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Ning Chen

Publications and source records attributed to Ning Chen.

At least 19 recordsLinked to original sources
PubMed2025

The evolutionary trajectories and gene regulatory roles of nuclear-integrated plastid DNA: clues for enhancing environmental adaptation in Caryophyllales.

Environmental stimuli can induce the transfer of chloroplast DNA to the nuclear genome, resulting in nuclear-integrated plastid DNAs (NUPTs). However, their role in plant adaptability remains unclear. Species within the Caryophyllales order, known for their adaptation to extreme environments, provide an ideal model for studying the evolutionary dynamics and functions of NUPTs. In this study, we analyzed NUPTs in 24 Caryophyllales species to investigate their evolution and regulatory roles in gene expression, particularly in response to environmental stimuli. We found significant interspecies variation in NUPT abundance, ranging from 566 insertions in Amaranthus cruentus to 3585 in Beta vulgaris, with sizes spanning from 100 bp to over 100 kb. Approximately 62% of NUPTs were inserted within the last 20 million years, while some species exhibit insertion peaks dating back 49 million years. NUPT presence/absence polymorphisms in six related species suggest that NUPT insertions and deletions are dynamic processes influenced by phylogeny. NUPTs predominantly integrate into intergenic regions but also insert into genes and promoters, with certain regions acting as hotspots. Notably, NUPTs introduce numerous environmental-responsive cis-acting elements in promoter regions. Genes with NUPT insertions in their promoters are significantly enriched for functions related to environmental response. Further luciferase assays in Spinacia oleracea demonstrated that NUPT insertions can regulate the expression of genes related to environmental responses, indicating their potential role in adaptive evolution. Overall, our study provides insights into NUPT evolution and their influence on gene function and plant adaptability to environmental stimuli.

Plastids↗
PubMed2007

Human retinoblastoma is not caused by known pRb-inactivating human DNA tumor viruses.

Retinoblastomas occur as the consequence of inactivation of the tumor suppressor retinoblastoma protein (pRb), classically upon biallelic inactivation of the RB1 gene locus. Recently, human papillomavirus (HPV) genomic DNA has been detected in retinoblastomas. To investigate the possibility that oncoproteins encoded by pRb-inactivating DNA tumor viruses play a role in the pathogenesis of human retinoblastoma, 40 fresh-frozen tumors were analyzed for the presence of HPV, adenovirus (HAdV) and polyomavirus (BKV, JCV and SV40) genomic DNA sequences by real-time polymerase chain reaction (PCR). Tumors were screened for genetic and epigenetic alterations in all 27 exons of the RB1 gene locus and promoter by exonic copy number detection, sequencing and methylation-specific PCR of the promoter region. Retinoblastoma tumors from children with bilateral familial (n=1), bilateral nonfamilial (n=1) and unilateral nonfamilial (n=38) disease were analyzed. Inactivating modifications to the RB1 gene locus were identified on both the alleles in 27 tumors, one allele in 8, and neither allele in 5 cases. A median of over 107,000 tumor cells were analyzed for viral genomic DNA in each PCR reaction. All tumor samples were negative for 37 HPV types, 51 HAdV types, BKV and JCV genomic sequences. Very low copy number (0.2-260 copies per 100,000 tumor cells) SV40 genomic DNA detected in 8 of 39 samples was demonstrated to be consistent with an artifact of plasmid-derived SV40. In contrast to recent reports, we obtained substantial quantitative evidence indicating that neither HPV nor any other pRb-inactivating human DNA tumor viruses play a role in the development of retinoblastoma, regardless of RB1 genotype.

Child↗
PubMed2007

Listeria monocytogenes mutants carrying Newcastle disease virus F gene fused to its actA and plcB: in vitro expression and immunogenicity in chickens.

