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  • 151. Ban, Liping
    et al.
    Ahmed, Elham
    Ninkovic, Velemir
    Delp, Gabriele
    Södertörn University, School of Life Sciences.
    Glinwood, Robert
    Infection with an insect virus affects olfactory behaviour and interactions with host plant and natural enemies in an aphid2008In: Entomologia Experimentalis et Applicata, ISSN 0013-8703, E-ISSN 1570-7458, Vol. 127, no 2, p. 108-117Article in journal (Refereed)
    Abstract [en]

    Aphid ecology and population dynamics are affected by a series of factors including behavioural responses to ecologically relevant chemical cues, capacity for population growth, and interactions with host plants and natural enemies. Using the aphid Rhopalosiphum padi (L.) (Homoptera: Aphididae), we showed that these factors were affected by infection with Rhopalosiphum padi virus (RhPV). Uninfected aphids were attracted to odour of uninfected aphids on the host plant, an aggregation mechanism. However, infected aphids were not attracted, and neither infected nor uninfected aphids were attracted to infected aphids on the plant. Infected aphids did not respond to methyl salicylate, a cue denoting host suitability. Infected aphids were more behaviourally sensitive to aphid alarm pheromone, and left the host plant more readily in response to it. RhPV reduced the lifespan and population growth rate of the aphid. The predacious ladybird, Coccinella septempunctata (L.) (Coleoptera: Coccinellidae), consumed more infected aphids than uninfected aphids in a 24-h period, and the aphid parasitoid Aphidius ervi Haliday (Hymenoptera: Aphidiidae) attacked more infected than uninfected aphids. However, the proportion of mummies formed was lower with infected aphids. The results represent further evidence that associated organisms can affect the behaviour and ecology of their aphid hosts.

  • 152.
    Banhart, Simon
    Södertörn University, School of Historical and Contemporary Studies, Archaeology.
    Varför används pollenanalys?: En studie av hur pollenanalys tillämpas i arkeologiska rapporter2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Why is pollen analysis used?

    This thesis has critically reviewed and examined archaeologist’s view and usage of pollen analysis, or palynology. Two research questions have been used and they are both directed towards archaeology reports and wants, together with the purpose, study how archaeologist have been using pollen analysis. In this thesis nine archaeology reports have been studied and analysed, and they have been compared with what archaeology literature have to say about pollen analysists abilities and limitations.

    The results presented in this thesis show that archaeologists are aware of how pollen analysis function, as well as the analysis methods abilities and limitations. Exceptions exists, but for the most parts archaeologists use pollen analysis for similar purposes namely, to examine vegetation history or to landscaping prehistoric mapping. In the exceptions, pollen analysis has shown to be a difficult method. But indications occur that pollen analysis, as a study method, can be used in more research questions than only vegetation history and landscape mapping.

  • 153. Bao, W J
    et al.
    Thullberg, M
    Zhang, H Q
    Onischenko, A
    Strömblad, Staffan
    Södertörn University, Avdelning Naturvetenskap.
    Cell attachment to the extracellular matrix induces proteasomal degradation of p21(CIP1) via Cdc42/Rac1 signaling2002In: Molecular and Cellular Biology, ISSN 0270-7306, E-ISSN 1098-5549, Vol. 22, no 13, p. 4587-4597Article in journal (Refereed)
    Abstract [en]

    The cyclin-dependent kinase 2 (Cdk2) inhibitors p21(CIP1) and p27(KIP1) are negatively regulated by anchorage during cell proliferation, but it is unclear how integrin signaling may affect these Cdk2 inhibitors. Here, we demonstrate that integrin ligation led to rapid reduction of p21(CIp1) and p27(KIP1) protein levels in three distinct cell types upon attachment to various extracellular matrix (ECM) proteins, including fibronectin (FN), or to immobilized agonistic anti-integrin monoclonal antibodies. Cell attachment to FN did not rapidly influence p21(CIp1) mRNA levels, while the protein stability of p21(CIp1) was decreased. Importantly, the down-regulation of p21(CIP1) and p27(KIP1) was completely blocked by three distinct proteasome inhibitors, demonstrating that integrin ligation induced proteasomal degradation of these Cdk2 inhibitors. Interestingly, ECM-induced proteasomal proteolysis of a ubiquitination-deficient p21(CIP1) mutant (p21K6R) also occurred, showing that the proteasomal degradation of p21(CIP1) was ubiquitin independent. Concomitant with our finding that the small GTPases Cdc42 and Rac1 were activated by attachment to FN, constitutively active (ca) Cdc42 and ca Rac1 promoted down-regulation of p21(CIP1). However, dominant negative (dn) Cdc42 and do Rac1 mutants blocked the anchorage-induced degradation of p21(CIP1), suggesting that an integrin-induced Cdc42/Rac1 signaling pathway activates proteasomal degradation of p21(CIP1). Our results indicate that integrin-regulated proteasomal proteolysis might contribute to anchorage-dependent cell cycle control.

  • 154.
    Barot, Camille
    et al.
    N Carolina State Univ, Dept Comp Sci, Raleigh, NC 27695 USA..
    Buro, Michael
    Univ Alberta, Dept Comp Sci, Edmonton, AB, Canada..
    Cook, Michael
    Univ London, Goldsmiths, London WC1E 7HU, England..
    Eladhari, Mirjam
    Stockholm Univiversity / University of Malta, Msida, Malta.
    Johansson, Magnus
    Uppsala universitet.
    Li, Boyang
    Disney Res, Pittsburgh, PA USA..
    Liapis, Antonios
    Univ Malta, Inst Digital Games, Msida, Malta..
    McCoy, Josh
    Amer Univ, Dept Comp, Washington, DC 20016 USA..
    Ontanon, Santiago
    Drexel Univ, Dept Comp Sci, Philadelphia, PA 19104 USA..
    Rowe, Jonathan
    N Carolina State Univ, Dept Comp Sci, Raleigh, NC 27695 USA..
    Tomai, Emmett
    Univ Texas Rio Grande Valley, Dept Comp Sci, Brownsville, TX USA..
    Verhagen, Harko
    Stockholm University.
    Zook, Alexander
    Georgia Inst Technol, Sch Interact Comp, Atlanta, GA 30332 USA..
    The AIIDE 2015 Workshop Program2016In: The AI Magazine, ISSN 0738-4602, Vol. 37, no 2, p. 91-94Article in journal (Refereed)
    Abstract [en]

    The workshop program at the 11th Annual AAAI Conference on Artificial Intelligence and Interactive Digital Entertainment was held November 14-15, 2015, at the University of California, Santa Cruz, USA. The program included four workshops (one of which was a joint workshop): Artificial Intelligence in Adversarial Real-Time Games, Experimental AI in Games, Intelligent Narrative Technologies and Social Believability in Games, and Player Modeling. This article contains the reports of three of the four workshops.

  • 155.
    Bartish, Galyna
    Södertörn University, School of Life Sciences. Stockholms universitet, Wenner-Grens institut.
    Elongation factor 2: A key component of the translation machinery in eukaryotes: Properties of yeast elongation factor 2 studied in vivo2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Synthesis of proteins is performed by the ribosome, a large ribonucleoprotein complex. Apart from the ribosome, numerous protein factors participate in this process. Elongation factor 2 (eEF2) is one of these factors. eEF2 is an essential protein with a mol. mass of about 100 kDa. The amino acid sequence of eEF2 is highly conserved in different organisms. eEF2 from S. cerevisiae contains 842 amino acids. The role of eEF2 in protein synthesis is to participate in the translocation of tRNAs from the A- and P-sites on the ribosome to the P- and E-sites. This movement of tRNAs is accompanied by a simultaneous movement of mRNA by one codon. eEF2 consists of six domains referred to as domains G, G′ and II-V, belongs to the G-protein super-family and possesses all structural motifs characterizing proteins in this family. eEF2 binds to the ribosome in complex with GTP. After GTP hydrolysis and translocation, it leaves the ribosome bound to GDP. The rate of protein synthesis in the cell can be regulated by phosphorylation of eEF2. Phosphorylation occurs on two threonine residues, situated in the G domain of the factor. Phosphorylation of eEF2 is catalysed by Rck2-kinase in yeast which is activated in response to osmotic stress. Despite the high degree of conservation of the threonine residues, they are not essential for yeast cell under normal growth conditions. However, under mild osmotic stress the growth rate of the cells lacking threonine residues was decreased. Region where threonine residues are located, called Switch I. Cryo-EM reconstruction shows that this region adopts ordered conformation when the eEF2•GTP complex is bound to the ribosome but became structurally disordered upon GTP hydrolysis. Mutagenesis of individual amino acids in Switch I resulted in both functional and non-functional eEF2 depending on the site of mutation and the substituting amino acid. Both functional and non-functional Switch I mutants were able to bind to the ribosome, indicating that mutations did not abolish the capacity of the factor to bind GTP. Yeast eEF2 with Switch I region from E. coli was able to substitute the wild type protein in vivo, though the growth rate of these cells was severely impaired. The eEF2-dependent GTP hydrolysis can be activated by ribosome from heterologous sources as seen in vitro. However, eEF2 from A. thaliana, D. melanogaster and S. solfataricus could not substi-tute yeast eEF2 in vivo. This may indicate additional roles of eEF2 in the yeast cell, apart from translocation itself.

