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Xin Du

Publications and source records attributed to Xin Du.

At least 19 recordsLinked to original sources
PubMed2026

Functional convergence of regulatory regions provides vital insights into mammalian gliding adaptation.

Uncovering the key genetic basis of complex phenotypic convergence in distantly related species has been a long-standing focus in evolutionary biology and genetics, and the convergent evolution of gliding in mammals offers a valuable opportunity to address this question. Here, we investigated the genomic basis of convergent evolution of gliding in mammals by analyzing both protein-coding genes and conserved non-coding elements (CNEs). We first de novo assembled and annotated two chromosome-level genomes of gliding mammals, the red and white giant flying squirrel (Petaurista alborufus) and sugar gliders (Petaurus breviceps), and conducted comprehensive comparative genomic analysis combined with another gliding mammal, the Sunda flying lemur (Galeopterus variegatus) and 14 background species. We found that the convergent evolution of protein-coding genes provided relatively limited but functionally relevant evidence linked to gliding phenotypes. By contrast, we found that gliding-accelerated CNEs (GACNEs) cluster near functionally equivalent genes and frequently aggregate into highly diverged yet functionally convergent hotspot regions. Across the three gliding lineages, both GACNEs and hotspot GACNEs show strong convergence in their functional enrichment profiles, suggesting a broad genetic basis underlying the convergent gliding phenotype. Furthermore, we identified 72 core transcription factors underpinning the genetic basis of gliding convergence, including EMX2 and ZFHX3, potentially involved in multiple aspects of gliding adaptation. Our study highlights the role of functional convergence in regulatory regions as a key mechanism in mammalian gliding convergence, offering valuable insights and strategies for uncovering the genetic basis of complex convergent traits, thereby advancing understanding of the molecular basis of convergent traits.

Petaurista alborufus↗
PubMed2005

CD14 is required for MyD88-independent LPS signaling.

The recessive mutation 'Heedless' (hdl) was detected in third-generation N-ethyl-N-nitrosourea-mutated mice that showed defective responses to microbial inducers. Macrophages from Heedless homozygotes signaled by the MyD88-dependent pathway in response to rough lipopolysaccharide (LPS) and lipid A, but not in response to smooth LPS. In addition, the Heedless mutation prevented TRAM-TRIF-dependent signaling in response to all LPS chemotypes. Heedless also abolished macrophage responses to vesicular stomatitis virus and substantially inhibited responses to specific ligands for the Toll-like receptor 2 (TLR2)-TLR6 heterodimer. The Heedless phenotype was positionally ascribed to a premature stop codon in Cd14. Our data suggest that the TLR4-MD-2 complex distinguishes LPS chemotypes, but CD14 nullifies this distinction. Thus, the TLR4-MD-2 complex receptor can function in two separate modes: one in which full signaling occurs and one limited to MyD88-dependent signaling.

Adaptor Proteins, Signal Transducing↗
PubMed2005

Crystallin {gamma}B-I4F mutant protein binds to {alpha}-crystallin and affects lens transparency.

A new mouse mutant line, Clapper, identified from N-ethyl-N-nitrosurea (ENU)-mutagenized mice, develops a dominant lamellar cataract. The cataract blocks the image of retinal fundus and transmits a fuzzy fluorescein image of retinal vasculature during angiography. The cataractous lens opacity decreases as the mice age. The Clapper mutation has been identified to be a missense mutation of the gammaB-crystallin gene that replaces the 4th isoleucine residue with a phenylalanine (gammaB-I4F). Unlike wild type gammaB, the gammaB-I4F mutant protein binds to alpha-crystallin to form high molecular weight complexes in vivo and in vitro. Circular dichroism measurements indicate that gammaB-I4F protein is less stable than wild type gammaB at high temperature. Darkly stained aggregates, enlarged interfiber spaces, and disorganized and smaller inner mature fibers were found in the regions of the cataract in homozygous Clapper mutant lenses. Thus, the lamellar cataract is likely due to the light-scattering effects of the enlarged interfiber spaces and protein aggregates caused by gammaB-I4F mutant proteins interacting with alpha-crystallin in the lens.

Angiography↗
PubMed2005

CD36 is a sensor of diacylglycerides.

