Proposal for a standard system for drawing structural diagrams of N‐ and O‐linked carbohydrates and related compounds

Symbolic diagrams are commonly used to depict N‐ and O‐linked glycans but there is no general consensus as to how individual constituent monosaccharides or linkages are shown. This article proposes a system that avoids ambiguities inherent in most other systems and is appropriate for both hand drawing and computer applications. Constituent monosaccharides are depicted by shapes modified to show OAc, deoxy, etc. Linkage is indicated by the bond angle and anomericity by solid (β) or dashed (α) lines.     

Exploratory evaluation of several teratogen warning symbols

BACKGROUND: Previous research has noted potential inadequacies in the warning labels and symbols used with some teratogenic medications. A clear teratogen warning symbol represents an important component of risk mitigation for accidental teratogen exposure. METHODS: Several teratogen warning symbols were developed through rapid prototyping and focus groups. A nationally distributed field trial (n = 300) examined the relative effectiveness of 6 candidate symbols, including the symbol in use at the time of the study. Measures included open-ended interpretation, closed-ended preference, and demographic surveys. Each participant was shown a single symbol and asked what it meant, to whom it applied, and what that person should do. Text statements were added to the symbol and participants were asked to reinterpret the warning. Participants were told the intended message of the warning, shown all 6 symbols, and asked to choose the most effective symbol. RESULTS: Four of 6 symbols achieved levels of correct interpretation close to or exceeding the American National Standards Institute (ANSI) benchmark of 85% and none exceeded the ANSI limit of 5% critical confusion. Symbols elicited varying conceptual responses. Respondents considered 1 symbol to be the most effective, by a 4 to 1 margin. Several outcomes varied by age and by ethnicity. CONCLUSIONS: Several symbols emerged as viable alternatives to the current symbol; however, no 1 symbol was clearly found to be the most effective. Instead, the symbol considered "best" depends on the messages that are considered most essential to the warning. Additionally, it appears a symbol without the addition of text can convey most, but possibly not all, of the meaning required of the warning label. Next steps should include further symbol refinement, closer examination of text additions to symbols, and validation of the candidate symbols and warnings through a large-scale field trial.     

D-glucose as a multivalent chiral scaffold for combinatorial chemistry

Due to their high density of functional groups and their availability in a variety of diastereomeric forms, monosaccharides are considered attractive scaffolds for combinatorial chemistry that allow the attachment and defined spatial alignment of up to five different pharmacophoric groups. For their application in combinatorial syntheses on solid phase, a set of selectively removable hydroxy protecting groups in combination with a cleavable anchor is required. Herein, we report on the construction and use of a versatile multivalent glucose building block for parallel synthesis on the solid phase.     

WildSpan: mining structured motifs from protein sequences

Background  

Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards) are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions) that incorporates several pruning strategies to largely reduce the mining cost.     

Antigenic reactivity: Molecular delineation of monohaptenic anaphylactogens

Anaphylactogenic, monohaptenic conjugates carrying a 2,4-dinitro-5-carboxyphenyl substituent as haptenic group and either one of two types of auxiliary groups essential for their anaphylactogenicity were studied. The “hydrocarbon auxiliary groups” require the presence of a hydrocarbon structure such as aliphatic chains of discrete length or planar rings such as provided by phenyl- or nicotinoyl residues and become particularly effective in conjunction with a carboxylate group. The benzylpenicilloyl group is an effective auxiliary structure, but the thiazolidine ring as such is not. It appears that the distance between haptenic and hydrocarbon auxiliary groups can be quite large. The “carbohydrate auxiliary group” becomes effective via a different mechanism. It requires disaccharide residues or two closely connected monosaccharides. Single monosaccharides are ineffective. A concept of interest with regard to drug allergy is the possibility that attachment of a single haptenic molecule to a glycoprotein constitutes an anaphylactogen.     

