FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data

We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell-wide metabolomics and fluxomics studies. In such studies, the structural information of the MS(n) product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MS(n) product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MS(n) product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well-known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single-step model that ignores intermediate fragmentation states and the multi-step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive- and negative-ion modes. The software has an easy-to-use graphical interface with built-in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar-phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Formation of a stable dicarbenoid and an unsaturated C2P2S2 ring from two-electron oxidation of the [C(PPh2S)2]2- dianion

Two-electron oxidation of the [C(PPh(2)S)(2)](2-) dianion with iodine afforded an unexpected mixture of a dimeric Li-I carbenoid [(Et(2)O)(mu-Li)][(mu(4)-Li){IC(PPh(2)S)(2)}(2)] and a novel, unsaturated six-membered C(2)P(2)S(2) ring in [(SPh(2)P)(2)C(2)(PPh(2))(2)S(2)].     

Determination of neutral carbohydrates by CZE with direct UV detection

A new CZE method relying on in-capillary reaction and direct UV detection at the wavelength 270 nm is presented for the simultaneous separation of the neutral carbohydrates xylitol, D-(-)-mannitol, sucrose, D-(+)-fucose, D-(+)-cellobiose, D-(+)-galactose, D-(+)-glucose, L-rhamnose, D-(+)-mannose, D-(-)-arabinose, D-(+)-xylose, and D-(-)-ribose. The alkaline electrolyte solution was prepared of 130 mM sodium hydroxide and 36 mM disodium hydrogen phosphate dihydrate. Separation of the sample mixture was achieved within 35 min. Calibration plots were linear in the range of 0.05-3 mM. Reproducibility of migration times was between 0.3 and 1.1%, and the detection limits for the analytes were 0.02 and 0.05 mM. The optimized method was applied for the determination of neutral monosaccharides in lemon, pineapple, and orange juices and a cognac sample. The methodology is fast since no other sample preparation except dilution is required.     

Thermoascus aurantiacus CBHI/Cel7A production in Trichoderma reesei on alternative carbon sources

To develop functional enzymes in cellulose hydrolysis at or above 70 degrees C the cellobiohydrolase (CBHI/Cel7A) of Thermoascus aurantiacus was cloned and expressed in Trichoderma reesei Rut-C30 under the strong cbh1 promoter. Cellulase production of the parental strain and the novel strain (RF6026) was examined in submerged fermentation experiments using various carbon sources, which were lactose, Solka Floc 200 cellulose powder, and steam pretreated corn stover. An industrially feasible production medium was used containing only distiller's spent grain, KH(2)PO(4), and (NH(4))(2)SO(4). Enzyme production was followed by measurements of protein concentration, total cellulase enzyme activity (filter paper activity), beta-glucosidase activity, CBHI activity, and endogenase I (EGI) activity. The Thermoascus CBHI/Cel7A activity was taken as an indication of the heterologous gene expression under the cbh1 promoter.     

Structure of anionic phospholipid coatings on silica by dissipative quartz crystal microbalance

The adsorption of anionic phospholipids on silica was investigated by the dissipative quartz crystal microbalance (QCM) technique. Liposomes composed of 1 mM 80:20 mol % of 1-palmitoyl-2-oleyl-sn-glycero-3-phosphatidylcholine (POPC)/phosphatidic acid, POPC/phosphatidylglycerol, or POPC/phosphatidylserine in N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) buffer at pH 7.4 (with or without 3 mM of CaCl2) were examined. We have previously demonstrated that similar phospholipid coatings can be used in capillary electrochromatography as a stationary phase for the separation of analytes. In this work, we focus on the formation of the coatings and on the type of lipid structure formed on silica. The QCM investigation comprised qualitative results based on changes in frequency and resistance, and quantitative modeling of the obtained results. The latter was performed using the dissipative QCM, which measures the quartz crystal impedance, combined with equivalent circuit analysis. A previously developed coating and cleaning procedure for phospholipid-coated fused silica capillaries was adopted in this study, and the same silica-coated crystal was used throughout the QCM study. We will demonstrate in this work that the type of lipid structure formed on silica, that is, a rather rigid supported lipid bilayer or a viscoelastic supported vesicle layer (SVL), is highly dependent on the lipid and solvent composition. We also show for the first time that the modeling of the dissipative QCM data can be used to extract a more quantitative picture of an adsorbed SVL, because, so far, published studies have merely used the QCM data in a qualitative sense.     

