Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes

Hen egg-white lysozyme has long been the paradigm for enzymatic glycosyl hydrolysis with retention of configuration, with a protonated carboxylic acid and a deprotonated carboxylate participating in general acid-base catalysis. In marked contrast, the retaining chitin degrading enzymes from glycosyl hydrolase families 18 and 20 all have a single glutamic acid as the catalytic acid but lack a nucleophile on the enzyme. Both families have a catalytic (βα)8-barrel domain in common. X-ray structures of three different chitinolytic enzymes complexed with substrates or inhibitors identify a retaining mechanism involving a protein acid and the carbonyl oxygen atom of the substrate’s C2 N-acetyl group as the nucleophile. These studies unambiguously demonstrate the distortion of the sugar ring toward a sofa conformation, long postulated as being close to that of the transition state in glycosyl hydrolysis.

The formation of peptide-like molecules on interstellar dust grains

Molecules with an amide functional group resemble peptide bonds, the molecular bridges that connect amino acids, and may thus be relevant in processes that lead to the formation of life. In this study, the solid state formation of some of the smallest amides is investigated in the laboratory. To this end, CH$_{4}$:HNCO ice mixtures at 20 K are irradiated with far-UV photons, where the radiation is used as a tool to produce the radicals required for the formation of the amides. Products are identified and investigated with infrared spectroscopy and temperature programmed desorption mass spectrometry. The laboratory data show that NH$_{2}$CHO, CH$_{3}$NCO, NH$_{2}$C(O)NH$_{2}$, CH$_{3}$C(O)NH$_{2}$ and CH$_{3}$NH$_{2}$ can simultaneously be formed. The NH$_{2}$CO radical is found to be key in the formation of larger amides. In parallel, ALMA observations towards the low-mass protostar IRAS 16293-2422B are analysed in search of CH$_{3}$NHCHO (N-methylformamide) and CH$_{3}$C(O)NH$_{2}$ (acetamide). CH$_{3}$C(O)NH$_{2}$ is tentatively detected towards IRAS 16293-2422B at an abundance comparable with those found towards high-mass sources. The combined laboratory and observational data indicates that NH$_{2}$CHO and CH$_{3}$C(O)NH$_{2}$ are chemically linked and form in the ice mantles of interstellar dust grains. A solid-state reaction network for the formation of these amides is proposed.Comment: Accepted for publication in MNRA

Brachytherapy for rhabdomyosarcoma: Survey of international clinical practice and development of guidelines.

BACKGROUND AND PURPOSE: The purpose of this study was to address the lack of published data on the use of brachytherapy in pediatric rhabdomyosarcoma by describing current practice as starting point to develop consensus guidelines. MATERIALS AND METHODS: An international expert panel on the treatment of pediatric rhabdomyosarcoma comprising 24 (pediatric) radiation oncologists, brachytherapists and pediatric surgeons met for a Brachytherapy Workshop hosted by the European paediatric Soft tissue Sarcoma Study Group (EpSSG). The panel's clinical experience, the results of a previously distributed questionnaire, and a review of the literature were presented. RESULTS: The survey indicated the most common use of brachytherapy to be in combination with tumor resection, followed by brachytherapy as sole local therapy modality. HDR was increasingly deployed in pediatric practice, especially for genitourinary sites. Brachytherapy planning was mostly by 3D imaging based on CT. Recommendations for patient selection, treatment requirements, implant technique, delineation, dose prescription, dose reporting and clinical management were defined. CONCLUSIONS: Consensus guidelines for the use of brachytherapy in pediatric rhabdomyosarcoma have been developed through multicenter collaboration establishing the basis for future work. These have been adopted for the open EpSSG overarching study for children and adults with Frontline and Relapsed RhabdoMyoSarcoma (FaR-RMS)

Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes

Rhabdomyosarcomas (RMS) are mesenchyme-derived tumors and the most common childhood soft tissue sarcomas. Treatment is intense, with a nevertheless poor prognosis for high-risk patients. Discovery of new therapies would benefit from additional preclinical models. Here, we describe the generation of a collection of 19 pediatric RMS tumor organoid (tumoroid) models (success rate of 41%) comprising all major subtypes. For aggressive tumors, tumoroid models can often be established within 4-8 weeks, indicating the feasibility of personalized drug screening. Molecular, genetic, and histological characterization show that the models closely resemble the original tumors, with genetic stability over extended culture periods of up to 6 months. Importantly, drug screening reflects established sensitivities and the models can be modified by CRISPR/Cas9 with TP53 knockout in an embryonal RMS model resulting in replicative stress drug sensitivity. Tumors of mesenchymal origin can therefore be used to generate organoid models, relevant for a variety of preclinical and clinical research questions

Methanol ice co-desorption as a mechanism to explain cold methanol in the gas-phase

Context. Methanol is formed via surface reactions on icy dust grains. Methanol is also detected in the gas-phase at temperatures below its thermal desorption temperature and at levels higher than can be explained by pure gas-phase chemistry. The process that controls the transition from solid state to gas-phase methanol in cold environments is not understood. Aims. The goal of this work is to investigate whether thermal CO desorption provides an indirect pathway for methanol to co-desorb at low temperatures. Methods. Mixed CH₃OH:CO/CH₄ ices were heated under ultra-high vacuum conditions and ice contents are traced using RAIRS (reflection absorption IR spectroscopy), while desorbing species were detected mass spectrometrically. An updated gas-grain chemical network was used to test the impact of the results of these experiments. The physical model used is applicable for TW Hya, a protoplanetary disk in which cold gas-phase methanol has recently been detected. Results. Methanol release together with thermal CO desorption is found to be an ineffective process in the experiments, resulting in an upper limit of ≤ 7.3 × 10−7 CH₃OH molecules per CO molecule over all ice mixtures considered. Chemical modelling based on the upper limits shows that co-desorption rates as low as 10−6 CH₃OH molecules per CO molecule are high enough to release substantial amounts of methanol to the gas-phase at and around the location of the CO thermal desorption front in a protoplanetary disk. The impact of thermal co-desorption of CH₃OH with CO as a grain-gas bridge mechanism is compared with that of UV induced photodesorption and chemisorption

Fungal chitinases: diversity, mechanistic properties and biotechnological potential

Chitin derivatives, chitosan and substituted chito-oligosaccharides have a wide spectrum of applications ranging from medicine to cosmetics and dietary supplements. With advancing knowledge about the substrate-binding properties of chitinases, enzyme-based production of these biotechnologically relevant sugars from biological resources is becoming increasingly interesting. Fungi have high numbers of glycoside hydrolase family 18 chitinases with different substrate-binding site architectures. As presented in this review, the large diversity of fungal chitinases is an interesting starting point for protein engineering. In this review, recent data about the architecture of the substrate-binding clefts of fungal chitinases, in connection with their hydrolytic and transglycolytic abilities, and the development of chitinase inhibitors are summarized. Furthermore, the biological functions of chitinases, chitin and chitosan utilization by fungi, and the effects of these aspects on biotechnological applications, including protein overexpression and autolysis during industrial processes, are discussed in this review