Synthesis and modifications of carbohydrates, using biotransformations

Enzymes continue to be used as important catalysts, for the generation of rare and 'unnatural' monosaccharides and for the selective formation of glycosidic linkages. Multi-enzyme systems have been employed in one-pot strategies for multistep reaction sequences and for co-factor regeneration. The efficiency of glycosidases for glycosylation reactions has been dramatically increased by active-site mutagenesis to generate glycosynthases. First reports have detailed the expansion and optimization of glycosynthase substrate specificity by directed evolution. Novel glycosyltransferases are being identified from genomic databases and have been shown to glycosylate complex metabolites, such as glycopeptide antibiotics, with exquisite selectivity and in good yields. An emerging field is the application of glycosynthases and glycosyltransferases to reactions on solid support, generating potential applications in microarrays.     

Correction to Yu (2010).

Reports an error in "Contemporary Chinese sex symbols in dreams: Correction to Yu" by Calvin Kai-Ching Yu (Dreaming, 2010[Mar], Vol 20[1], 25-41). The publishing year of the article in the correction notice was listed incorrectly as 2009. The correct publication year for the original article is 2010. The word were was also misspelled in the body of the correction as where. (The following abstract of the original article appeared in record 2010-05656-003.) [Correction Notice: An erratum for this article was reported in Vol 20(2) of Dreaming (see record 2010-12874-005). Three Chinese characters where printed incorrectly in the article. The correct symbols are shown along with the location of each in the original article. An error is also located on page 26, 3rd paragraph from the top, second symbol in the third sentence from the bottom of the paragraph. On page 28, 1st paragraph, the 1st symbol in line 7 of the paragraph is incorrect. The last error is on page 28, in which the 1st paragraph, 1st symbol in the last line of the paragraph is incorrect.] The present study aimed to determine how often Chinese people dream of sexual metaphors and to examine the association between the dreaming of sexual experiences and contemporary Chinese sex symbols. A list of sex symbols was derived from a thorough review of the sexual analogies that Chinese people most often use in slang language. This list, together with the Marlowe-Crowne Social Desirability Scale and the Eysenck Personality Questionnaire Revised–Short Form, was administrated to a sample of 608 upper-secondary school graduates from Hong Kong. It was found that the participants rarely dreamed about food analogies for sex, such as “eating litchis” and “bananas or banana-like objects.” By contrast, sex symbols involving weapons and aggressive behavior, such as “knives, swords, or daggers” and “shooting,” occurred in dreams with moderate prevalence rates. Moreover, gender, the frequency of dreaming sexual experiences, and social desirability significantly predicted the frequency scores on the scale formed by these aggressive symbols for sex. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Contemporary chinese sex symbols in dreams.

[Correction Notice: An erratum for this article was reported in Vol 20(3) of Dreaming (see record 2010-17362-003). The publishing year of the article in the correction notice was listed incorrectly as 2009. The correct publication year for the original article is 2010. The word were was also misspelled in the body of the correction as where.] [Correction Notice: An erratum for this article was reported in Vol 20(2) of Dreaming (see record 2010-12874-005). Three Chinese characters where printed incorrectly in the article. The correct symbols are shown along with the location of each in the original article. An error is also located on page 26, 3rd paragraph from the top, second symbol in the third sentence from the bottom of the paragraph. On page 28, 1st paragraph, the 1st symbol in line 7 of the paragraph is incorrect. The last error is on page 28, in which the 1st paragraph, 1st symbol in the last line of the paragraph is incorrect.] The present study aimed to determine how often Chinese people dream of sexual metaphors and to examine the association between the dreaming of sexual experiences and contemporary Chinese sex symbols. A list of sex symbols was derived from a thorough review of the sexual analogies that Chinese people most often use in slang language. This list, together with the Marlowe-Crowne Social Desirability Scale and the Eysenck Personality Questionnaire Revised–Short Form, was administrated to a sample of 608 upper-secondary school graduates from Hong Kong. It was found that the participants rarely dreamed about food analogies for sex, such as “eating litchis” and “bananas or banana-like objects.” By contrast, sex symbols involving weapons and aggressive behavior, such as “knives, swords, or daggers” and “shooting,” occurred in dreams with moderate prevalence rates. Moreover, gender, the frequency of dreaming sexual experiences, and social desirability significantly predicted the frequency scores on the scale formed by these aggressive symbols for sex. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

"Contemporary Chinese sex symbols in dreams": Correction to Yu (2009).

