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  • 51.
    Ohlson, Lena
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    In vivo studies of cell cycle regulating proteins in rats during liver regeneration and during promotion of liver carcinogenesis2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    There are more than one hundred different types of cancer in humans. However, the major platform for all types of cancer is automous and uncontrolled cell division and though most types of cancer are possible to treat and cure by surgery, chemical therapy or irradiation, more efficient and less toxic therapies are urgently needed. In the modern society we are exposed to more toxins than ever. The liver, as main detoxifier of our blood, is handling many hazardous compounds. Unfortunately, after being metabolised in the liver, many of these are able to act as promoters for one of the most lethal types of cancer, the hepatocellular carcinoma (HCC). Previous studies demonstrated that nuclear accumulation of p53 and other proteins is essential for efficient tumor suppression. Based on this, the aim of the study was to investigate whether altered localization and/or p53 protein expression is an early event in tumor development in liver that possibly contributes to the growth advantage of initiated hepatocytes. We also addressed the question of which impact 2-AAF exerts on cell cycle at early stages of tumor promotion. Preneoplastic foci were induced in rat liver by treatment with diethylnitroseamin (DEN), combined with either of the four tumor promoters, 2acetylaminofluorene, 17-alpha ethinylestradiol, choline-deficient diet or deoxycholic acid. This was combined with 2/3 partial hepatectomy as a proliferative stimulus. The immunohistochemical results showed that all four promoters decreased the focal expression of p53 and p21, two proteins known to inhibit replication upon DNA damage, in both nucleus and cytoplasm. In contrast, in surrounding tissue increased nuclear levels of p53 and p21 was observed. These data suggest that deregulation of p53 and p21 might be a common feature occurring early during promotion of HCC in vivo. We also found that treatment with 2-AAF prevented the induction of nuclear p53 in foci in response to gamma-irradiation in initiated male Wistar rats, which correlated with increased cytoplasmic expression of Mdm2 and Bcl-2 in foci. It is possible that complex formation with elevated Mdm2 together with increased Bcl-2 protein expression contributes to the sequestration and inactivation of p53 in cytoplasm. Growth signalling in regenerating liver was studied in non-initiated rats subjected to the tumor promoter 2-AAF. We found that 2-AAF exercise an almost complete mitoinhibitory effect in synchronised hepatocytes. Nuclear levels of cdk 4, cyclin D3, cyclin E, p53, p 130 and pRb were increased while the levels of PCNA, cdk 2, E2F- 1, -3 and -4 were decreased. Furthermore, both nuclear and cytoplasmic expression of cyclin A and - B proteins was lost. Finally, we found that p107 a member of the Rb-family and necessary for S-phase progression, but not pRB was increased in normal regenerating liver. In mitoinhibited liver the expression level of these two proteins was rather the opposit indicating slightly different roles for pRb and p107 during regeneration and cell cycle control, at least in this animal model.

  • 52.
    Ohlson, Lena C. E.
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Koroxenidou, Lena
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Porsch Hällström, Inger
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Tumor promotion in rat liver: low nuclear expression of p53 and p21 in preneoplastic foci compared with surrounding hepatocytesManuscript (preprint) (Other academic)
  • 53.
    Ohlson, Lena C. E.
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Koroxenidou, Lena
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Porsch Hällström, Inger
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Mitoinhibitory effects of the tumor promoter 2-acetylaminofluorene in rat liver: loss of E2F-1 and E2F-3 expression and cdk 2 kinase activity in late G12004In: Journal of Hepatology, ISSN 0168-8278, E-ISSN 1600-0641, Vol. 40, no 6, p. 957-962Article in journal (Refereed)
  • 54. Olsson, Björne
    et al.
    Bradley, Brian P.
    Gilek, Michael
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Reimer, Olof
    Shepard, Jenn L.
    Tedengren, Michael
    Physiological and proteomic responses in Mytilus edulis exposed to PCBs and PAHs extracted from Baltic Sea sediments2004In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 514, no 1-3, p. 15-27Article in journal (Refereed)
    Abstract [en]