  • 156.
    Bartish, Galyna I
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Jeppsson, N
    Bartish, I V
    Nybom, H
    Assessment of genetic diversity using RAPD analysis in a germplasm collection of sea buckthorn2000In: AGRICULTURAL AND FOOD SCIENCE IN FINLAND, ISSN 1239-0992, Vol. 9, no 4, p. 279-289Article in journal (Refereed)
    Abstract [en]

    Random amplified polymorphic DNA (RAPD) markers were used to characterize a part of a sea buckthorn gene bank collected for plant breeding purposes. Molecular markers were generated in 55 cultivars and accessions, representing five subspecies of Hippophae rhamnoides L. and intraspecific hybrids between different subspecies. Sixty-three markers were used to generate a Dice's similarity coefficient matrix of pairwise comparisons between individual RAPD profiles. Cluster (UPGMA) and principal co-ordinate analyses, based on this matrix, revealed clustering of plants into groups which generally correspond to their taxonomic classification or geographic origin. The analysis of molecular variance (AMOVA) was found useful for estimating components of genetic variation between and within taxonomic and geographic groups of accessions and cultivars. Whereas both alternatives for grouping the material (taxonomic or geographic origin) resulted in significant between-group variation, the major part of molecular variance (approximately 75%) was still attributed to variation within groups. We conclude that the RAPD analysis is useful for clarification of taxonomic and geographic origin of accessions and cultivars of sea buckthorn.

  • 157.
    Bartish, Galyna
    et al.
    Södertörn University, School of Life Sciences. Stockholm University.
    Moradi, Hossein
    Södertörn University, School of Life Sciences. Stockholm University.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    Amino acids Thr56 and Thr58 are not essential for elongation factor 2 function in yeast2007In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 274, no 20, p. 5285-5297Article in journal (Refereed)
    Abstract [en]

    Yeast elongation factor 2 is an essential protein that contains two highly conserved threonine residues, T56 and T58, that could potentially be phosphorylated by the Rck2 kinase in response to environmental stress. The importance of residues T56 and T58 for elongation factor 2 function in yeast was studied using site directed mutagenesis and functional complementation. Mutations T56D, T56G, T56K, T56N and T56V resulted in nonfunctional elongation factor 2 whereas mutated factor carrying point mutations T56M, T56C, T56S, T58S and T58V was functional. Expression of mutants T56C, T56S and T58S was associated with reduced growth rate. The double mutants T56M/T58W and T56M/T58V were also functional but the latter mutant caused increased cell death and considerably reduced growth rate. The results suggest that the physiological role of T56 and T58 as phosphorylation targets is of little importance in yeast under standard growth conditions. Yeast cells expressing mutants T56C and T56S were less able to cope with environmental stress induced by increased growth temperatures. Similarly, cells expressing mutants T56M and T56M/T58W were less capable of adapting to increased osmolarity whereas cells expressing mutant T58V behaved normally. All mutants tested were retained their ability to bind to ribosomes in vivo. However, mutants T56D, T56G and T56K were under-represented on the ribosome, suggesting that these nonfunctional forms of elongation factor 2 were less capable of competing with wild-type elongation factor 2 in ribosome binding. The presence of nonfunctional but ribosome binding forms of elongation factor 2 did not affect the growth rate of yeast cells also expressing wild-type elongation factor 2.

  • 158.
    Bartish, Galyna
    et al.
    Södertörn University, School of Life Sciences. Stockholm University.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    Importance of individual amino acids in the Switch I region in eEF2 studied by functional complementation in S. cerevisiae2008In: Biochimie, ISSN 0300-9084, E-ISSN 1638-6183, Vol. 90, no 5, p. 736-748Article in journal (Refereed)
    Abstract [en]

    Elongation factor 2 (eEF2) is a member of the G-protein super family. G-proteins undergo conformational changes associated with binding of the guanosine nucleotide and hydrolysis of the bound GTP. These structural rearrangements affects the Switch I region (also known as the Effector loop). We have studied the role of individual amino acids in the Switch I region (amino acids 25-73) of S. cerevisiae eEF2 using functional complementation in yeast. 21 point mutations in the Switch I region were created by site-directed mutagenesis. Mutants K49R, E52Q, A53G, F55Y, K60R, Q63A, T68S, 169M and A73G were functional while mutants R54H, F55N, D57A, D57E, D57S, R59K, R59M, Q63E, R65A, R65N, T68A and T68M were inactive. Expression of mutants K49R, A53G, Q63A, 169M and A73G was associated with markedly decreased growth rates and yeast cells expressing mutants A53G and 169M became temperature sensitive. The functional capacity of eEF2 in which the major part Switch I (amino acids T56 to 169) was converted into the homologous sequence found in EF-G from E. coli was also studied. This protein chimera could functionally replace yeast eEF2 in vivo. Yeast cells expressing this mutant grew extremely slowly, showed increased cell death and became temperature sensitive. The ability of the mutant to replace authentic eEF2 in vivo indicates that the structural rearrangement of Switch I necessary for eEF2 function is similar in eukaryotes and bacteria. The effect of two point mutations in the P-loop was also studied. Mutant A25G but not A25V could functionally replace yeast eEF2 even if cells expressing the mutant grew slowly. The A25G mutation converted the consensus sequences AXXXXGK[T/S] in eEF2 to the corresponding motif GXXXXGK[T/S] found in all other G-proteins, suggesting that the alanine found in the P-loop of peptidyltranslocases are not essential for function.

  • 159.
    Bartish, Galyna
    et al.
    Stockholms universitet.
    Nygård, Odd
    Södertörn University, School of Life Sciences.
    The functional importance of the N- and C-terminal regions in elongation factor 2 from S. cerevisiaeManuscript (preprint) (Other academic)
  • 160.
    Bathmann, Ulrich
    et al.
    Leibniz-Institute for Baltic Sea Research, Warnemünde, Germany.
    Schubert, Hendrik
    University of Rostock, Rostock, Germany.
    Andrén, Elinor
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Tuomi, Laura
    Finnish Meteorological Institute, Helsinki, Finland.
    Radziejewska, Teresa
    University of Szczecin, Szczecin, Poland.
    Kulinski, Karol
    Institute of Oceanology of the Polish Academy of Sciences, Sopot, Poland.
    Chubarenko, Irina
    Shirshov Institute of Oceanology of the Russian Academy of Sciences, Moscow, Russia.
    Editorial: Living Along Gradients: Past, Present, Future2020In: Frontiers in Marine Science, E-ISSN 2296-7745, Vol. 6, article id 801Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea is a geologically and evolutionarily young part of the coastal ocean that experienced, in its past, several severe environmental changes. In its present state, the Baltic Sea is characterized by both horizontal and vertical gradients of environmental conditions. As a huge estuary, it shows a west to east/south to north surface salinity gradient from 24 in Kattegat to nearly freshwater in the Bothnian Bay. The vertical salinity and oxygen gradients result in stratification which causes hypoxic and sulfidic anoxic conditions in deep basins. These gradient systems are impacted by natural and anthropogenic changes due to physico-chemical driving forces, varying over time and space. Gradient environments produce an imprint on both the structure and function of the biological systems and influence biogeochemical cycling. Besides, coastal seas in general and the Baltic Sea in particular, experience constant and direct influence from land with consequences to matter and energy cycles, biogeochemical interactions, energy fluxes, and sediment dynamics. “Living along gradients: past, present, future” in the Baltic are today’s very important aspects that rise questions like which of the effects we are detecting occur naturally, and which are driven by human activities. Deciphering past environmental changes and their causes provide keys to understand and simulate possible future scenarios, all of which should rise societal awareness and implementation of appropriate marine and coastal policies. Present-day knowledge on the dynamics of gradient systems, on the processes that affect the coastal sea environment, the results of interaction between coastal seas and society, the detection or reconstruction of past and present changes on time scales from inter-annual to millennial, and future change models are summarized here, with the idea to stimulate scientific exchange on most complex questions, addressing them from different perspectives.

