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  • 101.
    Arshamian, Artin
    et al.
    Karolinska Institute, Sweden; Radboud University of Nijmegen, Netherlands; Radboud University of Nijmegen, Netherlands; Stockholm University, Sweden.
    Laska, Matthias
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Gordon, Amy R.
    Karolinska Institute, Sweden; Monell Chemistry Senses Centre, PA 19104 USA.
    Norberg, Matilda
    Linköpings universitet, Institutionen för fysik, kemi och biologi. Linköpings universitet, Tekniska fakulteten.
    Lahger, Christian
    Linköpings universitet, Institutionen för fysik, kemi och biologi. Linköpings universitet, Tekniska fakulteten.
    Porada, Danja K.
    Karolinska Institute, Sweden.
    Jelvez Serra, Nadia
    Lund University, Sweden.
    Johansson, Emilia
    Karolinska Institute, Sweden.
    Schaefer, Martin
    Karolinska Institute, Sweden.
    Amundin, Mats
    Kolmarden Wildlife Pk, Sweden.
    Melin, Harald
    Karolinska Institute, Sweden.
    Olsson, Andreas
    Karolinska Institute, Sweden.
    Olsson, Mats J.
    Karolinska Institute, Sweden.
    Stensmyr, Marcus
    Lund University, Sweden.
    Lundstrom, Johan N.
    Karolinska Institute, Sweden; Monell Chemistry Senses Centre, PA 19104 USA; University of Penn, PA 19104 USA.
    A mammalian blood odor component serves as an approach-avoidance cue across phylum border - from flies to humans2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 13635Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Chemosignals are used by predators to localize prey and by prey to avoid predators. These cues vary between species, but the odor of blood seems to be an exception and suggests the presence of an evolutionarily conserved chemosensory cue within the blood odor mixture. A blood odor component, E2D, has been shown to trigger approach responses identical to those triggered by the full blood odor in mammalian carnivores and as such, is a key candidate as a food/alarm cue in blood. Using a multidisciplinary approach, we demonstrate that E2D holds the dual function of affecting both approach and avoidance behavior in a predator-prey predicted manner. E2D evokes approach responses in two taxonomically distant blood-seeking predators, Stable fly and Wolf, while evoking avoidance responses in the prey species Mouse. We extend this by demonstrating that this chemical cue is preserved in humans as well; E2D induces postural avoidance, increases physiological arousal, and enhances visual perception of affective stimuli. This is the first demonstration of a single chemical cue with the dual function of guiding both approach and avoidance in a predator-prey predicted manner across taxonomically distant species, as well as the first known chemosignal that affects both human and non-human animals alike.

  • 102.
    Arvidsson, Josefin
    Linköpings universitet, Institutionen för fysik, kemi och biologi.
    Development and application of an olfactory discrimination paradigm for Asian elephants (Elephas maximus)2011Independent thesis Advanced level (degree of Master (Two Years)), 40 poäng / 60 hpOppgave
    Abstract [en]

    The sense of smell plays an important role in regulating the behavior of Asian elephants but until now, no behavioral test to systematically assess the olfactory capabilities of this species existed. Using a voluntary, food-rewarded two-alternative operant conditioning procedure, three female Asian elephants were successfully taught to discriminate between rewarded and unrewarded odors and also succeeded in intramodal stimulus transfer tasks in which either the rewarded odor, or the unrewarded odor, or both odors were exchanged simultaneously for new odors. The animals readily mastered the initial task within only 120 stimulus contacts, demonstrating rapid olfactory learning and performing at least as good as rodents and dogs and even better than other species, including nonhuman primates, tested in similar studies before. When presented with pairs of structurally related odorants, the discrimination performance of the elephants decreased with increasing structural similarity of the odorants, but the animals still significantly discriminated between aliphatic acetic esters even when they only differed by one carbon chain length. The elephants also demonstrated an excellent long-term odor memory and successfully remembered the reward value of previously learned odor stimuli after two, four, eight and even 16 weeks of recess in testing. The paradigm developed and applied in the present study proved to be useful to assess the olfactory capabilities in Asian elephants.

  • 103.
    Arwin, Hans
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Tillämpad optik. Linköpings universitet, Tekniska högskolan.
    Magnusson, Roger
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Tillämpad optik. Linköpings universitet, Tekniska högskolan.
    Fernández del Río, Lia
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Tillämpad optik. Linköpings universitet, Tekniska högskolan.
    Åkerlind, Christina
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Tillämpad optik. Linköpings universitet, Tekniska högskolan. Swedish Defence Research Agency, Linköping, Sweden.
    Muñoz-Pineda, Eloy
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Tillämpad optik. Linköpings universitet, Tekniska högskolan. Cinvestav-IPN, Unidad Querétaro, Libramiento Norponiente 2000, 76230 Querétaro, Mexico.
    Landin, Jan
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Mendoza-Galván, Arturo
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Tillämpad optik. Cinvestav-IPN, Unidad Querétaro, Libramiento Norponiente 2000, 76230 Querétaro, Mexico.
    Järrendahl, Kenneth
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Tillämpad optik. Linköpings universitet, Tekniska fakulteten.
    Exploring optics of beetle cuticles with Mueller-matrix ellipsometry2014Inngår i: Materials Today, ISSN 1369-7021, E-ISSN 1873-4103, Vol. 1S, s. 155-160Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Spectroscopic Mueller-matrix ellipsometry at variable angles of incidence is applied to beetle cuticles using a small (50 -100 μm) spot size. It is demonstrated how ellipticity and degree of polarization of the reflected light can be derived from a Mueller matrix providing a detailed insight into reflection properties. Results from Cetonia aurata, Chrysina argenteola and Cotinis mutabilis are presented. The use of Mueller matrices in regression analysis to extract structural and optical parameters of cuticles is briefly described and applied to cuticle data from Cetonia aurata whereby the pitch of the twisted layered structure in the cuticle is determined as well as the refractive indices of the epicuticle and the exocuticle.

  • 104. Ashaduzzaman, Md
    et al.
    Parlak, Onur
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten.
    Turner, Anthony
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten.
    Tiwari, Ashutosh
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten.
    Fabrication of on/off-switchable enzymatic bioreactor for smart bioelectronics.2015Inngår i: Sweden-Japan Seminar on Nanomaterials and Nanotechnology – SJS-Nano, Linköping, Sweden, 10-11 March 2015., Japan Society for the Promotion of Science (JSPS), Stockholm , 2015, s. 36-37Konferansepaper (Fagfellevurdert)
  • 105.
    Aslan, Selcuk
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Molekylär genetik.
    The molecular genotyping of flower development genes and allelic variations in ‘historic’ barley accessions2010Independent thesis Advanced level (degree of Master (One Year)), 25 poäng / 37,5 hpOppgave
    Abstract [en]

    This is a genetic study of flowering time in cultivated barley with the aim to identify the alleles contributing to rapid flowering and frost resistance. We have genotyped a collection of 23 historic barley varieties for the crucial genes [VRN-1, VRN-2, VRN-3 (HvFT), Ppd-H1, CO, and Vrs1]. We have amplified the polymorphic mutations by PCR-based methods, and sequenced them to identify possible haplotype groups. The row type was not determined of all accessions, but all the Scandinavian varieties were found to carry mutant alleles of Vrs1, that indicates them to be six-row barleys. The deletion of the crucial segment of VRN-1 vernalization contributes dominant spring growth habit. We found haplotype groups 2 and 4 to be dominant in Northern barleys whereas haplotype groups 1 and 5 dominated in south. The presence of dominant allele VRN-2 gene is addressed to floral repression until plants get vernalized. Most of the 23 varieties were found to have deleted allele of VRN-2, which is connected with a spring growth habit. The only four of the accessions that have the dominant allele of Ppd-H1 that contribute flowering are generally from the south of Europe. HvFT and CO genes CO-interact to influence flowering time. CO haplotype grouping suggest a geographical distribution of different alleles but needs more disseminations. Certain HvFT alleles cause extremely early flowering during apex development in the varieties that have deletion of VRN-2 alleles under long days. VRN-3 alleles of 14 varieties were identified.

  • 106.
    Atikuzzaman, Mohammad
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Seminal Influence on the Oviduct: Mating and/or semen components induce gene expression changes in the pre-ovulatory functional sperm reservoir in poultry and pigs2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Internal fertilization occurs in birds and eutherian mammals. Foetal development, however, is either extra- respectively intra-corpore (egg vs uterus). In these animal classes, the female genital tract stores ejaculated spermatozoa into a restricted oviductal segment; the functional pre-ovulatory sperm reservoir, where they survive until ovulation/s occur. Paradoxically, this immunologically foreign sperm suspension in seminal fluid/plasma, often microbiologically contaminated, ought to be promptly eliminated by the female local immune defence which, instead, tolerates its presence. The female immune tolerance is presumably signalled via a biochemical interplay of spermatozoa, as well as the peptides and proteins of the extracellular seminal fluid, with female epithelial and immune cells. Such interplay can result in gene expression shifts in the sperm reservoir in relation to variations in fertility. To further aid our understanding of the underlying mechanisms, this thesis studied the proteome of the seminal fluid (using 2D SDS-PAGE and mass spectrometry) including cytokine content (using Luminex and/or ELISA) of healthy, sexually mature and fertile boars and cocks. As well, gene expression changes (using cDNA microarray) in the oviductal sperm reservoirs of sexually-mature females, mated or artificially infused with homologous sperm-free seminal fluid/plasma were studied. Pigs were of commercial, fertility-selected modern breeds (Landrace), while chicken belonged to the ancestor Red Junglefowl (RJF, low egg laying-capacity), a selected egg-layer White Leghorn (WL) and of their Advanced Intercross Line (AIL). Ejaculates were manually collected as single sample in cocks or as the sperm-rich fraction [SRF] and the post- SRF fraction in boars to harvest seminal fluid/plasma for proteome/cytokine and infusion-studies. Oviducts were retrieved for gene-expression analyses via microarray immediately post-mortem (chicken) or at surgery (pig), 24 h after mating or genital infusion. In pigs, the protein-rich seminal plasma showed the highest amounts of cytokines [interferon-γ, interferon gamma-induced protein 10 (IP-10/CXCL10), macrophage derived chemokine (MDC/CCL22), growth-regulated oncogene (GRO/CXCL1), granulocyte-macrophage colony-stimulating factor (GM-CSF), monocyte chemo-attractant protein-1 (MCP-1/ CCL2), interleukin (IL)-6, IL-8/CXCL8, IL-10, IL-15, IL-17 and transforming growth factor (TGF)-β1-3) in the larger, protein-rich and sperm-poor post-SRF, indicating its main immune signalling influence. Chicken showed also a plethora of seminal fluid proteins with serum albumin and ovotransferrin being conserved through selection/evolution. However, they showed fewer cytokines than pigs, as the anti-inflammatory/immune-modulatory TGF-β2 or the pro-inflammatory CXCL10. The RJF contained fewer immune system process proteins and lacked TGF-β2 compared to WL and AIL, suggesting selection for increased fertility could be associated with higher expression of immune-regulating peptides/proteins. The oviductal sperm reservoir reacted in vivo to semen exposure. In chicken, mating significantly changed the expression of immune-modulatory and pH-regulatory genes in AIL. Moreover, modern fertile pigs (Landrace) and chicken (WL), albeit being taxonomically distant, shared gene functions for preservation of viable sperm in the oviduct. Mating or SP/SF-infusion were able to change the expression of comparable genes involved in pH-regulation (SLC16A2, SLC4A9, SLC13A1, SLC35F1, ATP8B3, ATP13A3) or immune-modulation (IFIT5, IFI16, MMP27, ADAMTS3, MMP3, MMP12). The results of the thesis demonstrate that both mating and components of the sperm-free seminal fluid/plasma elicit gene expression changes in the pre-ovulatory female sperm reservoir of chickens and pigs, some conserved over domestication and fertility-selection.

