Biomedical subjects

Jun Li

Publications and source records attributed to Jun Li.

At least 91 records · Page 5Linked to original sources

PubMed2006

Theoretical probing of deltahedral closo-auroboranes B(x)Au(x)2- (x = 5-12).

Using density functional theory calculations, here we show that a series of B(x)Au(x)2- (x = 5-12) dianions possesses structure and bonding similar to the famous deltahedral closo-borane cages, B(x)H(x)2-. Effective atomic charges on Au in B(x)Au(x)2- are very similar to those on H in B(x)H(x)2-, indicating that Au in the closo-auroboranes is indeed analogous to H in the closo-boranes. The present theoretical predictions of B(x)Au(x)2- suggest that the closo-auroborane species are viable new chemical building blocks that may be synthesized in bulk. The Au atoms in the closo-auroboranes represent highly atomically dispersed Au and may potentially exhibit novel catalytic and chemical properties.

Journal Article↗

PubMed2006

High rate of chimeric gene origination by retroposition in plant genomes.

Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, despite abundant retrotransposons in plants and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons, confirming a previously observed role of retroelements in generating plant retrogenes. Substitution analyses revealed that the vast majority are subject to negative selection, suggesting, along with expression data and evidence of age, that they are likely functional retrogenes. In addition, 42% of these retrosequences have recruited new exons from flanking regions, generating a large number of chimerical genes. We also identified young chimerical genes, suggesting that gene origination through retroposition is ongoing, with a rate an order of magnitude higher than the rate in primates. Finally, we observed that retropositions have followed an unexpected spatial pattern in which functional retrogenes avoid centromeric regions, while retropseudogenes are randomly distributed. These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species.

Evolution, Molecular↗

PubMed2006

Density functional theory/time-dependent DFT studies on the structures, trend in DNA-binding affinities, and spectral properties of complexes [Ru(bpy)2(p-R-pip)]2+ (R = -OH, -CH3, -H, -NO2).

Studies on the electronic structures and trend in DNA-binding affinities of a series of Ru(II) complexes [Ru(bpy)2(p-R-pip)]2+ (bpy = 2,2-bipyridine; pip = 2-phenylimidazo[4,5-f] [1,10]-phenanthroline; R = -OH, -CH3, -H, -NO2) 1-4 have been carried out, using the density functional theory (DFT) at the B3LYP/LanL2DZ level. The electronic absorption spectra of these complexes were also investigated using time-dependent DFT (TDDFT) at the B3LYP//LanL2DZ/6-31G level. The computational results show that the substituents on the parent ligand (pip) have a significant effect on the electronic structures of the complexes, in particular, on the energies of the lowest unoccupied molecular orbital (LUMO) and near some unoccupied molecular orbitals (LUMO+x, x = 1-4). With the increase in electron-withdrawing ability of the substituent in this series, the LUMO+x (x = 0-4) energies of the complexes are substantially reduced in order, for example, epsilon(LUMO)(1) approximately epsilon(LUMO)(2) > epsilon(LUMO)(3) > epsilon(LUMO)(4), whereas the pi-component populations of the LUMO+x (x = 0-4) are not substantially different. Combining the consideration of the bigger steric hindrance of complex 2, the trend in DNA-binding affinities (K(b)) of the complexes, that is, K(b)(2) < K(b)(1) < K(b)(3) < K(b)(4) can be reasonably explained. In addition, the experimental singlet metal-to-ligand charge transfer ((1)MLCT) spectra of these complexes can be well simulated and discussed by the TDDFT calculations.

2,2'-Dipyridyl↗

PubMed2006

Contribution of 5-HT2A receptor gene -1438A>G polymorphism to outcome of attention-deficit/hyperactivity disorder in adolescents.

Attention-deficit/hyperactivity disorder (ADHD) typically emerges before 7 years of age and may persist into adolescence or adulthood. The adolescent outcome can be classified into four types, including non-remission, syndromatic remission, symptomatic remission, and functional remission. Genetic factors are believed to contribute to symptom stability and change across development, so adolescent outcome may be a sub-phenotype for molecular genetic studies of ADHD. Serotonin system genes are prime candidates for this sub-phenotype, since the development of this neurotransmitter system parallels the course of ADHD. The current study examined the association between adolescent outcome in ADHD and serotonin system genes, including the -1438A>G polymorphism of the serotonin 2A receptor gene (HTR2A) and the -759C>T polymorphism of the serotonin 2C receptor gene (HTR2C). The -1438A>G polymorphism was found to be related to remission in ADHD, especially functional remission (P = 0.029). Due to potential phenotypic and etiologic heterogeneity in ADHD, the results of this study must be replicated in additional samples before they can be generalized to other populations.

