Chemical variability of the volatile metabolites from the Caribbean corals of the genus Gorgonia

The chemical composition of the investigated gorgonians showed a high level of individual variation and the colonies, according to their major contributors, were assigned to 10 distinct chemical profiles, among which A, C, E, and G were the most abundant ones. From the metabolites identified in the present study, either by means of GC/MS or using NMR techniques after conventional separation procedures, the novel cyclic ether 5,10-epoxymuurolane is found in significant quantities in D and I chemical profiles. Furanotriene, isofuranotriene and furanodiene could be referred as the most common metabolites of the genus, since they are found in 6 out of 10 chemical profiles. Isosericenine is, also, a significant contributor of H and I chemical profiles. A number of sesquiterpene hydrocarbons, such as curzerene, bicyclogermacrene, valencene, beta-bourbonene and beta-elemene, along with the oxygenated sesquiterpenes elemanolide and furoventalene, are present at varying concentrations in the majority of the chemical profiles. Metabolites of high discriminant value are: alpha-himachalene for the K chemical profile, alpha-santalene and its oxygenated derivatives for the G chemical profile and the three geometrical isomers of germacrone for the F chemical profile. Several chemical profiles showed narrow geographic distribution. Most of the chemical profiles are located in the north, while F inhabits mainly southern sites and the others are equally distributed. Finally, 91% of the chemical profiles of the gorgonian colonies appeared to grow in all depths, while 9% did not inhabit deep-water environments. Most chemical profiles are less frequent at higher water depths with the exception of chemical profiles A and C.     

Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH

Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970–2978, 2001). The chemical shifts are determined at neutral pH in order to match the conditions of most studies of intrinsically disordered proteins. Temperature has a non-negligible effect on the ¹³C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series, which allows the accurate random coil chemical shifts to be obtained at any pH. By correcting the random coil chemical shifts for the effects of temperature and pH, systematic biases of the secondary chemical shifts are minimized, which will improve the reliability of detection of transient secondary structure in disordered proteins.     

Field programmable chemistry: integrated chemical and electronic processing of informational molecules towards electronic chemical cells

The topic addressed is that of combining self-constructing chemical systems with electronic computation to form unconventional embedded computation systems performing complex nano-scale chemical tasks autonomously. The hybrid route to complex programmable chemistry, and ultimately to artificial cells based on novel chemistry, requires a solution of the two-way massively parallel coupling problem between digital electronics and chemical systems. We present a chemical microprocessor technology and show how it can provide a generic programmable platform for complex molecular processing tasks in Field Programmable Chemistry, including steps towards the grand challenge of constructing the first electronic chemical cells. Field programmable chemistry employs a massively parallel field of electrodes, under the control of latched voltages, which are used to modulate chemical activity. We implement such a field programmable chemistry which links to chemistry in rather generic, two-phase microfluidic channel networks that are separated into weakly coupled domains. Electric fields, produced by the high-density array of electrodes embedded in the channel floors, are used to control the transport of chemicals across the hydrodynamic barriers separating domains. In the absence of electric fields, separate microfluidic domains are essentially independent with only slow diffusional interchange of chemicals. Electronic chemical cells, based on chemical microprocessors, exploit a spatially resolved sandwich structure in which the electronic and chemical systems are locally coupled through homogeneous fine-grained actuation and sensor networks and play symmetric and complementary roles. We describe how these systems are fabricated, experimentally test their basic functionality, simulate their potential (e.g. for feed forward digital electrophoretic (FFDE) separation) and outline the application to building electronic chemical cells.     

Relationship between nuclear magnetic resonance chemical shift and protein secondary structure

An analysis of the 1H nuclear magnetic resonance chemical shift assignments and secondary structure designations for over 70 proteins has revealed some very strong and unexpected relationships. Similar studies, performed on smaller databases, for 13C and 15N chemical shifts reveal equally strong correlations to protein secondary structure. Among the more interesting results to emerge from this work is the finding that all 20 naturally occurring amino acids experience a mean alpha-1H upfield shift of 0.39 parts per million (from the random coil value) when placed in a helical configuration. In a like manner, the alpha-1H chemical shift is found to move downfield by an average of 0.37 parts per million when the residue is placed in a beta-strand or extended configuration. Similar changes are also found for amide 1H, carbonyl 13C, alpha-13C and amide 15N chemical shifts. Other relationships between chemical shift and protein conformation are also uncovered; in particular, a correlation between helix dipole effects and amide proton chemical shifts as well as a relationship between alpha-proton chemical shifts and main-chain flexibility. Additionally, useful relationships between alpha-proton chemical shifts and backbone dihedral angles as well as correlations between amide proton chemical shifts and hydrogen bond effects are demonstrated.     