Toll-like receptor 2 (TLR2) is required for the recognition of numerous molecular components of bacteria, fungi and protozoa. The breadth of the ligand repertoire seems unusual, even if one considers that TLR2 may form heteromers with TLRs 1 and 6 (ref. 12), and it is likely that additional proteins serve as adapters for TLR2 activation. Here we show that an N-ethyl-N-nitrosourea-induced nonsense mutation of Cd36 (oblivious) causes a recessive immunodeficiency phenotype in which macrophages are insensitive to the R-enantiomer of MALP-2 (a diacylated bacterial lipopeptide) and to lipoteichoic acid. Homozygous mice are hypersusceptible to Staphylococcus aureus infection. Cd36(obl) macrophages readily detect S-MALP-2, PAM(2)CSK(4), PAM(3)CSK(4) and zymosan, revealing that some--but not all--TLR2 ligands are dependent on CD36. Already known as a receptor for endogenous molecules, CD36 is also a selective and nonredundant sensor of microbial diacylglycerides that signal via the TLR2/6 heterodimer.

Aging↗
PubMed2005

Antagonism between MyD88- and TRIF-dependent signals in B7RP-1 up-regulation.

Type I interferons (IFN) play a critical role in the Toll-like receptor (TLR)-mediated expression of B7 costimulatory family members. For example, LPS-induced up-regulation of CD80 (B7.1) and CD86 (B7.2) is abrogated in antigen-presenting cells (APC) deficient in TRIF or TRAM, two adaptors that are responsible for TLR4-mediated production of Type I IFN. In this report, we demonstrate that LPS-induced up-regulation of B7-related protein 1 (B7RP-1), a ligand for ICOS, is dependent primarily upon the MyD88-dependent signaling pathway. Signaling via the TRIF pathway sharply limits MyD88-dependent B7RP-1 up-regulation. Hence, LPS induces significantly higher B7RP-1 expression on TRIF- or TRAM-deficient mouse peritoneal macrophages and on TRIF-deficient mouse splenic B cells as compared to wild-type cells. Further studies reveal that Type I IFN are general suppressors of TLR-mediated up-regulation of B7RP-1. These data indicate that Type I IFN play a dual role in the TLR-mediated expression of B7 costimulatory family members and suggest that they may act to limit B7RP-1 expression and thus limit signals derived from B7RP-1-ICOS interaction.

Adaptor Proteins, Signal Transducing↗
PubMed2005

An essential role for Rxr alpha in the development of Th2 responses.

A viable hypomorphic allele of mouse retinoid X receptor alpha (Rxralpha) was created by random germline mutagenesis. The mutation (I273N) alters the ligand binding and heterodimerization domain, and causes a 90% decline in ligand-inducible transactivation. Homozygotes develop progressive alopecia and dermal cysts, and progressive exaggeration of Th1 and loss of Th2 responses to antigen. Th1 skewing is directly caused by aberrant function of both antigen-presenting cells and naïve CD4 T cells; the predominant Th1 response to antigen is attributable to decreased suppression of regulatory T cells in mutant mouse. Dietary depletion of vitamin A in Th2-prone wild-type mice mimics the immune phenotype caused by the mutation. Hence, RXRalpha plays an important post-developmental role in the regulation of adaptive immune responses, and provides a plausible link between nutritional environment and the type of adaptive response that results from immunization.

Aging↗
PubMed2005

Genetic analysis of innate immunity: identification and function of the TIR adapter proteins.

The innate immune system senses pathogens largely through signals initiated by a collection of phylogenetically related proteins known as "Toll-like receptors" (TLRs), of which ten representatives are encoded in the human genome. The sensing role of the TLRs first came to light when one member of this family, TLR4, was shown to serve the detection of endotoxin (lipopolysaccharide; LPS) in mice. This discovery was based upon positional cloning of a spontaneous mutation affecting a locus known as Lps. The recognition specificities of other TLRs have since been established by reverse genetic methods. The understanding of the biochemical circuitry that maintains the innate capacity for immune recognition and response has loomed as the next hurdle in the field. A total of five adapter proteins with cytoplasmic domain homology to the TLRs are known to exist in mammals. These proteins are not entirely promiscuous in their interaction with TLRs, but rather, show preferential association with individual family members, giving a particular character to the signals that distinct micro-organisms initiate. The adaptive immune response is dependent upon upregulation of costimulatory molecules (UCM) such as CD80 and CD86. Very recently, it has been shown that this upregulation is dependent upon an adapter encoded by a locus known as Lps2, known as Trif or Ticam-1, and upon type I interferon receptor signaling. LPS and dsRNA both signal via Trif, but dsRNA has an accessory pathway for UCM, that is independent of both Trif/Ticam-1 and the known dsRNA receptor, TLR3. Other key innate immunity genes have also been disclosed by germline mutagenesis, and are discussed in the present review.

