Prediction of Post-translational Modifications of Proteins from 2-DE/MS Data

The living cell is a complex entity consisting of nucleic acids, proteins, and otherbiomolecules that form an interrelated and dynamic network. The unraveling of this network is of great interest for scientists of different disciplines. With the sequencing of the genome a step was made to the understanding of the fundamental elements of the cells the genes. In humans, approximately 20,000 to 25,000 genes exist which encode about more than one million proteins. This complexity at the protein level is a result of alternative splicing and co- and post-translational modifications producing several protein species per transcript. Modifications are essential to the regulation of cellular processes and account for the activation or deactivation of enzymes and whole signaling pathways. The entirety of all proteins present in a cell at a fixed point of time and under particular biological conditions is called proteome, and the analysis of it is proteomics. One particular area of interest in proteomics is the identification of proteins and their post-translational modifications. Peptide mass fingerprinting is an established method and has proved useful to identify proteins by their amino acid sequence using mass spectrometry and protein sequence databases. This method relies on the idea of comparing experimental (measured) mass peaks to theoretical (calculated) masses, the latter being generated from a protein in a sequence database. As the mass of a modified protein differs from the mass of its unmodified counterpart, this mass distance is to be considered when detecting protein modifications with peptide mass fingerprinting. In the work described here, a novel algorithm was developed and implemented that allows for the identification of protein modifications from data derived by peptide mass fingerprinting. The algorithm transformed the process of predicting protein modifications to an extended Money Changing Problem of finding suitable combinations of modifications that explain the observed peak mass distances. Unlike common computational approaches the algorithm presented here will not be restricted in the number of modifications to be considered. Furthermore, this algorithm is efficient by calculating for a given list of modifications the combinations of modifications only once, independent of the number of queries. Although there exist hardly any frequencies of protein modifications, which turns the validation of the results very difficult, this novel approach is a promising step towards the unraveling of protein complexity

Reactions of High‐Energy, Excited I128 Ions with Gaseous Molecules

The manner in which molecular additives inhibit the reaction of (n, γ) activated I128 with CH4 was determined in an effort to observe indirectly reactions of I128 with the additives. The data suggest that (1) O2, N2, and CF4 serve only to remove excess I128 kinetic energy; (2) the ionization potential of O2 is greater than 12.16 ev, the potential energy of I+(1D2); (3) the ionization potential of C2F6 is less than 12.16 ev; (4) CH3I, CF3I, n‐C3H7I, and C6H6 inhibit the reaction principally as a result of I++additive ion‐molecule reactions and/or physical quenching.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70530/2/JCPSA6-36-2-287-1.pd

Pregnancy-associated breast cancer - Special features in diagnosis and treatment

For obvious psychological reasons it is difficult to associate pregnancy - a life-giving period of our existence with life-threatening malignancies. Symptoms pointing to malignancy are often ignored by both patients and physicians, and this, together with the greater difficulty of diagnostic imaging, probably results in the proven delay in the detection of breast cancers during pregnancy. The diagnosis and treatment of breast cancer are becoming more and more important, as the fulfillment of the desire to have children is increasingly postponed until a later age associated with a higher risk of carcinoma, and improved cure rates of solid tumors no longer exclude subsequent pregnancies. The following article summarizes the special features of the diagnosis and primary therapy of pregnancy-associated breast cancer with particular consideration of cytostatic therapy

Synchrotron-based radioscopy employing spatio-temporal micro-resolution for studying fast phenomena in liquid metal foams

High-speed synchrotron-based radioscopy is applied to study a coalescence event (which lasts ∼2 ms) in situ in a liquid metal foam

In vitro synchrotron-based radiography of micro-gap formation at the implant–abutment interface of two-piece dental implants

Micro-radiography using hard X-ray synchrotron radiation is the first potential tool to allow an evaluation of the mechanical behavior of the dental implant–abutment complex during force application, thus enabling the enhancement of the design of dental implants which has been based on theoretical analysis to date

Reflection on multilayer mirrors beam profile and coherence properties

The main advantage of Bragg reflection from a multilayer mirror as a monochromator for hard X rays, is the higher photon flux density because of the larger spectral bandpass compared with crystal lattice reflection. The main disadvantage lies in the strong modulations of the reflected beam profile. This is a major issue for micro imaging applications, where multilayer based monochromators are frequently employed to deliver high photon flux density. A subject of particular interest is the origin of the beam profile modifications, namely the irregular stripe patterns, induced by the reflection on a multilayer. For multilayer coatings in general it is known that the substrate and its surface quality significantly influence the performance of mirrors, as the coating reproduces to a certain degree the roughness and shape of the substrate. This proceedings article reviews recent experiments that indicate potential options for producing wave front preserving multilayer mirrors, as well as new details on the particular mirrors our group has extensively studied in the pas

A century of observed temperature change in the Indian Ocean

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wenegrat, J. O., Bonanno, E., Rack, U., & Gebbie, G. A century of observed temperature change in the Indian Ocean. Geophysical Research Letters, 49(13), (2022): e2022GL098217, https://doi.org/10.1029/2022GL098217.The Indian Ocean is warming rapidly, with widespread effects on regional weather and global climate. Sea-surface temperature records indicate this warming trend extends back to the beginning of the 20th century, however the lack of a similarly long instrumental record of interior ocean temperatures leaves uncertainty around the subsurface trends. Here we utilize unique temperature observations from three historical German oceanographic expeditions of the late 19th and early 20th centuries: SMS Gazelle (1874–1876), Valdivia (1898–1899), and SMS Planet (1906–1907). These observations reveal a mean 20th century ocean warming that extends over the upper 750 m, and a spatial pattern of subsurface warming and cooling consistent with a 1°–2° southward shift of the southern subtropical gyre. These interior changes occurred largely over the last half of the 20th century, providing observational evidence for the acceleration of a multidecadal trend in subsurface Indian Ocean temperature.GG is supported by U.S. NSF-OCE 82280500

Primary radiation damage in bone evolves via collagen destruction by photoelectrons and secondary emission self-absorption

X-rays are invaluable for imaging and sterilization of bones, yet the resulting ionization and primary radiation damage mechanisms are poorly understood. Here we monitor in-situ collagen backbone degradation in dry bones using second-harmonic-generation and X-ray diffraction. Collagen breaks down by cascades of photon-electron excitations, enhanced by the presence of mineral nanoparticles. We observe protein disintegration with increasing exposure, detected as residual strain relaxation in pre-stressed apatite nanocrystals. Damage rapidly grows from the onset of irradiation, suggesting that there is no minimal ‘safe’ dose that bone collagen can sustain. Ionization of calcium and phosphorous in the nanocrystals yields fluorescence and high energy electrons giving rise to structural damage that spreads beyond regions directly illuminated by the incident radiation. Our findings highlight photoelectrons as major agents of damage to bone collagen with implications to all situations where bones are irradiated by hard X-rays and in particular for small-beam mineralized collagen fiber investigations

The rupture of a single liquid aluminium alloy film

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG geförderten) Allianz- bzw. Nationallizenz frei zugänglich.This publication is with permission of the rights owner freely accessible due to an Alliance licence and a national licence (funded by the DFG, German Research Foundation) respectively.The present study is based on the idea of understanding the rupture of films in metal foams by studying free standing metallic films as a model system. Liquid dynamics, the velocity of the rupturing material as well as the behaviour of ceramic particles inside the melt were analysed optically ex situ and by synchrotron X-ray radiography in situ. It was found that the resistance of films to rupture is mainly based on the interaction between solid particles and an immobile oxide skin, the formation of which depends on the oxygen content of the surrounding atmosphere and the presence of magnesium