| 1. |
- Hakim Jaffer Ali, Mohammed, et al.
(författare)
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Benchmarking virus concentration methods for quantification of SARS-CoV-2 in raw wastewater
- 2021
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 755
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Tidskriftsartikel (refereegranskat)abstract
- Wastewater-based epidemiology offers a cost-effective alternative to testing large populations for SARS-CoV-2 virus, and may potentially be used as an early warning system for SARS-CoV-2 pandemic spread. However, viruses are highly diluted in wastewater, and a validated method for their concentration and further processing, and suitable reference viruses, are the main needs to be established for reliable SARS-CoV-2 municipal wastewater detection. For this purpose, we collected wastewater from two European cities during the Covid-19 pandemic and evaluated the sensitivity of RT-qPCR detection of viral RNA after four concentration methods (two variants of ultrafiltration-based method and two adsorption and extraction-based methods). Further, we evaluated one external (bovine corona virus) and one internal (pepper mild mottle virus) reference virus. We found a consistently higher recovery of spiked virus using the modified ultrafiltration-based method. This method also had a significantly higher efficiency (p-value <0.01) for wastewater SARS-CoV-2 detection. The ultracentrifugation method was the only method that detected SARS-CoV-2 in the wastewater of both cities. The pepper mild mottle virus was found to function as a potentially suitable internal reference standard.
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| 2. |
- Trushna, Tanwi, et al.
(författare)
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Interventions to promote household waste segregation: A systematic review
- 2024
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Ingår i: Heliyon. - 2405-8440. ; 10:2
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Forskningsöversikt (refereegranskat)abstract
- Waste segregation at source, particularly at the household level, is an integral component of sustainable solid waste management, which is a critical public health issue. Although multiple interventions have been published, often with contradictory findings, few authors have conducted a comprehensive systematic synthesis of the published literature. Therefore, we undertook a systematic review to synthesize all published interventions conducted in any country in the world which targeted household-level waste segregation with or without additional focus on recycling or composting.Following PRISMA guidelines, Web of Science, Medline, Global Health, and Google Scholar were searched using a search strategy created by combining the keywords ‘Waste’, ‘Segregation’, and ‘Household’. Two-stage blinded screening and consensus-based conflict resolution were done, followed by quality assessment, data extraction, and narrative synthesis.8555 articles were identified through the database searches and an additional 196 through grey literature and citation searching. After excluding 2229 duplicates and screening title abstracts of 6522 articles, 283 full texts were reviewed, and 78 publications reporting 82 intervention studies were included in the data synthesis.High methodological heterogeneity was seen, excluding the possibility of a meta-analysis. Most (n = 60) of the interventions were conducted in high-income countries. Interventions mainly focused on information provision. However, differences in the content of information communicated and mode of delivery have not been extensively studied. Finally, our review showed that the comparison of informational interventions with provision of incentives and infrastructural modifications needs to be explored in-depth. Future studies should address these gaps and, after conducting sufficient formative research, should aim to design their interventions following the principles of behaviour change.
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| 3. |
- Baumgarten, Thomas, et al.
(författare)
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Optimizing Recombinant Protein Production in the Escherichia coli Periplasm Alleviates Stress
- 2018
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 84:12
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Tidskriftsartikel (refereegranskat)abstract
- In Escherichia coli, many recombinant proteins are produced in the periplasm. To direct these proteins to this compartment, they are equipped with an N-terminal signal sequence so that they can traverse the cytoplasmic membrane via the protein-conducting Sec translocon. Recently, using the single-chain variable antibody fragment BL1, we have shown that harmonizing the target gene expression intensity with the Sec translocon capacity can be used to improve the production yields of a recombinant protein in the periplasm. Here, we have studied the consequences of improving the production of BL1 in the periplasm by using a proteomics approach. When the target gene expression intensity is not harmonized with the Sec translocon capacity, the impaired translocation of secretory proteins, protein misfolding/aggregation in the cytoplasm, and an inefficient energy metabolism result in poor growth and low protein production yields. The harmonization of the target gene expression intensity with the Sec translocon capacity results in normal growth, enhanced protein production yields, and, surprisingly, a composition of the proteome that is-besides the produced target-the same as that of cells with an empty expression vector. Thus, the single-chain variable antibody fragment BL1 can be efficiently produced in the periplasm without causing any notable detrimental effects to the production host. Finally, we show that under the optimized conditions, a small fraction of the target protein is released into the extracellular milieu via outer membrane vesicles. We envisage that our observations can be used to design strategies to further improve the production of secretory recombinant proteins in E. coli.IMPORTANCE The bacterium Escherichia coli is widely used to produce recombinant proteins. Usually, trial-and-error-based screening approaches are used to identify conditions that lead to high recombinant protein production yields. Here, for the production of an antibody fragment in the periplasm of E. coli, we show that an optimization of its production is accompanied by the alleviation of stress. This indicates that the monitoring of stress responses could be used to facilitate enhanced recombinant protein production yields.