Recombinant Listeria monocytogenes mutants carrying Newcastle disease virus (NDV) fusion protein gene F were constructed by homologous recombination. NDV F or its truncated fragment Fa was used as the model heterologous gene to be integrated into actA or plcB downstream of their signal sequences. Correct orientation of the inserted genes was verified by polymerase chain reaction amplification of F or Fa. The inserted F and Fa were expressed in the two recombinants Lm-DeltaactA-F and Lm-DeltaplcB-Fa as shown by sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blot. Both recombinants exhibited reduced virulence to embryonated eggs and mice by about 1.5-2.5 logs as compared with the parent wild strain 10403S. They were also less invasive than strain 10403S (P<0.05). Chickens receiving the recombinant strains orally or intraperitoneally were partially protected from virulent NDV challenge possibly due to enhancement of non-specific immunity because the antibody titers against the homologous virus strain or the recombinant truncated fusion protein were marginal. Further research is needed in other animal models to see if the low antibody response results from insufficient expression of the heterologous genes as a result of failure of L. monocytogenes or its recombinants to persist or replicate in chickens.

Animals↗
PubMed2006

C80 encaging four different atoms: the synthesis, isolation, and characterizations of ScYErN@C80.

The synthesis, isolation, and spectroscopic characterizations of an endohedral fullerene with four heteroatoms encapsulated (ScYErN@C80) are reported for the first time. The isomeric structure and electronic properties of this molecule are studied by various spectrometry methods such as high-performance liquid chromatography (HPLC), laser desorption time-of-flight (LD-TOF) mass spectroscopy, cyclic voltammetry, Fourier transform infrared (FTIR) spectroscopy, and visible-near infrared (vis-NIR) absorption spectroscopy. The carbon cage of ScYErN@C80 is assigned as Ih-C80, and the four-membered ScYErN cluster is suggested to rotate rapidly inside the fullerene cage. Six electrons are transferred from the nuclear cluster ScYErN to the fullerene cage, which leads to a closed-shell electronic structure of the Ih-C80 and results in excellent stability of this molecule.

Letter↗
PubMed2006

Sample preparation project for the subcellular proteome of mouse liver.

Organelle proteome has become one of the most important fields of proteomics, and the subcellular fractionation with high purity and yield has always been a challenge for cell biologists and also for the Human Liver Proteome Project (HLPP). The liver of a C57BL/6J mouse was chosen as the model to find the optimum method for subcellular preparation. The method we selected could obtain the multiple fractions including plasma membrane, mitochondria, nucleus, ER, and cytosol from a single homogenate. With the same procedure, it is for the first time that the preparation method of frozen homogenized livers was compared with that of the fresh livers and frozen livers. We systematically evaluated the purity, efficiency, and integrity by protein yield, immunoblotting, and transmission electron microscopy. Taken together, the method of multiple fractions from a single tissue is effective enough for subcellular fractionation of mouse liver. We give a selective sample preparation method for frozen homogenized livers, for rare clinical samples, which cannot easily be used for subcellular separation immediately. But the frozen livers are not recommended for organelles isolation. This result is especially useful for sample preparation of human liver for subcellular fractionation of HLPP.

Animals↗
PubMed2006

Novel cell therapy approaches for brain repair.

Numerous reports elucidate that tissue-specific stem cells are phenotypically plastic and their differentiation pathways are not strictly delineated. Although the identity of all the epigenetic factors which may trigger stem cells to make a lineage selection are still unknown, the plasticity of adult stem cells opens new approaches for their application in the treatment of various disorders. There is increasing researcher interest in hematopoietic stem cells for treatment of not only blood-related diseases but also various unrelated disorders including neurodegenerative diseases. Human umbilical cord blood (hUCB) cells, due to their primitive nature and ability to develop into nonhematopoietic cells of various tissue lineages, including neural cells, may be useful as an alternative cell source for cell-based therapies requiring either the replacement of individual cell types and/or substitution of missing substances. Here we focus on recent findings showing the robustness of adult stem cells derived from hUCB and their potential as a source of transplant cells for the treatment of diseased or injured brains and spinal cords. Depending upon the pathological microenvironment in which the hUCB cells are introduced, neuroprotective and/or trophic effects of these cells, from release of various growth or anti-inflammatory factors to moderation of immune-inflammatory effectors, may be more likely than neural replacement. These protective effects may prove essential to maintaining restored tissue integrity over the course of various diseases or injuries.

