| 1. |
- Bylund, Göran O, et al.
(författare)
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Alterations in the β flap and β' dock domains of the RNA polymerase abolish NusA-mediated feedback regulation of the metY-nusA-infB operon
- 2011
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Ingår i: Journal of Bacteriology. - 0021-9193 .- 1098-5530. ; 193:16, s. 4113-4122
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Tidskriftsartikel (refereegranskat)abstract
- The RimM protein in Escherichia coli is important for the in vivo maturation of 30S ribosomal subunits and a ΔrimM mutant grows poorly due to assembly and translational defects. These deficiencies are suppressed partially by mutations that increase the synthesis of another assembly protein, RbfA, encoded by the metY-nusA-infB operon. Among these suppressors are mutations in nusA that impair the NusA-mediated negative-feedback regulation at internal intrinsic transcriptional terminators of the metY-nusA-infB operon. We describe here the isolation of two new mutations, one in rpoB and one in rpoC (encoding the β and β' subunits of the RNA polymerase, respectively), that increase the synthesis of RbfA by preventing NusA from stimulating termination at the internal intrinsic transcriptional terminators of the metY-nusA-infB operon. The rpoB2063 mutation changed the isoleucine in position 905 of the β flap-tip helix to a serine, while the rpoC2064 mutation duplicated positions 415 to 416 (valine-isoleucine) at the base of the β' dock domain. These findings support previously published in vitro results, which have suggested that the β flap-tip helix and β' dock domain at either side of the RNA exit tunnel mediate the binding to NusA during transcriptional pausing and termination.
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| 2. |
- Fei, Y Y, et al.
(författare)
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Use of real-time, label-free analysis in revealing low-affinity binding to blood group antigens by Helicobacter pylori
- 2011
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 83:16, s. 6336-6341
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Tidskriftsartikel (refereegranskat)abstract
- Infectious diseases are often initiated by microbial adherence that is mediated by the binding of attachment molecules, termed adhesins, to cell surface receptors on host cells. We present an experimental system, oblique-incidence reflectivity difference (OI-RD) microscopy, which allows the detection of novel, low-affinity microbial attachment mechanisms that may be essential for infectious processes. OI-RD microscopy was used to analyze direct binding of the oncopathogen, Helicobacter pylori ( H. pylori ) to immobilized glycoconjugates in real time with no need for labeling tags. The results suggest the presence of additional Lewis b blood group antigen (Le(b)) binding adhesins that have not been detected previously. OI-RD microscopy also confirmed the high-affinity binding of H. pylori outer-membrane protein BabA to Le(b). The OI-RD microscopy method is broadly applicable to real-time characterization of intact microbial binding to host receptors and offers new strategies to elucidate the molecular interactions of infectious agents with human host cells.
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| 3. |
- Jin, Chunsheng, et al.
(författare)
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Human Synovial Lubricin Expresses Sialyl Lewis x Determinant and Has L-selectin Ligand Activity
- 2012
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 287:43, s. 35922-35933
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Tidskriftsartikel (refereegranskat)abstract
- Lubricin (or proteoglycan 4 (PRG4)) is an abundant mucin-like glycoprotein in synovial fluid (SF) and a major component responsible for joint lubrication. In this study, it was shown that O-linked core 2 oligosaccharides (Gal beta 1-3(GlcNAc beta 1-6)GalNAc alpha 1-Thr/Ser) on lubricin isolated from rheumatoid arthritis SF contained both sulfate and fucose residues, and SF lubricin was capable of binding to recombinant L-selectin in a glycosylation-dependent manner. Using resting human polymorphonuclear granulocytes (PMN) from peripheral blood, confocal microscopy showed that lubricin coated circulating PMN and that it partly co-localized with L-selectin expressed by these cells. In agreement with this, activation-induced shedding of L-selectin also mediated decreased lubricin binding to PMN. It was also found that PMN recruited to inflamed synovial area and fluid in rheumatoid arthritis patients kept a coat of lubricin. These observations suggest that lubricin is able to bind to PMN via an L-selectin-dependent and -independent manner and may play a role in PMN-mediated inflammation.
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| 4. |
- Sohlenius-Sternbeck, Anna-Karin, et al.