    Delarbeid
    1. The Seminal Plasma of the Boar is Rich in Cytokines, with Significant Individual and Intra-Ejaculate Variation
    Åpne denne publikasjonen i ny fane eller vindu >>The Seminal Plasma of the Boar is Rich in Cytokines, with Significant Individual and Intra-Ejaculate Variation
    Vise andre…
    2015 (engelsk)Inngår i: American Journal of Reproductive Immunology, ISSN 1046-7408, E-ISSN 1600-0897, Vol. 74, nr 6, s. 523-532Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Problem The boar, as human, sequentially ejaculates sperm-rich and sperm-poor fractions. Seminal plasma (SP) spermadhesins (PSP-I/PSP-II) induce a primary endometrial inflammatory response in female sows, similar to that elicited by semen deposition in other species, including human. However, the SP is also known to mitigate such response, making it transient to allow for embryo entry to a cleansed endometrium. Although cytokine involvement has been claimed, the exploration of cytokines in different SP fractions is scarce. This study determines Th1, Th2, Th17 and Th3 cytokine profiles in specific ejaculate SP fractions from boars of proven fertility. Methods SP samples from the sperm-rich fraction (SRF) and the sperm-poor post-SRF fraction (post-SRF) of manually collected ejaculates from eight boars (four ejaculates per boar) were analysed by commercial multiplex bead assay kits (Milliplex MAP, Millipore, USA) for interferon-gamma, interferon gamma-induced protein 10, macrophage-derived chemokine, growth-regulated oncogene, granulocyte-macrophage colony-stimulating factor, monocyte chemo-attractant protein-1, interleukins (IL)-6, IL-8, IL-10, IL-15, IL-17 and transforming growth factor (TGF)-beta 1-beta 3. Results Cytokine concentrations differed between the ejaculate fractions among boars, being highest in the post-SRF. Conclusion Boar SP is rich in Th1, Th2, Th17 and Th3 cytokines, with lowest concentrations in the sperm-peak-containing fraction, indicating its main immune influence might reside in the larger, protein-rich sperm-poor post-SRF.

    sted, utgiver, år, opplag, sider
    WILEY-BLACKWELL, 2015
    Emneord
    Ejaculate fractions; immunomodulatory molecules; pig; seminal plasma peptides
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-124497 (URN)10.1111/aji.12432 (DOI)000367669300006 ()26412440 (PubMedID)
    Merknad

    Funding Agencies|MINECO Madrid (Spain) [AGL2012-39903]; FEDER funds (EU); Formas (Stockholm, Sweden); MECD (Madrid, Spain); Seneca Foundation (Murcia, Spain)

    Tilgjengelig fra: 2016-02-02 Laget: 2016-02-01 Sist oppdatert: 2017-11-30
    2. Selection for higher fertility reflects in the seminal fluid proteome of modern domestic chicken
    Åpne denne publikasjonen i ny fane eller vindu >>Selection for higher fertility reflects in the seminal fluid proteome of modern domestic chicken
    Vise andre…
    2017 (engelsk)Inngår i: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, ISSN 1744-117X, E-ISSN 1878-0407, Vol. 21, s. 27-40Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The high egg-laying capacity of the modern domestic chicken (i.e. White Leghorn, WL) has arisen from the low egg-laying ancestor Red Junglefowl (RJF) via continuous trait selection and breeding. To investigate whether this long-term selection impacted the seminal fluid (SF)-proteome, 2DE electrophoresis-based proteomic analyses and immunoassays were conducted to map SF-proteins/cytokines in RJF, WL and a 9th generation Advanced Intercross Line (AIL) of RJF/WL-L13, including individual SF (n = 4, from each RJF, WL and AIL groups) and pools of the SF from 15 males of each group, analyzed by 2DE to determine their degree of intra-group (AIL, WL, and RJF) variability using Principal Component Analysis (PCA); respectively an inter-breed comparative analysis of intergroup fold change of specific SF protein spots intensity between breeds. The PCA clearly highlighted a clear intra-group similarity among individual roosters as well as a clear inter-group variability (e.g. between RJF, WL and AIL) validating the use of pools to minimize confounding individual variation. Protein expression varied considerably for processes related to sperm motility, nutrition, transport and survival in the female, including signaling towards immunomodulation. The major conserved SF-proteins were serum albumin and ovotransferrin. Aspartate aminotransferase, annexin A5, arginosuccinate synthase, glutathione S-transferase 2 and l-lactate dehydrogenase-A were RJF-specific. Glyceraldehyde-3-phosphate dehydrogenase appeared specific to the WL-SF while angiotensin-converting enzyme, γ-enolase, coagulation factor IX, fibrinogen α-chain, hemoglobin subunit α-D, lysozyme C, phosphoglycerate kinase, Src-substrate protein p85, tubulins and thioredoxin were AIL-specific. The RJF-SF contained fewer immune system process proteins and lower amounts of the anti-inflammatory/immunomodulatory TGF-β2 compared to WL and AIL, which had low levels- or lacked pro-inflammatory CXCL10 compared to RJF. The seminal fluid proteome differs between ancestor and modern chicken, with a clear enrichment of proteins and peptides related to immune-modulation for sperm survival in the female and fertility.

    sted, utgiver, år, opplag, sider
    Elsevier, 2017
    Emneord
    Rooster seminal fluid proteome, Cytokines, Egg-laying capacity, Red Junglefowl, White Leghorn, Advanced intercross line, Chicken
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-132624 (URN)10.1016/j.cbd.2016.10.006 (DOI)000395224100004 ()27852008 (PubMedID)
    Merknad

    Funding agencies: Research Council FORMAS, Stockholm, Sweden [221-2011-512]; Ministerio de Ciencia e Innovacion (Madrid, Spain) [BFU2013-42833-P]

    Tilgjengelig fra: 2016-11-17 Laget: 2016-11-17 Sist oppdatert: 2018-05-02bibliografisk kontrollert
    3. Mating induces the expression of immune- and pH-regulatory genes in the utero-vaginal junction containing mucosal sperm-storage tubuli of hens
    Åpne denne publikasjonen i ny fane eller vindu >>Mating induces the expression of immune- and pH-regulatory genes in the utero-vaginal junction containing mucosal sperm-storage tubuli of hens
    Vise andre…
    2015 (engelsk)Inngår i: Reproduction, Vol. 150, nr 6, s. 473-483Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The female chicken, as with other species with internal fertilization, can tolerate the presence of spermatozoa within specialized sperm-storage tubuli (SST) located in the mucosa of the utero-vaginal junction (UVJ) for days or weeks, without eliciting an immune response. To determine if the oviduct alters its gene expression in response to sperm entry, segments from the oviduct (UVJ, uterus, isthmus, magnum and infundibulum) of mated and unmated (control) hens, derived from an advanced inter-cross line between Red Junglefowl and White Leghorn, were explored 24 h after mating using cDNA microarray analysis. Mating shifted the expression of fifteen genes in the UVJ (53.33% immune-modulatory and 20.00% pH-regulatory) and seven genes in the uterus, none of the genes in the latter segment overlapping the former (with the differentially expressed genes themselves being less related to immune-modulatory function). The other oviductal segments did not show any significant changes. These findings suggest sperm deposition causes a shift in expression in the UVJ (containing mucosal SST) and the uterus for genes involved in immune-modulatory and pH-regulatory functions, both relevant for sperm survival in the hen's oviduct.

    sted, utgiver, år, opplag, sider
    Bioscientifica, 2015
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-122573 (URN)10.1530/REP-15-0253 (DOI)000365344400004 ()26370241 (PubMedID)
    Merknad

    Funding agencies: Research Council FORMAS, Stockholm [221-2011-512]; FORMAS [221-2012-667]; VR [621-2011-4802]

    Tilgjengelig fra: 2015-11-09 Laget: 2015-11-09 Sist oppdatert: 2017-02-20
  • 107.
    Atikuzzaman, Mohammad
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Alvarez-Rodriguez, Manuel
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för barns och kvinnors hälsa. Linköpings universitet, Medicinska fakulteten.
    Carrillo, Alejandro Vicente
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Johnsson, Martin
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Rodriguez-Martinez, Heriberto
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för barns och kvinnors hälsa. Linköpings universitet, Medicinska fakulteten.
    Conserved gene expression in sperm reservoirs between birds and mammals in response to mating.2017Inngår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 18, nr 1Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    BACKGROUND: Spermatozoa are stored in the oviductal functional sperm reservoir in animals with internal fertilization, including zoologically distant classes such as pigs or poultry. They are held fertile in the reservoir for times ranging from a couple of days (in pigs), to several weeks (in chickens), before they are gradually released to fertilize the newly ovulated eggs. It is currently unknown whether females from these species share conserved mechanisms to tolerate such a lengthy presence of immunologically-foreign spermatozoa. Therefore, global gene expression was assessed using cDNA microarrays on tissue collected from the avian utero-vaginal junction (UVJ), and the porcine utero-tubal junction (UTJ) to determine expression changes after mating (entire semen deposition) or in vivo cloacal/cervical infusion of sperm-free seminal fluid (SF)/seminal plasma (SP).

    RESULTS: In chickens, mating changed the expression of 303 genes and SF-infusion changed the expression of 931 genes, as compared to controls, with 68 genes being common to both treatments. In pigs, mating or SP-infusion changed the expressions of 1,722 and 1,148 genes, respectively, as compared to controls, while 592 genes were common to both treatments. The differentially expressed genes were significantly enriched for GO categories related to immune system functions (35.72-fold enrichment). The top 200 differentially expressed genes of each treatment in each animal class were analysed for gene ontology. In both pig and chicken, an excess of genes affecting local immune defence were activated, though frequently these were down-regulated. Similar genes were found in both the chicken and pig, either involved in pH-regulation (SLC16A2, SLC4A9, SLC13A1, SLC35F1, ATP8B3, ATP13A3) or immune-modulation (IFIT5, IFI16, MMP27, ADAMTS3, MMP3, MMP12).

    CONCLUSION: Despite being phylogenetically distant, chicken and pig appear to share some gene functions for the preservation of viable spermatozoa in the female reservoirs.

  • 108.
    Atikuzzaman, Mohammad
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Alvarez-Rodriguez, Manuel
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för barns och kvinnors hälsa. Linköpings universitet, Medicinska fakulteten.
    Vicente Carrillo, Alejandro
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Johnsson, Martin
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Rodriguez-Martinez, Heriberto
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för barns och kvinnors hälsa. Linköpings universitet, Medicinska fakulteten.
    Correction: Conserved gene expression in sperm reservoirs between birds and mammals in response to mating (vol 18, 98, 2017)2017Inngår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 18, artikkel-id 563Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    n/a

  • 109.
    Atikuzzaman, Mohammad
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Bhai Mehta, Ratnesh
    Linköpings universitet, Medicinska fakulteten. Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för neuro- och inflammationsvetenskap.
    Fogelholm, Jesper
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Rodriguez-Martinez, Heriberto
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Mating induces the expression of immune- and pH-regulatory genes in the utero-vaginal junction containing mucosal sperm-storage tubuli of hens2015Inngår i: Reproduction, Vol. 150, nr 6, s. 473-483Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The female chicken, as with other species with internal fertilization, can tolerate the presence of spermatozoa within specialized sperm-storage tubuli (SST) located in the mucosa of the utero-vaginal junction (UVJ) for days or weeks, without eliciting an immune response. To determine if the oviduct alters its gene expression in response to sperm entry, segments from the oviduct (UVJ, uterus, isthmus, magnum and infundibulum) of mated and unmated (control) hens, derived from an advanced inter-cross line between Red Junglefowl and White Leghorn, were explored 24 h after mating using cDNA microarray analysis. Mating shifted the expression of fifteen genes in the UVJ (53.33% immune-modulatory and 20.00% pH-regulatory) and seven genes in the uterus, none of the genes in the latter segment overlapping the former (with the differentially expressed genes themselves being less related to immune-modulatory function). The other oviductal segments did not show any significant changes. These findings suggest sperm deposition causes a shift in expression in the UVJ (containing mucosal SST) and the uterus for genes involved in immune-modulatory and pH-regulatory functions, both relevant for sperm survival in the hen's oviduct.

  • 110.
    Atikuzzaman, Mohammad
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Sanz, Libia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Pla, Davinia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Alvarez-Rodriguez, Manuel
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för barns och kvinnors hälsa. Linköpings universitet, Medicinska fakulteten.
    Rubér, Marie
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för barns och kvinnors hälsa. Linköpings universitet, Medicinska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Calvete, Juan J.
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Rodriguez-Martinez, Heriberto
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för barns och kvinnors hälsa. Linköpings universitet, Medicinska fakulteten.
    Selection for higher fertility reflects in the seminal fluid proteome of modern domestic chicken2017Inngår i: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, ISSN 1744-117X, E-ISSN 1878-0407, Vol. 21, s. 27-40Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The high egg-laying capacity of the modern domestic chicken (i.e. White Leghorn, WL) has arisen from the low egg-laying ancestor Red Junglefowl (RJF) via continuous trait selection and breeding. To investigate whether this long-term selection impacted the seminal fluid (SF)-proteome, 2DE electrophoresis-based proteomic analyses and immunoassays were conducted to map SF-proteins/cytokines in RJF, WL and a 9th generation Advanced Intercross Line (AIL) of RJF/WL-L13, including individual SF (n = 4, from each RJF, WL and AIL groups) and pools of the SF from 15 males of each group, analyzed by 2DE to determine their degree of intra-group (AIL, WL, and RJF) variability using Principal Component Analysis (PCA); respectively an inter-breed comparative analysis of intergroup fold change of specific SF protein spots intensity between breeds. The PCA clearly highlighted a clear intra-group similarity among individual roosters as well as a clear inter-group variability (e.g. between RJF, WL and AIL) validating the use of pools to minimize confounding individual variation. Protein expression varied considerably for processes related to sperm motility, nutrition, transport and survival in the female, including signaling towards immunomodulation. The major conserved SF-proteins were serum albumin and ovotransferrin. Aspartate aminotransferase, annexin A5, arginosuccinate synthase, glutathione S-transferase 2 and l-lactate dehydrogenase-A were RJF-specific. Glyceraldehyde-3-phosphate dehydrogenase appeared specific to the WL-SF while angiotensin-converting enzyme, γ-enolase, coagulation factor IX, fibrinogen α-chain, hemoglobin subunit α-D, lysozyme C, phosphoglycerate kinase, Src-substrate protein p85, tubulins and thioredoxin were AIL-specific. The RJF-SF contained fewer immune system process proteins and lower amounts of the anti-inflammatory/immunomodulatory TGF-β2 compared to WL and AIL, which had low levels- or lacked pro-inflammatory CXCL10 compared to RJF. The seminal fluid proteome differs between ancestor and modern chicken, with a clear enrichment of proteins and peptides related to immune-modulation for sperm survival in the female and fertility.

