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  • 201.
    Holmström, Therese E.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Wenner-Grens institut.
    Mattsson, Charlotte L.
    Stockholms universitet, Naturvetenskapliga fakulteten, Wenner-Grens institut.
    Wang, Yanling
    Stockholms universitet, Naturvetenskapliga fakulteten, Wenner-Grens institut.
    Iakovleva, Irina
    Stockholms universitet, Naturvetenskapliga fakulteten, Wenner-Grens institut.
    Petrovic, Natasa
    Stockholms universitet, Naturvetenskapliga fakulteten, Wenner-Grens institut.
    Nedergaard, Jan
    Stockholms universitet, Naturvetenskapliga fakulteten, Wenner-Grens institut.
    Non-transactivational, dual pathways for LPA-induced Erk1/2 activation in primary cultures of brown pre-adipocytes2010Inngår i: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 316, nr 16, s. 2664-75Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In many cell types, G-protein-coupled receptor (GPCR)-induced Erk1/2 MAP kinase activation is mediated via receptor tyrosine kinase (RTK) transactivation, in particular via the epidermal growth factor (EGF) receptor. Lysophosphatidic acid (LPA), acting via GPCRs, is a mitogen and MAP kinase activator in many systems, and LPA can regulate adipocyte proliferation. The mechanism by which LPA activates the Erk1/2 MAP kinase is generally accepted to be via EGF receptor transactivation. In primary cultures of brown pre-adipocytes, EGF can induce Erk1/2 activation, which is obligatory and determinant for EGF-induced proliferation of these cells. Therefore, we have here examined whether LPA, via EGF transactivation, can activate Erk1/2 in brown pre-adipocytes. We found that LPA could induce Erk1/2 activation. However, the LPA-induced Erk1/2 activation was independent of transactivation of EGF receptors (or PDGF receptors) in these cells (whereas in transformed HIB-1B brown adipocytes, the LPA-induced Erk1/2 activation indeed proceeded via EGF receptor transactivation). In the brown pre-adipocytes, LPA instead induced Erk1/2 activation via two distinct non-transactivational pathways, one G(i)-protein dependent, involving PKC and Src activation, the other, a PTX-insensitive pathway, involving PI3K (but not Akt) activation. Earlier studies showing LPA-induced Erk1/2 activation being fully dependent on RTK transactivation have all been performed in cell lines and transfected cells. The present study implies that in non-transformed systems, RTK transactivation may not be involved in the mediation of GPCR-induced Erk1/2 MAP kinase activation

  • 202.
    Hultengren, Svante
    et al.
    Naturcentrum.
    Bohman, Petter
    Naturcentrum.
    Ryrholm, Nils
    Högskolan i Gävle, Akademin för teknik och miljö, Avdelningen för elektronik, matematik och naturvetenskap, Biologi.
    Weibull, Henrik
    Naturcentrum.
    Inventeringar av kalkhällmarker i östra Dalsland2013Rapport (Annet vitenskapelig)
    Abstract [sv]

    Naturcentrum AB har på uppdrag av Länsstyrelsen i Västra Götaland genomfört inventeringar av naturvårdsintressanta arter på kalkhällmarker i östra Dalsland. Inventeringen har fokuserat på särskilt intressanta arter t ex rödlistade arter, sällsynta arter m m, inom grupperna fjärilar, bin, lavar, mossor och marksvampar. Dessutom har presenteras spridda observationer inom andra grupper, till exempel tvåvingar och trollsländor.

    De dalsländska kalkrika lerskifferhällmarkerna utgörs av någon mil breda, omvandlade berggrundsstråk i de mellersta och östra delarna av landskapet. Dessa kalkmarker skiljer sig från de geologiskt yngre och sedimentära kalkområdena som är typiska för till exempel Öland och Gotland. Förutsättningarna för floran och faunan i Dalslands kalkområden är unika genom det milda och fuktiga klimatet och att markke- min avviker något från de flesta andra kalkrika trakterna i Sverige. Dessa specifika förhållanden gynnar en lång rad sällsynta eller rödlistade arter.

    Fyra av de besökta områdena ligger på Ryrhalvön norr om Köpmannebro och den femte vid Ånimskogs kyrka. Samtliga delområden utgörs av västvända branter i direkt anslutning till sjöarna Ånimmen och Östebosjön. Miljöerna är generellt öppna och det västvända läget skapar ett varmt och solexponerat mikroklimat. I anslutning till de kala hällarna finns partier med tunna, kalkhaltiga jordlager och grusmarker. Graden av beskogning varierar både inom och mellan de olika delområdena.

    Inventeringarna genomfördes under några dagar under sommaren 2006 samt med en dags kompletterande lavinventering under februari 2008. Totalt på träffades 24 rödlistade arter fördelade enligt följande; sju fjärilsarter, två biarter, tre lavar, sex olika mossor och sex arter av svampar. Flera av dessa är ytterst sällsynta och har sin huvudsakliga utbredning i landet på dessa kalkrika lerskifferhällar. Vidare noterades ett 30-tal nya arter för landskapet Dalsland. Det största antalet nya fynd gjordes inom gruppen insekter vilket visar att kännedomen om landskapets insektsfauna är mycket bristfällig.

    Klot-tegellaven Psora globifera är klassad som starkt hotad (EN) och har huvuddelen av sina kända före- komster i kalkrika områden i Dalsland. Arten växer på lättvittrade, solexponerade, kalklerskifferhällar. I delområde 3 förekommer arten rikligt och i delområde 4 något mera sparsamt. Klotsporig skifferlav Sarcogyne distinguenda (VU) är en annan mycket sällsynt lav med få kända lokaler i landet av vilken den ena utgörs av delområde 5 (Carlsson 1998). Arten är knuten till klippor av kalklerskiffer. Det stora antalet arter gelélavar Collema spp. (sju stycken) är anmärkningsvärt även om ingen av arterna är rödlistade. Av mos-sorna bör särskilt nämnas hår-rosettmossa Riccia ciliata (VU), dvärgrosettmossa Riccia warnstorfii (VU) och trubbklockmossa Encalypta mutica (NT) vilka alla är mer eller mindre knutna till kalkhällar eller kalkrika jordar. Rosettmossorna växer rikligt i delområde 1 medan trubbklockmossan, som omfattas av habitatdi-rektivet inom Natura 2000, noterades i delområde 5. Brun fingersvamp Clavaria pullei (EN) noterades på gräsmarkerna i delområde 5. Arten verkar vara knuten till öppna och hävdade kalkrika marker. Bland in-sekterna utgör nyponsandbiet Andrena nitida (VU), fibblesandbiet A. fulvago (NT) och jungfrulinpraktmal Hypercallia citrinalis (NT) några av de mest anmärkningsvärda arterna. Nyponsandbiet som noterades i del-område 1 är mycket sällsynt och observerades senast 1949 i Dalsland.

    Inventeringarna som utförts är av stickprovskaraktär och det bedöms som sannolikt att fler värdefulla arter kan påträffas vid fördjupade inventeringar. Detta gäller både de behandlade delområdena och kalk-lerskiffermarker i allmänhet.

  • 203.
    Hägg, Sara
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologiska Beräkningar. Linköpings universitet, Tekniska högskolan.
    Alserius, Thomas
    Department of Cardiothoracic Surgery and Anaesthesiology and Department of Molecular Medicine and Surgery, Karolinska University Hospital Solna, Karolinska Institutet, Stockholm, Sweden.
    Noori, Peri
    Computational Medicine Group (www.CompMed.se), Center for Molecular Medicine, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.
    Skogsberg, Josefin
    Computational Medicine Group (www.CompMed.se), Center for Molecular Medicine, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.
    Ruusalepp, Arno
    Department of Thoracic Surgery, Tartu University Hospital, Tartu, Estonia.
    Ivert, Torbjörn
    Department of Cardiothoracic Surgery and Anaesthesiology and Department of Molecular Medicine and Surgery, Karolinska University Hospital Solna, Karolinska Institutet, Stockholm, Sweden.
    Tegnér, Jesper
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologiska Beräkningar. Linköpings universitet, Tekniska högskolan.
    Björkegren, Johan
    Computational Medicine Group (www.CompMed.se), Center for Molecular Medicine, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.
    Dual-Specificity Phosphatase-1—An Anti-Inflammatory Marker in Blood Independently Predicting Prolonged Postoperative Stay after Coronary Artery Bypass Grafting: DUSP1 – A Preoperative Blood Marker of Postoperative StayManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Objectives: Perform multi-organ expression profiling to identify gene markers predicting postoperative complications and hospitalization after coronary artery by-pass grafting (CABG) surgery.

    Background: Identifying patients who are at increased risk of morbidity and prolonged post-operative stay is of interest from both health-economic and individual patient perspectives. Patients with diabetes often present with inflammatory conditions and have prolonged hospitalization after CABG. The recent development of technologies to generate high-dimensional data provides an opportunity to identify preoperative markers that can be used to help optimize preoperative planning to minimize postoperative complications.

    Methods: We analyzed 198 whole-genome expression profiles of liver, skeletal muscle, and visceral fat isolated from 66 patients undergoing CABG in the Stockholm Atherosclerosis Gene Expression (STAGE) study. The findings were validated in pre-operative blood samples isolated from 181 patients undergoing CABG at Tartu University Hospital.

    Results: As shown in other studies, diabetic CABG patients in the STAGE cohort also had prolonged hospitalization time (P<0.02). Out of ~50 000 mRNAs measures in the liver, skeletal muscle and visceral fat in 66 STAGE patients, the mRNA levels of anti-inflammatory gene dual specificity phosphatase-1 (DUSP1) correlated independently with post-operative rehabilitation and separated the patients into those with normal (8 days) and prolonged hospitalization (>8 days). In the validation cohort, preoperative blood levels of DUSP1 separated patients with short and long hospitalization stay (P=9x10-10).

    Conclusions: From genome scans in three separate organs, we identified the anti-inflammatory gene DUSP1 as a pre-operative marker indicating risk for prolonged postoperative stay after CABG.

