Computational studies of the binding modes of A 2A adenosine receptor antagonists

A molecular docking study was performed on several structurally diverse A(2A) AR antagonists, including xanthines, and non-xanthine type antagonists to investigate their binding modes with A(2A) adenosine receptor (AR), one of the four subtypes of AR, which is currently of great interest as a target for therapeutic intervention, in particular for Parkinson's disease. The high-affinity binding site was found to be a hydrophobic pocket with the involvement of hydrogen bonding interactions as well as pi-pi stacking interactions with the ligands. The detailed binding modes for both xanthine and non-xanthine type A(2A) antagonists were compared and the essential features were extracted and converted to database searchable queries for virtual screening study of novel A(2A) AR antagonists. Findings from this study are helpful for elucidating the binding pattern of A(2A) AR antagonists and for the design of novel active ligands.

Polyubiquitin chains: functions, structures, and mechanisms

Ubiquitin is a highly conserved 76-amino acid polypeptide that is found throughout the eukaryotic kingdom. The covalent conjugation of ubiquitin (often in the form of a polymer) to substrates governs a variety of biological processes ranging from proteolysis to DNA damage tolerance. The functional flexibility of this post-translational modification has its roots in the existence of a large number of ubiquitinating enzymes that catalyze the formation of distinct ubiquitin polymers, which in turn encode different signals. This review summarizes recent advances in the field with an emphasis on the non-canonical functions of polyubiquitination. We also discuss the potential mechanism of chain linkage specification as well as how structural disparity in ubiquitin polymers may be distinguished by ubiquitin receptors to translate the versatile ubiquitin signals into various cellular functions.

Transcriptional differences between the male-sterile mutant bcms and wild-type Brassica campestris ssp. chinensis reveal genes related to pollen development

A novel male-sterile mutant which lacks mature pollen, Brassisa campestris male sterile (bcms), was identified in Brassica campestris L. ssp. chinensis Makino (syn. B. rapa ssp. chinensis). Genetic analysis revealed that bcms was controlled by a single recessive mutation locus. Genome-wide transcriptional profiling was performed on the flower buds of both the bcms mutant and the wild-type from which it originated, and profiling analysis indicated that there were numerous changes in gene expression attributable to the gene mutation. This mutation resulted in down-regulation of a variety of genes and up-regulated expression of a few other genes. A total of 51 transcript-derived fragments (TDFs) were isolated: 32 specifically and 12 predominantly accumulated in wild-type flower buds, and two specifically and five predominantly accumulated in bcms flower buds. Sequence analysis showed that some of these TDFs share significant similarities with genes involved in different aspects of cellular development, such as signal transduction, cell wall biosynthesis and regulation. Most other TDFs showed no or very poor sequence similarities to entries in any database and might represent new candidate proteins involved in pollen development. Furthermore, spatial and temporal expression pattern analysis of 20 genes derived from cDNA-amplified fragment length polymorphism in different tissues of both the bcms and wild-type plants revealed their complex and dynamic expression patterns. The bcms mutant and the genes isolated in this paper provide excellent material for future studies on the molecular mechanism of male sterility.

Combined method for artifact reduction in surface electroenterogram

Surface electroenterogram (EEnG) is a non-invasive method for monitoring the intestinal motility. However, surface EEnG recordings are contaminated by movement artifact, cardiac activity, respiratory artifact and other interferences. The aim of this work is to remove movement artifacts by means of a combined method of empirical mode decomposition (EMD) and independent component analysis (ICA). Four recording sessions were conducted on canine model. Surface signals from 4 different channels are decomposed using EMD. Resulting intrinsic mode functions are the inputs of ICA analysis which permits to separate and identify the activities of different origin. Signal components associated to movement artifacts are removed and the original signals are reconstructed by means of an inverse procedure. The results show that the proposed method allows extracting and cancelling movement artifacts from surface EEnG, avoiding the presence of irregular peaks in external intestinal motility indexes. Therefore, the proposed method could be useful to reduce artifacts in EEnG recording and to provide more robust non-invasive intestinal motility indicators.

