Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.

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Revealing noncovalent interactions.

Roles of glycine betaine and proline in improving plant abiotic stress resistance

Noncovalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these noncovalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define noncovalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their vdW radii. We recently developed an alternative perspective, derived from the electronic density: the non-covalent interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of noncova...

/pdf/nciplot-a-program-for-plotting-noncovalent-interaction-5bhkffn4zn.pdf

NCIPLOT: A Program for Plotting Noncovalent Interaction Regions

Arbuscular mycorrhizal (AM) fungi form mutualistic, symbiotic associations with the roots of more than 80% of land plants. The fungi are incapable of completing their life cycle in the absence of a host root. Their spores can germinate and grow in the absence of a host, but their hyphal growth is very limited. Little is known about the molecular mechanisms that govern signalling and recognition between AM fungi and their host plants. In one of the first stages of host recognition, the hyphae of AM fungi show extensive branching in the vicinity of host roots before formation of the appressorium, the structure used to penetrate the plant root. Host roots are known to release signalling molecules that trigger hyphal branching, but these branching factors have not been isolated. Here we have isolated a branching factor from the root exudates of Lotus japonicus and used spectroscopic analysis and chemical synthesis to identify it as a strigolactone, 5-deoxy-strigol. Strigolactones are a group of sesquiterpene lactones, previously isolated as seed-germination stimulants for the parasitic weeds Striga and Orobanche. The natural strigolactones 5-deoxy-strigol, sorgolactone and strigol, and a synthetic analogue, GR24, induced extensive hyphal branching in germinating spores of the AM fungus Gigaspora margarita at very low concentrations.

Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi

http://nhjy.hzau.edu.cn/kech/ssyy/qysd/njsl/21.pdf

Potential biochemical indicators of salinity tolerance in plants

Additional index words. Cuticular wax, cutin, blackspot disease, rose Abstract. The fungal pathogen Diplocarpon rosae causes rose blackspot disease, a serious problem for roses (Rosa) in the managed landscape. To prevent this disease, homeowners and professional growers often apply chemical fungicide. However, increased use of fungicides poses an environmental hazard and an economic burden to the user. New landscape rose cultivars like 'Knockout' possess increased disease resistance, but the biological basis for this resistance is still unknown. To investigate the potential role of leaf cuticle in blackspot resistance in rose, five rose cultivars known to vary greatly in blackspot resistance were examined for variation in the major lipids of the leaf cuticle, specifically the monomers of the cutin polyester and the free cuticular waxes. This is the first report of cutin monomers in the Rosa genera. The rose cultivars selected for this study were 'Knockout', 'Mister Lincoln', 'Garden Party', 'Purple Passion', and 'Bicolor'. 'Knockout' and 'Garden Party' had significantly lower total cutin monomer amount per leaf area than the other cultivars, whereas the most cutin monomers were observed on 'Purple Passion', 'Bicolor', and 'Mister Lincoln'. Five major cutin monomers (mostly hydroxylated 16 carbon fatty acids) dominated the cutin profiles of both adaxial and adaxial surfaces of all cultivars, with the 10,16-dihydroxy hexadecanoic acids being most abundant. The proportion of 10,16-dihydroxy hexadecanoic acids was slightly higher in the adaxial than abaxial leaf cuticles of all cultivars. Correspondingly, other cutin monomers were relatively lower in the adaxial cuticle, except 16-hydroxy hexadecanoic acid that differed little. Uniquely, this is the first report of cutin monomer composition of isolated abaxial and adaxial leaf cuticles of any plant. Total leaf cuticular wax amounts were lowest on 'Purple Passion' and 'Knockout', intermediate in 'Mister Lincoln' and 'Garden Party', and highest on 'Bicolor', with alkanes as the most abundant wax class. Consistent with previously published disease susceptibility ratings, our visual scores showed that 'Knockout' was most resistant to blackspot pathogen infection with a visual disease rating score of 1.0, followed by 'Mister Lincoln' at 1.8, 'Garden Party' at 5.4, 'Bicolor' at 7.5, and 'Purple Passion' with the most visible disease damage at 8.8. Regression analysis revealed that the alkane and ester proportions were most closely associated with blackspot disease susceptibility ratings, being inversely (R 2 = 0.63, P = 0.05) and directly (R 2 = 0.81, P = 0.05) correlated, respectively. More studies on the role of cuticle in rose susceptibility to blackspot are now clearly warranted.

https://journals.ashs.org/downloadpdf/journals/hortsci/42/7/article-p1631.pdf

Leaf cutin monomers, cuticular waxes, and blackspot resistance in rose

Optical fiber interface between a laser and a tandem mass spectrometer

MALDI-TOF MS analysis of supercritical CO2 extracted samples obtained from Mandevilla velutina cell cultures allowed the detection of the anti-bradykinin pregnanic steroid, velutinol A, using low amount of sample (1 g lyophilized cells), with minimum analyte isolation.

Supercritical CO2 extraction of velutinol A from Mandevilla velutina (Apocynaceae) cultured cells and MALDI-TOF MS analysis

Antimicrobial properties of three liverworts in axenic culture : Blasia pusilla, Pallavicinia lyellii and Radula obconica

Adhesion formation is a common complication in abdominal surgery with incidence as high as 93% and small bowel obstruction a common complication. Because the extracellular matrix material, small intestinal submucosa (SIS), is commonly used in various surgical procedures, methods to inhibit adhesiogenesis are of great interest. This study was undertaken to determine if incorporation of nimesulide (NM), a selective cyclooxygenase (COX)-2 inhibitor, could reduce the extent and tenacity of intraabdominal adhesion formation associated with SIS implantation. Female Sprague–Dawley rats underwent a cecal abrasion surgical procedure to induce adhesiogenesis. Rats were either left untreated or treated by direct application over the injured cecum with polypropylene mesh (PPM); SIS; SIS containing a low dose of NM; or SIS containing a high dose of NM. Rats were euthanized 21 days later, and adhesion extent and tenacity were evaluated using standard scales (0 = minimal adhesiogenesis; 4 = severe adhesiogenesis). Addition of NM to SIS resulted in a significant (p < 0.05) reduction in adhesion extent and in a similar reduction in adhesion tenacity for SIS containing a low dose of NM. Adhesions typically extended from the abraded cecal surface to the body wall and were characterized histologically by fibrous tissue adherent to the cecal wall. In conclusion, addition of the nonsteroidal anti-inflammatory, COX-2 selective drug, NM, to SIS attenuates adhesion extent and tenacity when compared with surgical placement of SIS or PPM alone. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2010

Karl V. Wood

Papers

Leaf cutin monomers, cuticular waxes, and blackspot resistance in rose

Optical fiber interface between a laser and a tandem mass spectrometer

Supercritical CO2 extraction of velutinol A from Mandevilla velutina (Apocynaceae) cultured cells and MALDI-TOF MS analysis

Antimicrobial properties of three liverworts in axenic culture : Blasia pusilla, Pallavicinia lyellii and Radula obconica

Addition of nimesulide to small intestinal submucosa biomaterial inhibits postsurgical adhesiogenesis in rats.