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Jie Song

Publications and source records attributed to Jie Song.

At least 19 recordsLinked to original sources
PubMed2024

Genome-wide copy number variation association study in anorexia nervosa.

This study represents the first large-scale investigation of rare (<1% population frequency) copy number variants (CNVs) in anorexia nervosa (AN). Large, rare CNVs are reported to be causally associated with anthropometric traits, neurodevelopmental disorders, and schizophrenia, yet their role in the genetic basis of AN is unclear. Using genome-wide association study (GWAS) array data from the Anorexia Nervosa Genetics Initiative (ANGI), which included 7414 AN case and 5044 controls, we investigated the association of 67 well-established syndromic CNVs and 178 pleiotropic disease-risk dosage-sensitive CNVs with AN. To identify novel CNV regions (CNVRs) that increase the risk of AN, we conducted genome-wide association studies with a focus on rare CNV-breakpoints (CNV-GWAS). We found no net enrichment of rare CNVs, either deletions or duplications, in AN, and none of the well-established syndromic or pleiotropic CNVs had a significant association with AN status. However, the CNV-GWAS found 21 nominally associated CNVRs that contribute to AN risk, covering protein-coding genes implicated in synaptic function, metabolic/mitochondrial factors, and lipid characteristics, like the CD36 (7q21.11) gene, which transports long-chain fatty acids into cells. CNVRs intersecting genes previously related to neurodevelopmental traits include deletions of NRXN1 intron 5 (2p16.3), IMMP2L (7q31.1), and PTPRD (9p23). Overall, given that our study is well powered to detect the CNV burden level reported for schizophrenia, we can conclude that rare CNVs have a limited role in the etiology of AN, as reported for bipolar disorder. Our nominal associations for the 21 discovered CNVRs are consistent with AN being a metabo-psychiatric trait, as demonstrated by the common genetic architecture of AN, and we provide association results to allow for replication in future research.

Humans↗
PubMed2007

Nanomechanical analysis of bone tissue engineering scaffolds.

Copolymers of (2-hydroxyethyl methacrylate) (HEMA) and methacrylamide monomers conjugated with amino acids were synthesized and crosslinked with ethylene glycol dimethacrylate. The resulting library of copolymers was mineralized in vitro using two distinct methods. In the first mineralization method, the copolymers were polymerized in the presence of a sub-micron hydroxyapatite (HA) suspension. In the second method, copolymers were mineralized with HA using a urea-mediated process. The mechanical properties of all of the copolymers, both mineralized and not, were determined using nanoindentation under both load and displacement control. A power law fit to the initial unloading curve was used to determine a reduced elastic modulus for each material. Between 30 and 300 indentations were performed on each material, and ANOVA analysis was run to determine the statistical significance of differences in modulus between samples. Using nanoindentation, the 22 different samples had reduced modulus values ranging from 840 MPa to 4.14 GPa. Aspartic acid-methacrylate (Asp-MA) copolymers were not distinguishable from the pHEMA control material. Polymerization in the presence of HA created a more uniform material than the urea method of mineralization. Several challenges and solutions encountered in the nanomechanical testing of soft, heterogeneous materials are discussed. These results demonstrate that with proper experimental design, the mechanical properties of tissue engineering scaffold materials based on polymer-ceramic composite materials can be determined using small samples and nanoindentation techniques.

Bone Substitutes↗
PubMed2006

[Capacitative Ca²⁺ entry is involved in ACh-induced distal colon smooth muscle contraction in rats].

