8383 research outputs found
Sort by
Identification of a C2-symmetric diol based human immunodeficiency virus protease inhibitor targeting Zika virus NS2B-NS3 protease
Get PDFZika virus (ZIKV) is an emerging mosquito-borne flavivirus and infection by ZIKV Asian lineage is known to cause fetal brain anomalies and Guillain-Barrés syndrome. The WHO declared ZIKV a global public health emergency in 2016. However, currently neither vaccines nor antiviral prophylaxis/treatments are available. In this study, we report the identification of a C2-symmetric diol-based Human immunodeficiency virus type-1 (HIV) protease inhibitor active against ZIKV NS2B-NS3 protease. The compound, referred to as 9b, was identified by in silico screening of a library of 6265 protease inhibitors. Molecular dynamics (MD) simulation studies revealed that compound 9b formed a stable complex with ZIKV protease. Interaction analysis of compound 9b's binding pose from the cluster analysis of MD simulations trajectories predicted that 9b mostly interacted with ZIKV NS3. Although designed as an aspartyl protease inhibitor, compound 9b was found to inhibit ZIKV serine protease in vitro with IC50 = 143.25 ± 5.45 µM, in line with the in silico results. Additionally, linear interaction energy method (LIE) was used to estimate binding affinities of compounds 9b and 86 (a known panflavivirus peptide hybrid with IC50 = 1.64 ± 0.015 µM against ZIKV protease). The LIE method correctly predicted the binding affinity of compound 86 to be lower than that of 9b, proving to be superior to the molecular docking methods in scoring and ranking compounds. Since most of the reported ZIKV protease inhibitors are positively charged peptide-hybrids, with our without electrophilic warheads, compound 9b represents a less polar and more drug-like non-peptide hit compound useful for further optimization.Communicated by Ramaswamy Sarma.Scandinavian Society for Antimicrobial Chemotherap
Split intein-mediated selection of cells containing two plasmids using a single antibiotic
Get PDF© The Author(s) 2019. The version of record of this article, first published in [Nature Communications], is available online at Publisher’s website: http://dx.doi.org/10.1038/s41467-019-12911-1To build or dissect complex pathways in bacteria and mammalian cells, it is often necessary to recur to at least two plasmids, for instance harboring orthogonal inducible promoters. Here we present SiMPl, a method based on rationally designed split enzymes and intein-mediated protein trans-splicing, allowing the selection of cells carrying two plasmids with a single antibiotic. We show that, compared to the traditional method based on two antibiotics, SiMPl increases the production of the antimicrobial non-ribosomal peptide indigoidine and the non-proteinogenic aromatic amino acid para-amino-L-phenylalanine from bacteria. Using a human T cell line, we employ SiMPl to obtain a highly pure population of cells double positive for the two chains of the T cell receptor, TCRα and TCRβ, using a single antibiotic. SiMPl has profound implications for metabolic engineering and for constructing complex synthetic circuits in bacteria and mammalian cells.Deutsche Forschungsgemeinschaft (DFG
Deleterious single nucleotide polymorphisms of protein kinase R identified by the computational approach
No full textThe human protein kinase R (PKR) recognizes invading RNA viruses and mediates the antiviral immune response by phosphorylating the eukaryotic translation initiation factor 2α (eIF-2α), thus blocking protein translation in infected cells and thus preventing viral replication. The observation that individuals show different degrees of susceptibility to viral infections gives rise to the hypothesis that single nucleotide polymorphisms (SNPs) in the protein kinase R may alter the response to an infection. Using different available servers (e.g. SIFT, PROVEAN, Polyphen2, SNAP2, SNP&GOs, SNP-PhD, I-Mutant Suite), 14 SNPs were identified that were predicted to have deleterious effects on the protein kinase R. Five SNPs, namely D266Y, Y323D, I398 K, Y465C and Y472C, were selected for homology modeling and the generated models were investigated with regard to their secondary structure, residue fluctuations and eIF-2α binding. Analysis with computational tools POLYVIEW-MM, SAAPdap, SRIDE, CMView, elNémo, NMsim and PatchDock revealed structural changes in all mutants yielding a more stable structure at the cost of reduced flexibility (except Y465C) and less conformational freedom compared to the native protein. The conformational changes in the mutant protein structures and the displacement of functional residues from their strategic positions are predicted to affect the functionality of PKR, and consequently will affect the efficiency of the individual's antiviral immune response negatively. This study will aid the physicians in precision medicine field to tailor optimal treatment for the patients.N/
Prevalence of polymorphisms with significant resistance to NS5A inhibitors in treatment-naive patients with hepatitis C virus genotypes 1a and 3a in Sweden
No full textBACKGROUND: The future treatment of hepatitis C virus (HCV) infection will be combinations of direct-acting antivirals (DAAs) that not only target multiple viral targets, but are also effective against different HCV genotypes. Of the many drug targets in HCV, one promising target is the non-structural 5A protein (NS5A), against which inhibitors, namely daclatasvir, ledipasvir and ombitasvir, have shown potent efficacy. However, since HCV is known to have very high sequence diversity, development of resistance is a problem against but not limited to NS5A inhibitors (i.e. resistance also found against NS3-protease and NS5B non-nucleoside inhibitors), when used in suboptimal combinations. Furthermore, it has been shown that natural resistance against DAAs is present in treatment-naïve patients and such baseline resistance will potentially complicate future treatment strategies.