    Stress responses in blue mussels (Mytilus edulis. L.) exposed to organic pollutants were measured using several physiological measures and as changes in protein expression. Blue mussels from the Baltic Sea were exposed for 6 days in a flow-through system to two fractions of extracted Baltic sediments (containing primarily PAHs or PCBs) from one industrially impacted site and one off-shore site. Exposure to Aroclor1248 (a commercial PCB mixture) was included as a reference treatment. Physiological response was measured as changes in respiration, excretion, clearance rates and scope for growth. Of the physiological responses, only clearance rate and scope for growth in the Aroclor and impacted site PCB treatments differed significantly (p < 0.05) from control organisms, perhaps due to a large variation among individuals. Seven proteins were observed, presumed to be from stress protein families (hsp60, hsp70 and hsp90) on one-dimensional electrophoresis gels. All protein levels, except three proteins, 62, 73 and 90 kDa, in response to PCB exposure from the industrial site, were significantly higher (p < 0.05) in treated than in control organisms, suggesting the use of stress-inducible proteins as diagnostics in risk assessment. A wider sample of proteins was observed using two-dimensional gel electrophoresis. The presence or absence of protein spots compared to control organisms was used as an indication of stress. Between 23 and 76 proteins or spots were present and 15 to 23 absent compared to controls, and the results supported the physiological and one-dimensional gel results, suggesting that the mussels were indeed suffering from stress. The methods used here represent stress monitoring at two different levels of biological organization; the cellular- and the level of individual organisms. In this experiment the protein response showed less variation among individuals compared to the physiological parameters. The protein response, however, still suffers from the lack of interpretation into commonly used monitoring terms, which emphasizes the need for more knowledge of whether the response is a momentary reflection of exposure or an early warning of higher order effects.

  • 55.
    Olsén, K Håkan
    et al.
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Stacey, N
    Crucian carp (Carassius carassius) male response toovulatory female in the wild2005In: List of Abstracts from the Sixteenth Annual Meeting of the European Chemoreception Research Organisation, 2005, p. -A54Conference paper (Other academic)
  • 56.
    Onischenko, Evgeny A
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Gubanova, N V
    Institute of Cytology and Genetics, Novosibirsk, Russia.
    Kieselbach, T
    Karolinska Institute.
    Kiseleva, E V
    Institute of Cytology and Genetics, Novosibirsk, Russia.
    Hallberg, Einar
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Annulate lamellae play only a minor role in the storage of excess nucleoporins in Drosophila embryos2004In: Traffic: the International Journal of Intracellular Transport, ISSN 1398-9219, E-ISSN 1600-0854, Vol. 5, no 3, p. 152-164Article in journal (Refereed)
    Abstract [en]

    The nuclear pore complexes (NPCs), multiprotein assemblies embedded in the nuclear envelope, conduct nucleo-cytoplasmic traffic of macromolecules. Mimics of NPCs, called annulate lamellae pore complexes (ALPCs), are usually found in cytoplasmic membranous stacks in oocytes and early embryonic cells. They are believed to constitute storage compartments for excess premade nucleoporins. To evaluate the extent to which ALPCs store nucleoporins in early embryonic cells we took advantage of syncytial Drosophila embryos, containing both AL and rapidly proliferating nuclei in the common cytoplasm. Electron microscopic morphometric analysis showed that the number of ALPCs did not decrease to compensate for the growing number of NPCs during syncytial development. We performed Western blot analysis to quantify seven different nucleoporins and analyzed their intraembryonal distribution by confocal microscopy and subcellular fractionation. Syncytial embryos contained a large maternally contributed stockpile of nucleoporins. However, even during interphases, only a small fraction of the excess nucleoporins was assembled into ALPCs, whereas the major fraction was soluble and contained at least one phosphorylated nucleoporin. We conclude that in Drosophila embryos ALPCs play only a minor role in storing the excess maternally contributed nucleoporins. Factors that may prevent nucleoporins from assembly into ALPCs are discussed.

  • 57. Pineda-Krch, M
    et al.
    Lehtilä, Kari
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Challenging the genetically homogeneous individual2004In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 17, no 6, p. 1192-1194Article in journal (Refereed)
  • 58.
    Rehn, Stanley
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Stensland, B
    The three-component reaction between isatin, alpha-amino acids, and dipolarophiles2004In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 2, p. 413-418Article in journal (Refereed)
    Abstract [en]

    3-Spiro[pyrrolidino-oxindoles] were prepared in high yields from a three-component reaction between isatin, an alpha-amino acid, and a dipolarophile. Both N-substituted and N-unsubstituted alpha-amino acids were used as the amine component.

  • 59.
    Rustum, Cecilia
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Stockholms universitet, Institutionen för neurokemi.
    Dynamic aspects of nucleocytoplasmic trafficking2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Cellular structures and compartmentalization is the result of a dynamic steady state exchange between its components. This thesis is focused in investigations of dynamic properties of green fluorescent protein (GFP)-labeled proteins in live cells using confocal laser microscopy in combination with bleaching techniques such as fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP).

