Translational control of coronaviruses

Coronaviruses represent a large family of enveloped RNA viruses that infect a large spectrum of animals. In humans, the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic and is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2002 and 2012, respectively. All viruses described to date entirely rely on the protein synthesis machinery of the host cells to produce proteins required for their replication and spread. As such, virus often need to control the cellular translational apparatus to avoid the first line of the cellular defense intended to limit the viral propagation. Thus, coronaviruses have developed remarkable strategies to hijack the host translational machinery in order to favor viral protein production. In this review, we will describe some of these strategies and will highlight the role of viral proteins and RNAs in this process.     

An integrated pathway system modeling of Saccharomyces cerevisiae HOG pathway: a Petri net based approach

Biochemical networks comprise many diverse components and interactions between them. It has intracellular signaling, metabolic and gene regulatory pathways which are highly integrated and whose responses are elicited by extracellular actions. Previous modeling techniques mostly consider each pathway independently without focusing on the interrelation of these which actually functions as a single system. In this paper, we propose an approach of modeling an integrated pathway using an event-driven modeling tool, i.e., Petri nets (PNs). PNs have the ability to simulate the dynamics of the system with high levels of accuracy. The integrated set of signaling, regulatory and metabolic reactions involved in Saccharomyces cerevisiae’s HOG pathway has been collected from the literature. The kinetic parameter values have been used for transition firings. The dynamics of the system has been simulated and the concentrations of major biological species over time have been observed. The phenotypic characteristics of the integrated system have been investigated under two conditions, viz., under the absence and presence of osmotic pressure. The results have been validated favorably with the existing experimental results. We have also compared our study with the study of idFBA (Lee et al., PLoS Comput Biol 4:e1000–e1086, 2008) and pointed out the differences between both studies. We have simulated and monitored concentrations of multiple biological entities over time and also incorporated feedback inhibition by Ptp2 which has not been included in the idFBA study. We have concluded that our study is the first to the best of our knowledge to model signaling, metabolic and regulatory events in an integrated form through PN model framework. This study is useful in computational simulation of system dynamics for integrated pathways as there are growing evidences that the malfunctioning of the interplay among these pathways is associated with disease.     

Effects of the interactions between glutaraldehyde and the polymeric matrix on the efficacy of the biocide against pseudomonas fluorescens biofilms

Glutaraldehyde (GTA) is a widely used biocide due to its high effectiveness. The experimental work reported here was carried out to assess the effectiveness of GTA in controlling biofilms formed by Pseudomonas fluorescens on stainless steel slides, and to compare efficacy against both planktonic and sessile micro‐rganisms. The tests were performed using two concentrations of GTA (50 and 100mg 1^‐1), biofilms of two ages (7 and 15 d), several pH values (5,7 and 9) and a range of exposure times (from 0 (control) to 1,3,7 and 24 h). The action of GTA on biofilm and planktonic populations was assessed by means of activity tests, zeta potential, and the wet weight of the biofilms. Biofilms were not completely removed after treatment with GTA in any of the conditions studied. The higher GTA concentration was more effective in reducing the bacterial activity of the biofilm. The biocide proved to be more effective for longer exposure times. GTA showed good antimicrobial activity against P. fluorescens in suspension, with higher activity at pH 9. The findings of this study suggest that when GTA is used to control biofilms, it reacts with one of the components of the matrix, the proteins, thereby reducing its antimicrobial action.     

Effect of photosynthetic biofilms on the open‐circuit potential of stainless steel

Periodic illumination of photosynthetic biofilms on AISI* 316L stainless steel resulted in evolution of oxygen (1–7 mg.1^‐1) and a corresponding increase in open circuit potential (E_corr) from 2 to 15 mV. The change in E^ depended on the interval of illumination. When the dark cycle began, elevation in potential was followed by an immediate drop. Illumination did not affect E_corr in sterile systems or in systems that contained only nonphotosynthetic eubacteria. Radiated heat from illumination accounted for changes of 4 to 5°C in temperature which, in the absence of oxygen production, should decrease dissolved oxygen by 0.75 mgl^‐1 and decrease E_corr by 1 mV. Positive shifts of E_corr induced by periodic illumination of photosynthetic biofilms are primarily the result of oxygen production.     