  • 111.
    Atterby, Clara
    et al.
    Uppsala University, Sweden.
    Borjesson, Stefan
    National Vet Institute SVA, Sweden.
    Ny, Sofia
    Public Health Agency Sweden, Sweden; Karolinska Institute, Sweden.
    Jarhult, Josef D.
    Uppsala University, Sweden.
    Byfors, Sara
    Public Health Agency Sweden, Sweden.
    Bonnedahl, Jonas
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten. Linnaeus University, Sweden; Kalmar County Council, Sweden.
    ESBL-producing Escherichia coli in Swedish gulls: A case of environmental pollution from humans?2017Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, nr 12, artikkel-id e0190380Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    ESBL-producing bacteria are present in wildlife and the environment might serve as a resistance reservoir. Wild gulls have been described as frequent carriers of ESBL-producing E. coli strains with genotypic characteristics similar to strains found in humans. Therefore, potential dissemination of antibiotic resistance genes and bacteria between the human population and wildlife need to be further investigated. Occurrence and characterization of ESBL-producing E. coli in Swedish wild gulls were assessed and compared to isolates from humans, livestock and surface water collected in the same country and similar time-period. Occurrence of ESBL-producing E. coli in Swedish gulls is about three times higher in gulls compared to Swedish community carriers (17% versus 5%) and the genetic characteristics of the ESBL-producing E. coli population in Swedish wild gulls and Swedish human are similar. ESBL-plasmids IncF-and IncI1-type carrying ESBL-genes blaCTX-M-15 or blaCTX-M-14 were most common in isolates from both gulls and humans, but there was limited evidence of clonal transmission. Isolates from Swedish surface water harbored similar genetic characteristics, which highlights surface waters as potential dissemination routes between wildlife and the human population. Even in a low-prevalence country such as Sweden, the occurrence of ESBL producing E. coli in wild gulls and the human population appears to be connected and the occurrence of ESBL-producing E. coli in Swedish gulls is likely a case of environmental pollution.

  • 112.
    Averhed, Björn
    Linköpings universitet, Institutionen för fysik, kemi och biologi. Linköpings universitet.
    Kan förändringar i bottenfaunan påvisas två år efter en bäckrestaurering?2010Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    The aim of this work is to analyze if a change in the benthic community can be detected two years after a restoration of a small stream. The samples were taken in a small stream at Tinnerö Eklandskap just south of Linköping. In addition to the restored area, two reference sites upstream and downstream of the restored area were sampled to compare to the restored site. The method used for sampling of benthic fauna in the stream was kick sampling. ASPT, Berger-Parker and Renkonen-indices were used to find out if there was any difference between the reference areas and the restored area. In addition to indices, rank-abundance curves and species lists were made to see if there was any trend difference between the different areas. The only index that showed a difference between the different areas was Berger-Parker diversity index. The reason why there were no greater differences between the areas may be due to the fact that two years is too short to allow time for the benthos to re-colonize the restored area.

  • 113.
    Azzouzi, Sawsen
    et al.
    University of Sousse, Tunisia.
    Ben Ali, M
    University of Sousse, Tunisia.
    Abbas, M.N.
    Analytical Laboratory, National Research Center, Egypt.
    Bala, C
    University of Bucharest, Romania.
    Dridi, C
    University of Sousse, Tunisia.
    Errachid, A
    University of Lyon, France.
    Turner, Anthony
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten.
    Electrochemical detection of cancer biomarkers using nano-materials based sensors as early warning system of prostate cancer2016Inngår i: Cancer Diagnostics Symposium, Swedish Exhibition and Congres Centre, Gothenburg, Sweden, 28 May 2016, Elsevier, 2016Konferansepaper (Annet vitenskapelig)
  • 114.
    Azzouzi, Sawsen
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten. University of sousse, Tunisia.
    Kor, Kalamodin
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten. Damghan University, Iran.
    Ben Ali, Mounir
    University of sousse, Tunisia.
    Turner, Anthony
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten.
    Mak, Wing Cheung
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten.
    Beni, Valerio
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten.
    A single probe based impedimetric biosensor for the label free, real time monitoring of microRNA-21 biomarker2016Inngår i: Biosensors 2016 – The World Congress on Biosensors, Gothenburg, Sweden, 25-27 May 2016, Elsevier, 2016Konferansepaper (Annet vitenskapelig)
  • 115.
    Babu Moparthi, Satish
    et al.
    Aix Marseille University, France.
    Carlsson, Uno
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten.
    Vincentelli, Renaud
    University of Aix Marseille, France.
    Jonsson, Bengt-Harald
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten.
    Hammarström, Per
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten.
    Wenger, Jerome
    Aix Marseille University, France.
    Differential conformational modulations of MreB folding upon interactions with GroEL/ES and TRiC chaperonin components2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, nr 28386Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Here, we study and compare the mechanisms of action of the GroEL/GroES and the TRiC chaperonin systems on MreB client protein variants extracted from E. coli. MreB is a homologue to actin in prokaryotes. Single-molecule fluorescence correlation spectroscopy (FCS) and time-resolved fluorescence polarization anisotropy report the binding interaction of folding MreB with GroEL, GroES and TRiC. Fluorescence resonance energy transfer (FRET) measurements on MreB variants quantified molecular distance changes occurring during conformational rearrangements within folding MreB bound to chaperonins. We observed that the MreB structure is rearranged by a binding-induced expansion mechanism in TRiC, GroEL and GroES. These results are quantitatively comparable to the structural rearrangements found during the interaction of beta-actin with GroEL and TRiC, indicating that the mechanism of chaperonins is conserved during evolution. The chaperonin-bound MreB is also significantly compacted after addition of AMP-PNP for both the GroEL/ES and TRiC systems. Most importantly, our results showed that GroES may act as an unfoldase by inducing a dramatic initial expansion of MreB (even more than for GroEL) implicating a role for MreB folding, allowing us to suggest a delivery mechanism for GroES to GroEL in prokaryotes.

  • 116.
    Babu Moparthi, Satish
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska fakulteten. Institut Fresnel, CNRS UMR 7249, Aix-Marseille Université, Marseille, France.
    Sjölander, Daniel
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska högskolan.
    Villebeck, Laila
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Molekylär Bioteknik. Linköpings universitet, Tekniska högskolan.
    Jonsson, Bengt-Harald
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska högskolan.
    Hammarström, Per
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska högskolan.
    Carlsson, Uno
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Kemi. Linköpings universitet, Tekniska högskolan.
    Transient conformational remodeling of folding proteins by GroES - Individually and in concert with GroEL2014Inngår i: Journal of chemical biology, ISSN 1864-6158, E-ISSN 1864-6166, Vol. 7, nr 1, s. 1-15Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    The commonly accepted dogma of the bacterial GroE chaperonin system entails protein folding mediated by cycles of several ATP-dependent sequential steps where GroEL interacts with the folding client protein. In contrast, we herein report GroES-mediated dynamic remodeling (expansion and compression) of two different protein substrates during folding: the endogenous substrate MreB and carbonic anhydrase (HCAII), a well-characterized protein folding model. GroES was also found to influence GroEL binding induced unfolding and compression of the client protein underlining the synergistic activity of both chaperonins, even in the absence of ATP. This previously unidentified activity by GroES should have important implications for understanding the chaperonin mechanism and cellular stress response. Our findings necessitate a revision of the GroEL/ES mechanism.

  • 117.
    Backlund, Emma
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan.
    Assessment of ventricular morphology using echocardiography in Ornate tinamous (Nothoprocta ornata) and domestic chickens (Gallus domesticus)2014Independent thesis Basic level (degree of Bachelor), 10,5 poäng / 16 hpOppgave
    Abstract [en]

    The Ornate Tinamou (Nothoprocta ornata), an ancient bird, has adapted to life at high altitude (>2.400 m.a.s.l) for a longer period than the domestic chicken (Gallus domesticus), which came to South America with the Spanish conquerors. Ornate tinamous have a smaller heart in relation to body size than domestic chickens. This study was made to evaluate heart morphometric measurements comparing Ornate Tinamou and domestic chicken using echocardiography measurements to determine wall thickness and chamber size and to evaluate whether it can retrieve measurements consistent with previous results on dissected hearts. I was also interested in evaluating potential adaptations of the Ornate Tinamou to life in hypoxic environments by exposing the heart to positive inotropic stimulation. The results were compared with those previously obtained on dissected hearts. The results showed that the chamber size of the domestic chicken was significantly larger than in Ornate Tinamou, both in conscious and anesthetized birds. Injection of 1µg/kg isoproterenol caused domestic chickens’ systolic chamber size to decrease significantly and fractional shortening to increase significantly. The same changes were seen in the Ornate Tinamou but they were not significant. In conclusion, this study confirms that echocardiography is a valid method for retrieving cardiac measurements without euthanizing animals, opening for the possibility of taking several measurements at different ages.

  • 118.
    Backteman, Karin
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för inflammationsmedicin. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Diagnostikcentrum, Klinisk immunologi och transfusionsmedicin.
    T Cells and NK Cells in Coronary Artery Disease: Longitudinal and methodological studies in humans2014Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Coronary artery disease (CAD) is the leading cause of death worldwide and most often due to atherosclerosis. Atherosclerosis is a chronic inflammatory process that involves the arteries, inclouding those that supply blood to the heart muscle. Although inflammation is an important contributing factor to atherosclerosis, the mechanisms are not fully understood. One mechanism contributing to atherogenesis may involve some infectious microorganisms such as cytomegalovirus (CMV). In atherosclerosis, the arterial wall becomes infiltrated with lipids followed by different types of leukocytes and inflammatory mediators (atherogenesis). Leukocytes recirculate continuously between the blood and lymphoid organs, such as lymph nodes, where the adaptive immune response is started and regulated.

    The general aim of this thesis was to increase the understanding of associations between lymphocyte populations and different conditions of CAD (unstable and stable). To assess changes over time, a longitudinal follow up design was mostly used. Therefore, also perspectives of longitudinal variation were included in the thesis.

    Paper I showed that flow cytometric evaluation of lymphocyte populations is a robust technique that can be used in longitudinal studies, both in clinical and research settings. It was also shown that the time of sampling over the year did not have a major impact on the findings.

    In paper II, thoracic lymph nodes were investigated to assess whether CAD-associated changes were more prominent in comparison with blood. As expected, there were several major differences in lymphocyte composition between lymph nodes and blood. However, the analysis of thoracic lymph nodes did not reveal any further changes that were not detected in blood. Thus, blood is still the most reliable compartment for studies of lymphocyte populations in CAD since it is not possible to examine the local findings in the artery wall.

    Natural killer (NK) cells are innate lymphocytes with both regulatory and effector functions. In paper II and III we confirmed previous findings that CAD patients have lower proportions of NK cells in blood. However, the NK subtype and cytokine profile (paper III, measured by subtype markers and intra-cellular cytokine staining) did not differ between patients and controls. During a 12-month follow-up, the proportions of NK cells increased, although not in all patients. Failure to reconstitute NK cell levels was associated with several components of the metabolic syndrome and with a persistent low-grade inflammation as measured by plasma IL-6 levels. The findings support the notion of a protective role for NK cells in inflammation.

    CD4+ but not CD8+ T cells were significantly increased in patients with both unstable and stable conditions compared with healthy individuals (paper IV). Subpopulations of CD4+ T cells (CD4+CD28null) have previously been associated with CAD. However, we show that CD28null and CD28null57+ cells within the CD4+ and CD8+ T cell populations were similar in CAD patients and healthy controls. Instead, CMV seropositivity was the major determinant of expanded CD28null and CD57+ T cell fractions in both patients and healthy individuals. During the 1 year follow up the proportion of CD4+CD28null and CD8+CD28null cells increased in patients, which may reflect an accelerated immunological ageing occurring after the cardiac event.