Cell death in mammalian development

During embryogenesis there is an exquisite orchestration of cellular division, movement, differentiation, and death. Cell death is one of the most important aspects of organization of the developing embryo, as alteration in timing, level, or pattern of cell death can lead to developmental anomalies. Cell death shapes the embryo and defines the eventual functions of the organs. Cells die using different paths; understanding which path a dying cell takes helps us define the signals that regulate the fate of the cell. Our understanding of cell death in development stems from a number of observations indicating genetic regulation of the death process. With today's increased knowledge of the pathways of cell death and the identification of the genes whose products regulate the pathways we know that, although elimination of some of these gene products has no developmental phenotype, alteration of several others has profound effects. In this review we discuss the types and distributions of cell death seen in developing mammalian embryos as well as the gene products that may regulate the process.

Quantification of combined method for interferences reduction in multichannel surface electroenterogram

Surface electroenterogram (EEnG) is a non-invasive method for monitoring the intestinal motility. However, surface EEnG signals are contaminated by strong physiological interferences. The main interferences which affect high-frequency components of surface EEnG are cardiac activity and movement artifacts. The aim of this work is to quantify the effectiveness of a combined method based on empirical mode decomposition and independent component analysis to remove these interferences from multichannel surface EEnG. In order to do so, several parameters were calculated from five recording sessions: Signal-to-ECG interference ratio (S/I) and variation of energy over 2 Hz (EF2). The results show that the S/I of processed signals was significantly higher than that of original signals, moreover the improvement of the S/I ratio is due to the attenuation of energy associated to interference. The proposed method also allows cancelling movement artifacts from surface EEnG, reducing considerably the non-physiological variation of EF2. Furthermore after the application of the combined method, correlation coefficient between EF2 of internal recording with EF2 of surface recording is greatly higher. Therefore, the proposed method could be helpful to reduce high-frequency interferences in EEnG recording and to provide more robust non-invasive intestinal motility indicators.

High resolution spectroscopy of (lambda)(12)B by electroproduction

An experiment measuring electroproduction of hypernuclei has been performed in hall A at Jefferson Lab on a 12C target. In order to increase counting rates and provide unambiguous kaon identification two superconducting septum magnets and a ring imaging Cherenkov detector were added to the hall A standard equipment. An unprecedented energy resolution of less than 700 keV FWHM has been achieved. Thus, the observed (Lambda)(12)B spectrum shows for the first time identifiable strength in the core-excited region between the ground-state s-wave Lambda peak and the 11 MeV p-wave Lambda peak.

The study of the relationship between Notch signal transduction pathway and polycomb protein Bmi1 in colorectal caner cells

14501

Background: As is known the polycomb group protein BMI1 has been shown to support normal stem cell proliferation via its putative stem cell factor function. However, the potential molecular mechanism of BMI1 act as a cancer stem cell factor may also promote cancer development is unclear. In this study we demonstrated for the first time that Notch signal transduction pathway regulating expression of Bmi1 in colorecta caner cells and investigate the Notch1 mRNA and Bmi1 mRNA level in human colorectal cancer samples and their correlation with clinicopathological parameters of colorectal cancer. Methods and Results: We assessed Notch1 and Bmi1 mRNA in 50 cases of colorectal cancer and adjacent normal tissue by RT-PCR. The immunohistochemistry was used to determine the expression of ICN and in the 50 tissues of colorectal cancer and normal mucosa. Bmi1 SW480 cells were treated with DAPT (g-secretase inhibitor) at different times. MTT assay and flow cytometry were used to measure the proliferation and apoptosis of SW480 cells. The expression of ICN, Bmi1 were measured by western blot. Notch1 and Bmi1 mRNA level were increased in colorectal cancer compared with adjacent normal mucosa (P<0.05), the median values were 1.97-fold, 1.88-fold, respectively. It was found that overexpression of Notch1 and Bmi1 was related to differentiation and lymph nodes metastasis in colorectal cancer (P<0.05). The correlation between Notch1 and Bmi1 mRNA level, ICN and Bmi1 protein level are significant at the 0.01 level. Treating SW480 with DAPT, resulted in significant growth inhibition, apoptosis induction and downregulation of ICN and Bmi1. Conclusion: Our results show that overexpression of Notch1 and Bmi1 may play a critical role in the development of colorectal cancer. Notch1 signal transduction pathway regulating expression of Bmi1 in colorectal cancer cells.Blockade of Notch1 signal pathway can inhibit proliferation and accelerate apoptosis of colorectal cancer. [Key words] Colorectal cancer; BMI1; Signal transducers and activators of transcription3; Western blotting

