Computational optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2

The coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the coronavirus disease 2019 pandemic, and the closely related SARS-CoV coronavirus enter cells by binding at the human angiotensin converting enzyme 2 (hACE2). The stronger hACE2 affinity of SARS-CoV-2 has been connected with its higher infectivity. In this work, we study hACE2 complexes with the receptor-binding domains (RBDs) of the human SARS-CoV-2 and human SARS-CoV viruses, using all-atom molecular dynamics simulations and computational protein design with a physics-based energy function. The molecular dynamics simulations identify charge-modifying substitutions between the CoV-2 and CoV RBDs, which either increase or decrease the hACE2 affinity of the SARS-CoV-2 RBD. The combined effect of these mutations is small, and the relative affinity is mainly determined by substitutions at residues in contact with hACE2. Many of these findings are in line and interpret recent experiments. Our computational protein design calculations redesign positions 455, 493, 494, and 501 of the SARS-CoV-2 receptor binding motif, which contact hACE2 in the complex and are important for ACE2 recognition. Sampling is enhanced by an adaptive importance sampling Monte Carlo method. Sequences with increased affinity replace CoV-2 glutamine by a negative residue at position 493; serine by a nonpolar or aromatic residue or an asparagine at position 494; and asparagine by valine or threonine at position 501. Substitutions at positions 455 and 501 have a smaller effect on affinity. Substitutions suggested by our design are seen in viral sequences encountered in other species, including bat and pangolin. Our results might be used to identify potential virus strains with higher human infectivity and assist in the design of peptide-based or peptidomimetic compounds with the potential to inhibit SARS-CoV-2 binding at hACE2.     

The effect of the elongation of the proximal aorta on the estimation of the aortic wall distensibility

The compliance of the proximal aortic wall is a major determinant of cardiac afterload. Aortic compliance is often estimated based on cross-sectional area changes over the pulse pressure, under the assumption of a negligible longitudinal stretch during the pulse. However, the proximal aorta is subjected to significant axial stretch during cardiac contraction. In the present study, we sought to evaluate the importance of axial stretch on compliance estimation by undertaking both an in silico and an in vivo approach. In the computational analysis, we developed a 3-D finite element model of the proximal aorta and investigated the discrepancy between the actual wall compliance to the value estimated after neglecting the longitudinal stretch of the aorta. A parameter sensitivity analysis was further conducted to show how increased material stiffness and increased aortic root motion might amplify the estimation errors (discrepancies between actual and estimated distensibility ranging from − 20 to − 62%). Axial and circumferential aortic deformation during ventricular contraction was also evaluated in vivo based on MR images of the aorta of 3 healthy young volunteers. The in vivo results were in good qualitative agreement with the computational analysis (underestimation errors ranging from − 26 to − 44%, with increased errors reflecting higher aortic root displacement). Both the in silico and in vivo findings suggest that neglecting the longitudinal strain during contraction might lead to severe underestimation of local aortic compliance, particularly in the case of women who tend to have higher aortic root motion or in subjects with stiff aortas.

     

Response of greenhouse tomato to salt stress and K+ supplement

Abstract

The effect of NaCl salinity and potassium supplement on growth, tissue ion concentration, photosynthesis, yield and fruit quality characteristics of tomato plants was studied. Tomato plants, hyb. Belladonna, were grown in 8.5 l pots, filled with 1:3 sand:perlite mixture and irrigated with a half-strength Hoagland solution through a closed hydroponic system. Six irrigation treatments were applied, including combinations of 3 salinity (0, 35 and 70 mM NaCl) and two potassium levels (K1: 200 ppm and K2: 400 ppm) in the nutrient solution. Salinity reduced photosynthesis resulting in reduced plant height and dry weight. Yield was reduced by 25% and 69% at 35 and 70 mM, respectively, as compared to control plants (0 mM NaCl). Both total soluble solids and titratable acidity of the fruit increased with increasing salinity and K levels. The application of high potassium level (K2) reduced the concentration of Na and increased that of K in the leaves and roots of the plants, as compared to K1 treatment. Toxicity symptoms were mostly observed in the leaves of 70K1 plants, while no visual symptoms of toxicity were observed in 70K2 treatment. Despite the positive effects of potassium supplement in reducing Na concentration and the absence of toxicity symptoms in the leaves, plant growth was not improved, while leaf photosynthesis was reduced. Furthermore, no positive effects in the percentage of marketable fruit, mean fruit weight and yield were observed in the plants receiving extra K.     

