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| 2. |
- Alattar, AG, et al.
(författare)
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Gene editing of CD34+ progenitor cells from single blood donor waste bags to create cultured early erythroid cells for study of blood group knock-outs
- 2020
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Ingår i: Vox Sanguinis. - : Wiley. - 1423-0410 .- 0042-9007. ; 115:Suppl. s1, s. 363-363
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Konferensbidrag (refereegranskat)abstract
- Background: Many blood group antigens are carried by red cell surface proteins, thefunctions of which are not yet fully characterized or in some cases completelyunknown. By investigating red cells with naturally-occurring blood group variants,much has been learnt about the underlying molecules. However, interindividualvariation affecting other molecules than the one(s) of interest may confound orotherwise hamper such studies. As an alternative, a reductionistic approach whereonly a single factor differs between test and control cells significantly facilitatesinterpretation of functional studies. Using various siRNA, shRNA and various gene-editing tools blood group expression can be manipulated and useful modelsdeveloped. Applying the latter on primary hematopoietic stem and progenitor cells(HSPCs) can be challenging.Aims: We evaluated a protocol for gene editing of CD44 using a CRISPR/Cas9hybrid system on HSPCs isolated from blood donation leukocyte waste bags fromsingle donors to develop a model for study of blood group molecular function inerythropoiesis.Methods: Peripheral blood mononuclear cells (PBMCs) were from anonymizedleucocyte waste bags obtained after whole blood unit processing in the Reveosautomated blood component system. Cells were harvested following Lymphoprepgradient separation and CD34+HSPCs enriched and collected using magnetic beads.CD34+cells were cultured in 2-phase culture medium to generate erythroid cellsfrom HSPCs (Vidovic, Vox Sang 2017). For CRISPR/Cas9 gene editing, a short guideRNA (sgRNA) targeting CD44 was designed and cloned into the lentiCRISPR v2vector (Addgene plasmid #52961). A non-targeting sgRNA cloned into the vectorwas used as control. Lentivirus particles were produced in the human 293T cell lineas described previously (Galeev, Methods Mol Biol 2017). Equal number of CD34+cells were transduced 24 hours after collection using RetroNectin following theRetroNectin-Bound Virus (RBV) Infection Method according to manufacturer’sprotocol. Cells were transduced at a multiplicity of infection (MOI) of 10 with atarget transduction efficiency of 20–30%. Cells were cultured at 37°C, 5% CO2 for72 hours in phase I culture medium and then electroporated with Cas9 mRNA usingthe ECM 830 Electroporation System as described previously for cord blood-derivedCD34+cells (Backstrom, Exp Hematol 2019). GFP+CD44-edited cell frequencieswere monitored by flow cytometry at day 7 of the HSPC expansion phase and atday 14 of the erythroid expansion-differentiation phase using antibodies againsterythroid-specific cell surface markers GPA and Band3 in addition to CD49d toassess the erythroid development stage.Results: We tested the above protocol and observed that the frequencies of editedcells lacking CD44 expression within the GFP+population at day 7 of culture were10–25% while the edited frequencies were increased at day 14 of culture to 60–80%within the GFP+cells. Whilst this stage corresponds to erythroblasts, earlier or laterstages can be tested.Summary/Conclusions: The previously established hybrid system for CRISPR/Cas9gene editing in cord blood-derived CD34+HSPCs, which combines lentiviraldelivery of the sgRNA with transient delivery of Cas9 mRNA by electroporation, isalso applicable to primary human adult HSPCs from Reveos-processed single-donorwhole blood donation, resulting in a traceable high-yield gene-editing system tostudy blood group function and erythroid development
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| 3. |
- Lê, A D, et al.
(författare)
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Neurobiological processes in alcohol addiction.
- 2001
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Ingår i: Alcoholism, clinical and experimental research. - 0145-6008. ; 25:5 Suppl ISBRA
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Forskningsöversikt (refereegranskat)abstract
- This article represents the proceedings of a symposium at the ISBRA Meeting in Yokohama, Japan. The chairs were A. D. Lê and K. Kiianmaa. The presentations were (1) Alcohol reward and aversion, by C. L. Cunningham; (2) The role of sensitization of neuronal mechanisms in ethanol self-administration, by J. A. Engel, M. Ericson, and B. Söderpalm; (3) Alcohol self-administration in dependent animals: Neurobiological mechanisms, by G. F. Koob, A. J. Roberts, and F. Weiss; (4) Stress and relapse to alcohol, by A. D. Lê; (5) Alcohol-preferring AA and alcohol-avoiding ANA rats differ in locomotor activation induced by repeated morphine injections, by P. Hyytiä, S. Janhunen, J. Mikkola, P. Bäckström, and K. Kiianmaa; and (6) Initial sensitivity and acute functional tolerance to the hypnotic effects of ethanol in mice genetically selected for mild and severe ethanol withdrawal convulsions, by I. Ponomarev and J. C. Crabbe.
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| 4. |
- Qin, Yue, et al.