METHODS: A pan-genotypic population-sequencing method with degenerated primers targeting the NS5A region was developed. We have investigated the prevalence of baseline resistant variants in 127 treatment-naïve patients of HCV genotypes 1a, 1b, 2b and 3a.
RESULTS: The method could successfully sequence more than 95% of genotype 1a, 1b and 3a samples. Interpretation of fold resistance data against the NS5A inhibitors was done with the help of earlier published phenotypic data. Baseline resistance variants associated with high resistance (1000-50,000-fold) was found in three patients: Q30H or Y93N in genotype 1a patients and further Y93H in a genotype 3a patient.
CONCLUSION: Using this method, baseline resistance can be examined and the data could have a potential role in selecting the optimal and cost-efficient treatment for the patient.N/
Transmission of hepatitis C virus among intravenous drug users in the Uppsala region of Sweden
Get PDFBACKGROUND: Epidemiology and transmission patterns of hepatitis C virus (HCV) are important subjects as we enter a new era of treatment with directly acting antivirals (DAAs). The highest prevalence of HCV in developed countries is found among intravenous drug users (IDUs), where unsafe needle sharing practices provide the main route of infection. Efforts to prohibit the continuous spread of HCV among these groups have been initiated by the community services and health care providers. Our goal was to understand how HCV was transmitted among IDUs within a limited population group. We provide a retrospective study (2005-2007) of the HCV transmission patterns in a population of IDUs in the Uppsala region of Sweden.
METHOD: Eighty-two serum samples were collected from IDUs in Uppsala County. Our reverse transcription nested polymerase chain reaction (RT-nested PCR) and sequencing method enabled a comprehensive genetic analysis for a broad spectrum of genotypes of two relatively conserved regions, NS5B and NS3, that encodes for the viral polymerase and protease, respectively. HCV RNA in serum samples was amplified and sequenced with in-house primers. Sequence similarities between individuals and subgroups were analyzed with maximum likelihood (ML) phylogenetic trees. Published HCV reference sequences from other geographic regions and countries were also included for clarity.
RESULTS: Phylogenetic analysis was possible for 59 NS5B (72%) and 29 NS3 (35%) sequences from Uppsala patients. Additionally, we also included 15 NS3 sequences from Örebro patients, making a total of 44 NS3 sequences for the analysis. By analyzing the NS3 sequences, two transmission sets were found between the IDUs (>98% sequence identity), with one set consisting of two individuals and another set consisting of three individuals. In addition, the phylogenetic analysis done with our serum samples displayed clusters that distinguished them from the reference sequences.
CONCLUSION: Our method seems to enable us to trace the HCV transmission between IDUs. Furthermore, the method is fairly independent of the time of infection because the method uses relatively conserved HCV sequence regions (i.e. NS5B and NS3).N/
Are we witnessing a revolution of the Italian citizenship regime? Postscript to the special issue
No full textThis is an Author's Accepted Manuscript of the article Bargel, L., Bottecchia, G., Donati, S., Fusari, V., Gargiulo, E., Rigo, E., Sredanovic, D., & Tuorto, D. (2025). Are we witnessing a revolution of the Italian citizenship regime? Postscript to the special issue. Journal of Modern Italian Studies, vol(issue), 1-10, as published in the Journal of Modern Italian Studies on 5th June 2025. © Taylor and Francis, available online at: https://www.tandfonline.com/doi/full/10.1080/1354571X.2025.2510081#d1e213.While we were completing this special issue, in spring 2025, three possible changes to the Italian citizenship law developed that could lead to a deep transformation in the way Italian citizenship has been historically ruled and produce multiple effects on the citizenship/mobility nexus. We therefore felt the need to acknowledge them through adding this collective post-script, even if it is too early to provide a comprehensive in-depth analysis
(Un)sustainability of the elite parasport development system in a Least Developed Country: an investigation of Cambodian para-Athletic career pathways
Get PDFPurpose: Establishing athletic career pathways is important for the sustainable development of elite parasport, but there is a paucity of literature on parasport athletic career pathways in economically disadvantaged, Least Developed Countries. The current study investigated how para-athletes, coaches, and administrators in Cambodia experience their athletic careers. Methodology: Individual, semi-structured interviews were conducted with four para-athletics coaches, six para-athletics athletes, and two parasport administrators in Cambodia. The transcripts were analyzed with thematic analysis. Findings and practical implications: Key themes indicated that the lack of parasport equipment limits new athlete recruitment, the lack of a positive career outlook after athletic retirement is a cause of distress among athletes, and specialized parasport coaches are lacking. These problems suggest alack of sustainability. The Cambodian government could invest in a clearer retirement preparation system for para-athletes. In this respect, retired para-athletes could continue contributing to parasport development in the country as elite and grassroots-level coaches. Research contribution: This is the first study examining the experience of para-athletes, coaches, and administrators in a Least Developed Country. Our findings identified recruitment, retirement preparation, and coach training as major areas for development. Value: The findings would assist evidence-based policy making for more sustainable development of elite parasport.The Japan Sports Agency of the government of Japa
