Simple example of structure versus property relationship applied to a reduced-friction biosystem,a quite personal opinion

Structure versus property (small-scale) relationship enters when something interesting is going to happen in a biosystem. This special-type “happening” is actually appearing to be manifested at both micro- and mesoscopic levels of always productive soft-matter organization under dynamic response, especially the one characteristic of the articular cartilage—an efficient, designed-by-nature multi-membrane, and virtually, with-ion-channels equipped, absorber and load relaxor.     

Plant architecture: a dynamic, multilevel and comprehensive approach to plant form, structure and ontogeny

BACKGROUND AND AIMS: The architecture of a plant depends on the nature and relative arrangement of each of its parts; it is, at any given time, the expression of an equilibrium between endogenous growth processes and exogenous constraints exerted by the environment. The aim of architectural analysis is, by means of observation and sometimes experimentation, to identify and understand these endogenous processes and to separate them from the plasticity of their expression resulting from external influences. SCOPE: Using the identification of several morphological criteria and considering the plant as a whole, from germination to death, architectural analysis is essentially a detailed, multilevel, comprehensive and dynamic approach to plant development. Despite their recent origin, architectural concepts and analysis methods provide a powerful tool for studying plant form and ontogeny. Completed by precise morphological observations and appropriated quantitative methods of analysis, recent researches in this field have greatly increased our understanding of plant structure and development and have led to the establishment of a real conceptual and methodological framework for plant form and structure analysis and representation. This paper is a summarized update of current knowledge on plant architecture and morphology; its implication and possible role in various aspects of modern plant biology is also discussed.     

Synthesis, crystal structure, electronic structure, bonding, photoluminescence and spectroscopic property investigations of a mononuclear 1,10-phenanthroline and 5-bromo-salicylate ternary indium(III) complex

The synthesis, X-ray structure, electronic structure, bonding, photoluminescence, spectroscopic property and characterization of an indium(III) complex, [In(Hbsac)₃(phen)] (1) (H₂bsac = 5-bromo-salicylic acid, and phen = 1,10-phenanthroline) are presented. Complex 1 is octacoordinate and carboxylate chelating, being novel and rarely reported for main group complexes. The electronic structure, bonding and the charge transfer properties of light excitation and light emission are discussed in detail using first-principles theory, including partial density of states (PDOSs), crystal orbital overlap population (COOP), the density functional theory (DFT/TDDFT) analysis schemes. The charge transfer is mainly π → π^∗ intraligand charge transfer transition (ILCT) for excitation, and π → π^∗ ligand-to-ligand charge transfer transition (LL′CT) for emission in nature.     

Synthesis of a metal-dicarboxylate hybrid with three dimensional Na-O-Cu connectivity: structure, magnetic property and controlled solid state thermolysis leading to CuO nanorod

A one-pot reaction of CuCl₂ · 2H₂O and malonic acid leads to a novel three dimensional inorganic-organic hybrid framework, [Na₂Cu(mal)₂(H₂O)₂]_n, (1) (mal = malonate dianion). Single crystal X-ray structure of 1 reveals that it is a novel heterometallic three dimensional coordination-polymeric network which consists of interlocked anionic Cu-malonate and cationic Na-water-malonate sheets, where malonate dianion functions as an unprecedented heptadentate ligand. Low temperature magnetic study reveals that the compound is weak ferromagnetically coupled and this is supported by magneto-structural correlation. Thermogravimetric analyses are performed and it is observed that complex 1 upon heating finally transforms to CuO, which is evident by X-ray powder diffraction technique. Controlled solid state thermolysis of complex 1 at ∼850 °C for 24 h leads to the formation of CuO nanorods, which is confirmed by scanning electron microscopy and X-ray powder diffraction technique. The nanorods formed here have average diameters of ca. 40-200 nm and lengths up to 13 μm.     