Contraction of smooth muscle cells is triggered by an increase in cytosolic Ca(2+) upon agonist stimulation. Ca(2+) influx across the plasma membrane constitutes a major component of the agonist-induced response in smooth muscle cells. Traditionally, voltage-operated Ca(2+) channel (VOCC) is considered as the channel mediating the Ca(2+) entry. However, this view has been challenged by recent discoveries, which demonstrated that other types of ion channels, such as store-operated and/or receptor-operated Ca(2+) channels (SOCC and/or ROCC), also participate in Ca(2+) response induced by agonists in smooth muscle cells. SOCC is defined as the channel activated in response to the depletion of the internal Ca(2+) stores, an event secondary to G protein coupled receptor or receptor tyrosine kinase stimulation. The Ca(2+) flow mediated by SOCC is termed as capacitative Ca(2+) entry (CCE). Previous study from other group has demonstrated that VOCC played a predominant role in ACh-induced contraction of distal colon smooth muscle in guinea pig. However, whether SOCC participates in the agonist-induced contractile response in this particular tissue is unknown. The present study was performed to investigate the role of CCE in ACh-induced mechanical activity of distal colon smooth muscle in rats. The contractile function of the smooth muscle was assessed by measuring isometric force of isolated rat distal colon rings. We showed that both high extracellular K(+) (40 mmol/L) and ACh (5 mumol/L) evoked striking contraction of the smooth muscle. The contractile responses were almost abolished by removal of extracellular Ca(2+) with ethylene glycol-bis(2-aminoethylether)-N,N,N',N' tetraacetic acid (EGTA), suggesting a critical contribution of extracellular source of Ca(2+) to the contraction. Verapamil (5 mumol/L), an L-type VOCC blocker, significantly attenuated, but didn't completely eliminate the high K(+)- and ACh-induced contraction (74% and 41% for high K(+) and ACh, respectively), indicating that additional channels might be involved in the contractile mechanism. Furthermore, ACh only induced transient contractions in the absence of extracellular Ca(2+). Readmission of Ca(2+) into the extracellular compartment resulted in a significant and sustained increase in the tension of the smooth muscle. This response was not affected by verapamil (5 mumol/L) and Cd(2+) (5 mumol/L), both of which efficiently block VOCC at the doses. However, La(3+), a known inhibitor of SOCC, significantly suppressed the Ca(2+) readdition-induced contraction in a dose-dependent manner. On the basis of these results, we conclude that contraction of smooth muscle in the distal colon is regulated by multiple Ca(2+) channels. In addition to VOCC-mediated Ca(2+) influx, SOCC-mediated CCE participates in agonist-induced contractile response of distal colon smooth muscle in rats.

Acetylcholine↗
PubMed2006

Nutritional and osmotic roles of nitrate in a euhalophyte and a xerophyte in saline conditions.

The effects of salinity and nitrogen (N) on growth and the role of NO3- in osmotic adjustment in the leaf-succulent euhalophyte Suaeda physophora and the stem-succulent xerophyte Haloxylon persicum were evaluated. Seedlings were exposed to 1 or 300 mm NaCl in 0.05, 1 or 10 mm NO3- -N treatments for 24 d. At 10 mm NO3-, 300 mm NaCl had no adverse effect on the concentration of NO3-, the content of organic N, and the estimated contribution of NO3- to osmotic potential in leaves of S. physophora, but markedly reduced these in stems of H. persicum. At 300 mm NaCl, more NO3- but less Cl- and Na+ were involved in osmotic adjustment in leaves of S. physophora compared with that in stems of H. persicum. The contribution of NO3- to osmotic potential was much higher in S. physophora, but lower in H. persicum, than that of amino acids at 300 mm NaCl. The nutritional and osmotic roles of NO3- -N seem to be more important in the euhalophyte S. physophora than in the xerophyte H. persicum under saline conditions. These characteristics may determine the natural distributions of the two species in saline or arid environments.

Amino Acids↗
PubMed2005

Comparing the Dictyostelium and Entamoeba genomes reveals an ancient split in the Conosa lineage.