No significant financial relationships to disclose.

Empirical mode decomposition: a method to reduce low frequency interferences from surface electroenterogram

The surface electroenterogram (EEnG) is a non-invasive method of studying myoelectrical bowel activity. However, surface EEnG recordings are contaminated by cardiac activity, respiratory and motion artifacts, and other sources of interference. The aim of this work is to remove the respiration artifact and the very low frequency components from surface EEnG by means of empirical mode decomposition (EMD). Eleven recording sessions were carried out on canine model. Several parameters were calculated before and after the application of the method: signal-to-interference ratio (S/I ratio) and the attenuation level of the signal and of interference. The results show that the S/I ratio was significantly higher after the application of the method (3.68+/-5.54 dB vs. 10.45+/-3.65 dB), the attenuation level of signal and of interference is -0.49+/-0.80 dB versus -7.26+/-5.42 dB, respectively. Therefore, EMD could be a useful aid in identifying the intestinal slow wave and in removing interferences from EEnG recordings.

Amplification and specific expression of T-bet gene in nasal NK/T-cell lymphoma

To define the specific genetic alterations in nasal natural killer/T-cell lymphoma (N-NK/T-L), the assay of restriction landmark genomic scanning (RLGS), a genome-wide method, was used to investigate a pair of genomic DNA from N-NK/T-L cells and peripheral blood leukocytes of the same patient. The intensified spots in displayed N-NK/T-L gel of RLGS were subjected to bioinformatic analysis by virtual genome scan (VGS) and one of candidate spots proved to be T-bet gene (T-box expressed in T-cell). The pair of samples was consequently analysed by Southern hybridization, revealing genomic amplification of T-bet but not different status of DNA methylation. The amplification of T-bet was also discovered in other cases of N-NK/T-L by dot blotting. The expression of T-bet was investigated by in situ hybridization (ISH) and immunohistochemistry (IHC). The results showed that T-bet predominantly expressed in N-NK/T-L (ISH: 90.0%, 18/20; IHC: 80%, 16/20), while few cases of B-cell lymphoma (ISH: 11.8%, 2/17; IHC: 17.6%, 3/17) or T-cell lymphoma (ISH: 33.3%, 2/6; IHC: 16.7%, 1/6) were positive. The difference of T-bet expression in either ISH or IHC between N-NK/T-L and B-cell lymphoma or T-cell lymphoma was statistically significant (P < 0.05). Moreover, the expression of T-bet was not detected in normal spleen tissue and chronic inflammatory nasal mucosa. The results suggested that the amplification of T-bet gene or resulting its over-expression of T-bet gene might be involved in the development of N-NK/T-L and thus it should be worth confirming whether the over-expression of T-bet be helpful to the diagnosis of N-NK/T-L in further study.

Stilbenoids from Stemona sessilifolia

Two new dihydrostilbenes, stilbostemins H (1), I (2), and a new dihydrophenanthrene, stemanthrene E (3), were isolated and identified from the roots of Stemona sessilifolia, together with known stilbostemins B, D and G, and stemanthrenes A and C (4-8). Structures of new stilbenoids were established by 1D and 2D (1)H NMR and (13)C NMR spectroscopic analyses.

