High Structural Diversity Research Articles

Synthesis of Crystalline Chalcogenides in Ionic Liquids.

Crystalline chalcogenides belong to the most promising class of materials. In addition to dense solid-state structures, they may form molecular cluster arrangements and networks with high porosity, as in the so-called "zeotype" chalcogenidometalates. The high structural diversity comes along with interesting physical properties such as semi-/photoconductivity, ion transport capability, molecular trapping potential, as well as chemical and catalytic activity. The great interest in the development of new and tailored chalcogenides has provoked a continuous search for new and better synthesis strategies over the years. The trend has clearly been towards lower temperatures for both economic and ecological reasons as well as for better reaction control. This led to the application of ionic liquids as a designer-like medium for materials synthesis. In this Review, we summarize recent developments and present a survey of different chalcogenide families along with their properties.

Chemical constituents, antioxidant and potential allelopathic effect of the essential oil from the aerial parts of Cullen plicata

The intensive use of synthetic chemical pesticides has a serious impact on humans and the environment. The essential oil is a proper class of allelochemicals to be used as bio herbicides due to their biodegradability, high structural diversity and reduced natural resistance to weeds. The essential oil from the aerial parts of Cullen plicata (Delile) C.H. Stirt. was extracted by hydrodistillation and analyzed by gas chromatography/mass spectrometry. A concentrations of 50, 100, 150 and 200μLL−1 of the essential oil were prepared for studying their allelopathic activities on germination and seedling growth of Bidens pilosa and Urospermum picroides. In addition, the antioxidant activity was investigated. Thirty five compounds were determined, mainly sesquiterpenes (77.14%). The dominant sesquiterpenes are (−)-caryophyllene oxide (33.42%), Z-nerolidol (17.92%), .tau.cadinol (9.06%) and α-cadinol (6.66%). At 200μLL−1, the germination of both B. pilosa and U. picroides was completely inhibited. The IC50 value of the essential oil on germination inhibition of B. pilosa and U. picroides were 49.39 and 17.86μLL−1, respectively. On the other hand, the inhibition seedling growth of both B. pilosa and U. picroides showed significant dose-proportional increases in the inhibition under the treatment of the essential oil. However, B. pilosa was strongly inhibited than U. picroides. The antioxidant activity of the C. plicata essential oil has IC50 value of 1.31μLmL−1 compared to 0.03μLmL−1 for catechol. From this study, we can say that C. plicata essential oil could give a hope toward production of eco-friendly bio herbicides at least against B. pilosa and U. picroides and also as a source of natural antioxidants that could be used as food additives.

N-glycoprotein macroheterogeneity: biological implications and proteomic characterization.

Glycosylation is a co- and post-translational modification that is critical for the regulation of the biophysical properties and biological activities of diverse proteins. Biosynthetic pathways for protein glycosylation are inherently inefficient, resulting in high structural diversity in mature glycoproteins. Macroheterogeneity is the structural diversity due to the presence or absence of glycans at specific glycosylation sites, and is caused by inefficiency in the initial transfer of glycans to proteins. Here, we review the enzymatic and evolutionary mechanisms controlling macroheterogeneity, its biological consequences in physiological and disease states, its relevance to heterologous production and glycoengineering of glycoproteins, and mass spectrometry based methods for its analysis. We highlight the importance of the analysis of macroheterogeneity for a complete understanding of glycoprotein biosynthesis and function, and emphasize how advances in mass spectrometry glycoproteomics will enable analysis of this critical facet of glycoprotein structural diversity.

Separation and characterization of bufadienolides in toad skin using two-dimensional normal-phase liquid chromatography×reversed-phase liquid chromatography coupled with mass spectrometry.

Bufadienolides possess various bioactivities especially antitumor. Due to the high structural diversity, the separation of bufadienolides often suffers from coelution problem on conventional RP columns. In this work, an off-line two-dimensional normal-phase liquid chromatography×reversed-phase liquid chromatography (2D-NPLC×RPLC) method was developed to separate and characterize bufadienolides in toad skin. Several RP and NP columns were evaluated with five reference bufadienlides. The XUnion C18 and XAmide columns exhibited superior chromatographic performances for bufadienlide separation, and were selected in RPLC and NPLC, respectively. RPLC was used in the second-dimension for the good compatibility with MS, while NPLC was adopted in the first-dimension. The orthogonality of the 2D-NPLC×RPLC system was investigated by the geometric approach using fifteen bufadienolide mixtures. The result was 49.6%, demonstrating reasonable orthogonality of this 2D-LC system. By combining the 2D-LC system with MS, 64 bufadienlides including 33 minor ones and 11 pairs of isomers in toad skin were identified. This off-line 2D-NPLC×RPLC allowed to solve the coelution problem of bufadienlides in one-dimension RPLC, and thus facilitated the identification significantly.