Alcohol Drinking Cessation and the Risk of Laryngeal and Pharyngeal Cancers: A Systematic Review and Meta-Analysis

Objective

To evaluate the effect of alcohol cessation on the risk of developing laryngeal and pharyngeal cancers, combining available evidence in the scientific literature in a meta-analysis.

Methods

A systematic literature review was conducted, and a meta-analysis was applied on the retrieved studies. The generalised least squares method was used to estimate the trend from dose-response data to assess changes in the risks of laryngeal and pharyngeal cancers after drinking cessation.

Results

A total of 9 case-control studies were included in the meta-analysis (4 and 8 estimates for laryngeal and pharyngeal cancers, respectively). On average, alcohol drinking cessation was associated with a 2% yearly reduction in the risk of developing laryngeal and pharyngeal cancers. There was a considerable heterogeneity between the studies of pharyngeal cancer, but this was mostly due to two studies. The increased risk of laryngeal and pharyngeal cancers caused by alcohol was reversible; the time periods until the risks became equal to those of never drinkers were 36 (95% CI 11–106) and 39 (95% CI 13–103) years, respectively. Moreover, 5 years of drinking cessation was associated with a reduction of around 15% in the alcohol-related elevated risk of laryngeal and pharyngeal cancers.

Conclusion

Although a long time period is required to completely eliminate the alcohol-related elevated risk of laryngeal and pharyngeal cancers, a substantial risk reduction can be seen in the short term (5–10 years), and drinking cessation should therefore be encouraged to reduce the incidence of these cancers.     

Economic Recession and Emergence of an HIV-1 Outbreak among Drug Injectors in Athens Metropolitan Area: A Longitudinal Study

Background

During 2011, a dramatic increase (1600%) of reported HIV-1 infections among injecting drug users (IDUs) was noted in Athens, Greece. We herein assess the potential causal pathways associated with this outbreak.

Methods

Our study employed high resolution HIV-1 phylogenetic and phylogeographic analyses. We examined also longitudinal data of ecological variables such as the annual growth of gross domestic product (GDP) of Greece in association with HIV-1 and HCV sentinel prevalence in IDUs, unemployment and homelessness rates and HIV transmission networks in Athens IDUs before and during economic recession (2008–2012).

Results

IDU isolates sampled in 2011 and 2012 suggested transmission networks in 94.6% and 92.7% of the cases in striking contrast with the sporadic networking (5%) during 1998–2009. The geographic origin of most HIV-1 isolates was consistent with the recently documented migratory waves in Greece. The decline in GDP was inversely correlated with annual prevalence rates of HIV and HCV and with unemployment and homelessness rates in IDUs (all p<0.001). The slope of anti-HCV prevalence in the sentinel populations of IDUs and in “new” drug injectors was found 120 and 1.9-fold (p = 0.007, p = 0.08 respectively) higher in 2008–2012 (economic recession) compared with 2002–2006. The median (25th, 75th) size of transmission networks were 34 (12, 58) and 2 (2, 2) (p = 0.057) in 2008–2012 and 1998–2007, respectively. The coverage of harm reduction services was low throughout the study period.

Conclusions

Scaling-up harm reduction services and addressing social and structural factors related to the current economic crisis should be urgently considered in environments where HIV-1 outbreaks may occur.     

