Nonribosomal cyclic peptides: specific markers of fungal infections

Some cyclic peptides and depsipeptides are synthesized in microorganisms by large multienzymes called nonribosomal peptide synthetases. The structures of peptide products originating in this way are complex and diverse and are microorganism-specific. This work proposes the use of fungal cyclic peptides and depsipeptides as extremely specific markers of fungal infections. Since a reliable molecular tool for diagnosing fungal infections at an early stage is still missing, we present mass spectrometry as a new, modern, broadband (with respect to fungal strain) and specific tool for clinical mycologists. More than 40 different fungal species can be rapidly characterized according to specific families of cyclic peptides, and in some cases, a particular fungal strain can be identified on the basis of its cyclopeptide profile. This paper is also aimed at initiating discussion on the biological role of these secondary metabolites, especially of those synthesized by medically important strains. Proven cytotoxic, anti-inflammatory or immunosuppressive activities of some cyclic peptides indicate that these molecules may contribute to the synergistic array of fungal virulence factors and support microbial invasion during fungal infection. In addition to an overview on recent mass spectrometric protocols for cyclic peptide sequencing, the structures of new peptides from Paecilomyces and Pseudallescheria are presented.     

Features of X-ray fluorescence determination of rock-forming elements in powder samples of peat sediments

The features of rock-forming elements determination in powder samples of peat sediments are considered. Based on theoretical calculations and experimental data, the mineralogical and particle size effects on the X-ray fluorescence intensity have been estimated. For routine analysis, powder rock samples are usually milled to a particle size of 10–60 μm. Theoretically, estimated variations of rock-forming elements analytical lines intensities in different minerals are up to 30%, and the particle size effect cannot be eliminated simultaneously for all rock-forming elements. Experimental estimation shows that the impossibility of the particle size distribution control can lead to significant variations in the intensities of the analytical lines (3%–18%) that is mainly corresponding to theoretical estimation. Fine milling allowed us to achieve an average particle size of fewer than 20 μm and reduce the measurement uncertainty by 1.5–2 times. 12 samples of peat sediments with organic matter content up to 70 wt% were analyzed by X-ray fluorescence analysis using different sample preparation techniques, as well as by certified methods. The accuracy of X-ray fluorescence analysis of peat sediments prepared as pressed pellets varies from 1.5 to 11 rel% depending on compound contents. It is more than for samples prepared as fused beads, however, the proposed method can be used to determine the variations of rock-forming elements contents in peat sediments where the content variations exceed the measurement uncertainty, and accuracy of analysis is sufficient for further paleoecological reconstructions.     

Global alignment of molecular sequences via ancestral state reconstruction

We consider the trace reconstruction problem on a tree (TRPT): a binary sequence is broadcast through a tree channel where we allow substitutions, deletions, and insertions; we seek to reconstruct the original sequence from the sequences received at the leaves. The TRPT is motivated by the multiple sequence alignment problem in computational biology. We give a simple recursive procedure giving strong reconstruction guarantees at low mutation rates. To our knowledge, this is the first rigorous trace reconstruction result on a tree in the presence of indels.     

Magnetocaloric effect and multifunctional properties of Ni–Mn-based Heusler alloys

The studies of magnetocaloric properties, phase transitions, and phenomena related to magnetic heterogeneity in the vicinity of the martensitic transition (MT) in Ni–Mn–In and Ni–Mn–Ga off-stoichiometric Heusler alloys are summarized. The crystal structure, magnetocaloric effect (MCE), and magnetotransport properties were studied for the following alloys: Ni₅₀Mn_50−xIn_x, Ni_50−xCo_xMn₃₅In₁₅, Ni₅₀Mn_35−xCo_xIn₁₅, Ni₅₀Mn₃₅In₁₄Z (Z=Al, Ge), Ni₅₀Mn₃₅In_15−xSi_x, Ni_50−xCo_xMn_25+yGa_25−y, and Ni_50–xCo_xMn_32−yFeyGa₁₈. It was found that the magnetic entropy change, ΔS, associated with the inverse MCE in the vicinity of the temperature of the magneto-structural transition, TM, persists in a range of (125-5) J/(kg K) for a magnetic field change ΔH=5 T. The corresponding temperature varies with composition from 143 to 400 K. The MT in Ni₅₀Mn_50−xIn_x (x=13.5) results in a transition between two paramagnetic states. Associated with the paramagnetic austenite-paramagnetic martensite transition ΔS=24 J/(kg K) was detected for ΔH=5 T at T=350 K. The variation in composition of Ni₂MnGa can drastically change the magnetic state of the martensitic phase below and in the vicinity of TM. The presence of the martensitic phase with magnetic moment much smaller than that in the austenitic phase above TM leads to the large inverse MCE in the Ni₄₂Co₈Mn_32−yFeyGa₁₈ system. The adiabatic change of temperature (ΔT_ad) in the vicinity of TC and TM of Ni₅₀Mn₃₅In₁₅ and Ni₅₀Mn₃₅In₁₄Z (Z=Al, Ge) was found to be ΔT_ad=−2 K and 2 K for ΔH=1.8 T, respectively. It was observed that |ΔT_ad|≈1 K for ΔH=1 T for both types of transitions. The results on resistivity, magnetoresistance, Hall resistivity in some In-based alloys are discussed.     