Amyotrophic Lateral Sclerosis↗
PubMed2006

Virulence phenotyping and molecular characterization of a low-pathogenicity isolate of Listeria monocytogenes from cow's milk.

A low-pathogenicity isolate of Listeria monocytogenes from cow's milk, as screened in mouse and chicken embryonated egg models, was examined for virulence-related phenotypic traits. Corresponding virulence genes (iap, prfA, plcA, hly, mpl, actA, plcB, InlA and InlB) were compared with L. monocytogenes reference strains 10403S and EGD to elucidate the possible molecular mechanisms of low virulence. Although L. monocytogenes H4 exhibited similar patterns to strain 10403S in terms of hemolytic activity, in vitro growth and invasiveness and even had higher adhesiveness, faster intracellular growth and higher phospholipase activity in vitro, it was substantially less virulent than the strain 10403S in mouse and chicken embryo models (50% lethal dose: 10(8.14) vs. 10(5.49) and 10(6.73) vs. 10(1.9), respectively). The genes prfA, plcA and mpl were homologous among L. monocytogenes strains H4, 10403S and EGD (>98%). Genes iap, hly, plcB, InlA and InlB of L. monocytogenes 10403S had higher homology to those of strain EGD (>98%) than isolate H4. The homology of the gene hly between strain 10403S and isolate H4 was 96.9% at the nucleotide level, but 98.7% at the amino acid level. The actA gene of isolate H4 had deletions of 105 nucleotides corresponding to 35 amino acid deletions falling within the proline-rich region. Taken together, this study presents some clues as to reduced virulence to mice and chicken embryos of the isolate H4 probably as a result of deletion mutations of actA.

Amino Acid Sequence↗
PubMed2006

Immunogenicity of formaldehyde and binary ethylenimine inactivated infectious bursal disease virus in broiler chicks.

Infectious bursal disease virus (IBDV) was inactivated by two different chemicals--formaldehyde and binary ethylenimine (BEI). Formaldehyde was used at 0.1% and 0.2%, while BEI was used at concentrations of 0.001 and 0.002 mol/L. These four vaccines were tested for their efficiency in generating humoral immune response in different groups of broiler chicks. Both BEI-inactivated vaccines gave relatively higher antibody titers and were almost twice as efficient as formaldehyde-inactivated ones.

Animals↗
PubMed2006

[Observation on therapeutic effects of bird-pecking needling and needle warming moxibustion on bulging of lumbar intervertebral disc].

OBJECTIVE: To explore the best manipulating method for bulging of lumbar intervertebral disc. METHODS: Eighty cases were randomly divided into a treatment group (n=58) and a control group (n=22). The treatment group were treated with bird-pecking needling and needle warming moxibustion, and the control group with needle warming moxibustion of uniform reinforcing and reducing method. Their therapeutic effects were compared. RESULTS: The total effective rate was 100.0% in the treatment group and 81. 8% in the control group with a significant difference between the two groups (P < 0.01). CONCLUSION: Therapeutic effects of bird-pecking needling and needle warming moxibustion on bulging of lumbar intervertebral disc is significantly superior to that of needle warming moxibustion of uniform reinforcing and reducing method.

Animals↗
PubMed2006

[Characterization of a recombinant Listeria monocytogenes strain containing the fusion protein gene of Newcastle disease virus].