Reports an error in "Contemporary Chinese sex symbols in dreams" by Calvin Kai-Ching Yu (Dreaming, 2010[Mar], Vol 20[1], 25-41). Three Chinese characters where printed incorrectly in the article. The correct symbols are shown along with the location of each in the original article. On page 26, 3rd paragraph from the top, the second symbol in the third sentence from the bottom of the paragraph is incorrect. On page 28, 1st paragraph, the 1st symbol in line 7 of the paragraph is also incorrect. The last error on page 28, in which the 1st paragraph, 1st symbol in the last line of the paragraph is incorrect. (The following abstract of the original article appeared in record 2010-05656-003.) The present study aimed to determine how often Chinese people dream of sexual metaphors and to examine the association between the dreaming of sexual experiences and contemporary Chinese sex symbols. A list of sex symbols was derived from a thorough review of the sexual analogies that Chinese people most often use in slang language. This list, together with the Marlowe-Crowne Social Desirability Scale and the Eysenck Personality Questionnaire Revised–Short Form, was administrated to a sample of 608 upper-secondary school graduates from Hong Kong. It was found that the participants rarely dreamed about food analogies for sex, such as “eating litchis” and “bananas or banana-like objects.” By contrast, sex symbols involving weapons and aggressive behavior, such as “knives, swords, or daggers” and “shooting,” occurred in dreams with moderate prevalence rates. Moreover, gender, the frequency of dreaming sexual experiences, and social desirability significantly predicted the frequency scores on the scale formed by these aggressive symbols for sex. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Solid Lipid Nanoparticles as Delivery Systems for Bioactive Food Components

The inclusion of bioactive compounds, such as carotenoids, omega-3 fatty acids, or phytosterols, is an essential requisite for the production of functional foods designed to improve the long-term health and well-being of consumers worldwide. To incorporate these functional components successfully in a food system, structurally sophisticated encapsulation matrices have to be engineered, which provide maximal physical stability, protect ingredients against chemical degradation, and allow for precise control over the release of encapsulated components during mastication and digestion to maximize adsorption. A novel encapsulation system initially developed in the pharmaceutical industries to deliver lipophilic bioactive compounds is solid lipid nanoparticles (SLN). SLN consist of crystallized nanoemulsions with the dispersed phase being composed of a solid carrier lipid–bioactive ingredient mixture. Contrary to larger colloidal solid lipid particles, specific crystal structures can be “dialed-in” in SLN by using specific surfactant mixtures and ensuring that mean particle sizes are below 100–200 nm. Moreover, in SLN, microphase separations of the bioactive compound from the solidifying lipid matrix can be prevented resulting in an even dispersion of the encapsulated compound in the solid matrix thereby improving chemical and physical stability of the bioactive. In this review article, we will briefly introduce the structure, properties, stability, and manufacturing of solid lipid particles and discuss their emerging use in food science.     

Impacts of chronic nitrogen additions vary seasonally and by microbial functional group in tundra soils

Previous studies have shown that fertilization with nitrogen depresses overall microbial biomass and activity in soil. In the present study we broaden our understanding of this phenomenon by studying the seasonality of responses of specific microbial functional groups to chronic nitrogen additions in alpine tundra soils. We measured soil enzyme activities, mineralization kinetics for 8 substrates, biomass of 8 microbial functional groups, and changes in N and carbon pools in the soil. Our approach allowed us to compare the ability of the soil microbial biomass to utilize various substrates in addition to allowing us to estimate changes in biomass of microbial functional groups that are involved in carbon and nitrogen cycling. Overall microbial activity and biomass was reduced in fertilized plots, whereas pools of N in the soil and microbial biomass N were higher in fertilized plots. The negative effects of N were most prominent in the summer. Biomass of the dominant microbial functional groups recovered in fertilized soils during the winter and nitrogen storage in microbial biomass was higher in fertilized soils in the autumn and winter than in the summer. Microbial immobilization of N may therefore be a significant sink for added N during autumn and winter months when plants are not active. One large microbial group that did not recover in the winter in fertilized soils was phenol mineralizers, possibly indicating selection against microbes with enzyme systems for the breakdown of phenolic compounds and complex soil organic matter. Overall, this work is a step towards understanding how chronic N additions affect the structure and biogeochemical functioning of soil microbial communities.     

