A graphical method to construct a phylogenetic tree

A 3D graphical representation of DNA sequences, which has no circuit or degeneracy, is derived for mathematical denotation of DNA sequence. Based on this graphical representation, we propose a new sequence distance measure. We make use of the corresponding similarity matrix to construct a phylogenic tree by virtue of the fuzzy theory. The examination of phylogenic tree belong to eight species illustrates the utility of our approach. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Compactification of a myelin mimetic Langmuir monolayer upon adsorption and unfolding of myelin basic protein

The surface shear viscosity of a myelin mimetic Langmuir monolayer is investigated upon adsorption of myelin basic protein (MBP). We measure an increase of the surface shear viscosity at picomolar concentrations of the protein, suggesting that the globular conformation of MBP changes upon adsorption at the monolayer. The conformational change enables hydrodynamic interactions of the proteins, with a typical separation of hundreds of nanometers. This unfolding is essential for the compactification of the myelin sheath, serving an enhanced saltatory signal transduction in vertebrates. The viscometry used extends the sensitivity of standard surface viscometers toward lower viscosities.     

Tocopherols and Triterpenoids from Sida acuta

A new tocopherol derivative, 7_a‐methoxy‐α‐tocopherol ( 1 ), and a new taraxastane triterpene, taraxast‐1,20(30)‐dien‐3‐one ( 5 ), together with four known compounds, β‐tocopherol ( 2 ), α‐tocopherol ( 3 ), α‐tocospiro B ( 4 ) and taraxasterone ( 6 ) were isolated from the whole plant of Sida acuta. Their structures were elucidated by spectral analysis including MS, 1D and 2D‐NMR spectroscopy. Among those compounds, compounds 1 , 2 , and 3 showed significant antioxidant effect (EC₅₀ = 86.9, 68.2, and 70.9 μM, respectively) in the DPPH radicals scavenging activity assay.     

Four Novel Eremophilanolides from Ligularia sagitta

Four new eremophilanolides, isolated from Ligularia sagitta, were identified as (1β,3β,6β,8β,10β)‐6‐acetoxy‐3‐(angeloyloxy)‐1,10‐epoxy‐8‐hydroxyeremophil‐7(11)‐en‐8,12α‐olide ( 1 ), (1β,3β,6β,8β,10β)‐3‐(angeloyloxy)‐1,10‐epoxy‐6,8‐dihydroxyeremophil‐7(11)‐en‐8,12α‐olide ( 2 ), (1β,3β,6β,8β,10β)‐3‐(angeloyloxy)‐1,10‐epoxy‐8‐ethoxy‐6‐hydroxyeremophil‐7(11)‐en‐8,12α‐olide ( 3 ), and (1β,3β,8β,10β)‐3‐(angeloyloxy)‐1,10‐epoxy‐8‐hydroxyeremophil‐7(11)‐en‐8,12α‐olide ( 4 ). Their structures were elucidated by spectroscopic methods, including 2D‐NMR techniques and chemical transformations.     

catena‐Poly[[tetra­aqua­manganese(II)]‐μ‐4‐(carboxyl­ato­methyl­sulfanyl)­phenoxy­acetato]

The title compound, [Mn(C₁₀H₈O₅S)(H₂O)₄]_n, a one‐dimensional manganese(II) complex comprising helical chains bridged by 4‐(carboxylatomethylsulfanyl)phenoxyacetate ligands has been characterized by single‐crystal X‐ray diffraction analysis. Hydrogen‐bonding inter­actions between adjacent chains extend the complex into a three‐dimensional supra­molecular architecture.     

Development of a competitive liposome-based lateral flow assay for the rapid detection of the allergenic peanut protein Ara h1

A competitive lateral flow assay for detecting the major peanut allergen, Ara h1, has been developed. The detector reagents are Ara h1-tagged liposomes, and the capture reagents are anti-Ara h1 polyclonal antibodies. Two types of rabbit polyclonal antibodies were raised either against the entire Ara h1 molecules (anti-Ara h1 Ab) or against an immunodominant epitope on Ara h1 (anti-peptide Ab). All of them reacted specifically with Ara h1 in Western Blot against crude peanut proteins. Moreover, the anti-Ara h1 Ab was chosen for this assay development because of its highest immunoactivity to Ara h1-tagged liposomes in the lateral flow assay. The calculated limit of detection (LOD) of this assay is 0.45 g mL^–1 of Ara h1 with a dynamic range between 0.1 and 10 g mL^–1 of Ara h1 in buffer. Additionally, the visually determined detection range is from 1 to 10 g mL^–1 of Ara h1 in buffer. Results using this assay can be obtained within 30 min without the need of sophisticated equipment or techniques; therefore, this lateral flow assay has the potential to be a cost-effective, fast, simple, and sensitive method for on-site screening of peanut allergens.     

