chromosome-level draft genome, we found a recent (evolved 0.26 million years ago), highly homologous, and dmrt1 containing sex-determination locus with slightly reduced recombination in large yellow croaker (Larimichthys crocea), a teleost species with genetic sex determination (GSD) and with undifferentiated sex chromosomes. We observed genomic homology and polymorphic segregation of the proto-sex locus between sexes. Expression of dmrt1 showed a stepwise increase in the development of testis, but not in the ovary. We infer that the inception of the proto-sex locus involves a few divergences in nucleotide sequences and slight suppression of recombination in an autosome region. In androgen-induced sex reversal of genetic females, in addition to dmrt1, genes in the conserved dmrt1 cluster, and the rest of the sex determination network were activated. We provided evidence that broad functional links were shared by genetic sex determination and environmental sex reversal.

evolutionary biology↗

bioRxiv2020

TMT-Based Quantitative Proteomic Analysis of Intestinal Organoids Infected by Listeria monocytogenes with Different Virulence

Listeria monocytogenes (Lm) is an opportunistic food-borne pathogen that cause listeriosis. L. monocytogenes belonged to different serovars presents with different virulence in the host and caused different host reactions. To investigate the remodeling of host proteome by differently toxic strains, the cellular protein responses of intestinal organoids were analyzed using TMT labeling and high performance liquid chromatography-mass spectrometry. Quantitative proteomic analysis revealed 6564 differentially expressed proteins, of which 5591 proteins were quantified. The fold-change cutoff was set at 1.3 (Lm vs control), the virulent strain caused 102 up-regulated proteins and 52 down-regulated proteins, while the low virulent strain caused 188 up-regulated proteins and 25 down-regulated proteins. These identified proteins were involved in the regulation of essential processes such as biological metabolism, energy metabolism, and immune system process. Some selected proteins were screened by Real-time PCR and Western blotting. These results revealed that differently toxic L. monocytogenes induced similar biological functions and immune responses while had different regulation on differential proteins in the pathway.

microbiology↗

bioRxiv2020

Chromosome-scale genome assembly of Fusarium oxysporum strain Fo47, a fungal endophyte and biocontrol agent

Here, we report a chromosome-level genome assembly of Fusarium oxysporum strain Fo47 (12 pseudomolecules; contig N50: 4.52Mb), generated using a combination of PacBio long-read, Illumina pair-ended and Hi-C sequencing data. Although F. oxysporum causes vascular wilt to over 100 plant species, the strain Fo47 is classified as an endophyte and widely used as a biocontrol agent for plant disease control. The Fo47 genome carries a single accessory chromosome of 4.23 Mb, compared to the reference genome of F. oxysporum f.sp. lycopersici strain Fol4287. The high-quality assembly and annotation of the Fo47 genome will be a valuable resource for studying the mechanisms underlying the endophytic interactions between F. oxysporum and plants, as well as deciphering the genome evolution of the F. oxysporum species complex.

genomics↗

bioRxiv2020

MSIsensor-pro: fast, accurate and matched-normal-sample-free detection of microsatellite instability

We developed MSIsensor-pro (https://github.com/xjtu-omics/msisensor-pro), an open-source single sample microsatellite instability (MSI) scoring method for research and clinical applications. MSIsensor-pro introduces a multinomial distribution model to quantify polymerase slippages for each tumor sample and a discriminative sites selection method to enable MSI detection without matched normal samples. For samples of various sequencing depths and tumor purities, MSIsensor-pro significantly outperformed the current leading methods in terms of both accuracy and computational cost.