Influence of yeasts and of their constituents on nucleoside uptake in peritoneal murine macrophages

A marked reduction of [3H]-uridine uptake was observed when mouse peritoneal macrophages (pM phi) were exposed to heat-killed Candida albicans or Saccharomyces cerevisiae. By contrast, an increased nucleoside uptake was promoted by yeast products such as zymosan, laminarin, or yeast cell-wall extracts, which are mainly composed of beta-glucans and alpha-mannans. In a search for the active fungal component(s), the uptake process was shown to be differently affected by monosaccharides and polysaccharides. These findings support the view that a specific recognition of a pM phi membrane receptor is mediating the effect of the various substances.     

Marine algal lectins: new developments

Lectins can be extracted more readily from marine algae if the plant material is freeze-dried or frozen in liquid nitrogen prior to homogenisation. The addition of detergents, such as Tween 80, to the extraction medium and diluents, enhances extraction and detection of the lectins. Marine algal lectins can be isolated by affinity chromatography using a general affinity complex such as yeast mannan-Cellulofine which facilitates the isolation of purified lectin for biochemical characterisation. Red algal lectins exist as three types: low molecular weight molecules which bind glycoproteins, but not monosaccharides and have no requirement for divalent cations; lectins which bind monosaccharides and related small molecules, but have no divalent cation requirements; larger lectins (M.W. > 64000) which bind monosaccharides in the presence of divalent cations. No green algal lectin characterised so far requires divalent cations for haemagglutination. Possibly, only green algal lectins capable of forming oligomers have the capacity to bind monosaccharides.     

Biochemical and structural analyses of the extracellular matrix fibrils of Myxococcus xanthus.

It is characteristic of myxobacteria to produce large amounts of extracellular material. This report demonstrates that this material in Myxococcus xanthus is fibrillar and describes the structure and chemical composition of the fibrils. The extracellular matrix fibrils are the mediators of cell-cell cohesion in M. xanthus. As such, the fibrils play an important role in the cell-cell interactions that form the basis for the social and developmental lifestyle of this organism. The fibrils are composed of protein and carbohydrate in a 1.0:1.2 ratio. Combined, the two fractions accounted for greater than 85% of the mass of isolated fibrils, and the fibrils were found to compose up to 10% of the dry weight of cells grown at high density on a solid surface. The polysaccharide portion of the fibrils was shown to be composed of five different monosaccharides: galactose, glucosamine, glucose, rhamnose, and xylose. Glucosamine, one of the component monosaccharides of the fibrils and a known morphogen for M. xanthus, inhibited cohesion to a level near that of Congo red (the positive control for cohesion inhibition). Glucose and xylose also inhibited cohesion but less than did glucosamine. Analysis of the morphology of the fibrils, the periodicities within the distribution of fibril diameters observed by field emission scanning electron microscopy, and the observation of fibrils on hydrated cells strongly suggested that the extracellular matrix of M. xanthus was indeed arranged as fibrils. Furthermore, results suggested that the fibrils were constructed as carbohydrate structures with associated proteins.     

MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes

The identification of orthologous genes shared by multiple genomes plays an important role in evolutionary studies and gene functional analyses. Based on a recently developed accurate tool, called MSOAR 2.0, for ortholog assignment between a pair of closely related genomes based on genome rearrangement, we present a new system MultiMSOAR 2.0, to identify ortholog groups among multiple genomes in this paper. In the system, we construct gene families for all the genomes using sequence similarity search and clustering, run MSOAR 2.0 for all pairs of genomes to obtain the pairwise orthology relationship, and partition each gene family into a set of disjoint sets of orthologous genes (called super ortholog groups or SOGs) such that each SOG contains at most one gene from each genome. For each such SOG, we label the leaves of the species tree using 1 or 0 to indicate if the SOG contains a gene from the corresponding species or not. The resulting tree is called a tree of ortholog groups (or TOGs). We then label the internal nodes of each TOG based on the parsimony principle and some biological constraints. Ortholog groups are finally identified from each fully labeled TOG. In comparison with a popular tool MultiParanoid on simulated data, MultiMSOAR 2.0 shows significantly higher prediction accuracy. It also outperforms MultiParanoid, the Roundup multi-ortholog repository and the Ensembl ortholog database in real data experiments using gene symbols as a validation tool. In addition to ortholog group identification, MultiMSOAR 2.0 also provides information about gene births, duplications and losses in evolution, which may be of independent biological interest. Our experiments on simulated data demonstrate that MultiMSOAR 2.0 is able to infer these evolutionary events much more accurately than a well-known software tool Notung. The software MultiMSOAR 2.0 is available to the public for free.     

