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  • 1.
    Abadi, Mehrdad Sardar
    et al.
    Leibniz Inst Appl Geophys, LIAG, Rock Phys & Borehole Geophys, Hannover, Germany..
    Voeten, Dennis F. A. E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Kulagina, Elena, I
    Russian Acad Sci, Ufa Fed Res Ctr, Inst Geol, Ufa, Russia..
    Boulvain, Frederic
    Univ Liege, Dept Geol, Lab Petrol Sedimentaire, Bat B20, Liege, Belgium..
    Da Silva, Anne-Christine
    Univ Liege, Dept Geol, Lab Petrol Sedimentaire, Bat B20, Liege, Belgium..
    A comment on overlooked storm sensitivity of the carbonate factory recorded in the Mississippian Mobarak Formation (Alborz Mountains, Iran)2022Ingår i: Geological Journal, ISSN 0072-1050, E-ISSN 1099-1034, Vol. 57, nr 10, s. 4388-4392Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    New interpretations of depositional palaeoenvironments in the Mississippian (Lower Carboniferous) Mobarak Formation (Alborz Mountains, Iran) suggest a significant and persistent influence of storms. This deviates from previous conclusions that these deposits recorded mounds, patch reefs, and extensive lagoons deposited under stagnant environmental conditions. We here clarify and discuss the origin and nature of this misconception by explaining "unexpected" observations that are informed by outdated interpretations of the depositional environment of the Mobarak Formation. This evaluation offers the context required for appropriately interpreting and correlating Mississippian depositional records across the Alborz Basin.

  • 2.
    Abarenkov, Kessy
    et al.
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    Adams, Rachel I.
    Univ Calif Berkeley, Plant & Microbial Biol, Berkeley, CA 94720 USA..
    Irinyi, Laszlo
    Westmead Hosp, Ctr Infect Dis & Microbiol, Mol Mycol Res Lab, Sydney Med Sch, Sydney, NSW, Australia.;Univ Sydney, Marie Bashir Inst Infect Dis & Biosecur, Sydney, NSW, Australia.;Westmead Inst Med Res, Westmead, NSW, Australia..
    Agan, Ahto
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Ambrosio, Elia
    Univ Tartu, Nat Hist Museum, Tartu, Estonia.;Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.;Via Calamandrei 2, I-53035 Siena, Italy..
    Antonelli, Alexandre
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden.;Gothenburg Bot Garden, Carl Skottsbergs Gata 22A, S-41319 Gothenburg, Sweden..
    Bahram, Mohammad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Bengtsson-Palme, Johan
    Univ Gothenburg, Sahlgrenska Acad, Dept Infect Dis, Guldhedsgatan 10, S-41346 Gothenburg, Sweden..
    Bok, Gunilla
    SP Tech Res Inst Sweden, Box 857, S-50115 Boras, Sweden..
    Cangren, Patrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Coimbra, Victor
    Univ Fed Pernambuco UFPE, Dept Micol, CCB, Av Prof Nelson Chaves S-N, BR-50670901 Recife, PE, Brazil..
    Coleine, Claudia
    Univ Tuscia, Dept Ecol & Biol Sci, I-01100 Viterbo, Italy..
    Gustafsson, Claes
    Univ Gothenburg, Herbarium GB, Box 461, S-40530 Gothenburg, Sweden..
    He, Jinhong
    Chinese Acad Sci, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China..
    Hofmann, Tobias
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Kristiansson, Erik
    Chalmers, Dept Math Sci, S-41296 Gothenburg, Sweden..
    Larsson, Ellen
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Larsson, Tomas
    Univ Gothenburg, Dept Marine Sci, Box 460, S-40530 Gothenburg, Sweden..
    Liu, Yingkui
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Martinsson, Svante
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Meyer, Wieland
    Westmead Hosp, Ctr Infect Dis & Microbiol, Mol Mycol Res Lab, Sydney Med Sch, Sydney, NSW, Australia.;Westmead Inst Med Res, Westmead, NSW, Australia..
    Panova, Marina
    Univ Gothenburg, Dept Marine Sci Tjarno, S-45296 Stromstad, Sweden..
    Pombubpa, Nuttapon
    Univ Calif Riverside, Dept Plant Pathol & Microbiol, Riverside, CA 92521 USA.;Univ Calif Riverside, Inst Integrat Genome Biol, Riverside, CA 92521 USA..
    Ritter, Camila
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Ryberg, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Svantesson, Sten
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Scharn, Ruud
    Univ Gothenburg, Dept Earth Sci, Box 460, S-40530 Gothenburg, Sweden..
    Svensson, Ola
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Töpel, Mats
    Univ Gothenburg, Dept Marine Sci, Box 460, S-40530 Gothenburg, Sweden..
    Unterseher, Martin
    Ernst Moritz Arndt Univ Greifswald, Inst Bot & Landscape Ecol, Soldmannstr 15, D-17487 Greifswald, Germany..
    Visagie, Cobus
    Agr & Agri Food Canada, Biodivers Mycol, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.;Univ Ottawa, Dept Biol, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada..
    Wurzbacher, Christian
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Taylor, Andy F. S.
    James Hutton Inst, Aberdeen AB15 8QH, Scotland.;Univ Aberdeen, Inst Biol & Environm Sci, Cruickshank Bldg, Aberdeen AB24 3UU, Scotland..
    Köljalg, Urmas
    Univ Tartu, Nat Hist Museum, Tartu, Estonia.;Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Schriml, Lynn
    Univ Maryland, Sch Med, Dept Epidemiol & Publ Hlth, Baltimore, MD 21201 USA.;Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA..
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard - a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)2016Ingår i: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, nr 16, s. 1-15Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data - for example, "retrieve all fungal sequences recovered from bathrooms" - a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http:// gensc.org/ mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http:// its. mycologylab.org).

