Biomedical subjects
Publications and source records attributed to Bin Liu.
A novel spin trap containing an iodoacetamide group has been synthesized and then used to target polypeptides, i.e. glutathione and bovine serum albumin, by which the resulting covalently bonded bioconjugates exhibit great potential for the application of spin trapping of transient radicals in biological systems.
The identification of serum biomarkers as a means of the early diagnosis and finding possible therapeutic targets in cancers is of increasing interest. In the present study, cells of human tongue cancer cell line Tca8113 were subcutaneously inoculated into nude mice, while control nude mice were injected with phosphate-buffered saline. Two weeks after injection, serum from mice was collected for proteomic analysis using two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). Comparing the serum 2-DE maps from the tumor-bearing mice with those produced from control mice, we found that squamous cell carcinoma antigen 1 was over-expressed only in tumor-bearing mice. Squamous cell carcinoma antigen 1 was also up-regulated in clinical tongue cancer patients by RT-PCR and Western-blotting. These results indicate that squamous cell carcinoma antigen 1 may be of great potential as the biomarker of tongue cancer and as the potential therapeutic target for gene therapy.
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are two types of noncoding RNAs involved in developmental regulation, genome maintenance, and defense in eukaryotes. The activity of Dicer or Dicer-like (DCL) proteins is required for the maturation of miRNAs and siRNAs. In this study, we cloned and sequenced 66 candidate rice (Oryza sativa) miRNAs out of 1,650 small RNA sequences (19 to approximately 25 nt), and they could be further grouped into 21 families, 12 of which are newly identified and three of which, OsmiR528, OsmiR529, and OsmiR530, have been confirmed by northern blot. To study the function of rice DCL proteins (OsDCLs) in the biogenesis of miRNAs and siRNAs, we searched genome databases and identified four OsDCLs. An RNA interference approach was applied to knock down two OsDCLs, OsDCL1 and OsDCL4, respectively. Strong loss of function of OsDCL1IR transformants that expressed inverted repeats of OsDCL1 resulted in developmental arrest at the seedling stage, and weak loss of function of OsDCL1IR transformants caused pleiotropic developmental defects. Moreover, all miRNAs tested were greatly reduced in OsDCL1IR but not OsDCL4IR transformants, indicating that OsDCL1 plays a critical role in miRNA processing in rice. In contrast, the production of siRNA from transgenic inverted repeats and endogenous CentO regions were not affected in either OsDCL1IR or OsDCL4IR transformants, suggesting that the production of miRNAs and siRNAs is via distinct OsDCLs.
Centromeres are required for faithful segregation of chromosomes in cell division. It is not clear what kind of sequences act as functional centromeres and how centromere sequences are organized in Oryza punctata, a BB genome species. In this study, we found that the CentO centromeric satellites in O. punctata share high homology with the CentO satellites in O. sativa. The O. punctata centromeres are characterized by megabase tandem arrays that are flanked by centromere-specific retrotransposons. Immunostaining with an antibody specific to CENH3 indicates that the 165-bp CentO satellites are the major component for functional centromeres. Moreover, both strands of CentO satellites are highly methylated and transcribed and produce small interfering RNA, which may be important for the maintenance of centromeric heterochromatin and centromere function.
Shigella strains are important human pathogens and are normally identified by their O antigens. O antigen is an essential part of the lipopolysaccharide present in the outer membrane of Gram-negative bacteria and plays a role in pathogenicity. Structural and genetic organization of the Shigella boydii type 18 O antigen was investigated. As judged by sugar and methylation analyses and NMR spectroscopy data, the O antigen has a linear pentasaccharide repeating unit (O unit), which consists of three L-rhamnose residues, and one residue each of D-galacturonic acid (D-GalA) and N-acetylgalactosamine (D-GalNAc), and the following structure of the O unit was established. -->3)-beta-L-Rhap-(1-->4)-alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->2)-alpha-D-GalpA-(1-->3)-alpha-D-GalpNAc-(1--> The O antigen gene cluster of S. boydii type 18, which contains nine open reading frames (ORFs), was found between galF and gnd. Based on homology, all of the ORFs were identified as O antigen synthesis genes, involved in the synthesis of rhamnose, transfer of sugars, and processing of O unit. Genes specific for S. boydii type 18 were identified, which can be potentially used for the development of a PCR-based assay for the identification and detection of this strain.