(författare)
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Practical use of the regression offset approach for the prediction of in vivo intrinsic clearance from hepatocytes
- 2012
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Ingår i: Xenobiotica. - : Informa UK Limited. - 0049-8254 .- 1366-5928. ; 42:9, s. 841-853
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Tidskriftsartikel (refereegranskat)abstract
- 1. Systematic under-prediction of clearance is frequently associated with in vitro kinetic data when extrapolated using physiological scaling factors, appropriate binding parameters and the well-stirred model. The present study describes a method of removing this systematic bias through application of empirical correction factors derived from regression analyses applied to the in vitro and in vivo data for a defined set of reference compounds.2. Linear regression lines were established with in vivo intrinsic clearance (CLint), derived from in vivo clearance data and scaled in vitro intrinsic clearance from isolated hepatocyte incubations. The scaled CLint was empirically corrected to a predicted in vivo CLint using the slope and intercept from a uniform weighted linear regression applied to the in vitro to in vivo extrapolation.3. Cross validation of human data demonstrated that 66% of the reference compounds had a predicted in vivo CLint within two-fold of the observed value. The average absolute fold error (AAFE) for the in vivo CLint predictions was 1.90. For rat, 54% of the compounds had a predicted value within two-fold of the observed and the AAFE was 1.98.4. Three AstraZeneca projects are used to exemplify how a two-sided prediction interval, applied to the rat regression corrected reference data, can form the basis for assessing the likelihood that, for a given chemical series, the in vitro kinetic data is predictive of in vivo clearance and is therefore appropriate to guide optimisation of compound metabolic stability.
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| 5. |
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| 6. |
- Tenow, Olle, et al.
(författare)
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Geometrid outbreak waves travel across Europe
- 2013
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Ingår i: Journal of Animal Ecology. - : Wiley. - 0021-8790 .- 1365-2656. ; 82:1, s. 84-95
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Tidskriftsartikel (refereegranskat)abstract
- We show that the population ecology of the 9- to 10-year cyclic, broadleaf-defoliating winter moth (Operophtera brumata) and other early-season geometrids cannot be fully understood on a local scale unless population behaviour is known on a European scale. Qualitative and quantitative data on O. brumata outbreaks were obtained from published sources and previously unpublished material provided by authors of this article. Data cover six decades from the 1950s to the first decade of twenty-first century and most European countries, giving new information fundamental for the understanding of the population ecology of O. brumata. Analyses on epicentral, regional and continental scales show that in each decade, a wave of O. brumata outbreaks travelled across Europe. On average, the waves moved unidirectionally ESE-WNW, that is, toward the Scandes and the Atlantic. When one wave reached the Atlantic coast after 9-10 years, the next one started in East Europe to travel the same c. 3000 km distance. The average wave speed and wavelength was 330 km year-1 and 3135 km, respectively, the high speed being incongruous with sedentary geometrid populations. A mapping of the wave of the 1990s revealed that this wave travelled in a straight E-W direction. It therefore passed the Scandes diagonally first in the north on its way westward. Within the frame of the Scandes, this caused the illusion that the wave moved N-S. In analogy, outbreaks described previously as moving S-N or occurring contemporaneously along the Scandes were probably the result of continental-scale waves meeting the Scandes obliquely from the south or in parallel. In the steppe zone of eastern-most and south-east Europe, outbreaks of the winter moth did not participate in the waves. Here, broadleaved stands are small and widely separated. This makes the zone hostile to short-distance dispersal between O. brumata subpopulations and prevents synchronization within meta-populations. We hypothesize that hostile boundary models, involving reciprocal host-herbivore-enemy reactions at the transition between the steppe and the broadleaved forest zones, offer the best explanation to the origin of outbreak waves. These results have theoretical and practical implications and indicate that multidisciplinary, continentally coordinated studies are essential for an understanding of the spatio-temporal behaviour of cyclic animal populations.
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| 7. |
- Yousefzadeh, Matthew J, et al.
(författare)
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Mechanism of suppression of chromosomal instability by DNA polymerase POLQ
- 2014
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Ingår i: PLOS Genetics. - : Public library science. - 1553-7390 .- 1553-7404. ; 10:10, s. e1004654-
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Tidskriftsartikel (refereegranskat)abstract
- Although a defect in the DNA polymerase POLQ leads to ionizing radiation sensitivity in mammalian cells, the relevant enzymatic pathway has not been identified. Here we define the specific mechanism by which POLQ restricts harmful DNA instability. Our experiments show that Polq-null murine cells are selectively hypersensitive to DNA strand breaking agents, and that damage resistance requires the DNA polymerase activity of POLQ. Using a DNA break end joining assay in cells, we monitored repair of DNA ends with long 3' single-stranded overhangs. End joining events retaining much of the overhang were dependent on POLQ, and independent of Ku70. To analyze the repair function in more detail, we examined immunoglobulin class switch joining between DNA segments in antibody genes. POLQ participates in end joining of a DNA break during immunoglobulin class-switching, producing insertions of base pairs at the joins with homology to IgH switch-region sequences. Biochemical experiments with purified human POLQ protein revealed the mechanism generating the insertions during DNA end joining, relying on the unique ability of POLQ to extend DNA from minimally paired primers. DNA breaks at the IgH locus can sometimes join with breaks in Myc, creating a chromosome translocation. We found a marked increase in Myc/IgH translocations in Polq-defective mice, showing that POLQ suppresses genomic instability and genome rearrangements originating at DNA double-strand breaks. This work clearly defines a role and mechanism for mammalian POLQ in an alternative end joining pathway that suppresses the formation of chromosomal translocations. Our findings depart from the prevailing view that alternative end joining processes are generically translocation-prone.
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