How to change the oligomeric state of a circular protein assembly: switch from 11-subunit to 12-subunit TRAP suggests a general mechanism

Many critical cellular functions are performed by multisubunit circular protein oligomers whose internal geometry has evolved to meet functional requirements. The subunit number is arguably the most critical parameter of a circular protein assembly, affecting the internal and external diameters of the assembly and often impacting on the protein's function. Although accurate structural information has been obtained for several circular proteins, a lack of accurate information on alternative oligomeric states has prevented engineering such transitions. In this study we used the bacterial transcription regulator TRAP as a model system to investigate the features that define the oligomeric state of a circular protein and to question how the subunit number could be manipulated.We find that while Bacillus subtilis and Bacillus stearothermophilus TRAP form 11-subunit oligomers, the Bacillus halodurans TRAP exclusively forms 12-subunit assemblies. Significantly, the two states of TRAP are related by a simple rigid body rotation of individual subunits around inter-subunit axes. We tested if such a rotation could be induced by insertion or deletion mutations at the subunit interface. Using wild type 11-subunit TRAP, we demonstrate that removal of five C-terminal residues at the outer side of the inter-subunit axis or extension of an amino acid side chain at the opposite, inner side, increased the subunit number from 11 to 12. Our findings are supported by crystal structures of TRAP oligomers and by native mass spectrometry data.The subunit number of the TRAP oligomer can be manipulated by introducing deletion or addition mutations at the subunit interface. An analysis of available and emerging structural data on alternative oligomeric states indicates that the same principles may also apply to the subunit number of other circular assemblies suggesting that the deletion/addition approach could be used generally to engineer transitions between different oligomeric states

First Crystal Structure for a Gold Carbene-Protein Adduct

The X-ray structure of the adduct formed in the reaction between the gold N-heterocyclic carbene compound Au(NHC)Cl (with NHC = 1-butyl-3-methyl-imidazole-2-ylidene) and the model protein thaumatin is reported here. The structure reveals binding of Au(NHC)(+) fragments to distinct protein sites. Notably, binding of the gold compound occurs at lysine side chains and at the N-terminal tail; the metal binds the protein after releasing Cl- ligand, but retaining NHC fragment

Differences in run-up, take-off, and flight characteristics: successful vs. unsuccessful high jump attempts at the IAAF world championships

Studies previously conducted on high jump have yielded important information regarding successful performance. However, analyses in competitive scenarios have often disregarded athletes’ unsuccessful attempts. This study aimed to investigate the biomechanical differences between successful and unsuccessful jumps during competition. High-speed video footage (200 Hz) was obtained from 11 athletes during the 2018 Men's World Athletics Indoor Championship Final. From each athlete, one successful (SU) and one unsuccessful (UN) jump at the same bar height were included in the analysis, leaving seven athletes in total. Following whole-body 3D manual digitization, several temporal and kinematic variables were calculated for the run-up, take-off, and flight phases of each jump. During SU jumps, athletes raised the center of mass to a greater extent (p < 0.01) from take-off. Touchdown in SU jumps was characterized by a faster anteroposterior velocity (p < 0.05), lower backward lean (p < 0.05), and changes in joint angles for the stance and trail limbs (p < 0.05). Athletes also shortened the final contact time during SU jumps (p < 0.01) after producing a longer flight time in the final step of the run-up (p < 0.05). Elite-level high jumpers undertake a series of adjustments to successfully clear the bar after UN jumps. These adjustments reinforce the importance of the run-up in setting the foundations for take-off and bar clearance. Furthermore, the findings demonstrate the need for coaches to be mindful of the adjustments required in stance and trail limbs when looking to optimize feedback to athletes during training and competition