    Studies of dynamic properties of c-Myc in living cells showed that c-Myc is shuttling between the nucleus and the cytoplasm. c-Myc also enters the nucleoli during certain conditions. Nucleolar c-Myc is dynamically associated to structural component(s) of nucleoli, but can exchange with soluble pools in the nucleoplasm and cytoplasm.

    Photobleaching experiments showed that a significant fraction of HIV-1 Vpr is dynamically associated with the NE and rapidly exchanges between the nucleoplasm and the cytoplasm. The yeast two-hybrid system, pull-down experiments and co-immunoprecipitating was used to show that Vpr interacts specifically and directly with a domain in the N-terminal portion of the NPC protein hCG1. The results suggest that the specific interaction of HIV-1 Vpr with the nucleoporin hCG1 results in the dynamic retention of Vpr at the nuclear envelope.

    The distribution and dynamic properties of NPC proteins was investigated in NIH/3T3 cells, lacking the pore membrane protein gp210. Confocal laser scanning microscopy and FRAP experiments showed that the absence of gp210 from nuclear pores of NIH/3T3 cells did neither alter the distribution nor dynamic properties of POM121 and NUP107 (two NPC proteins stably integrated in the NPC).

    Degradation of the integral nuclear pore membrane protein POM121 during apoptosis was investigated in relation to other apoptotic events. POM121 cleavage, which is the earliest sign of dismantling of the nuclear membrane, is due to caspase-3-dependent cleavage at aspartate-531. Loss of nuclear compartmentalization in live cells undergoing apoptosis was monitored as appearance of GFP-NLS in the cytoplasm. The time of appearance of cytoplasmic GFP-NLS correlated with caspase-3-dependent cleavage of POM121. Both events occured concomitantly with collapsing of chromatin against the nuclear periphery, but preceded the onset of nucleosomal DNA fragmentation.

    Translocation ability of the cell-penetrating peptide, transportan, into living cells was investigated. Recombinantly expressed GFP was purified and conjugated to chemically synthesized transportan via a disulfide bond and added to tissues culture cells. Transportan was able to internalize a 27 kDa protein such as GFP in a native folded state into living cells.

  • 60.
    Rytkönen, Paulina
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Tillväxtens Tal och Verklighet: erfarenheter från Latinamerika2005In: Världens eko: en antologi om miljö- och utvecklingsfrågor / [ed] Suzanne Påhlman, Stockholm: Atlas , 2005, p. 100-116Chapter in book (Other academic)
  • 61.
    Saunders, Fred
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science, Environmental science. Södertörn University, School of Chemistry, Biology, Geography and Environmental Science, Geography.
    The Sustainability and Social Equity of Alternative Agrofood Systems2004In: Finnish Journal of Rural Research and Policy (Maaseudun uusi aika), ISSN 1237-413X, Vol. 12, no 4, p. 57-70Article in journal (Refereed)
  • 62. Scherfer, C
    et al.
    Karlsson, C
    Loseva, O
    Bidla, G
    Goto, A
    Havemann, J
    Dushay, Mitchell S
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Theopold, U
    Isolation and characterization of hemolymph clotting factors in Drosophila melanogaster by a pullout method2004In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 14, no 7, p. 625-629Article in journal (Refereed)
    Abstract [en]

    Clotting is critical in limiting loss of hemolymph and initiating wound healing in insects as well as in vertebrates [1]. Clotting is also an important immune defense, quickly forming a secondary barrier to infection, thereby immobilizing, and possibly killing bacteria directly [2, 3]. Here, we describe methods to assess clotting and to extract the clot from Drosophila larval hemolymph by using aggregation of paramagnetic beads. The validity of the assay was demonstrated by characterization of mutants. We show that clotting occurs in the absence of phenoloxidase and that the Drosophila clot binds bacteria. We also describe a pullout assay to purify the clot as a whole, free from entrapped hemocytes and cellular debris. Proteins subsequently identified by mass spectrometry include both predicted and novel clot proteins. Immune induction has been shown for three of the latter, namely Tiggrin and two unknown proteins (GC15825 and CG15293) [4,5] that we now propose function in hemolymph clotting. The most abundant clot protein is Hemolectin [6], and we confirm that hemolectin mutant larvae show clotting defects.