    Delarbeid
    1. Biological and methodological variation of lymphocyte subsets in blood of human adults
    Åpne denne publikasjonen i ny fane eller vindu >>Biological and methodological variation of lymphocyte subsets in blood of human adults
    2007 (engelsk)Inngår i: JIM - Journal of Immunological Methods, ISSN 0022-1759, E-ISSN 1872-7905, Vol. 322, nr 1-2, s. 20-27Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Although lymphocyte populations are often monitored over time, information about the biological variation over time is limited. Three-colour-flow cytometry was used to investigate the biological and methodological variation of lymphocyte populations in blood. Fifteen healthy individuals (11 females and 4 males) were longitudinally monitored for 2-8 years. Blood samples were drawn monthly when possible. In total, 493 observations were included. Absolute counts and proportions were determined for T-cells (CD3+), T-helper cells (CD3+ CD4+), cytolytic T-cells (CD3+ CD8+), B-cells (CD3- CD19+) and NK-cells (CD3- CD16+/56+). As to variation over the year, ANOVA testing showed only a minor monthly variation for absolute counts of the CD8+ population (p < 0.05) for October compared with June and July, whereas no significant differences were found for the other populations or in the proportions of lymphocyte subsets. Although lower than the longitudinal variation, the methodological variation, expressed as coefficient of variation (CV %), was in a similar range as the variation over time, indicating that the normal biological variation should not be overestimated, while the methodological inter-assay should be taken into consideration in longitudinal studies or monitoring of patients. © 2007 Elsevier B.V. All rights reserved.

    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-41169 (URN)10.1016/j.jim.2007.01.021 (DOI)55291 (Lokal ID)55291 (Arkivnummer)55291 (OAI)
    Tilgjengelig fra: 2009-10-10 Laget: 2009-10-10 Sist oppdatert: 2017-12-13
    2. Lymphocyte Subpopulations in Lymph Nodes and Peripheral Blood: A Comparison between Patients with Stable Angina and Acute Coronary Syndrome
    Åpne denne publikasjonen i ny fane eller vindu >>Lymphocyte Subpopulations in Lymph Nodes and Peripheral Blood: A Comparison between Patients with Stable Angina and Acute Coronary Syndrome
    2012 (engelsk)Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, nr 3Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Objective: Atherosclerosis is characterized by a chronic inflammatory response involving activated T cells and impairment of natural killer (NK) cells. An increased T cell activity has been associated with plaque instability and risk of acute cardiac events. Lymphocyte analyses in blood are widely used to evaluate the immune status. However, peripheral blood contains only a minor proportion of lymphocytes. In this study, we hypothesized that thoracic lymph nodes from patients with stable angina (SA) and acute coronary syndrome (ACS) might add information to peripheral blood analyses. less thanbrgreater than less thanbrgreater thanMethods: Peripheral blood and lymph nodes were collected during coronary by-pass surgery in 13 patients with SA and 13 patients with ACS. Lymphocyte subpopulations were assessed by flow cytometry using antibodies against CD3, CD4, CD8, CD19, CD16/56, CD25, Foxp3, CD69, HLA-DR, IL-18 receptor (R) and CCR4. less thanbrgreater than less thanbrgreater thanResults: Lymph nodes revealed a lymphocyte subpopulation profile substantially differing from that in blood including a higher proportion of B cells, lower proportions of CD8(+) T cells and NK cells and a 2-fold higher CD4/CD8 ratio. CD4(+)CD69(+) cells as well as Foxp3(+) regulatory T cells were markedly enriched in lymph nodes (p andlt; 0.001) while T helper 1-like (CD4(+)IL-18R(+)) cells were more frequent in blood (p andlt; 0.001). The only significant differences between ACS and SA patients involved NK cells that were reduced in the ACS group. However, despite being reduced, the NK cell fraction in ACS patients contained a significantly higher proportion of IL-18R(+) cells compared with SA patients (p andlt; 0.05). less thanbrgreater than less thanbrgreater thanConclusion: There were several differences in lymphocyte subpopulations between blood and lymph nodes. However, the lymphocyte perturbations in peripheral blood of ACS patients compared with SA patients were not mirrored in lymph nodes. The findings indicate that lymph node analyses in multivessel coronary artery disease may not reveal any major changes in the immune response that are not detectable in blood.

    sted, utgiver, år, opplag, sider
    Public Library of Science, 2012
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-77542 (URN)10.1371/journal.pone.0032691 (DOI)000303005000033 ()
    Merknad
    Funding Agencies|Swedish Heart-Lung Foundation|20090489|Swedish Research Council|2008-2282|Tilgjengelig fra: 2012-05-25 Laget: 2012-05-22 Sist oppdatert: 2017-12-07
    3. Natural killer (NK) cell deficit in coronary artery disease: no aberrations in phenotype but sustained reduction of NK cells is associated with low-grade inflammation
    Åpne denne publikasjonen i ny fane eller vindu >>Natural killer (NK) cell deficit in coronary artery disease: no aberrations in phenotype but sustained reduction of NK cells is associated with low-grade inflammation
    2014 (engelsk)Inngår i: Clinical and Experimental Immunology, ISSN 0009-9104, E-ISSN 1365-2249, Vol. 175, nr 1, s. 104-112Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Although reduced natural killer (NK) cell levels have been reported consistently in patients with coronary artery disease (CAD), the clinical significance and persistence of this immune perturbation is not clarified. In this study we characterized the NK cell deficit further by determining (i) differentiation surface markers and cytokine profile of NK cell subsets and (ii) ability to reconstitute NK cell levels over time. Flow cytometry was used to analyse NK cell subsets and the intracellular cytokine profile in 31 patients with non-ST elevation myocardial infarction (non-STEMI), 34 patients with stable angina (SA) and 37 healthy controls. In blood collected prior to coronary angiography, the proportions of NK cells were reduced significantly in non-STEMI and SA patients compared with controls, whereas NK cell subset analyses or cytokine profile measurements did not reveal any differences across groups. During a 12-month follow-up, the proportions of NK cells increased, although not in all patients. Failure to reconstitute NK cell levels was associated with several components of metabolic syndrome. Moreover, interleukin (IL)-6 levels remained high in patients with sustained NK cell deficit, whereas a decline in IL-6 (P < 0·001) was seen in patients with a pronounced increase in NK cells. In conclusion, we found no evidence that reduction of NK cells in CAD patients was associated with aberrations in NK cell phenotype at any clinical stage of the disease. Conversely, failure to reconstitute NK cell levels was associated with a persistent low-grade inflammation, suggesting a protective role of NK cells in CAD.

    sted, utgiver, år, opplag, sider
    Wiley-Blackwell, 2014
    Emneord
    coronary artery disease; cytokines; inflammation; leukocytes; natural killer cell
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-103363 (URN)10.1111/cei.12210 (DOI)000329165400012 ()24298947 (PubMedID)
    Tilgjengelig fra: 2014-01-17 Laget: 2014-01-17 Sist oppdatert: 2017-12-06bibliografisk kontrollert
    4. Cytomegalovirus seropositivity is a major determinant of CD28null T cell expansion in patients with coronary artery disease
    Åpne denne publikasjonen i ny fane eller vindu >>Cytomegalovirus seropositivity is a major determinant of CD28null T cell expansion in patients with coronary artery disease
    2014 (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Objective: Accumulation of CD4+28null cells, with a proinflammatory and senescent phenotype, has been associated with unstable conditions of coronary artery disease (CAD). Human cytomegalovirus (HCMV) is known to exert profound effects on T cells, including loss of CD28. Here, we longitudinally assessed the proportions of CD28null and CD28nullCD57+ cells in CD4+ and CD8+ T cell populations of patients with CAD and related the findings to HCMV seropositivity.

    Methods: HCMV antibody levels and expression of CD28 and CD57 on CD4+ and CD8+ T cells were analysed in 31 patients with acute coronary syndrome (ACS), 34 patients with stable angina (SA) and 37 healthy controls. Samples were taken prior to 34 coronary angiography and after 3 and 12 months. In a subsample, HCMV-specific IFN-γ and  TNF production was assessed ex vivo.

    Results: Increased proportions of CD4+CD28null, but not CD8+CD28null cells, were significantly associated with presence of CAD. Significant increases in CD28null 37 and CD28nullCD57+ cells occurred within CD4+ and CD8+ T cell compartments in both ACS and SA patients during 12-month follow-up. HCMV was the major determinant of CD28null and CD28nullCD57+ T cell levels in both patients and controls (p <0.001). There were no obvious signs of CMV reactivation in patients.

    Conclusion: HCMV was a major determinant of the presence of CD28null and CD28nullCD57+ T cells in patients with CAD, independent of clinical stage. Findings also indicate that HCMV might have a large impact on the T cell aging process that occurred in patients after a cardiac event.

    Emneord
    Coronary artery disease, acute coronary syndrome, CD28null T cells, CD57+ 49 T cells, Human cytomegalovirus
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-111049 (URN)
    Tilgjengelig fra: 2014-10-06 Laget: 2014-10-06 Sist oppdatert: 2015-03-25bibliografisk kontrollert
  • 119.
    Backteman, Karin
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för inflammationsmedicin. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Diagnostikcentrum, Klinisk immunologi och transfusionsmedicin.
    Ernerudh, Jan
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för inflammationsmedicin. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Diagnostikcentrum, Klinisk immunologi och transfusionsmedicin.
    Jonasson, Lena
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för kardiovaskulär medicin. Linköpings universitet, Hälsouniversitetet. Östergötlands Läns Landsting, Hjärt- och Medicincentrum, Kardiologiska kliniken US.
    Cytomegalovirus seropositivity is a major determinant of CD28null T cell expansion in patients with coronary artery disease2014Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Objective: Accumulation of CD4+28null cells, with a proinflammatory and senescent phenotype, has been associated with unstable conditions of coronary artery disease (CAD). Human cytomegalovirus (HCMV) is known to exert profound effects on T cells, including loss of CD28. Here, we longitudinally assessed the proportions of CD28null and CD28nullCD57+ cells in CD4+ and CD8+ T cell populations of patients with CAD and related the findings to HCMV seropositivity.

    Methods: HCMV antibody levels and expression of CD28 and CD57 on CD4+ and CD8+ T cells were analysed in 31 patients with acute coronary syndrome (ACS), 34 patients with stable angina (SA) and 37 healthy controls. Samples were taken prior to 34 coronary angiography and after 3 and 12 months. In a subsample, HCMV-specific IFN-γ and  TNF production was assessed ex vivo.

    Results: Increased proportions of CD4+CD28null, but not CD8+CD28null cells, were significantly associated with presence of CAD. Significant increases in CD28null 37 and CD28nullCD57+ cells occurred within CD4+ and CD8+ T cell compartments in both ACS and SA patients during 12-month follow-up. HCMV was the major determinant of CD28null and CD28nullCD57+ T cell levels in both patients and controls (p <0.001). There were no obvious signs of CMV reactivation in patients.

    Conclusion: HCMV was a major determinant of the presence of CD28null and CD28nullCD57+ T cells in patients with CAD, independent of clinical stage. Findings also indicate that HCMV might have a large impact on the T cell aging process that occurred in patients after a cardiac event.

  • 120.
    Bagheryan, Zahra
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten. University of Mazandaran, Iran.
    Raoof, Jahan-Bakhsh
    University of Mazandaran, Iran.
    Golabi, Mohsen
    Linköpings universitet, Institutionen för fysik, kemi och biologi. Linköpings universitet, Tekniska fakulteten.
    Turner, Anthony
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten.
    Beni, Valerio
    Linköpings universitet, Institutionen för fysik, kemi och biologi. Linköpings universitet, Tekniska fakulteten. Acreo Swedish ICT AB, Sweden.
    Diazonium-based impedimetric aptasensor for the rapid label-free detection of Salmonella typhimurium in food sample2016Inngår i: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 80, s. 566-573Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Fast and accurate detection of microorganisms is of key importance in clinical analysis and in food and water quality monitoring. Salmonella typhimurium is responsible for about a third of all cases of food borne diseases and consequently, its fast detection is of great importance for ensuring the safety of foodstuffs. We report the development of a label-free impedimetric aptamer-based biosensor for S. typhimurium detection. The aptamer biosensor was fabricated by grafting a diazonium-supporting layer onto screen printed carbon electrodes (SPEs), via electrochemical or chemical approaches, followed by chemical immobilisation of aminated-aptamer. FTIR-ATR, contact angle and electrochemical measurements were used to monitor the fabrication process. Results showed that electrochemical immobilisation of the diazonium-grafting layer allowed the formation of a denser aptamer layer, which resulted in higher sensitivity. The developed aptamer-biosensor responded linearly, on a logarithm scale, over the concentration range 1 x 10(1) to 1 x 10(8) CFU mL(-1), with a limit of quantification (LOQ) of 1 x 10(1) CFU mL(-1) and a limit of detection (LOD) of 6 CFU mL(-1). Selectivity studies showed that the aptamer biosensor could discriminate S. typhimurium from 6 other model bacteria strains. Finally, recovery studies demonstrated its suitability for the detection of S. typhimurium in spiked (1 x 10(2), 1 x 10(4) and 1 x 10(6) CFU mL(-1)) apple juice samples. (C) 2016 Elsevier B.V. All rights reserved.