Integrins are modular (alphabeta) heterodimeric proteins that mediate cell adhesion and convey signals across the plasma membrane. Interdomain motions play a key role in signal transduction by propagating structural changes through the molecule, thus controlling the activation state and adhesive properties of the integrin. We expressed a soluble fragment of the human integrin beta2 subunit comprising the plexin-semaphorin-integrin domain (PSI)/hybrid domain/I-EGF1 fragment and present its crystal structure at 1.8-A resolution. The structure reveals an elongated molecule with a rigid architecture stabilized by nine disulfide bridges. The PSI domain is located centrally and participates in the formation of extended interfaces with the hybrid domain and I-EGF1 domains, respectively. The hybrid domain/PSI interface involves the burial of an Arg residue, and contacts between PSI and I-EGF1 are mainly mediated by well conserved Arg and Trp residues. Conservation of key interacting residues across the various integrin beta subunits sequences suggests that our structure represents a good model for the entire integrin family. Superposition with the integrin beta3 receptor in its bent conformation suggests that an articulation point is present at the linkage between its I-EGF1 and I-EGF2 modules and underlines the importance of this region for the control of integrin-mediated cell adhesion.
Raman and FT-IR spectra were employed to investigate the dispersion of molybdena on mixed TiO2 (rutile and anatase, signed as R and A) with different BET surface ratios of rutile/TiO2(R + A). The results showed that (1) molybdena would preferentially disperse on the rutile surface in mixed TiO2; (2) for MoO3/rutile with low molybdena loading (e.g., 0.20 mmol/100 m2 rutile), a dispersed molybdena species existed on the rutile surface in an isolated tetrahedral coordination environment, while for MoO3/rutile with high molybdena loading (e.g. 0.82 mmol/100 m2 rutile), a polymeric molybdena species could be detected on the rutile surface; (3) for the MoO3/anatase sample, a dispersed molybdena species existed on the anatase surface in a polymeric coordination environment; and (4) the formation of the Bronsted acid site on the surface of rutile and anatase should be related to the polymeric molybdena species. All these results have been discussed via the interaction between OH groups of molybdena and OH groups of rutile and anatase, and it seems reasonable to suggest that, for the lower molybdena loading, the different states of the dispersed molybdena species should result from the different dehydration orders of OH groups of the molybdena and surface OH groups of rutile and anatase.
Four mixed-valent ruthenium diphosphonates, namely, Na(4)[Ru(2)(hedp)(2)X]x16H(2)O [X = Cl (1), Br (2)], K(3)[Ru(2)(hedp)(2)(H(2)O)(2)]x6H(2)O (3), and Na(7)[Ru(2)(hedp)(2)Fe(CN)(6)]x24H(2)O (4), where hedp represents 1-hydroxyethylidenediphosphonate [CH(3)C(OH)(PO(3))(2)](4-), were synthesized and structurally characterized. Compounds 1, 2, and 4 show linear chain structures in which the mixed-valent [Ru(2)(hedp)(2)](3-) dimers are linked by X(-) or [Fe(CN)(6)](4-) bridges. Compound 3 contains discrete species of [Ru(2)(hedp)(2)(H(2)O)(2)](3-) where the axial positions of [Ru(2)(hedp)(2)](3-) paddlewheel are terminated by water molecules. Magnetic studies show that significant antiferromagnetic exchanges are mediated between the [Ru(2)(hedp)(2)](3-) (S = 3/2) units through halide bridges in compounds 1 and 2.
[reaction: see text] A novel chiral monodentate spiro phenylphospholane ligand 4 was prepared from a readily accessible, enantiomerically pure 1,1'-spirobiindane-7,7'-diol in high yield. This ligand has proven to be efficient for Pd-catalyzed enantioselective allylation of aldehydes with allylic alcohols. Aromatic, heteroaromatic, and aliphatic aldehydes gave homoallylic alcohols in good enantioselectivities (up to 83% ee) and excellent anti diastereoselectivities (up to 99:1 dr).