Adolescent↗

PubMed2006

Sn12(2-): stannaspherene.

Stannaspherene. The Sn122- cluster is discovered to be a highly stable and highly symmetric icosahedral cage bonded by four delocalized radial pi bonds and nine delocalized on-sphere sigma bonds from the 5p orbitals of the Sn atoms. It has a diameter of 6.1 A, with a large empty interior volume, and can host most transition metal atoms inside, giving rise to a large class of endohedral chemical building blocks for cluster-assembled nanomaterials.

Journal Article↗

PubMed2006

High efficient mammalian expression and secretion of a functional humanized single-chain Fv/human interleukin-2 molecules.

AIM: To construct and produce a recombinant bispecific humanized single-chain Fv (sFv) /Interleukin-2 (IL-2) fusion protein by using mammalian cells. METHODS: The sFv/IL-2 protein was genetically engineered, and transfected to mammalian cells to determine whether the mammalian protein folding machinery can produce and secrete active sFv/IL-2 with high efficiency. RESULTS: The fusion protein was constructed and high efficiently expressed with yields up to 102 +/- 4.2 mg/L in culture supernatant of the stably transfected 293 cell line. This recombinant fusion protein consisted of humanized variable heavy (V(H)) and light (V(L)) domains of monoclonal antibody (mAb) 520C9 directed against the human HER-2/neu (c-erbB2) proto-oncogene product p185, and human IL-2 connected by polypeptide linker. The fusion protein was shown to retain the immunostimulatory activities of IL-2 as measured by IL-2-dependent cell proliferation and cytotoxicity assays. In addition to its IL-2 activities, this fusion protein also possessed antigen-binding specificity against p185, as determined by indirect ELISA using p185 positive SKOV 3ip1 cells. CONCLUSION: The large-scale preparation of the recombinant humanized sFv antibody/IL-2 fusion protein is performed with 293 cells. The recombinant humanized sFv antibody/IL-2 fusion protein may provide an effective means of targeting therapeutic doses of IL-2 to p185 positive tumors without increasing systemic toxicity or immunogenicity.

Animals↗

PubMed2006

A negative feedback loop of transcription factors that controls stem cell pluripotency and self-renewal.

Embryonic stem (ES) cells possess the ability to renew themselves while maintaining the capacity to differentiate into virtually all cell types of the body. Current evidence suggests that ES cells maintain their pluripotent state by expressing a battery of transcription factors including Oct4 and Nanog. However, little is known about how ES cells maintain the expression of these pluripotent factors in ES cells. Here we present evidence that Oct4, Nanog, and FoxD3 form a negative feedback loop to maintain their expression in pluripotent ES cells. First, Oct4 maintains Nanog activity by directly activating its promoter at sub-steady-state concentration but repressing it at or above steady-state levels. On the other hand, FoxD3 behaves as a positive activator of Nanog to counter the repressive effect of Oct4. The expression of Oct4 is activated by FoxD3 and Nanog but repressed by Oct4 itself, thus, exerting an important negative feedback loop to limit its own activity. Indeed, overexpression of either FoxD3 or Nanog in ES cells failed to increase the concentration of Oct4 beyond the steady-state concentration, whereas knocking down either FoxD3 or Nanog reduces the expression of Oct4 in ES cells. Finally, overexpression of Oct4 or Nanog failed to compensate the loss of Nanog or Oct4, respectively, suggesting that both are required for ES self-renewal and pluripotency. Our results suggest the FoxD3-Nanog-Oct4 loop anchors an interdependent network of transcription factors that regulate stem cell pluripotency.

Animals↗

PubMed2006

The OH radical-H2O molecular interaction potential.

The OH radical is one of the most important oxidants in the atmosphere due to its high reactivity. The study of hydrogen-bonded complexes of OH with the water molecules is a topic of significant current interest. In this work, we present the development of a new analytical functional form for the interaction potential between the rigid OH radical and H(2)O molecules. To do this we fit a selected functional form to a set of high level ab initio data. Since there is a low-lying excited state for the H(2)O.OH complex, the impact of the excited state on the chemical behavior of the OH radical can be very important. We perform a potential energy surface scan using the CCSD(T)/aug-cc-pVTZ level of electronic structure theory for both excited and ground states. To model the physics of the unpaired electron in the OH radical, we develop a tensor polarizability generalization of the Thole-type all-atom polarizable rigid potential for the OH radical, which effectively describes the interaction of OH with H(2)O for both ground and excited states. The stationary points of (H(2)O)(n)OH clusters were identified as a benchmark of the potential.