bioinformatics↗

bioRxiv2019

Modularized Transcriptional Regulatory Networks of Fusarium graminearum

The filamentous fungus Fusarium graminearum causes devastating crop disease and produces harmful mycotoxins worldwide. Understanding the complex F. graminearum transcriptional regulatory networks (TRNs) is vital for effective disease management. Reconstructing F. graminearum dynamic TRNs, an NP-hard problem, remains unsolved using commonly adopted reductionist or co-expression based approaches. Multi-omic data such as fungal genomic, transcriptomic data and phenomic data are vital to but so far have been largely isolated and untapped for unraveling phenotype-specific TRNs. Here for the first time, we harnessed these resources to infer global TRNs for F. graminearum using a Bayesian network based algorithm, "module networks". The inferred TRNs contain 49 regulatory modules that show condition-specific gene regulation. Through a robust validation based on prior biological knowledge including functional annotations and TF binding site enrichment, our network prediction displayed high accuracy and concordance with existing knowledge, highlighted by its accurate capture of the well-known trichothecene gene cluster. In addition, we developed a new computational method to calculate the associations between modules and phenotypes, and discovered subnetworks responsible for fungal virulence, sexual reproduction and mycotoxin production. Finally, we found a clear compartmentalization of TRN modules in core and lineage-specific genomic regions in F. graminearum, reflecting the evolution of the TRNs in fungal speciation. This system-level reconstruction of filamentous fungal TRNs provides novel insights into the intricate networks of gene regulation that underlie key processes in F. graminearum pathobiology and offers promise for the development of improved disease control strategies.

microbiology↗

bioRxiv2019

Admixture-enabled selection for rapid adaptive evolution in the Americas

BackgroundAdmixture occurs when previously isolated populations come together and exchange genetic material. We hypothesized that admixture can enable rapid adaptive evolution in human populations by introducing novel genetic variants (haplotypes) at intermediate frequencies, and we tested this hypothesis via the analysis of whole genome sequences sampled from admixed Latin American populations in Colombia, Mexico, Peru, and Puerto Rico.\n\nResultsOur screen for admixture-enabled selection relies on the identification of loci that contain more or less ancestry from a given source population than would be expected given the genome-wide ancestry frequencies. We employed a combined evidence approach to evaluate levels of ancestry enrichment at (1) single loci across multiple populations and (2) multiple loci that function together to encode polygenic traits. We found cross-population signals of African ancestry enrichment at the major histocompatibility locus on chromosome 6, consistent with admixture-enabled selection for enhanced adaptive immune response. Several of the human leukocyte antigen genes at this locus (HLA-A, HLA-DRB51 and HLA-DRB5) showed independent evidence of positive selection prior to admixture, based on extended haplotype homozygosity in African populations. A number of traits related to inflammation, blood metabolites, and both the innate and adaptive immune system showed evidence of admixture-enabled polygenic selection in Latin American populations.\n\nConclusionsThe results reported here, considered together with the ubiquity of admixture in human evolution, suggest that admixture serves as a fundamental mechanism that drives rapid adaptive evolution in human populations.

genomics↗

bioRxiv2019

Lentivirus-mediated long-term overexpression of specific microRNA in mammalian cells

The establishment of a method that would overexpress or suppress of specific microRNA activity is essential for the functional analysis of these molecules and for the development of miRNA therapeutic applications. There already exist excellent ways to inhibit miRNA function in vitro and in vivo by overexpressing miRNA target sequences, which include miRNA decoys, sponges, or antagomirs that are complementary to an miRNA seed region. Conversely, no methods to induce stable gain-of-function phenotypes for specific miRNAs have, as yet, been reported. Furthermore, the discovery of complementary miRNA pairs raises suspicion regarding the existing methods used for miRNA overexpression. In our study, we will study whether the traditional methods for miRNA overexpression can be used for specific miRNA overexpression while complementary miRNA pairs exist. In addition, we test various miRNA-expression cassettes that were designed to efficiently overexpress specific miRNA through the shRNA lentivirus expression system. We report the optimal conditions that were established for the design of such miRNA-expression cassettes. We finally demonstrate that the miRNA-expression cassettes achieve efficient and long-term overexpression of specific miRNAs. Meanwhile, our results also support the notion that miRNA-miRNA interactions are implicated in potential, mutual regulatory patterns and beyond the seed sequence of miRNA, extensive pairing interactions between a miRNA and its target also lead to target-directed miRNA degradation. Our results indicate that our method offers a simple and efficient means to over-express the specific miRNA with long-term which will be very useful for future studies in miRNA biology, as well as contributed to the development of miRNA-based therapy for clinical applications.

molecular biology↗

bioRxiv2019

The Norepinephrine Metabolite DOPEGAL Confers Locus Coeruleus Tau Vulnerability and Propagation via Asparagine Endopeptidase