  • 161. Bauer, S H J
    et al.
    Månsson, Martin
    Södertörn University, Avdelning Naturvetenskap.
    Hood, D W
    Richards, J C
    Moxon, E R
    Schweda, Elke K H
    Södertörn University, Avdelning Naturvetenskap.
    A rapid and sensitive procedure for determination of 5-N-acetyl neuraminic acid in lipopolysaccharides of Haemophilus influenzae: a survey of 24 non-typeable H-influenzae strains2001In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 335, no 4, p. 251-260Article in journal (Refereed)
    Abstract [en]

    In view of the importance of 5-N-acetyl neuraminic acid in bacterial pathogenesis, a sensitive, reproducible and reliable method for the determination of 5-N-acetyl neuraminic acid levels in lipopolysaccharide (LPS) is described and applied to 24 different non-typeable Haemophilus influenzae (NTHi) strains. The method involves analysis by high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD) of terminal 5-N-acetyl neuraminic acid residues released by neuraminidase treatment of O-deacylated LPS. The procedure is relatively fast and the instrumental effort is moderate. The results of the procedure were compared with data obtained by H-1 NMR and electrospray ionisation-mass spectrometry (ESI-MS). The analysis of LPS from 24 NTHi strains showed that 5-N-acetyl neuraminic acid was found to be a common constituent of LPS in NTHi. Only one strain (NTHi 432) did not show any sialylation. Molar ratios (LPS /5-N-acetyl neuraminic acid) ranged between 5/1 and 500/1. Several strains in which no 5-N-acetyl neuraminic acid could be determined by other methods including 1H NMR and ESI-MS were shown to contain 5-N-acetyl neuraminic acid by this HPAEC-PAD procedure. The method was applied to determine levels of terminal 5-N-acetyl neuraminic acid in LPS from NTHi strains grown under different conditions and mutant strains containing inactive LPS biosynthetic genes.

  • 162.
    Bauge Sheard, Rebecca
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Svanberg, Kathrin
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    "Good" versus "Bad" Fishermen: A case study on fishermen’s perceptions of illegal fishing and the failure of co-management initiatives in Lake Babati2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Small-scale fisheries represent an important sector for Tanzania’s economy and the contribution to the livelihood of people. In Lake Babati, fish stocks are decreasing, mainly because of illegal fishing methods. This study therefore aims at examining how the problems of illegal fishing affect the fishermen, as well as their perceptions of the implemented fish ban. By using semi-structured interviews, a seasonal calendar and a Venn diagram, the data was analysed through a Critical Institutionalist lens. The results show that the fish ban has not improved the situation and that the fisheries co-management in Lake Babati is weakly practiced. Furthermore, the complexity of socially embedded relations constrains the organisation among the fishermen. As a response to the inadequate management, the fishermen suggest other solutions for preventing illegal fishing. 

  • 163. Bayne, Elizabeth H.
    et al.
    Portoso, Manuela
    Kagansky, Alexander
    Kos-Braun, Isabelle C.
    Urano, Takeshi
    Ekwall, Karl
    Södertörn University, School of Life Sciences.
    Alves, Flavia
    Rappsilber, Juri
    Allshire, Robin C.
    Splicing factors facilitate RNAi-directed silencing in fission yeast2008In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 322, no 5901, p. 602-606Article in journal (Refereed)
    Abstract [en]

    Heterochromatin formation at fission yeast centromeres is directed by RNA interference (RNAi). Noncoding transcripts derived from centromeric repeats are processed into small interfering RNAs (siRNAs) that direct the RNA-induced transcriptional silencing (RITS) effector complex to engage centromer transcripts, resulting in recruitment of the histone H3 lysine 9 methyltransferase Clr4, and hence silencing. We have found that defects in specific splicing factors, but not splicing itself, affect the generation of centromeric siRNAs and consequently centromeric heterochromatin integrity. Moreover, splicing factors physically associate with Cid12, a component of the RNAi machinery, and with centromeric chromatin, consistent with a direct role in RNAi. We propose that spliceosomal complexes provide a platform for siRNA generation and hence facilitate effective centromere repeat silencing.

  • 164.
    Bazancir, Star
    et al.
    Södertörn University College, School of Communication, Technology and Design.
    Carnö, Tim
    Södertörn University College, School of Communication, Technology and Design.
    Fildelning bortom rätt och fel: en studie om fildelning och filbytare2004Independent thesis Basic level (degree of Bachelor)Student thesis
    Abstract [sv]

    All utveckling av ny teknologi åtföljs av nya möjligheter, framkallar nya aktiviteter, intentioner och återuppväcker idéer som tidvis kolliderar med kraftfulla kommersiella intressen och lagar. Fildelning är i den bemärkelsen ett ytterst intressant och aktuellt exempel. I följande uppsats överträds den offentliga debatten om fildelning, vad vi istället avser är att belysa området utifrån filbytarens perspektiv. Vad vi avser är att studera filbytarens inställningar, motiveringar och värderingar för att därigenom försöka kasta ett nytt ljus över fildelningsfrågan. Empiriskt material som behandlas i studien, har insamlats genom strukturerade enkätintervjuer samt tre personliga intervjuer. Urvalet för undersökningen har huvudsakligen framtagits genom en direkt subjektiv urvalsprocess, vi har helt enkelt uppsökt personer som vi vet ägnar sig åt fildelning. Analysen av undersökningsresultaten underbyggs av Siva Vaidhyanathans teorier om fildelningens kulturella och ideologiska aspekter. Resultatet av följande undersökning tyder på att fildelning ger tillgång till ett bredare utbud av kulturprodukter och att aktiviteten i viss mån också bidrar till att filbytare utvecklar nya intressen. Priserna på kulturprodukter som film och musik, framfördes som en motivering till nerladdning av upphovsrättsskyddat material. Fildelning beskrevs som en reaktion mot missförhållanden i den kommersiella marknaden, eller som ett uttryck för idén om gemensam tillgång till kultur.

  • 165. Beckman, M
    et al.
    Kihlmark, Madeleine
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Iverfeldt, K
    Hallberg, Einar
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Degradation of GFP-labelled POM121, a non-invasive sensor of nuclear apoptosis, precedes clustering of nuclear pores and externalisation of phosphatidylserine2004In: Apoptosis (London), ISSN 1360-8185, E-ISSN 1573-675X, Vol. 9, no 3, p. 363-368Article in journal (Refereed)
    Abstract [en]

    The nuclear pore membrane protein POM121 is specifically degraded during apoptosis by a caspase-3-dependent process enabling early detection of apoptosis in living cells expressing POM121-GFP. Here we further investigated temporal aspects of apoptotic degradation of POM121-GFP. We demonstrate that decreased POM121-GFP fluorescence precedes annexin V-labelling of apoptotic cells. This indicates that degradation of the nuclear pore complex starts prior to redistribution of plasma membrane phosphatidylserine, which serves as a signal for phagocytotic elimination of apoptotic cells. Furthermore, a caspase-resistant GFP-labelled mutant of POM121 resisted degradation even in late apoptosis and was detected in clustered nuclear pores. Thus, it can be concluded that loss of POM121-GFP is a specific sensor of the activation of caspase-3-dependent proteolysis at the nuclear pores.