The Amoebozoa are a sister clade to the fungi and the animals, but are poorly sampled for completely sequenced genomes. The social amoeba Dictyostelium discoideum and amitochondriate pathogen Entamoeba histolytica are the first Amoebozoa with genomes completely sequenced. Both organisms are classified under the Conosa subphylum. To identify Amoebozoa-specific genomic elements, we compared these two genomes to each other and to other eukaryotic genomes. An expanded phylogenetic tree built from the complete predicted proteomes of 23 eukaryotes places the two amoebae in the same lineage, although the divergence is estimated to be greater than that between animals and fungi, and probably happened shortly after the Amoebozoa split from the opisthokont lineage. Most of the 1,500 orthologous gene families shared between the two amoebae are also shared with plant, animal, and fungal genomes. We found that only 42 gene families are distinct to the amoeba lineage; among these are a large number of proteins that contain repeats of the FNIP domain, and a putative transcription factor essential for proper cell type differentiation in D. discoideum. These Amoebozoa-specific genes may be useful in the design of novel diagnostics and therapies for amoebal pathologies.

Animals↗
PubMed2005

Structural properties of benzimidazole cavitand and its selective recognition toward 4-methylbenzamide over 4-methylanilide.

The conformations and properties of cavitand 5 with four benzimidazole flaps are studied by (1)H NMR. The benzimidazole cavitand 5 can form very stable vase structures with an enforced concave cavity by intermolecular hydrogen bonding with four hydroxyl-containing molecules, X-OH, such as methanol (X = Me), acetic acid (X = CH(3)CO), and trifluoroacetic acid (X = CF(3)CO). The stronger hydrogen bond donor strengths of X-OH are, the stronger hydrogen bonds are formed between the NH and N atoms of the neighboring benzimidazole fragments and the more vase structures of 5.4HOX are stable. The annular tautomerism of 5 in CDCl(3)/CD(3)OD (9:1, v/v) due to the proton exchange between NH and N atoms of the neighboring benzimidazole fragments is observed by 400 MHz (1)H NMR, and the free energy of activation is measured as DeltaG++(210) = 10.2 kcal/mol at a coalescence temperature of 210 K. Cavitand 5 forms inclusion complexes with 4-methylbezamide guests such as 4-methyl-N-p-tolylbenzamide 6 and N,4-dimethylbenzamide 7 in water-saturated CDCl(3). However, an isomorphic 4-methylanilide guest such as N-4-tolylacetamide 8 cannot be recognized in the concave cavity of 5. This high selectivity toward 4-methylbenzamide over 4-methylanilide seems attributable to the hydrogen-binding interaction between the NH proton of 4-methylbezamide guest 7 and the oxygen atom of the closest water molecule.

Journal Article↗
PubMed2005

Strategies for adaptation of Suaeda physophora, Haloxylon ammodendron and Haloxylon persicum to a saline environment during seed-germination stage.

BACKGROUND AND AIMS: Germination is very important for plant establishment in arid regions. The strategies taken by halophytes during the seed germination stage to adapt to saline environments in an arid zone were investigated in Suaeda physophora (euhalophyte), Haloxylon ammodendron (xero-halophyte) and Haloxylon persicum (xerophyte). METHODS: Seeds of S. physophora, H. ammodendron and H. persicum were exposed to a range of iso-osmotic NaCl and PEG solutions. Seed germination in, and recovery germination from, high NaCl were recorded. The effects of iso-osmotic NaCl and PEG on seed water uptake and changes in ion content were measured. In addition, the structure of seeds and Na+ distribution in the seed coat and embryos of dry seeds were investigated. KEY RESULTS: The relative increase in fresh weight of germinating seeds was markedly reduced in -2.24 MPa PEG compared with that in -2.24 MPa NaCl, while the opposite trend was found in concentration of K+ during the initial 9 h for all species. Haloxylon ammodendron and S. physophora had a higher recovery germination from -3.13 MPa NaCl compared with H. persicum. Seeds of all species had no endosperm. More Na+ was compartmentalized in the seed coats of the two halophytic species compared with that in the xerophyte H. persicum. CONCLUSIONS: The effect of NaCl on seed germination was due to both osmotic stress and ion toxicity for the three species. High soil salinity and a high content of Na+ in seeds may induce more seeds to remain ungerminated in S. physophora and H. ammodendron. Morphological structure and adaptation to salinity during seed germination may determine the geographical distribution of H. ammodendron and S. physophora in certain saline regions.

Adaptation, Physiological↗
PubMed2005

A new 2-D graphical representation of DNA sequences and their numerical characterization.