  • 63.
    Shi, Lan-Xin
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. University of California, One Shields Avenue, Davis, United States .
    Schröder, W. P.
    The low molecular mass subunits of the photosynthetic supracomplex, photosystem II2004In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1608, no 2-3, p. 75-96Article in journal (Refereed)
    Abstract [en]

    The photosystem II (PSII) complex is located in the thylakoid membrane of higher plants, algae and cyanobacteria and drives the water oxidation process of photosynthesis, which splits water into reducing equivalents and molecular oxygen by solar energy. Electron and X-ray crystallography analyses have revealed that the PSII core complex contains between 34 and 36 transmembrane α-helices, depending on the organism. Of these helices at least 12-14 are attributed to low molecular mass proteins. However, to date, at least 18 low molecular mass (<10 kDa) subunits are putatively associated with the PSII complex. Most of them contain a single transmembrane span and their protein sequences are conserved among photosynthetic organisms. In addition, these proteins do not have any similarity to any known functional proteins in any type of organism, and only two of them bind a cofactor. These findings raise intriguing questions about why there are so many small protein subunits with single-transmembrane spans in the PSII complex, and their possible functions. This article reviews our current knowledge of this group of proteins. Deletion mutations of the low molecular mass subunits from both prokaryotic and eukaryotic model systems are compared in an attempt to understand the function of these proteins. From these comparisons it seems that the majority of them are involved in stabilization, assembly or dimerization of the PSII complex. The small proteins may facilitate fast dynamic conformational changes that the PSII complex needs to perform an optimal photosynthetic activity.

  • 64. Sjögren, M
    et al.
    Göransson, U
    Johnson, Ann-Louise
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Dahlström, M
    Andersson, R
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Jonsson, P R
    Bohlin, L
    Antifouling activity of brominated cyclopeptides from the marine sponge Geodia barretti2004In: Journal of natural products (Print), ISSN 0163-3864, E-ISSN 1520-6025, Vol. 67, no 3, p. 368-372Article in journal (Refereed)
    Abstract [en]

    In this work, we show the potent antifouling effects of two compounds, barettin (cyclo[(6-bromo-8-entryptophan)arginine]) (1), isolated as a Z/E mixture (87/13), and 8,9-dihydrobarettin (cyclo[(6-bromotryptophan)arginine]) (2), isolated from the marine sponge Geodia barretti. The compounds were isolated guided by their ability to inhibit the settlement of cyprid larvae of the barnacle Balanus improvisus, and their structures were determined by means of mass spectrometry, NMR, and quantitative amino acid analysis. The activities of these brominated diketopiperazine-like cyclic dipeptides are in the range of antifouling agents in use today, as shown by their EC50 values of 0.9 and 7.9 muM, respectively. However, contrary to today's antifouling agents, the effects of barettin and 8,9-dihydrobarettin are nontoxic and reversible. A small set of synthetic analogues, including L-arginine, L-tryptophan, 5-bromo-D,L-tryptophan, 6-bromo-D,L-tryptophan, and 6-fluoro-D,L-tryptophan, were tested for possible structure-activity relationships. None of these compounds showed any effect at a concentration of 10 muM. We hypothesize that the isolated compounds are part of the sponge's chemical defense to deter fouling organisms. This theory is supported by the fact that barettin is found in water exposed to living specimens of G. barretti in concentrations that completely inhibit barnacles from settling.

  • 65.
    Sjöling, Sara
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Mohammed, S M
    Lyimo, T J
    Kyaruzi, J J
    Benthic bacterial diversity and nutrient processes in mangroves: impact of deforestation2005In: Estuarine, Coastal and Shelf Science, ISSN 0272-7714, E-ISSN 1096-0015, Vol. 63, no 3, p. 397-406Article in journal (Refereed)
    Abstract [en]

    The bacterial diversity and nutrient dynamics of mangrove sediments in Kisakasaka, Tanzania, was investigated in order to evaluate potential changes associated with deforestation of mangroves. Study sites included relatively undisturbed, recently protected mangroves and clear-cut mangrove areas that were sampled during both the wet and dry seasons. Physicochemical parameters, nitrogenase activity, pore water nutrient concentrations and bacterial diversity were measured in sediment depth profiles using both molecular and chemical techniques. Results show that there are significant differences in sediment pore water nutrient concentrations and bacterial diversity in sediments of mangrove areas which have been deforested compared to those which have been protected. Average measured values for protected and deforested areas, respectively, were: sulphide (S-2-),S- < 42 +/- 10 mu M and > 1.9 +/- 0.5 mM at 30 cm depth; ammonium (NH4+), 58 +/- 2 mu M and 113 +/- 12 mu M at 4-5 cm depth; soluble reactive phosphate, 40.2 +/- 11 mu M and 18.4 +/- 1.2 at 4-5 cm depth. Nitrogen fixation rates were lower in deforested areas during day and night, organic content was higher in protected areas (20 +/- 5%) compared to deforested areas (12 +/- 3%). The bacterial diversity was lower in deforested areas as determined by Shannon index using 16S rRNA gene analysis with terminal restriction fragment length polymorphism.