  • 204.
    Hägg, Sara
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologiska Beräkningar. Linköpings universitet, Tekniska högskolan.
    Salehpour, Mehran
    Ion Physics, Angström Laboratory, Department of Engineering Sciences, Uppsala University, Uppsala, Sweden.
    Noori, Peri
    From the Computational Medicine Group, Center for Molecular Medicine, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.
    Lundström, Jesper
    From the Computational Medicine Group, Center for Molecular Medicine, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.
    Skogsberg, Josefin
    From the Computational Medicine Group, Center for Molecular Medicine, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.
    Konrad, Peter
    Department of Surgery, Stockholm Söder Hospital, Karolinska Institutet, Stockholm, Sweden.
    Rosfors, Stefan
    Department of Clinical Physiology, Stockholm Söder Hospital, Karolinska Institutet, Stockholm, Sweden.
    Tegnér, Jesper
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologiska Beräkningar.
    Björkegren, Johan
    From the Computational Medicine Group, Center for Molecular Medicine, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden.
    Carbon-14 Dating to Determine Carotid Plaque Age: Carbon-14 Dating of Carotid PlaquesManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Rationale: The exact nature of atherosclerotic plaque development and the molecular mechanisms that lead to clinical manifestations of carotid stenosis are unclear. After nuclear bomb tests in the 1950s, atmospheric 14C concentrations rapidly increased. Since then, the concentrations have been declining, and the curve of declination can be used to date biological samples synthesized during the last five to six decades.

    Objective: To investigate plaque age as a novel characteristic of atherosclerotic plaques in patients with carotid stenosis.

    Methods and Results: Carotid plaques from 29 well-characterized endarterectomy patients with symptomatic carotid stenosis were analyzed by accelerator mass spectrometry, and global gene expression of 25 plaque samples was profiled with HG-U133 Plus 2.0 arrays. The average plaque age was 9.3 years, and inter- and intrasample standard variations were low (1–3.5 years); thus, most of the plaques were generated 5–15 years before surgery. Plaque age was not associated with patient age or plaque size, determined by intima-media thickness, but was inversely related to plasma insulin levels (P=0.0014). A cluster of functionally related genes enriched with genes involved in immune responses was activated in plaques with low plaque age, as were oxidative phosphorylation genes.

    Conclusion: Patients with mild insulin resistance have increased immune and inflammatory gene activity in their carotid plaques causing them to become instable, rapidly progressing into clinical manifestations at a relatively young age. These results show that plaque age, determined by 14C dating, is a novel and important characteristic of atherosclerotic plaques that will improve our understanding of the clinical significance and molecular underpinnings of atherosclerosis.

  • 205.
    Hägglund, Anna-Carin
    et al.
    Umeå universitet, Medicinska fakulteten, Umeå centrum för molekylär medicin (UCMM).
    Dahl, Lina
    Umeå universitet, Medicinska fakulteten, Umeå centrum för molekylär medicin (UCMM).
    Carlsson, Leif
    Umeå universitet, Medicinska fakulteten, Umeå centrum för molekylär medicin (UCMM).
    Lhx2 is required for patterning and expansion of a distinct progenitor cell population committed to eye development2011Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, nr 8, s. e23387-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Progenitor cells committed to eye development become specified in the prospective forebrain and develop subsequently into the optic vesicle and the optic cup. The optic vesicle induces formation of the lens placode in surface ectoderm from which the lens develops. Numerous transcription factors are involved in this process, including the eye-field transcription factors. However, many of these transcription factors also regulate the patterning of the anterior neural plate and their specific role in eye development is difficult to discern since eye-committed progenitor cells are poorly defined. By using a specific part of the Lhx2 promoter to regulate Cre recombinase expression in transgenic mice we have been able to define a distinct progenitor cell population in the forebrain solely committed to eye development. Conditional inactivation of Lhx2 in these progenitor cells causes an arrest in eye development at the stage when the optic vesicle induces lens placode formation in the surface ectoderm. The eye-committed progenitor cell population is present in the Lhx2(-/-) embryonic forebrain suggesting that commitment to eye development is Lhx2-independent. However, re-expression of Lhx2 in Lhx2(-/-) progenitor cells only promotes development of retinal pigment epithelium cells, indicating that Lhx2 promotes the acquisition of the oligopotent fate of these progenitor cells. This approach also allowed us to identify genes that distinguish Lhx2 function in eye development from that in the forebrain. Thus, we have defined a distinct progenitor cell population in the forebrain committed to eye development and identified genes linked to Lhx2’s function in the expansion and patterning of these progenitor cells.

  • 206. Hälldahl, Filip
    Gymnasielärares upplevelser av utomhusdidaktik i biologi2015Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
  • 207.
    Härkönen, Tero
    et al.
    Naturhistoriska riksmuseet, Enheten för miljöforskning och övervakning.
    Karlsson, Olle
    Naturhistoriska riksmuseet, Enheten för miljöforskning och övervakning.
    Bäcklin, Britt-Marie
    Naturhistoriska riksmuseet, Enheten för miljöforskning och övervakning.
    Moraeus, Charlotta
    Naturhistoriska riksmuseet, Enheten för miljöforskning och övervakning.
    Sälpopulationer och sälhälsa2014Inngår i: Havet, ISSN 1654-6741, s. 93-94Artikkel i tidsskrift (Annet (populærvitenskap, debatt, mm))
  • 208.
    Högberg, Peter
    et al.
    Department of Forest Ecology, SLU, Umeå, Sweden.
    Ekblad, Alf
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Nordgren, Anders
    Department of Forest Ecology, SLU, Umeå, Sweden.
    Plamboeck, Agneta H.
    Swedish Defence Research Agency Division of NBC-Defence, Umeå, Sweden.
    Ohlsson, Anders
    Department of Forest Ecology, SLU, Umeå, Sweden.
    Bhupinderpal-Singh, Singh
    Department of Forest Ecology, SLU, Umeå, Sweden.
    Högberg, Mona
    Department of Forest Ecology, SLU, Umeå, Sweden.
    Factors determining the 13C abundance of soil-respired CO2 in Boreal forests2005Inngår i: Stable isotopes and biosphere-atmosphere interactions: processes and biological controls / [ed] Lawrence B. Flanagan, James R. Ehleringer, Diane E. Pataki, Elsevier, 2005, s. 47-68Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    Analysis of the isotopic composition of the CO2 respired from soils may reveal information about the important component of the ecosystem C balance. This is crucial, since a large terrestrial sink for atmospheric CO2 has been located in the northern hemisphere, and the vast boreal forests may be largely responsible. At the same time, boreal and arctic ecosystems have large amounts of C stored in the soil, and could potentially become a source of CO2 in a warmer climate promoting more rapid decomposition of soil organic matter. Furthermore, the northern hemisphere has complex dynamics in terms of annual fluctuations in both the concentration of CO2 in the atmosphere and its δl3C. It is of utmost importance to understand the causes of this variability, since it interferes with the partitioning between the ocean and the terrestrial contributions in global models. This chapter aims to provide an update on the reviews by Flanagan and Ehleringer and Ehleringer et al. on the causation of the δ13C of the soil CO2 efflux and, in doing this, focuses on the boreal forests.

  • 209.
    Ingberg, Edvin
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för neuro- och inflammationsvetenskap. Linköpings universitet, Medicinska fakulteten. Östergötlands Läns Landsting, Diagnostikcentrum, Klinisk kemi.
    Theodorsson, Elvar
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten. Region Östergötland, Diagnostikcentrum, Klinisk kemi.
    Theodorsson, Annette
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för neuro- och inflammationsvetenskap. Linköpings universitet, Medicinska fakulteten. Region Östergötland, Sinnescentrum, Neurokirurgiska kliniken US. Östergötlands Läns Landsting, Diagnostikcentrum, Klinisk kemi.
    Ström, Jakob
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten. Region Östergötland, Diagnostikcentrum, Klinisk kemi. veÖrebro University Hospital, Sweden; Unirsity of Örebro, Sweden.
    Effects of high and low 17 beta-estradiol doses on focal cerebral ischemia in rats2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, nr 20228Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The majority of the numerous animal studies of the effects of estrogens on cerebral ischemia have reported neuroprotective results, but a few have shown increased damage. Differences in hormone administration methods, resulting in highly different 17 beta-estradiol levels, may explain the discrepancies in previously reported effects. The objective of the present study was to test the hypothesis that it is the delivered dose per se, and not the route and method of administration, that determines the effect, and that high doses are damaging while lower doses are protective. One hundred and twenty ovariectomized female Wistar rats (n = 40 per group) were randomized into three groups, subcutaneously administered different doses of 17 beta-estradiol and subjected to transient middle cerebral artery occlusion. The modified sticky tape test was performed after 24 h and the rats were subsequently sacrificed for infarct size measurements. In contrast to our hypothesis, a significant negative correlation between 17 beta-estradiol dose and infarct size was found (p = 0.018). Thus, no support was found for the hypothesis that 17 beta-estradiol can be both neuroprotective and neurotoxic merely depending on dose. In fact, on the contrary, the findings indicate that the higher the dose of 17 beta-estradiol, the smaller the infarct.

  • 210.
    Ingvarsson, Pär K
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Street, Nathaniel R
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Association genetics of complex traits in plants2011Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 189, nr 4, s. 909-922Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Association mapping is rapidly becoming the main method for dissecting the genetic architecture of complex traits in plants. Currently most association mapping studies in plants are preformed using sets of genes selected to be putative candidates for the trait of interest, but rapid developments in genomics will allow for genome-wide mapping in virtually any plant species in the near future. As the costs for genotyping are decreasing, the focus has shifted towards phenotyping. In plants, clonal replication and/or inbred lines allows for replicated phenotyping under many different environmental conditions. Reduced sequencing costs will increase the number of studies that use RNA sequencing data to perform expression quantitative trait locus (eQTL) mapping, which will increase our knowledge of how gene expression variation contributes to phenotypic variation. Current population sizes used in association mapping studies are modest in size and need to be greatly increased if mutations explaining less than a few per cent of the phenotypic variation are to be detected. Association mapping has started to yield insights into the genetic architecture of complex traits in plants, and future studies with greater genome coverage will help to elucidate how plants have managed to adapt to a wide variety of environmental conditions.