We use first-principles quantum-chemical approaches to study absorption and emission properties of recently synthesized distyrylbenzene (DSB) derivative chromophores and their dimers (two DSB molecules linked through a [2.2]paracyclophane moiety). Several solvent models are applied to model experimentally observed shifts and radiative lifetimes in Stokes nonpolar organic solvents (toluene) and water. The molecular environment is simulated using the implicit solvation models, as well as explicit water molecules and counterions. Calculations show that neither implicit nor explicit solvent models are sufficient to reproduce experimental observations. The contact pair between the chromophore and counterion, on the other hand, is able to reproduce the experimental data when a partial screening effect of the solvent is taken into account. Based on our simulations we suggest two mechanisms for the excited-state lifetime increase in aqueous solutions. These findings may have a number of implications for organic light-emitting devices, electronic functionalities of soluble polymers and molecular fluorescent labels, and their possible applications as biosensors and charge/energy conduits in nanoassemblies.
A series of compounds were designed and synthesized to examine how through-space and through-bond electron delocalization respond to solvent effects. The general strategy involves the study of "dimers" of the distyrylbenzene chromophore held in close proximity by the [2.2]paracyclophane core and a systematic dissection of the chromophore into components with through-space and through-bond electronic delocalization. Steady state and time-resolved fluorescence spectroscopy in a range of solvents reveals a red-shift in emission and an increase in the intrinsic fluorescence lifetime for the emitting state in polar solvents when donor substituents are absent. We propose that through-space delocalization across the [2.2]paracyclophane core is more polarizable in the excited state, relative to the through-bond (distyrylbenzene based) excited state. When strong donors are attached to the distyrylbenzene chromophore, the charge transfer character of the distyrylbenzene-based excited state dominates fluorescence properties.
A selective fluorescent chemodosimeter for mercury ion based on the mercury-promoted intramolecular cyclic guanylation of thiourea connected on 1, 8-naphthalimide is described.
The shear viscosity of a two-dimensional (2D) liquid was calculated using molecular dynamics simulations with a Yukawa potential. The viscosity has a minimum at a Coulomb coupling parameter Gamma of about 17, arising from the temperature dependence of the kinetic and potential contributions. Previous calculations of 2D viscosity were less extensive as well as for a different potential. The stress autocorrelation function was found to decay rapidly, contrary to earlier work. These results are useful for 2D condensed matter systems and are compared to a dusty plasma experiment.
BACKGROUND: Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the artiodactyls. RESULTS: We have generated approximately 3.84 million shotgun sequences (0.66X coverage) from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project") together with an initial evolutionary analysis. The non-repetitive fraction of the sequences was aligned to the UCSC human-mouse alignment and the resulting three-species alignments were annotated using the human genome annotation. Ultra-conserved elements and miRNAs were identified. The results show that for each of these types of orthologous data, pig is much closer to human than mouse is. Purifying selection has been more efficient in pig compared to human, but not as efficient as in mouse, and pig seems to have an isochore structure most similar to the structure in human. CONCLUSION: The addition of the pig to the set of species sequenced at low coverage adds to the understanding of selective pressures that have acted on the human genome by bisecting the evolutionary branch between human and mouse with the mouse branch being approximately 3 times as long as the human branch. Additionally, the joint alignment of the shot-gun sequences to the human-mouse alignment offers the investigator a rapid way to defining specific regions for analysis and resequencing.
Phonons in a one-dimensional chain of charged microspheres suspended in a plasma were studied in an experiment. The phonons correspond to random particle motion in the chain; no external manipulation was applied to excite the phonons. Two modes were observed, longitudinal and transverse. The velocity fluctuations in the experiment are analyzed using current autocorrelation functions and a phonon spectrum. The phonon energy was found to be unequally partitioned among phonon modes in the dusty plasma experiment. The experimental phonon spectrum was characterized by a dispersion relation that was found to differ from the dispersion relation for externally excited phonons. This difference is attributed to the presence of frictional damping due to gas, which affects the propagation of externally excited phonons differently from phonons that correspond to random particle motion. A model is developed and fit to the experiment to explain the features of the autocorrelation function, phonon spectrum, and the dispersion relation.