  • 121.
    Bagheryan, Zahra
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten. University of Mazandaran, Iran.
    Raoof, J-B
    University of Mazandaran, Iran.
    Ozalp, V.C.
    Istanbul Kemerburgaz University, Turkey.
    Turner, Anthony
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten.
    Beni, Valerio
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biosensorer och bioelektronik. Linköpings universitet, Tekniska fakulteten.
    Diazonium-based impedimetric aptasensor for the rapid label-free detection of Salmonella typhimurium in food samples2016Inngår i: Biosensors 2016 – The World Congress on Biosensors, Gothenburg, Sweden, 25-27 May 2016, Elsevier, 2016Konferansepaper (Annet vitenskapelig)
  • 122.
    Bahrampour, Shahrzad
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten.
    Genetic mechanisms regulating proliferation and cell specification in the Drosophila embryonic CNS2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The central nervous system (CNS) consists of an enormous number of cells, and large cellular variance, integrated into an elaborate network. The CNS is the most complex animal organ, and therefore its establishment must be controlled by many different genetic programs. Considering the high level of complexity in the human CNS, addressing issues related to human neurodevelopment represents a major challenge. Since comparative studies have revealed that neurodevelopmental programs are well conserved through evolution, on both the genetic and functional levels, studies on invertebrate neurodevelopmental programs are often translatable to vertebrates. Indeed, the basis of our current knowledge about vertebrate CNS development has been greatly aided by studies on invertebrates, and in particular on the Drosophila melanogaster (fruit fly) model system.

    This thesis attempted to identify novel genes regulating neural cell specification and proliferation in the CNS, using the Drosophila model system. Moreover, I aimed to address how those genes govern neural progenitor cells (neuroblasts; NBs) to obtain/maintain their stemness identity and proliferation capacity, and how they drive NBs through temporal windows and series of programmed asymmetric division, which gradually reduces their stemness identity in favor of neural differentiation, resulting in appropriate lineage progression. In the first project, we conducted a forward genetic screen in Drosophila embryos, aimed at isolating genes involved in regulation of neural proliferation and specification, at the single cell resolution. By taking advantage of the restricted expression of the neuropeptide FMRFa in the last-born cell of the NB lineage 5-6T, the Ap4 neuron, we could monitor the entire lineage progression. This screen succeeded in identifying 43 novel genes controlling different aspects of CNS development. One of the genes isolated, Ctr9, displayed extra Ap4/FMRFa neurons. Ctr9 encodes a component of the RNA polymerase II complex Paf1, which is involved in a number of transcriptional processes. The Paf1C, including Ctr9, is highly conserved from yeast to human, and in the past couple of years, its importance for transcription has become increasingly appreciated. However, studies in the Drosophila system have been limited. In the screen, we isolated the first mutant of Drosophila Ctr9 and conducted the first detailed phenotypic study on its function in the Drosophila embryonic CNS. Loss of function of Ctr9 leads to extra NB numbers, higher proliferation ratio and lower expression of neuropeptides. Gene expression analysis identified several other genes regulated by Ctr9, which may explain the Ctr9 mutant phenotypes. In summary, we identified Ctr9 as an essential gene for proper CNS development in Drosophila, and this provides a platform for future study on the Drosophila Paf1C. Another interesting gene isolated in the screen was worniou (wor), a member of the Snail family of transcription factors. In contrast to Ctr9, whichdisplayed additional Ap4/FMRFa neurons, wor mutants displayed a loss of these neurons. Previous studies in our group have identified many genes acting to stop NB lineage progression, but how NBs are pushed to proliferate and generate their lineages was not well known. Since wor may constitute a “driver” of proliferation, we decided to study it further. Also, we identified five other transcription factors acting together with Wor as pro-proliferative in both NBs and their daughter cells. These “drivers” are gradually replaced by the previously identified late-acting “stoppers.” Early and late factors regulate each other and the cell cycle, and thereby orchestrate proper neural lineage progression.

    Delarbeid
    1. Novel Genes Involved in Controlling Specification of Drosophila FMRFamide Neuropeptide Cells
    Åpne denne publikasjonen i ny fane eller vindu >>Novel Genes Involved in Controlling Specification of Drosophila FMRFamide Neuropeptide Cells
    Vise andre…
    2015 (engelsk)Inngår i: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 200, nr 4, s. 1229-1244Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The expression of neuropeptides is often extremely restricted in the nervous system, making them powerful markers for addressing cell specification . In the developing Drosophila ventral nerve cord, only six cells, the Ap4 neurons, of some 10,000 neurons, express the neuropeptide FMRFamide (FMRFa). Each Ap4/FMRFa neuron is the last-born cell generated by an identifiable and well-studied progenitor cell, neuroblast 5-6 (NB5-6T). The restricted expression of FMRFa and the wealth of information regarding its gene regulation and Ap4 neuron specification makes FMRFa a valuable readout for addressing many aspects of neural development, i.e., spatial and temporal patterning cues, cell cycle control, cell specification, axon transport, and retrograde signaling. To this end, we have conducted a forward genetic screen utilizing an Ap4-specific FMRFa-eGFP transgenic reporter as our readout. A total of 9781 EMS-mutated chromosomes were screened for perturbations in FMRFa-eGFP expression, and 611 mutants were identified. Seventy-nine of the strongest mutants were mapped down to the affected gene by deficiency mapping or whole-genome sequencing. We isolated novel alleles for previously known FMRFa regulators, confirming the validity of the screen. In addition, we identified novel essential genes, including several with previously undefined functions in neural development. Our identification of genes affecting most major steps required for successful terminal differentiation of Ap4 neurons provides a comprehensive view of the genetic flow controlling the generation of highly unique neuronal cell types in the developing nervous system.

    sted, utgiver, år, opplag, sider
    Genetics Society of America, 2015
    Emneord
    Drosophila; CNS development; neural cell fate specification; forward genetic screening; FMRFamide
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-121318 (URN)10.1534/genetics.115.178483 (DOI)000359917000020 ()26092715 (PubMedID)
    Tilgjengelig fra: 2015-09-16 Laget: 2015-09-14 Sist oppdatert: 2019-03-13bibliografisk kontrollert
    2. Ctr9, a Key Component of the Paf1 Complex, Affects Proliferation and Terminal Differentiation in the Developing Drosophila Nervous System
    Åpne denne publikasjonen i ny fane eller vindu >>Ctr9, a Key Component of the Paf1 Complex, Affects Proliferation and Terminal Differentiation in the Developing Drosophila Nervous System
    2016 (engelsk)Inngår i: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, nr 10, s. 3229-3239Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The Paf1 protein complex (Paf1C) is increasingly recognized as a highly conserved and broadly utilized regulator of a variety of transcriptional processes. These include the promotion of H3K4 and H3K36 trimethylation, H2BK123 ubiquitination, RNA Pol II transcriptional termination, and also RNA-mediated gene silencing. Paf1C contains five canonical protein components, including Paf1 and Ctr9, which are critical for overall complex integrity, as well as Rtf1, Leo1, and Cdc73/Parafibromin(Hrpt2)/Hyrax. In spite of a growing appreciation for the importance of Paf1C from yeast and mammalian studies, there has only been limited work in Drosophila. Here, we provide the first detailed phenotypic study of Ctr9 function in Drosophila. We found that Ctr9 mutants die at late embryogenesis or early larval life, but can be partly rescued by nervous system reexpression of Ctr9. We observed a number of phenotypes in Ctr9 mutants, including increased neuroblast numbers, increased nervous system proliferation, as well as downregulation of many neuropeptide genes. Analysis of cell cycle and regulatory gene expression revealed upregulation of the E2f1 cell cycle factor, as well as changes in Antennapedia and Grainy head expression. We also found reduction of H3K4me3 modification in the embryonic nervous system. Genome-wide transcriptome analysis points to additional downstream genes that may underlie these Ctr9 phenotypes, revealing gene expression changes in Notch pathway target genes, cell cycle genes, and neuropeptide genes. In addition, we find significant effects on the gene expression of metabolic genes. These findings reveal that Ctr9 is an essential gene that is necessary at multiple stages of nervous system development, and provides a starting point for future studies of the Paf1C in Drosophila.

    sted, utgiver, år, opplag, sider
    Genetics Society of America, 2016
    Emneord
    neuroblast, lineage tree, cell cycle, epigenetics, terminal differentiation, FlyBook
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-132856 (URN)10.1534/g3.116.034231 (DOI)000386581200018 ()27520958 (PubMedID)
    Merknad

    Funding Agencies|Swedish Research Council [621-2013-5258]; Knut and Alice Wallenberg Foundation [KAW2011.0165]; Swedish Cancer Foundation [120531]; Swedish Royal Academy of Sciences

    Tilgjengelig fra: 2016-12-06 Laget: 2016-11-30 Sist oppdatert: 2017-11-29
    3. Neural Lineage Progression Controlled by a Temporal Proliferation Program.
    Åpne denne publikasjonen i ny fane eller vindu >>Neural Lineage Progression Controlled by a Temporal Proliferation Program.
    Vise andre…
    2017 (engelsk)Inngår i: Developmental Cell, ISSN 1534-5807, E-ISSN 1878-1551, Vol. 43, nr 3, s. 332-348Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Great progress has been made in identifying transcriptional programs that establish stem cell identity. In contrast, we have limited insight into how these programs are down-graded in a timely manner to halt proliferation and allow for cellular differentiation. Drosophila embryonic neuroblasts undergo such a temporal progression, initially dividing to bud off daughters that divide once (type I), then switching to generating non-dividing daughters (type 0), and finally exiting the cell cycle. We identify six early transcription factors that drive neuroblast and type I daughter proliferation. Early factors are gradually replaced by three late factors, acting to trigger the type I→0 daughter proliferation switch and eventually to stop neuroblasts. Early and late factors regulate each other and four key cell-cycle genes, providing a logical genetic pathway for these transitions. The identification of this extensive driver-stopper temporal program controlling neuroblast lineage progression may have implications for studies in many other systems.less thanbr /greater than (Copyright © 2017 Elsevier Inc. All rights reserved.)

    sted, utgiver, år, opplag, sider
    Cell Press, 2017
    HSV kategori
    Identifikatorer
    urn:nbn:se:liu:diva-143117 (URN)10.1016/j.devcel.2017.10.004 (DOI)000414584300011 ()29112852 (PubMedID)
    Merknad

    Funding agencies: Swedish Research Council [621-2013-5258]; Knut and Alice Wallenberg Foundation [KAW2011.0165, KAW2012.0101]; Swedish Cancer Foundation [140780, 150633]

    Tilgjengelig fra: 2017-11-20 Laget: 2017-11-20 Sist oppdatert: 2017-11-20bibliografisk kontrollert
  • 123.
    Bahrampour, Shahrzad
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten.
    Gunnar, Erika
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten.
    Jönsson, Carolin
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten.
    Ekman, Helen
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten.
    Thor, Stefan
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten.
    Neural Lineage Progression Controlled by a Temporal Proliferation Program.2017Inngår i: Developmental Cell, ISSN 1534-5807, E-ISSN 1878-1551, Vol. 43, nr 3, s. 332-348Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Great progress has been made in identifying transcriptional programs that establish stem cell identity. In contrast, we have limited insight into how these programs are down-graded in a timely manner to halt proliferation and allow for cellular differentiation. Drosophila embryonic neuroblasts undergo such a temporal progression, initially dividing to bud off daughters that divide once (type I), then switching to generating non-dividing daughters (type 0), and finally exiting the cell cycle. We identify six early transcription factors that drive neuroblast and type I daughter proliferation. Early factors are gradually replaced by three late factors, acting to trigger the type I→0 daughter proliferation switch and eventually to stop neuroblasts. Early and late factors regulate each other and four key cell-cycle genes, providing a logical genetic pathway for these transitions. The identification of this extensive driver-stopper temporal program controlling neuroblast lineage progression may have implications for studies in many other systems.less thanbr /greater than (Copyright © 2017 Elsevier Inc. All rights reserved.)