Synthesis, crystal structure and surface photo-electric property of a series of Co(II) coordination polymers and supramolecules

Four new Co(II) coordination complexes, [Co(o-phta)(pz)₂]_n1, [Co(PTA)₂(Imh)₂]·(HPTA)·H₂O 2, {[Co(pdc)₂(H₂O)]·(ppz)·2H₂O}_n3, [K₂Co₂(ox)(btec)(CH₃OH)₂]_n4, (H₂phta = o-phthalic acid, pz = pyrazole, HPTA = p-toluic acid, ppz = piperazine, Imh = imidazole, H₂pdc = pyridine-2,5-dicarboxylic acid, H₂(ox) = oxalic acid, H₄btec = 1,2,4,5-benzenetetracarboxylic acid), were hydrothermally synthesized and characterized by X-ray single crystal diffraction, IR, UV–Vis absorption spectrum, TG analysis and elemental analysis. The surface photovoltage properties of the four Co(II) complexes were investigated by the surface photovoltage spectroscopy (SPS). The structural analyses indicate that complexes 1 and 3 are 1D coordination polymers and complex 2 is a mononuclear molecular complex. Complexes 1, 2 and 3 are connected into 2D supramolecules by hydrogen bonds, respectively. Complex 4 is a coordination polymer with 3D structure, exhibiting a 4-nodal(4,5,6,12)-connected topology with a Schläfli symbol of (4¹⁰)₂(4²⁴·6³²·8¹⁰)(4⁵·6)₂(4⁹·6⁵·8). The results of SPS show the four complexes exhibit obvious photovoltaic responses in 300–800 nm, which indicates they all possess photo-electric conversion properties. By the comparative analysis of the SPS, it is found that structure of the complex, species of ligand and coordination micro-environment of the Co(II) ion affect the SPS. The relationships between SPS and UV–Vis absorption spectra are discussed.     

NMR structure and dynamics of inhibitory repeat domain variant 12, a plant protease inhibitor from Capsicum annuum,and its structural relationship to other plant protease inhibitors

Abstract

Although several plant protease inhibitors have been structurally characterized using X-ray crystallography, very few have been studied using NMR techniques. Here, we report an NMR study of the solution structure and dynamics of an inhibitory repeat domain (IRD) variant 12 from the wound-inducible Pin-II type proteinase inhibitor from Capsicum annuum. IRD variant 12 (IRD12) showed strong anti-metabolic activity against the Lepidopteran insect pest, Helicoverpa armigera. The NMR-derived three-dimensional structure of IRD12 reveals a three-stranded anti-parallel β-sheet rigidly held together by four disulfide bridges and shows structural homology with known IRDs. It is interesting to note that the IRD12 structure containing ～75% unstructured part still shows substantial amount of rigidity of N–H bond vectors with respect to its molecular motion.

Communicated by Ramaswamy H. Sarma     

Crystal structure of DeSI-1, a novel deSUMOylase belonging to a putative isopeptidase superfamily

Post-translational modification by small ubiquitin-like modifier (SUMO) can be reversed by sentrin/SUMO-specific proteases (SENPs), the first known class of deSUMOylase. Recently, we identified a new deSUMOylating enzyme DeSI-1, which is distinct from SENPs and belongs to the putative deubiquitinating isopeptidase PPPDE superfamily. Herein, we report the crystal structure of DeSI-1, revealing that this enzyme forms a homodimer and that the groove between the two subunits is the active site harboring two absolutely conserved cysteine and histidine residues that form a catalytic dyad. We also show that DeSI-1 exhibits an extremely low endopeptidase activity toward precursor forms of SUMO-1 and SUMO-2, unlike SENPs.     

Using chiral peptide substitutions to probe the structure function relationship of a key residue of Aβ42

Amyloid beta‐protein 42 plays an important role in the onset and progression of Alzheimer's disease. Familial mutations have identified the glutamate residue 22 as a hotspot with regard to peptide neurotoxicity. We introduce an approach to study the influence of systematic sidechain modification at this residue, employing chirality as a structural probe. Circular dichroism experiments reveal that charge‐preserving alterations of the amino acid sidechain attenuate the characteristic random coil to β‐sheet transition associated with the wildtype peptide. Removal of the negative charge from residue 22, a trait observed with all known familial mutations at this residue, gives rise to a peptide with limited random coil propensity and high β‐sheet characteristics. Our approach can be extended to other residues of Aβ, as well as further amyloidogenic peptides.     