Vinyl sulfone functionalization: a feasible approach for the study of the lectin-carbohydrate interactions

Carbohydrate-mediated molecular recognition is involved in many biological aspects such as cellular adhesion, immune response, blood coagulation, inflammation, and infection. Considering the crucial importance of such biological events in which proteins are normally involved, synthetic saccharide-based systems have emerged as powerful tools for the understanding of protein-carbohydrate interactions. As a new approach to create saccharide-based systems, a set of representative monosaccharides (D-mannose, D-glucose, N-acetyl-D-glucosamine, and L-fucose) and disaccharides (lactose, maltose, and melibiose) were derivatized at their anomeric carbon with a vinyl sulfone group spanned by an ethylthio linker. This vinyl sulfone functionalization is demonstrated to be a general strategy for the covalent linkage of a saccharide in mild conditions via Michael-type additions with the amine and thiol groups from functionalized supports and those naturally present in biomolecules. The introduction of the ethylthio linker between the biorecognizable element (i.e., saccharide) and the reactive group (i.e., vinyl sulfone) was found to preserve the functionality of the former. The capability of the vinyl sulfone saccharides for the study of lectin-carbohydrate interactions was demonstrated by (i) immobilizing them on both amine-functionalized supports (glass slides and microwell plates) and polylysine-coated glass slides to create sugar arrays that selectively bind lectins (ii) coupling to model proteins to yield neoglycoproteins that are recognized by lectins and (iii) using vinyl sulfone saccharides as tags to allow the detection of the labeled biomolecule by HRP-lectins. The above results were further put tothe test with a real case: detection of carbohydrate binding proteins present in rice ( Oryza sativa ).     

Sugar-derived glasses support thermal and photo-initiated electron transfer processes over macroscopic distances

Trehalose-derived glasses are shown to support long range electron transfer reactions between spatially well separated donors and protein acceptors. The results indicate that these matrices can be used not only to greatly stabilize protein structures but also to facilitate both thermal and photo-initiated hemeprotein reduction over large macroscopic distances. To date the promise of exciting new protein-based technologies that can harness the exceptional tunability of protein functionality has been significantly thwarted by both intrinsic instability and stringent solvent/environment requirements for the expression of functional properties. The presented results raise the prospect of overcoming these limitations with respect to incorporating redox active proteins into solid state devices such as tunable batteries, switches, and solar cells. The findings also have implications for formulations intended to enhance long term storage of biomaterials, new protein-based synthetic strategies, and biophysical studies of functional intermediates trapped under nonequilibrium conditions. In addition, the study shows that certain sugars such as glucose or tagatose, when added to redox-inactive glassy matrices, can be used as a source of thermal electrons that can be harvested by suitable redox active proteins, raising the prospect of using common sugars as an electron source in solid state thermal fuel cells.     

Ontogenetic constructions of some fossil plants

This article presents a survey of ontogenetic studies in paleobotany, and of biologically relevant mathematical results available from such techniques as finite element analyses, algorithmic systems, and computer simulation. Dynamic representations of growth are possible when the observed cellular arrangements in fossils are mathematically described. Successive computer solutions of parameterizing equations allow for the extrapolation of ontogenetic trends forwards and backwards in time (i.e., more and less mature stages, respectively), as well as the interpolation of missing stages or portions of an organism's development. The hypothetical constructions derived from these techniques may be tested against direct comparisons with the fossil being simulated and/pr proposed modern analogues. Similarly, multicellular organisms or portions of organisms (e.g., leaves, sporangia) may be constructed as arrays of symbols — each symbol representing a cell or group of cells. Development in such models is simulated by providing instructions for cell division, cell death, or alteration in cellular states, e.g., vegetative to reproductive. Illustrative simulations of Parka, Mastopora, Rhynia and Calamites are presented and paleobotanical conclusions concerning their respective growth patterns are drawn.