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| 4. |
- Dash-Wagh, Suvarna, et al.
(författare)
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PepFect6 Mediated SiRNA Delivery into Organotypic Cultures
- 2016
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Ingår i: SiRNA Delivery Methods. - TOTOWA : HUMANA PRESS INC. - 9781493931125 - 9781493931118 ; 1364, s. 27-35
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Bokkapitel (refereegranskat)abstract
- Gene silencing by small interfering RNA (SiRNA) is an attractive therapeutic approach for pathological disorders that targets a specific gene. However, its applications are limited, as naked RNA is rapidly degraded by RNases and is inadequately internalized by the target cells in the body. Several viral and non-viral vectors have been described to improve the delivery of SiRNAs both in cultured cells as well as in vivo. Increasing evidence suggests that cell-penetrating peptides (CPPs) are an efficient, non-cytotoxic tool for intracellular delivery of SiRNA. Recently, a new peptide, PepFect6 (PF6), based system has been described for efficient SiRNA delivery in various cell types. PF6 is an amphipathic stearyl-TP10 peptide carrying a pH titratable trifluoromethylquinoline moiety that facilitate endosomal release. PF6 forms stable non-covalent complexes with SiRNA. Upon internalization, the complexes rapidly escape the endosomal compartment, resulting in robust RNA interference (RNAi) responses. This chapter describes a protocol to use the PF6-nanoparticle technology for SiRNA delivery into organotypic cultures of the inner ear i.e., cochlea. We also highlight different critical points in the peptide/SiRNA complex preparation, transfection and in analyzing the efficacy of PF6-SiRNA associated RNAi response.
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| 5. |
- Ewels, Philip, et al.
(författare)
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MultiQC : summarize analysis results for multiple tools and samples in a single report
- 2016
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 32:19, s. 3047-3048
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis.Results: We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization.
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| 6. |
- Hagey, Daniel W., et al.
(författare)
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Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells
- 2016
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 26:7, s. 908-917
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Tidskriftsartikel (refereegranskat)abstract
- Spatially distinct gene expression profiles in neural stem cells (NSCs) are a prerequisite to the formation of neuronal diversity, but how these arise from the regulatory interactions between chromatin accessibility and transcription factor activity has remained unclear. Here, we demonstrate that, despite their distinct gene expression profiles, NSCs of the mouse cortex and spinal cord share the majority of their DNase I hypersensitive sites (DHSs). Regardless of this similarity, domain-specific gene expression is highly correlated with the relative accessibility of associated DHSs, as determined by sequence read density. Notably, the binding pattern of the general NSC transcription factor SOX2 is also largely cell type specific and coincides with an enrichment of LHX2 motifs in the cortex and HOXA9 motifs in the spinal cord. Interestingly, in a zebrafish reporter gene system, these motifs were critical determinants of patterned gene expression along the rostral-caudal axis. Our findings establish a predictive model for patterned NSC gene expression, whereby domain-specific expression of LHX2 and HOX proteins act on their target motifs within commonly accessible cis-regulatory regions to specify SOX2 binding. In turn, this binding correlates strongly with these DHSs relative accessibility-a robust predictor of neighboring gene expression.
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| 7. |
- Lindskog, Cecilia, et al.
