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Chang, Y.

Publications and source records attributed to Chang, Y..

At least 145 records · Page 8Linked to original sources

Initial data release and announcement of the Fish10K: Fish 10,000 Genomes Project

With more than 30,000 species, fish are the largest and most ancient vertebrate group. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish. Here, we announce the Fish10K project, an international collaborative project or initiative? aiming to sequence 10,000 representative fish genomes under a systematic context within ten years, and officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, and sequencing and assembly strategies. To illustrate, we present the genomes of ten fish species from a cohort of 93 species chosen for technology development.

genomics↗

The efficiency for recombineering is dependent on the source of the phage recombinase function unit

Phage recombinase function units (PRFUs) such as lambda-Red or Rac RecET have been proven to be powerful genetic tools in the recombineering of Escherichia coli. Studies have focused on developing such systems in other bacteria as it is believed that these PRFUs have limited efficiency in distant species. However, how the species evolution distance relates to the efficiency of recombineering remains unclear. Here, we present a thorough study of PRFUs to find features that might be related to the efficiency of PRFUs for recombineering. We first identified 59 unique sets of PRFUs in the genus Corynebacterium and classified them based on their sequence as well as secondary structure similarities. Then both PRFUs from this genus and other bacteria were chosen for experiment based on sequential and secondary structure similarity as well as species distance. These PRFUs were compared for their ability in mediating recombineering with oligo or double-stranded DNA substrates in Corynebacterium glutamicum. We demonstrate that the source of the PRFU is more critical than species distance for the efficiency of recombineering. Our work will provide new ideas for efficient recombineering using PRFUs.\n\nImportanceRecombineering using phage recombinase function units (PRFUs) such as lambda-Red or Rac RecET has gained success in Escherichia coli, while efforts applying these systems in other bacteria were limited by the efficiency. It is believed that the species distance may be a major reason for the low efficiency. In this study, however, we showed that it is the source of PRFU rather than the species distance that matters for the recombineering in Corynebacterium glutamicum. Besides, we also showed that the lower transformation efficiency in other bacteria compared to that of E. coli could be a major reason for the low performance of heterogeneously expressed RecET. These findings will be helpful for the recombineering using PRFUs.

bioinformatics↗

Depletion of intermediate filament IFB-1 negatively affects mobility and physiological function of mitochondria in C. elegans sensory neurons

Mitochondria and intermediate filament (IF) accumulations often occur during imbalanced axonal transport leading to various types of neurological diseases. It is still poorly understood whether a link between neuronal IFs and mitochondrial mobility exist. In C. elegans, among the 11 cytoplasmic IF family proteins, IFB-1 is of particular interest as it is expressed in a subset of sensory neurons. Depletion of IFB-1 leads to mild dye-filling and significant chemotaxis defects as well as reduced life span. Sensory neuron development is affected and mitochondria transport is slowed down leading to reduced densities of these organelles. Mitochondria tend to cluster in neurons of IFB-1 mutants likely dependent on fission but independent of fusion events. Oxygen consumption and mitochondrial membrane potential is measurably reduced in worms carrying mutations in the ifb-1 gene. Membrane potential also seems to play a role in transport such as FCCP treatment led to increased directional switching of mitochondria. Mitochondria colocalize with IFB-1 in worm neurons and appear in a complex with IFB-1 in pull-down assays. In summary, we propose a model in which neuronal intermediate filaments may serve as critical (transient) anchor points for mitochondria during their long-range transport in neurons for steady and balanced transport. Abstract Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/723205v3_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1c6fc73org.highwire.dtl.DTLVardef@e7fd9aorg.highwire.dtl.DTLVardef@ba9742org.highwire.dtl.DTLVardef@20a9ed_HPS_FORMAT_FIGEXP M_FIG C_FIG SynopsisVarious neurological diseases are both associated with abnormal accumulations of neuronal intermediate filaments as well as mitochondria. Here, we report a link between these two phenomena employing the model organisms C. elegans. Depletion of neuronal intermediate filament IFB-1 impairs the transport of mitochondria in sensory neurons leading to clustered and accumulated mitochondria affecting neuronal growth and oxygen consumption in nematodes.