  • 211.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Data Analysis and Next Generation Sequencing : Applications in Microbiology.2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Next Generation Sequencing (NGS) is a new technology that has revolutionized the way we study living organisms. Where previously only a few genes could be studied at a time through targeted direct probing, NGS offers the possibility to perform measurements for a whole genome at once. The drawback is that the amount of data generated in the process is large and extracting useful information from it requires new methods to process and analyze it.

    The main contribution of this thesis is the development of a novel experimental method coined tagRNA-seq, combining 5’tagRACE, a previously developed technique, with RNA-sequencing technology. Briefly, tagRNA-seq makes it possible to identify the 5’ ends of RNAs in bacteria and directly probe for their type, primary or processed, by ligating short RNA sequences, the tags, to the beginnings of RNA molecules. We used the method to directly probe for transcription start and processing sites in two bacterial species, Escherichiacoli and Enterococcus faecalis. It was also used to study polyadenylation in E. coli, where the ability to identify processed RNA molecules proved to be useful to separate direct and indirect regulatory effects of this mechanism. We also demonstrate how data from tagRNA-seq experiments can be used to increase confidence on the discovery of anti-sense transcripts in bacteria. Analyses of RNA-seq data obtained in the context of these experiments revealed subtle artifacts in the coverage signal towards gene ends, that we were able to explain and quantify based Kolmogorov’s broken stick model. We also discovered evidences for circularization of a few RNA transcripts, both in our own data sets and publicly available data.

    Designing the tags used in tagRNA-seq led us to the problem of words absent from a text. We focus on a particular subset of these, the minimal absent words (MAWs), and develop a theory providing a complete description of their size distribution in random text. We also show that MAWs in genomes from viruses and living organisms almost always exhibit a behavior different from random texts in the tail of the distribution, and that MAWs from this tail are closely related to sequences present in the genome that preferentially appear in regions with important regulatory functions.

    Finally, and independently from tagRNA-seq, we propose a new approach to the problem of bacterial community reconstruction in metagenomic, based on techniques from compressed sensing. We provide a novel algorithm competing with state-of-the-art techniques in the field.

  • 212.
    Jacobsen, Annette
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Reference gene selection and validation for HT29 and VK2/E6E7 human epithelial cell lines treated with probiotic and pathogenic bacteria: HT29 and EK2/V6V7 reference gene selection2013Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    The ability of commensal bacteria to influence gene expression in host cells under the influence of pathogenic bacteria has already been demonstrated. Investigation of the extent of this interaction is important to understanding how bacteria can be used as probiotics in the future. Currently, real-time quantitative polymerase chain reaction (qPCR) is the most sensitive tool for evaluating relative changes to gene expression levels. However as a result of its sensitivity an appropriate method of normalisation must be used to account for any variation incurred in preparatory experimental procedures. These variations may result from differences in the amount of starting material, quality of extracted RNA, or in the efficiency of the reverse transcriptase or polymerase enzymes. Although selection of an endogenous control gene is the preferred method of normalisation, this selection is often made without proper validation of the gene’s appropriateness for the study in question. In this study we used qPCR data and applied four different algorithms (genormPLUS, BestKeeper, Normfinder, and comparative ΔCq) to evaluate eight different genes as to their suitability as endogenous controls for use in studies involving HT29 (colonic) and VK2/E6E7 (vaginal) human mucosal epithelial cells treated with probiotic and pathogenic bacteria. We found phosphoglycerate kinase 1 (PGK1) to be most appropriate for HT29 cells, and transmembrane protein 222 (TMEM222) to be the best choice for VK2/E6E7 cells. In both cell lines reference stability would be improved by use of multiple endogenous controls. This study provides recommendations for stable endogenous control genes for use in further studies involving HT29 and VK2/E6E7 cells after bacterial challenge.

  • 213.
    Jakobsson, Tell
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Klinisk mikrobiologi. Linköpings universitet, Hälsouniversitetet.
    Forsum, Urban
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Klinisk mikrobiologi. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Laboratoriemedicinskt centrum, Klinisk mikrobiologi.
    Changes in the predominant human Lactobacillus flora during in vitro fertilisation2008Inngår i: Annals of Clinical Microbiology and Antimicrobials, ISSN 1476-0711, E-ISSN 1476-0711, Vol. 7, artikkel-id 14Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Signature matching of nucleotide sequences in the V1 and V3 regions 16S rRNA genes using pyrosequencing technology is a powerful tool for typing vaginal Lactobacilli to the species level and has been used for investigating the vaginal microbial niche. Methods: This study has characterized the normal cultivable vaginal Lactobacillus flora at varying estradiol levels in plasma, the study comprised 17 patients undergoing ovarian stimulation for In Vitro Fertilization (IVF) treatment. The vaginal status of each participant was initially assessed as normal according to Amsel and Nugent criteria. Results: L. crispatus, L. gasseri and/or L. jensenii were present in 10of the patients throughout the study period, and little variation among these three species was encountered in individual patients. The flora of three women was dominated by L. delbrüeckii, L. rhamnosus or L. vaginalis. One woman exhibited a dominance of L. iners. The flora of the remaining three women were initially dominated by L. rhamnosus or L. reuteri, but as their estrogen levels rose, their flora composition altered, to become dominated by one of the three species most common in a normal, healthy vagina. Conclusion: Signature matching of nucleotide sequences in the V1 and V3 regions of 16S rRNA genes is a discriminative tool for the study of vaginal Lactobacilli and can be used to track the Lactobacillus flora under a variety of physiological conditions. © 2008 Jakobsson and Forsum, licensee BioMed Central Ltd.

  • 214.
    Jepson, Paul D.
    et al.
    Zool Soc London, Inst Zool, London NW1 4RY, England..
    Deaville, Rob
    Zool Soc London, Inst Zool, London NW1 4RY, England..
    Barber, Jonathan L.
    Ctr Environm Fisheries & Aquaculture Sci, Lowestoft NR33 0HT, Suffolk, England..
    Aguilar, Alex
    Univ Barcelona, Dept Anim Biol, Barcelona, Spain.;Univ Barcelona, Biodivers Res Inst IRBio, Barcelona, Spain..
    Borrell, Asuncion
    Univ Barcelona, Dept Anim Biol, Barcelona, Spain.;Univ Barcelona, Biodivers Res Inst IRBio, Barcelona, Spain..
    Murphy, Sinead
    Zool Soc London, Inst Zool, London NW1 4RY, England..
    Barry, Jon
    Ctr Environm Fisheries & Aquaculture Sci, Lowestoft NR33 0HT, Suffolk, England..
    Brownlow, Andrew
    Scottish Marine Anim Stranding Scheme, SRUC Vet Serv Drummondhill, Inverness IV2 4JZ, Scotland..
    Barnett, James
    Univ Exeter, Environm & Sustainabil Inst, Penryn TR10 9EZ, Cornwall, England..
    Berrow, Simon
    Galway Mayo Inst Technol, Marine & Freshwater Res Ctr, Galway, Ireland..
    Cunningham, Andrew A.
    Zool Soc London, Inst Zool, London NW1 4RY, England..
    Davison, Nicholas J.
    Scottish Marine Anim Stranding Scheme, SRUC Vet Serv Drummondhill, Inverness IV2 4JZ, Scotland..
    ten Doeschate, Mariel
    Scottish Marine Anim Stranding Scheme, SRUC Vet Serv Drummondhill, Inverness IV2 4JZ, Scotland..
    Esteban, Ruth
    CIRCE, Conservat Informat & Res Cetaceans, Algeciras 11390, Spain..
    Ferreira, Marisa
    Univ Minho, Dept Biol, Soc Portuguesa Vida Selvagem, Marine Anim Tissue Bank Portugal, P-4719 Braga, Portugal.;CESAM, Oporto, Portugal..
    Foote, Andrew D.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Genov, Tilen
    Morigenos Slovenian Marine Mammal Soc, Piran 6330, Slovenia.;Univ Primorska, Sci & Res Ctr, Inst Biodivers Studies, Koper, Slovenia.;Univ Primorska, Fac Math Nat Sci & Informat Technol, Dept Biodivers, Koper, Slovenia..
    Gimenez, Joan
    CSIC, EBD, Dept Conservat Biol, Seville 42092, Spain..
    Loveridge, Jan
    Cornwall Wildlife Trust Marine Strandings Network, Truro TR4 9DJ, England..
    Llavona, Angela
    Coordinadora Estudio Mamiferos Marinos CEMMA, Gondomar 36380, Pontevedra, Spain..
    Martin, Vidal
    Soc Estudios Cetaceos Canarias SECAC, Lanzarote, Spain..
    Maxwell, David L.
    Ctr Environm Fisheries & Aquaculture Sci, Lowestoft NR33 0HT, Suffolk, England..
    Papachlimitzou, Alexandra
    Ctr Environm Fisheries & Aquaculture Sci, Lowestoft NR33 0HT, Suffolk, England..
    Penrose, Rod
    Marine Environm Monitoring, Cardigan SA43 2PS, Ceredigion, England..
    Perkins, Matthew W.
    Zool Soc London, Inst Zool, London NW1 4RY, England..
    Smith, Brian
    Nat Hist Museum, London SW7 5BD, England..
    de Stephanis, Renaud
    CSIC, EBD, Dept Conservat Biol, Seville 42092, Spain..
    Tregenza, Nick
    Cornwall Wildlife Trust Marine Strandings Network, Truro TR4 9DJ, England..
    Verborgh, Philippe
    CIRCE, Conservat Informat & Res Cetaceans, Algeciras 11390, Spain..
    Fernandez, Antonio
    Univ Las Palmas Gran Canaria, Fac Vet, Gran Canaria, Spain..
    Law, Robin J.
    Zool Soc London, Inst Zool, London NW1 4RY, England.;Ctr Environm Fisheries & Aquaculture Sci, Lowestoft NR33 0HT, Suffolk, England..
    PCB pollution continues to impact populations of orcas and other dolphins in European waters2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 18573Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Organochlorine (OC) pesticides and the more persistent polychlorinated biphenyls (PCBs) have well-established dose-dependent toxicities to birds, fish and mammals in experimental studies, but the actual impact of OC pollutants on European marine top predators remains unknown. Here we show that several cetacean species have very high mean blubber PCB concentrations likely to cause population declines and suppress population recovery. In a large pan-European meta-analysis of stranded (n = 929) or biopsied (n = 152) cetaceans, three out of four species:-striped dolphins (SDs), bottlenose dolphins (BNDs) and killer whales (KWs) had mean PCB levels that markedly exceeded all known marine mammal PCB toxicity thresholds. Some locations (e.g. western Mediterranean Sea, south-west Iberian Peninsula) are global PCB "hotspots" for marine mammals. Blubber PCB concentrations initially declined following a mid-1980s EU ban, but have since stabilised in UK harbour porpoises and SDs in the western Mediterranean Sea. Some small or declining populations of BNDs and KWs in the NE Atlantic were associated with low recruitment, consistent with PCB-induced reproductive toxicity. Despite regulations and mitigation measures to reduce PCB pollution, their biomagnification in marine food webs continues to cause severe impacts among cetacean top predators in European seas.

