Comparing the binding interactions in the receptor binding domains of SARS-CoV-2 and SARS-CoV

COVID-19, since emerged in Wuhan, China, has been a major concern due to its high infection rate, leaving more than one million infected people around the world. Huge number of studies tried to reveal the structure of the SARS-CoV-2 compared to the SARS-CoV-1, in order to suppress this high infection rate. Some of these studies showed that the mutations in the SARS-CoV-1 Spike protein might be responsible for its higher affinity to the ACE2 human cell receptor. In this work, we used molecular dynamics simulations and Monte Carlo sampling to compare the binding affinities of the spike proteins of SARS-CoV and SARS-CoV-2 to the ACE2. We found that the SARS-CoV-2 binds to ACE2 stronger than SARS-CoV by 7 kcal/mol, due to enhanced electrostatic interactions. The major contributions to the electrostatic binding energies are resulting from the salt-bridges formed between R426 and ACE2-E329 in case of SARS-CoV and K417 and ACE2-D30 for SARS-CoV2. In addition, there is no significant contribution from a single mutant to the binding energies. However, these mutations induce sophisticated structural changes that enhance the binding energies. Our results also indicate that the SARS-CoV-2 is unlikely a lab engineered virus

Placemaking from Interstitial Spaces: Participatory planning and collaborative community design as strategies to revitalize a service alleyway in Montreal (Bishop/Mackay)

This project explores participatory planning and community design methodologies (i.e. pattern language design, placemaking, community planning charrettes, planning-in-situ, open planning and peer to peer urbanism) to revitalize a service alleyway in downtown Montreal. The objective of this project is to democratize planning and urban design practices and to engage ordinary citizens in the planning of their own spaces. After a series of visioning workshops, brainstorming sessions and a community planning charrette, this project incorporates inputs from stakeholders, students and ordinary citizens into a collaborative urban design project. The project proposes interventions such as a woonerf, a planning committee, a cubic/fractal scaffolding structure, art murals and wall projections (among others). With the objective of encouraging future adaptations and transformations, this project is published under a Creative Commons license. Adopt and adapt these ideas (but cite and acknowledge accordingly)

Sorption and desorption of phosphorus as influenced by corn stalk residue, pH, and ionic strength in a gleysol from Québec, Canada

The Pike River watershed has a history of phosphorus (P) pollution due to surface and subsurface leaching, and erosion of agricultural soil rich in P. It is therefore important to consider factors that may change the dynamics of P sorption and desorption behaviours and potentially increase the P concentration in the soil solution. This thesis investigates the effect of corn stalk residue presence and application rate on P sorption and desorption. This thesis also investigates the effect of varying solution pH and ionic strength on P release. Batch experiments were used to investigate P sorption followed by experiments to test the reversibility of the sorption process under different corn stalk residue applications (0.3,5.3,10.3,15.3, and 20.3%) and at different P concentrations (0, 12.9, 27.7, 42.2, 57.0, and 71.8 mg L-1). The quantity of P sorbed to soil was found to decrease significantly as residue application rates increased (p<0.0001). Phosphorus remaining in the soil after desorption decreased significantly as application of residues increased (p<0.0001). Varying the P concentration under a constant dosage of residue (5.3%) showed that the concentration of P sorbed increased with increases in P application; however sorption efficiency decreased with increasing P application. Sorption in the presence of residues was significantly lower (p<0.0001) than sorption in the absence of residues for P treatments higher than 42.2 mg L-1. Percent sorbed P remaining after desorption was similar in the presence (85-91%) and absence (86-91%) of the 5.3% corn stalk residue treatment. A second study was performed to investigate the effect of varying ionic strength and pH on P release into solution and to identify which factor had a greater effect on P release. It was found that at low ionic strengths the pH effects on P release were more pronounced whereas at high ionic strengths the P concentrations were not significantly different regardless of pH level. Since residue incorporation increased the availability of P in this soil, then due to the P pollution history of the area it is suggested that a large scale study be conducted taking into account a temporal component (including microbial interaction), depth, and a leaching component. A study of such scale would allow for a more conclusive quantification of P loss associated with the incorporation of different residue applications. It is also recommended to evaluate P release under varying pH and ionic strengths at a larger scale. Results from this study can be used to further inform soil chemistry models as well as advise for or against the use of soil amendments that induce long term changes to soil pH and solution ionic strength with respect to the overall effect on P loss from this Gleysol.Le basin versant de la Rivière aux Brochets présente un historique de pollution par le phosphore (P) liée à son lessivage en surface et par voie souterraine, ainsi que suite à l’érosion des sols agricoles. Il est donc important de prendre en considération les facteurs pouvant changer la dynamique de sorption et désorption du phosphore au sol pouvant contribuer à une augmentation du P dans la solution du sol. Les présentes recherches étudièrent les effets de l’amendement (ou non-amendement) d’un sol avec différentes quantités de résidus de tige de maïs sur la sorption et désorption du P. Également, l’effet de modifier le pH et la force ionique de la solution du sol sur la libération du phosphore fut évalué. Des essais par agitation servant à évaluer la sorption du P, suivis par des expériences visant à évaluer la réversibilité du processus de sorption, furent entrepris en absence (0%) et présence de différentes fractions massiques de résidus de tige de maïs (0.3, 5.3, 10.3, 15.3, et 20.3% à sec) combinés avec différentes concentrations de P (0, 12.9, 27.7, 42.2, 57.0, et 71.8 mg L-1 ). En un premier volet la quantité de P sorbée au sol, et en second volet le P demeurant dans le sol après désorption, diminuèrent significativement (p<0.0001) avec une augmentation du taux d’application de résidus. L’application de P à des taux croissants sous un niveau de résidus constant (5.3%) augmenta la quantité de P sorbée, mais diminua l’efficacité de la sorption. Pour les apports de P de plus de 42.2 mg L-1, la sorption du P en présence de résidus fut significativement inférieure à celle en absence de résidus. Le pourcentage de P sorbé demeurant après la désorption fut semblable en présence (5.3% résidus — 85-91%) et absence (0% résidus — 86-91%) de résidus. Une seconde étude visa à établir l’effet prédominant sur la libération de P vers la solution du sol entre les variations en pH et la force ionique de la solution du sol. À une force ionique faible, les effets du pH sur la libération du P s’avérèrent plus prononcés qu’à une force ionique élevée, lorsque le P libéré ne montra aucune différence significative entre différents pH. Comme d’incorporer les résidus dans le sol augmenta la disponibilité du P et donné l’historique régionale de pollution par le P, il est à suggérer qu’une étude à grande échelle soit entreprise prenant en compte un aspect temporel (incluant les interactions microbiennes), la profondeur, et le lessivage. Une étude à une telle échelle permettrait une quantification plus concluante des pertes en P advenant de l’incorporation des divers résidus. Il serait à recommander d’évaluer si le P libéré sous divers pH et forces ioniques demeurent valables à une plus grande échelle. Les résultats de la présente étude peuvent servir à éclairer davantage les modèles de chimie des sols, et aider à se prononcer pour ou contre l’utilisation d’amendements au sol causant des changements à long terme du pH ou de la force ionique du sol, quant à leur effet global sur les pertes en P d’un gleysol