Journal Article↗

PubMed2006

Bioremediation of environmental endocrine disruptor di-n-butyl phthalate ester by Rhodococcus ruber.

In this study DBP-degradation strain CQ0301 was isolated from rubbish landfill soil. According to the biophysical, biochemical characteristics and analysis of 16S rRNA, the strain was identified as Rhodococcus ruber. Three new protein bands could be fractioned after DBP-inducing, which were suspected to participate the process of DBP-degrading. Catechol was suspected to be an intermediate product of DBP and cleaving the benzene ring was catalyzed by catechol 1,2-dioxygenase, because a highly activity of catechol 1,2-dioxygenase could be detected after DBP-inducing. The results of this study also showed the optimal pH value, optimal temperature which influenced the degradation rate in soil: pH 7.0-8.0, 30-35 degrees C. Kinetics of degradation reaction had been performed at different initial concentration and different time. Analyzed with SPSS10.0 software, the DBP degradation can be described as the same exponential model when the initial DBP concentration was lower than 50 mg/kg. The kinetics equation was lnC=-0.1332t + A, with the degradation half-life of DBP in soil (5.20 d). Inoculating CQ0301 could relieve DBP content in plant. We also found that adding nutrient materials into soil was useful for decreasing the DBP content in plant. In summary, we isolated a bacterium capable of degrading DBP and decreasing DBP content in plant. We also explored the mechanism of biodegradation and characterized the environmental factors influencing the degradation process in contaminated soil. Based on this work, we hope that these findings can provide some information for applying of bioremediation of DBP contaminated soil.

Biodegradation, Environmental↗

PubMed2006

Computing Ka and Ks with a consideration of unequal transitional substitutions.

BACKGROUND: Approximate methods for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) among protein-coding sequences have adopted different mutation (substitution) models. In the past two decades, several methods have been proposed but they have not considered unequal transitional substitutions (between the two purines, A and G, or the two pyrimidines, T and C) that become apparent when sequences data to be compared are vast and significantly diverged. RESULTS: We propose a new method (MYN), a modified version of the Yang-Nielsen algorithm (YN), for evolutionary analysis of protein-coding sequences in general. MYN adopts the Tamura-Nei Model that considers the difference among rates of transitional and transversional substitutions as well as factors in codon frequency bias. We evaluate the performance of MYN by comparing to other methods, especially to YN, and to show that MYN has minimal deviations when parameters vary within normal ranges defined by empirical data. CONCLUSION: Our comparative results deriving from consistency analysis, computer simulations and authentic datasets, indicate that ignoring unequal transitional rates may lead to serious biases and that MYN performs well in most of the tested cases. These results also suggest that acquisitions of reliable synonymous and nonsynonymous substitution rates primarily depend on less biased estimates of transition/transversion rate ratio.

Algorithms↗

PubMed2006

The varying microsporidian genome: existence of long-terminal repeat retrotransposon in domesticated silkworm parasite Nosema bombycis.

Microsporidia are a group of intracellular parasites with an extremely compact genome and there is no confirmed evidence that retroelements are parasitised in these organisms. Using the dataset of 200,000 genomic shotgun reads of the silkworm pebrine Nosema bombycis, we have identified the eight complete N. bombycis long-terminal repeat retrotransposon (Nbr) elements. All of the Nbr elements are Ty3/gypsy members and have close relationships to Saccharomycetes long-terminal repeat retrotransposons identified previously, providing further evidence of their relationship to fungi. To explore the effect of retrotransposons in microsporidian genome evolution, their distribution was characterised by comparisons between two N. bombycis contigs containing the Nbr elements with the completed genome of the human parasite Encephalitozoon cuniculi, which is closely related to N. bombycis. The Nbr elements locate between or beside syntenic blocks, which are often clustered with other transposable-like sequences, indicating that they are associated with genome size variation and syntenic discontinuities. The ratios of the number of non-synonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site of the open reading frames among members of each of the eight Nbr families were estimated, which reveal the purifying selection acted on the N. bombycis long-terminal repeat retrotransposons. These results strongly suggest that retrotransposons play a major role in reorganization of the microsporidian genome and they might be active. The present study presents an initial characterization of some transposable elements in the N. bombycis genome and provides some insight into the evolutionary mechanism of microsporidian genomes.

