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.

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

Mapping the onion value chain of Dhaka, Bangladesh

Onion is the most commonly used spice in Bangladesh, and the most market sensitive agricultural- commodity, well-known for its huge price volatility. In recent years, the country has faced a steep increase in the price of onions, which made the commodity unaffordable for poor- and low middle-income people. Wageningen Research (WUR) and the Food and Agriculture Organization of the United Nations (FAO) conducted an onion value chain mapping study to identify and understand the flow of the product from producer to the consumer in Dhaka, the role of the value chain actors, their relationships, the leverage points, and the constraints

X-ray crystallographic validation of structure predictions used in computational design for protein stabilization

Protein engineering aimed at enhancing enzyme stability is increasingly supported by computational methods for calculation of mutant folding energies and for the design of disulfide bonds. To examine the accuracy of mutant structure predictions underlying these computational methods, crystal structures of thermostable limonene epoxide hydrolase variants obtained by computational library design were determined. Four different predicted effects indeed contributed to the obtained stabilization: (i) enhanced interactions between a flexible loop close to the N-terminus and the rest of the protein; (ii) improved interactions at the dimer interface; (iii) removal of unsatisfied hydrogen bonding groups; and (iv) introduction of additional positively charged groups at the surface. The structures of an eightfold and an elevenfold mutant showed that most mutations introduced the intended stabilizing interactions, and side-chain conformations were correctly predicted for 72-88% of the point mutations. However, mutations that introduced a disulfide bond in a flexible region had a larger influence on the backbone conformation than predicted. The enzyme active sites were unaltered, in agreement with the observed preservation of catalytic activities. The structures also revealed how a c-Myc tag, which was introduced for facile detection and purification, can reduce access to the active site and thereby lower the catalytic activity. Finally, sequence analysis showed that comprehensive mutant energy calculations discovered stabilizing mutations that are not proposed by the consensus or B-FIT methods. This article is protected by copyright. All rights reserved

Adaptation to changing water resource availability in Northern India with respect to Himalayan Glacier retreat and changing monsoons using participatory approaches

Changes in rainfall patterns and temperatures are likely to affect water resources in India. Also, changes in the extreme events will have direct implications on life and property. Adapting to the adverse effects of climate change becomes critical to avoid huge material and immaterial damages. This paper discusses the use of a multi-level and participatory approach to develop adaptation options to deal with climate related risks in a manner that contributes to stakeholder engagement, understanding of the risks, identification of the adaptation responses as well as its prioritization for risk reduction. It highlights the importance of involving stakeholders from multiple levels as each level corresponds with different priorities in adaptation options

Land use classification Bangladesh : combining and downscaling existing databases

Bangladesh is a south Asian country with lush greenery and many natural waterways. Bangladesh consists mostly out of fertile flat lands. Due to urbanisation, agricultural expansion and intensification as result of population and economic growth the use of the natural land system is changing rapidly. Understanding current land cover and how the land is being used is elementary for land management and land use planning. In this study we developed a spatial land use classification database of Bangladesh based on existing land cover classifications, census data of agricultural yields, cropping areas, and supplemented with local knowledge

The unique characteristics of intussusception after renal tumor surgery in children

Introduction To further optimize survival rates as well as quality of cure for pediatric kidney tumors, attention for treatment related morbidity and mortality has become increasingly important. Intussusception is a rare but important complication after tumornephrectomy in children, causing morbidity, mortality and prolonged hospitalization. In this study, we describe two recent cases in our institute and provide a comprehensive review of the literature. Methods For our narrative review, we searched for all reported cases of post tumor nephrectomy intussusception published until November 2016, using Pubmed and Embase libraries. Results A total of 52 pediatric renal tumor cases who developed intussusception after tumor nephrectomy were identified. Median age was 23 months (range 3–84). Median time of onset was postoperative day 6 (range 1–18). Of 41 patients described in detail, only 4/41 were ileocolic, the others suffered from a small bowel intussusception. Most frequent presenting symptom was bilious vomiting. Preceding treatment approach was documented in 47 cases; i.e. preoperative chemotherapy had been administered to 10/47 patients. In 29 of 30 well documented cases, successful manually reduction during re-laparotomy was described and only 1 patient needed resection. All patients survived without recurrence of intussusception. Conclusion In pediatric renal tumor patients, small bowel obstruction seems to reflect mostly post nephrectomy intussusception cases in contrast to the ileocolic idiopathic intussusceptions that are observed in healthy children. Symptoms of intussusception mimic chemotherapy related toxicity and general post-surgical symptoms, thereby initiating a significant delay in diagnosis. Awareness of intussusception after renal tumor surgery is warranted

Surgical treatment of childhood hepatoblastoma in the Netherlands (1990-2013)

Achievement of complete surgical resection plays a key role in the successful treatment of children with hepatoblastoma. The aim of this study is to assess the surgical outcomes after partial liver resections for hepatoblastoma, focusing on postoperative complications, resection margins, 30-day mortality, and long-term survival. Chart reviews were carried out on all patients treated for hepatoblastoma in the Netherlands between 1990 and 2013. A total of 103 patients were included, of whom 94 underwent surgery. Partial hepatectomy was performed in 76 patients and 18 patients received a liver transplant as a primary procedure. In 42 of 73 (58 %) patients, one or more complications were reported. In 3 patients, information regarding complications was not available. Hemorrhage necessitating blood transfusion occurred in 33 (45 %) patients and 9 (12 %) patients developed biliary complications, of whom 8 needed one or more additional surgical interventions. Overall, 5-year disease-specific survival was 82, 92 % in the group of patients who underwent partial hepatectomy, and 77 % in the group of patients who underwent liver transplantation. Partial hepatectomy after chemotherapy in children with hepatoblastoma offers good chances of survival. This type of major surgery is associated with a high rate of surgical complications (58 %), which is not detrimental to surviva