cell biology↗

Chromosome-level genome assembly of a butterflyfish, Chelmon rostratus

Chelmon rostratus (Teleostei, Perciformes, Chaetodontidae) is a copperband butterflyfish. As an ornamental fish, the genome information for this species might help understanding the genome evolution of Chaetodontidae and adaptation/evolution of coral reef fish.\n\nIn this study, using the stLFR co-Barcode reads data, we assembled a genome of 638.70 Mb in size with contig and scaffold N50 sizes of 294.41 kb and 2.61 Mb, respectively. 94.40% of scaffold sequences were assigned to 24 chromosomes using Hi-C data and BUSCO analysis showed that 97.3% (2,579) of core genes were found in our assembly. Up to 21.47 % of the genome was found to be repetitive sequences and 21,375 protein-coding genes were annotated. Among these annotated protein-coding genes, 20,163 (94.33%) proteins were assigned with possible functions.\n\nAs the first genome for Chaetodontidae family, the information of these data helpfully to improve the essential to the further understanding and exploration of marine ecological environment symbiosis with coral and the genomic innovations and molecular mechanisms contributing to its unique morphology and physiological features.

genomics↗

Chromosome level draft genomes of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), an alien invasive pest in China

The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a severely destructive pest native to the Americas, but has now become an alien invasive pest in China, and causes significant economic loss. Therefore, in order to make effective management strategies, it is highly essential to understand genomic architecture and its genetic background. In this study, we assembled two chromosome scale genomes of the fall armyworm, representing one male and one female individual procured from Yunnan province of China. The genome sizes were identified as 542.42 Mb with N50 of 14.16 Mb, and 530.77 Mb with N50 of 14.89 Mb for the male and female FAW, respectively. We predicted about 22,201 genes in the male genome. We found the expansion of cytochrome P450 and glutathione s-transferase gene families, which are functionally related to the intensified detoxification and pesticides tolerance. Further population analyses of corn strain (C strain) and rice strain (R strain) revealed that the Chinese fall armyworm was most likely invaded from Africa. These strain information, genome features and possible invasion source described in this study will be extremely important for making effective strategies to manage the fall armyworms.

genomics↗

Meiosis related cancer-testis genes correlate with tumor aneuploidy and immune infiltration in 21 cancer types

The meiosis stage of spermatogenesis and the aneuploidy generation in tumorigenesis are highly linked. Cancer-testis genes (CT genes) were specifically expressed in testis and cancers and may serve as the molecular basis of the shared features between spermatogenesis and tumorigenesis. In the present study, we integrated multi-omics data from bulk samples and cell lines, and single cell RNA-Seq data from testis and two tumors to systematically investigate the association between CT genes and aneuploidy. After ranking genes according to their association with aneuploidy level, we found that CT genes, especially CT genes specifically expressed in meiosis, showed a consistently positive correlation with aneuploidy and homologous recombination deficiency (HRD) level. Similar results were also found in the CT non-coding genes. Then, we constructed a regulatory network based on the single cell RNA-seq data and revealed that the gain of accelerator transcriptional factors (TFs) E2F7 and E2F8 and the loss of the stabilizer TFs RFX2 and NFYA aberrantly activated CT genes in the cancers and were associated with the increase of HRD level. Finally, we found that the association between CT genes and cytotoxic infiltrating lymphocytes can be influenced by the HRD level. In sum, our results revealed the evidence of pseudomeiotic functions of CT genes in the aneuploidy generation process in the cancer cells. The results may help illuminate the origin of aneuploidy in cancers and guide future immunotherapy targeting CT antigens.

genomics↗

New logic facilitated identification of novel phage recombinase function units

Phage recombinase function unit (PRFU) contains one single strand annealing protein (SSAP) and one 5-3 exonuclease (EXO). Well-known PRFU such as lambda-Red or Rac RecET has been proved to be useful tool in the recombineering of Escherichia coli but had limited efficiency in distant species. Therefore, PRFUs from closely related species were often searched and developed as specific genetic tools. However, there are still many bacteria with few PRFU identified. Here, we hypothesised that the occurrence of PRFU might be related to specific strains. Based on this assumption, we managed to identify 59 unique sets of PRFUs in over 23 species of the genus Corynebacterium, a taxonomic group that were reported to be lacking in such system. The identified PRFUs were then classified to show their similarities and relation to species based on both sequential and structural information. Representative PRFUs were verified to be highly effective in mediating recombineering using ssDNA or dsDNA substrates. Analysis of the functional PRFUs indicated that they share similar local genome contexts, which might suggest their common origin. Our findings reveal the relation of PRFUs, species and strains and provide novel candidate genetic manipulation tools in genus Corynebacterium.\n\nAuthor SummaryGenus Corynebacterium is a taxonomic group with highly diversified species that are of medical, veterinary, or biotechnological relevance. However, being lack of genetic tools limits the study of these species. Our new verified phage recombinase function units (PRFUs) in this genus that are highly effective in mediating recombineering will provide new candidate genetic tools in this genus. Besides, reference genomes were often used for genome study and data mining. While for the mobile genetic elements, their transferable characteristic may affect their occurrence among genomes. Here we provide evidence for this idea by showing that the occurrence of PRFU is strain related but not species related. This may be helpful for the functional genomics study of mobile genetic elements among genomes.