  • 166.
    Beckman, Marie
    et al.
    Södertörn University, School of Life Sciences, Molecular biology.
    Freeman, Craig
    Parish, Christopher R.
    Small, David H.
    Activation of cathepsin D by glycosaminoglycans2009In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 276, no 24, p. 7343-7352Article in journal (Refereed)
    Abstract [en]

    We have previously shown that heparin can increase the activity of the proenzyme form of Alzheimer's beta-site amyloid precursor protein cleaving enzyme 1 (BACE1). Cathepsin D (CD) is a member of the aspartic protease family and has sequence similarity to BACE1. Therefore, we examined whether heparin and other glycosaminoglycans (GAGs) can influence the activity of CD. Heparin and other GAGs were found to stimulate the activity of recombinant proCD. Desulfation of heparin almost abolished the stimulation, indicating that sulfate groups were important for the stimulatory effect. In addition, the stimulation was dependent on the length of the GAG chain, as larger GAGs were more potent in their ability to stimulate proCD than shorter fragments. In the presence of heparin, limited autocatalytic proteolysis of the proenzyme was increased, suggesting that heparin increases the activity of proCD by accelerating the conversion of proCD, which has little activity, to pseudoCD, an active form lacking residues 1-26 of the prodomain. Furthermore, the activity of spleen-derived mature CD, which lacks the entire 44 amino acid residue prodomain, was also increased by heparin, indicating that the catalytic domain of CD contains at least one region to which GAGs bind and stimulate enzyme activity. Because heparin also stimulated the activity of pseudoCD, proenzyme activation was probably accelerated by the interaction of heparin with the catalytic domain of pseudoCD. However, it is possible that heparin may also activate the proenzyme directly. On the basis of this study, we propose that GAGs may regulate CD activity in vivo.

  • 167. Belyaev, I Y
    et al.
    Eriksson, S
    Nygren, Jonas
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute / Stockholm University.
    Torudd, J
    Harms-Ringdahl, M
    Effects of ethidium bromide on DNA loop organisation in human lymphocytes measured by anomalous viscosity time dependence and single cell gel electrophoresis1999In: Biochimica et Biophysica Acta - General Subjects, ISSN 0304-4165, E-ISSN 1872-8006, Vol. 1428, no 2-3, p. 348-356Article in journal (Refereed)
    Abstract [en]

    The effects of ethidium bromide (EtBr) on human lymphocytes were studied by the method of anomalous viscosity time dependence (AVTD) and by the comet assay. EtBr at low concentrations increased the maximum viscosity and time of radial migration as measured with AVTD at neutral conditions of lysis. A pronounced relaxation of DNA loops was observed with the neutral comet assay. The maximal comet length corresponded to 2 Mb DNA loops. At high concentrations of EtBr, 2. mg/ml, significant reduction in AVTD below control level was seen that suggested hypercondensation of chromatin. The hypercondensation was directly observed with the neutral comet assay. EtBr did not induce DNA strand breaks as measured by the alkaline comet assay. The hypercondensed nuclei could be decondensed by irradiation with gamma-rays or exposure to light. The data provide evidence that EtBr at high concentrations resulted in hypercondensation of chromatin below control level. The comet assay confirmed that the increase in AVTD peaks deals with relaxation of loops and AVTD decrease is caused by chromatin condensation. The prediction of the AVTD theory for a correlation between time of radial migration and condensation of chromatin was verified. Further, the data show that the comet assay at neutral conditions of lysis is rather sensitive to DNA loop relaxation in the absence of DNA damage. Finally, donor specificity was found for the hypercondensation.

  • 168. Benach, J
    et al.
    Filling, C
    Oppermann, U C T
    Roversi, P
    Bricogne, G
    Berndt, Kurt D
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Jörnvall, H
    Ladenstein, R
    Structure of bacterial 3 beta/17 beta-hydroxysteroid dehydrogenase at 1.2 angstrom resolution: A model for multiple steroid recognition2002In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 41, no 50, p. 14659-14668Article in journal (Refereed)
    Abstract [en]

    The enzyme 3beta/17beta-hydroxysteroid dehydrogenase (3beta/17beta-HSD) is a steroid-inducible component of the Gram-negative bacterium Conramonas testosteroni. It catalyzes the reversible reduction/ dehydrogenation of the oxo/beta-hydroxy groups at positions 3 and 17 of steroid compounds, including hormones and isobile acids. Crystallographic analysis at 1.2 Angstrom resolution reveals the enzyme to have nearly identical subunits that form a tetramer with 222 symmetry. This is one of the largest oligomeric structures refined at this resolution. The subunit consists of a monomer with a single-domain structure built around a seven-stranded beta-sheet flanked by six alpha-helices. The active site contains a Ser-Tyr-Lys triad, typical for short-chain dehydrogenases/reductases (SDR). Despite their highly diverse substrate specificities, SDR members show a close to identical folding pattern architectures and a common catalytic mechanism. In contrast to other SDR apostructures determined, the substrate binding loop is well-defined. Analysis of structure-activity relationships of catalytic cleft residues, docking analysis of substrates and inhibitors, and accessible surface analysis explains how 3beta/17beta-HSD accommodates steroid substrates of different conformations.

  • 169.
    Bengtsson, Ellen
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Media Technology.
    Hoff, Isabelle
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Media Technology.
    Digitalisering av brädspel: Hur automation av spelmekanik kan förändra sociala interaktioner vid spelande2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Enjoyment and social interaction are closely connected, and board games can be synonymous with both of these things. Board games and digital versions of those games are often used in parallel, which offers a unique position of inquiry. Automation is a tool commonly used in the creation of digital board games, but how does it affect the sociality and how does it differ from physical board games? This is the question that this paper explores through an observational study of the game Ticket to Ride, both in its original, physical form as well as its digital counterpart. Two groups of players were recorded while playing both versions of the game in a different order. Throughout the observation of these game sessions, seven different game mechanics have been used as the lens to determine how the difference in social interaction is connected to the game itself. These game mechanics were turn-taking (time), game surface (space), object (state), actions (strategy), rules (automation), bookkeeping and chance, but social interactions unrelated to the game were also examined. Two of the seven game mechanics turned out to have the most effect on social interaction in the different versions of the game; rules and turn-taking. These two mechanics were important to the learning of the game and for maintaining focus throughout the game.

  • 170.
    Bengtsson, Joakim
    et al.
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Nyberg, Jessica
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Vad i den grafiska spelmiljön påverkar spelarens problemlösning i spelet Brothers: A tale of two sons?2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Den här studien undersöker hur miljön i spelet Brothers: A tale of two sons (Starbreeze Studios, 2013) tolkas av spelarna. Studien fokuserar på spelmiljön och hur grafik med interagerbara objekt tolkas och hur spelaren lägger märke till objekten. En kvalitativ undersökning genomfördes där fyra personer intervjuades. Semi-strukturerad intervjuform användes och varje spelare fick testa utvalda scener ur spelet under observation. Spelet har fokus på problemlösning och det är inte alltid tydligt vad spelaren ska göra. Många andra spelutvecklare gör interagerbara objekt enkla att se genom att särskilja dem från andra objekt, genom highlights och iögonfallande färger. Målet med studien var att undersöka vilka objekt spelaren tolkar som interagerbara och hur dessa objekt utmärker sig visuellt jämfört med andra grafiska element. Genom intervjuer och observationer, blev slutsatsen att den grafiska miljön hade påverkan på spelarna, en del objekt var mer utmärkande än andra att de skulle användas som nyckelobjekt för problemlösning. Objekt som var avvikande och hade unika former som särskilde sig från bakgrunden var lättare att uppfatta som interagerbara objekt.