Tasty figs and tasteless flies: plant chemical discrimination but no prey chemical discrimination in the cordylid lizard<Emphasis Type="Italic"> Platysaurus broadleyi</Emphasis>

Lizards use visual and/or chemical cues to locate and identify food. The ability to discriminate prey chemical cues is affected by phylogeny, diet, and foraging mode. Augrabies flat lizards (Platysaurus broadleyi) are omnivorous members of the lizard clade Scleroglossa. Within Scleroglossa, all previously tested omnivores are capable of both prey and plant chemical discrimination. At Augrabies Falls National Park, P. broadleyi feed on both insects (black flies) and plant material (figs), and as scleroglossans, are predicted to discriminate both plant and prey chemicals. However, Platysaurus broadleyi use visual, not chemical cues, to detect and capture black flies, which occur in large concentrations in the study area. We tested free-ranging individuals for the ability to discriminate insect and plant chemicals from controls. There was a significant stimulus effect such that lizards tongue-flicked fig-labelled tiles significantly more than the remaining stimuli, spent more time at the fig-labelled tile, and attempted to eat fig-labelled tiles more often than tiles labelled with control or insect stimuli. Platysaurus broadleyi is exceptional in being the first lizard shown to possess plant chemical discrimination but to lack prey chemical discrimination. We suggest that an absence of prey chemical discrimination may be a consequence of foraging behaviour and environmental effects. Because insect prey are highly clumped, abundant, and aerial, profitable ambushing using visual cues may have relaxed any selective pressure favouring insect prey chemical discrimination. However, a more likely alternative is that responses to figs are gustatory, whereas as prey chemical discrimination and plant chemical discrimination are usually mediated by vomerolfaction.Communicated by P.K. McGregor     

Responses to chemical cues from animal and plant foods by actively foraging insectivorous and omnivorous scincine lizards

If tongue-flicking is important to lizards to sample chemical cues permitting identification of foods, tongue-flicking and subsequent feeding responses should be adjusted to match diet. This hypothesis can be examined for plant foods because most lizards are insectivores, but herbivory/omnivory has evolved independently in many lizard taxa. Here we present experimental data on chemosensory responses to chemical cues from animal prey and palatable plants by three species of the scincine lizards. When tested with chemical stimuli presented on cotton swabs, the insectivorous Eumeces fasciatus responded strongly to prey chemicals but not to chemicals from plants palatable to omnivorous lizards or to pungent or odorless control stimuli. Two omnivorous species, E. schneideri and Scincus mitranus, responded more strongly to chemical cues from both prey and food plants than to the control chemicals. All available data for actively foraging lizards, including these skinks, show that they are capable of prey chemical discrimination, and insectivores do not exhibit elevated tongue-flicking or biting responses to chemical cues from palatable plants. In all of the several species of herbivores/omnivores tested, the lizards show elevated responses to both animal and plant chemicals. We suggest two independent origins of both omnivory and plant chemical discrimination that may account for the evolution of diet and food chemical discriminations in the eight species of skinks studied, five of which are omnivores. All data are consistent with the hypothesis that acquisition of omnivory is accompanied by acquisition of plant chemical discrimination, but data on a broad diversity of taxa are needed for a definitive comparative test of the evolutionary hypothesis. J. Exp. Zool. 287:327-339, 2000.     

An Analysis of Chemical Ingredients Network of Chinese Herbal Formulae for the Treatment of Coronary Heart Disease

As a complex system, the complicated interactions between chemical ingredients, as well as the potential rules of interactive associations among chemical ingredients of traditional Chinese herbal formulae are not yet fully understood by modern science. On the other hand, network analysis is emerging as a powerful approach focusing on processing complex interactive data. By employing network approach in selected Chinese herbal formulae for the treatment of coronary heart disease (CHD), this article aims to construct and analyze chemical ingredients network of herbal formulae, and provide candidate herbs, chemical constituents, and ingredient groups for further investigation. As a result, chemical ingredients network composed of 1588 ingredients from 36 herbs used in 8 core formulae for the treatment of CHD was produced based on combination associations in herbal formulae. In this network, 9 communities with relative dense internal connections are significantly associated with 14 kinds of chemical structures with P<0.001. Moreover, chemical structural fingerprints of network communities were detected, while specific centralities of chemical ingredients indicating different levels of importance in the network were also measured. Finally, several distinct herbs, chemical ingredients, and ingredient groups with essential position in the network or high centrality value are recommended for further pharmacology study in the context of new drug development.     