bioinformatics↗

Clinical pattern of antibiotic overuse and misuse in primary healthcare hospitals in the southwest of China

PurposeOveruse and misuse of antibiotics are the primary risk factors for antibiotics resistance. Inadequate professional competence of primary care physicians might exacerbate these problems in China. This retrospective study aims to document the clinical pattern of antibiotics use and its overuse and misuse rates in rural primary care institutions, and to evaluate the association between antibiotics use and characteristics of the physicians and their patients.\n\nMethodsMedical records from 16 primary care hospitals in rural areas of Guizhou province, China were obtained from the Health Information System in 2018. Classification of incorrect and/or unnecessary use, escalated use and combined antibiotics use was based on the Guiding Principle of Clinical Use of Antibiotics (2015, China) and the standard of USA Centers for Disease Control and Prevention. Generalized Estimating Equations were employed to determine predictive factors for inappropriate antibiotics use.\n\nResultsA total of 74,648 antibiotics prescriptions were retrieved. Uncomplicated respiratory infection was the most common disease accounting for 58.6% of all prescriptions. The main antibiotic group used was penicillins (51.5%) followed by cephalosporins and macrolides (14% each). Of 57,009 patient visits, only 8.7% of the antibiotic prescriptions were appropriate. Combined, escalated, and incorrect and/or unnecessary antibiotics use was found in 7.8%, 6.2% and 77.3% of patient visits, respectively, of which 28.7% were given intravenously. Antibiotics misuse was significantly more likely among newly employed physicians with lower levels of professional education. Adult patients and those who had public insurance had a higher risk of being prescribed incorrect and/or unnecessary antibiotics.\n\nConclusionOveruse of antibiotics for uncomplicated respiratory infection and use of cephalosporins, macrolides and injection antibiotics in primary care are the major problems of clinical practice in rural areas of Guizhou.

epidemiology↗

Dosing regimen of gentamicin and the effect of antenatal steroids on clearance in preterm infants

ObjectiveDetermine the gentamicin pharmacokinetic and pharmacodynamic (PK/PD) profiles of once daily dosing (ODD) versus every 18-hour (q18h) regimens and to characterize the effect of antenatal steroid on gentamicin clearance (GentCL).\n\nStudy DesignRetrospective cohort of preterm infants ([&le;]34 weeks gestation; [&le;]7 days) who received gentamicin for >48 hours from January 2005 to June 2007. Serum gentamicin peak and trough concentrations were determined, and PK/PD profiles calculated using standard noncompartmental methods.\n\nResult122 (63%) infants received ODD and 73 (37%) received q18h regimen. Desired gentamicin peak (5 to 12 mcg/mL) and trough (<2 mcg/mL) concentrations were achieved in 80% (95%CI, 72-86) on ODD vs. 47% (95%CI, 36-58) on q18h (p<0.001). Target drug exposure (AUC >72 mcg/mL/hr) was achieved in 73% (89/122) of infants on ODD vs. 22% (16/73) on q18h (p < 0.001). GentCL was significantly lower in those who receive antenatal steroid (37+/-8 mL/kg/hr vs. 42+/-13 mL/kg/hr, p=0.04) but not affected by postnatal indomethacin treatment (p>0.86).\n\nConclusionPK/PD profile of gentamicin is improved by ODD in preterm infants. GentCl was significantly less in infants exposed to antenatal steroids but not in those treated with indomethacin.

pharmacology and toxicology↗

An Integrated Framework for Genome Analysis Reveals Numerous Previously Unrecognizable Structural Variants in Leukemia Patients' Samples

While genomic analysis of tumors has stimulated major advances in cancer diagnosis, prognosis and treatment, current methods fail to identify a large fraction of somatic structural variants in tumors. We have applied a combination of whole genome sequencing and optical genome mapping to a number of adult and pediatric leukemia samples, which revealed in each of these samples a large number of structural variants not recognizable by current tools of genomic analyses. We developed computational methods to determine which of those variants likely arose as somatic mutations. The method identified 97% of the structural variants previously reported by karyotype analysis of these samples and revealed an additional fivefold more such somatic rearrangements. The method identified on average tens of previously unrecognizable inversions and duplications and hundreds of previously unrecognizable insertions and deletions. These structural variants recurrently affected a number of leukemia associated genes as well as cancer driver genes not previously associated with leukemia and genes not previously associated with cancer. A number of variants only affected intergenic regions but caused cis-acting alterations in expression of neighboring genes. Analysis of TCGA data indicates that the status of several of the recurrently mutated genes identified in this study significantly affect survival of AML patients. Our results suggest that current genomic analysis methods fail to identify a majority of structural variants in leukemia samples and this lacunae may hamper diagnostic and prognostic efforts.

