| 1. |
- Afanasyeva, Elena A., et al.
(författare)
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Kalirin-RAC controls nucleokinetic migration in ADRN-type neuroblastoma
- 2021
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Ingår i: Life Science Alliance. - : Life Science Alliance, LLC. - 2575-1077. ; 4:5
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Tidskriftsartikel (refereegranskat)abstract
- The migrational propensity of neuroblastoma is affected by cell identity, but the mechanisms behind the divergence remain unknown. Using RNAi and time-lapse imaging, we show that ADRN-type NB cells exhibit RAC1- and kalirin-dependent nucleokinetic (NUC) migration that relies on several integral components of neuronal migration. Inhibition of NUC migration by RAC1 and kalirin-GEF1 inhibitors occurs without hampering cell proliferation and ADRN identity. Using three clinically relevant expression dichotomies, we reveal that most of up-regulated mRNAs in RAC1- and kalirin-GEF1-suppressed ADRN-type NB cells are associated with low-risk characteristics. The computational analysis shows that, in a context of overall gene set poverty, the upregulomes in RAC1- and kalirin-GEF1-suppressed ADRN-type cells are a batch of AU-rich element-containing mRNAs, which suggests a link between NUC migration and mRNA stability. Gene set enrichment analysis-based search for vulnerabilities reveals prospective weak points in RAC1- and kalirin-GEF1-suppressed ADRN-type NB cells, including activities of H3K27- and DNA methyltransferases. Altogether, these data support the introduction of NUC inhibitors into cancer treatment research.
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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Chapman, Henry N, et al.
(författare)
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Femtosecond X-ray protein nanocrystallography.
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 470:7332, s. 73-7
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Tidskriftsartikel (refereegranskat)abstract
- X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
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| 4. |
- Edlund, Lena, 1965-
(författare)
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Att fånga det flyktiga : Om existentiell mening och objektivitet
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This work attempts an answer to two questions. Firstly, is it possible to experience meaning when everything is transient? And secondly, in what way is objectivity possible when it comes to such phenomena as existential meaning? The questions originate from our insideperspective, and it is from what we have experienced ourselves that we try to make intelligible existential meaning. We are to a great extent part of the context in which we live. Our ability to contemplate our situation and our own contemplation is taking place in interplay with others. To make room for the small things meaningful in life, the expression existential meaning is used. In this expression both the meaningless and the meaningful are included, since both are needed for our understanding of meaning. Without the Other and that which is different, the individual person’s formation of existential meaning becomes just more of the same, it becomes an enclosure in the present. The encounter with the Other makes room for that which is different to break through.Objectivity is possible when it comes to existential meaning, if one views objectivity as a process between people. It is performed in conversation. Those who converse, refer to their bodily experiences of the Time that remains and help each other, using language as the tool, to formulate their experiences. They compare each others’ manifestations of existential meaning,and with the help of language they go further in the formation of what is meaningless and meaningful. Their conversations imply a normative presupposition that they can justify the claims that they make. Because it is actually not possible to make intelligible existential meaning in words other than by doing it as a mix of descriptions of that which is manifesting itself and linguistic rewritings in the form of stories. This expression of objectivity has a normative aspect, namely in relation to the possibility that we can be wrong. Therefore, we need each other in the act of judging, and together we are guided by the fact that it later on can emerge things that show that our judgment has not been fully correct.
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| 5. |
- Elfaitouri, Amal, et al.