A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme

The occurrence of large domain motions associated with the mechanism of action of many proteins is well established. We present a general method of predicting domain closure applicable to proteins containing domains separated by an apparent hinge. The method attempts to allow for natural directional bias within the closing protein by repeatedly applying a weak pulling force over a short distance between pairs of atoms chosen at random in the two domains in question. Appropriate parameters governing the pulling function were determined empirically. The method was applied to the bi-lobal protein PGK and a closed-form activated ternary complex generated for Bacillus stearothermophilus PGK. This model was compared with the recently determined crystal structure of closed-form Trypanosoma brucei PGK. The model predicts the correct hinge regions, although the magnitude of movement at one hinge point was overestimated, and provides a reasonable representation of the closed-form ternary complex. Proteins 30:372–380, 1998. © 1998 Wiley-Liss, Inc.     

Crystal structure of PHYHD1A, a 2OG oxygenase related to phytanoyl-CoA hydroxylase

Phytanoyl-CoA hydroxylase (PAHX) catalyzes an important step in the metabolism of the fatty acid side chain of chlorophyll. PHYHD1 exists in three isoforms and is the closest human homologue of PAHX. We show that like PAHX, the PHYHD1A but likely not the PHYHD1B/C isoforms, is a functional Fe(II) and 2-oxoglutarate (2OG) dependent oxygenase. Crystallographic and biochemical analyses reveal that PHYHD1A has the double-stranded β-helix fold and Fe(II) and cosubstrate binding residues characteristic of the 2-oxoglutarate dependent oxygenases and catalyzes the conversion of 2-oxoglutarate to succinate and CO₂ in an iron-dependent manner. However, PHYHD1A did not couple 2OG turnover to the hydroxylation of acyl-coenzyme A derivatives that are substrates for PAHX, implying that it is not directly involved in phytanoyl coenzyme-A metabolism.     

Behavioral responses of female adult Trichoplusia ni to volatiles from soybeans versus a preferred host, lima bean

Volatiles from different plants may have quite distinct effects on insect behaviors, i.e., attraction, repulsion or neutrality. Our study used Tenax^® to trap volatiles from plants at room temperature, and assayed female adult Trichoplusia ni's (Lepidoptera: Noctuidae) responses to such volatiles. The results showed that volatiles from PI 227687 soybean leaves were repellent to T. ni, while those from Davis soybean were attractive to the moth, and those from an unnumbered PI soybean had no significant behavioral effect. Odors from Henderson lima bean, one of the more preferred hosts of T. ni, also did not influence the insect's behavior. The HPLC, GLC and GLC-MS analyses indicated that qualitative and quantitative differences among volatiles from plant species, varieties or plant introductions account for these effects. The attractive volatiles from Davis soybean contain much more 4-hexen-1-ol acetate, 2,2-dimethyl hexanal and 2-hexenal than those of PI 227678, but do not have the repellent tetradecene and dodecene which are major components in PI 227687 soybean odors. The composition of the neutral volatiles from Henderson lima bean is more complex than that of the volatiles from soybeans.     

Novel autoxidation and Michael addition of a butenolide-containing sugar leading to a C-branched-chain glucopyranosidulose,and X-ray structure of intermediates

A butenolide-containing sugar available from the aldol condensation of methyl 4,6-O-benzylidene-alpha-D-glucopyranosid-2-ulose with diethyl malonate is autoxidized at the C-3 position into the corresponding alpha,beta-unsaturated gamma-lactone sugar by air, which subsequently undergoes 1,4-conjugate (Michael) addition of hydroxide ion (or water) leading to a C-branched-chain glucopyranosidulose. The autoxidations are also performed in weakly basic, neutral and weakly acidic medium, respectively.     