  • 171. Bensch, Staffan
    et al.
    Grahn, Mats
    Södertörn University, School of Life Sciences, Biology. Södertörn University, School of Life Sciences, Environmental science.
    Müller, Nils
    Gay, Laurene
    Åkesson, Susanne
    Genetic, morphological, and feather isotope variation of migratory willow warblers show gradual divergence in a ring.2009In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 18, no 14, p. 3087-96Article in journal (Refereed)
    Abstract [en]

    The circular distribution of the willow warbler Phylloscopus trochilus around the Baltic Sea shares many features with the classic examples of ring species; however, the system is much younger. It has previously been shown that a secondary contact zone is located in central Scandinavia, where there are narrow clines for several morphological traits coincident with a migratory divide. Here we analyse multiple traits and genes from > 1700 males captured on breeding territories at 77 sites spread around the Baltic Sea to test the following hypothesis. If the secondary contact zone in Scandinavia is a result of divergence in two allopatric refuge populations during the last glaciation, we expect to find a similar secondary contact zone somewhere else around the circular distribution. Our results show that the trait clines were wider and displaced from each other along the eastern side of the Baltic Sea. Analyses of 12 microsatellite loci confirmed that the genome is very similar between the terminal forms (F(ST) = 0). Two AFLP-derived markers filtered out from a genomic scan instead appear to be maintained by selection. These markers exhibited steep clines at the secondary contact zone in Scandinavia, but as for the phenotypic traits, had vastly different cline centres east of the Baltic Sea. The trait clines along the ring distribution outside the Scandinavian secondary contact zone thus seem to have been shaped by independent action of selection or drift during the process of postglacial colonization.

  • 172.
    Benulic, Kajsa-Stina
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    A Beef with Meat: Media and Audience Framings of Environmentally Unsustainable Production and Consumption2016Doctoral thesis, monograph (Other academic)
    Abstract [en]

    The aim of this thesis is to identify potential routes of participation in environmentally sustainable changes of the Swedish meat production and consumption. Changes are needed as meat production and consumption have been linked to serious environmental problems, such as climate change, biodiversity loss, and land use change. Scientists, international organizations, and Swedish government authorities have identified individual consumer responsibility as key in making that change happen. The public is to be informed and educated to make more environmentally sustainable choices as meat consumers, and become more supportive of policy instruments. This strategy, which mirrors the dominant approach to solving environmental problems, is suggested by government authorities despite their suspicion that media should have made most Swedes aware of the environmental impacts of meat.

    In this thesis potential participatory routes are identified through the analysis of Swedish news media and audience framings of meat production and consumption. Media framing is studied as an important source of information, and perhaps motivation, crucial in the individualized consumer responsibility approach. The media framing is studied through content analysis of mainstream and alternative radical newspapers. The audiences’ framing of meat may be influenced by media, but also by their everyday experiences, beliefs, values, and opinions. Focus group discussions with reception elements are the methods used for studying how audiences frame meat and use media in the process. The concept of participation is broadened to include passive and active forms to capture in which roles individuals consider to contribute to changing meat production and consumption. It is not self-evident that routes to change must include individual participation, since responsibility may be attributed to other actors, both by media and their audiences.

    The results imply only participatory route supported by media and audience framing. It is the one that mirrors the individualized consumer responsibility approach to solving environmental problems. The major barrier to the route is the audiences’ perceived inability to act. In an alternative route supported by both media and audience framing, state centered actors are made responsible for enforcing change. Here, the major barrier is the perceived unlikeliness of powerful actors assuming responsibility. Audiences construct no citizen roles for themselves to participate in. Neither does media, who only address audiences as consumers. Based on these findings it is suggested that the outlook for the individualized responsibility approach to making meat production and consumption environmentally sustainable is gloomy. At least if it the approach is to continuously rely on the information and motivation offered by media.

  • 173. Berg, H
    et al.
    Francis, J
    Souter, Petra
    Södertörn University, Avdelning Naturvetenskap.
    Support to marine research for sustainable management of marine and coastal resources in the Western Indian Ocean2002In: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 31, no 7-8, p. 597-601Article in journal (Refereed)
  • 174. Berg, Mikko
    et al.
    Marttila, Topias
    Kaipainen, Mauri
    Kojo, Ilpo
    Exploring Political Agendas with Advanced Visualizations and Interface Tools.2006In: e-Service Journal, ISSN 1528-8226, E-ISSN 1528-8234, Vol. 4, p. 47-63Article in journal (Refereed)
    Abstract [en]

    With Web-based e-services called "election engines," citizens can search for and compare candidates in local and national elections using issue-based questionnaires. The results of such services are generally in the form of search engine lists. However, data on political issues andagendas is very complex, i.e., highly multidimensional. Hence, we argue that relevant votingdecisions should not be based on simple search engine results, but on more encompassing cognitive operations. In our project, the service was redesigned to extend the function from a meresearch engine to a navigation toolset with real-time feedback. Two types of visualization components, a similarity map and sector diagrams, help citizens to make sense of multidimensional political spaces by facilitating exploration at will. As the result of an extended researchproject, our redesigned service was published by a major commercial broadcasting company forthe Finnish EU elections in June 2004 and in local elections in October 2004. 

  • 175. Berger, Juerg
    et al.
    Senti, Kirsten-Andre
    Senti, Gabriele
    Södertörn University, School of Life Sciences. Karolinska Institute.
    Newsome, Timothy P.
    Åsling, Bengt
    Dickson, Barry J.
    Suzuki, Takashi
    Systematic identification of genes that regulate neuronal wiring in the Drosophila visual system2008In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 4, no 5, p. Online-Article in journal (Refereed)
    Abstract [en]

    Forward genetic screens in model organisms are an attractive means to identify those genes involved in any complex biological process, including neural circuit assembly. Although mutagenesis screens are readily performed to saturation, gene identification rarely is, being limited by the considerable effort generally required for positional cloning. Here, we apply a systematic positional cloning strategy to identify many of the genes required for neuronal wiring in the Drosophila visual system. From a large-scale forward genetic screen selecting for visual system wiring defects with a normal retinal pattern, we recovered 122 mutations in 42 genetic loci. For 6 of these loci, the underlying genetic lesions were previously identified using traditional methods. Using SNP-based mapping approaches, we have now identified 30 additional genes. Neuronal phenotypes have not previously been reported for 20 of these genes, and no mutant phenotype has been previously described for 5 genes. The genes encode a variety of proteins implicated in cellular processes such as gene regulation, cytoskeletal dynamics, axonal transport, and cell signalling. We conducted a comprehensive phenotypic analysis of 35 genes, scoring wiring defects according to 33 criteria. This work demonstrates the feasibility of combining large-scale gene identification with large-scale mutagenesis in Drosophila, and provides a comprehensive overview of the molecular mechanisms that regulate visual system wiring.

  • 176.
    Berger, Tony
    et al.
    Södertörn University College, School of Communication, Media and it.
    Törnqvist, Carl
    Södertörn University College, School of Communication, Media and it.
    EmoWheel: En metodutveckling för utvärdering av emotionellt engagemang2009Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This is a study of how emotional engagement can be measured and be taken into account in the development of websites. We believe that emotions become relevant only when viewed in correlation to how users experiencing a webpage. In this study, we developed a tool for use together with user tests where the information about the user's emotional engagement can add new value to the evaluation. The tool allows the user to mark, on the website, his/her emotions and level of engagement represented by colored circles, generating quantiative data on how users feel about the website. The tool is part of a method for evaluating the emotional engagement that we have developed which consists of user testing supported by the tool and accompanied by interviews.

  • 177.
    Bergfeldt, Vendela
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Microbes that never sleep: A multidisciplinary study of the antibiotic resistance management in Sweden2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The hypotheses of this study are that reduction and rational usage of antibiotics reduces development of antibiotic resistance. In Sweden, the trends do not follow this pattern. Despite a decrease in prescriptions of antibiotics, there is an increase in the number of patients infected with Methicillin-resistant Staphylococcus Aureus (MRSA), Extended Spectrum Beta-Lactamases (ESBL) and ESBL selecting for carbapenem-resistance (ESBLCARBA). This study aims to study factors affecting antibiotic resistance management. An additional aim is to use a multidisciplinary approach for a subject that has mostly been studied with quantitative methods. First, linear regressions investigated any possible significant changes of prescription rates in outpatient care, hospital usage of antibiotic groups and antibiotic resistance. After this, nine interviews were conducted with physicians in outpatient care, hospital care and with representatives from the Swedish Strategic Programme for the Rational Use of Antimicrobial Agents and Surveillance of Resistance (Strama), a network working for Swedish prevention against antibiotics resistance. There was a significant decrease in the number of prescriptions of antibiotics in outpatient care among all Swedish counties and a small, but significant increase of antibiotics used in hospitals. The number of patients infected with multidrug resistant bacteria also show a significant increase. The interviews revealed that health care workers in all counties follow the same guidelines and try to be as specific as possible in choosing antibiotics to hit specific bacteria. The respondents suggested migration and extended travelling as explanations to the growing number of cases of multidrug resistant bacteria. Further, two major factors emerged as important for an efficient antibiotic resistance management; Education/knowledge and Discussion. The results indicate a need for further research on rational usage of antibiotics and the use of broad-spectrum antibiotics in hospital care, rather than the reduction through prescriptions. The results indicate that rational usage has a bigger impact than reduction. Using a multidisciplinary approach gave a broader perspective on the issue and future studies should see the possibilities of mixing quantitative and qualitative studies.

