Introduction to Protein Structure Prediction

This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence. We give an overview of the different classes of modelling techniques, notably template-based and template free. We also discuss the way in which structural predictions are validated within the global com- munity, and elaborate on the extent to which predicted structures may be trusted and used in practice. Finally we discuss whether the concept of a sin- gle fold pertaining to a protein structure is sustainable given recent insights. In short, we conclude that the general protein three-dimensional structure prediction problem remains unsolved, especially if we desire quantitative predictions. However, if a homologous structural template is available in the PDB model or reasonable to high accuracy may be generated

The Ross Procedure : Outdated or Up-to-date?

Background: The Ross procedure uses a patient’s own pulmonary valve to replace the diseased aortic valve. It is an alternative to conventional valve replacement especially in the younger patient population. This patient group, and patients with contraindications against conventional valve re- p lacements, may benefit from a Ross procedure if it can be performed safely and with adequate durability. The aim of this study was to assess the reproducibility, survival, and durability of pulmo- nary autograft replacements in our institution. Methods: Bet ween December 1995 and December 2020, 202 patients (male 73%; mean age 35.4±11.4 years) underwent the Ross procedure at our institution. Eight patients were lost to follow up and were excluded from the long term analysis. One patient was intraoperatively c onverted to a Bentall procedure. Five patients underwent a cylinder Ross procedure and 196 patients a full root replacement. Aortic v alve morphology was unicuspid in 87 ( bicuspid in 76 ( and tricus- pid in 25 ( patients. Fourteen patients had undergone valve replacement previously, and the morphology could not be determined. Results: Overall, 202 patients were analyzed, 10 patients died, and 8 patients were lost to follow up. The pulmonary valve was replaced with a ho mograft in 156 patients, with a bovine jugular vein graft in 35 patients, and in 10 patients with a stentless bio logical valve prosthesis Mean myocardial ischemia time was 91±20minutes; mean perfusion time was 125±33 minutes. Fifty eight patients required a concomitant procedure during their Ross operation, most commonly as- cending aortic replacement (n= There was one perioperative death, no myocardial infarction, and one neurological complication. A permanent pacemaker was implanted in four cases ( There was one late deat h from a non cardiac cause. Twenty three patients required reinterventions after the Ross procedure (pulmonary autograft n=16, pulmonary conduit n= 7). A valve sparing pro- cedure was performed in the majority of cases. At 10 years, survival was 93%, simila r to that of the age and gender matched German population. Freedom from autograft reintervention at 10 years was 89% and freedom from RV PA reintervention was 93%. Median and mean follow up were 5.7 [range 0.1 24.4] years and 7.8 ±7 years. Clinical and echocardiography follow up were 95% and 92% complete (1467 patient years). Conclusion The Ross procedure represents a safe and valid option in young and middle aged patients. It is associated with low perioperative morbidity and mortality. The probabilit y of reinterven- tions is low and long term survival is excellent, similar to that of the age and gender matched gen- eral German population

Heat capacity and high pressure exploration of YbB2

The compound YbB2 has been reported to order anti-ferromagnetically at temperatures around 5.6 K. This transition was verified from heat capacity data taken in different magnetic fields by our Quantum Design PPMS system. X-ray diffraction measurements have been performed using this sample under different pressures at the APS facility in Argonne National Laboratory. A sudden change in resistivity measurements of the sample indicated a possible structural phase transition around 3 GPa. The data indicates the YbB2 compound is not responsible for the anomaly

Preface to Introduction to Structural Bioinformatics

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which is where the previous topics meet to explore three dimensional protein structures through computational analysis. We provide an overview of existing computational techniques, to validate, simulate, predict and analyse protein structures. More importantly, it will aim to provide practical knowledge about how and when to use such techniques. We will consider proteins from three major vantage points: Protein structure quantification, Protein structure prediction, and Protein simulation & dynamics

Achieving a high‐density oleaginous yeast culture: Comparison of four processing strategies using <i>Metschnikowia pulcherrima</i>

Microbial lipids have the potential to displace terrestrial oils for fuel, value chemical, and food production, curbing the growth in tropical oil plantations and helping to reduce deforestation. However, commercialization remains elusive partly due to the lack of suitably robust organisms and their low lipid productivity. Extremely high cell densities in oleaginous cultures are needed to increase reaction rates, reduce reactor volume, and facilitate downstream processing. In this investigation, the oleaginous yeast Metschnikowia pulcherrima, a known antimicrobial producer, was cultured using four different processing strategies to achieve high cell densities and gain suitable lipid productivity. In batch mode, the yeast demonstrated lipid contents more than 40% (w/w) under high osmotic pressure. In fed‐batch mode, however, high‐lipid titers were prevented through inhibition above 70.0 g L−1 yeast biomass. Highly promising were a semi‐continuous and continuous mode with cell recycle where cell densities of up to 122.6 g L−1 and maximum lipid production rates of 0.37 g L−1 h−1 (daily average), a nearly two‐fold increase from the batch, were achieved. The findings demonstrate the importance of considering multiple fermentation modes to achieve high‐density oleaginous yeast cultures generally and indicate the limitations of processing these organisms under the extreme conditions necessary for economic lipid production.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 665992

Effects of a combined supercritical extraction/thermal cycle on binder removal cycle time, yield, residual carbon, and defect formation in multilayer ceramic capacitors

The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Title from PDF of title page (University of Missouri--Columbia, viewed on March 31, 2011).Thesis advisor: Dr. Stephen J. Lombardo.M. S. University of Missouri--Columbia 2010.In this work, a combined cycle consisting of a supercritical extraction cycle (SCE) followed by a thermal cycle (TC), was used to remove binder from green multilayer ceramic capacitors. The dielectric was barium titanate and the binder consisted of poly(vinyl butyral) plasticized with phthalates. Supercritical extraction of approximately one-third of the binder leads to an increase in the porosity and gas permeability of samples and to a decrease in the adhesion strength between layers. The partial removal of the binder also resulted in a decrease in cycle time and defects following the combined SCE/TC. Samples subjected to the combined SCE/TC also had 25-30% less residual carbon as compared to samples subjected to a thermal cycle alone. This work also presents the binder removal efficiencies from tape cast films fabricated with titanate-based dielectrics. The organic systems evaluated were plasticized acrylic, poly(propylene carbonate), and poly(vinyl butyral) binders. The effect of temperature on binder removal and defect formation are assessed.Includes bibliographical reference