OBJECTIVE: To evaluate whether RNA interference can protect porcine endothelial cells from complement mediated cytotoxicity. METHODS: Immortalized porcine aortic endothelial cells of the line PED were cultured and transfected with alpha1,3-galactosyltransferase (alpha1, 3-GT) specific siRNAs. Cells transfected with mismatch SiRNA was used as negative controls. Forty-eight hours later the cells were collected. The expression of alpha1, 3-GT mRNA was examined by RT-PCR. The expression of alpha-Gal was examined by flow cytometry. PED cells ere labeled with (51)Cr and mixed with normal human serum (NHS). The release of (51)Cr was measured by gamma-ray counter. Heat inactivated NHS (HINHS) was used as control. RESULTS: Two isoforms (isoform 1 and isoform 2) were amplified from the PED cells. The expression of alpha1, 3-GT in the PED cells transfected with SiRNA-1 was lower by 70% in comparison with the mock group (69% for the isoform 1 and 72% for the isoform 2, both P < 0.05). However, the expression of alpha1, 3-GT in the PED cells transfected with SiRNA21 was not different from those in the mock group and mismatch group (both P > 0.05). Flow cytometry showed that the average fluorescence intensity of the PED cells transfected with SiRNA-1 was 52, 9, significantly lower than that of the mismatch group and mock group (493.9 and 5-5.7 respectively, both P < 0.0). Fluorescence microscopy observed the "silence effect" of alphaGal after SiRNA-1 transfection. Added with 20% and 40% NHS, the cell dissolution rate of the SiRNA transfection group was lower than that of the mock group by 70% and 60% respectively. CONCLUSIONS: alpha1, 3GT gene silencing actually occurs following transfection of SiRNA-1. Porcine endothelial cells can be the targets of RNAi.
The importance of cyclooxygenase-2 (COX-2) in mediating Parkinson's disease (PD) was suggested in reports, indicating that COX-2 selective inhibitors or genetic knockout reduce 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced dopaminergic (DA) neurotoxicity in a mouse model of PD. However, cell types and mechanisms underlying the activation of COX-2 have not been clearly elucidated in these animal studies. Using primary neuron-glia cultures, we aimed to determine 1) whether microglia participate in 1-methyl-4-phenylpryridinium (MPP)-induced COX-2 activation and 2) whether the activation of COX-2 contributes to subsequent neurotoxicity. MPP, in a concentration-dependent manner, increased prostaglandin E2 (PGE2) production in mixed neuron-microglia cultures but not in enriched neuron, microglia, or astroglia cultures nor in mixed neuron-astroglia cultures. MPP-induced PGE2 increase was completely abolished by treatment with DuP697, a COX-2 selective inhibitor. DuP697 also significantly reduced MPP-induced DA neurotoxicity as determined by DA uptake assay. Immunocytochemistry and confocal microscopy studies showed enhanced COX-2 expression in both microglia and neurons after MPP treatment. However, neuronal increase in COX-2 expression was not totally dependent on the production of PGE2 from microglia, since microglia deficient in COX-2 only attenuated, but did not completely block, MPP-increased PGE2 production in mixed neuron-microglia cultures, suggesting that part of PGE2 production was originated from neurons. Together, these results indicate that MPP-induced COX-2 expression and subsequent PGE2 production depend on interactions between neurons and microglia. Microgliosis may also be responsible for the COX-2 activation in neurons, leading to the enhanced DA neurotoxicity, which, in turn, reinforces microgliosis. Thus inhibition of microgliosis and COX-2 activity may stop this vicious circle and be valuable strategies in PD therapy.
Orbilia querci, a new nematode-trapping fungus, was found on rotten wood of Quercus sp. in Huai-rou County, Beijing, China. It is characterized by having a tear-shaped spore body in the cylindrical ascospore. Pure culture was obtained from the ascospores. Conidiophores were simple or occasionally branched, bearing a single conidium on the tip. Conidia were spindle-shaped, mostly with 3-septa. Nematodes were captured by means of adhesive stalked knobs. The adhesive knobs were produced frequently on nutritional agar plates even in the absence of challenging nematodes. Its anamorph is placed in Dactylellina and named as D. querci. The sequence divergence of the ITS1 region between the fungus and the other knob-forming species tested was 23.8-33.4%, supporting O. querci as a distinct species. This is the first report of the connection between a knob-forming nematophagous hyphomycete and an Orbilia teleomorph.