Beneficial effects of chromium in people with type 2 diabetes, and urinary chromium response to glucose load as a possible indicator of status

No reliable method for the estimation of chromium (Cr) status is available yet. The aim of this study is to investigate the possibility of using urinary Cr response to glucose load as an indicator of Cr status. Seventy-eight non-insulin-dependent diabetes mellitus patients were divided randomly into two groups and given Cr supplements as brewer’s yeast and CrCl₃ sequentially with placebo in between, in a double-blind, crossover design of four stages, each lasting 8 wk. At the beginning and end of each stage, subjects were weighed, their dietary data and drug dosage recorded, and blood and urine samples collected for analysis of glucose and urinary chromium (fasting and 2 h post-75-g glucose load) and fructosamine. The mean urinary Cr after the glucose load was significantly higher than the fasting mean at zero time (p<0.01). However, only 52 of the patients showed an obvious increase; the others showed a slight decrease or no change. Both supplements caused a significant increase in the means of urinary Cr and a significant decrease in the means of glucose and fructosamine. Only those subjects responding to Cr supplement by improved glucose control showed an increase in post-glucose-load urinary Cr over fasting level, after the supplement but not at zero time. Therefore, it was concluded that urinary Cr response to glucose load could be used as an indicator of Cr status.     

Population structure of a threatened plant, Pulsatilla patens, in boreal forests: modelling relationships to overgrowth and site closure

Pulsatilla patens (L.) Mill. (Ranunculaceae) is a threatened plant which in Fennoscandia favours south-facing, warm slopes of pine-dominated esker forests. The cessation of cattle grazing, modern forestry practices, and especially efficient fire prevention have resulted in closure of undergrowth vegetation in these forests. Using generalized linear models (GLM), we studied the relationships between habitat factors (covers of field and ground layer and amount of litter) and the population structure of P. patens in 48 populations in Finland in order to identify favourable conditions for regeneration. The largest populations occurred at sites with intermediate values of both ground and field layer. The number of juvenile plants was also highest at intermediate values of ground layer. Dense moss layer and abundant litter had a negative effect on the flowering of P. patens. In conclusion, creation and maintenance of habitat heterogeneity to prevent the closure of undergrowth vegetation is of paramount importance for the successful reproduction of P. patens.     

Genetic diversity, population structure, and conservation of Sophora moorcroftiana (Fabaceae), a shrub endemic to the Tibetan Plateau

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the middle reaches of Yarlung Zangbo River in Tibet. It is an important species to fix sand dunes and to avoid the formation of shifting sands; therefore, its progressive over-exploitation may enhance land desertification. The levels and distribution of genetic variability of this species were evaluated from 10 natural populations at 24 loci encoding 13 enzymes, using allozyme analysis by starch gel electrophoresis. Data obtained revealed moderate levels of genetic variation within populations (Pp=27.5%, Ap=1.5, Hep=0.122) and a considerable divergence among populations (FST=0.199). Significant positive correlations (r2=0.49, p<0.05; r2=0.46, p<0.05) were found between elevation and both mean number of alleles per locus (A) and gene diversity (He) in the studied populations of S. moorcroftiana. Lower genetic diversity in lower elevation populations might be due to the negative effects of human pressures and habitat fragmentation, to adaptation to high altitudes as a consequence of a peripatric speciation process, or to directional gene flow along the river basin from the source populations located in the west at higher altitudes. The evaluation of the degree of threat has led to the inclusion of this species in the category of EN ("endangered"), and conservation strategies for this endemic species are discussed on the basis of these findings.     

Fundulus heteroclitus vitellogenin: The deduced primary structure of a piscine precursor to noncrystalline,liquid-phase yolk protein

