Making sense of molecular signatures in the immune system

The development of Functional Genomics technologies has opened new avenues to investigate the complexity of the immune system. Microarray technology has been particularly successful because of its relatively low cost and high genome coverage. Consequently to our ability to monitor the expression of a significant proportion of an organism genome, our understanding of the molecular dynamics behind cell differentiation and cell response has greatly improved. Molecular signatures associated to immune cells have provided important tools to investigate the molecular basis of diseases and have been often associated to diagnostic and prognostic markers. The availability of such large collection of data has stimulated the application of complex machine learning techniques in the attempt to link molecular signatures and cell physiology. Here we review the most recent developments in the analysis of molecular signatures in the immune system.     

Synthese von Dimethyl-4a,8a-methanophthalazin-1,4-dicarboxylat und Derivaten

Synthesis of Dimethyl 4a,8a-Methanophthalazine-1,4-dicarboxylate and Derivatives Diels-Alder reaction with inversed electron demand of 1H-cyclopropabenzol 1 with dimethyl 1,2,4,5-tetrazine-3,6-dicarboxylate ( 2 ) yields dimethyl-4a,8a-methanophthalazine-1,4-dicarboxylate ( 3 ). The reactions of 3 with nucleophiles are also described.     

An assessment of the relative contributions of redox and steric issues to laccase specificity towards putative substrates

Laccases catalyze the one-electron oxidation of a broad range of substrates coupled to the 4 electron reduction of O2 to H2O. Phenols are typical substrates, because their redox potentials (ranging from 0.5 to 1.0 V vs. NHE) are low enough to allow electron abstraction by the T1 Cu(II) that, although a relatively modest oxidant (in the 0.4-0.8 V range), is the electron-acceptor in laccases. The present study comparatively investigated the oxidation performances of Trametes villosa and Myceliophthora thermophila laccases, two enzymes markedly differing in redox potential (0.79 and 0.46 V). The oxidation efficiency and kinetic constants of laccase-catalyzed conversion of putative substrates were determined. Hammett plots related to the oxidation of substituted phenols by the two laccases, in combination with the kinetic isotope effect determination, confirmed a rate-determining electron transfer from the substrate to the enzyme. The efficiency of oxidation was found to increase with the decrease in redox potential of the substrates, and the Marcus reorganisation energy for electron transfer to the T1 copper site was determined. Steric hindrance to substrate docking was inferred because some of the phenols and anilines investigated, despite possessing a redox potential compatible with one-electron abstraction, were scarcely oxidised. A threshold value of steric hindrance of the substrate, allowed for fitting into the active site of T. villosa laccase, was extrapolated from structural information provided by X-ray analysis of T. versicolor lac3B, sharing an identity of 99% at the protein level, thus enabling us to assess the relative contribution of steric and redox properties of a substrate in determining its susceptibility to laccase oxidation. The inferred structural threshold is compatible with the distance between two phenylalanine residues that mark the entrance to the active site. Interaction of the substrate with other residues of the active site is commented on.     

Recent developments in stripping analysis of trace metals

Development of sensing systems for trace metals is highly important because the abnormal concentration of some metals or the presence of some traces of toxic metals is very dangerous. The stripping analysis is an efficient way to detect metals even at low concentrations. Much work has been carried out to develop highly sensitive, stable, reproducible, and cheap electrochemical sensors for metal ions. This review summarizes the recent progress is stripping analysis of trace metals, focusing on works published from 2015 to 2019.     

1,3‐Ninhydrin dihydrazone featuring an R44(12) motif with symmetry and comprising only N and H atoms

In the title compound [systematic name: (1Z,3Z)‐1,3‐dihydrazinylidene‐1H‐inden‐2(3H)‐one], C₉H₈N₄O, isolated molecules possess approximate noncrystallographic C_2v symmetry and their cis conformation and planarity are assisted by a pair of short intramolecular N—H...O hydrogen bonds. Each molecule is asymmetrically involved in an extensive three‐dimensional network of N—H...O and N—H...N hydrogen bonds, and the structure also exhibits weaker π–π and C=O...C interactions. The structure features an R₄⁴(12) motif consisting solely of N and H atoms and possessing crystallographic symmetry.     