  • 215.
    Jerkert, Jesper
    KTH, Skolan för elektro- och systemteknik (EES), Ljud- och bildbehandling (Stängd 130101).
    Europarådet gör skarp markering mot kreationism2007Inngår i: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 104, nr 43, s. 3216-Artikkel i tidsskrift (Fagfellevurdert)
  • 216.
    Joandi, Linnéa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    The impact of climate change on aquatic systems and phytoplankton communities: A quantitative study of the impacts of altering food-quality on microzooplankton growth rate2013Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    A global increase in atmospheric CO2 and temperature is assumed to affect the marine ecosystems in numerous ways, e.g. by altering ocean circulation patterns and changing nutrient regimes. The changes are expected to impact heavily on both phytoplankton communities as well as the rest of the marine food-web. Based on previous experimental studies that have investigated the impacts of varied algae food-quality on zooplankton, this quantitative study hypothesizes that (i) the tested microzooplankton species Brachionus plicatilis (rotifer) and Euplotes sp. (ciliate) will show high population growth rates (g) when fed with Nannochloropsis sp. grown under nutrient replete conditions, (ii) that the species will show a population growth rate close to zero when fed with algae grown on phosphorous-deficient media and (iii) that microzooplankton will be negatively affected by the algae grown in nitrogen-deficient media. The study thus aims to investigate how changes in the balance of energy and several chemical elements in ecological interactions, ecological stoichiometry, affect the growth rates of algal grazers. The results show that food-independent factors had a large impact on growth rates and resulted in unexpected, deviating trends. However, as the growth rates for B. plicatilis fed with phosphorous-deficient algae were lower than those of B. plicatilis fed with nitrogen-deficient algae, there is some support for the

  • 217.
    Johannesson, Karin M.
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan.
    Lindström, G.
    Swedish Meteorological and Hydrological Institute, SMHI.
    Heeb, A.
    Swedish Board of Agriculture (Jordbruksverket).
    Milver, A.
    Gothenburg University.
    Rönnberg, R.
    Stockholm Vatten, Sweden.
    Sundblad-Tonderski, Karin
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan.
    Andersson, L.
    Swedish Meteorological and Hydrological Institute, SMHI.
    Can spatial and temporal nutrient concentration variability be captured by catchment agro-geographical characteristics and water quality modelling?2015Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    In water management, source areas need to be identified and seasonal variability of nutrient flows assessed to facilitate design of cost-efficient mitigation programs. This study aimed at investigating to what degree sub-catchment spatial and temporal nutrient concentration variability could be captured by their agro-geographical characteristics and water quality modelling.

    An agricultural catchment (160 km2) in Southeast Sweden was investigated with respect to source areas for phosphorus (P), nitrogen and particle losses. The specific aims were to 1) investigate the spatial variability of nutrient and particle concentrations and transport from different sub-catchments, 2) analyze if sub-catchment characteristics could explain differences in nutrient and particle concentration dynamics and overall nutrient losses, and 3) evaluate how well monitored temporal and spatial variability in nutrient concentrations could be simulated by a catchment model (HYPE). The purpose with the latter was to find recommendations for further model development and identify limitations for the use of catchment models in local water management.

    Water flow was measured in two stations during 2009-2011. Grab samples were collected in synoptic sampling campaigns covering 10 sampling points during periods that represented various water flow regimes. Water samples were analyzed for total P (TP), dissolved phosphate (PO4-P), nitrate (NO3-N) and suspended matter (SUSP). The HYPE model was setup with the same detailed agro-geographical data as used for the statistical analyses of spatial and temporal correlations. The results showed that the sub-catchment variability of all measured nutrient concentrations were correlated with agro-geographical characteristics. All fractions of P concentrations were strongly correlated with soil type, whereas NO3-N concentrations were more related to crop factors. With regard to temporal dynamics of monitored concentrations, links to seasonality and water flow were more significant for NO3-N than for TP. Concentrations generated from the water quality model (HYPE) did not capture the subcatchment or temporal variability indicated from monitoring, particularly not for P concentrations. Neither did the modelled correlation between agro-geographical factors and concentrations correspond to that found for monitored concentrations. Some suggestions for model improvement were identified. Although water quality models are useful for local water management when it comes to modelling the impact of e.g. measures or climate change, our results suggest that their value might still be more limited when assessing variability on the subcatchment scale.

  • 218.
    Johannesson, Karin
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk Biologi. Linköpings universitet, Tekniska högskolan.
    Tonderski, Karin S.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan.
    Ehde, Per Magnus
    Wetland Research Centre, Halmstad University, Sweden.
    Weisner, Stefan E.B.
    Wetland Research Centre, Halmstad University, Sweden.
    Temporal phosphorus dynamics affecting retention estimates in agricultural constructed wetlands2017Inngår i: Ecological Engineering: The Journal of Ecotechnology, ISSN 0925-8574, E-ISSN 1872-6992, Vol. 103, s. 436-445Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Data from seven constructed wetlands (CWs) in the south of Sweden were analyzed to investigate the effects of water flow and season on inflow phosphorus (P) concentrations and temporal P retention variations in CWs receiving runoff from arable land. The form of P (dissolved or particulate) during different water flows (high and low) and seasons (warm and cold) was investigated using the results of total P (TP) and phosphate analyzed in grab samples that had been collected regularly or occasionally during two to nine years, along with continuous water flow measurements.

    The form of inflow and outflow P (particulate or dissolved P) differed between CWs, and also varied with season and flow. For instance, in three of the CWs, particulate P (PP) dominated the inflow during the cold period with high flow, while during the other periods the proportion of PP was approximately 50%. In one CW situated in a catchment with high clay content, PP dominated both inflow and outflow at all times. The average clay content in catchment top soils was positively correlated to the flow-weighted inflow TP concentrations.

    In three CWs receiving runoff through drainage pipes, the relationship between TP concentrations (TPin) and water flow was positive, both during high and low flow, and during warm and cold period. However, in four CWs that received surface water runoff, the relationship between TPin and water flow was positive during high flow periods (i.e. the 25% sampling occasions with the highest flow), and during low flow and warm period, the relationship was negative in these four wetlands, indicating either anoxic stagnant water upstream or influence from rural wastewater.

    The temporal dynamics of P concentrations mean that in some of the CWs, the main part of the annual P retention may occur during a few days with high water flows. The correlation between concentration and water flow suggests that the water sampling strategy may have a considerable impact on retention estimates, as exemplified by some calculation examples.

  • 219.
    Johannesson, Malin
    Högskolan i Halmstad, Sektionen för ekonomi och teknik (SET).
    Prey choice of the snow leopard (Panthera uncia) in the Gobi desert in southern Mongolia.2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    To properly plan a conservation strategy for large, elusive carnivores that lives in remote areas, there is a need for correct information about their diet. Problematically, endangered species such as the snow leopard are difficult to obtain information on, due to their camouflage, secretiveness and isolated lives in rugged ecosystems. Global positioning system (GPS) collars can thus provide useful information on snow leopard ecology and behavior. This study took place in the Gobi desert in southern Mongolia, and aimed to investigate the prey choices of the snow leopard. In total there were 19 snow leopards captured between 2008 and 2013 that were fitted with GPS collars. These collars registered a position every fifth to seventh hour. Kill sites were found by visiting clusters of GPS locations. Ibex was the prey most dominated (66 %), followed by goat, sheep (20 %), and argali (8 %). The ibex and argali were sex- and age-classified.  Age and sex ratio of the killed ibex differed from the age and sex ratio of the ibex population. Adult ibex males seemed to be overrepresented among the kills (males <5 years 10 % and males >5 years 35 %), whereas females seemed underrepresented. Also in argali, the category most killed were males (56 %). The results show that snow leopards do not only kill prey larger than themselves, they also seem to select the largest age and sex categories among ibex and argali, although the different categories killed varied between seasons. Possible explanations for the results are discussed. The findings of this study will help to understand the feeding ecology of the snow leopard, and how to address the conservation and management issues in how to conserve this felid and its most important preys.

  • 220.
    Johanson, Ida
    Karlstads universitet, Fakulteten för hälsa, natur- och teknikvetenskap (from 2013).
    Utbildning i sex och samlevnad för lärarstudenter: - ett bortglömt kapitel?2013Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Såväl internationell som nationell forskning visar att den sex- och samlevnadsundervisning som ges i skolan spelar roll för ungdomars sexuella hälsa och att läraren i detta sammanhang ses som en viktig kunskapskälla. Syftet med denna studie var att försöka ge en bild av på vilket sätt blivande lärare i Sverige blir förberedda för att undervisa i sex och samlevnad genom sin utbildning. För att undersöka detta användes följande frågeställning: Vad krävs för att läraren ska kunna bedriva en tillfredsställande sex- och samlevnadsundervisning? I studien användes kvalitativa intervjuer med en relativt hög grad av strukturering och en låg grad av standardisering. Fyra lärarstudenter på ett universitet i Mellansverige intervjuades. Det som framkommer är att det som krävs för att en lärare/lärarstudent ska kunna bedriva en tillfredsställande sex- och samlevnadsundervisning är en form av trygghet. Trygghet som kan upplevas när läraren har fått erfarenhet, kunskap om ämnet och verktyg att använda i undervisningen. Studien visar också ett samband mellan den utbildning som ges på lärarprogrammet och lärarstudenternas upplevda förmåga att undervisa elever i sex och samlevnad, men personliga egenskaper har också viss betydelse i detta sammanhang. Det framgår tydligt att det är svårt att få en relevant sex- och samlevnadsutbildning inom ramen för lärarutbildningen.