Stereoselective aza Diels-Alder reaction on solid phase: a facile synthesis of hexahydrocinnoline derivatives

As part of our continuing studies of polymer-supported pericyclic reactions for preparing biologically interesting heterocyclic compounds, we have introduced a traceless solid-phase synthesis of hexahydrocinnolines. We developed a method in which mild reaction conditions can be used for the hetero-Diels-Alder reactions on a polymeric support. The dienoic 3-vinyl-2-cyclohexenol attached to a Wang resin through an ether linkage undergoes [4 + 2] cycloaddition reaction with several azadienophiles. The highly stereoselective Diels-Alder reaction showed preferential formation of a single cycloadduct resulting from an anti attack of the dienophile on the polymer-bound diene. Trifluoroacetic acid-mediated cleavage of the polymer-bound cycloadducts yields fused nonaromatic hexahydrocinnolines in moderate yields in three steps.     

Determination of differential heavy metal and trace element accumulation in liver, gills, intestine and muscle of sterlet (Acipenser ruthenus) from the Danube River in Serbia by ICP-OES

The accumulation of heavy metals in fish has been extensively studied and well documented. However, the research has been mainly focused on the muscle tissue, while the distribution patterns among other tissues, such as liver and gills, have been mostly neglected. Within the present study, the concentrations of Ag, Al, As, B, Ba, Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Se, Sr, Zn and Li in the muscle, gills, liver and intestine of the sterlet (Acipenser ruthenus) from the Danube River have been assessed by using the inductively-coupled plasma optical spectrometry. The analysis has revealed a high degree of differential accumulation of the studied heavy metals and trace elements in the tissues of the Danube sterlet. Liver appeared to be the main heavy metal storage tissue, while the lowest levels of analyzed metals were found in muscles. Heavy metal concentrations in the muscle were at acceptable levels for human consumption, except partly for cadmium. We conclude that, in order to enable a more efficient control of contaminants in fish products, there is an apparent need to resolve the problem of lack of legal limits for many metals in European legislation.     

Chemical ecology of tannins: recent developments in tannin chemistry reveal new structures and structure-activity patterns

Tannins are chemically complex plant polyphenols and only little is known of their true molecule-specific anti-herbivore activities. Here we will show that modern tannin chemistry is able to reveal fully new types of tannins in plants together with new types of biological activities for the tannins. Most of these new findings relate to ellagitannins, one of the least studied and underestimated classes of bioactive plant polyphenols.     

Excitation energy transfer in isolated chlorosomes from Chlorobaculum tepidum and Prosthecochloris aestuarii

Excitation energy transfer in chlorosomes from photosynthetic green sulfur bacteria, Chlorobaculum (Cba.) tepidum and Prosthecochloris (Pst.) aestuarii, have been studied at room temperature by time-resolved femtosecond transient absorption spectroscopy. Bleach rise times from 117 to 270 fs resolved for both chlorosomes reflect extremely efficient intrachlorosomal energy transfer. Bleach relaxation times, from 1 to 3 ps and 25 to 35 ps, probed at 758 nm were tentatively assigned to intrachlorosomal energy transfer based on amplitude changes of the global fits and model calculations. The anisotropy decay constant of about 1 ps resolved at 807 nm probe wavelength for the chlorosomes from Chloroflexus aurantiacus, Pst. aestuarii and Cba. tepidum was related to energy transfer between bacteriochlorophyll a molecules of the baseplate and partly to intrachlorosomal energy transfer. The longer anisotropy components 6.6, 8.8 and 12.1 ps resolved for the three chlorosomes, respectively, were assigned to chlorosome to baseplate energy transfer. Global fits of magic-angle data also revealed longer chlorosome to baseplate energy transfer components from 95 to 135 ps, in accord with results from simulations.     

Temporal networks

A great variety of systems in nature, society and technology–from the web of sexual contacts to the Internet, from the nervous system to power grids–can be modeled as graphs of vertices coupled by edges. The network structure, describing how the graph is wired, helps us understand, predict and optimize the behavior of dynamical systems. In many cases, however, the edges are not continuously active. As an example, in networks of communication via e-mail, text messages, or phone calls, edges represent sequences of instantaneous or practically instantaneous contacts. In some cases, edges are active for non-negligible periods of time: e.g., the proximity patterns of inpatients at hospitals can be represented by a graph where an edge between two individuals is on throughout the time they are at the same ward. Like network topology, the temporal structure of edge activations can affect dynamics of systems interacting through the network, from disease contagion on the network of patients to information diffusion over an e-mail network. In this review, we present the emergent field of temporal networks, and discuss methods for analyzing topological and temporal structure and models for elucidating their relation to the behavior of dynamical systems. In the light of traditional network theory, one can see this framework as moving the information of when things happen from the dynamical system on the network, to the network itself. Since fundamental properties, such as the transitivity of edges, do not necessarily hold in temporal networks, many of these methods need to be quite different from those for static networks. The study of temporal networks is very interdisciplinary in nature. Reflecting this, even the object of study has many names—temporal graphs, evolving graphs, time-varying graphs, time-aggregated graphs, time-stamped graphs, dynamic networks, dynamic graphs, dynamical graphs, and so on. This review covers different fields where temporal graphs are considered, but does not attempt to unify related terminology—rather, we want to make papers readable across disciplines.