  • 66. Skarstein, Frode
    et al.
    Folstad, Ivar
    Liljedal, Ståle
    Grahn, Mats
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    MHC and fertilization success in the Arctic charr (Salvelinus alpinus)2005In: Behavioral Ecology and Sociobiology, ISSN 0340-5443, E-ISSN 1432-0762, Vol. 57, no 4, p. 374-380Article in journal (Refereed)
    Abstract [en]

    Genes of the major histocompatibility complex (MHC) are remarkably polymorphic. Several selection mechanisms have been invoked to account for this diversity, including disassortative mating preferences. In addition, eggs may discriminate between sperm based on MHC. To investigate the effects of MHC-genotype on fertilization success, we obtained mature gametes from ripe Arctic charr (Salvelinus alpinus) males and females captured on spawning grounds. The eggs of each female were divided into two batches, and by letting each of 2 males fertilize 1 of the batches, we obtained a total of 36 half-sibling batch-pairs. The semen was diluted to ensure that the two males in each half-sibling batch-pair contributed with the same number of sperm cells. We found that MHC-heterozygous males had significantly higher fertilization success than MHC-homozygous males and neither initial spermatocrit, sperm motility nor swimming velocity co-varied with difference in fertilization success. There was no effect of female genotype or female-male MHC-similarity on fertilization success. However, one MHC-allele was associated with increased fertilization success. It seems plausible that the difference in fertilization success between homo-and heterozygous males may be due to MHC-dependent sperm selection by the ovum.

  • 67.
    Slätt, Johnny
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Cyanoacetylation of indoles, pyrroles and amines, and synthetic uses of these products2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on an organic synthetic project aimed towards development of small molecules acting on the P2 receptor as well as development of synthetic methods to such molecules (primarily indoles and featuring isatogens in particular). The new methodology includes cyanoacetylation of indoles, pyrroles, amines, and enamines using cyanoacetic acid in acetic anhydride. The molecules obtained (e.g. 3-cyanoacetylindole) could be further functionalized by nitrosation followed by reduction. Cyanoacetylated anilines carrying an appropriate substituent (e.g NO2) could be cyclized to quinoxaline-N-oxides, a class of molecules which have been considered as analogues to isatogens. The molecule 2,2'-pyridylisatogen tosylate (PIT) is particularly interesting within this class because of its documented interaction with the P2 receptor.

  • 68.
    Slätt, Johnny
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Reinvestigation of a synthesis of quinoxaline-N-oxidesManuscript (preprint) (Other academic)
  • 69.
    Slätt, Johnny
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Beslic, Senad
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Stensland, Birgitta
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Intitutet.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Functionalizations of 3-(cyanoacetyl)indole and 2-(cyanoacetyl)pyrroleManuscript (preprint) (Other academic)
  • 70.
    Slätt, Johnny
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Janosik, Tomasz
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Wahlström, Niklas
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Synthetic applications of 3-(cyanoacetyl)indoles and related compounds2005In: Journal of Heterocyclic Chemistry, ISSN 0022-152X, E-ISSN 1943-5193, Vol. 42, no 1, p. 141-145Article in journal (Refereed)
    Abstract [en]

    Various synthetic applications of 3-(cyanoacetyl)indoles, as well as syntheses of some related indoles, have been investigated. Diethyl 2-(1H-indol-3-yl)-2-oxoethylphosphonate and a methyl derivative thereof have been prepared in one step from indole. Moreover, it was demonstrated that 3-(cyanoacetyl)indoles are useful starting materials for the preparation of for example 3-(1H-indol-3-yl)-3-oxopropanamides, 3-heteroarylindoles or 3-heteroaroylindoles.