  • 178.
    Berggren, My
    Södertörn University, Teacher Education.
    Det kreativa matematiska resonemanget i dagens klassrum: Undersökning om möjligheter till att utveckla ett kreativt matematiskt resonemang i undervisning på mellanstadiet2019Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The purpose of this study is to try to gain a deeper understanding of teachers' views on how teaching should be designed to promote creative mathematical reasoning in problem-solving. This will be examined on the basis of the following two questions: What opportunities in problem solving teaching can students use conceptual as well as procedural knowledge in order to develop a creative reasoning? And what opportunities for developing a creative reasoning are there in problem solving teaching? The teachers´ lessons were observed to answer the questions. Interviews of the teachers were conducted to supplement the observations and get a picture of their knowledge of the creative reasoning.

    Previous studies show that students rarely use a creative reasoning because teaching materials and examinations do not give students the opportunity to do so. Instead the students tend to use more imitative reasoning which is not built on deeper knowledge but is based on memorizing information. Therefore, it becomes relevant to investigate what opportunities classroom activities give students to make use of a creative mathematical reasoning. This study concludes that students are given a limited opportunity to use creative mathematical reasoning. Students can use both conceptual and procedural knowledge during the teacher-led teaching. The type of teaching that requires students to use creative reasoning is lacking. From interviews of the teachers, it emerges that the teachers do not know about the different types of mathematical reasoning. This may explain why students rarely need to use a creative reasoning that is based on a deeper understanding of the lessons learned on problem solving.

  • 179. Bergh, F T
    et al.
    Flinn, Elisabeth M
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Svaren, J
    Wright, Anthony P
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Horz, W
    Comparison of nucleosome remodeling by the yeast transcription factor Pho4 and the glucocorticoid receptor2000In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 275, no 12, p. 9035-9042Article in journal (Refereed)
    Abstract [en]

    Chromatin reorganization of the PHO5 and murine mammary tumor virus (MMTV) promoters is triggered by binding of either Pho4 or the glucocorticoid receptor (GR), respectively. In order to compare the ability of Pho4 and GR to remodel chromatin and activate transcription, hybrid promoter constructs were created by insertion of the MMTV B nucleosome sequence into the PHO5 promoter and then transformed into a yeast strain expressing GR, Activation of either Pho4 (by phosphate depletion) or GR (by hormone addition) resulted in only slight induction of hybrid promoter activity. However, simultaneous activation of both Pho4 and GR resulted in synergistic activation to levels exceeding that of the wild type PHO5 promoter. Under these conditions, Pho4 completely disrupted the nucleosome containing its binding site. In contrast, GR had little effect on the stability of the MMTV B nucleosome. A minimal transactivation domain of the GR fused to the Pho4 DNA-binding domain is capable of efficiently disrupting the nucleosome with a Pho4-binding site, whereas the complementary hybrid protein (Pho4 activation domain, GR DNA-binding domain) does not labilize the B nucleosome. Therefore, we conclude that significant activation by Pho4 requires nucleosome disruption, whereas equivalent transcriptional activation by GR is not accompanied by overt perturbation of nucleosome structure. Our results show that the DNA-binding domains of the two factors play critical roles in determining how chromatin structure is modified during promoter activation.

  • 180.
    Bergman, Daniella
    Södertörn University College, School of Discourse Studies.
    Om arternas överlevnad: en artikelserie om den biologiska mångfalden i Sverige2007Independent thesis Basic level (degree of Bachelor), 10 points / 15 hpStudent thesis
    Abstract [sv]

    Överingress:

    Tänk att du är på en skogspromenad, alla träd har smala

    stammar och är antingen gran eller tall. Kvittret och sången

    har försvunnit eftersom här inte finns några insekter för

    fåglarna att äta. Den biologiska mångfalden i Sverige är

    viktig för att vi ska må bra. I dag bryter många skogsägare

    mot lagen när de avverkar skog och det påverkar den

    biologiska mångfalden negativt.

    När valet nu står mellan gamla träd och nya hus, i ett

    samhälle med bostadsbrist, är prioriteringarna inte självklara.

  • 181.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Engqvist, Robert
    Karolinska Institute.
    Stålhandske, C
    Chemical Centre, Lund.
    Wallberg, H
    KTH.
    Studies of the reactions between indole-2,3-diones (isatins) and 2-aminobenzylamine2003In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 59, no 7, p. 1033-1048Article in journal (Refereed)
  • 182.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Janosik, T
    Koch, E
    Pelcman, B
    Acid-induced dimerization of 3-(1H-indol-3-yl)maleimides. Formation of cyclopentindole derivatives2000In: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 1, ISSN 1470-4358, no 16, p. 2615-2621Article in journal (Refereed)
    Abstract [en]

    Acid-induced dimerizations of 3-substituted maleimides have been investigated, leading to e.g. the cyclopentindole 9 and the deeply coloured spiro compounds 24 and 25 in good yields. 3-(1H-Indol-3-yl)maleimide 6b readily gave the cycloaddition products 13-15 on treatment with appropriate dienophiles. In addition, several related 3,3-di-(1H-indol-3-yl)succinimides have been prepared and studied.

  • 183.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Janosik, T
    Yudina, L
    Desarbre, E
    Lidgren, G
    Venemalm, L
    Reactions of 1,2-bis(1H-indol-2-yl)ethane: Formation of indolo[2,3-c]carbazole and cyclohept[1,2-b : 5,4-b ']bisindole derivatives2000In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 56, no 13, p. 1911-1916Article in journal (Refereed)
    Abstract [en]

    1,2-Bis(1H-indol-2-yl)ethane (9) has been prepared and converted into indolo[2,3-c]carbazole (8) using palladium acetate in refluxing acetic acid. Reaction of 9 with CoF3 in hot TFA led to isolation of cyclohept[1,2-b:5,4-b']bisindole derivatives 11 and 12, which could be elaborated into further derivatives. Treatment of 9 with orthoesters, aldehydes and ketones under acidic conditions afforded additional bisindoles containing a seven-membered ring.

  • 184.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Janosik, Tomasz
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Recent progress in the chemistry of sulfur-containing indoles2002In: Progress in Heterocyclic Chemistry, ISSN 0959-6380, Vol. 14, no C, p. 1-18Article in journal (Refereed)
  • 185.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Janosik, Tomasz
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Wahlström, Niklas
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institutet.
    Indolocarbazoles2001In: Advances in Heterocyclic Chemistry, ISSN 0065-2725, E-ISSN 1557-8429, Vol. 80, p. 1-71Article, review/survey (Refereed)
  • 186.
    Bergman, Jan
    et al.
    Södertörn University, School of Life Sciences.
    Johnson, Ann-Louise
    A short synthesis of the carbazole alkaloid clausine E2006In: Organic preparations and procedures international, ISSN 0030-4948, E-ISSN 1945-5453, Vol. 38, no 6, p. 593-599Article in journal (Refereed)
  • 187.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Koch, E
    Pelcman, B
    Coupling reactions of indole-3-acetic acid derivatives. Synthesis of arcyriaflavin A2000In: JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 1, ISSN 1470-4358, no 16, p. 2609-2614Article in journal (Refereed)
    Abstract [en]

    The bisindolesuccinic acid methyl ester 10 was obtained by an iodine-promoted coupling of the dianion 9. The diester was converted to the N-benzylimide 12, which was oxidatively cyclized to the indolo[2,3-a]pyrrolo[3,4-c]carbazole 15. The diester 10 could be directly transformed to the known indolocarbazole diester 27 via acid-induced intramolecular cyclization in TFA. The same methodology gave arcyriaflavin A 4 from the succinimide 18b.