The plant microbiome explored: implications for experimental botany.

The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habitats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorganisms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are co-evolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. Our study of the current literature shows that analysis of plant microbiome data has brought about a paradigm shift in our understanding of the diverse structure and functioning of the plant microbiome with respect to the following: (i) the high interplay of bacteria, archaea, fungi, and protists; (ii) the high specificity even at cultivar level; (iii) the vertical transmission of core microbiomes; (iv) the extraordinary function of endophytes; and (v) several unexpected functions and metabolic interactions. The plant microbiome should be recognized as an additional factor in experimental botany and breeding strategies.

Strain Selection for Generation of O-Antigen-Based Glycoconjugate Vaccines against Invasive Nontyphoidal Salmonella Disease.

Nontyphoidal Salmonellae, principally S. Typhimurium and S. Enteritidis, are a major cause of invasive bloodstream infections in sub-Saharan Africa with no vaccine currently available. Conjugation of lipopolysaccharide O-antigen to a carrier protein constitutes a promising vaccination strategy. Here we describe a rational process to select the most appropriate isolates of Salmonella as source of O-antigen for developing a bivalent glycoconjugate vaccine. We screened a library of 30 S. Typhimurium and 21 S. Enteritidis in order to identify the most suitable strains for large scale O-antigen production and generation of conjugate vaccines. Initial screening was based on growth characteristics, safety profile of the isolates, O-antigen production, and O-antigen characteristics in terms of molecular size, O-acetylation and glucosylation level and position, as determined by phenol sulfuric assay, NMR, HPLC-SEC and HPAEC-PAD. Three animal isolates for each serovar were identified and used to synthesize candidate glycoconjugate vaccines, using CRM197 as carrier protein. The immunogenicity of these conjugates and the functional activity of the induced antibodies was investigated by ELISA, serum bactericidal assay and flow cytometry. S. Typhimurium O-antigen showed high structural diversity, including O-acetylation of rhamnose in a Malawian invasive strain generating a specific immunodominant epitope. S. Typhimurium conjugates provoked an anti-O-antigen response primarily against the O:5 determinant. O-antigen from S. Enteritidis was structurally more homogeneous than from S. Typhimurium, and no idiosyncratic antibody responses were detected for the S. Enteritidis conjugates. Of the three initially selected isolates, two S. Typhimurium (1418 and 2189) and two S. Enteritidis (502 and 618) strains generated glycoconjugates able to induce high specific antibody levels with high breadth of serovar-specific strain coverage, and were selected for use in vaccine production. The strain selection approach described is potentially applicable to the development of glycoconjugate vaccines against other bacterial pathogens.

Morphological diversity and evolution of Centrolepidaceae (Poales), a species‐poor clade with diverse body plans and developmental patterns

• Premise of the study: The small primarily Australian commelinid monocot family Centrolepidaceae displays remarkably high structural diversity that has been hitherto relatively poorly explored. Data on Centrolepidaceae are important for comparison with other Poales, including grasses and sedges.• Methods: We examined vegetative and reproductive morphology in a global survey of Centrolepidaceae based on light and scanning electron microscopy of 18 species, representing all three genera. We used these data to perform a cladistic analysis to assess character evolution.• Key results: Each of the three genera is monophyletic; Centrolepis is sister to Aphelia. Some Centrolepidaceae show a change from spiral to distichous phyllotaxy on inflorescence transition. In Aphelia and most species of Centrolepis, several morphologically distinct leaf types develop along the primary shoot axis and flowers are confined to dorsiventral lateral spikelets. Centrolepis racemosa displays secondary unification of programs of leaf development, absence of the leaf hyperphyll and loss of shoot dimorphism. Presence or absence of a leaf ligule and features of inflorescence and flower morphology are useful as phylogenetic characters in Centrolepidaceae.• Conclusions: Ontogenetic changes in phyllotaxy differ fundamentally between some Centrolepidaceae and many grasses. Inferred evolutionary transformations of phyllotaxy in Centrolepidaceae inflorescences also differ from those in grasses. In contrast with grasses, some Centrolepidaceae possess ligulate leaves where the ligule represents the boundary between the bifacial hypophyll and unifacial hyperphyll. All the highly unusual features of the morphological‐misfit species Centrolepis racemosa could result from the same saltational event. Centrolepidaceae offer good perspectives for studies of evolutionary developmental biology.