  • 71.
    Slätt, Johnny
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Romero, Ivan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Cyanoacetylation of indoles, pyrroles and aromatic amines with the combination cyanoacetic acid and acetic anhydride2004In: Synthesis (Stuttgart), ISSN 0039-7881, E-ISSN 1437-210X, no 16, p. 2760-2765Article in journal (Refereed)
    Abstract [en]

    Cyanoacetic acid was activated with acetic anhydride and when heated this reagent reacted with a variety of both activated and deactivated pyrroles, indoles and aniline derivatives.

  • 72. Srivastava, R.
    et al.
    Varshney, G. K.
    Kitambi, Satish Srinivas
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Amla, D. V.
    Analysis of glutamine synthetase (glnA) gene from prokaryotic and eukaryotic organisms2004In: Physiology and Molecular Biology of Plants, ISSN 0971-5894, Vol. 10, no 2, p. 197-202Article in journal (Refereed)
    Abstract [en]

    Glutamine synthetase (GS) is a key enzyme involved in nitrogen metabolism that performs the essential biochemical function of ammonium assimilation and glutamine synthesis. The enzyme and its isoforms are present universally in all organisms and display diverse regulatory patterns. In this study, we have analyzed some sequences upstream and downstream the initiation codon of the structural gene of GS (glnA) to show that these sequences are involved in regulation and stable expression of the enzyme. GS is known to be regulated by adenylylation-deadenylylation cascade in some organisms. Analysis of the adenylylation site from several organisms revealed that the site could also be deciphered from those organisms where regulation of the enzyme is not known by adenylylation. The adenylylation site was mutated by the use of Swiss-PdbViewer and possible reasons were assigned to the functional and nonfunctional properties of this site in various organisms. This analysis has also helped in assigning functional relationships to some conserved sequences within and in the proximity of the glnA gene.

  • 73. Söderqvist, Tore
    et al.
    Hammer, Monica
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Gren, Ing-Marie
    Samverkan för människa och natur: en introduktion till ekologisk ekonomi2004Book (Other academic)
  • 74. Theopold, U
    et al.
    Schmidt, O
    Söderhäll, K
    Dushay, Mitchell S
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Coagulation in arthropods: defence, wound closure and healing2004In: Trends in immunology, ISSN 1471-4906, E-ISSN 1471-4981, Vol. 25, no 6, p. 289-294Article in journal (Refereed)
    Abstract [en]

    Arthropods have open circulatory systems and must seal wounds and keep bacteria from entering the hemocoel using efficient clotting systems. Enzymes that crosslink the clot include transglutaminase, which is phylogenetically conserved, and phenoloxidase, which is not found in vertebrates. Prophenoloxidase is usually activated through a proteolytic cascade similar to the vertebrate clotting cascade. The well-characterized clotting cascade in horseshoe crabs is strongly activated by bacterial elicitors, in contrast to vertebrate clotting where induction relies more on endogenous signals. Many arthropod clotting factors are not orthologues of blood clotting factors, but show novel architectures assembled from domains that are also found in their vertebrate counterparts. The cellular mechanisms that lead to coagulation of blood and hemolymph appear to be similar. Recent findings in Drosophila reveal parallels between developmental processes that involve epithelial fusion and wound healing, enabling genetic dissection of the signal pathways involved. This Review is the first in a series on interactions between haemostasis and inflammation.

  • 75.
    Wahlström, Niklas
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Synthesis of 2,3 '-biindolyls and indolo[3,2-a]carbazoles2004In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 45, no 39, p. 7273-7275Article in journal (Refereed)
    Abstract [en]

    Several highly activated 2,3'-biindolyls were prepared from methyl 5,6-dimethoxyindole-2-carboxylate and oxindoles. The 2,3'-biindolyls were further transformed into a hydroxy indolo[3,2-a]carbazole and a bisindole amde.

  • 76.
    Wahlström, Niklas
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science.
    Romero, I
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Synthesis of metabolites of the Ah receptor ligand 6-formylindolo[3,2-b]carbazole2004In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 12, p. 2593-2602Article in journal (Refereed)
    Abstract [en]

    Synthesis of the five mono- and di-hydroxylated metabolites of the aryl hydrocarbon receptor high affinity ligand 6-formylindolo[3,2-b]carbazole is described. The structures of the metabolites were unequivocally established as 2-hydroxy-, 8-hydroxy-, 2,10-dihydroxy-, 4,8-dihydroxy- and 2,8-dihydroxyindolo[3,2-b]carbazole-6-carboxaldehyde.