21世纪植物化学生态学前沿领域

植物和其它有机体通过次生物质为媒介的化学作用关系近年引入注目,其中植物的诱导化学防御,植物的化学通讯,植物次生物质和进化的关系,植物与人类的化学关系和海洋植物化学生态学是21世纪植物化学生态学值得关注的前沿领域。植物化学生态学前沿领域的进展将为实现21世纪的持续,发展是在生态安全条件下提高农业产量并达到对病虫草害的有效控制方面具有重要意义。     

Validation of archived chemical shifts through atomic coordinates

The public archives containing protein information in the form of NMR chemical shift data at the BioMagResBank (BMRB) and of 3D structure coordinates at the Protein Data Bank are continuously expanding. The quality of the data contained in these archives, however, varies. The main issue for chemical shift values is that they are determined relative to a reference frequency. When this reference frequency is set incorrectly, all related chemical shift values are systematically offset. Such wrongly referenced chemical shift values, as well as other problems such as chemical shift values that are assigned to the wrong atom, are not easily distinguished from correct values and effectively reduce the usefulness of the archive. We describe a new method to correct and validate protein chemical shift values in relation to their 3D structure coordinates. This method classifies atoms using two parameters: the per‐atom solvent accessible surface area (as calculated from the coordinates) and the secondary structure of the parent amino acid. Through the use of Gaussian statistics based on a large database of 3220 BMRB entries, we obtain per‐entry chemical shift corrections as well as Z scores for the individual chemical shift values. In addition, information on the error of the correction value itself is available, and the method can retain only dependable correction values. We provide an online resource with chemical shift, atom exposure, and secondary structure information for all relevant BMRB entries ( http://www.ebi.ac.uk/pdbe/nmr/vasco ) and hope this data will aid the development of new chemical shift‐based methods in NMR. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Systemtheoretische analyse der chemischen atmungsregulation unter berücksichtigung ihres mehrdimensionalen charakters

The chemical control of respiration provides for the maintanence of energy and substance equilibrium primarily and for the homoeostatic stability of the chemical blood parameters secondarily. Based on results having been obtained from an appropriate state space model some findings on respiration can be reproduced. In addition to the true qualitative reflecting the steady state at work performance, the contribute of separate chemical drives to the whole ventilation are represented correctly, suggesting the unnecessarity of any additional specific work drives. Nervous influences of ventilation besides of its chemical control are not suitable to guarantee its controlability, they represent only disturbaces mobilizing it. Coupled organ systems take part on transmitting primary afferent infromation about the chemical condition of the total metabolism, which proved to be necessary and sufficient for the chemical control activity.     

Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds

A novel technique to annotate, query, and analyze chemical compounds has been developed and is illustrated by using the inhibitor data on HIV protease-inhibitor complexes. In this method, all chemical compounds are annotated in terms of standard chemical structural fragments. These standard fragments are defined by using criteria, such as chemical classification; structural, chemical, or functional groups; and commercial, scientific or common names or synonyms. These fragments are then organized into a data tree based on their chemical substructures. Search engines have been developed to use this data tree to enable query on inhibitors of HIV protease (http://xpdb.nist.gov/hivsdb/hivsdb.html). These search engines use a new novel technique, Chemical Block Layered Alignment of Substructure Technique (Chem-BLAST) to search on the fragments of an inhibitor to look for its chemical structural neighbors. This novel technique to annotate and query compounds lays the foundation for the use of the Semantic Web concept on chemical compounds to allow end users to group, sort, and search structural neighbors accurately and efficiently. During annotation, it enables the attachment of "meaning" (i.e., semantics) to data in a manner that far exceeds the current practice of associating "metadata" with data by creating a knowledge base (or ontology) associated with compounds. Intended users of the technique are the research community and pharmaceutical industry, for which it will provide a new tool to better identify novel chemical structural neighbors to aid drug discovery.     

The application of 1H NMR chemical shift calculations to diastereotopic groups in proteins.

We have calculated chemical shifts for a range of diastereotopic protons in proteins (i.e. methylene protons, and the methyl groups of valine and leucine residues), using a recently optimised method for chemical shift calculation. The calculations are based on crystal structure coordinates, and have been compared with experimental stereospecific assignments. The results indicate that chemical shifts can be used to suggest stereospecific assignments with about 80% probability of being correct, in cases where both the experimental and the calculated chemical shift differences between a pair of diastereotopic protons are greater than 0.3 ppm. Inaccurate calculations are shown to be caused in most cases by differences between crystal and solution structures. Furthermore, chemical shift calculations based on NMR structures are shown to be capable of acting as a further constraint on structure, by limiting the range of side-chain conformations adopted in structures calculated from NMR data.     

Can microbial-based insecticides replace chemical pesticides in agricultural production?