Virtual screening and synthesis of novel antitubercular agents through interaction-based pharmacophore and molecular docking studies.

Tuberculosis continues to become a major threat and wide spreading disease though out the world. Therefore it is required to identify the new drugs for the treatment of tuberculosis with better activity profile than the prevalent compounds. In present study we have screened and modified the antitubercular compounds from commercial chemical database using the interaction-based pharmacophore and molecular docking studies. In the first step different pharmacophores of cocrystal structures of enyol acyl carrier reductase (also known as InhA) proteins (2B36 and 3FNG) were generated and employed for screening of ChemDiv database. Four different pharmacophore hypothesis retrieved 3456 hits from approximately 0.67 million compounds. In the second filter, these hit molecules were subjected to the molecular docking studies in 2NSD and 3FNG crystal structures. On the basis of high fit values, GScore, structural diversity and visual inspection, one hundred compounds were selected, purchased and subjected to experimental validation for antitubercular activity against H37Rv Mycobacterium tuberculosis (MTB) strain. Three compounds showed the minimal inhibitory concentration (MIC) value at 16 μg/mL and one compound VH04 showed the value at 1 μg/mL. Then a more active amidoethylamine compound was developed by chemical modifications of the virtual hit VH04 against the MTB strain. We believe that this newly identified scaffold could be useful for the optimization of lead from hit compounds of new antitubercular agents.

Immune and stress responses in oysters with insights on adaptation.

Oysters are representative bivalve molluscs that are widely distributed in world oceans. As successful colonizers of estuaries and intertidal zones, oysters are remarkably resilient against harsh environmental conditions including wide fluctuations in temperature and salinity as well as prolonged air exposure. Oysters have no adaptive immunity but can thrive in microbe-rich estuaries as filter-feeders. These unique adaptations make oysters interesting models to study the evolution of host-defense systems. Recent advances in genomic studies including sequencing of the oyster genome have provided insights into oyster's immune and stress responses underlying their amazing resilience. Studies show that the oyster genomes are highly polymorphic and complex, which may be key to their resilience. The oyster genome has a large gene repertoire that is enriched for immune and stress response genes. Thousands of genes are involved in oyster's immune and stress responses, through complex interactions, with many gene families expanded showing high sequence, structural and functional diversity. The high diversity of immune receptors and effectors may provide oysters with enhanced specificity in immune recognition and response to cope with diverse pathogens in the absence of adaptive immunity. Some members of expanded immune gene families have diverged to function at different temperatures and salinities or assumed new roles in abiotic stress response. Most canonical innate immunity pathways are conserved in oysters and supported by a large number of diverse and often novel genes. The great diversity in immune and stress response genes exhibited by expanded gene families as well as high sequence and structural polymorphisms may be central to oyster's adaptation to highly stressful and widely changing environments.

ChemInform Abstract: Metal‐Mediated Post‐Ugi Transformations for the Construction of Diverse Heterocyclic Scaffolds

AbstractReview: 50 refs.

Separation and characterization of phenolic compounds and triterpenoid saponins in licorice (Glycyrrhiza uralensis) using mobile phase-dependent reversed-phase × reversed-phase comprehensive two-dimensional liquid chromatography coupled with mass spectrometry

Licorice is one of the most popular herbal medicines worldwide. It contains a big array of phenolic compounds (flavonoids, coumarins, and diphenylethanones). Due to high structural diversity, low abundance, and co-elution with licorice saponins, these phenolic compounds are difficult to be separated by conventional chromatography. In this study, a mobile phase-dependent reversed-phase×reversed phase comprehensive two-dimensional liquid chromatography (RP×RP 2DLC) method was established to separate phenolic compounds in licorice (the roots of Glycyrrhiza uralensis). Organic solvents in the mobile phase were optimized to improve orthogonality of the first and second dimensions, and a synchronized gradient mode was used to improve chromatographic resolution. Finally, licorice extracts were eluted with methanol/water/formic acid in the first dimension (Acquity CSH C18 column), and acetonitrile/water/formic acid in the second dimension (Poroshell Phenyl-Hexyl column). By using this 2DLC system, a total of 311 compounds were detected within 40min. The practical and effective peak capacity was 1329 and 524, respectively, and the orthogonality was 79.8%. The structures of 21 selected unknown compounds were tentatively characterized by mass spectrometry, and 8 of them were discovered from G. uralensis for the first time. The mobile phase-dependent 2DLC/MS system could benefit the separation and characterization of natural products in complicated herbal extracts.