Anti-malarial agent artesunate inhibits TNF-alpha-induced production of proinflammatory cytokines via inhibition of NF-kappaB and PI3 kinase/Akt signal pathway in human rheumatoid arthritis fibroblast-like synoviocytes

OBJECTIVES

Recent studies indicate that the anti-malarial agent artemisinin and its derivatives may exert an anti-inflammatory effect. In this study, we explored the effect of artesunate, an artemisinin derivative, on tumour necrosis factor (TNF)-alpha-induced production of interleukins, IL-1beta, IL-6 and IL-8, in human rheumatoid arthritis (RA) fibroblast-like synoviocytes (FLS), and further investigated the signal mechanism by which this compound modulates those cytokines' production.

METHODS

RA FLS obtained from patients with active RA were stimulated with TNF-alpha and incubated with artesunate, and IL-1beta, IL-6 and IL-8 production was measured by ELISA. DNA-binding activity and nuclear translocation of nuclear factor kappa B (NF-kappaB) were measured by a sensitive multi-well colourimetric assay and confocal fluorescence microscopy, respectively. Signal transduction proteins expression was measured by western blot.

RESULTS

Artesunate decreased the secretion of IL-1beta, IL-6 and IL-8 from TNF-alpha-stimulated RA FLS in a dose-dependent manner. Artesunate also prevented TNF-alpha-induced nuclear NF-kappaB translocation, DNA-binding activity and gene transcriptional activity, as well as phosphorylation and degradation of IkappaBalpha, but phosphorylation of p38 mitogen-activated protein kinase, extracellular signal-regulated kinase and c-Jun N-terminal kinase were unaffected. The production of IL-1beta, IL-6 and IL-8 induced by TNF-alpha was decreased by pyrrolidine dithiocarbamate (PDTC), a chemical inhibitor of NF-kappaB. These observations suggest that artesunate inhibits production of IL-1beta, IL-6 and IL-8 through inhibition of NF-kappaB signalling pathway. We also showed that artesunate prevented Akt phosphorylation. TNF-alpha-induced production of IL-1beta, IL-6 and IL-8 was hampered by treatment with the phosphatidylinositol 3 (PI3) kinase inhibitor LY294002, suggesting that inhibition of Akt activation might inhibit IL-1beta, IL-6 and IL-8 production induced by TNF-alpha.

CONCLUSIONS

Our results indicate that artesunate exerts an anti-inflammatory effect in RA FLS and provide the evidence that artesunate may have therapeutic potential for RA.

Precision measurements of the nucleon strange form factors at Q2 approximately 0.1 GeV2

We report new measurements of the parity-violating asymmetry A(PV) in elastic scattering of 3 GeV electrons off hydrogen and 4He targets with <theta(lab)> approximately 6.0 degrees . The 4He result is A(PV)=(+6.40+/-0.23(stat)+/-0.12(syst))x10(-6). The hydrogen result is A(PV)=(-1.58+/-0.12(stat)+/-0.04(syst))x10(-6). These results significantly improve constraints on the electric and magnetic strange form factors G(E)(s) and G(M)(s). We extract G(E)(s)=0.002+/-0.014+/-0.007 at <Q(2)>=0.077 GeV2, and G(E)(s)+0.09G(M)(s)=0.007+/-0.011+/-0.006 at <Q(2)>=0.109 GeV2, providing new limits on the role of strange quarks in the nucleon charge and magnetization distributions.

Labdane diterpenes from the seeds of Platycladus orientalis

Two new labdane diterpenes, 14(R),15-dihydroxy-8(17),12(E)-labdadien-19-oic acid (1) and 16-methyl-12,15-epoxy-8(17),13-labdadien-19-oic acid (2), together with four known compounds, were isolated from the seeds of Platycladus orientalis. Their structures were established by spectroscopic methods. The stereochemistry of compound 1 was defined by X-ray crystallographic analysis.