We consider a novel 2-D graphical representation of DNA sequences according to chemical structures of bases, reflecting distribution of bases with different chemical structure, preserving information on sequential adjacency of bases, and allowing numerical characterization. The representation avoids loss of information accompanying alternative 2-D representations in which the curve standing for DNA overlaps and intersects itself. Based on this representation we present a numerical characterization approach by the leading eigenvalues of the matrices associated with the DNA sequences. The utility of the approach is illustrated on the coding sequences of the first exon of human beta-globin gene.

Base Composition↗
PubMed2005

Mineralization of synthetic polymer scaffolds: a bottom-up approach for the development of artificial bone.

The controlled integration of organic and inorganic components confers natural bone with superior mechanical properties. Bone biogenesis is thought to occur by templated mineralization of hard apatite crystals by an elastic protein scaffold, a process we sought to emulate with synthetic biomimetic hydrogel polymers. Cross-linked polymethacrylamide and polymethacrylate hydrogels were functionalized with mineral-binding ligands and used to template the formation of hydroxyapatite. Strong adhesion between the organic and inorganic materials was achieved for hydrogels functionalized with either carboxylate or hydroxy ligands. The mineral-nucleating potential of hydroxyl groups identified here broadens the design parameters for synthetic bonelike composites and suggests a potential role for hydroxylated collagen proteins in bone mineralization.

Acrylamides↗
PubMed2005

Statin-inhibited endothelial permeability could be associated with its effect on PECAM-1 in endothelial cells.

UNLABELLED: The 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors (statins) are known to inhibit leukocyte recruitment to endothelium but the mechanism is less understood. Platelet endothelial cell adhesion molecule-1 (PECAM-1) is an endothelial junction protein involved in leukocyte diapedesis. We hypothesize that in endothelial cells, statins may well recruit PECAM-1 to exert their inhibitory effect on leukocyte trans-endothelial migration (TEM). In lovastatin-treated resting human umbilical vein endothelial cells (HUVECs), increased levels of mRNA and protein of PECAM-1 as well as its bio-synthesis (all approximately 2-fold) were observed by real-time PCR, Western blotting and 35S-labeled methionine incorporation assay, respectively. Moreover, in lovastatin treated resting cells as well as TNF-alpha activated endothelial cells, unanimously decreased Triton X-100 insoluble and soluble PECAM-1 ratio was observed. Such changes were accompanied by decreased TEM of U-937 cells (a promonocyte cell line). All lovastatin's effects were abrogated by mevalonic acid. In resting HUVECs, geranylgeranyl pyrophosphate (GGPP), but not farnesyl pyrophosphate (FPP) (both are isoprenoid intermediates in the cholesterol biosynthesis pathway) compromised the effect of lovastatin on PECAM-1 expression, whereas C3 toxin, an inhibitor of small G proteins, exerted statin-like effect. CONCLUSION: Statin-reduced endothelial permeability could be attributed to altered intracellular distribution of PECAM-1 in endothelial cells. We speculate that lovastatin regulates PECAM-1 expression in HUVECs through the mevalonate-GGPP pathway by inhibiting of Rho small GTPase.

Cells, Cultured↗
PubMed2005

Association of Leu125Val polymorphism of platelet endothelial cell adhesion molecule-1 (PECAM-1) gene & soluble level of PECAM-1 with coronary artery disease in Asian Indians.