A Novel Fluorescent Aminoacid Designed for Fluorometric Detection of Cu （Ⅱ）

A fluorescent aminoacid was designed for selective and sensitive detection of Cu(II) in aqueous solution. The designing of this Cu(II) fluorescent chemosensing molecule, N ± (1‐naphthyl). aminoacetic acid (NAA), was based on the binding of Cu(II) to aminoacetic acid and the novel charge transfer photophysics of 1‐aminonaphthalenes. The fluorescence of NAA was found quenched by Cu (II) and several other metal ions of similar electronic structure such as Co(II), Ni(II) and Zn(II). The quenching was shown to occur via electron transfer within the metal‐NAA complex, which required an optimal combination of high binding affinity and favorable redox properties of the components in the metal‐NAA complex and hence afforded selective fluorometric detection of Cu(II). The calibration graph obeyed Stern‐Volmer theory and was shown for Cu(II) over the range of 0–2.75 ± 10–⁴ mol/L. The quenching constant of Cu(II) was measured as 8.0 ± 10³ mol/L that was two orders of magnitude higher than those of Co(II), Ni(II) and Zn(II). The 3SD limit of detection for Cu(II) was 8.00 ± 10^?6 mol/L with a coefficient of variation of 1.65%. Linear range for quantitative detection of Cu(II) was 2.67 ± 10^?5‐2.75 ± 10^?4 mol/L. The method was applied to synthetic sample measurements which gave recoveries of 105%‐112%.     

A zwitterion of 1,5‐bis­(2‐hydroxy­benzamido)‐3‐aza­pentane: a two‐dimensional hydrogen‐bonding network involving dimers

The title compound, 2‐{N‐[2‐(2‐hydroxy­benzamido)ethyl­ammonio­ethyl]amino­carbon­yl}phenolate, C₁₈H₂₁N₃O₄, crystallizes in a zwitterionic form as a result of inter­molecular proton transfer and possesses a negatively charged phenolate group and a protonated amino group. The 2‐hydroxy­benzamide and 2‐(amino­carbonyl)­phenolate moieties attached to the two ends of the C—C—N—C—C backbone adopt a cis conformation in relation to this backbone. All N‐ and O‐bound H atoms are involved in hydrogen‐bond formation; the zwitterions are first linked into head‐to‐tail dimers, which are further organized into a two‐dimensional network parallel to the crystallographic bc plane.     

Folding, conformational changes, and dynamics of cytochromes C probed by NMR spectroscopy

NMR spectroscopy has become a vital tool for studies of protein conformational changes and dynamics. Oxidized Fe(III)cytochromes c are a particularly attractive target for NMR analysis because their paramagnetism (S = (1)/(2)) leads to high (1)H chemical shift dispersion, even for unfolded or otherwise disordered states. In addition, analysis of shifts induced by the hyperfine interaction reveals details of the structure of the heme and its ligands for native and nonnative protein conformational states. The use of NMR spectroscopy to investigate the folding and dynamics of paramagnetic cytochromes c is reviewed here. Studies of nonnative conformations formed by denaturation and by anomalous in vivo maturation (heme attachment) are facilitated by the paramagnetic, low-spin nature of native and nonnative forms of cytochromes c. Investigation of the dynamics of folded cytochromes c also are aided by their paramagnetism. As an example of this analysis, the expression in Escherichia coli of cytochrome c(552) from Nitrosomonas europaea is reported here, along with analysis of its unusual heme hyperfine shifts. The results are suggestive of heme axial methionine fluxion in N. europaea ferricytochrome c(552). The application of NMR spectroscopy to investigate paramagnetic cytochrome c folding and dynamics has advanced our understanding of the structure and dynamics of both native and nonnative states of heme proteins.     

16-脱氢孕烯醇酮醋酸酯的环境友好合成法

Instead of environmentally toxic chromium oxidant, singlet oxygen generated photcchemically was used as environmentally friendly and benign oxidizing agent to accomplish the transformation of pseudodiosgenin diacetate to diosone efficiently in a low toxic and less expensive solvent acetone. Accordingly 16-dehydropregnenolone acetate(16-DPA), an important intermediate for preparation of steroidal drugs, was prepared in good yield (75%) when photoreaction was run in acetone/acetic anhydride/pyridine system. The mild reaction condition as well as simple and environmentally friendly process made the method commercially viable and important for production of 16-DPA in industrial scale.