  • 77.
    Wahlström, Niklas
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Stensland, B
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Synthesis of 2,3 '-diindolylmethanes and substituted indolo[3,2-b]carbazoles2004In: Synthesis (Stuttgart), ISSN 0039-7881, E-ISSN 1437-210X, no 8, p. 1187-1194Article in journal (Refereed)
    Abstract [en]

    Three different synthetic routes to substituted 2,3'-diindolylmethanes, and the syntheses of substituted indolo[3,2-b]carbazoles are described. The first rigid proof of an acylation in the 2-position of a 1,3-unsubstituted indole is also presented in the form of an X-ray structure.

  • 78.
    Wahlström, Niklas
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Stensland, B
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Synthesis of the marine alkaloid caulersin2004In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 60, no 9, p. 2147-2153Article in journal (Refereed)
    Abstract [en]

    A three-step synthesis of caulersin (3) from indole-2-acetic acid methyl ester and indole-2-carbonyl chloride is described. As the spectral data of the synthetic sample differed from those reported for the natural product, the structure was determined by X-ray crystallography.

  • 79.
    Wiklund, Per
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Synthesis of heterocycles from anthranilic acid and its derivatives2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Anthranilic acid (2-aminobenzoic acid, Aa) is the biochemical precursor to the amino acid tryptophan, as well as a catabolic product of tryptophan in animals. It is also integrated into many alkaloids isolated from plants. Aa is produced industrially for production of dyestuffs and pharmaceuticals. The dissertation gives a historical background and a short review on the reactivity of Aa. The synthesis of several types of nitrogen heterocycles from Aa is discussed. Treatment of anthranilonitrile (2-aminobenzonitrile, a derivative of Aa) with organomagnesium compounds gave deprotonation and addition to the nitrile triple bond to form amine-imine complexed dianions. Capture of these intermediate with acyl halides normally gave aromatic quinazolines, a type of heterocyclic compounds that is considered to be highly interesting as scaffolds for development of new drugs. When the acyl halide was a tertiary 2-haloacyl halide, the reaction instead gave 1,4-benzodiazepine-3-ones via rearrangement. These compounds are isomeric to the common benzodiazepine drugs (such as diazepam, Valium®) which are 1,4-benzodiazepine-2-ones. Capture of the dianions with aldehydes or ketones, led to 1,2-dihydroquinazolines. Unsubstituted imine anions could be formed by treatment of anthranilonitrile with diisobutylaluminium hydride. Also in this case capture with aldehydes gave 1,2-dihydroquinazolines. Several different dicarboxylic acid derivatives of Aa were treated with dehydrating reagents, and the resulting products were more or less complex 1,3-benzoxazinones, one of which required X-ray crystallography confirm its structure. During the work on preparation of N-substituted derivatives of Aa, necessary for synthesis of 1,4-benzodiazepine-3,5-diones, it was noted that many of the obtained products were in fact not N-substituted, but O-substituted. This challenged the established notion that Aa reacts nucleophilically at the N-terminal under most conditions. Several grave errors in the recent literature were revealed. In 1976 researchers from the group that originally developed the common benzodiazepine drugs published a retraction of a claim of synthesis of a benzodiazepine by Gärtner in 1904. They found that the method actually gave a 6-membered ring system, not a 7-membered 1,4-benzodiazepine-3,5-dione as originally claimed. Because the 1,4-benzodiazepine skeleton is highly interesting as a scaffold for development of new drugs, a few publications on synthesis of this target has appeared. However, repetition of several of the described syntheses failed to yield the poorly described products. Studies on how to ring close N-carbamoyl derivatives of Aa were undertaken. It became clear that Umpolung of the substrates by N-derivatisation was a necessary prerequisite for ring closure. The introduction of the N-nitroso group was developed to this end, leading to N1-nitroso substituted 1,4-benzodiazepine-3,5-diones. The nitroso group could be removed after ring closure. Heating of one of these compounds induced a ring contraction rearrangement. A proposed mechanism involves elimination of HNO (nitrosyl) and proton mediated loss of CO.

  • 80.
    Wiklund, Per
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Alkylation and acylation of basic salts of anthranilic acid2004In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 45, no 5, p. 969-972Article in journal (Refereed)
    Abstract [en]

    The O-nucleophilicity of basic anthranilic acid salts was documented, analyzed, and utilized in synthesis. Specifically substitutions leading to esters instead of secondary amines, and formation of anthranilic acid anhydrides were studied.