BACKGROUND & OBJECTIVES: Platelet endothelial cell adhesion molecule-1 (PECAM-1) plays a key role in the transendothelial migration of circulating leukocytes (diapedesis) during vascular inflammation. We hypothesized that genetic variation and the level of soluble PECAM-1 could be associated with the development of atherosclerosis and conducted a study on gene polymorphisms of PECAM-1 and soluble PECAM-1 levels in Asian Indian patients with coronary artery disease (CAD) in Singapore. METHODS: Of the 137 angiographically confirmed patients (> or =70% stenosis) of CAD and 110 controls in Asian Indian population, two single nucleotide polymorphisms (SNPs) of PECAM-1 gene, C+373G (Leu125Val) at exon 3 and G+1688A (Ser563Asn) at exon 8 were analyzed by polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP) strategy. In addition, plasma soluble PECAM-1, P-selection and lipid profile were measured. Chi- square test and student t test were adopted to compare categorical and continuous variables, respectively. RESULTS: A significant decrease in C allele frequency but increase in G allele frequency of the Leu125Val (C/G) polymorphism were observed in CAD patients as compared with controls (0.54/0.46 vs 0.663/0.337 respectively, P=0.008). Alteration in genotype distributions (CC, CG and GG) of the Leu125Val polymorphism between CAD patients and controls (P=0.009) was also significant. A similar trend was observed on the allele frequencies (G/A) and genotype distributions of Ser563Asn (G/A) polymorphism, though the difference did not reach significance. On the other hand, plasma level of soluble PECAM-1 (sPECAM-1) was markedly elevated in CAD patients (P=0.006), and associated with soluble P-selectin and lipid profiles. INTERPRETATION & CONCLUSION: Our study showed that Leu125Val polymorphism of PECAM-1 gene and elevated soluble PECAM-1 were related to severe coronary artery stenosis in CAD patients of Asian Indian origin in Singapore. Our data also suggest that PECAM-1 plays an important role in the development of atherosclerosis.

Base Sequence↗
PubMed2005

[Effects of the Radix Ranuncoli Ternati extracts on Mycobacterium tuberculosis proteome profiling revealed by 2D electrophoresis].

Radix Ranuncoli Ternati is clinically effective traditional Chinese medicine for multidrug resistant tuberculosis. Its active components and mechanism of action remain unsolved. Two dimensional gel electrophoresis (2-DE) was employed to address this problem. Globlal proteome of Mycobacterium tuberculosis untreated and treated with Radix Ranuncoli Ternati were compared, and 22 protein spots were found to be expressed differentially. 3 protein spots which remarkably decreased in Mycobacterium tuberculosis treated with Radix Ranuncoli Ternati were subjected to matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) analysis. The data obtained from peptide mass finger printing were used for database search. The 3 protein spots in gel were identified as cysA2 (thiosulfate sulfurtransferase), tsf (elongation factor EF-Ts) and hspX (heat shock protein X). These data provide insights into the changed global protein patterns of Mycobacterium tuberculosis treated with Radix Ranuncoli Ternati and may prove useful for further study in the mechanism in how Radix Ranuncoli Ternati influence the life of Mycobacterium tuberculosis. The differentially expressed proteins may be potential novel antituberculosis drug targets.

Antigens, Bacterial↗
PubMed2004

Identification of a novel transcript of human PECAM-1 and its role in the transendothelial migration of monocytes and Ca2+ mobilization.

Platelet-endothelial cell adhesion molecule-1 (PECAM-1) is an integral component of endothelial cells and has been implicated in the transendothelial migration (TEM) of circulating leukocytes mediated by its 1st and 2nd extracellular immunoglobulin (Ig)-like domains and regulation of intracellular Ca(2+) homeostasis with its 6th domain. Up-to-date, little is known about the role of the 5th extracellular (Ig)-like domain. We have discovered a novel human PECAM-1 transcript missing the entire 7th exon, which encodes the 5th extracellular (Ig)-like domain of PECAM-1. A synthetic peptide with sequence homology to the 5th domain of PECAM-1 (JHS-7 peptide) and a corresponding polyclonal antibody (JHS-7 Ab) were prepared and their potential role in transendothelial migration and Ca(2+) influx was measured. The JHS-7 peptide and the antibody exerted a dose dependent decrease (50-80%) in the transendothelial migration of freshly isolated human monocytes and a promonocytic cell line (U-937) in resting HUVECs and HUVECs activated with tumor necrosis factor-alpha. This was accompanied by an increase in Ca(2+) influx and decrease in refilling of the intracellular Ca(2+) stores in HUVECs. In summary, we have identified a novel PECAM-1 transcript (Deltaexon 7) and shown that the 5th (Ig)-like domain of PECAM-1 plays a role in monocyte TEM and Ca(2+) homeostasis.