Comparing the Binding Interactions in the Receptor Binding Domains of SARS-CoV-2 and SARS-CoV

SARS-CoV-2, since emerging in Wuhan, China, has been a major concern because of its high infection rate and has left more than six million infected people around the world. Many studies endeavored to reveal the structure of the SARS-CoV-2 compared to the SARS-CoV, in order to find solutions to suppress this high infection rate. Some of these studies showed that the mutations in the SARS-CoV spike (S) protein might be responsible for its higher affinity to the ACE2 human cell receptor. In this work, we used molecular dynamics simulations and Monte Carlo sampling to compare the binding affinities of the S proteins of SARS-CoV and SARS-CoV-2 to the ACE2. Our results show that the protein surface of the ACE2 at the receptor binding domain (RBD) exhibits negative electrostatic potential, while a positive potential is observed for the S proteins of SARS-CoV/SARS-CoV-2. In addition, the binding energies at the interface are slightly higher for SARS-CoV-2 because of enhanced electrostatic interactions. The major contributions to the electrostatic binding energies result from the salt bridges forming between R426 and ACE-2-E329 in the case of SARS-CoV and K417 and ACE2-D30 in the SARS-CoV-2. In addition, our results indicate that the enhancement in the binding energy is not due to a single mutant but rather because of the sophisticated structural changes induced by all these mutations together. This finding suggests that it is implausible for the SARS-CoV-2 to be a lab-engineered virus

Comparing the binding interactions in the receptor binding domains of SARS-CoV-2 and SARS-CoV

SARS-CoV-2, since emerging in Wuhan, China, has been a major concern because of its high infection rate and has left more than six million infected people around the world. Many studies endeavored to reveal the structure of the SARS-CoV-2 compared to the SARS-CoV, in order to find solutions to suppress this high infection rate. Some of these studies showed that the mutations in the SARS-CoV spike (S) protein might be responsible for its higher affinity to the ACE2 human cell receptor. In this work, we used molecular dynamics simulations and Monte Carlo sampling to compare the binding affinities of the S proteins of SARS-CoV and SARS-CoV-2 to the ACE2. Our results show that the protein surface of the ACE2 at the receptor binding domain (RBD) exhibits negative electrostatic potential, while a positive potential is observed for the S proteins of SARS-CoV/SARS-CoV-2. In addition, the binding energies at the interface are slightly higher for SARS-CoV-2 because of enhanced electrostatic interactions. The major contributions to the electrostatic binding energies result from the salt bridges forming between R426 and ACE-2-E329 in the case of SARS-CoV and K417 and ACE2-D30 in the SARS-CoV-2. In addition, our results indicate that the enhancement in the binding energy is not due to a single mutant but rather because of the sophisticated structural changes induced by all these mutations together. This finding suggests that it is implausible for the SARS-CoV-2 to be a lab-engineered virus

A multivariate morphometrics study of the Solidago altissima complex and S. canadensis (Aateraceae: Astereae)

The Solidago altissima complex stretches across much of North America on the prairies and in the eastern deciduous forest. A multivariate morphometric analysis including 28 vegetative and floral traits scored on 162 specimens was performed to assess the classification of the complex in eastern North America proposed by Semple (2014). Discriminant analysis indicated support for recognizing the following taxa: Solidago altiplanities, Solidago altissima vars. altissima, gilvocanescens, and pluricephala, S. canadensis vars. canadensis and hargeri, and S. juliae. A lectotype is designated for Solidago pruinosa Greene, which is a synonym of S. altissima var. gilvocanescens.Fil: Semple, John C.. University of Waterloo; CanadáFil: Rahman, Hammad. University of Waterloo; CanadáFil: Sbovski, Sofia. University of Waterloo; CanadáFil: Sorour, Mariam K.. University of Waterloo; CanadáFil: Kornobis, Katherine. University of Waterloo; CanadáFil: Lopez Laphitz, Rita Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentina. University of Waterloo; Canadá. Universidad Nacional del Comahue; ArgentinaFil: Tong, Lan. University of Waterloo; Canad