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| 2. |
- Grüning, Björn, et al.
(författare)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 3. |
- Kang, Wenjing, 1988-, et al.
(författare)
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MapToCleave : High-throughput profiling of microRNA biogenesis in living cells
- 2021
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Ingår i: Cell Reports. - : Elsevier BV. - 2211-1247. ; 37:7
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Tidskriftsartikel (refereegranskat)abstract
- Previous large-scale studies have uncovered many features that determine the processing of microRNA (miRNA) precursors; however, they have been conducted in vitro. Here, we introduce MapToCleave, a method to simultaneously profile processing of thousands of distinct RNA structures in living cells. We find that miRNA precursors with a stable lower basal stem are more efficiently processed and also have higher expression in vivo in tissues from 20 animal species. We systematically compare the importance of known and novel sequence and structural features and test biogenesis of miRNA precursors from 10 animal and plant species in human cells. Lastly, we provide evidence that the GHG motif better predicts processing when defined as a structure rather than sequence motif, consistent with recent cryogenic electron microscopy (cryo-EM) studies. In summary, we apply a screening assay in living cells to reveal the importance of lower basal stem stability for miRNA processing and in vivo expression.
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| 5. |
- Shen, Ruidan, et al.
(författare)
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Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases
- 2022
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Ingår i: Chemical Science. - : Royal Society of Chemistry. - 2041-6520 .- 2041-6539. ; 13:45, s. 13524-13540
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Tidskriftsartikel (refereegranskat)abstract
- Protein tyrosine phosphatases (PTPs) possess a conserved mobile catalytic loop, the WPD-loop, which brings an aspartic acid into the active site where it acts as an acid/base catalyst. Prior experimental and computational studies, focused on the human enzyme PTP1B and the PTP from Yersinia pestis, YopH, suggested that loop conformational dynamics are important in regulating both catalysis and evolvability. We have generated a chimeric protein in which the WPD-loop of YopH is transposed into PTP1B, and eight chimeras that systematically restored the loop sequence back to native PTP1B. Of these, four chimeras were soluble and were subjected to detailed biochemical and structural characterization, and a computational analysis of their WPD-loop dynamics. The chimeras maintain backbone structural integrity, with somewhat slower rates than either wild-type parent, and show differences in the pH dependency of catalysis, and changes in the effect of Mg2+. The chimeric proteins' WPD-loops differ significantly in their relative stability and rigidity. The time required for interconversion, coupled with electrostatic effects revealed by simulations, likely accounts for the activity differences between chimeras, and relative to the native enzymes. Our results further the understanding of connections between enzyme activity and the dynamics of catalytically important groups, particularly the effects of non-catalytic residues on key conformational equilibria.
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| 6. |
- Shen, Ruidan, et al.
(författare)
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Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases
- 2021
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Ingår i: JACS Au. - : American Chemical Society (ACS). - 2691-3704. ; 1:5, s. 646-659
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Tidskriftsartikel (refereegranskat)abstract
- Catalysis by protein tyrosine phosphatases (PTPs) relies on the motion of a flexible protein loop (the WPD-loop) that carries a residue acting as a general acid/base catalyst during the PTP-catalyzed reaction. The orthogonal substitutions of a noncatalytic residue in the WPD-loops of YopH and PTP1B result in shifted pH-rate profiles from an altered kinetic pKa of the nucleophilic cysteine. Compared to wild type, the G352T YopH variant has a broadened pH-rate profile, similar activity at optimal pH, but significantly higher activity at low pH. Changes in the corresponding PTP1B T177G variant are more modest and in the opposite direction, with a narrowed pH profile and less activity in the most acidic range. Crystal structures of the variants show no structural perturbations but suggest an increased preference for the WPD-loop-closed conformation. Computational analysis confirms a shift in loop conformational equilibrium in favor of the closed conformation, arising from a combination of increased stability of the closed state and destabilization of the loop-open state. Simulations identify the origins of this population shift, revealing differences in the flexibility of the WPD-loop and neighboring regions. Our results demonstrate that changes to the pH dependency of catalysis by PTPs can result from small changes in amino acid composition in their WPD-loops affecting only loop dynamics and conformational equilibrium. The perturbation of kinetic pKa values of catalytic residues by nonchemical processes affords a means for nature to alter an enzyme’s pH dependency by a less disruptive path than altering electrostatic networks around catalytic residues themselves.
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| 7. |
- Smith, Roger O., et al.
(författare)
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Assistive technology products : a position paper from the first global research, innovation, and education on assistive technology (GREAT) summit
- 2018
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Ingår i: Disability and Rehabilitation. - : Informa Healthcare. - 1748-3107 .- 1748-3115. ; 13:5, s. 473-485
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Tidskriftsartikel (refereegranskat)abstract
- This paper is based on work from the Global Research, Innovation, and Education on Assistive Technology (GREAT) Summit that was coordinated by WHO's Global Cooperation on Assistive Technology (GATE). The purpose of this paper is to describe the needs and opportunities embedded in the assistive product lifecycle as well as issues relating to the various stages of assistive product mobilization worldwide. The paper discusses assistive technology product terminology and the dangers of focusing on products outside the context and rolling out products without a plan. Additionally, the paper reviews concepts and issues around technology transfer, particularly in relation to meeting global needs and among countries with limited resources. Several opportunities are highlighted including technology advancement and the world nearing a state of readiness through a developing capacity of nations across the world to successfully adopt and support the assistive technology products and applications. The paper is optimistic about the future of assistive technology products reaching the people that can use it the most and the excitement across large and small nations in increasing their own capacities for implementing assistive technology. This is expressed as hope in future students as they innovate and in modern engineering that will enable assistive technology to pervade all corners of current and potential marketplaces. Importantly, the paper poses numerous topics where discussions are just superficially opened. The hope is that a set of sequels will follow to continue this critical dialog.Implications for RehabilitationSuccessful assistive technology product interventions are complex and include much more than the simple selection of the right product.Assistive technology product use is highly context sensitive in terms of an individual user's environment.The development of assistive technology products is tricky as it must be contextually sensitive to the development environment and market as well.As a field we have much to study and develop around assistive technology product interventions from a global perspective.
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