  • 221.
    Johansson, Cecilia
    Karlstads universitet, Fakulteten för humaniora och samhällsvetenskap (from 2013), Institutionen för pedagogiska studier.
    Biologi på landsbygdens respektive tätortens förskolor: En intervjustudie om eventuella skillnader beroende på förskolans geografiska placering2016Independent thesis Basic level (professional degree), 10 poäng / 15 hpOppgave
  • 222. Johansson, Jessica
    et al.
    Rankinen, Juha
    Inventering av flodpärlmussla i Fylleån norr om Gyltigesjön2015Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Freshwater environments are threatened worldwide, of which many of the species associatedwith freshwater. In 2014, 243 freshwater mussels were on the international Red List. One ofthem is the freshwater pearl mussel, Margaritifera margaritifera, which because of itscomplex life cycle can be counted as an indicator of whether a stream is worth protecting. It's since the early 1900's in decline throughout their range. Sweden is counted as a core area which is why we have not only a national but an international responsibility to conserve the species. The mussel is covered by the County Administrative Board of Hallands action plans for threatened species. The County Administrative Board has since 2004 made a number of inventories in the county to get an overview of the occurrence of the freshwater pearl mussel. Still, there are some streams that are not fully inventoried. We have inventoried the mainstream Fylleån from outlet to Gyltigesjön to Bygget, as well as tributaries. In the 80's some parts further downstream in Fylleån were inventoried and then no freshwater pearl mussels were found. Per Ingvarsson who is leading the inventories of freshwater pearl mussels in Halland has pointed out the upper part as an interesting area for mussels. This upper part of Fylleån has previously only been inventoried on two locations, therefore, we have now done a complete inventory to examine the presence of mussels.

    Some of the results of our survey:

    • No fresh water pearl mussels were found in the investigated waters.

    • The water in the river was heavily colored which complicated the inventory.

    • The majority of the route consisted of flowing water with a bottom of stone and/or blocks which are suitable habitat for mussels, but there were silt on the bottom.

    • No fish or fish larvae were found.

    • One duck mussel was found in the outlet to Gyltigesjön.

    In closing, we discuss what could be causing our results.

  • 223. Johansson, Karin S. L.
    et al.
    Luhrig, Katharina
    Klaminder, Jonatan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Rengefors, Karin
    Development of a quantitative PCR method to explore the historical occurrence of a nuisance microalga under expansion2016Inngår i: Harmful Algae, ISSN 1568-9883, E-ISSN 1878-1470, Vol. 56, s. 67-76Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A number of marine and freshwater harmful algal bloom (HAB) species have colonized new areas and expanded their habitat range in recent years. Nevertheless it is notoriously difficult to establish when colonization first occurred, what the dispersal routes are, and to separate recent invasion from increases in existent but small populations. The freshwater raphidophyte Gonyostomum semen is a nuisance species that has expanded its habitat range and increased in abundance in northern Europe during the past decades. To evaluate to what extent sediments can be used for determining historic occurrence of G. semen, a quantitative real-time PCR method for detecting cysts of this algae was developed. This paper presents a qPCR protocol with a set of primers that are specific to Gonyostomum and with PCR conditions optimized for sediment samples from humic lakes, which are the common habitat of G. semen. With this sensitive method as few as 1.6 cysts per PCR reaction could be reliably quantified, corresponding to 320 cysts per g wet weight sediment Cysts were present in sediments with ages ranging from years to decades and their persistence allows detection of historic populations up to at least 50 years old. With this qPCR assay it will be possible to trace the presence of G. semen in environments prior to the onset of algae-specific monitoring programs as well as for quantification in water column samples.

  • 224. Jonsell, Bengt
    et al.
    Åhlander, Erik
    Naturhistoriska riksmuseet, Enheten för zoologi.
    The Linnean Anders Sparrman as traveller and collector in South Africa2016Inngår i: Symbolae Botanicae Upsalienses, ISSN 0082-0644, Vol. 38, s. 75-80Artikkel i tidsskrift (Fagfellevurdert)
  • 225.
    Jonsson, Annie
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Vetenskaplig utvärdering av åtgärdseffekter mot almsjukan inom projektet LifeELMIAS: Rapport till Naturvårdsverket 2017-10-312017Rapport (Annet vitenskapelig)
    Abstract [sv]

    EU-projektet ”LifeELMIAS - Saving wooded Natura 2000 habitats from invasive alien fungi species on the Island of Gotland, Sweden” startade i augusti 2013 och avslutas under 2018. Projektet har haft sitt fokus på att bekämpa och i bästa fall utrota almsjukan på Gotland, samt långsiktigt skydda och bevara den biologiska mångfalden som är speciellt knuten till alm och även ask. Projektet drivs av Skogsstyrelsen med flera samarbetspartners bland annat Naturvårdsverket. Från 2013 har bekämpningsåtgärderna finansierats i projektet LifeElmias och det kostar i medeltal 5 miljoner kronor per år. För att kunna ta ställning till hur almsjukan ska hanteras på Gotland efter projektavslut har Naturvårdsverket beställt följande utvärdering. I uppdraget har det ingått att sammanställa vad som genomförts i LifeElmias och vilka slutsatser man kan göra, samt en diskussion om framtida möjligheter.

     

    Så snart almsjukan upptäcktes på Gotland 2005 sattes bekämpningsåtgärder in som har pågått fram till idag. Till och med 2009 spred sig sjukdomen mycket snabbt på ön. Därefter har den stoppats upp och dess spridningstakt har inte ökat signifikant sedan dess. Det finns tyvärr inget som tyder på att det skulle vara möjligt att utrota sjukdomen på Gotland. Ett uppehåll i bekämpningen kommer att innebära att almsjukan återigen går in i en starkt växande fas. Då skulle upp till 90% av almbeståndet kunna slås ut på bara några år. Fram till idag har endast 3% av beståndet på 1 miljon almar insjuknat. Almarterna dör inte ut helt om man slutar med bekämpningen men förekomsterna kommer till största delen bestå av unga träd och buskartade bestånd. Vilken total effekt det har på den biologiska mångfalden generellt går inte att förutsäga. Artsammansättningen kommer dock att förändras och populationsstorlekar påverkas i både negativ och positiv riktning.

     

    Den hittills mest effektiva metoden att bekämpa almsjukan har varit att upptäcka sjuka träd och destruera dem. Nya möjligheter med fjärranalys för att inventera finns inom räckhåll och med hjälp av ekologisk geografisk modellering skulle man kunna finna strategier för att effektivisera kontrollen eller upprätta skyddszoner för specifikt bevarande av almbestånden inom Natura 2000-områdena. Både fjärranalys och ekologisk modellering kräver dock ett utvecklingsarbete med anpassningar för de specifika situationerna med almsjuka, Gotlands geografi, klimat med flera faktorer. Men dessa metoder skulle långsiktigt kunna effektivisera arbetet och minska kostnaderna för ett fortsatt kontrollprogram.

  • 226.
    Jonsson, Ann-Louise
    Högskolan i Gävle, Akademin för teknik och miljö, Avdelningen för elektronik, matematik och naturvetenskap.
    Summoner's Garden: Ett gestaltningsförslag på en corporate garden baserad på ett pc-spel2015Independent thesis Basic level (university diploma), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Detta examensarbete syftar till att skapa ett gestaltningsförslag till en trädgård baseratpå pc-spelet League of Legends. Arbetet följer konceptet corporate garden då detbaseras på en produkt som är skapad av ett företag. Arbetet ska besvara frågan ”Hur kanett gestaltningsförslag för en corporate garden för spelföretaget Riot Games medinspiration från spelet League of Legends se ut?”, ”Hur uppfattar spelarna landskapet ispelet?” samt ”Vilka växter kan passa i en miljö med halvskugga till skugga, lågt pHvärdesamt relativt hög markfuktighet i zon 1? ”. Metoderna som nyttjades var en kortlitteratursökning åtföljt av en mer omfattande studie av spelets landskapsgrafik samtenkätfrågor till målgruppen spelarna. Motiven till tagna beslut presenteras tillsammansmed växtvalen, varpå illustrationsplanen presenteras. Som komplement till dennaanvänds exempelskisser i mindre skala för att kunna peka på detaljer, såsom placeringav växtval. Resultatet pekar på 25 stycken olika växter som passar i de olikaståndorterna. Växtvalen består av lignoser, perenner, mossor och knölar/lökar.Illustrationsplanen visar en stor parkliknande trädgård i pc-spelet League of Legendsanda.

  • 227.
    Kalathil, Aravind Nambiar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    The effect of Magnetic Fields on Dictyostelium discoideum, Osteoblasts and Fibroblasts2016Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The effect of EM waves on cells has been a subject of growing interest for many years. In this project we tried to recreate the increased proliferation rate noticed in the Dictyostelium discoideum.

    The effect was not initially observed in the osteoblasts, since the experiments were attempted without a complete understanding of all the parameters involved that increased the proliferation rate.

    However, with the fibroblast cell, a similar trendline was achieved, with the highest difference in growth peaking at 22% using a magnetic field of 20Hz and 2300μT.

    In this project we try to explore the implications of such an effect, why it refused to work with one cell line, and why it worked with another, even though the effect was not as pronounced as it was with the amoebas. 

  • 228.
    Kallio, Sakari
    et al.
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Koivisto, Mika
    University of Turku, Finland.
    Seeing Blue As Red: A Hypnotic Suggestion Can Alter Visual Awareness of Colors2016Inngår i: International journal of clinical and experimental hypnosis, ISSN 0020-7144, E-ISSN 1744-5183, Vol. 64, nr 3, s. 261-284Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Some highly hypnotizable individuals have reported changes in objects' color with suggestions given in normal waking state. However, it is not clear whether this occurs only in their imagination. The authors show that, although subjects could imagine colors, a posthypnotic suggestion was necessary for seeing altered colors, even for a hypnotic virtuoso. She reported posthypnotic color alterations also selectively in response to specific target shapes in briefly presented object arrays. Surprisingly, another highly hypnotizable person showed a very different pattern of results. The control participants could not simulate virtuosos' results by applying cognitive strategies. The results imply that hypnosis can alter the functioning of automatic visual processes but only in some of the most hypnotizable individuals.