Metal-sensitive and thermostable trypsin from the crevalle jack (<Emphasis Type="Italic">Caranx hippos</Emphasis>) pyloric caeca: purification and characterization

Background

Over the past decades, the economic development and world population growth has led to increased for food demand. Increasing the fish production is considered one of the alternatives to meet the increased food demand, but the processing of fish leads to by-products such as skin, bones and viscera, a source of environmental contamination. Fish viscera have been reported as an important source of digestive proteases with interesting characteristics for biotechnological processes. Thus, the aim of this study was to purify and to characterize a trypsin from the processing by-products of crevalle jack (Caranx hippos) fish.

Results

A 27.5 kDa trypsin with N-terminal amino acid sequence IVGGFECTPHVFAYQ was easily purified from the pyloric caeca of the crevalle jack. Its physicochemical and kinetic properties were evaluated using N-α-benzoyl-_DL-arginine-p-nitroanilide (BApNA) as substrate. In addition, the effects of various metal ions and specific protease inhibitors on trypsin activity were determined. Optimum pH and temperature were 8.0 and 50°C, respectively. After incubation at 50°C for 30 min the enzyme lost only 20% of its activity. K _m , k_cat, and k _cat /K _m values using BApNA as substrate were 0.689 mM, 6.9 s^-1, and 10 s^-1 mM^-1, respectively. High inhibition of trypsin activity was observed after incubation with Cd²⁺, Al³⁺, Zn²⁺, Cu²⁺, Pb²⁺, and Hg²⁺ at 1 mM, revealing high sensitivity of the enzyme to metal ions.

Conclusions

Extraction of a thermostable trypsin from by-products of the fishery industry confirms the potential of these materials as an alternative source of these biomolecules. Furthermore, the results suggest that this trypsin-like enzyme presents interesting biotechnological properties for industrial applications.

     

A multi‐MHz single‐shot data acquisition scheme with high dynamic range: pump–probe X‐ray experiments at synchrotrons

The technical implementation of a multi‐MHz data acquisition scheme for laser–X‐ray pump–probe experiments with pulse limited temporal resolution (100 ps) is presented. Such techniques are very attractive to benefit from the high‐repetition rates of X‐ray pulses delivered from advanced synchrotron radiation sources. Exploiting a synchronized 3.9 MHz laser excitation source, experiments in 60‐bunch mode (7.8 MHz) at beamline P01 of the PETRA III storage ring are performed. Hereby molecular systems in liquid solutions are excited by the pulsed laser source and the total X‐ray fluorescence yield (TFY) from the sample is recorded using silicon avalanche photodiode detectors (APDs). The subsequent digitizer card samples the APD signal traces in 0.5 ns steps with 12‐bit resolution. These traces are then processed to deliver an integrated value for each recorded single X‐ray pulse intensity and sorted into bins according to whether the laser excited the sample or not. For each subgroup the recorded single‐shot values are averaged over ～10⁷ pulses to deliver a mean TFY value with its standard error for each data point, e.g. at a given X‐ray probe energy. The sensitivity reaches down to the shot‐noise limit, and signal‐to‐noise ratios approaching 1000 are achievable in only a few seconds collection time per data point. The dynamic range covers 100 photons pulse^?1 and is only technically limited by the utilized APD.     

Probing proteins on functionalized silicon surfaces using matrix-assisted laser desorption/ionization mass spectrometry

Flat H-terminated Si(111) substrates modified with alkyl monolayers terminated with hydrophobic and hydrophilic functional groups were prepared using known surface functionalization methods and characterized by FTIR, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The surfaces were then used for the study of non-specific binding of proteins from complex mixtures (using standard mixture of proteins with average molecular weight approximately 6-66 kDa) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Protein adsorption on these surfaces (following on-probe fractionation of the mixture) was found to be dependent on the nature of surface functional groups, and nature and pH of rinsing solutions used. The results obtained in this work demonstrate that simple silicon-based surface modifications can be effective for direct analysis of complex mixtures by MALDI-MS. Preliminary results obtained using similarly functionalized porous silicon substrates proved that such substrates are (due to their increased surface areas) better performing than flat silicon.     

Nuclear orbiting and anomalies in nuclear reactions

In this paper, we report our measurements of back-angle oxygen and carbon particle yields from ¹⁶O+⁸⁹Y, ¹²C+⁹³Nb reactions forming the same compound nucleus ¹⁰⁵Ag at the same excitation energy and spin distribution. We find anomalously large oxygen yield and entrance channel dependence at high excitation energies from ¹⁶O+⁸⁹Y reaction implying formation of a dinuclear orbiting complex. Possible connection between nuclear orbiting and fast fission is also discussed.