(författare)
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Epitopes of Microbial and Human Heat Shock Protein 60 and Their Recognition in Myalgic Encephalomyelitis
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:11, s. 55-
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Tidskriftsartikel (refereegranskat)abstract
- Myalgic encephalomyelitis (ME, also called Chronic Fatigue Syndrome), a common disease with chronic fatigability, cognitive dysfunction and myalgia of unknown etiology, often starts with an infection. The chaperonin human heat shock protein 60 (HSP60) occurs in mitochondria and in bacteria, is highly conserved, antigenic and a major autoantigen. The anti-HSP60 humoral (IgG and IgM) immune response was studied in 69 ME patients and 76 blood donors (BD) (the Training set) with recombinant human and E coli HSP60, and 136 30-mer overlapping and targeted peptides from HSP60 of humans, Chlamydia, Mycoplasma and 26 other species in a multiplex suspension array. Peptides from HSP60 helix I had a chaperonin-like activity, but these and other HSP60 peptides also bound IgG and IgM with an ME preference, theoretically indicating a competition between HSP60 function and antibody binding. A HSP60-based panel of 25 antigens was selected. When evaluated with 61 other ME and 399 non-ME samples (331 BD, 20 Multiple Sclerosis and 48 Systemic Lupus Erythematosus patients), a peptide from Chlamydia pneumoniae HSP60 detected IgM in 15 of 61 (24%) of ME, and in 1 of 399 non-ME at a high cutoff (p<0.0001). IgM to specific cross-reactive epitopes of human and microbial HSP60 occurs in a subset of ME, compatible with infection-induced autoimmunity.
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| 6. |
- Grenholm, Carl-Henric, et al.
(författare)
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Kristen feminism : Gudsbild och filosofisk bakgrund
- 1982
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- I denna bok behandlas den kritik som sådana feministteologer som Mary Daly och Sheila Collins riktat mot traditionella kristna gudssymboler och gudsföreställningar. Den alternativa gudsbild som framträder hos dessa feminististiska teologer analyseras och kritiseras. Boken klargör den kristna feminismens filosofiska bakgrund och förutsättning och påvisar främst dess beroende av Paul Tillichs ontologi och symbolteori. Dess tes är att den som rationellt önskar ta ställning till nutida feministteologi bör kritiskt granska även dessa dess filosofiska förutsättningar.
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| 7. |
- Herrmann, Björn, et al.
(författare)
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Comparison of a duplex quantitative real-time PCR assay and the COBAS Amplicor CMV Monitor test for detection of cytomegalovirus
- 2004
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Ingår i: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 42:5, s. 1909-14
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Tidskriftsartikel (refereegranskat)abstract
- A duplex quantitative real-time PCR (qPCR) assay was designed to detect both the polymerase gene (pol) and the glycoprotein gene (gB) of cytomegalovirus (CMV). The detection limit of the qPCR was determined to be 1 to 3 copies/reaction and the linear measure interval was 10(3) to 10(8) copies/ml. The qPCR system was compared to the COBAS Amplicor CMV Monitor test (COBAS) by an analysis of 138 plasma samples. Both systems detected CMV in 71 cases and had negative results for 33 samples. In addition, 34 samples were positive by qPCR and negative by the COBAS assay, but in no case was the COBAS result positive and the qPCR result negative. Thus, qPCR detected 48% more positive cases than the COBAS method. For samples with > or = 10(5) copies/ml by qPCR, a saturation effect was seen in the COBAS assay and quantification required dilution. Copy numbers for pol and gB by qPCR generally agreed. However, the reproducibility of qPCR assays and the need for an international standard are discussed. Discrepant copy numbers for pol and gB by qPCR were found for samples from two patients, and sequence analysis revealed that the corresponding CMV strains were mismatched at four nucleotide positions compared with the gB fragment primer sequences. In conclusion, a duplex qPCR assay in a real-time format facilitates quantitative measurements and minimizes the risk of false-negative results.
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| 8. |
- Herrmann, Björn, et al.
(författare)
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Differentiation and Phylogenetic Relationships in Mycobacterium spp with Special Reference to the RNase P RNA Gene rnpB
- 2014
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Ingår i: Current Microbiology. - : Springer Science and Business Media LLC. - 0343-8651 .- 1432-0991. ; 69:5, s. 634-639
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Tidskriftsartikel (refereegranskat)abstract
- The rnpB gene encodes for the RNA subunit of the catalytic ribonuclease RNase P and is present in all bacteria and has both conserved and highly variable sequence regions. Determination of rnpB in 35 Mycobacterium spp. showed species specific sequences for all species except the Mycobacterium tuberculosis complex (four species). High sequence variation was seen in the P3, P15 and P19 regions of suggested secondary structures of the corresponding RNase P RNA molecules. Phylogenetic analysis showed that rnpB gave similar tree topologies as 16S rRNA and hsp65 genes. A combined analysis of the three genes increased the number of nodes with significant support from 10 to 19. The results indicate that rnpB is useful for phylogenetic studies and is a possible target for identification and detection of Mycobacterium spp.