Homologous recombination was utilized for construction of a recombinant strain of L. monocytogenes carrying a gene from the Newcastle diseases virus by insertional mutation targeting its listeriolysin O gene (hly). The gene encoding fusion protein of the Newcastle disease virus (NDV-F) was used as the model heterologous gene. The F gene was inserted into hly downstream to its promoter and signal sequence by overlapping extension polymerase chain reaction, which was then subcloned into the shuttle plasmid pKSV7 for allelic exchange with L. monocytogenes chromosome. PCR amplification of the target genes indicated insertion of the F gene into the chromosome DNA of L. monocytogenes. RT-PCR showed transcription of F gene from the recombinant L. monocytogenes strain. Comparisons were then made between the recombinant strain and its wild parent strain in terms of the hemolytic activity, adhesion and invasiveness to cultured HeLa cells, virulence to mice and chicken embryos, and growth kinetics in broth medium as well as its stability upon repeated subculturing and serial passages in mice. The recombinant L. monocytogenes lost its hemolytic activity on the blood agar and had no hemolytic titer from its culture supernatants as compared with the titer of 24 in the supernatant from the wild parent strain. The recombinant strain also had lower adhesiveness (P > 0.05) and significantly lower relative invasiveness to the HeLa cells than its wild type strain (P < 0.05). Such insertional mutation resulted in reduced virulence, about 3.7 logs and 6.5 logs less than its parent strain L. monocytogenes 10403S as shown by the 50% lethal dose assays in the mouse and chicken embryonated egg models respectively. The recombinant strain was relatively stable as shown by amplification of the target gene NDV-F from its genomic DNA after subculturing in BHI broth or in mice for 5 times.

Animals↗
PubMed2005

First-in-class pan caspase inhibitor developed for the treatment of liver disease.

A series of oxamyl dipeptides were optimized for pan caspase inhibition, anti-apoptotic cellular activity and in vivo efficacy. This structure-activity relationship study focused on the P4 oxamides and warhead moieties. Primarily on the basis of in vitro data, inhibitors were selected for study in a murine model of alpha-Fas-induced liver injury. IDN-6556 (1) was further profiled in additional in vivo models and pharmacokinetic studies. This first-in-class caspase inhibitor is now the subject of two Phase II clinical trials, evaluating its safety and efficacy for use in liver disease.

Adult↗
PubMed2005

Specific formation of beads-on-a-chain structures on giant DNA using a designed polyamine derivative.

Fluorescence microscopy was used to study the folding transition of giant DNAs, T4 DNA (ca. 166 kbp), and lambda DNA (ca. 48 kbp), which proceeds through intermediates with intramolecular segregation induced by pteridine-polyamine conjugates, i.e., 2-amino-6,7-dimethyl-4-(4,9,13-triazatridecylamino)pteridine and -4-(3-(aminopropyl)amino)pteridine. According to the results of DNA denaturation, UV and fluorescent spectroscopy, and transmission electron microscopic observations, it became clear that DNA folding induced by the polyamine derivative is not a continuous shrinking process but a combination of discontinuous processes.

Bacteriophage T4↗
PubMed2005

Dramatic change in the tertiary structure of giant DNA without distortion of the secondary structure caused by pteridine-polyamine conjugates.

Pteridine-polyamine conjugates, such as 2-polyamine (1,3-diaminopropane and spermine) substituted 6,7-dimethyl-3H-pteridine-4-one, induce a folding transition of a giant DNA molecule more effectively than the corresponding polyamines. However, since neither a DNA high-temperature shift of denaturation (Tm) curve nor distortion of the UV/fluorescence spectra is observed in a mixture of these compounds with DNA, they do not interact with the DNA duplex strongly.

Bacteriophage T4↗
PubMed2005

Human umbilical cord blood progenitors: the potential of these hematopoietic cells to become neural.

The mononuclear fraction from human umbilical cord blood (HUCB) contains a significant number of stem/progenitor cells that in theory could be come any cell in the body, including neurons. Taking into consideration that transdifferentiation would be a very rare event and also knowing that overlapping genetic programs for hematopoiesis and neuropoiesis exist, we undertook a characterization of the HUCB mononuclear fraction, including analysis of cellular subpopulations and their morphology, cell viability, proliferation, and expression of neural and hematopoietic antigens. Two cell populations were apparent-adherent and floating fractions. The adherent fraction was mainly lymphocytes (~53%) expressing hematopoietic antigens. Upon replate, the floating population had many cells that expressed stem cell antigens. More of the cells in this subfraction expressed neural proteins. Neurotrophin receptors trkB and trkC were present in both cell fractions, although expression was higher in the floating fraction. Our initial characterization suggests that a subpopulation of cells exists within the HUCB mononuclear fraction that seems to have the potential to become neural cells, which could then be used in the development of cell-based therapies for brain injuries and diseases.

