Proteomic evaluation of nanotoxicity in aquatic organisms : a review

The alteration of organisms protein functions by engineered nanoparticles (ENPs) is dependent on the complex interplay between their inherent physicochemical properties (e.g., size, surface coating, shape) and environmental conditions (e.g., pH, organic matter). To date, there is increasing interest on the use of ‘omics’ approaches, such as proteomics, genomics, and others, to study ENPs-biomolecules interactions in aquatic organisms. However, although proteomics has recently been applied to investigate effects of ENPs and associated mechanisms in aquatic organisms, its use remain limited. Herein, proteomics techniques widely applied to investigate ENPs–protein interactions in aquatic organisms are reviewed. Data demonstrates that 2DE and mass spectrometry and/or their combination, thereof, are the most suitable techniques to elucidate ENPs–protein interactions. Furthermore, current status on ENPs and protein interactions, and possible mechanisms of nanotoxicity with emphasis on those that exert influence at protein expression levels, and key influencing factors on ENPs–proteins interactions are outlined. Most reported studies were done using synthetic media and essay protocols and had wide variability (not standardized); this may consequently limit data application in actual environmental systems. Therefore, there is a need for studies using realistic environmental concentrations of ENPs, and actual environmental matrixes (e.g., surface water) to aid better model development of ENPs–proteins interactions in aquatic systems.The Botswana International University of Science and Technology, the University of Pretoria and Water Research Commission.http://www.proteomics-journal.comhj2023Chemical Engineerin

Timing Constraints of In Vivo Gag Mutations during Primary HIV-1 Subtype C Infection

Background: Aiming to answer the broad question “When does mutation occur?” this study examined the time of appearance, dominance, and completeness of in vivo Gag mutations in primary HIV-1 subtype C infection. Methods: A primary HIV-1C infection cohort comprised of 8 acutely and 34 recently infected subjects were followed frequently up to 500 days post-seroconversion (p/s). Gag mutations were analyzed by employing single-genome amplification and direct sequencing. Gag mutations were determined in relation to the estimated time of seroconversion. Time of appearance, dominance, and completeness was compared for different types of in vivo Gag mutations. Results: Reverse mutations to the wild type appeared at a median (IQR) of 62 (44;139) days p/s, while escape mutations from the wild type appeared at 234 (169;326) days p/s (p<0.001). Within the subset of mutations that became dominant, reverse and escape mutations appeared at 54 (30;78) days p/s and 104 (47;198) days p/s, respectively (p<0.001). Among the mutations that reached completeness, reverse and escape mutations appeared at 54 (30;78) days p/s and 90 (44;196) days p/s, respectively (p = 0.006). Time of dominance for reverse mutations to and escape mutations from the wild type was 58 (44;105) days p/s and 219 (90;326) days p/s, respectively (p<0.001). Time of completeness for reverse and escape mutations was 152 (100;176) days p/s and 243 (101;370) days p/s, respectively (p = 0.001). Fitting a Cox proportional hazards model with frailties confirmed a significantly earlier time of appearance (hazard ratio (HR): 2.6; 95% CI: 2.3–3.0), dominance (4.8 (3.4–6.8)), and completeness (3.6 (2.3–5.5)) of reverse mutations to the wild type Gag than escape mutations from the wild type. Some complex mutational pathways in Gag included sequential series of reversions and escapes. Conclusions: The study identified the timing of different types of in vivo Gag mutations in primary HIV-1 subtype C infection in relation to the estimated time of seroconversion. Overall, the in vivo reverse mutations to the wild type occurred significantly earlier than escape mutations from the wild type. This shorter time to incidence of reverse mutations remained in the subsets of in vivo Gag mutations that reached dominance or completeness

Characterization of Primary Murine Alveolar Epithelial Cells and their Responses to Respiratory Viral Infections

Alveolar epithelial cells are important targets of respiratory viral infections that cause severe diseases in the lung. The alveolar epithelium, which covers more than 99% of the large internal surface area of the lung, is composed of two morphologically distinct cell types. The alveolar type I (ATI) cells are large thin cells that function in gas exchange. The alveolar type II (ATII) cells are cuboidal and produce surfactant that is required to prevent collapse of the air spaces. ATII cells divide and transdifferentiate into ATI cells to repair damaged epithelium. Both ATI and ATII cells are infected by viruses and contribute to cytokine production during infection. The goal of this dissertation was to establish an in vitro model of murine ATI and ATII cells and determine their susceptibility and responses to infection by respiratory viruses used in murine models: influenza A virus strain PR8 and murine coronavirus, MHV-1. Isolated ATII cells were cultured to maintain an ATII phenotype as determined by expression of LBP180 or transdifferentiate into an ATI-like cell phenotype determined by expression of T1?. Primary cultures of either phenotype supported replication of PR8 and MHV-1. Further, both viruses induced cytokine expression by ATI cells. Expression of several cytokines and chemokines were induced by both viruses, while MHV-1 infection resulted in expression of an additional set of cytokines that were not expressed by PR8-infected cells. To help better understand the dynamics of PR8 and cellular proteins interactions, proteomics analysis using liquid chromatography-tandem mass spectrometry was examined on ATII cells. Protein profiles in PR8 infected and uninfected ATII cells were compared. Influenza disrupted various functional classes of proteins that may allow productive infection of ATII cells, altering their homeostatic functions. These data will help identify cellular proteins whose functions in the virus life cycle could be targeted for antiviral strategies. Moreover, differentiated cultures of murine alveolar epithelial cells will be critical for identifying mechanisms of viral damage to the alveolar epithelium during respiratory infections, by providing an in vitro model to perform mechanistic studies that can be correlated with in vivo studies in well-established murine models.Thesis (Ph.D., Biology)--University of Idaho, June 201

