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- Andersson, Axel, et al.
(författare)
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ISTDECO : In Situ Transcriptomics Decoding by Deconvolution
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In Situ Transcriptomics (IST) is a set of image-based transcriptomics approaches that enables localisation of gene expression directly in tissue samples. IST techniques produce multiplexed image series in which fluorescent spots are either present or absent across imaging rounds and colour channels. A spot’spresence and absence form a type of barcoded pattern that labels a particular type of mRNA. Therefore, the expression of agene can be determined by localising the fluorescent spots and decode the barcode that they form. Existing IST algorithms usually do this in two separate steps: spot localisation and barcode decoding. Although these algorithms are efficient, they are limited by strictly separating the localisation and decoding steps. This limitation becomes apparent in regions with low signal-to-noise ratio or high spot densities. We argue that an improved gene expression decoding can be obtained by combining these two steps into a single algorithm. This allows for an efficient decoding that is less sensitive to noise and optical crowding. We present IST Decoding by Deconvolution (ISTDECO), a principled decoding approach combining spectral and spatial deconvolution into a single algorithm. We evaluate ISTDECOon simulated data, as well as on two real IST datasets, and compare with state-of-the-art. ISTDECO achieves state-of-the-art performance despite high spot densities and low signal-to-noise ratios. It is easily implemented and runs efficiently using a GPU.ISTDECO implementation, datasets and demos are available online at: github.com/axanderssonuu/istdeco
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- Elezagic, D., et al.
(författare)
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Antimicrobial peptides derived from the cartilage.-specific C-type Lectin Domain Family 3 Member A (CLEC3A) – potential in the prevention and treatment of septic arthritis
- 2019
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Ingår i: Osteoarthritis and Cartilage. - : Elsevier BV. - 1063-4584.
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To investigate the antimicrobial activity of peptides derived from C-type Lectin Domain Family 3 Member A (CLEC3A), shed light on the mechanism of antimicrobial activity and assess their potential application in prevention and treatment of septic arthritis. Design: We performed immunoblot to detect CLEC3A peptides in human cartilage extracts. To investigate their antimicrobial activity, we designed peptides and recombinantly expressed CLEC3A domains and used them to perform viable count assays using E.coli, P.aeruginosa and S.aureus. We investigated the mechanism of their antimicrobial activity by fluorescence and scanning electron microscopy, performed ELISA-style immunoassays and transmission electron microscopy to test for lipopolysaccharide binding and surface plasmon resonance to test for lipoteichoic acid (LTA) binding. We coated CLEC3A peptides on titanium, a commonly used prosthetic material, and performed fluorescence microscopy to quantify bacterial adhesion. Moreover, we assessed the peptides’ cytotoxicity against primary human chondrocytes using MTT cell viability assays. Results: CLEC3A fragments were detected in human cartilage extracts. Moreover, bacterial supernatants lead to fragmentation of recombinant and cartilage-derived CLEC3A. CLEC3A-derived peptides killed E.coli, P.aeruginosa and S.aureus, permeabilized bacterial membranes and bound lipopolysaccharide and LTA. Coating CLEC3A antimicrobial peptides (AMPs) on titanium lead to significantly reduced bacterial adhesion to the material. In addition, microbicidal concentrations of CLEC3A peptides in vitro displayed no direct cytotoxicity against primary human chondrocytes. Conclusions: We identify cartilage-specific AMPs originating from CLEC3A, resolve the mechanism of their antimicrobial activity and point to a novel approach in the prevention and treatment of septic arthritis using potent, non-toxic, AMPs.
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