  • 229.
    Karlsson , Eva-Lena
    et al.
    Karlstads universitet, Fakulteten för samhälls- och livsvetenskaper.
    Frenander Lake, Karin
    Karlstads universitet, Fakulteten för samhälls- och livsvetenskaper.
    Hållbar utveckling med början i förskolan?2009Independent thesis Basic level (professional degree), 10 poäng / 15 hpOppgave
    Abstract [en]

    Abstract

     

    The objective of our study was to get knowledge about how teachers think when they make purchases to preschool. Do they consider making environmentally conscious purchases? Do they work actively to transfer environmental consciousness to the children?

    We chose to interview nine preschool teachers and one cook in two different local municipalities. Our investigation showed that there was a very low engagement in these issues. The teachers said that they were very strictly bound to already existing public contracts and did not see any possibilities to influence the preschools consumption.

    The teachers hade no idea that not only their work could result in environmental savings in the school, but also result in attitudes changes among the children, their parents and, in the long term, society in general. The teachers wished they had a concrete environmental mission and they did what they could with the available resources.

    With our essay we aim to show teachers in the primary school that their choices are important and that it is possible to influence, even on a small scale.

  • 230.
    Karlsson, Anna-Carin
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan.
    Fallahshahroudi, Amir
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan.
    Johnsen, Hanna
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan.
    Hagenblad, Jenny
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan.
    Andersson, Leif
    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
    Jensen, Per
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan.
    The effect of a domestication related mutation in the thyroid stimulating hormone receptor (TSHR) on photoperiodic response and reproduction in chickenManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The thyroid stimulating hormone receptor (TSHR) has been suggested to be a “domestication locus” in the chicken. A strong selective sweep over the gene in domestic breeds of chicken, but not in the ancestral Red Junglefowl, and significant effects of a mutation in TSHR on domestication related traits in chicken, indicate that the gene has been important for the chicken domestication. The TSHR play a key role in the signal transduction of seasonal reproduction, which is characteristically less strict in domestic animals. We investigated the effect of the mutation on reproductive traits as well as TSHB, TSHR, DIO2 and DIO3 gene expression during altered day length (photoperiod) in females and males intercross chickens homozygous for the mutation (d/d) or wild type homozygotes (w/w). This allowed an assessment of the effect of genotype at this locus against a random mix of RJF and WL genotypes throughout the rest of the genome. The TSHR gene expression was significantly lower in both d/d females and males, in comparison to w/w individuals, indicating a strong effect of the “domestic” mutation on gene expression. The d/d females showed a faster increase in the onset of laying than w/w females, and d/d males showed a reduced response to altered day length in testicular size and significant lower levels of TSHB and DIO3 expression, in comparison to w/w males. Additionally, pure White Leghorn females kept under natural day length in Sweden during December showed active ovaries and significant lower levels of TSHR and DIO3 expression in comparison to Red Junglefowl females kept under similar conditions. Our study suggest that the TSHR mutation affects photoperiodic response in chicken in the direction of being less dependent on seasonal reproduction, a typical domestication feature, and may therefore have been important for the chicken domestication.

  • 231.
    Karlsson, Pauline
    Högskolan i Halmstad.
    Anläggande av naturstig: ett sätt att främja intresset för och öka kunskapen om naturen2016Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    En naturstig utgörs vanligtvis av ett antal skyltar längst med en promenadslinga. Genom attgå stigen och ta del av texter och bilder får besökaren en flexibel form av guidning inaturområdet. Naturstigar är på det sättet ett bra sätt att locka ut människor i naturen. Ennaturstig kan bli forum för bland annat undervisning, rekreation och närturism. Stigarnaerbjuder en mer tillgänglig och tillrättalagd natur, som i vissa sammanhang är mer attraktivän den helt vilda.Som en del av mitt syfte har jag anlagt en naturstig vid Stadsbondgården i Fyllinge utanförHalmstad. I linje med syftet innehåller rapporten även forskning relaterat till ekoturism ochnaturstigar, för att kunna fungera som en metodvägledning för framtida anläggande avnaturstigar.Via mina skyltar ville jag uppmuntra till upptäckarlust, och ge naturstigsbesökaren enbegynnande eller fördjupad relation till naturen. Jag jobbade med en grundtanke om att visapå den rika biologiska mångfalden som även den stadsnära naturen besitter.En utvärdering av den färdiga stigen visade på brister i tydlighet och vägvisning. Innehålletpå skyltarna beskrevs av de flesta som positivt. Naturstigen uppfattades av en majoritet somvacker, lärorik och värd ett återbesök.

  • 232.
    Karlsson, Simon
    et al.
    Karlstads universitet, Fakulteten för hälsa, natur- och teknikvetenskap (from 2013), Institutionen för miljö- och livsvetenskaper.
    Christiansson, Jonas
    Karlstads universitet, Fakulteten för hälsa, natur- och teknikvetenskap (from 2013), Institutionen för miljö- och livsvetenskaper.
    Calles, Olle
    Karlstads universitet, Fakulteten för hälsa, natur- och teknikvetenskap (from 2013), Institutionen för miljö- och livsvetenskaper.
    Granö fiskavledare2015Rapport (Annet vitenskapelig)
    Abstract [sv]

    Utvinning av vattenkraft från Granö kraftstation påbörjades på slutet av 1950-talet. Ålen har sedan dess varit hindrad att passera genom kraftverket av ett finmaskigt och höglutande nät under ålens vandringssäsonger. Den alternativa vägen runt stationen har varit med spillvatten eller ner i den gamla ålkistan placerad i intagskanalen. Det är okänt hur många ålar som faktiskt vandrat ut med spillvattnet, men fångsterna i den gamla ålkistan har varit begränsade och mängder med ålar har dött på nätet. Ålen är nu akut hotad och åtgärder att mildra kraftverkens negativa inverkan på utvandrande blankål har högsta prioritet.

    Till följd av problem med igensättning av den så kallade ålspärren uppstod ett dammbrott 2010. För att öka dammsäkerheten och effektiviteten för åluppsamling designades och uppfördes en ny fiskavledare med åluppsamlingsanläggning 2011. Granö fiskavledare är unik i sitt slag då den har intagsgaller av kompositmaterial, ställbara lutningar (30-40˚), samt flyktöppningar som leder till en uppsamlingsbur. Vattnet från uppsamlingen pumpas tillbaka till intagskanalen, för att undvika onödigt spill.

    En stor del av utvärderingen bestod i märkning och spårning av blankål i anslutning till avledaren. Märkningsförsöken under 2012 och 2013 visade att endast en liten proportion av fisken hittar flyktöppningarna och kommer till uppsamlingsburen, dessutom har skador på fisken kunna relateras till avledaren och uppsamlingsburen. Totalt har 284 ålar märkts och 475 har visuellt bedömts för skador efter passage genom avledaren eller referensfisket Havbältan. Trots två dåliga ålvandringsår har majoriteten av den radiomärkta fisken ankommit till avledaren och totalt har 15 fisk återfångades. Hydrauliska mätningar i flyktöppningarna visar att vattenflödena igenom avledarsystemet är låga och andelen (vatten genom avledaren/totalflöde) är långt under rekommenderat vilket kan vara en anledning till de få återfångsterna av fisk.

  • 233.
    Karthikraj, Karthikraj
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Crosstalk between DNA repair and chromatin modifications2013Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
  • 234.
    Kellner, Eva
    Högskolan i Gävle, Akademin för hälsa och arbetsliv, Avdelningen för arbets- och folkhälsovetenskap, Biologi.
    (I) gapet mellan teori och praktik - utveckling av lärarkunskap i biologi2016Inngår i: Ämnesdidaktiska utmaningar - inom matematik, naturvetenskap och teknik / [ed] Mikael Björling, Gävle: Gävle University Press , 2016, 1, s. 47-60Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 235.
    Kellner, Eva
    et al.
    Högskolan i Gävle, Akademin för hälsa och arbetsliv, Avdelningen för arbets- och folkhälsovetenskap, Biologi.
    Attorps, Iiris
    Högskolan i Gävle, Akademin för teknik och miljö, Avdelningen för elektronik, matematik och naturvetenskap, Matematik.
    Kollegialt lärande: aktionsforskning i biologi- och matematikundervisning2016Inngår i: Ämnesdidaktiska utmaningar - inom matematik, naturvetenskap och teknik / [ed] Mikael Björling, Gävle: Gävle University Press , 2016, 1, s. 61-74Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 236.
    Kellner, Martin
    et al.
    Sodertorn Univ, Sch Nat Sci Technol & Environm Studies, Sodertorn, Sweden.
    Porseryd, Tove
    Sodertorn Univ, Sch Nat Sci Technol & Environm Studies, Sodertorn, Sweden.
    Hallgren, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Miljötoxikologi.
    Porsch-Hällström, Inger
    Sodertorn Univ, Sch Nat Sci Technol & Environm Studies, Sodertorn, Sweden.
    Hansen, S.H.
    Univ Copenhagen, Fac Hlth & Med Sci, Dept Pharm, DK-1168 Copenhagen, Denmark.
    Olsén, K. Håkan
    Sodertorn Univ, Sch Nat Sci Technol & Environm Studies, Sodertorn, Sweden.
    Waterborne citalopram has anxiolytic effects and increases locomotor activity in the three-spine stickleback (Gasterosteus aculeatus)2016Inngår i: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 173, s. 19-28Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Citalopram is an antidepressant drug, which acts by inhibiting the re-uptake of serotonin from the synaptic cleft into the pre-synaptic nerve ending. It is one of the most common drugs used in treatment of depression, it is highly lipophilic and frequently found in sewage treatment plant effluents and surface waters around the world. Citalopram and other selective serotonin re-uptake inhibitors have, at concentrations that occur in nature, been shown to have behavioural as well as physiological effects on fish and other animals. This study is the result of several different experiments, intended to analyse different aspects of behavioural effects of chronic citalopram exposure in fish. Our model species the three-spine stickleback is common in the entire northern hemisphere and is considered to be a good environmental sentinel species. Female three-spine sticklebacks were exposed to 0, 1.5 and 15 μg/l nominal concentrations of citalopram for 21 days and subjected to the novel tank (NT) diving test. In the NT test, the fish exposed to 1.5 μg/l, but not the 15 μg/l fish made a significantly higher number of transitions to the upper half and stayed there for significantly longer time than the fish exposed to 0 μg/l. The 15 μg/l group, however, displayed a significantly lower number of freeze bouts and a shorter total freezing time. The test for locomotor activity included in the NT test showed that fish treated with 1.5 and 15 μg/l displayed a significantly higher swimming activity than control fish both 5–7 and 15–17 minutes after the start of the experiment. In the next experiment we compared fish exposed to 1.5 μg/l and 0.15 μg/l to pure water controls with regard to shoaling intensity and found no effect of treatment. In the final experiment the propensity of fish treated with 1.5 μg/l to approach an unknown object and aggressive behaviour was investigated using the Novel Object test and a mirror test, respectively. The exposed fish ventured close to the unknown object significantly more often and stayed there for significantly longer time than unexposed fish. The aggression test yielded no statistically significant effects. It is concluded that citalopram changes the behaviour of the three-spine stickleback in a way that is likely to have ecological consequences and that it must not be considered an environmentally safe pharmaceutical.