Aberrant Tau inclusions in the locus coeruleus (LC) are the earliest detectable Alzheimers disease (AD)-like neuropathology in the human brain; however, why LC neurons are selectively vulnerable to developing early Tau pathology and degenerating later in disease and whether the LC might seed the stereotypical spread of Tau pathology to the rest of the brain remain unclear. Here we show that 3,4-dihydroxyphenylglycolaldehyde (DOPEGAL), which is produced exclusively in noradrenergic neurons by monoamine oxidase A (MAO-A) metabolism of norepinephrine (NE), activates asparagine endopeptidase (AEP) that cleaves Tau at residue N368 into aggregation- and propagation-prone forms, thereby leading to LC degeneration and the spread of Tau pathology. DOPEGAL triggers AEP-cleaved Tau aggregation in vitro and in intact cells, resulting in LC neurotoxicity and propagation of pathology to the forebrain. Thus, our findings reveal a novel molecular mechanism underlying the selective vulnerability of LC neurons in AD.

neuroscience↗

bioRxiv2018

Tau accumulation activates STAT1 triggering memory deficits via suppressing NMDA receptor expression

Intracellular tau accumulation forming neurofibrillary tangles is hallmark pathology of Alzheimer's disease (AD), but how tau accumulation induces synapse impairment is elusive. By overexpressing human full-length wildtype tau (termed hTau) to mimic tau abnormality as seen in the brain of sporadic AD patients, we found that hTau accumulation activated JAK2 to phosphorylate STAT1 (Signal Transducer and Activator of Transcription 1) at Tyr701 leading to STAT1 dimerization, nuclear translocation and its activation. STAT1 activation suppressed expression of N-methyl-D-aspartate receptors (NMDARs) through direct binding to the specific GAS element of GluN1, GluN2A and GluN2B promoters, while knockdown STAT1 by AAV-Cre in STAT1flox/flox mice or expressing dominant negative Y701F-STAT1 efficiently rescued hTau-induced suppression of NMDARs expression with amelioration of synaptic functions and memory performance. These findings indicate that hTau accumulation impairs synaptic plasticity through JAK2/STAT1-induced suppression of NMDARs expression, revealing a novel mechanism for hTau-associated synapse and memory deficits.

neuroscience↗

bioRxiv2018

Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half assembled intermediate

Assembly of eukaryotic ribosome is a complicated and dynamic process that involves a series of intermediates. How the highly intertwined structure of 60S large ribosomal subunits is established is unknown. Here, we report the structure of an early nucleolar pre-60S ribosome determined by cryo-electron microscopy at 3.7 [A] resolution, revealing a half assembled subunit. Domains I, II and VI of 25S/5.8S rRNA tightly pack into a native-like substructure, but domains III, IV and V are not assembled. The structure contains 12 assembly factors and 19 ribosomal proteins, many of which are required for early processing of large subunit rRNA. The Brx1-Ebp2 complex would interfere with the assembly of domains IV and V. Rpf1, Mak16, Nsa1 and Rrp1 form a cluster that consolidates the joining of domains I and II. Our structure reveals a key intermediate on the path to the establishment of the global architecture of 60S subunits.

biophysics↗

bioRxiv2017

Adaptation of the FADS gene family in Europe: Variation across time, geography and subsistence

Fatty acid desaturase (FADS) genes encode rate-limiting enzymes for the biosynthesis of omega-6 and omega-3 long chain polyunsaturated fatty acids (LCPUFAs). This biosynthesis is essential for individuals subsisting on LCPUFAs-poor, plant-based diets. Positive selection on FADS genes has been reported in multiple populations, but its presence and pattern in Europeans remain elusive. Here, with analyses of ancient and modern DNA, we demonstrated that positive selection acted on the same FADS variants both before and after the advent of farming in Europe, but on opposite alleles. Selection in recent farmers also varied geographically, with the strongest signal in Southern Europe. These varying selection patterns concur with anthropological evidence of differences in diets, and with the association of recently-adaptive alleles with higher FADS1 expression and enhanced LCPUFAs biosynthesis. Genome-wide association studies revealed associations of recently-adaptive alleles with not only LCPUFAs, but also other lipids and decreased risk of several inflammation-related diseases.

genomics↗