Review lipopeptides biosurfactants: Mean classes and new insights for industrial, biomedical, and environmental applications.

Lipopeptides are microbial surface active compounds produced by a wide variety of bacteria, fungi, and yeast. They are characterized by high structural diversity and have the ability to decrease the surface and interfacial tension at the surface and interface, respectively. Surfactin, iturin, and fengycin of Bacillus subtilis are among the most popular lipopeptides. Lipopepetides can be applied in diverse domains as food and cosmetic industries for their emulsification/de-emulsification capacity, dispersing, foaming, moisturizing, and dispersing properties. Also, they are qualified as viscosity reducers, hydrocarbon solubilizing and mobilizing agents, and metal sequestering candidates for application in environment and bioremediation. Moreover, their ability to form pores and destabilize biological membrane permits their use as antimicrobial, hemolytic, antiviral, antitumor, and insecticide agents. Furthermore, lipopeptides can act at the surface and can modulate enzymes activity permitting the enhancement of the activity of certain enzymes ameliorating microbial process or the inhibition of certain other enzymes permitting their use as antifungal agents. This article will present a detailed classification of lipopeptides biosurfactant along with their producing strain and biological activities and will discuss their functional properties and related applications.

Improved genome inference in the MHC using a population reference graph.

While much is known about human genetic variation, such information is typically ignored in assembling novel genomes. Instead, reads are mapped to a single reference, which can lead to poor characterization of regions of high sequence or structural diversity. We introduce a population reference graph, which combines multiple reference sequences and catalogues of variation. The genomes of novel samples are reconstructed as paths through the graph using an efficient hidden Markov model, allowing for recombination between different haplotypes and additional variants. By applying the method to the 4.5Mb extended MHC region on human chromosome 6, combining eight assembled haplotypes, sequences of known classical HLA alleles and 87,640 SNP variants from the 1000 Genomes Project, we demonstrate, using simulations, SNP genotyping, short-read and long-read data, how the method improves the accuracy of genome inference and reveals regions where the current set of reference sequences is substantially incomplete.

ChemInform Abstract: Ring Opening of Heterocycles Containing a C—N Double Bond: A Simple Synthesis of Imides Promoted by Acyl Palladium Species.

Abstract A detailed study on the reactivity of various heterocycles, containing a C–N double bond, with acyl palladium species, generated in situ from allyl or benzyl halides and CO, has been performed. While the cyclic imine 2-methyl-1-pyrroline reacted with acyl-palladium intermediates to give a bicyclic β-lactam, other heterocycles containing a C–N double bond conjugated with a heteroatom (O or N), showed a ring-opening reaction leading to functionalized imides with high structural diversity. Such methodology represents a simple and direct way to prepare structurally complex imides. Moreover, a reaction mechanism, involving cationic intermediates, was also proposed.

Cleavage of C–N bonds in guanidine derivatives and its relevance to efficient C–N bonds formation

Efficient nonenzymatic decomposition of guanidine derivatives with high structural and functional diversity into anilide products is achieved in the presence of PdII/Cu(II) carboxylates/CO, relying on a dual C–N bonds cleavage strategy. In this decomposition process, the cooperative action of PdII species, Cu(II) carboxylates, and CO provides not only the N-acylating agents but also an initiator to trigger this C–N bonds cleavage sequence. The current results indicate that PdII/Cu(II) carboxylates/CO system provides a convenient and practical method for highly selective cleavage of unreactive C–N single bonds.

Isolation of novel indole diterpenes and dihydrodibenzofuran from the marine fungus <i>Aspergillus</i> sp.

Twelve secondary metabolites were earlier isolated from two marine-derived fungal strains, Aspergillus sp. AF-119 and Aspergillus sp. JQG a-6f. The objectives of this investigation were to isolate and purify natural products produced in these fungi, and identify possible drug candidates. The chemical structures of these compounds were elucidated and characterized by the analysis of 1D and 2D NMR spectra, UV, optical rotation and massspectroscopy data. Three of the isolated compounds are novel derivatives of indole diterpenes (1& 2), and dihydrodibenzofuran, namely, 9-hydroxy-7-methyl-2, 3-dihydrodibenzo [b, d] furan-1, 4-dione (3). The rest of the compounds were also determined from spectroscopy data to be known. These included three indole diterpenes – paspalinine (4), paspalicine (5) and paspaline (6); two ditetopiperazines –fumitremorgin B and lanosulin (7 & 8); methyl 2,8-dihydroxy-6-methyl-9-oxo-9H-xanthene-1 carboxylate (9); 1,3,8-trihydroxy-6-methylanthracene-9,10- dione (10); terphenyl (11) and 2-(3-chloro-2-hydroxyphenyl)-5-hydroxy-3,7,8-trimethoxy-4H-chromen-4-one (12). Paper disc diffusion assays showed that the novel compounds exhibit antibacterial activity on S. aureus, B. subtilis, and E. coli, but no activity on C. niger. MTT assays showed that the three novel compounds have antibacterial activity in vitro. These findings further enhanced the concept that natural products synthesized by marine-derived fungi possessed high structural diversity, antimicrobial and antitumor activities. Hence, they are a rich resource for drug discovery.Keywords: Marine Fungi; Natural product; Indole diterpenes; Cytotoxicity Assay