A novel epidermal growth factor receptor-signaling platform and its targeted translation in pancreatic cancer

Epidermal growth factor (EGF)-induced EGFR tyrosine kinase receptor activation in cancer cell survival responses has become a strategic molecular-targeting clinical therapeutic intent, but the failures of these targeted approaches in the clinical setting demand alternate strategies. Here, we uncover a novel neuraminidase-1 (Neu1) and matrix metalloproteinase-9 (MMP-9) cross-talk in alliance with GPCR neuromedin B, which is essential for EGF-induced receptor activation and cellular signaling. Neu1 and MMP-9 form a complex with EGFR on the cell surface. Tamiflu (oseltamivir phosphate), anti-Neu1 antibodies, broad range MMP inhibitor galardin (GM6001), neuromedin B GPCR specific antagonist BIM-23127, the selective inhibitor of whole heterotrimeric G-protein complex BIM-46174 and MMP-9 specific inhibitor dose-dependently inhibited Neu1 activity associated with EGF stimulated 3T3–hEGFR cells. Tamiflu, anti-Neu1 antibodies and MMP9i attenuated EGFR phosphorylation associated with EGF-stimulated cells. Preclinical data provide the proof-of-evidence for a therapeutic targeting of Neu1 with Tamiflu in impeding human pancreatic cancer growth and metastatic spread in heterotopic xenografts of eGFP-MiaPaCa-2 tumors growing in RAGxCγ double mutant mice. Tamiflu-treated cohort exhibited a reduction of phosphorylation of EGFR-Tyr1173, Stat1-Tyr701, Akt-Thr308, PDGFRα-Tyr754 and NFκBp65-Ser311 but an increase in phospho-Smad2-Ser465/467 and -VEGFR2-Tyr1175 in the tumor lysates from the xenografts of human eGFP-MiaPaCa-2 tumor-bearing mice. The findings identify a novel promising alternate therapeutic treatment of human pancreatic cancer.     

Emergence of gp120 V3 Variants Confers Neutralization Resistance in an R5 Simian-Human Immunodeficiency Virus-Infected Macaque Elite Neutralizer That Targets the N332 Glycan of the Human Immunodeficiency Virus Type 1 Envelope Glycoprotein

Neutralization-resistant simian-human immunodeficiency virus AD8 (SHIV_AD8) variants that emerged in an infected macaque elite neutralizer targeting the human immunodeficiency virus type 1 (HIV-1) gp120 N332 glycan acquired substitutions of critical amino acids in the V3 region rather than losing the N332 glycosylation site. One of these resistant variants, carrying the full complement of gp120 V3 changes, was also resistant to the potent anti-HIV-1 monoclonal neutralizing antibodies PGT121 and 10-1074, both of which are also dependent on the presence of the gp120 N332 glycan.     

Is the caste-ratio of the oligolectic bumblebee Bombus gerstaeckeri Morawitz (Hymenoptera: Apidae) biased to queens?

Three bumblebee species, foraging on Aconitum spp. have been commonly observed in Eyne (France, East Pyrénées): Bombus gerstaeckeri, B. hortorum and B. wurflenii. We estimated the population of these three species. For B. hortorum and B. wurflenii, the total workers populations foraging on Aconitum spp. ranged from 101 to 523 and 156 to 270, respectively. These two species also forage on other plants while B. gerstaeckeri visits only Aconitum spp. The population of B. gerstaeckeri observed was extremely small, founded by 33 queens only in 2001. With a total number of workers estimated from 40 to 102, the observed workers/queens ratio, 1 to 3 workers for each queen, is very unusual for a eusocial species. Also we observed queens foraging during the whole life of the colony. This kind of social organisation is similar to that of some high arctic species. It could be interpreted as the result of an insularity syndrome.     

Habitat associations of Eurasian Skylarks Alauda arvensis breeding on Irish farmland and implications for agri-environment planning

Capsule Skylarks breeding in Ireland prefer extensive grassland habitats and almost completely avoid tillage habitats.

Aims To describe the distribution and habitat use of breeding Skylarks in Ireland, particularly in lowland agricultural habitats, and to use this information to inform conservation measures for this species.

Methods Countryside Bird Survey (CBS) and Farmland Bird Project (FBP) data were examined to determine large-scale (national) distribution and habitat selection, in addition to smaller-scale (farm- and field-level) habitat use. The CBS is a national breeding bird monitoring scheme involving 397 1-km squares. The FBP collected detailed bird and habitat data from 122 farms.

Results CBS and FBP data both showed significant regional differences in breeding Skylark densities, with the highest relative abundances in the northwest and west. Dry grassland/grass moor habitats supported the highest densities of breeding Skylarks in the CBS, which were significantly higher than in improved grassland or tillage. At the farm-level, Skylark numbers were positively related to wetland habitats but negatively associated with trees in field boundaries, dense ground vegetation and overall density of farm boundaries. At the field-scale, larger fields and unimproved grasslands were preferred.

Conclusion Agri-environment measures tailored to region-specific requirements and to the relatively local habitat preferences of target species are required if population declines of species of conservation concern, including Skylarks, are to be reversed.