Amino Acid Sequence↗

PubMed2006

Correlation between TIMP-1 expression and liver fibrosis in two rat liver fibrosis models.

AIM: To evaluate serum TIMP-1 level and the correlation between TIMP-1 expression and liver fibrosis in immune-induced and CCL4-induced liver fibrosis models in rats. METHODS: Immune-induced and CCL4-induced liver fibrosis models were established by dexamethasone (0.01 mg) and CCL4 respectively. Serum TIMP-1 level was detected with ELISA, while histopathological grade of liver biopsy was evaluated. Spearman rank-correlation test was used to analyse the difference of the correlation between the TIMP-1 expression and hepatic fibrosis in the two fibrosis models. Furthermore, in situ hybridization was used to determine the expression difference of TIMP-1 mRNA in the two models. RESULTS: Positive correlation existed between serum TIMP-1 level of immune induced group and the histopathological stages of fibrosis liver of corresponding rats (Spearman rank-correlation test, r(s) = 0.812, P < 0.05), and the positive in situ hybridization signal of TIMP-1 mRNA was strong. In CCL4-induced liver fibrosis model, the correlation between the serum TIMP-1 level and the severity of hepatic fibrosis was not statistically significant(Spearman rank-correlation test, r(s) = 0.229, P > 0.05). And compared with immune-induced model, the positive in situ hybridization signal of TIMP-1 mRNA was weaker, while the expression variation was higher in hepatic fibrosis of the same severity. CONCLUSION: The correlations between TIMP-1 expression and liver fibrosis in two rat liver fibrosis models are different. In immune-induced model, serum TIMP-1 level could reflect the severity of liver fibrosis, while in CCL4-induced model, the correlation between the serum TIMP-1 level and the severity of hepatic fibrosis was not statistically significant.

Animals↗

PubMed2006

No association of attention-deficit/hyperactivity disorder with genes of the serotonergic pathway in Han Chinese subjects.

Attention-deficit/hyperactivity disorder (ADHD) is a complex psychiatric syndrome with cardinal symptoms of inattention, hyperactivity and impulsivity, and is a significant risk factor for poor health outcomes in both adolescence and adulthood. Etiology is clearly multifactoral, with probable contributions from both genetic and environmental factors. The genetic contribution is prominent, with estimated heritability at about 0.80. Although effects in dopamine metabolism have long been implicated in the etiology of ADHD, the role for serotonin has gained more attention in recent years. The current study examined five variants in three serotonin genes [those that code for serotonin receptors 2A (HTR2A), 5A (HTR5A) and 6 (HTR6)] in a relatively large sample of ADHD nuclear families. The transmission disequilibrium test (TDT) and the extended transmission disequilibrium test (ETDT) were performed to test for evidence of distorted transmission of alleles or haplotypes. No significant biased transmission was observed. These results do not support a substantial role of these serotonin gene in ADHD, however, additional work may be warranted before this association is definitively discounted.

Asian People↗

PubMed2006

Experimental and theoretical investigations of IR spectra and electronic structures of the U(OH)2, UO2(OH), and UO2(OH)2 molecules.

Reactions of laser-ablated U atoms and H2O2 molecules produce UO2, H2UO2, and UO2(OH)2 as major products and U(OH)2 and HU(O)OH as minor products. Complementary information is obtained from similar reactions of U atoms with D2O2, with H2 + O2 mixtures, and with H2O in excess Ar. Through extensive relativistic density functional theory calculations, we have determined the geometry structures and ground states of these U species with a variety of oxidation states U(II), U(IV), U(V), and U(VI). The calculated vibrational frequencies, IR intensities, and isotopic frequency ratios are in good agreement with the experimental values, thus supporting assignments of the observed matrix IR spectra. We propose that the reactions proceed by forming an energized [U(OH)4] intermediate from reactions of the excited U atom with two H2O2 molecules. Because of the special stability of the U(VI) oxidation state, this intermediate decomposes to the UO2(OH)2 molecule, which reveals a distinctive difference between the chemistries of U and Th, where the major product in analogous Th reactions is the tetrahedral Th(OH)4 molecule owing to the stable Th(IV) oxidation state.

Journal Article↗

PubMed2006

Immunofluorescent labeling of cancer cells with quantum dots synthesized in aqueous solution.