High temperatures are associated with reduced cognitive performance in wild southern pied babblers
Get PDF© 2023 The Authors. Published by the Royal Society.Global temperatures are increasing rapidly. While considerable research is accumulating regarding the lethal and sublethal effects of heat on wildlife, its potential impact on animal cognition has received limited attention. Here, we tested wild southern pied babblers (Turdoides bicolor) on three cognitive tasks (associative learning, reversal learning and inhibitory control) under naturally occurring heat stress and non-heat stress conditions. We determined whether cognitive performance was explained by temperature, heat dissipation behaviours, individual and social attributes, or proxies of motivation. We found that temperature, but not heat dissipation behaviours, predicted variation in associative learning performance. Individuals required on average twice as many trials to learn an association when the maximum temperature during testing exceeded 38°C compared with moderate temperatures. Higher temperatures during testing were also associated with reduced inhibitory control performance, but only in females. By contrast, we found no temperature-related decline in performance in the reversal learning task, albeit individuals reached learning criterion in only 14 reversal learning tests. Our findings provide novel evidence of temperature-mediated cognitive impairment in a wild animal and indicate that its occurrence depends on the cognitive trait examined and individual sex.This work was funded by the Australian Government Research Training Program through a scholarship awarded to C.S. at The University of Western Australia (UWA) and by the Australian Research Council through a Discovery Project grant (no. DP220103823) awarded to A.R.R., B.J.A. and A.T. This work was also supported by the Rotary Club of Melville and the Postgraduate Student Association of UWA through two awards to C.S. The KRR, the study site where this research was based, was financed by the Universities of Cambridge and Zurich, the MAVA Foundation and the European Research Council (grant no. 294494) and received logistical support from the Mammal Research Institute of the University of Pretoria
Extra food provisioning does not affect behavioral lateralization in nestling lesser kestrels
Get PDF© The Author(s) 2022. Published by Oxford University Press on behalf of Editorial Office, Current Zoology.Costs and benefits of brain lateralization may depend on environmental conditions. Growing evidence indicates that the development of brain functional asymmetries is adaptively shaped by the environmental conditions experienced during early life. Food availability early in life could act as a proxy of the environmental conditions encountered during adulthood, but its potential modulatory effect on lateralization has received little attention. We increased food supply from egg laying to early nestling rearing in a wild population of lesser kestrels Falco naumanni, a sexually dimorphic raptor, and quantified the lateralization of preening behavior (head turning direction). As more lateralized individuals may perform better in highly competitive contexts, we expected that extra food provisioning, by reducing the level of intra-brood competition for food, would reduce the strength of lateralization. We found that extra food provisioning improved nestling growth, but it did not significantly affect the strength or direction of nestling lateralization. In addition, maternal body condition did not explain variation in nestling lateralization. Independently of extra food provisioning, the direction of lateralization differed between the sexes, with female nestlings turning more often toward their right. Our findings indicate that early food availability does not modulate behavioral lateralization in a motor task, suggesting limited phenotypic plasticity in this trait.The study was supported by institutional funding from the Università degli Studi di Milano (to D.R.), Università degli Studi di Padova (to C.S.), and the Istituto Nazionale per la Protezione e la Ricerca Ambientale (ISPRA) (to J.G.C.). Nest-boxes were installed with support from the European Commission through the LIFE Project “Rapaci Lucani” (LIFE05NAT/IT/00009) and were designed by G. Ceccolini
Make university placements work for students and employers
No full textThis item is not available on ChesterRep.To access this item click on the URL in Additional LinksArticle for THE campus based on research exploring students' and employers' perspectives of placement on the Childhood Studies and Applied Psychology programmeUnfunde
Data sources:
Access Repository Dashboard
Do you manage ChesterRep? Access insider analytics, issue reports and manage access to outputs from your repository in the CORE Repository Dashboard!