Adaptor Proteins, Signal Transducing↗
PubMed2005

A toll-like receptor 2-responsive lipid effector pathway protects mammals against skin infections with gram-positive bacteria.

flake (flk), an N-ethyl-N-nitrosourea-induced recessive germ line mutation of C57BL/6 mice, impairs the clearance of skin infections by Streptococcus pyogenes and Staphylococcus aureus, gram-positive pathogens that elicit innate immune responses by activating Toll-like receptor 2 (TLR2). Positional cloning and sequencing revealed that flk is a novel allele of the stearoyl coenzyme A desaturase 1 gene (Scd1). flake homozygotes show reduced sebum production and are unable to synthesize the monounsaturated fatty acids (MUFA) palmitoleate (C(16:1)) and oleate (C(18:1)), both of which are bactericidal against gram-positive (but not gram-negative) organisms in vitro. However, intradermal MUFA administration to S. aureus-infected mice partially rescues the flake phenotype, which indicates that an additional component of the sebum may be required to improve bacterial clearance. In normal mice, transcription of Scd1-a gene with numerous NF-kappaB elements in its promoter--is strongly and specifically induced by TLR2 signaling. Similarly, the SCD1 gene is induced by TLR2 signaling in a human sebocyte cell line. These observations reveal the existence of a regulated, lipid-based antimicrobial effector pathway in mammals and suggest new approaches to the treatment or prevention of infections with gram-positive bacteria.

Animals↗
PubMed2005

[Evaluation of early invasive or initially conservative strategies in patients with non-ST-segment elevation acute coronary syndrome at intermediate or high risk].

OBJECTIVE: To demonstrate the effect of early strategies and revascularization patterns on in-hospital major adverse cardiac events (MACE) in patients with non-ST-segment elevation acute coronary syndrome (ACS) at intermediate or high risk. METHODS: 910 Patients with non-ST-segment elevation ACS at intermediate or high risk were divided into either early invasive (n = 237) or initially conservative (n = 673) group according to whether or when coronary angiography (CAG) was performed after admission ( 48 h) in order to demonstrate the impact of early strategies and revascularization patterns on in-hospital MACE events (death, new-onset myocardial infarction or repeat revascularization). RESULTS: Compared with those of the initially conservative group, patients in the early invasive group had a shorter hospital stay and increased rate of MACE (6.3% vs 2.5%, OR 0.384, 95% CI 0.188 - 0.781, P = 0.006) or new-onset myocardial infarction (4.6% vs 0.9%, OR 0.185, 95% CI 0.068 - 0.505, P = 0.001), which was partly due to increased procedures of revascularization (86.9% vs 67.5%, P < 0.001). No differences were found among in-hospital mortality or rate of repeat revascularization between the two groups. During subgroup analysis, patients receiving PCI in the early invasive or initially conservative group had comparable rates of new-onset myocardial infarction, repeat revascularization or MACE events, whereas patients receiving CABG in the early invasive group had a higher rate of new-onset myocardial infarctions than those in the initially conservative group (7.5% vs 1.8%, P = 0.027). CONCLUSIONS: An early invasive strategy in patients with non-ST-segment elevation ACS had comparable in-hospital mortality and higher rate of in-hospital myocardial infarction compared with an initially conservative strategy, an early invasive strategy with PCI seems safe and feasible without increased risk of adverse clinical events. The impact of early CABG on in-hospital adverse events warrants further investigation.

Acute Coronary Syndrome↗
PubMed2005

[The study on effect of Sarcandra glabra on prevention and treatment of thrombocytopenia by chemotherapy].