  • 188.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap.
    Rehn, S
    Synthesis of 4-oxo-4,5-dihydro-3H-pyrrolo[2,3-c]quinoline-1-carboxylic acid ethyl ester and its isomer 1-oxo-2,9-dihydro-1H-beta-carboline-4-carboxylic acid ethyl ester2002In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 58, no 45, p. 9179-9185Article in journal (Refereed)
    Abstract [en]

    4-Oxo-4,5-dihydro-3H-pyrrolo[2,3-c]quinoline-1-carboxylic acid ethyl ester was obtained when TosMIC was reacted with 3-methylene-oxindole acetic acid ethyl ester. An alternative synthesis to this pyrroloquinolone was performed via a reduction of a 2,3,4-trisubstituted pyrrole obtained in turn by treatment of a vinyl sulfone with ethyl isocyanoacetate under basic conditions. A beta-carboline, isomeric with the pyrroloquinolone, was synthesised utilizing a tosylimine.

  • 189.
    Bergman, Jan
    et al.
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Wahlström, Niklas
    Södertörn University, Avdelning Naturvetenskap. Karolinska Institute.
    Yudina, L N
    Tholander, J
    Lidgren, G
    Synthesis of indolocarbazole quinones; potent aryl hydrocarbon receptor ligands2002In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 58, no 7, p. 1443-1452Article in journal (Refereed)
    Abstract [en]

    Syntheses of indolo[2,3-b]carbazole-6,12-dione and the isomeric indolo[3,2-b]carbazole-6,12-dione, an extremely efficient inducer of the aryl hydrocarbon (Ah) receptor are described. Initial oxidation of the parent indolo[3,2-b]carbazole followed by several different ring-closing strategies produced the latter compound. Entries into syntheses of unsymmetrical 6,12-disubstituted indolo[2,3-b]carbazoles are also described.

  • 190.
    Bergström, Emma
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Media Technology.
    Den mobilanpassade jobbrekryteringsprocessen: En kvalitativ undersökning om två intressentgruppers användarupplevelse av tjänsten Uptrail2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This study aims to examine two user groups experience and usage of the mobile job advertising service Uptrail. The two groups that are the focus of this work are the companies that use the service for job recruitment and job-seekers that have applied for work through Uptrail. In which context job-seekers apply for work through the service and why is also examined in this study. This is to give an understanding of how the mobile interface might influence users behaviour during the job recruitment process. The study is based on a qualitative research method where individual in-depth interviews with representatives from the different groups are used for gathering data. Also a shorter observation has been applied during the interviews with the job seekers. Collected data were then analyzed through an inductive interpretation method and combined with previous research and theories regarding mobile usage, context, digital recruitment (e-recruitment) and user experience (UX).

    The result of the study implies that Uptrail has impacted the motives behind job advertising by affecting the user experience of the recruitment process. Job applicants experienced that the mobile format and the process of the service changed their habits on applying for work through digital application. In line with previous research results from this study also suggest that the usage of mobile services largely takes place in “home like” environments. This is explained as a consequence of existing attitudes and thoughts regarding the job search process. 

  • 191.
    Bergström, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Effektmätning inom eventbranschen: En plan för mätning av effekt och ROI inom eventbranschen2015Independent thesis Basic level (university diploma), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The competition in the event industry is tough; the event agencies have to work hard to keep customers. Event marketing is partly about changing the receivers’ attitudes about a specific topic. The only way to find out whether attitudes have been changed is to measure the effects of the event.

    This report discusses in what way event agencies evaluate the effect of their events. I came to the conclusion that it is not common for event agencies to measure the effect. The reason is mostly because it is expensive to hire a company that does it, but also because it takes a lot of time. The solution is to define a method for evaluation that is simple, flexible and inexpensive for everyone involved.

    Even though this report is about evaluation in the event industry, I also look at evaluation in the advertising business, to find possible similarities. The outcome is a possible solution used for smartphones. One possible method to use is called Telia Mobil Respons and it is both easy to understand and manage, but also cost effective. 

  • 192.
    Berini, Francesca
    et al.
    Politecnico di Milano and University of Insubria, Varese, Italy.
    Presti, Ilaria
    Politecnico di Milano and University of Insubria, Varese, Italy / Chemo Biosynthesis, Corana, Pavia, Italy.
    Beltrametti, Fabrizio
    Actygea, Gerenzano, Varese, Italy.
    Pedroli, Marco
    Vårum, Kjell M
    Norwegian University of Science and Technology, Trondheim, Norway.
    Pollegioni, Loredano
    Politecnico di Milano and University of Insubria, Varese, Italy.
    Sjöling, Sara
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies, Environmental Science.
    Marinelli, Flavia
    Politecnico di Milano and University of Insubria, Varese, Italy.
    Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome2017In: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 16, no 1, article id 16Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Through functional screening of a fosmid library, generated from a phytopathogen-suppressive soil metagenome, the novel antifungal chitinase-named Chi18H8 and belonging to family 18 glycosyl hydrolases-was previously discovered. The initial extremely low yield of Chi18H8 recombinant production and purification from Escherichia coli cells (21 μg/g cell) limited its characterization, thus preventing further investigation on its biotechnological potential.

    RESULTS: We report on how we succeeded in producing hundreds of milligrams of pure and biologically active Chi18H8 by developing and scaling up to a high-yielding, 30 L bioreactor process, based on a novel method of mild solubilization of E. coli inclusion bodies in lactic acid aqueous solution, coupled with a single step purification by hydrophobic interaction chromatography. Chi18H8 was characterized as a Ca(2+)-dependent mesophilic chitobiosidase, active on chitin substrates at acidic pHs and possessing interesting features, such as solvent tolerance, long-term stability in acidic environment and antifungal activity against the phytopathogens Fusarium graminearum and Rhizoctonia solani. Additionally, Chi18H8 was found to operate according to a non-processive endomode of action on a water-soluble chitin-like substrate.

    CONCLUSIONS: Expression screening of a metagenomic library may allow access to the functional diversity of uncultivable microbiota and to the discovery of novel enzymes useful for biotechnological applications. A persisting bottleneck, however, is the lack of methods for large scale production of metagenome-sourced enzymes from genes of unknown origin in the commonly used microbial hosts. To our knowledge, this is the first report on a novel metagenome-sourced enzyme produced in hundreds-of-milligram amount by recovering the protein in the biologically active form from recombinant E. coli inclusion bodies.

  • 193.
    Berkmann, Anna
    Södertörn University, School of Natural Sciences, Technology and Environmental Studies.
    Greening Potentials and Limits of Eco-Labelling Schemes in the EU: A policy evaluation with a focus on small firms in the German coffee-processing sector2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    As SMEs transformation to sustainable practices in manufacturing, processing and services, is declared to be the key to a green growth model, the research in this thesis aims to understand in what way eco-labelling can be a part of that. In order to approach this complex issue, the thesis aims to identify the greening potential and the limits of contemporary eco-labelling schemes for SME product within the German coffee-processing sector. With regard to that, the thesis applied the policy evaluation method "Program Theory Evaluation" (PTE), which assesses a policy in place and thus provides information how the introduction and the function of eco-labelling schemes is observed and perceived by German coffee-processing SMEs (GCPS). Hence, based on a policy evaluation from a rational perspective, which has the focus on the policy’s problem-solving process and implementation cycle, the thesis reveals how eco-labelling schemes’ underlying theoretical greening strategy act in practice to German coffee-processing SME (GCPS). Thereby it could be evaluated that eco-labelling schemes imply shortcomings to address and green GCPS high quality coffee products. As the PTE-method aims also on optimizing the policy’s rationalisation, the inappropriate or failed implementation of eco-labelling schemes by GCPS has been further explored. To grasp the eco-labelling schemes extent of limits to green GCPS products, the thesis compares and analyses the policy evaluation results against the backdrop of eco-labelling schemes’ normative theoretical policy conception and in the light of "Environmental Authority of Political Consumerism (Ecological Modernisation Theory)". With regard to that, the thesis fosters a policy learning process and uncovers that eco-labelling scheme eco-labelling schemes potential to green GCPS products is limited and conditioned to this a lower level of sustainable value as they are focused to supply mainly the demand for mainstream coffee products. Hence, the thesis concludes that it is not the underlying rationality of eco-labelling schemes, namely being a consumer-oriented and market-based policy instrument that does not apply to green GCPS products. However, this opens up a new perspective as it points out a sustainable quality gap between products using eco-labelling schemes and non-labelled GCPS high quality products. In return this raises considerations in terms of improving eco-labelling schemes’ contribution to sustainable development. Thus the thesis argues to optimize their rationalization with regard to GCPS high quality products as frontrunners of tomorrow’s sustainability.