Amino Acid Sequence↗
PubMed2004

Functional self-assembling bolaamphiphilic polydiacetylenes as colorimetric sensor scaffolds.

Conjugated polymers capable of responding to external stimuli by changes in optical, electrical, or electrochemical properties can be used for the construction of direct sensing devices. Polydiacetylene-based systems are attractive for sensing applications due to their colorimetric response to changes in the local environment. Here we present the design, preparation, and characterization of self-assembling functional bolaamphiphilic polydiacetylenes (BPDAs) inspired by nature's strategy for membrane stabilization. We show that by placing polar headgroups on both ends of the diacetylene lipids in a transmembranic fashion and by altering the chemical nature of the polar surface residues, the conjugated polymers can be engineered to display a range of radiation-, thermal-, and pH-induced colorimetric responses. We observed dramatic nanoscopic morphological transformations accompanying charge-induced chromatic transitions, suggesting that both side-chain disordering and main-chain rearrangement play important roles in altering the effective conjugation lengths of the poly(ene-yne). These results establish the foundation for further development of BPDA-based colorimetric sensors.

Journal Article↗
PubMed2004

Functional lipid microstructures immobilized on a gold electrode for voltammetric biosensing of cholera toxin.

Redox functionalized microstructures of diacetylene lipids containing cell surface ligand GM1 have been prepared for the construction of an electrochemical biosensor for cholera toxin from Vibrio cholerae. Incorporation of lipid molecules with disulfide functionality into the microstructures allows for firm attachment of the microstructures on a gold surface to form a sensing interface. The observed morphology of the microstructures is platelet, with size around 240 nm as determined by dynamic light scattering and transmission electron microscopy. The electrochemical response stems from electron transfer between the electrode and the redox sites on the microstructures, and the Faradaic current is influenced by the binding events of protein toxins to the ligands displayed on the crystalline surface. Electrochemical characterization indicates that electron transfer of surface ferrocene on the gold electrode is facile. Differential pulse voltammetry was used to measure the current magnitude as a function of toxin concentration, and a working range expanding from 1.0 x 10(-8) to 5.0 x 10(-7) M was obtained. Bovine serum albumin (BSA) was used as a control agent with which no interference to Faradaic response was found in the same concentration range. Atomic force microscopy (AFM) was used to characterize the morphology and distribution of microstructures on the gold surface. The effectiveness of the design for bypassing surface fouling of proteins in electrochemical detection has been demonstrated, and a binding regulated electron hopping mechanism for the observed electrochemical behavior has been proposed.

Biosensing Techniques↗
PubMed2004

Activation of gene expression by triplex-directed psoralen crosslinks.

Psoralen-conjugated triplex-forming oligonucleotides (pso-TFOs) can target photochemical adducts to specific DNA sequences. Here, we have used pso-TFOs to activate gene expression on a plasmid. We designed a pso-TFO adapter, consisting of a single-stranded TFO for targeting DNA, linked to a double-stranded hairpin segment that contains a hybrid ecdysone response element (E/GRE) enhancer for binding activated ecdysone receptors. When targeted to the 5' flanking region of a minimal promoter, this pso-TFO adapter increased the expression of a downstream reporter gene three- to four-fold. Gene activation, however, was independent of both the E/GRE hairpin of the adapter and ecdysone receptors, suggesting it was due to an intrinsic effect of triplex. Gene activation was dependent on psoralen photo-crosslinking. Gene activation by pso-TFOs in which the psoralen was linked to the TFO via a disulfide bond was similar before and after detachment of the TFO and its release from the triplex. These results indicate that psoralen photo-crosslinks play a prominent role in activation. Gene activation was undiminished in XPA, XPD and XPG human cell lines, indicating that activation was not dependent on the complete nucleotide excision repair (NER) pathway. Collectively, these results demonstrate that TFOs can be used to direct psoralen crosslinks adjacent to a gene as a way of activating gene expression.

Binding Sites↗