OBJECTIVE: To investigate the effect of Sarcandra glabra Thunb on prevention and treatment of thrombocytopenia after chemotherapy with a large dosage. METHODS: The Babl/c mice model of thrombocytopenia was made by intraperitoneal injection of 5-FU at a large dosage. All mice were poured Sarcandra glabra Thunb dilution to the mice's stomach once daily from the beginning of the experiment. Then the effect was analyzed by measuring peripheral blood cell counts of the mice on the 2nd day, the 4th day and the 7th day after chemotherapy. On the end of 7th day, all mice were killed, and then bone marrow biopsy was employed to investigate the hemapoietic condition. RESULTS: Before the chemotherapy, the platelet counts of mice treated by Sarcandra glabra Thunb were higher than that in the control group (P < 0.05). After chemotherapy with 5-FU, the platelet counts were not significantly decreased in two all experimental groups compared with negative control group (P < 0.05), while there was not significantly different between two experimental groups (P > 0.05). Moreover the marrow biopsy showed that bone marrow hyperplasia was active in two intervention study groups with some megaryocytes in the medullary cavity of bone while bone marrow hyperplasia was low in the control group without any megaryocyte in the medullary cavity of bone. CONCLUSION: The Sarcandra glabra Thunb had obvious activity in treatment to therombocytopenia and can prevent thrombocytopenia by 5-FU.

Animals↗
PubMed2004

The extracellular matrix gene Frem1 is essential for the normal adhesion of the embryonic epidermis.

Fraser syndrome is a rare recessive disorder characterized by cryptophthalmos, syndactyly, renal defects, and a range of other developmental abnormalities. Because of their extensive phenotypic overlap, the mouse blebbing mutants have been considered models of this disorder, and the recent isolation of mutations in Fras1 in both the blebbed mouse and human Fraser patients confirms this hypothesis. Here we report the identification of mutations in an extracellular matrix gene Fras1-related extracellular matrix gene 1 (Frem1) in both the classic head blebs mutant and in an N-ethyl-N-nitrosourea-induced allele. We show that inactivation of the gene results in the formation of in utero epidermal blisters beneath the lamina densa of the basement membrane and also in renal agenesis. Frem1 is expressed widely in the developing embryo in regions of epithelial/mesenchymal interaction and epidermal remodeling. Furthermore, Frem1 appears to act as a dermal mediator of basement membrane adhesion, apparently independently of the other known "blebs" proteins Fras1 and Grip1. Unlike both Fras1 and Grip1 mutants, collagen VI and Fras1 deposition in the basement membrane is normal, indicating that the protein plays an independent role in epidermal differentiation and is required for epidermal adhesion during embryonic development.

Amino Acid Sequence↗
PubMed2004

Toll-like receptors 9 and 3 as essential components of innate immune defense against mouse cytomegalovirus infection.

Several subsets of dendritic cells have been shown to produce type I IFN in response to viral infections, thereby assisting the natural killer cell-dependent response that eliminates the pathogen. Type I IFN production can be induced both by unmethylated CpG-oligodeoxynucleotide and by double-stranded RNA. Here, we describe a codominant CpG-ODN unresponsive phenotype that results from an N-ethyl-N-nitrosourea-induced missense mutation in the Tlr9 gene (Tlr9(CpG1)). Mice homozygous for the Tlr9(CpG1) allele are highly susceptible to mouse cytomegalovirus infection and show impaired infection-induced secretion of IFN-alpha/beta and natural killer cell activation. We also demonstrate that both the Toll-like receptor (TLR) 9 --> MyD88 and TLR3 --> Trif signaling pathways are activated in vivo on viral inoculation, and that each pathway contributes to innate defense against systemic viral infection. Whereas both pathways lead to type I IFN production, neither pathway offers full protection against mouse cytomegalovirus infection in the absence of the other. The Tlr9(CpG1) mutation alters a leucine-rich repeat motif and lies within a receptor domain that is conserved within the evolutionary cluster encompassing TLRs 7, 8, and 9. In other TLRs, including three mouse-specific TLRs described in this paper, the affected region is not represented. The phenotypic effect of the Tlr9(CpG1) allele thus points to a critical role for TLR9 in viral sensing and identifies a vulnerable amino acid within the ectodomain of three TLR proteins, essential for a ligand response.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Genetic analysis of innate immunity: TIR adapter proteins in innate and adaptive immune responses.

The innate immune system senses pathogens largely through signals initiated by a collection of phylogenetically related proteins known as "Toll-like receptors" (TLRs), of which 10 representatives are encoded in the human genome. Our understanding of the sensing role played by the TLRs began with the positional cloning of a spontaneous mutation (Lps(d)) in the gene encoding the mammalian lipopolysaccharide (LPS) receptor. Other key innate immunity proteins have been disclosed by germline mutagenesis, and are discussed in the present review.

Animals↗
PubMed2004

Velvet, a dominant Egfr mutation that causes wavy hair and defective eyelid development in mice.