  • 237.
    Klaminder, Jonatan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Hellström, Gustav
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Fahlman, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Jonsson, Micael
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Fick, Jerker
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Lagesson, Annelie
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Bergman, Eva
    Brodin, Tomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Drug-Induced Behavioral Changes: Using Laboratory Observations to Predict Field Observations2016Inngår i: Frontiers in Environmental Science, E-ISSN 2296-665X, Vol. 4, artikkel-id 81Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Behavioral assays constitute important research tools when assessing how fish respond to environmental change. However, it is unclear how behavioral modifications recorded in laboratory assays are expressed in natural ecosystems, a limitation that makes it difficult to evaluate the predictive power of laboratory-based measurements. In this study, we hypothesized that exposure to a benzodiazepine (i.e., oxazepam) increases boldness and activity in laboratory assays as well as in field assays – that is, laboratory results can be used to predict field results. Moreover, we expected the modified behavior to affect other important ecological measures such as habitat selection and home range. To test our hypothesis, we exposed European perch (Perca fluviatilis) to oxazepam and measured subsequent changes in behavioral trials both in laboratory assays and in a lake ecosystem populated with a predatory fish species, pike (Esox lucius). In the lake, the positions of both perch and pike were tracked every three minutes for a month using acoustic telemetry. In the laboratory assay, the oxazepam-exposed perch were bolder and more active than the non-exposed perch. In the lake assay, the oxazepam-exposed perch were also more bold and active, had a larger home range, and used pelagic habitats more than the non-exposed perch. We conclude that ecotoxicological behavioral assays are useful for predicting the effects of exposure in natural systems. However, although individual responses to exposure were similar in both the laboratory and field trials, effects were more obvious in the field study, mainly due to reduced variability in the behavior measures from the lake. Hence, short-term behavioral assays may fail to detect all the effects expressed in natural environments. Nevertheless, our study clearly demonstrates that behavior modifications observed in laboratory settings can be used to predict how fish perform in aquatic ecosystems. 

  • 238.
    Klevebring, Daniel
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    On Transcriptome Sequencing2009Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis is about the use of massive DNA sequencing to investigate the transcriptome. During recent decades, several studies have made it clear that the transcriptome comprises a more complex set of biochemical machinery than was previously believed. The majority of the genome can be expressed as transcripts; and overlapping and antisense transcription is widespread. New technologies for the interroga- tion of nucleic acids have made it possible to investigate such cellular phenomena in much greater detail than ever before. For each application, special requirements need to be met. The work presented in this thesis focuses on the transcrip- tome and the development of technology for its analysis. In paper I, we report our development of an automated approach for sample preparation. The procedure was benchmarked against a publicly available reference data set, and we note that our approach outperformed similar manual procedures in terms of reproducibility. In the work reported in papers II-IV, we used different massive sequencing technologies to investigate the transcriptome. In paper II we describe a concatemerization approach that increased throughput by 65% using 454 sequencing,and we identify classes of transcripts not previously described in Populus. Papers III and IV both report studies based on SOLiD sequencing. In the former, we investigated transcripts and proteins for 13% of the human gene and detected a massive overlap for the upper 50% transcriptional levels. In the work described in paper IV, we investigated transcription in non-genic regions of the genome and detected expression from a high number of previ- ously unknown loci.

  • 239.
    Klevebring, Daniel
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Bjursell, Magnus K
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Emanuelsson, Olof
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Lundeberg, Joakim
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Several recent studies have indicated that transcription is pervasive in regions outside of protein coding genes and that short antisense transcripts can originate from the promoter and terminator regions of genes. Here we investigate transcription of fragments longer than 200 nucleotides, focusing on antisense transcription for known protein coding genes and intergenic transcription. We find that roughly 12% to 16% of all reads that originate from promoter and terminator regions, respectively, map antisense to the gene in question. Furthermore, we detect a high number of novel transcriptionally active regions (TARs) that are generally expressed at a lower level than protein coding genes. We also investigate the correlation between RNA-seq data and microarray data and conclude that the correlation is dependant on gene length such that longer genes show a better correlation.

  • 240.
    Klevebring, Daniel
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Fagerberg, Linn
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Lundberg, Emma
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Emanuelsson, Olof
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Uhlén, Mathias
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Lundeberg, Joakim
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Analysis of transcript and protein overlap in a human osteosarcoma cell line2010Inngår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, nr 1, s. 684-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins. In this study, we used massive transcriptome sequencing (RNA-seq) to investigate the transcriptome of a human osteosarcoma cell line and compared the expression levels with in situ protein data obtained in-situ from antibody-based immunohistochemistry (IHC) and immunofluorescence microscopy (IF).

    Results: A large-scale analysis based on 2749 genes was performed, corresponding to approximately 13% of the protein coding genes in the human genome. We found the presence of both RNA and proteins to a large fraction of the analyzed genes with 60% of the analyzed human genes detected by all three methods. Only 34 genes (1.2%) were not detected on the transcriptional or protein level with any method. Our data suggest that the majority of the human genes are expressed at detectable transcript or protein levels in this cell line. Since the reliability of antibodies depends on possible cross-reactivity, we compared the RNA and protein data using antibodies with different reliability scores based on various criteria, including Western blot analysis. Gene products detected in all three platforms generally have good antibody validation scores, while those detected only by antibodies, but not by RNA sequencing, generally consist of more low-scoring antibodies.

    Conclusion: This suggests that some antibodies are staining the cells in an unspecific manner, and that assessment of transcript presence by RNA-seq can provide guidance for validation of the corresponding antibodies.

  • 241.
    Klevebring, Daniel
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Gry, Marcus
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Lindberg, Johan
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Eidefors, Anna
    Lundeberg, Joakim
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Automation of cDNA Synthesis and Labelling Improves Reproducibility2009Inngår i: Journal of Biomedicine and Biotechnology, ISSN 1110-7243, E-ISSN 1110-7251, Vol. 2009, s. 396808-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background. Several technologies, such as in-depth sequencing and microarrays, enable large-scale interrogation of genomes and transcriptomes. In this study, we asses reproducibility and throughput by moving all laboratory procedures to a robotic workstation, capable of handling superparamagnetic beads. Here, we describe a fully automated procedure for cDNA synthesis and labelling for microarrays, where the purification steps prior to and after labelling are based on precipitation of DNA on carboxylic acid-coated paramagnetic beads. Results. The fully automated procedure allows for samples arrayed on a microtiter plate to be processed in parallel without manual intervention and ensuring high reproducibility. We compare our results to a manual sample preparation procedure and, in addition, use a comprehensive reference dataset to show that the protocol described performs better than similar manual procedures. Conclusions. We demonstrate, in an automated gene expression microarray experiment, a reduced variance between replicates, resulting in an increase in the statistical power to detect differentially expressed genes, thus allowing smaller differences between samples to be identified. This protocol can with minor modifications be used to create cDNA libraries for other applications such as in-depth analysis using next-generation sequencing technologies.

  • 242.
    Klevebring, Daniel
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Street, Nathaniel
    Fahlgren, Noah
    Kasschau, Kristin D.
    Carrington, James C.
    Lundeberg, Joakim
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Jansson, Stefan
    Genome-wide profiling of Populus small RNAs2009Inngår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 10, s. Article number 620-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing. Results: The most abundant size class of sRNAs were 24 nt and these were generally associated with a number of classes of retrotransposons and repetitive elements. Some repetitive elements were also associated with 22 nt RNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the sex-determining loci and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified. We identified 15 novel predicted microRNAs (miRNAs), including miRNA∗ sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs). Conclusions: The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.

  • 243.
    Klutsch, Cornelya F. C.
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    de Caprona, M. Dominique Crapon
    The IGF1 small dog haplotype is derived from Middle Eastern grey wolves: a closer look at statistics, sampling, and the alleged Middle Eastern origin of small dogs2010Inngår i: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 8, s. 119-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This paper is a response to Gray MM, Sutter NB, Ostrander EA, Wayne RK: The IGF1 small dog haplotype is derived from Middle Eastern grey wolves. BMC Biology 2010, 8:16. See research article at http://www.biomedcentral.com/1741-7007/8/16.