STRUCTURE AND DYNAMICS OF MICROBIAL COMMUNITIES IN ANAEROBIC DIGESTION PROCESSES

Nowadays world energy needs rely mostly on fossil fuels (oil, coal and natural gas) which accounts for more than 80% of global energy production. Fossil fuels reserves are estimated to deplete in the next future. In this context, it arises the need to establish new renewable energetic sources. A well-established technology for bioenergy production in the form of biogas is anaerobic digestion (AD). This process involves a complex consortium of different functional groups of microbes which, degrading the organic matter, produce biogas composed mainly of methane and carbon dioxide. In the latest 10 years there has been renewed interest for energy production from biomass through AD because of its versatility and potentiality. So far, the control and performance of AD process has typically been performed working on operational parameters (such as T, pH, COD, loading rate, etc.). However, recent studies concerning the microbial consortia involved in this complex process have been developing with the final aim to get an exhaustive knowledge of microbiology of the process and how it correlates to the operation of the reactor in order to improve the digester performance making preventive action possible. the general aim of this PhD thesis was to investigate the microbiology of both batch and continuous, single and two-stage anaerobic systems. The goals were (i) to elucidate the structure of the microbial communities, (ii) to investigate the dynamics, interactions and responses of the key metabolic groups responsible for the degradation of substrates and (iii) to give valuable information on the correlation between structure and function inside the microbial consortiums

Stress Hyperglycemia Does Not Affect Clinical Outcome of Diabetic Patients Receiving Intravenous Thrombolysis for Acute Ischemic Stroke

Although stress hyperglycemia represents a main risk factor for poor outcome among patients with acute ischemic stroke (AIS) undergoing recanalization therapy, we have limited information regarding a possible influence of the premorbid diabetic status on this association. We recruited consecutive patients admitted to the Udine University Hospital with AIS who were treated with intravenous thrombolysis (IVT) from January 2015 to September 2020. On the basis of the premorbid diabetic status, our sample was composed of 130 patients with and 371 patients without diabetes. The glucose-to-glycated hemoglobin ratio (GAR) was used to measure stress hyperglycemia. Patients were stratified into 3 groups by tertiles of GAR (Q1–Q3). The higher GAR index was, the more severe stress hyperglycemia was considered. Among diabetic patients we did not observe any significant association between severe stress hyperglycemia and outcome measures (three-month poor outcome: Q1, 53.7%; Q2, 53.5%; Q3, 58.7%; p = 0.854; three-month mortality: Q1, 14.6%; Q2, 9.3%; Q3, 23.9%; p = 0.165; symptomatic intracranial hemorrhage: Q1, 7.3%; Q2, 14%; Q3, 19.6%; p = 0.256). Differently, non-diabetic subjects with more severe stress hyperglycemia showed a higher prevalence of three-month poor outcome (Q1, 32.2%; Q2, 27.7%; Q3, 60.3%; p = 0.001), three-month mortality (Q1, 9.1%; Q2, 8.4%; Q3, 18.3%; p = 0.026), and symptomatic intracranial hemorrhage (Q1, 0.8%; Q2, 0.8%; Q3, 9.9; p = 0.001). After controlling for several confounders, severe stress hyperglycemia remained a significant predictor of three-month poor outcome (OR 2.1, 95% CI 1.03–4.28, p = 0.041), three-month mortality (OR 2.39, 95% CI 1.09–5.26, p = 0.029) and symptomatic intracranial hemorrhage (OR 12.62, 95% CI 1.5–106, p = 0.02) among non-diabetics. In conclusion, premorbid diabetic status seems to influence outcome in AIS patients receiving IVT. Indeed, odds of functional dependency, mortality and hemorrhagic complications were significantly increased in patients with more severe stress hyperglycemia only when they were not affected by diabetes

Architecture of collaborating frameworks: simulation, visualisation, user interface and analysis

The Anaphe project is an ongoing effort to provide an Object Oriented software environment for data analysis in HENP experiments. A range of commercial and public domain libraries is used to cover basic functionalities; on top of these libraries a set of HENP-specific C++ class libraries for histogram management, fitting, plotting and ntuple-like data analysis has been developed. In order to comply with the user requirements for a command-line driven tool, we have chosen to use a scripting language (Python) as the front-end for a data analysis tool. The loose coupling provided by the consequent use of (AIDA compliant) Abstract Interfaces for each component in combination with the use of shared libraries for their implementation provides an easy integration of existing libraries into modern scripting languages thus allowing for rapid application development. This integration is simplified even further using a specialised toolkit (SWIG) to create "shadow classes" for the Python language, which map the definitions of the Abstract Interfaces almost at a one-to-one level. This paper will give an overview of the architecture and design choices and will present the current status and future developments of the project