  • 194. Bernard, Pascal
    et al.
    Schmidt, Christine Katrin
    Vaur, Sabine
    Dheur, Sonia
    Drogat, Julie
    Genier, Sylvie
    Ekwall, Karl
    Södertörn University, School of Life Sciences.
    Uhlmann, Frank
    Javerzat, Jean-Paul
    Cell-cycle regulation of cohesin stability along fission yeast chromosomes2008In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 27, no 1, p. 111-121Article in journal (Refereed)
    Abstract [en]

    Sister chromatid cohesion is mediated by cohesin, but the process of cohesion establishment during S-phase is still enigmatic. In mammalian cells, cohesin binding to chromatin is dynamic in G1, but becomes stabilized during S-phase. Whether the regulation of cohesin stability is integral to the process of cohesion establishment is unknown. Here, we provide evidence that fission yeast cohesin also displays dynamic behavior. Cohesin association with G1 chromosomes requires continued activity of the cohesin loader Mis4/Ssl3, suggesting that repeated loading cycles maintain cohesin binding. Cohesin instability in G1 depends on wpl1, the fission yeast ortholog of mammalian Wapl, suggestive of a conserved mechanism that controls cohesin stability on chromosomes. wpl1 is nonessential, indicating that a change in wpl1-dependent cohesin dynamics is dispensable for cohesion establishment. Instead, we find that cohesin stability increases at the time of S-phase in a reaction that can be uncoupled from DNA replication. Hence, cohesin stabilization might be a pre-requisite for cohesion establishment rather than its consequence.

  • 195.
    Berndt, Kurt D
    University of Chicago, USA.
    Design, synthesis, and characterization of amphiphilic helical peptides as models of protein structure1989Doctoral thesis, monograph (Other academic)
  • 196.
    Berndt, Kurt D
    et al.
    Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland.
    Beunink, J
    Schröder, W
    Wüthrich, K
    Designed replacement of an internal hydration water molecule in BPTI: structural and functional implications of a glycine-to-serine mutation.1993In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 32, p. 4564-4570Article in journal (Refereed)
    Abstract [en]

    The three-dimensional structure of the basic pancreatic trypsin inhibitor (BPTI) contains four internal water molecules, which form a total of nine intermolecular hydrogen bonds with the BPTI polypeptide chain. To investigate the effect of such internal hydration on protein structure and stability, we displaced one of the internal water molecules in a recombinant BPTI analogue, BPTI(G36S), in which Gly 36 is replaced by serine. The replacement of a water molecule by the seryl side chain was established by the absence of the protein-water nuclear Overhauser effects (NOE) that had been attributed to the water molecule near Gly 36 in wild-type BPTI and by the presence of new, intramolecular NOEs to the hydroxyl proton of Ser 36. BPTI(G36S) has slightly reduced thermal stability compared to BPTI, corresponding to a destabilization by delta (delta G) approximately 0.7 kcal/M in 6 M guanidinium hydrochloride solution. Additionally, the stabilities of the complexes formed between BPTI(G36S) and trypsin, plasmin, or kallikrein are significantly reduced when compared to the corresponding complexes with wild-type BPTI.

  • 197.
    Berndt, Kurt D
    et al.
    Eidgenossische TH-Honggerberg, Zürich, Switzerland.
    Güntert, P
    Wüthrich, K
    Nuclear-Magnetic-Resonance Solution Structure of Dendrotoxin-K from the Venom of Dendroaspis-Polylepis-Polylepis1993In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 234, no 3, p. 735-750Article in journal (Refereed)
  • 198.
    Berndt, Kurt D
    et al.
    Eidgenösische Technische Hochschule-Hönggerberg, Zürich, Switzerland.
    Güntert, Peter
    Orbons, Leonard P.M.
    Wüthrich, Kurt
    Determination of a high-quality nuclear magnetic resonance solution structure of the bovine pancreatic trypsin inhibitor and comparison with three crystal structures1992In: Journal of Molecular Biology, Vol. 227, p. 757-775Article in journal (Refereed)
    Abstract [en]

    A high-quality three-dimensional structure of the bovine pancreatic trypsin inhibitor (BPTI) in aqueous solution was determined by 1H nuclear magnetic resonance (n.m.r.) spectroscopy and compared to the three available high-resolution X-ray crystal structures. A newly collected input of 642 distance constraints derived from nuclear Overhauser effects and 115 dihedral angle constraints was used for the structure calculations with the program DIANA, followed by restrained energy minimization with the program AMBER. The BPTI solution structure is represented by a group of 20 conformers with an average root-mean-square deviation (RMSD) relative to the mean solution structure of 0.43 A for backbone atoms and 0.92 A for all heavy atoms of residues 2 to 56. The pairwise RMSD values of the three crystal structures relative to the mean solution structure are 0.76 to 0.85 A for the backbone atoms and 1.24 to 1.33 A for all heavy atoms of residues 2 to 56. Small local differences in backbone atom positions between the solution structure and the X-ray structures near residues 9, 25 to 27, 46 to 48 and 52 to 58, and conformational differences for individual amino acid side-chains were analyzed for possible correlations with intermolecular protein-protein contacts in the crystal lattices, using the pairwise RMSD values among the three crystal structures as a reference.

  • 199.
    Berndt, Kurt D
    et al.
    Eidgenössische TH-Hönggerberg, Zürich, Switzerland.
    Güntert, Peter
    Wüthrich, Kurt
    Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water1996In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 24, p. 304-313Article in journal (Refereed)
    Abstract [en]

    The NMR solution structure of bovine pancreatic trypsin inhibitor (BPTI) obtained by distance geometry calculations with the program DIANA is compared with groups of conformers generated by molecular dynamics (MD) simulations in explicit water at ambient temperature and pressure. The MD simulations started from a single conformer and were free or restrained either by the experimental NOE distance restraints or by time-averaged restraints; the groups of conformers were collected either in 10 ps intervals during 200 ps periods of simulation, or in 50 ps intervals during a 1 ns period of simulation. Overall, these comparisons show that the standard protein structure determination protocol with the program DIANA provides a picture of the protein structure that is in agreement with MD simulations using "realistic" potential functions over a nanosecond timescale. For well-constrained molecular regions there is a trend in the free MD simulation of duration 1 ns that the sampling of the conformation space is slightly increased relative to the DIANA calculations. In contrast, for surface-exposed side-chains that are less extensively constrained by the NMR data, the DIANA conformers tend to sample larger regions of conformational space than conformers selected from any of the MD trajectories. Additional insights into the behavior of surface side-chains come from comparison of the MD runs of 200 ps or 1 ns duration. In this time range the sampling of conformation space by the protein surface depends strongly on the length of the simulation, which indicates that significant side-chain transitions occur on the nanosecond timescale and that much longer simulations will be needed to obtain statistically significant data on side-chain dynamics.

  • 200. Berndtsson, Johan
    et al.
    Normark, Maria
    The coordinative functions of flight strips: air traffic control revisited1999In: Proceedings of the international ACM SIGGROUP conference on Supporting group work, GROUP '99 / [ed] Stephen C Hayne, New York: ACM , 1999, p. 101-110Conference paper (Refereed)
    Abstract [en]

    Cooperation in time-critical and physically distributed worksettings, such as air traffic control, requires extensive coordinationbetween the involved actors. For this coordination to beefficient the controllers rely both on the comprehensive use ofrules and procedures, and on artifacts supporting them infollowing these procedures. At the Copenhagen Air TrafficControl Center this coordination is largely carried out throughthe use of a flight plan database system, paper flight strips, anda closed-circuit television system. In relation to the introductionof a new and increasingly automated system in the year 2003 this paper discusses the coordinative functions served bythese three, soon to be replaced, artifacts from a design perspective.Despite the skepticism expressed in previous research,our results show that a further computerization couldbe successful if the coordinative functions the system currentlyfulfills are properly preserved.

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