Differently coloured polymorphs of 4‐[(2‐nitrophenyl)azo]phenol

The crystal structures of the brown–yellow and orange polymorphs of the title compound, 4‐[(2‐nitro­phenyl)­diazenyl]­phenol, C₁₂H₉N₃O₃, have been determined and their visible reflection spectra recorded. Both structures adopt a stacking arrangement with interstack hydrogen bonds. Ab initio and semi‐empirical (AM1 and INDO‐CISD) calculations were performed in order to rationalize the difference in colour. It can be attributed neither to the subtle distinctions in molecular geometry nor to the effect of intermolecular electrostatic interactions. The most probable origin of this difference is the mixing of intramolecular n π* and intermolecular charge‐transfer excitations.     

Effect of thermosensitive matrix-phase transition on urease-catalyzed urea hydrolysis

Temperature dependencies of kinetic and equilibrium parameters of urea hydrolysis catalyzed by native urease and the urease immobilized in a thermosensitive poly-N-isopropylacrylamide gel have been studied. The swelling ratio of the collapsed urease-containing gel is shown to increase in the presence of urea. Below a lower critical solution temperature (LCST) of the polymer, the immobilized u reaseactually has thesame catalytic properties as the native enzyme. At temperatures above LCST, the observed catalytic activity of the immobilized enzyme depends chiefly not only on the thermoreversible matrix state, but also on gel water content.     

Impact of slow gain dynamics on soliton molecules in mode-locked fiber lasers

We theoretically demonstrate and experimentally confirm the major influence of gain dynamics on soliton molecules that self-assemble in mode-locked lasers. Both slow gain recovery and depletion play a pivotal role in the formation of chirped soliton molecules characterized by an increasing separation from leading to trailing pulses. These chirped molecules actually consist of many pulses and may be termed macromolecules. They are experimentally observed in a fiber laser and numerically modeled by an approach that properly includes the slow gain dynamics. Furthermore, it is shown that these processes stabilize soliton trains in fiber lasers by inhibiting internal oscillations.     

NMR and X-ray crystallography, complementary tools in structural proteomics of small proteins

NMR spectroscopy and X-ray crystallography, the two primary experimental methods for protein structure determination at high resolution, have different advantages and disadvantages in terms of sample preparation and data collection and analysis. It is therefore of interest to assess their complementarity when applied to small proteins. Structural genomics/proteomics projects provide an ideal opportunity to make such comparisons as they generate data in a systematic manner for large enough numbers of proteins to allow firm conclusions to be drawn. Here we report a comparison for 263 unique proteins screened by both NMR spectroscopy and X-ray crystallography in our structural proteomics pipeline. Only 21 targets (8%) were deemed amenable to both methods based on an initial 2D 15N-HSQC NMR spectrum and optimized crystallization trials. However, the use of both methods in the pipeline increased the total number of targets amenable to structure determination to 107, with 43 amenable to NMR only and 43 amenable to X-ray crystallographic methods only. We did not observe a correlation between 15N-HSQC spectral quality and the success of the same protein in crystallization screens. Similar results were found for an independent set of 159 proteins as reported in the accompanying paper by Snyder et al. Thus, we conclude that both methods are highly complementary, and in order to increase the number of proteins suited for structure determination, we suggest that both methods be used in parallel in screening of all small proteins for structure determination.