Genetic and epidemiological analysis of norovirus from children with gastroenteritis in Botswana, 2013–2015

Background: Norovirus is a leading cause of viral gastroenteritis worldwide with a peak of disease seen in children. The epidemiological analysis regarding the virus strains in Africa is limited. The first report of norovirus in Botswana was in 2010 and currently, the prevalence and circulating genotypes of norovirus are unknown, as the country has no systems to report the norovirus cases. This study investigated the prevalence, patterns and molecular characteristics of norovirus infections among children ≤5 years of age admitted with acute gastroenteritis at four hospitals in Botswana. Methods: A total of 484 faecal samples were collected from children who were admitted with acute gastroenteritis during the rotavirus vaccine impact survey between July 2013 and December 2015. Norovirus was detected using real-time RT-PCR. Positive samples were genotyped using conventional RT-PCR followed by partial sequencing of the capsid and RdRp genes. Norovirus strains were determined by nucleotide sequence analysis using the online Norovirus Genotyping Tool Version 1.0, and confirmed using maximum likelihood tree construction as implemented in MEGA 6.0. Results: The prevalence of norovirus was 9.3% (95% CI 6.7–11.9). The genotype diversity was dominated by the GII.4 strain at 69.7%. This was followed by GII.2, GII.12 each at 9.1%, GI.9 at 6.6% and GII.6, GII.10 each at 3.0%. The most common combined RdRp/Capsid genotype was the GII.Pe/GII.4 Sydney 2012. Norovirus was detected during most part of the year; however, there was a preponderance of cases in the wet season (December to March). Conclusion: The study showed a possible decline of norovirus infections in the last 10 years since the first report. An upward trend seen between 2013 and 2015 may be attributable to the success of rotavirus vaccine introductions in 2012. Knowledge of circulating genotypes, seasonal trends and overall prevalence is critical for prevention programming and possible future vaccine design implications.Medicine, Faculty ofNon UBCPathology and Laboratory Medicine, Department ofReviewedFacult

Additional file 1: of Genetic and epidemiological analysis of norovirus from children with gastroenteritis in Botswana, 2013–2015

Table S1. GII.4 Variants and similarity to published sequences. Query data from NCBI database of previously unassigned samples. (DOCX 24 kb

Occurrence, fate, effects, and risks of dexamethasone : ecological implications post-COVID-19

The recent outbreak of respiratory syndrome-coronavirus-2 (SARS-CoV-2), which causes coronavirus disease (COVID-19), has led to the widespread use of therapeutics, including dexamethasone (DEXA). DEXA, a synthetic glucocorticoid, is among the widely administered drugs used to treat hospitalized COVID-19 patients. The global COVID-19 surge in infections, consequent increasing hospitalizations, and other DEXA applications have raised concerns on eminent adverse ecological implications to aquatic ecosystems. Here, we aim to summarize published studies on DEXA occurrence, fate, and effects on organisms in natural and engineered systems as, pre-COVID, the drug has been identified as an emerging environmental contaminant. The results demonstrated a significant reduction of DEXA in wastewater treatment plants, with a small portion, including its transformation products (TPs), being released into downstream waters. Fish and crustaceans are the most susceptible species to DEXA exposure in the parts-per-billion range, suggesting potential deleterious ecological effects. However, there are data deficits on the implications of DEXA to marine and estuarine systems and wildlife. To improve DEXA management, toxicological outcomes of DEXA and formed TPs should entail long-term studies from whole organisms to molecular effects in actual environmental matrices and at realistic exposure concentrations. This can aid in striking a fine balance of saving human lives and protecting ecological integrity.SUPPLEMENTARY MATERIAL : Table S1: The ecotoxicological effects of DEXA on organisms at different levels of organization, Table S2: Removal of DEXA during wastewater treatment in WWTPs, with techniques utilized across geographical regions globally in selected studies.The Water Research Commission, the Department of Science and Innovation/National Research Foundation SARChI (DSI/NRF SARChI, South Africa) and Botswana International University of Science and Technology.https://www.mdpi.com/journal/ijerpham2022Chemical Engineerin

Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus

AbstractInfection of type II alveolar epithelial (ATII) cells by influenza A viruses (IAV) correlates with severe respiratory disease in humans and mice. To understand pathogenic mechanisms during IAV infection of ATII cells, murine ATII cells were cultured to maintain a differentiated phenotype, infected with IAV-PR8, which causes severe lung pathology in mice, and proteomics analyses were performed using liquid chromatography–mass spectrometry. PR8 infection increased levels of proteins involved in interferon signaling, antigen presentation, and cytoskeleton regulation. Proteins involved in mitochondrial membrane permeability, energy metabolism, and chromatin formation had reduced levels in PR8-infected cells. Phenotypic markers of ATII cells in vivo were identified, confirming the differentiation status of the cultures. Surfactant protein B had decreased levels in PR8-infected cells, which was confirmed by immunoblotting and immunofluorescence assays. Analysis of ATII cell protein profiles will elucidate cellular processes in IAV pathogenesis, which may provide insight into potential therapies to modulate disease severity