Thioglycolic-acid-stabilized CdTe quantum dots, synthesized directly in aqueous solution, are successfully conjugated with biotin and polyethylene glycol. Using these conjugates, we report the development of this kind of water-soluble quantum dot for immunofluorescent labeling of cancer cells. The results show that these conjugates have very low nonspecific binding and good stability against photobleaching, enabling them to be applied in many biological fields, such as cellular labeling, intracellular tracking, and other imaging applications.

Cell Line, Tumor↗

PubMed2006

Natural malaria infection in Anopheles gambiae is regulated by a single genomic control region.

We surveyed an Anopheles gambiae population in a West African malaria transmission zone for naturally occurring genetic loci that control mosquito infection with the human malaria parasite, Plasmodium falciparum. The strongest Plasmodium resistance loci cluster in a small region of chromosome 2L and each locus explains at least 89% of parasite-free mosquitoes in independent pedigrees. Together, the clustered loci form a genomic Plasmodium-resistance island that explains most of the genetic variation for malaria parasite infection of mosquitoes in nature. Among the candidate genes in this chromosome region, RNA interference knockdown assays confirm a role in Plasmodium resistance for Anopheles Plasmodium-responsive leucine-rich repeat 1 (APL1), encoding a leucine-rich repeat protein that is similar to molecules involved in natural pathogen resistance mechanisms in plants and mammals.

Alleles↗

PubMed2006

Prevention of hepatic injury by a traditional Chinese formulation, BJ-JN, in mice treated with Bacille-Calmette-Guérin and lipopolysaccharide.

The hepatoprotective effects of BJ-JN (a traditional Chinese formulation) were evaluated in Bacille-Calmette-Guérin and lipopolysaccharide (BCG/LPS)-induced immunological liver injury (ILI) in mice. BJ-JN (0.75, 1.5, 3 g/kg) was administered via gavage daily for 10 days. Liver index (liver weight/body weight), serum levels of alanine aminotransferase (ALT), hepatic nitric oxide (NO), malondialdehyde (MDA) content, superoxide dismutase (SOD) activity, splenocyte proliferation, production of tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1) by peritoneal macrophages, and histopathologic changes of the liver were evaluated following the 10 days treatment. BJ-JN (0.75, 1.5, 3 g/kg) effectively reduced the BCG/LPS-induced elevated liver index, serum ALT levels, hepatic NO and MDA content, and restored hepatic SOD activity in ILI mice. BJ-JN treatment also alleviated diminished splenocyte proliferation induced by concanavalin A (ConA) and repressed abnormally high levels of TNF-alpha and IL-1 from peritoneal macrophages. The histopathological analysis suggested that BJ-JN reduced the degree of liver injury of ILI mice. These results suggest that BJ-JN has a protective and therapeutic effect on ILI mice, which might be associated with its antioxidant properties, ability to reduce NO production and immunoregulatory function.

Alanine Transaminase↗

PubMed2006

Chemical and biological assessment of a chinese herbal decoction containing Radix Astragali and Radix Angelicae Sinensis: Determination of drug ratio in having optimized properties.

Danggui Buxue Tang (DBT), a Chinese medicinal decoction that is commonly used as a dietary supplement in treating woman with menopausal irregularity, contains two herbs: Radix Astragali (Huangqi) and Radix Angelicae Sinensis (Danggui). The ratio of Radix Astragali and Radix Angelicae Sinensis used in DBT should be 5:1 as described in China in 1247 A.D.; however, the rationale of this formula has not been given. Here, the chemical and biological properties of DBT, prepared from different ratios of the drugs, were determined. Significantly, higher amounts of Radix Astragali-derived astragaloside IV, calycosin, and formononetin and Radix Angelicae Sinensis-derived ferulic acid were found in DBT with Radix Astragali and Radix Angelicae Sinensis in a 5:1 ratio. By using the biological effects of DBT in stimulating osteoblast proliferation, estrogen promoter activation, and anti-platelet aggregation activity, the drug ratio of 5:1 produced the best effects. In addition, the use of ethanol-treated Radix Angelicae Sinensis enhanced the efficacy of DBT, and the treatment further increased the solubilities of chemical constituents. By analyzing the correlation of chemical and biological results, several chemicals showed positive correlation with DBT-induced bioactivities. The current results support the ancient formulation of DBT, and the identified chemicals could serve as markers for quality control of DBT.

Angelica sinensis↗