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| 9. |
- Herrmann, Maria, et al.
(författare)
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40Ar/39Ar age evidence for an impact-generated hydrothermal system in the Devonian Siljan crater, Sweden
- 2021
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Ingår i: Large Meteorite Impacts and Planetary Evolution VI. - : Geological Society of America. - 0072-1077. - 9780813795508 ; 550, s. 569-583
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Bokkapitel (refereegranskat)abstract
- Crater-forming events are generally followed by the development of hydrothermal systems due to the rapid heating of the target rock. Such hydrothermal systems are a feature of nearly all large terrestrial impact structures. For the Siljan impact structure in Sweden, there is evidence for such a fossil hydrothermal system, possibly triggered by the impact event ca. 380 Ma. To investigate the thermal regime of the near-surface hydrothermal activity of the Siljan crater, biotite and amphibole grains extracted from samples collected in a transect across the high-pressure regime recorded by the central uplift, as well as from distal localities outside the central uplift of the crater, were dated using the 40Ar/39Ar laser step-heating technique. Our results show that biotite from inside the central uplift, which was strongly altered to chlorite by low-temperature (200-340°C) hydrothermal reactions, yields strongly disturbed age spectra. The first and second (low laser power) step ages range from ca. 1300 to 190 Ma. In contrast, biotite from outside the central uplift and amphibole, irrespective of location inside or outside of the central uplift, are much less altered, which is reflected in less disturbed, near-flat age spectra. This result indicates that the hydrothermal temperatures inside the central uplift were >200°C, sufficient to disturb the K-Ar system of biotite during its chloritization, but too low to affect the amphibole (closure temperature of 480-580°C). In contrast, the temperature of the hydrothermal system outside of the central uplift was <200°C, as no significant reset of the K-Ar system can be observed in either biotite or amphibole. Our results are consistent with estimated trapping temperatures from fluid inclusion studies, which show a decrease from 327-342°C within the central uplift to 40-225°C toward outside the central uplift. We conclude that the near-surface hydrothermal system in the Siljan impact structure was an impact-triggered system. This system was strongly active, with its highest temperature inside the central uplift and decreasing rapidly toward the outlying part of the crater.
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| 10. |
- Herrmann, Maria, et al.
(författare)
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The effect of low-temperature annealing on discordance of U–Pb zircon ages
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Discordant U–Pb data of zircon are commonly attributed to Pb loss from domains with variable degree of radiation damage that resulted from α-decay of U and Th, which often complicates the correct age interpretation of the sample. Here we present U–Pb zircon data from 23 samples of ca. 1.7–1.9 Ga granitoid rocks in and around the Siljan impact structure in central Sweden. Our results show that zircon from rocks within the structure that form an uplifted central plateau lost significantly less radiogenic Pb compared to zircon grains in rocks outside the plateau. We hypothesize that zircon in rocks within the central plateau remained crystalline through continuous annealing of crystal structure damages induced from decay of U and Th until uplifted to the surface by the impact event ca. 380 Ma ago. In contrast, zircon grains distal to the impact have accumulated radiation damage at shallow and cool conditions since at least 1.26 Ga, making them vulnerable to fluid-induced Pb-loss. Our data are consistent with studies on alpha recoil and fission tracks, showing that annealing in zircon occurs at temperatures as low as 200–250 °C. Zircon grains from these samples are texturally simple, i.e., neither xenocrysts nor metamorphic overgrowths have been observed. Therefore, the lower intercepts obtained from regression of variably discordant zircon data are more likely recording the age of fluid-assisted Pb-loss from radiation-damaged zircon at shallow levels rather than linked to regional magmatic or tectonic events.
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