In the course of a large-scale program of ENU mutagenesis, we isolated a dominant mutation, called Velvet. The mutation was found to be uniformly lethal to homozygotes, which do not survive E13.5. Mice heterozygous for the Velvet mutation are born with eyelids open and demonstrate a wavy coat and curly vibrissae. The mutation was mapped to the proximal end of chromosome 11 by genome-wide linkage analysis. On 249 meioses, the locus was confined to a 2.7-Mb region, which included the epidermal growth factor receptor gene (Egfr). An A --> G transition in the Egfr coding region of Velvet mice was identified, causing the amino acid substitution D833G. This substitution alters an essential triad of amino acids (DFG --> GFG) that is normally required for coordination of the ATP substrate. As such, kinase activity is at least mostly abolished, but quaternary structure of the receptor is presumably maintained, accounting for the dominant effect. Velvet is the first known dominant representative of the Egfr allelic series that is fully viable, a fact that makes it particularly useful for developmental studies.

Animals↗
PubMed2004

A simple rectification method for linear multi-baseline stereovision system.

The linear multi-baseline stereo system introduced by the CMU-RI group has been proven to be a very effective and robust stereovision system. However, most traditional stereo rectification algorithms are all designed for binocular stereovision system, and so, cannot be applied to a linear multi-baseline system. This paper presents a simple and intuitional method that can simultaneously rectify all the cameras in a linear multi-baseline system. Instead of using the general 8-parameter homography transform, a two-step virtual rotation method is applied for rectification, which results in a more specific transform that has only 3 parameters, and more stability. Experimental results for real stereo images showed the presented method is efficient.

Journal Article↗
PubMed2003

The effect of human tissue factor pathway inhibitor-2 on the growth and metastasis of fibrosarcoma tumors in athymic mice.

Human tissue factor pathway inhibitor-2 (TFPI-2) is a matrix-associated Kunitz inhibitor that inhibits the plasmin- and trypsin-mediated activation of zymogen matrix metalloproteinases involved in tumor progression, invasion, and metastasis. To directly assess its role in tumor growth and metastasis in vivo, we stably transfected HT-1080 fibrosarcoma cells expressing either fully active wild-type human TFPI-2 (WT) or inactive R24Q TFPI-2 (QT) and examined their ability to form tumors and metastasize in athymic mice in comparison to mock-transfected cells (MT). MT and QT fibrosarcoma tumors grew 2 to 3 times larger than WT tumors. Tumor metastasis was confined to the lung and was observed in 75% of mice treated with either MT or QT cells, whereas only 42% of mice treated with WT cells developed lung metastases. Real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) analyses of each tumor group revealed 3- to 6-fold lower levels of murine vascular endothelial growth factor gene expression in WT tumors in relation to either MT or QT tumors. Comparative tumor gene expression analysis revealed that several human genes implicated in oncogenesis, invasion, metastasis, apoptosis, and angiogenesis had significantly altered levels of expression in WT tumors. Our collective data demonstrate that secretion of inhibitory TFPI-2 by a highly metastatic tumor cell markedly inhibits its growth and metastasis in vivo by regulating pericellular extracellular matrix (ECM) remodeling and angiogenesis.

Animals↗
PubMed2003

Molecular cloning, expression, and characterization of bovine tissue factor pathway inhibitor-2.

Human tissue factor pathway inhibitor-2 (TFPI-2) is a matrix-associated Kunitz-type serine proteinase inhibitor that is secreted by all cells of the vasculature, and presumably plays a role in the regulation of plasmin-mediated matrix remodeling. In this report, we describe the cloning and expression of a full-length cDNA for bovine TFPI-2 that exhibits 72% sequence identity with that of human TFPI-2. Following a 22 residue signal peptide, the mature protein contains 212 amino acids with 18 cysteines, three putative N-glycosylation sites, and one putative O-glycosylation site. The deduced sequence of mature bovine TFPI-2 revealed a short acidic amino-terminal region, three tandem Kunitz-type domains, and a carboxy-terminal tail highly enriched in basic amino acids. Recombinant bovine TFPI-2 was expressed in HEK 293 cells and resolved into two isoforms, designated as alpha-TFPI-2 (M(r) 33 kDa) and beta-TFPI-2 (M(r) 31 kDa), which presumably represent differentially glycosylated forms of the inhibitor. Similar to human TFPI-2, both bovine TFPI-2 isoforms exhibited strong inhibitory activity towards trypsin and plasmin, and weak inhibitory activity towards the factor VIIa-tissue factor complex.

Amino Acid Motifs↗