  • 244.
    Kohout, Manuel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Prioritizing islands for the eradication of invasive predators: Which islands in the Western Indian Ocean should be protected first2014Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    Islands, constituting merely 5% of our planet’s land area, hold more than 20% of all existing terrestrial plant and vertebrate species. Dauntingly, islands are also among the places most severely affected by the extinction crisis we are facing today. Next to habitat destruction, the greatest threat to island biodiversity is invasive predators and the most effective way to deal with them is their removal. Crucially, eradication is an absolutely essential prerequisite for any subsequent restoration to be successful. In an aspiration to add to the gradually emerging efforts of channelling limited resources to the islands in most urgent need of protection, this study informs about island priorities in the Western Indian Ocean for the eradication of rats (Rattus spp.), cats (Felis catus) and mice (Mus musculus). Considering 318 islands within the region and using 77 affected bird species as surrogates for an island’s total conservation value, the overall strategy of the approach is one of return on investment, i.e. of conservation gain divided by conservation cost. The method strives to be complex and flexible enough to be adjustable to the specific goals of any conservation practitioner in the region, while, at the same time, simple and transparent enough, to be repeatable anywhere in the world. Novel is the inclusion of two variables increasing along probability curves, and measuring an island’s inundation and reinvasion risk. The result of the triage is a set of robust lists presenting the most important islands for immediate conservation actions. 

  • 245.
    Koivisto, Mika
    et al.
    Department of Psychology, University of Turku, Turku, Finland / Centre for Cognitive Neuroscience, University of Turku, Turku, Finland.
    Salminen-Vaparanta, Niina
    Department of Psychology, University of Turku, Turku, Finland / Centre for Cognitive Neuroscience, University of Turku, Turku, Finland.
    Grassini, Simone
    Department of Psychology, University of Turku, Turku, Finland / Centre for Cognitive Neuroscience, University of Turku, Turku, Finland.
    Revonsuo, Antti
    Högskolan i Skövde, Institutionen för biovetenskap. Högskolan i Skövde, Forskningscentrum för Systembiologi. Department of Psychology, University of Turku, Turku, Finland / Centre for Cognitive Neuroscience, University of Turku, Turku, Finland.
    Subjective visual awareness emerges prior to P32016Inngår i: European Journal of Neuroscience, ISSN 0953-816X, E-ISSN 1460-9568, Vol. 43, nr 12, s. 1601-1611Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Studies on the neural basis of visual awareness, the subjective experience of seeing, have found several potential neural corre- lates of visual awareness. Some of them may not directly correlate with awareness but with post-perceptual processes, such as reporting one’s awareness of the stimulus. We dissociated potential electrophysiological correlates of visual awareness from those occurring during response selection and thus co-occurring with post-perceptual processing. The participants performed two GO-NOGO conditions. In the aware-GO condition they responded with a key press when they were aware of the stimulus and withheld responding when they were unaware of it. In the unaware-GO condition they withheld responding when they were aware and responded when they were not aware of the stimulus. Thus, event-related potentials could be measured to aware and una- ware trials when responding was required and when not required. The results revealed that the N200 amplitude (180–280 ms) over the occipital and posterior temporal cortex was enhanced in aware trials as compared with trials without awareness. This effect (visual awareness negativity, VAN) did not depend on responding. The amplitude of P3 (350–450 ms) also was enhanced in aware trials as compared with unaware trials. In addition, the amplitudes in the P3 time window depended on responding: they were greater when awareness was mapped to GO-response than when not, suggesting that P3 reflects post-perceptual process- ing, that is, it occurs after awareness has emerged. These findings support theories of visual awareness that assume a relatively early onset of visual awareness before P3. 

  • 246.
    Konn, Cécile
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologi och geokemi.
    Charlou, Jean-Luc
    Laboratoire de géochimie et métallogénie, Ifremer, Brest, France.
    Testemale, Denis
    Institut Néel, Grenoble, France.
    Querellou, Joel
    UMR6197 LM2E, Ifremer, Brest, France.
    Holm, Nils
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologi och geokemi.
    New insight on the origin of organic compounds in fluids from ultramafic-hosted hydrothermal systemsManuskript (Annet vitenskapelig)
    Abstract [en]

    Hydrocarbons gases (C1-C4) as well as larger organic compounds were reported elsewhere in fluids from the Rainbow and the Lost City ultramafic-hosted hydrothermal fields. Whereas hydrocarbon gases are likely abiogenic (Fischer-Tropsch Type reaction), the origin of larger molecules remains unclear. Our ability to differentiate between biotic and abiotic sources of organic compounds in deep-sea hydrothermal systems may give clues to the understanding of organic geochemistry on the early Earth. Here, we report a series of experiments of hydrothermal degradation (40 MPa / 200, 350 and 450°C) of the piezophile archaea Pyrococcus abyssi biomass, which provides supporting lines of evidence of the abiogenic origin of saturated hydrocarbons as well as of the possible biogenic origin of alkylated aromatic hydrocarbons, Polycyclic Aromatic Hydrocarbons (PAH) and C12:0-C16:0 fatty acids in fluids from ultramafic-hosted hydrothermal systems.

  • 247.
    Korol, Sergiy V.
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Fysiologi.
    Tafreshiha, Atieh
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Fysiologi.
    Bhandage, Amol K.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Fysiologi.
    Birnir, Bryndis
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Fysiologi.
    Jin, Zhe
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Fysiologi.
    Insulin enhances GABAA receptor-mediated inhibitory currents in rat central amygdala neurons2018Inngår i: Neuroscience Letters, ISSN 0304-3940, E-ISSN 1872-7972, Vol. 671, s. 76-81Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Insulin, a pancreatic hormone, can access the central nervous system, activate insulin receptors distributed in selective brain regions and affect various cellular functions such as neurotransmission. We have previously shown that physiologically relevant concentration of insulin potentiates the GABAA receptor-mediated tonic inhibition and reduces excitability of rat hippocampal CA1 neurons. The central nucleus of the amygdala (CeA) comprises heterogeneous neuronal populations that can respond to hormonal stimulus. Using quantitative PCR and immunofluorescent labeling, we report that the mRNA and protein of the insulin receptor are abundantly expressed in the rat CeA. The insulin receptor mRNA is also detected in the CeA from post-mortem human brain samples. Furthermore, our whole-cell patch-clamp recordings show that the application of insulin (5 and 50 nM) selectively enhances the frequency and amplitude of spontaneous inhibitory postsynaptic currents (sIPSCs) in rat CeA neurons. Our findings reveal that GABAergic synaptic transmission is a target in the CeA for insulin receptor signaling that may underlie insulin modulation of emotion- and feeding-related behaviors.

  • 248.
    Kotova, Natalia
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för genetik, mikrobiologi och toxikologi.
    Vare, Daniel
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för genetik, mikrobiologi och toxikologi.
    Schultz, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för genetik, mikrobiologi och toxikologi.
    Gradecka Meesters, Dobrosława
    Stępnik, Maciej
    Grawé, Jan
    Helleday, Thomas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för genetik, mikrobiologi och toxikologi.
    Jenssen, Dag
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för genetik, mikrobiologi och toxikologi.
    Genotoxicity of alcohol is linked to DNA replication-associated damage and homologous recombination repairInngår i: Carcinogenesis, ISSN 0143-3334, E-ISSN 1460-2180Artikkel i tidsskrift (Fagfellevurdert)
  • 249.
    Kremnev, Dmitry
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Get in tune: chloroplast and nucleus harmony2014Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Photosynthetic eukaryots emerged as a result of several billion years of evolution between proeukaryotic cell and ancestral cyanobacteria that formed modern chloroplasts. The symbiotic relationship led to significant rearrangements in the genomes of the plastid and the nucleus: as many as 90 % of all the plastid genes were transferred to the nucleus. The gene transfer has been accompanied by the development of sophisticated regulatory signaling networks originating in the organelle (retrograde) and in the nucleus (anterograde) that coordinate development of the plastid and ensure adequate cell responses to stress signals. In this thesis I have demonstrated that transcriptional activity of PEP in the chloroplast is essential for proper embryo and seedling development in Arabidopsis thaliana. The function of PEP is dependent on the nuclear encoded PEPassociated factor PRIN2 that is able to sense the redox status of the plastid during seedling development and different stress. In response to the plastid status PRIN2 modulates the transcription activity of the PEP enzyme complex. We further established that PRIN2, as an essential component for full PEP activity, is also required to emit the Plastid Gene Expression (PGE) retrograde signal to regulate the Photosynthesis-Associated Nuclear Genes (PhANG) in the nucleus during early seedling growth via GUN1. On the other hand, regulation of PhANG expression during the High Light (HL) conditions requires functional PRIN2 and PEP activity but is GUN1-independent. Another retrograde signal produced by the developing chloroplast is associated with the tetrapyrrole biosynthesis pathway. We have established that accumulation of the chlorophyll intermediate MgProtoIX-ME in the crd mutant triggers repression of the PhANG expression, and this negative signal is mediated by a cytoplasmic protein complex containing the PAPP5 phosphatase. The nuclear targets that receive the tetrapyrrole mediated signal are GLK1 and GLK2 transcription factors that control the PhANG expression and the expression of the enzymes involved in the biosynthesis of chlorophyll.

  • 250.
    Kremnev, Dmitry
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Plastid encoded RNA polymerase activity and expression of photosynthesis genes required for embryo and seed development in Arabidopsis2014Inngår i: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462XArtikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chloroplast biogenesis and function is essential for proper plant embryo and seed development but the molecular mechanisms underlying the role of plastids during embryogenesis are poorly understood. Expression of plastid encoded genes is dependent on two different transcription machineries; a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. However, the division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear. We show here that PLASTID REDOX INSENSITIVE 2 (PRIN2) and CHLOROPLAST STEM-LOOP BINDING PROTEIN 41 kDa (CSP41b), two proteins identified in plastid nucleoid preparations, are essential for proper plant embryo development. Using Co-IP assays and native PAGE we have shown a direct physical interaction between PRIN2 and CSP41b. Moreover, PRIN2 and CSP41b form a distinct protein complex in vitro that binds DNA. The prin2.2 and csp41b-2 single mutants displayed pale phenotypes, abnormal chloroplasts with reduced transcript levels of photosynthesis genes and defects in embryo development. The respective csp41b-2prin2.2 homo/heterozygote double mutants produced abnormal white colored ovules and shrunken seeds. Thus, the csp41b-2prin2.2 double mutant is embryo lethal. In silico analysis of available array data showed that a large number of genes traditionally classified as PEP dependent genes are transcribed during early embryo development from the pre-globular stage to the mature-green-stage. Taken together, our results suggest that PEP activity and consequently the switch from NEP to PEP activity, is essential during embryo development and that the PRIN2-CSP41b DNA binding protein complex possibly is important for full PEP activity during this process.

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