  • 124.
    Bahrampour, Shahrzad
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten. Inst Rech Clin Montreal, Canada; Karolinska Inst, Sweden.
    Jönsson, Carolin
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten.
    Thor, Stefan
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten. Univ Queensland, Australia.
    Brain expansion promoted by polycomb-mediated anterior enhancement of a neural stem cell proliferation program2019Inngår i: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 17, nr 2, artikkel-id e3000163Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    During central nervous system (CNS) development, genetic programs establish neural stem cells and drive both stem and daughter cell proliferation. However, the prominent anterior expansion of the CNS implies anterior-posterior (A-P) modulation of these programs. In Drosophila, a set of neural stem cell factors acts along the entire A-P axis to establish neural stem cells. Brain expansion results from enhanced stem and daughter cell proliferation, promoted by a Polycomb Group (PcG)-amp;gt;Homeobox (Hox) homeotic network. But how does PcG-amp;gt;Hox modulate neural-stem-cell-factor activity along the A-P axis? We find that the PcG-amp;gt;Hox network creates an A-P expression gradient of neural stem cell factors, thereby driving a gradient of proliferation. PcG mutants can be rescued by misexpression of the neural stem cell factors or by mutation of one single Hox gene. Hence, brain expansion results from anterior enhancement of core neural-stem-cell-factor expression, mediated by PcG repression of brain Hox expression.

  • 125.
    Bahrampour, Shahrzad
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten.
    Thor, Stefan
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för mikrobiologi och molekylär medicin. Linköpings universitet, Medicinska fakulteten.
    Ctr9, a Key Component of the Paf1 Complex, Affects Proliferation and Terminal Differentiation in the Developing Drosophila Nervous System2016Inngår i: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, nr 10, s. 3229-3239Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Paf1 protein complex (Paf1C) is increasingly recognized as a highly conserved and broadly utilized regulator of a variety of transcriptional processes. These include the promotion of H3K4 and H3K36 trimethylation, H2BK123 ubiquitination, RNA Pol II transcriptional termination, and also RNA-mediated gene silencing. Paf1C contains five canonical protein components, including Paf1 and Ctr9, which are critical for overall complex integrity, as well as Rtf1, Leo1, and Cdc73/Parafibromin(Hrpt2)/Hyrax. In spite of a growing appreciation for the importance of Paf1C from yeast and mammalian studies, there has only been limited work in Drosophila. Here, we provide the first detailed phenotypic study of Ctr9 function in Drosophila. We found that Ctr9 mutants die at late embryogenesis or early larval life, but can be partly rescued by nervous system reexpression of Ctr9. We observed a number of phenotypes in Ctr9 mutants, including increased neuroblast numbers, increased nervous system proliferation, as well as downregulation of many neuropeptide genes. Analysis of cell cycle and regulatory gene expression revealed upregulation of the E2f1 cell cycle factor, as well as changes in Antennapedia and Grainy head expression. We also found reduction of H3K4me3 modification in the embryonic nervous system. Genome-wide transcriptome analysis points to additional downstream genes that may underlie these Ctr9 phenotypes, revealing gene expression changes in Notch pathway target genes, cell cycle genes, and neuropeptide genes. In addition, we find significant effects on the gene expression of metabolic genes. These findings reveal that Ctr9 is an essential gene that is necessary at multiple stages of nervous system development, and provides a starting point for future studies of the Paf1C in Drosophila.

  • 126.
    Bai, Sai
    et al.
    Zhejiang University, Peoples R China.
    He, Shasha
    Zhejiang University, Peoples R China.
    Jin, Yizheng
    Zhejiang University, Peoples R China.
    Wu, Zhongwei
    Soochow University, Peoples R China.
    Xia, Zhouhui
    Soochow University, Peoples R China.
    Sun, Baoquan
    Soochow University, Peoples R China.
    Wang, Xin
    Zhejiang University, Peoples R China.
    Ye, Zhizhen
    Zhejiang University, Peoples R China.
    Gao, Feng
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska högskolan.
    Shao, Shuyan
    Zhang, Fengling
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska högskolan.
    Electrophoretic deposited oxide thin films as charge transporting interlayers for solution-processed optoelectronic devices: the case of ZnO nanocrystals2015Inngår i: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 5, nr 11, s. 8216-8222Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A promising fabrication method of electron transporting interlayers for solution-processed optoelectronic devices by electrophoretic deposition (EPD) of colloidal zinc oxide (ZnO) nanocrystals was demonstrated. A low voltage of 3-5 V and a short deposition time of 40 s at room temperature were found to be sufficient to generate dense and uniform ZnO thin films. The EPD ZnO nanocrystal films were applied as ETLs for inverted organic solar cell and polymer light emitting diodes (PLEDs). By optimizing the EPD processing of ZnO nanocrystal electron transporting layers (ETLs), inverted organic solar cells based on [3,4-b]-thiophene/benzodithiophene (PTB7): [6-6]-phenyl-C71-butyric acid methyl ester (PC71BM) and poly(3-hexylthiophene) (P3HT): [6-6]-phenyl-C-61-butyric acid methyl ester (PC61BM) with an average PCE of 8.4% and 4.0% were fabricated. In combination with the PLEDs and flexible devices results, we conclude that the EPD processed ZnOnanocrystal thin films can serve as high quality ETLs for solution-processed optoelectronic devices.

  • 127.
    Bai, Sai
    et al.
    Zhejiang University, Peoples R China; Zhejiang University, Peoples R China.
    Jin, Yizheng
    Zhejiang University, Peoples R China; Zhejiang University, Peoples R China.
    Liang, Xiaoyong
    Zhejiang University, Peoples R China; Zhejiang University, Peoples R China.
    Ye, Zhizhen
    Zhejiang University, Peoples R China; Zhejiang University, Peoples R China.
    Wu, Zhongwei
    Soochow University, Peoples R China.
    Sun, Baoquan
    Soochow University, Peoples R China.
    Ma, Zaifei
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska högskolan.
    Tang, Zheng
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska högskolan.
    Wang, Jianpu
    Nanjing Technical University, Peoples R China.
    Wuerfel, Uli
    Fraunhofer Institute Solar Energy Syst ISE, Germany; University of Freiburg, Germany.
    Gao, Feng
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska högskolan.
    Zhang, Fengling
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska högskolan.
    Ethanedithiol Treatment of Solution-Processed ZnO Thin Films: Controlling the Intragap States of Electron Transporting Interlayers for Efficient and Stable Inverted Organic Photovoltaics2015Inngår i: ADVANCED ENERGY MATERIALS, ISSN 1614-6832, Vol. 5, nr 5, s. 1401606-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The surface defects of solution-processed ZnO films lead to various intragap states. When the solution-processed ZnO films are used as electron transport interlayers (ETLs) in inverted organic solar cells, the intragap states act as interfacial recombination centers for photogenerated charges and thereby degrade the device performance. Here, a simple passivation method based on ethanedithiol (EDT) treatment is demonstrated, which effectively removes the surface defects of the ZnO nanocrystal films by forming zinc ethanedithiolates. The passivation by EDT treatment modulates the intragap states of the ZnO films and introduces a new intragap band. When the EDT-treated ZnO nanocrystal films are used as ETLs in inverted organic solar cells, both the power conversion efficiency and stability of the devices are improved. The control studies show that the solar cells with EDT-treated ZnO films exhibit reduced charge recombination rates and enhanced charge extraction properties. These features are consistent with the fact that the modulation of the intragap states results in reduction of interfacial recombination as well as the improved charge selectivity and electron transport properties of the ETLs. It is further demonstrated that the EDT treatment-based passivation method can be extended to ZnO films deposited from sol-gel precursors.

  • 128.
    Bailey, Richard I.
    et al.
    Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden .
    Innocenti, Paolo
    Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden .
    Morrow, Edward H.
    Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden .
    Friberg, Urban
    Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden .
    Qvarnström, Anna
    Department of Ecology and Genetics, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden .
    Female Drosophila melanogaster Gene Expression and Mate Choice: The X Chromosome Harbours Candidate Genes Underlying Sexual Isolation2011Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, nr 2, artikkel-id e17358Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: The evolution of female choice mechanisms favouring males of their own kind is considered a crucial step during the early stages of speciation. However, although the genomics of mate choice may influence both the likelihood and speed of speciation, the identity and location of genes underlying assortative mating remain largely unknown. Methods and Findings: We used mate choice experiments and gene expression analysis of female Drosophila melanogaster to examine three key components influencing speciation. We show that the 1,498 genes in Zimbabwean female D. melanogaster whose expression levels differ when mating with more (Zimbabwean) versus less (Cosmopolitan strain) preferred males include many with high expression in the central nervous system and ovaries, are disproportionately X-linked and form a number of clusters with low recombination distance. Significant involvement of the brain and ovaries is consistent with the action of a combination of pre- and postcopulatory female choice mechanisms, while sex linkage and clustering of genes lead to high potential evolutionary rate and sheltering against the homogenizing effects of gene exchange between populations. Conclusion: Taken together our results imply favourable genomic conditions for the evolution of reproductive isolation through mate choice in Zimbabwean D. melanogaster and suggest that mate choice may, in general, act as an even more important engine of speciation than previously realized.

  • 129.
    Baiser, Benjamin
    et al.
    Univ Florida, FL 32611 USA.
    Gravel, Dominique
    Univ Sherbrooke, Canada.
    Cirtwill, Alyssa
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk Biologi. Linköpings universitet, Tekniska fakulteten.
    Dunne, Jennifer A.
    Santa Fe Inst, NM 87501 USA.
    Fahimipour, Ashkaan K.
    Univ Oregon, OR 97403 USA.
    Gilarranz, Luis J.
    Eawag Swiss Fed Inst Aquat Sci and Technol, Switzerland.
    Grochow, Joshua A.
    Univ Colorado, CO 80309 USA.
    Li, Daijiang
    Univ Florida, FL 32611 USA.
    Martinez, Neo D.
    Univ Arizona, AZ USA.
    McGrew, Alicia
    Univ Florida, FL USA.
    Poisot, Timothee
    Univ Montreal, Canada.
    Romanuk, Tamara N.
    Dalhousie Univ, Canada.
    Stouffer, Daniel B.
    Univ Canterbury, New Zealand.
    Trotta, Lauren B.
    Univ Florida, FL 32611 USA.
    Valdovinos, Fernanda S.
    Univ Michigan, MI 48109 USA.
    Williams, Richard J.
    Vibrant Data Inc, CA USA.
    Wood, Spencer A.
    Univ Washington, WA 98195 USA.
    Yeakel, Justin D.
    Santa Fe Inst, NM 87501 USA; Univ Calif Merced, CA USA.
    Ecogeographical rules and the macroecology of food webs2019Inngår i: Global Ecology and Biogeography, ISSN 1466-822X, E-ISSN 1466-8238, Vol. 28, nr 9, s. 1204-1218Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aim

    How do factors such as space, time, climate and other ecological drivers influence food web structure and dynamics? Collections of well‐studied food webs and replicate food webs from the same system that span biogeographical and ecological gradients now enable detailed, quantitative investigation of such questions and help integrate food web ecology and macroecology. Here, we integrate macroecology and food web ecology by focusing on how ecogeographical rules [the latitudinal diversity gradient (LDG), Bergmann's rule, the island rule and Rapoport's rule] are associated with the architecture of food webs.

    Location

    Global.

    Time period

    Current.

    Major taxa studied

    All taxa.

    Methods

    We discuss the implications of each ecogeographical rule for food webs, present predictions for how food web structure will vary with each rule, assess empirical support where available, and discuss how food webs may influence ecogeographical rules. Finally, we recommend systems and approaches for further advancing this research agenda.

    Results

    We derived testable predictions for some ecogeographical rules (e.g. LDG, Rapoport's rule), while for others (e.g., Bergmann's and island rules) it is less clear how we would expect food webs to change over macroecological scales. Based on the LDG, we found weak support for both positive and negative relationships between food chain length and latitude and for increased generality and linkage density at higher latitudes. Based on Rapoport's rule, we found support for the prediction that species turnover in food webs is inversely related to latitude.

    Main conclusions

    The macroecology of food webs goes beyond traditional approaches to biodiversity at macroecological scales by focusing on trophic interactions among species. The collection of food web data for different types of ecosystems across biogeographical gradients is key to advance this research agenda. Further, considering food web interactions as a selection pressure that drives or disrupts ecogeographical rules has the potential to address both mechanisms of and deviations from these macroecological relationships. For these reasons, further integration of macroecology and food webs will help ecologists better understand the assembly, maintenance and change of ecosystems across space and time.