genomics↗

In situ structures of periplasmic flagella in Borrelia reveals conformational changes essential for flagellar rotation

The bacterial flagellar motor is a molecular machine that rotates the flagellar filament at high speed. Torque is generated by the stator-rotor interaction coupled to an ion flux through the torque-generating stator. Here, we employed cryo-electron tomography to visualize the intact flagellar motor in the Lyme disease spirochete Borrelia burgdorferi. By analysis of the motor structures of wild-type and stator mutants, we localize the torque-generating units precisely and determine three-dimensional structure of the stator and its interactions with the rotor. Our study shows that the cytoplasmic domains of the stator are packed regularly around the circumference of the flagellar C-ring. The stator-rotor interaction induces a profound conformational change in the C-ring. Analysis of the motors of a less motile motB-D24E mutant and a non-motile motB-D24N mutant, in which the proton translocation is reduced and blocked, respectively, provides evidence that the conformational change of the C-ring is essential for flagellar rotation.

microbiology↗

A chromosome-level genome of black rockfish, Sebastes schlegelii, provides insights into the evolution of live birth

Black rockfish (Sebastes schlegelii) is a teleost species where eggs are fertilized internally and retained in the maternal reproductive system, where they undergo development until live birth (termed viviparity). In the present study, we report a chromosome-level black rockfish genome assembly. High-throughput transcriptome analysis (RNA-seq and ATAC-seq), coupled with in situ hybridization (ISH) and immunofluorescence, identify several candidate genes for maternal preparation, sperm storage and release, and hatching. We propose that zona pellucida (ZP) genes retain sperm at the oocyte envelope, while genes in two distinct astacin metalloproteinase subfamilies serve to release sperm from the ZP and free the embryo from chorion at pre-hatching stage. Finally, we present a model of black rockfish reproduction, and propose that the rockfish ovarian wall has a similar function to uterus of mammals. Taken together, these genomic data reveal unprecedented insights into the evolution of an unusual teleost life history strategy, and provide a sound foundation for studying viviparity in non-mammalian vertebrates and an invaluable resource for rockfish ecology and evolution research.

genomics↗

Recent origin of an XX/XY sex-determination system in the ancient plant lineage Ginkgo biloba

Sexual dimorphism like dioecy (separate male and female individuals) have evolved in diverse multicellular eukaryotes while the molecular mechanisms underlying the development of such a key biological trait remains elusive (1). The living fossil Ginkgo biloba represents an early diverged lineage of land plants with dioecy. However, its sex-determination system and molecular basis have long been controversial or unknown. In the present research, we assembled the first and largest to date chromosome-level genome of a non-model tree species using Hi-C data. With this reference genome, we addressed both questions using genome resequencing data gathered from 97 male and 265 female trees of ginkgo, as well as transcriptome data from three developmental stages for both sexes. Our results support vertebrate-like XY chromosomes for ginkgo and five potential sex-determination genes, which may originate ~14 million years ago. This is the earliest diverged sex determination region in all reported plants as yet. The present research resolved a long-term controversy, lay a foundation for future studies on the origin and evolution of plant sexes, and provide genetic markers for sex identification of ginkgo which will be valuable for both nurseries and field ecology of ginkgo.

evolutionary biology↗

Immunomodulatory activity of Ganoderma lucidum immunomodulatory protein via PI3K/Akt and MAPK signaling pathways in macrophage RAW264.7 cells

Ganoderma lucidum, a traditional edible and medicinal fungus, holds an important status in health care systems in China and other Asian countries. Fungal immunomodulatory protein (FIP), one of the active ingredients isolated from G. lucidum, is a class of naturally occurring proteins and possesses potential biological functions. This study was conducted to explore the molecular mechanism of its immunomodulatory potency in immune responses of macrophages. In vitro assays of biological activity indicated that rFIP-glu significantly activated macrophage RAW264.7 cells, and possessed the ability of pro-and anti-inflammation the cells. RNA sequencing analysis showed that macrophage activation involved Toll-like receptors and mitogen-activated protein kinases pathways. Furthermore, qRT-PCR indicated that phosphoinositide 3 kinase inhibitor LY294002 blocked the mRNA levels of MCP-1, MEK1/2 inhibitor U0126 reduced the mRNA levels of TNF- and MCP-1, and JNK inhibitor SP600125 prevented the up-regulation of iNOS mRNA in the rFIP-glu-induced cells. FIP-glu mediated these inflammatory effects not through a general pathway, instead through a different pathway for different inflammatory mediator. These data indicate the possibility that rFIP-glu has an important immune-regulation function and thus has potential therapeutic uses.