Extensive use of chemical insecticides to control insect pests in agriculture has improved yields and production of high-quality food products. However, chemical insecticides have been shown to be harmful also to beneficial insects and many other organisms like vertebrates. Thus, there is a need to replace those chemical insecticides by other control methods in order to protect the environment. Insect pest pathogens, like bacteria, viruses or fungi, are interesting alternatives for production of microbial-based insecticides to replace the use of chemical products in agriculture. Organic farming, which does not use chemical pesticides for pest control, relies on integrated pest management techniques and in the use of microbial-based insecticides for pest control. Microbial-based insecticides require precise formulation and extensive monitoring of insect pests, since they are highly specific for certain insect pests and in general are more effective for larval young instars. Here, we analyse the possibility of using microbial-based insecticides to replace chemical pesticides in agricultural production.     

Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue’s effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict ¹³C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve the identification of small populations of transient structure in disordered proteins.     

植物种间和种内的化学作用

植物间相互作用是生态学基础科学问题之一,植物能感受和识别共存同种或异种植物,进而调整生长、繁殖和防御策略。植物种间和种内的感受和识别大多是由植物产生释放的次生物质所介导,这类化学识别通讯可以启动相应的植物化感作用机制。近年发现,植物亲属间也存在着化学识别、地下根系通讯调控地上开花繁殖等植物种间和种内的化学作用关系。目前植物通过地上挥发物介导的植物化学作用已基本澄清,但根分泌物介导的植物地下化学作用机制及其信号物质还所知甚少。地下化学作用不仅决定根系侵入(接近)和躲避(排斥)行为,也能调控地上开花时间和花期。这样,植物间的化学作用还涉及植物地下和地上的协调互作。本文以植物化感作用和植物化学识别通讯及相应的化感物质和信号物质为基点,从植物亲属识别、根系化学识别和行为模式、地下化学作用调控地上开花繁殖3个方面综述植物种间和种内化学作用的研究进展,为全面理解植物间相互作用提供新视野。     

Chemical images: technical approaches and issues.

Chemical mapping techniques using Raman microscopy are introduced, and using an example of a pharmaceutical tablet, the practical aspects of data collection and processing to produce a chemical image of the sample are detailed. Issues related to data processing, instrument standards, chemical image reportable errors, and the interpretation of chemical images are presented to encourage debate, develop solutions, and promote use in other challenging scientific applications. applications.     

The use of enzymes in the chemical industry in Europe

Many European chemical industries are in a phase of reorganization resulting in a general opening towards life sciences. Traditional chemical markets are served increasingly with products derived from bioprocesses or hybrid chemical/biocatalytic processes. Biocatalytic steps are already being used to produce a wide range of products, including agricultural chemicals, organics, drugs and plastic materials, to name but a few. Apart from the rapidly growing number of commercialized bioprocesses, a partial survey of exploratory activities points to future applications of enzymes in the European chemical industry, which will bring new products and technologies and, in some cases, replace traditional syntheses.     

生物的化学通讯

生物个体（同种或异种）相互之间的有着化学信息联系,昆虫,特别是社会性昆虫化学通讯是其沟通信息的主要方式,我们关于化学通讯的知识大多来自于对昆虫信息素的研究,近来的研究已揭示在植物和植物以及植物和动物之间也存在着化学信息交流。     

蚧虫蜡泌物的化学研究进展

总结了国内外对蚧虫蜡泌物及其化学成分的研究进展 ,内容包括蜡泌物形成介壳的主要类型 ;蜡泌物的化学研究方法及已涉及的种类 ;蜡泌物的主要化学组成 ,并对 5类物质 ,即蜡、烃类、树脂或萜类、色素类、内蜜露作了重点叙述。最后 ,讨论了研究蚧虫蜡泌物的化学成分具有的意义和应用前景 ,包括蜡泌物作为生物资源的利用 ;以蚧虫作为农林、果树和花卉业的重要害虫 ,针对蜡泌物的特点研制相应的新型杀虫剂 ;利用蜡泌物的化学信息素对天敌的诱导作用 ,开展蚧虫生物防治 ;利用蜡泌物作为化学分类性状的应用等。     

Metabolism and motility in prebiotic structures

Easily accessible, primitive chemical structures produced by self-assembly of hydrophobic substances into oil droplets may result in self-moving agents able to sense their environment and move to avoid equilibrium. These structures would constitute very primitive examples of life on the Earth, even more primitive than simple bilayer vesicle structures. A few examples of simple chemical systems are presented that self-organize to produce oil droplets capable of movement, environment remodelling and primitive chemotaxis. These chemical agents are powered by an internal chemical reaction based on the hydrolysis of an oleic anhydride precursor or on the hydrolysis of hydrogen cyanide (HCN) polymer, a plausible prebiotic chemistry. Results are presented on both the behaviour of such droplets and the surface-active properties of HCN polymer products. Such motile agents would be capable of finding resources while escaping equilibrium and sustaining themselves through an internal metabolism, thus providing a working chemical model for a possible origin of life.