  • 130.
    Baker, Maggie
    et al.
    NIAAA, USA.
    Lindell, Stephen G.
    NIAAA, USA.
    Driscoll, Carlos A.
    NIAAA, USA.
    Zhou, Zhifeng
    NIAAA, USA.
    Yuan, Qiaoping
    NIAAA, USA.
    Schwandt, Melanie L.
    NIAAA, USA.
    Miller-Crews, Isaac
    NIAAA, USA.
    Simpson, Elizabeth A.
    Eunice Shriver Kennedy National Institute Child Health and Huma, MD 20837 USA.
    Paukner, Annika
    Eunice Shriver Kennedy National Institute Child Health and Huma, MD 20837 USA.
    Francesco Ferrari, Pier
    University of Claude Bernard Lyon, France.
    Kumar Sindhu, Ravi
    NIAAA, MD 20852 USA.
    Razaqyar, Muslima
    NIAAA, USA.
    Sommer, Wolfgang H.
    Heidelberg University, Germany; Heidelberg University, Germany.
    Lopez, Juan F.
    University of Michigan, MI 48109 USA.
    Thompson, Robert C.
    University of Michigan, MI 48109 USA.
    Goldman, David
    NIAAA, USA.
    Heilig, Markus
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Centrum för social och affektiv neurovetenskap. Linköpings universitet, Medicinska fakulteten. Region Östergötland, Närsjukvården i centrala Östergötland, Psykiatriska kliniken.
    Dee Higley, J.
    Brigham Young University, UT 84602 USA.
    Suomi, Stephen J.
    Eunice Shriver Kennedy National Institute Child Health and Huma, MD 20837 USA.
    Barr, Christina S.
    NIAAA, USA.
    Early rearing history influences oxytocin receptor epigenetic regulation in rhesus macaques2017Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, nr 44, s. 11769-11774Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Adaptations to stress can occur through epigenetic processes and may be a conduit for informing offspring of environmental challenge. We employed ChIP-sequencing for H3K4me3 to examine effects of early maternal deprivation (peer-rearing, PR) in archived rhesus macaque hippocampal samples (male, n = 13). Focusing on genes with roles in stress response and behavior, we assessed the effects of rearing on H3K4me3 binding by ANOVA. We found decreased H3K4me3 binding at genes critical to behavioral stress response, the most robust being the oxytocin receptor gene OXTR, for which we observed a corresponding decrease in RNA expression. Based on this finding, we performed behavioral analyses to deter mine whether a gain-of-function nonsynonymous OXTR SNP inter acted with early stress to influence relevant behavioral stress reactivity phenotypes (n = 194), revealing that this SNP partially rescued the PR phenotype. PR infants exhibited higher levels of separation anxiety and arousal in response to social separation, but infants carrying the alternative OXTR allele did not exhibit as great a separation response. These data indicate that the oxytocin system is involved in social-separation response and suggest that epigenetic down-modulation of OXTR could contribute to behavior al differences observed in PR animals. Epigenetic changes at OXTR may represent predictive adaptive responses that could impart readiness to respond to environmental challenge or maintain proximity to a caregiver but also contribute to behavioral pathology. Our data also demonstrate that OXTR polymorphism can permit animals to partially overcome the detrimental effects of early maternal deprivation, which could have translational implications for human psychiatric disorders.

  • 131.
    Bakovic, Vid
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Univ Nat Resources and Life Sci Vienna, Austria.
    Schuler, Hannes
    Free Univ Bozen Bolzano, Italy.
    Schebeck, Martin
    Univ Nat Resources and Life Sci Vienna, Austria.
    Feder, Jeffrey L.
    Univ Notre Dame, IN 46556 USA.
    Stauffer, Christian
    Univ Nat Resources and Life Sci Vienna, Austria.
    Ragland, Gregory J.
    Univ Colorado, CO 80202 USA.
    Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi2019Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, nr 20, s. 4648-4666Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher F-ST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host-related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.

  • 132.
    Bakulin, Artem A.
    et al.
    FOM Institute AMOLF, Netherlands; University of Cambridge, England.
    Xia, Yuxin
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska fakulteten.
    Bakker, Huib J.
    FOM Institute AMOLF, Netherlands.
    Inganäs, Olle
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska fakulteten.
    Gao, Feng
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska fakulteten.
    Morphology, Temperature, and Field Dependence Separation in High-Efficiency Solar Cells Based on Polyquinoxaline Copolymer2016Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, nr 8, s. 4219-4226Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Charge separation and recombination are key processes determining the performance of organic optoelectronic devices. Here we combine photoluminescence and photovoltaic characterization of organic solar cell devices with ultrafast multipulse photocurrent spectroscopy to investigate charge generation mechanisms in the organic photovoltaic devices based on a blend of an alternating polyquinoxaline copolymer with fullerene. The combined use of these techniques enables the determination of the contributions of geminate and bimolecular processes to the solar cell performance. We observe that charge separation is not a temperature-activated process in the studied materials. At the same time, the generation of free charges shows a dear external field and morphology dependence. This indicates that the critical step of charge separation involves the nonequilibrium state that is formed at early times after photoexcitation, when the polaronic localization is not yet complete. This work reveals new aspects of molecular level charge dynamics in the organic light-conversion systems.

  • 133.
    Banerji, Shantanu
    et al.
    Manitoba Institute of Cell Biology, Winnipeg, Manitoba, Canada .
    Los, Marek Jan
    Manitoba Institute of Cell Biology, Cancer Care Manitoba; Manitoba Institute of Child Health; Department of Biochemistry and Medical Genetics; Department of Human Anatomy and Cell Science, University Manitoba, Winnipeg, Canada.
    Important differences between topoisomerase-I and -II targeting agents2006Inngår i: Cancer Biology & Therapy, ISSN 1538-4047, E-ISSN 1555-8576, Vol. 5, nr 8, s. 965-966Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Commentary to: Activation of ATM and Histone H2AX Phosphorylation Induced by Mitoxantrone But Not by Topotecan is Prevented by the Antioxidant N-acetyl-L-Cysteine Xuan Huang, Akira Kurose, Toshiki Tanaka, Frank Traganos, Wei Dai and Zbigniew Darzynkiewicz

     

  • 134.
    Bao, Qinye
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska fakulteten.
    Fabiano, Simone
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Fysik och elektroteknik. Linköpings universitet, Tekniska fakulteten.
    Andersson, Mattias
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska högskolan.
    Braun, Slawomir
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska fakulteten.
    Sun, Zhengyi
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska högskolan.
    Crispin, Xavier
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Fysik och elektroteknik. Linköpings universitet, Tekniska fakulteten.
    Berggren, Magnus
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Fysik och elektroteknik. Linköpings universitet, Tekniska fakulteten.
    Liu, Xianjie
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska fakulteten.
    Fahlman, Mats
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska fakulteten.
    Energy Level Bending in Ultrathin Polymer Layers Obtained through Langmuir-Shafer Deposition2016Inngår i: Advanced Functional Materials, ISSN 1616-301X, E-ISSN 1616-3028, Vol. 26, nr 7, s. 1077-1084Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The semiconductor-electrode interface impacts the function and the performance of (opto) electronic devices. For printed organic electronics the electrode surface is not atomically clean leading to weakly interacting interfaces. As a result, solution-processed organic ultrathin films on electrodes typically form islands due to dewetting. It has therefore been utterly difficult to achieve homogenous ultrathin conjugated polymer films. This has made the investigation of the correct energetics of the conjugated polymer-electrode interface impossible. Also, this has hampered the development of devices including ultrathin conjugated polymer layers. Here, LangmuirShafer-manufactured homogenous mono-and multilayers of semiconducting polymers on metal electrodes are reported and the energy level bending using photoelectron spectroscopy is tracked. The amorphous films display an abrupt energy level bending that does not extend beyond the first monolayer. These findings provide new insights of the energetics of the polymer-electrode interface and opens up for new high-performing devices based on ultrathin semiconducting polymers.

  • 135.
    Bao, Qinye
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska högskolan.
    Liu, Xianjie
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska högskolan.
    Braun, Slawomir
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska högskolan.
    Gao, Feng
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska högskolan.
    Fahlman, Mats
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska högskolan.
    Energetics at Doped Conjugated Polymer/Electrode Interfaces2015Inngår i: ADVANCED MATERIALS INTERFACES, ISSN 2196-7350, Vol. 2, nr 2Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    n/a

  • 136.
    Bao, Qinye
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska högskolan.
    Liu, Xianjie
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska högskolan.
    Xia, Yuxin
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska högskolan.
    Gao, Feng
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biomolekylär och Organisk Elektronik. Linköpings universitet, Tekniska högskolan.
    Kauffmann, Louis-Dominique
    GenesInk, France.
    Margeat, Olivier
    Aix Marseille University, France.
    Ackermann, Jorg
    Aix Marseille University, France.
    Fahlman, Mats
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Ytors Fysik och Kemi. Linköpings universitet, Tekniska högskolan.
    Effects of ultraviolet soaking on surface electronic structures of solution processed ZnO nanoparticle films in polymer solar cells2014Inngår i: Journal of Materials Chemistry A, ISSN 2050-7488, Vol. 2, nr 41, s. 17676-17682Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We systematically show the effect of UV-light soaking on surface electronic structures and chemical states of solution processed ZnO nanoparticle (ZnONP) films in UHV, dry air and UV-ozone. UV exposure in UHV induces a slight decrease in work function and surface-desorption of chemisorbed oxygen, whereas UV exposure in the presence of oxygen causes an increase in work function due to oxygen atom vacancy filling in the ZnO matrix. We demonstrate that UV-light soaking in combination with vacuum or oxygen can tune the work function of the ZnONP films over a range exceeding 1 eV. Based on photovoltaic performance and diode measurements, we conclude that the oxygen atom vacancy filling occurs mainly at the surface of the ZnONP films and that the films consequently retain their n-type behavior despite a significant increase in the measured work function.

  • 137.
    Barabas, György
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk Biologi. Linköpings universitet, Tekniska fakulteten.
    The coexistence problem revisited2017Inngår i: NATURE ECOLOGY and EVOLUTION, ISSN 2397-334X, Vol. 1, nr 10, s. 1425-1426Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    A new theoretical study warns against common misinterpretations of classical ideas on the limits to species diversity.

  • 138.
    Barabas, György
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk Biologi. Linköpings universitet, Tekniska fakulteten.
    D'Andrea, Rafael
    Univ Illinois, IL 61801 USA.
    Stump, Simon Maccracken
    Yale Sch Forestry and Environm Studies, CT 06511 USA.
    Chesson's coexistence theory2018Inngår i: Ecological Monographs, ISSN 0012-9615, E-ISSN 1557-7015, Vol. 88, nr 3, s. 277-303Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    We give a comprehensive review of Chesson's coexistence theory, summarizing, for the first time, all its fundamental details in one single document. Our goal is for both theoretical and empirical ecologists to be able to use the theory to interpret their findings, and to get a precise sense of the limits of its applicability. To this end, we introduce an explicit handling of limiting factors, and a new way of defining the scaling factors that partition invasion growth rates into the different mechanisms contributing to coexistence. We explain terminology such as relative nonlinearity, storage effect, and growth-density covariance, both in a formal setting and through their biological interpretation. We review the theory's applications and contributions to our current understanding of species coexistence. While the theory is very general, it is not well suited to all problems, so we carefully point out its limitations. Finally, we critique the paradigm of decomposing invasion growth rates into stabilizing and equalizing components: we argue that these concepts are useful when used judiciously, but have often been employed in an overly simplified way to justify false claims.

  • 139.
    Barabas, György
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Teoretisk Biologi. Linköpings universitet, Tekniska fakulteten. University of Chicago, IL 60637 USA.
    Michalska-Smith, Matthew J.
    University of Chicago, IL 60637 USA.
    Allesina, Stefano
    University of Chicago, IL 60637 USA; Northwestern University, IL 60208 USA.
    Self-regulation and the stability of large ecological networks2017Inngår i: NATURE ECOLOGY and EVOLUTION, ISSN 2397-334X, Vol. 1, nr 12, s. 1870-+Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The stability of complex ecological networks depends both on the interactions between species and the direct effects of the species on themselves. These self-effects are known as self-regulation when an increase in a species abundance decreases its per-capita growth rate. Sources of self-regulation include intraspecific interference, cannibalism, time-scale separation between consumers and their resources, spatial heterogeneity and nonlinear functional responses coupling predators with their prey. The influence of self-regulation on network stability is understudied and in addition, the empirical estimation of self-effects poses a formidable challenge. Here, we show that empirical food web structures cannot be stabilized unless the majority of species exhibit substantially strong self-regulation. We also derive an analytical formula predicting the effect of self-regulation on network stability with high accuracy and show that even for random networks, as well as networks with a cascade structure, stability requires negative self-effects for a large proportion of species. These results suggest that the aforementioned potential mechanisms of self-regulation are probably more important in contributing to the stability of observed ecological networks than was previously thought.