(författare)
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The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling
- 2015
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- Background: To understand cardiac and skeletal muscle function, it is important to define and explore their molecular constituents and also to identify similarities and differences in the gene expression in these two different striated muscle tissues. Here, we have investigated the genes and proteins with elevated expression in cardiac and skeletal muscle in relation to all other major human tissues and organs using a global transcriptomics analysis complemented with antibody-based profiling to localize the corresponding proteins on a single cell level. Results: Our study identified a comprehensive list of genes expressed in cardiac and skeletal muscle. The genes with elevated expression were further stratified according to their global expression pattern across the human body as well as their precise localization in the muscle tissues. The functions of the proteins encoded by the elevated genes are well in line with the physiological functions of cardiac and skeletal muscle, such as contraction, ion transport, regulation of membrane potential and actomyosin structure organization. A large fraction of the transcripts in both cardiac and skeletal muscle correspond to mitochondrial proteins involved in energy metabolism, which demonstrates the extreme specialization of these muscle tissues to provide energy for contraction. Conclusions: Our results provide a comprehensive list of genes and proteins elevated in striated muscles. A number of proteins not previously characterized in cardiac and skeletal muscle were identified and localized to specific cellular subcompartments. These proteins represent an interesting starting point for further functional analysis of their role in muscle biology and disease.
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| 8. |
- Mahmudi, Owais, et al.
(författare)
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Gene-pseudogene evolution : a probabilistic approach
- 2015
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Ingår i: BMC Genomics. - 1471-2164. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- Over the last decade, methods have been developed for the reconstruction of gene trees that take into account the species tree. Many of these methods have been based on the probabilistic duplication-loss model, which describes how a gene-tree evolves over a species-tree with respect to duplication and losses, as well as extension of this model, e.g., the DLRS (Duplication, Loss, Rate and Sequence evolution) model that also includes sequence evolution under relaxed molecular clock. A disjoint, almost as recent, and very important line of research has been focused on non protein-coding, but yet, functional DNA. For instance, DNA sequences being pseudogenes in the sense that they are not translated, may still be transcribed and the thereby produced RNA may be functional. We extend the DLRS model by including pseudogenization events and devise an MCMC framework for analyzing extended gene families consisting of genes and pseudogenes with respect to this model, i.e., reconstructing gene-trees and identifying pseudogenization events in the reconstructed gene-trees. By applying the MCMC framework to biologically realistic synthetic data, we show that gene-trees as well as pseudogenization points can be inferred well. We also apply our MCMC framework to extended gene families belonging to the Olfactory Receptor and Zinc Finger superfamilies. The analysis indicate that both these super families contains very old pseudogenes, perhaps so old that it is reasonable to suspect that some are functional. In our analysis, the sub families of the Olfactory Receptors contains only lineage specific pseudogenes, while the sub families of the Zinc Fingers contains pseudogene lineages common to several species.
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| 9. |
- Mirzadeh, Kiavash, et al.
(författare)
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Increased production of periplasmic proteins in Escherichia coli by directed evolution of the translation initiation region
- 2020
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Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859 .- 1475-2859. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Recombinant proteins are often engineered with an N-terminal signal peptide, which facilitates their secretion to the oxidising environment of the periplasm (gram-negative bacteria) or the culture supernatant (gram-positive bacteria). A commonly encountered problem is that the signal peptide influences the synthesis and secretion of the recombinant protein in an unpredictable manner. A molecular understanding of this phenomenon is highly sought after, as it could lead to improved methods for producing recombinant proteins in bacterial cell factories.Results: Herein we demonstrate that signal peptides contribute to an unpredictable translation initiation region. A directed evolution approach that selects a new translation initiation region, whilst leaving the amino acid sequence of the signal peptide unchanged, can increase production levels of secreted recombinant proteins. The approach can increase production of single chain antibody fragments, hormones and other recombinant proteins in the periplasm of E. coli.Conclusions: The study demonstrates that signal peptide performance is coupled to the efficiency of the translation initiation region.
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| 10. |
- Prager, Maria, et al.
(författare)
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ASV portal : an interface to DNA-based biodiversity data in the Living Atlas
- 2023
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Ingår i: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited func-tionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Ampli-con Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.Results: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. Conclusion: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.
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