(författare)
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A multi-scale map of cell structure fusing protein images and interactions
- 2021
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 600:7889, s. 536-
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Tidskriftsartikel (refereegranskat)abstract
- The cell is a multi-scale structure with modular organization across at least four orders of magnitude(1). Two central approaches for mapping this structure-protein fluorescent imaging and protein biophysical association-each generate extensive datasets, but of distinct qualities and resolutions that are typically treated separately(2,3). Here we integrate immunofluorescence images in the Human Protein Atlas(4) with affinity purifications in BioPlex(5) to create a unified hierarchical map of human cell architecture. Integration is achieved by configuring each approach as a general measure of protein distance, then calibrating the two measures using machine learning. The map, known as the multi-scale integrated cell (MuSIC 1.0), resolves 69 subcellular systems, of which approximately half are to our knowledge undocumented. Accordingly, we perform 134 additional affinity purifications and validate subunit associations for the majority of systems. The map reveals a pre-ribosomal RNA processing assembly and accessory factors, which we show govern rRNA maturation, and functional roles for SRRM1 and FAM120C in chromatin and RPS3A in splicing. By integration across scales, MuSIC increases the resolution of imaging while giving protein interactions a spatial dimension, paving the way to incorporate diverse types of data in proteome-wide cell maps.
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| 5. |
- Bäckström, Disa
(författare)
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Exploring the diversity and evolution of giant viruses in deep sea sediments using genome-resolved metagenomics
- 2018
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Viruses are the most abundant biological entities on this planet, which is impressive considering that they are completely dependent on their hosts for reproduction. Recently the idea of what viruses are has changed dramatically, with the discovery of giant viruses that belong to the Nucleocytoplasmic Large DNA Viruses (NCLDV), such as Mimiviridae, Marseilleviridae, and the proposed families Pandoraviruses, and Pithoviruses. Not only are some of these viruses as large as bacteria in size, their genomes also exceed the size of some prokaryotic genomes. The evolutionary path to viral giganticism is not yet fully understood, and several opposing theories have been proposed. The more examples of giant viruses we have to study, the clearer the picture becomes. The rate of discovery, however, is limited by the low capacity of culturing. In an effort to contribute through culture-independent methods, I used genome-resolved metagenomics to retrieve genomes of 23 new members of the NCLDV from deep sea sediment samples that were taken near Loki’s Castle hydrothermal vent field. This method has previously been used to study uncultured Bacteria and Archaea, but few successful cases of metagenomic binning of NCLDV have been documented. New methods for refinement and quality control of the binned genomes were developed, combining reads profiling with differential coverage binning, and composition-based cleaning of potentially contaminating sequences. The binned genomes represent several novel clades of NCLDV, the most noteworthy ones distantly related to Pithoviruses and Marseilleviridae, and greatly expand their overall diversity. Phylogenetic analysis of their genome content supports the independent evolution of viral giganticism from smaller viruses. Continued use of metagenomics to explore the presence of NCLDV in environmental samples will lead to new insights into their diversity, evolution, and biology.
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| 9. |
- Kunze, J., et al.
(författare)
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Optical study of competition between ordering and metallicity in La(2-2x)Sr(1+2x)Mn(2)O(7)
- 2003
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Ingår i: Physical Review B Condensed Matter. - 0163-1829 .- 1095-3795. ; 67
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Tidskriftsartikel (refereegranskat)abstract
- We study by spectroscopic ellipsometry the optical in-plane anisotropies in La(2-2x)Sr(1+2x)Mn(2)O(7) with 0.32less than or equal toxless than or equal to0.40 above and below the metal to insulator (MI) transition. Spectral-weight changes in the optical conductivity occur at a cross-over temperature T(’)=280 K for all dopings. Local ordering of orbital and charge degrees of freedom sets in doping dependently at temperatures of 145 Kless than or equal toT(*)less than or equal to310 K. Below the MI transition we observe for all dopings except x=0.36 a vanishing of the charge ordering and an isotropic and metallic state at low frequencies, whereas the local orbital ordering persists. For x=0.36 we observe two different characteristic developments of the ordering processes, one being compatible with the parabolic doping dependence on T(*) established by the other doping levels and the second showing ordering at a temperature slightly above the MI transition. We argue that our observations are compatible with a phase separation scenario.
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| 10. |
- Maple-Grødem, Jodi, et al.
(författare)
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Lack of Association between GBA Mutations and Motor Complications in European and American Parkinson's Disease Cohorts
- 2021
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Ingår i: Journal of Parkinson's Disease. - : IOS Press. - 1877-7171 .- 1877-718X. ; 11:4, s. 1569-1578
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Tidskriftsartikel (refereegranskat)abstract
- Background: Motor complications are a consequence of the chronic dopaminergic treatment of Parkinson's disease (PD) and include levodopa-induced dyskinesia (LIDs) and motor fluctuations (MF). Currently, evidence is on lacking whether patients with GBA-associated PD differ in their risk of developing motor complications compared to the general PD population.Objective: To evaluate the association of GBA carrier status with the development of LIDS and MFs from early PD.Methods: Motor complications were recorded prospectively in 884 patients with PD from four longitudinal cohorts using part IV of the UPDRS or MDS-UPDRS. Subjects were followed for up to 11 years and the associations of GBA mutations with the development of motor complications were assessed using parametric accelerated failure time models.Results: In 439 patients from Europe, GBA mutations were detected in 53 (12.1%) patients and a total of 168 cases of LIDs and 258 cases of MF were observed. GBA carrier status was not associated with the time to develop LIDs (HR 0.78, 95%CI 0.47 to 1.26, p = 0.30) or MF (HR 1.19, 95%CI 0.84 to 1.70, p = 0.33). In the American cohorts, GBA mutations were detected in 36 (8.1%) patients and GBA carrier status was also not associated with the progression to LIDs (HR 1.08, 95%CI 0.55 to 2.14, p = 0.82) or MF (HR 1.22, 95%CI 0.74 to 2.04, p = 0.43).Conclusion: This study does not provide evidence that GBA-carrier status is associated with a higher risk of developing motor complications. Publication of studies with null results is vital to develop an accurate summary of the clinical features that impact patients with GBA-associated PD.
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