immunology↗

Clathrin-coated Pits are Shredded Organelles Presorting Receptors in the Plasma Membrane

A myriad of receptor types crowds the plasma membrane of cells. Here, we revealed that clathrin-coated pits (CCPs) presort receptors to modulate receptor activation on the plasma membrane. We visualized individual molecules of receptors, including epidermal growth factor receptor (EGFR), ErbB2, transferrin receptor (TfR), and beta2-adrenergic receptors ({beta}2-AR), inside a single CCP in a living cell using single-molecule diffusivity-based colocalization analysis. The spatially distinct subsets of CCPs selectively allocated for these receptors were observed in a resting state. The EGFR pre-allocated CCP subset was partially shared with that for ErbB2, whereas the EGFR and TfR pre-allocated CCP subsets were mutually exclusive. PICALM was necessary for the pre-allocation of CCPs for EGFR. Furthermore, EGFR dimerization was markedly elevated inside the pre-allocated CCP subset after dynamin recruitment. The pre-sorting function of CCPs provides an efficient mechanism to control competition and cooperation between receptors on the crowded plasma membrane.\n\nOne Sentence SummaryClathrin-coated pits are small-sized organelles pre-sorting receptor kinds to modulate receptor activation on the crowded plasma membrane.

cell biology↗

Construction of an index system for big data application in health care enterprises: A study based on the Delphi method

This study explored the theory of medical enterprise management and big data. Based on the Delphi method, two rounds of expert opinions were consulted on the capability of a health care enterprise big data application index system covering 11 dimensions, 46 first-level indicators and 111 second-level indicators. The index system includes two categories of input and capacity. The input category includes five dimensions: human resources, material resources, financial resources, government policies, and social service system or social environment. The capabilities category includes six dimensions: data integration capabilities, service capabilities, data analysis capabilities, information security, profitability, and innovation capabilities. This index system aims to appraise the application capability of big data scientifically and systematically, and fills the gaps of such research in China so far, which has positive significance for further research in the future.

scientific communication and education↗

The GTPase Nog1 couples polypeptide exit tunnel quality control with ribosomal stalk assembly

Eukaryotic ribosome precursors acquire translation competence in the cytoplasm through stepwise release of bound assembly factors, and proofreading of their functional centers. In case of the large subunit precursor (pre-60S), these essential steps include eviction of placeholders Arx1 and Mrt4 that prevent premature loading of the protein-folding machinery at the polypeptide exit tunnel (PET), and the ribosomal stalk, respectively. Here, we reveal that sequential ATPase and GTPase activities license release factors Rei1 and Yvh1 recruitment to the pre-60S in order to trigger Arx1 and Mrt4 removal. Drg1-ATPase activity extracts the C-terminal tail of Nog1 from the PET, enabling Rei1 to probe PET integrity, and then catalyze Arx1 release. Subsequently, GTPase hydrolysis stimulates Nog1 removal from the pre-60S, permitting Yvh1 to mediate Mrt4 release, and initiate ribosomal stalk assembly. Thus, Nog1 couples quality control and assembly of spatially distant functional centers during ribosome formation.

biochemistry↗

Snapshots of single particles from single cells using electron microscopy

Cryo-electron microscopy has become an indispensable tool for structural studies of biological macromolecules. There are two predominant methods for studying the architectures of multi-protein complexes: (1) single particle analysis of purified samples and (2) tomography of whole cells or cell sections. The former can produce high-resolution structures but is limited to highly purified samples, while the latter can capture proteins in their native state but is hindered by a low signal-to-noise ratio and results in lower-resolution structures. Here, we present a method combining microfluidic single cell extraction with single particle analysis by electron microscopy to characterize protein complexes from individual C. elegans embryos. Using this approach, we uncover three-dimensional structures of ribosomes directly from single embryo extracts. In addition, we investigate structural dynamics during development by counting the number of ribosomes per polysome in early and late embyros. This approach has significant potential applications for counting protein complexes and studying protein architectures from single cells in developmental, evolutionary and disease contexts.

biochemistry↗