Chemical characterisation and allelopathic potential of essential oils from leaves and rhizomes of white ginger

Essential oils have the potential to be used as bioherbicides, and possess the advantage of their biodegradability, high structural diversity and reduced natural resistance to weeds. The essential oils of the leaves and rhizomes of Hedychium coronarium, an exotic invasive plant adapted to different regions of Brazil, were extracted by hydrodistillation and characterised chemically by Gas-Liquid Chromatography and Gas-Liquid Chromatography/Mass Spectrometry. Allelopathic activity was determined using methodologies that evaluate the effects of volatility and direct contact on seed germination and seedling vigour in the lettuce. The major constituents of the essential oil from the leaves were β-pinene (46.9%), α-pinene (19.2%) and β-caryophyllene (13.2%) and from the rhizomes, β-pinene (41.5%), 1.8-cineole (23.6%) and α-pinene (13.1%). When analysing the volatile effects of the essential oils, it was seen that their concentration did not affect seedling first germination count or total germination. The essential oil from the rhizomes was more effective than the essential oil from the leaves in reducing seedling response for SGI, dry weight, and length of the roots and shoots. When evaluating the effect of direct contact with the essential oils, it was seen that both oils reduced the response of all the variables under evaluation, and that in addition, the oil from the rhizomes caused greater reductions than that from the leaves, again for all variables. These results can be attributed to the higher levels of monoterpenes present in the essential oil from the rhizomes, mainly the presence of 1.8-cineole.

English

Pollens and seeds of Hypoestes and Rhinacanthus collected from different field localities in Taiz and Soqotra Island, Yemen were investigated by using light and scanning electron microscopes. Pollen grains of Hypoestes were prolate in equatorial view, lobate trigonal to lobate circular in polar view whereas those of Rhinacanthus were subspheroidal and rounded trigonal in polar view. The aperture was tricolporate and exine ornamentation was coarsely reticulate for all species in the two genera. Scanning electron microscopy and morphological observations showed that mature dry seeds of Hypoestes and Rhinacanthus have various sizes and shapes, the surface ornamentations observed were reticulate to cristate, an addition to the tuberculum and papillae. The three Hypoestes species differ in the seed structure which are useful for identification and their high structural diversity provides an important taxonomic value for species differentiation.

Retention Indices for Identification of Aroma Compounds by GC: Development and Application of a Retention Index Database

In this paper we focus on the development and application of a retention index database for aroma compounds with high structural diversity. Retention indices of over 300 aroma compounds were determined on three capillary columns of different polarity. The capability of the retention index database was evaluated by identification of the components of tobacco flavor. The results showed that the database can be used for qualitative identification. The database also contains a good set of retention index data for study of quantitative structure–retention relationships.

Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis.

Strigolactones (SLs) are a class of phytohormones and rhizosphere signaling compounds with high structural diversity. Three enzymes, carotenoid isomerase DWARF27 and carotenoid cleavage dioxygenases CCD7 and CCD8, were previously shown to convert all-trans-β-carotene to carlactone (CL), the SL precursor. However, how CL is metabolized to SLs has remained elusive. Here, by reconstituting the SL biosynthetic pathway in Nicotiana benthamiana, we show that a rice homolog of Arabidopsis More Axillary Growth 1 (MAX1), encodes a cytochrome P450 CYP711 subfamily member that acts as a CL oxidase to stereoselectively convert CL into ent-2'-epi-5-deoxystrigol (B-C lactone ring formation), the presumed precursor of rice SLs. A protein encoded by a second rice MAX1 homolog then catalyzes the conversion of ent-2'-epi-5-deoxystrigol to orobanchol. We therefore report that two members of CYP711 enzymes can catalyze two distinct steps in SL biosynthesis, identifying the first enzymes involved in B-C ring closure and a subsequent structural diversification step of SLs.