  • 81.
    Wiklund, Per
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Rogers-Evans, M
    F. Hoffmann-La Roche Ltd, Basel, Switzerland .
    Bergman, Jan
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Synthesis of 1,4-benzodiazepine-3,5-diones2004In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 69, no 19, p. 6371-6376Article in journal (Refereed)
    Abstract [en]

    Even though benzodiazepines have a strong position in medicinal chemistry, very few synthetic routes to 1H-1,4-benzodiazepine-3,5(2H,4H)-diones have ever been published and the claimed products have often been poorly characterized. Through the present work several 1H-1,4-benzodiazepine-3,5(2H,4H)-diones have become available from N-carbamoylmethylanthranilic acids. The required ring closures were achieved only when the amino groups of the starting materials were substituted with electron withdrawing groups such as acetyl, alkyloxycarbonyl, or nitroso. During the synthetic work a novel ring contraction rearrangement from a 1-nitroso-1H-1,4-benzodiazepine-3,5(2H,4H)-dione to a 3H-quinazoline-4-one was observed. The proposed mechanism involves elimination of HNO followed by a proton-mediated loss of CO. The 1-nitrosated 1,4-benzodiazepinediones could be separately denitrosated to the corresponding amino compounds.

  • 82. Wu, X.
    et al.
    Jörnvall, H.
    Berndt, Kurt D.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institutet.
    Oppermann, U.
    Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance2004In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 313, no 1, p. 89-96Article in journal (Refereed)
    Abstract [en]

    Expression patterns in Escherichia coli of two small archaeal proteins with a natural content of about 30% rare codons were analyzed. The proteins, a histone-like protein from Sulfolobus shibatae (Ssh10), and a glutaredoxin-like protein from Methanobacterium thermoautotrophicum (mtGrx), were produced with expression plasmids encoding wild-type genes, codon-optimized synthetic, and GST-fusion genes. These constructs were expressed in BL21 (DE3), its LysS derivative, and modified strains carrying copies for rare codon tRNAs or deletions in the RNAseE gene. Both Ssh10 and mtGrx expression levels were constitutively high in BL21(DE3) and its derivatives, with the exception of the LysS phenotype, which prevented high level expression of the Ssh10 wild-type gene. Surprisingly, a codon-optimized mtGrx gene construct displayed undetectable levels of protein production. The translational block observed with the synthetic mtGrx gene could be circumvented by using a synthetic mtGrx-glutathione S-transferase (GST) fusion construct or by in vitro translation. Taken together, the results underscore the importance of mRNA levels and RNA stability, but not necessarily tRNA abundance for efficient heterologous protein production in E. coli.

  • 83.
    Xue, Yongtao
    et al.
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Haas, S A
    Max-Plank Institute for Molecular Genetics, Berlin, Germany.
    Brino, L
    Eurogentec SA, Seraing, Belgium.
    Gusnanto, A
    Karolinska Institute.
    Reimers, M
    Karolinska Institute.
    Talibi, D
    Eurogentec SA, Seraing, Belgium.
    Vingron, M
    Max-Plank Institute for Molecular Genetics, Berlin, Germany.
    Ekwall, Karl
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    Wright, Anthony P H
    Södertörn University, School of Chemistry, Biology, Geography and Environmental Science. Karolinska Institute.
    A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift2004In: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 21, no 1, p. 25-39Article in journal (Refereed)
    Abstract [en]

    Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission yeast. The microarray contains DNA fragments, PCR-amplified from a genomic DNA template, that represent >99% of the 5000 or so annotated fission yeast genes, as well as a number of control sequences. The GenomePRIDE software used attempts to design similarly sized DNA fragments corresponding to gene regions within single exons, near the 3'-end of genes that lack homology to other fission yeast genes. To validate the design and utility of the array, we studied expression changes after a 2 h temperature shift from 25degreesC to 36degreesC, conditions widely used when studying temperature-sensitive mutants. Obligingly, the vast majority of genes do not change more than two-fold, supporting the widely held view that temperature-shift experiments specifically reveal phenotypes associated with temperature-sensitive mutants. However, we did identify a small group of genes that showed a reproducible change in expression. Importantly, most of these corresponded to previously characterized heat-shock genes, whose expression has been reported to change after more extreme temperature shifts than those used here.. We conclude that the DNA microarray represents a useful resource for fission yeast researchers as well as the broader yeast community, since it will facilitate comparison with the distantly related budding yeast, Saccharomyces cerevisiae. To maximize the utility of this resource, the array and its component parts are fully described in On-line Supplementary Information and are also available commercially.

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