Antigens, CD↗
PubMed2005

Transendothelial migration of melanoma cells involves N-cadherin-mediated adhesion and activation of the beta-catenin signaling pathway.

Cancer metastasis is a multistep process involving many types of cell-cell interactions, but little is known about the adhesive interactions and signaling events during extravasation of cancer cells. Transendothelial migration of cancer cells was investigated using an in vitro assay, in which melanoma cells were seeded on top of a monolayer of endothelial cells. Attachment of melanoma cells on the endothelium induced a twofold increase in N-cadherin expression in melanoma cells and the redistribution of N-cadherin to the heterotypic contacts. Transendothelial migration was inhibited when N-cadherin expression was repressed by antisense RNA, indicating a key role played by N-cadherin. Whereas N-cadherin and beta-catenin colocalized in the contact regions between melanoma cells and endothelial cells during the initial stages of attachment, beta-catenin disappeared from the heterotypic contacts during transmigration of melanoma cells. Immunolocalization and immunoprecipitation studies indicate that N-cadherin became tyrosine-phosphorylated, resulting in the dissociation of beta-catenin from these contact regions. Concomitantly, an increase in the nuclear level of beta-catenin occurred in melanoma cells, together with a sixfold increase in beta-catenin-dependent transcription. Transendothelial migration was compromised in cells expressing a dominant-negative form of beta-catenin, thus supporting a regulatory role of beta-catenin signaling in this process.

Active Transport, Cell Nucleus↗
PubMed2005

Neutrophil-specific chemokines are produced by astrocytic cells but not by neuronal cells.

BACKGROUND: Neutrophils have a central role in the inflammatory conditions of the central nervous system (CNS). ELR chemokines direct neutrophil migration, but the source of chemokines in the CNS is unclear. We quantified chemokine production using cell-line models of astrocytic and neuronal cells, specifically NT2.N cells, a human line with characteristics of immature neurons, and NT2.A cells, a line with characteristics of astrocytes. OBJECTIVE: In NT2.N and NT2.A cells, and their parent cell line NT2, we sought to: (1) quantify ELR chemokines, (2) determine receptor (CXCR-1 and CXCR-2) expression, and (3) measure the function of the chemokines generated from these cells. DESIGN/METHODS: NT2 cells were differentiated into NT2.N cells and NT2.A cells with all trans retinoic acid and mitosis inhibitors. Chemokine concentrations in culture supernatants were determined by ELISA. Immunofluorescence was used to detect CXCR-1 and CXCR-2. RT-PCR was used to determine chemokine and chemokine receptor mRNA. Chemotaxis assays were used to assess function. RESULTS: ELR chemokines were not detected in supernatants of NT2 or NT2.N cells, although mRNA for GRO-gamma/CXCL3 was found in both. In contrast, in NT2.A cells, mRNA and protein were present for GCP-2/CXCL6, GRO-alpha/CXCL1, GRO-gamma/CXCL3, and IL-8/CXCL8. CXCR-1 and CXCR-2 were expressed on NT2, NT2.N, and NT2.A cells detected by immunofluorescent staining and RT-PCR. Supernatants of NT2.A cells resulted in neutrophil chemotactic function of 30.5 +/- 3.9%, greater than NT2 cells (12.3 +/- 1.6%, mean +/- SEM, P < 0.01). CONCLUSIONS: We speculate that astrocytes are a source of ELR chemokines in the human CNS and that neurons and astrocytes can respond to those chemokines.

Astrocytes↗
PubMed2005

Melanocortin subtype-4 receptor agonists containing a piperazine core with substituted aryl sulfonamides.

The biological activity for a set of melanocortin-4 receptor (MC4R) agonists containing a piperazine core with an ortho-substituted aryl sulfonamide is described. Compounds from this set had binding and functional activities at MC4R less than 30 nM. The most selective compound in this series was >25,000-fold more potent at MC4R than MC3R, and 490-fold more potent at MC4R than MC5R. This compound also reduced food intake after oral dosing at 25, 50, and 100 mg kg(-1) in fasted mice.

Animals↗