  • 140.
    Barczyk, K.
    et al.
    Department of Immunology, Faculty of Biotechnology, Jagiellonian University, Krakow, Poland; Institute of Experimental Dermatology, University of Münster, Münster, Germany.
    Kreuter, M.
    Department of Medicine/Hematology and Oncology, University of Münster, Münster, Germany.
    Pryjma, J.
    Department of Immunology, Faculty of Biotechnology, Jagiellonian University, Krakow, Poland.
    Booy, Evan P.
    Manitoba Institute of Cell Biology, and Department of Biochemistry and Medical Genetics, Univ. Manitoba, Winnipeg, Canada.
    Maddika, Subbareddy
    Manitoba Institute of Cell Biology, Cancer Care Manitoba; Department of Biochemistry and Medical Genetics,University of Manitoba, Winnipeg, Canada .
    Ghavami, Saeid
    Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, Cancer Care Manitoba, Winnipeg, Manitoba, Canada.
    Berdel, W. E.
    Department of Medicine/Hematology and Oncology, University of Münster, Münster, Germany.
    Roth, J.
    Institute of Experimental Dermatology, University of Münster, Münster, Germany.
    Los, Marek Jan
    Institute of Experimental Dermatology, University of Münster, Münster, Germany Manitoba Institute of Cell Biology, Cancer Care Manitoba; Manitoba Institute of Child Health; Department of Biochemistry and Medical Genetics; Department of Human Anatomy and Cell Science, University Manitoba, Winnipeg, Canada, .
    Serum cytochrome c indicates in vivo apoptosis and can serve as a prognostic marker during cancer therapy2005Inngår i: International Journal of Cancer, ISSN 0020-7136, E-ISSN 1097-0215, Vol. 116, nr 2, s. 167-173Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Despite significant progress in cancer therapy, the outcome of the treatment is often unfavorable. Better treatment monitoring would not only allow an individual more effective, patient-adjusted therapy, but also it would eliminate some of the side effects. Using a cytochrome c ELISA that was modified to increase sensitivity, we demonstrate that serum cytochrome c is a sensitive apoptotic marker in vivo reflecting therapy-induced cell death burden. Furthermore, increased serum cytochrome c level is a negative prognostic marker. Cancer patients whose serum cytochrome c level was normal 3 years ago have a twice as high probability to be still alive, as judged from sera samples collected for years, analyzed recently and matched with survival data. Moreover, we show that serum cytochrome c and serum LDH-activity reflect different stages and different forms of cell death. Cellular cytochrome c release is specific for apoptosis, whereas increased LDH activity is an indicator of (secondary) necrosis. Whereas serum LDH activity reflects the "global" degree of cell death over a period of time, the sensitive cytochrome c-based method allows confirmation of the individual cancer therapy-induced and spontaneous cell death events. The combination of cytochrome c with tissue-specific markers may provide the foundation for precise monitoring of apoptosis in vivo, by "lab-on-the-chip" technology. (c) 2005 Wiley-Liss, Inc.

  • 141.
    Barranco, Isabel
    et al.
    Univ Murcia, Spain.
    Padilla, Lorena
    Univ Murcia, Spain.
    Parrilla, Inmaculada
    Univ Murcia, Spain.
    Alvarez-Barrientos, Alberto
    Univ Extremadura, Spain.
    Perez-Patino, Cristina
    Univ Murcia, Spain.
    Pena, Fernando J.
    Univ Extremadura, Spain.
    Martinez, Emilio A.
    Univ Murcia, Spain.
    Rodriguez-Martinez, Heriberto
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för barns och kvinnors hälsa. Linköpings universitet, Medicinska fakulteten.
    Roca, Jordi
    Univ Murcia, Spain.
    Extracellular vesicles isolated from porcine seminal plasma exhibit different tetraspanin expression profiles2019Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, artikkel-id 11584Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Seminal extracellular vesicles (EVs) include exosomes (phi 40-120 nm) and microvesicles (MVs, phi 120-1000 nm), which would be involved in multiple functional reproductive roles. The study aimed to establish which EV subtypes are present in pig semen, using a high-resolution flow cytometer to explore differences in their tetraspanin expression profile. The EVs were isolated from 12 pig ejaculates using serial ultracentrifugation and characterized by dynamic light scattering and electron microscopy for size and morphology as well as for tetraspanin expression using flow cytometry with Carboxyfluorescein succinimidyl ester (CFSE) and antibodies against CD9, CD63 and CD81. Pig semen contained a heterogeneous EV-population regarding size and morphology. Flow cytometric analysis demonstrated that the proportion of EVs expressing CD63 and CD9 was higher in MVs (P amp;lt; 0.001 and P amp;lt; 0.05, respectively) than in exosomes, while the opposite was true for CD81; higher (P amp;lt; 0.001) in exosomes than in MVs. In conclusion, (1) the new generation of flow cytometers are able to accurately identify EVs and to gate them in two size-different populations named exosomes and MVs. (2) Tetraspanins CD9, CD63 and CD81 are present in both seminal EVs, albeit with exosomes and MVs differing in expression profiles, suggesting dissimilar cargo and binding affinity.

  • 142.
    Barrefelt, Linnea
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi.
    Populationsutveckling och bärkraft för lodjur (Lynx lynx) i Östergötland2019Independent thesis Basic level (degree of Bachelor), 10,5 poäng / 16 hpOppgave
    Abstract [sv]

    Jordens biologiska mångfald minskar i en allt snabbare takt, men mitt i denna ekologiska katastrof börjar arter på vissa håll att återkomma. De stora rovdjuren i Europa är ett sådant exempel. Från att ha varit försvunna från stora delar av sina utbredningsområden är de flesta populationer numera stabila eller ökande. I Skandinavien har lodjurspopulationen expanderat och efter närmare 100 års reproduktiv frånvaro förekommer åter föryngringar i Sydsverige. I Östergötland finns i dagsläget ca 50–55 individer och mycket tyder på att stammen kommer att fortsätta öka. Genom att sammanställa och analysera data från inventeringsrapporter, observationsloggar och avskjutningsstatistik har jag undersökt lodjurspopulationens utveckling i Östergötland och beräknat länets bärkraft för lo. Beräkningen av bärkraften har utgått från klövviltförekomsten samt mängden lämpligt habitat. Resultaten visar att Östergötland har gott om lämpligt habitat och en hög bytesdensitet, som är jämförbar med flera lodjurstäta områden i Europa. Givet dessa förutsättningar har Östergötland en bärkraft för lo som ligger långt över dagens populationsnivå. Uppskattningsvis kan Östergötland hålla mellan 80–140 självständiga individer. Detta skulle innebära en fördubbling av dagens antal och kunna leda till såväl positiva som negativa konsekvenser för samhället. Lodjur kan innebära ett hot mot tamboskap, men de senaste årens rapportering visar att angreppen orsakade av lodjur är begränsade. Även påverkan på klövviltstammarna är i dagsläget försumbar. På sikt skulle dock en större lodjurspopulation kunna reglera klövviltet och på så vis minska mängden trafikolyckor och skador på skog.

  • 143.
    Barrientos-Somarribas, Mauricio
    et al.
    Karolinska Inst, Sweden.
    Messina, David N.
    Stockholm Univ, Sweden.
    Pou, Christian
    Karolinska Inst, Sweden.
    Lysholm, Fredrik
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Bioinformatik. Linköpings universitet, Tekniska fakulteten.
    Bjerkner, Annelie
    Karolinska Univ Hosp, Sweden.
    Allander, Tobias
    Karolinska Univ Hosp, Sweden.
    Andersson, Björn
    Karolinska Inst, Sweden.
    Sonnhammer, Erik L. L.
    Stockholm Univ, Sweden.
    Discovering viral genomes in human metagenomic data by predicting unknown protein families2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 28Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families. We applied this method to 17 virus-enriched libraries originating from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fluid samples. This resulted in 32 predicted putative novel gene families. Some families showed detectable homology to sequences in metagenomics datasets and protein databases after reannotation. Notably, one predicted family matches an ORF from the highly variable Torque Teno virus (TTV). Furthermore, follow-up from a predicted ORFan resulted in the complete reconstruction of a novel circular genome. Its organisation suggests that it most likely corresponds to a novel bacteriophage in the microviridae family, hence it was named bacteriophage HFM.

  • 144.
    Bartoszek, Krzysztof
    Department of Mathematics, Uppsala University, Uppsala, Sweden.
    Phylogenetic effective sample size2016Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 407, s. 371-386Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this paper I address the question—how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes-the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.

  • 145.
    Bartoszek, Krzysztof
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Quantifying the effects of anagenetic and cladogenetic evolution2014Inngår i: Mathematical Biosciences, ISSN 0025-5564, E-ISSN 1879-3134, Vol. 254, s. 42-57Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both types of change, quantify the effects of speciational change via the correlation between species and attribute the proportion of change to each type. I discuss results of parameter estimation of Hominoid body size in this light. I derive mathematical formulae related to this problem, the probability generating functions of the number of speciation events along a randomly drawn lineage and from the most recent common ancestor of two randomly chosen tip species for a conditioned Yule tree. Additionally I obtain in closed form the variance of the distance from the root to the most recent common ancestor of two randomly chosen tip species.

  • 146.
    Bartoszek, Krzysztof
    Department of Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Göteborg Sweden.
    The Laplace Motion in Phylogenetic Comparative Methods2012Inngår i: Proceedings of the 18th National Conference on Applications of Mathematics in Biology and Medicine, 2012, s. 25-30Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The majority of current phylogenetic comparative methods assume that the stochastic evolutionaryprocess is homogeneous over the phylogeny or offer relaxations of this in rather limited and usually parameter expensive ways. Here we make a preliminary investigation, bymeans of a numerical experiment, whether the Laplace motion process can offer an alternative approach.

  • 147.
    Bartoszek, Krzysztof
    Linköpings universitet, Institutionen för datavetenskap, Statistik och maskininlärning. Linköpings universitet, Filosofiska fakulteten.
    Trait evolution with jumps: illusionary normality2017Inngår i: Proceedings of the XXIII National Conference on Applications of Mathematics in Biology and Medicine, 2017, s. 23-28Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Phylogenetic comparative methods for real-valued traits usually make use of stochastic process whose trajectories are continuous.This is despite biological intuition that evolution is rather punctuated thangradual. On the other hand, there has been a number of recent proposals of evolutionarymodels with jump components. However, as we are only beginning to understandthe behaviour of branching Ornstein-Uhlenbeck (OU) processes the asymptoticsof branching  OU processes with jumps is an even greater unknown. In thiswork we build up on a previous study concerning OU with jumps evolution on a pure birth tree.We introduce an extinction component and explore via simulations, its effects on the weak convergence of such a process.We furthermore, also use this work to illustrate the simulation and graphic generation possibilitiesof the mvSLOUCH package.

  • 148.
    Bartoszek, Krzysztof
    et al.
    Linköpings universitet, Institutionen för datavetenskap, Statistik och maskininlärning. Linköpings universitet, Filosofiska fakulteten. Uppsala University, Sweden.
    Glemin, Sylvain
    Uppsala University, Sweden; CNRS University of Montpellier IRD EPHE, France.
    Kaj, Ingemar
    Uppsala University, Sweden.
    Lascoux, Martin
    Uppsala University, Sweden.
    Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations2017Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 429, s. 35-45Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the evolution of phenotypic traits along phylogenies. The standard OU process includes random perturbations and stabilizing selection and assumes that species evolve independently. However, evolving species may interact through various ecological process and also exchange genes especially in plants. This is particularly true if we want to study phenotypic evolution among diverging populations within species. In this work we present a straightforward statistical approach with analytical solutions that allows for the inclusion of adaptation and migration in a common phylogenetic framework, which can also be useful for studying local adaptation among populations within the same species. We furthermore present a detailed simulation study that clearly indicates the adverse effects of ignoring migration. Similarity between species due to migration could be misinterpreted as very strong convergent evolution without proper correction for these additional dependencies. Finally, we show that our model can be interpreted in terms of ecological interactions between species, providing a general framework for the evolution of traits between "interacting" species or populations.(C) 2017 Elsevier Ltd. All rights reserved.

  • 149.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Jones, Graham
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden / Department of Biological and Environmental Science, University of Gothenburg, Gothenburg, Sweden.
    Oxelman, Bengt
    Department of Biological and Environmental Science, University of Gothenburg, Gothenburg, Sweden.
    Sagitov, Serik
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Time to a single hybridization event in a group of species with unknown ancestral history2013Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 322, s. 1-6Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We consider a stochastic process for the generation of species which combines a Yule process with a simple model for hybridization between pairs of co-existent species. We assume that the origin of the process, when there was one species, occurred at an unknown time in the past, and we condition the process on producing n species via the Yule process and a single hybridization event. We prove results about the distribution of the time of the hybridization event. In particular we calculate a formula for all moments, and show that under various conditions, the distribution tends to an exponential with rate twice that of the birth rate for the Yule process.

  • 150.
    Bartoszek, Krzysztof
    et al.
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Sweden.
    Krzeminski, Michal
    Gdansk University of Technology.
    Critical case stochastic phylogenetic tree model via the Laplace transform2014Inngår i: Demonstratio Matematicae, ISSN 0420-1213, Vol. 47, nr 2, s. 474-481Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Birth-and-death models are now a common mathematical tool to describe branching patterns observed in real-world phylogenetic trees. Liggett and Schinazi (2009) is one such example. The authors propose a simple birth-and-death model that is compatible with phylogenetic trees of both in uenza and HIV, depending on the birth rate parameter. An interesting special case of this model is the critical case where the birth rate equals the death rate. This is a non-trivial situation and to study its asymptotic behaviour we employed the Laplace transform. With this we correct the proof of Liggett and Schinazi (2009) in the critical case.

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