We have cloned and sequenced a cDNA encoding a vitellogenin (Vtg) from the mummichog, Fundulus heteroclitus, an estuarine teleost. We constructed a liver cDNA library against RNA from estrogen-treated male mummichogs. Five overlapping cDNA clones totalling 5,197 by were isolated through a combination of degenerate oligonucleotide probing of the library and PCR. The cDNA sequence contains a 5,112 by open reading frame. The predicted primary structure of the deduced 1,704-amino-acid protein is 30–40% identical to other documented chordate Vtgs, establishing this Vtg as a member of the ancient Vtg gene family. Of the previously reported chordate Vtg sequences (Xenopus laevis, Gallus domesticus, Ichthyomyzon unicuspis, and Acipenser transmontanus), all four act as precursor proteins to a yolk which is eventually rendered insoluble under physiological conditions, either as crystalline platelets or as noncrystalline granules. The yolk of F. heteroclitus, on the other hand, remains in a soluble state throughout oocyte growth. The putative F. heteroclitus Vtg contains a polyserine region with a relative serine composition that is 10–20% higher than that observed for the other Vtgs. The trinucleotide repeats encoding the characteristic polyserine tracts of the phosvitin region follow a previously reported trend: TCX codons on the 5 end and AGY codons toward the 3 end. Whether the difference in Vtg primary structure between F. heteroclitus and that of other chordates is responsible for the differences in yolk structure remains to be elucidated. As the first complete teleost Vtg to be reported, these data will aid in designing nucleotide and immunological probes for detecting Vtg as a reproductive status indicator in F. heteroclitus and other piscine species.Abbreviations AGY AG(T or C) - TCX TC(AGC or T) - Lv lipovitellin - Pv phosvitin - Vtg vitellogenin Correspondence to: G.J. LaFleur, Jr.     

Use of a generalised linear model to test habitat preferences: the example of Zingel asper, an endemic endangered percid of the River Rhône

SUMMARY 1. A study of microhabitat preferences was conducted on Zingel asper , an endangered endemic species from the Rhône catchment. A generalised linear model allowed us to test statistically the non-random habitat selection and the effect of season and site on this habitat selection.
2. The analysis detected significant preferences for the three physical variables considered: water depth, water velocity and substratum size.
3. A seasonal shift in the substratum size preference was found: preference for stones increasing during the spawning season. Depth preference varied between sites, suggesting a possible plasticity in habitat selection.
4. These results suggest that the availability of suitable physical habitat plays a significant role in determining fish distribution in the River Beaume.     

Biogeochemical fluxes of iron from rainwater,rivers and sewage to a Galician Ria (NW Iberian Peninsula). Natural versus anthropogenic contributions

The total iron (TFe) concentrations in five rivers to a Galician Ria (averages 1.0–4.5 μM) was within the pristine range, but in rainwater it was higher (17 μM). TFe values of small sewage treatment plants (STP) ranged between 3 and 4 μM, whereas in the largest was 11 μM. Particulate iron in rivers was five times more abundant than dissolved iron, except in the Lagares where it was 20 times higher, but in the STDs the dissolved/particulate coefficients varied from 0.1 to 1.1 and in the rainwater it was lower than 0.4. Equations of water flow versus iron flux were obtained to quantify the iron contribution from the freshwater sources to the Vigo Ria. It receives annually 490 tons of iron (6% in dissolved form) and 90% of this comes from industries focused on metal processes. The contaminated Lagares River accounts for the main input of TFe (327 t a⁻¹), followed by rainwater (78 t a⁻¹), the Oitavén River (28 t a⁻¹) and Vigo STP (33 t a⁻¹). Anthropogenic activities have increased the amount of iron flowing into the Ria by roughly ten times and this could upset the biogeochemical cycle in similar coastal systems.     

Response of microbial community structure to the hydrochemical evolution during riverbank filtration: a case study in Shenyang,China

Abstract

Microorganisms are widely involved in the transformation process of physical and chemical properties in the geological and hydrogeological environment. Active participation of microorganisms is important features of the biogeochemical reactions during groundwater exploiting along the riverbank filtration. Hydrodynamic condition has a direct or indirect difference control of the biological effectiveness, chemical activity and mobility of the pollution components, which can affect biogeochemical process. In different biogeochemistry, there will be some exclusive functional bacteria, which is of great significance to understand the biogeochemical mechanism of river water infiltration. This study confirms that there are two main different flow paths from river to the center of the depression cone due to different hydrodynamic conditions and spatial characteristics and scaling effects of redox zonation during riverbank filtration. In different flow paths, the microbial abundance shows obvious spatial heterogeneity. The microbial abundance and species similarity degree of the riverbed and deep flow path sediments has significant correlation. There is a significant correlation between the dominant bacteria and the environmental factors in different hydrodynamic conditions on a spatial scale. This study is the first to reveal the response of microbial community structure to water chemical evolution during riparian filtration. Due to significant positive correlation between the Fe/Mn and As, it brings the potential danger for drinking water.