Quantitative Phosphoproteome Analysis Unveils LAT as a Modulator of CD3ζ and ZAP-70 Tyrosine Phosphorylation

Signaling through the T cell receptor (TCR) initiates adaptive immunity and its perturbation may results in autoimmunity. The plasma membrane scaffolding protein LAT acts as a central organizer of the TCR signaling machinery to activate many functional pathways. LAT-deficient mice develop an autoimmune syndrome but the mechanism of this pathology is unknown. In this work we have compared global dynamics of TCR signaling by MS-based quantitative phosphoproteomics in LAT-sufficient and LAT-defective Jurkat T cells. Surprisingly, we found that many TCR-induced phosphorylation events persist in the absence of LAT, despite ERK and PLCγ1 phosphorylation being repressed. Most importantly, the absence of LAT resulted in augmented and persistent tyrosine phosphorylation of CD3ζ and ZAP70. This indicates that LAT signaling hub is also implicated in negative feedback signals to modulate upstream phosphorylation events. Phosphorylation kinetics data resulting from this investigation is documented in a database (phosphoTCR) accessible online. The MS data have been deposited to the ProteomeXchange with identifier PXD000341.     

Meander: visually exploring the structural variome using space-filling curves

The introduction of next generation sequencing methods in genome studies has made it possible to shift research from a gene-centric approach to a genome wide view. Although methods and tools to detect single nucleotide polymorphisms are becoming more mature, methods to identify and visualize structural variation (SV) are still in their infancy. Most genome browsers can only compare a given sequence to a reference genome; therefore, direct comparison of multiple individuals still remains a challenge. Therefore, the implementation of efficient approaches to explore and visualize SVs and directly compare two or more individuals is desirable. In this article, we present a visualization approach that uses space-filling Hilbert curves to explore SVs based on both read-depth and pair-end information. An interactive open-source Java application, called Meander, implements the proposed methodology, and its functionality is demonstrated using two cases. With Meander, users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference. The application was developed using Java version 1.6 and Processing.org and can be run on any platform. It can be found at http://homes.esat.kuleuven.be/~bioiuser/meander.     

Early Miocene herpetofaunas from the Greek localities of Aliveri and Karydia – bridging a gap in the knowledge of amphibians and reptiles from the early Neogene of southeastern Europe

Abstract

We here describe new remains of amphibians and reptiles from the early Miocene (MN 4) of two different Greek localities, Aliveri and Karydia. The newly described material consists of urodelans, alytids, indeterminate anurans, turtles, crocodylians, lacertids, indeterminate scincomorphs, anguids, colubrids, viperids, and indeterminate snakes. The presence of the frog Latonia cf. gigantea in Greece is documented for the first time. Additionally, the presence of viperids in Aliveri implies a much wider distribution for these snakes during the early Miocene of Europe. Of special interest is the presence of a peculiar colubrid that seems to possess a hitherto unknown vertebral structure, which is herein defined as the ‘paracentral ridge’. Although incomplete, the new material has important taxonomic and biogeographic implications, as it enhances our understanding of southeastern European herpetofaunas from the early Miocene, a time period that was characterised by major dispersal and extinction events and climatic change that affected the whole continent.     

The fossil turtles of Greece: An overview of taxonomy and distribution

Turtle remains are common in the Miocene-Holocene deposits of Greece, and are a key focus of the growing research interest in Neogene herpetofaunas from the Aegean region. Some of the most important finds include one of Europe's stratigraphically youngest pleurodiran taxa, Nostimochelone lampra, from the Early Miocene of Macedonia, together with arguably the richest record of fossil tortoises from the Eastern Mediterranean. This incorporates the presently oldest definitive representatives of the quintessential genus Testudo sensu stricto from the Late Miocene of Attica and Macedonia, and numerous specimens of the colossal (carapace ∼2 m-length) testudinid Cheirogaster from Late Miocene-Late Pliocene sediments in southern and northern Greece, as well as on the eastern Aegean islands of Samos and Lesvos. Tantalising, but as yet unconfirmed Miocene accounts of the geoemydid Mauremys in Macedonia, and indeterminate emydid-like remains from Euboea, also provide potentially significant range extensions. Although hampered by a historically sparse documentation, the fossil turtles of Greece are a significant resource that record both assemblage changes and the origin of modern lineages.