    Ladda ner fulltext (pdf)
    fulltext
  • 3.
    Abarenkov, Kessy
    et al.
    Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia..
    Kristiansson, Erik
    Chalmers Univ Technol, Dept Math Sci, Gothenburg, Sweden.;Univ Gothenburg, Gothenburg, Sweden..
    Ryberg, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Nogal-Prata, Sandra
    Real Jardin Bot CSIC, Dept Mycol, Madrid, Spain..
    Gomez-Martinez, Daniela
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Stueer-Patowsky, Katrin
    Tech Univ Munich, Chair Urban Water Syst Engn, Coulombwall 3, D-85748 Garching, Germany..
    Jansson, Tobias
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Polme, Sergei
    Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia..
    Ghobad-Nejhad, Masoomeh
    Iranian Res Org Sci & Technol, Dept Biotechnol, POB 3353-5111, Tehran 3353136846, Iran..
    Corcoll, Natalia
    Univ Gothenburg, Gothenburg Global Biodivers Ctr, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Scharn, Ruud
    Univ Gothenburg, Dept Earth Sci, Box 460, S-40530 Gothenburg, Sweden..
    Sanchez-Garcia, Marisol
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden..
    Khomich, Maryia
    Univ Bergen, Dept Clin Sci, Box 7804, N-5020 Bergen, Norway..
    Wurzbacher, Christian
    Tech Univ Munich, Chair Urban Water Syst Engn, Coulombwall 3, D-85748 Garching, Germany..
    Nilsson, R. Henrik
    Univ Gothenburg, Gothenburg Global Biodivers Ctr, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    The curse of the uncultured fungus2022Ingår i: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, nr 86, s. 177-194Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget lowresolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length that represent truly unidentifiable fungal taxa - and what proportion of them that would have deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.

    Ladda ner fulltext (pdf)
    FULLTEXT01
  • 4.
    Abbassi, Nasrollah
    et al.
    Univ Zanjan, Dept Geol, Fac Sci, Zanjan, Iran..
    Kundrat, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Ataabadi, Majid Mirzaie
    Univ Zanjan, Dept Geol, Fac Sci, Zanjan, Iran..
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Uppsala Univ, Sub Dept Evolut & Dev, Evolutionary Biol Ctr, Dept Organismal Biol, Uppsala, Sweden..
    Avian ichnia and other vertebrate trace fossils from the Neogene Red Beds of Tarom valley in north-western Iran2016Ingår i: Historical Biology, ISSN 0891-2963, E-ISSN 1029-2381, Vol. 28, nr 8, s. 1075-1089Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Neogene Red Beds of the Tarom valley (north-western Iran) include conglomerate, sandstone, marl and gypsum. Avian and mammal footprints were discovered in one of the sandstone layers at the base of a third Miocene stratigraphical unit in the Gilankesheh area located in the east Tarom valley. The avian ichnia include Aviadactyla vialovi, Avipeda filiportatis, Charadriipeda disjuncta, Charadriipeda isp. A and B and cf. Ornithotarnocia lambrechti. Bird feeding traces are preserved as bilobate, loop-shaped, sinusoidal and ring-like traces. We have also identified a reticulate texture of sole scale imprints in some of the avian ichnia. Two mammal footprints of camelid-like artiodactyls are also present with the avian ichno-assemblage.

  • 5. Abrahamson, Alexandra
    et al.
    Andersson, Carin
    Jönsson, Maria E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Miljötoxikologi.
    Fogelberg, Oscar
    Orberg, Jan
    Brunstrom, Bjorn
    Brandt, Ingvar
    Gill EROD in monitoring of CYP1A inducers in fish - A study in rainbow trout (Oncorhynchus mykiss) caged in Stockholm and Uppsala waters2007Ingår i: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 85, nr 1, s. 1-8Artikel i tidskrift (Refereegranskat)
  • 6. Achatz, Johannes Georg
    et al.
    Hooge, Matthew
    Wallberg, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Jondelius, Ulf
    Tyler, Seth
    Systematic revision of acoels with 9+0 sperm ultrastructure (Convolutida) and the influence of sexual conflict on morphology2010Ingår i: Journal of Zoological Systematics and Evolutionary Research, ISSN 0947-5745, E-ISSN 1439-0469, Vol. 48, nr 1, s. 9-32Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    We have used newly discerned morphological characters as well as molecular-sequence data from 18S and 28S rDNA to revise the families recently designated as the '9+0' acoels - what we call Convolutida. Characters from the ultrastructure of sperm, with their '9+0' axonemes, are useful in delineating the Convolutida, but are either species-specific or too conserved within the group to be used to infer relationships within it. Male genital organs, prostatoid organs, and sagittocysts, on the other hand, give a good phylogenetic signal for reconstructing relationships of such genera as Conaperta, Anaperus, and Achoerus; some features of the reproductive organs correlate with habitat and show how the Convolutida probably originated as epiphytic predators and radiated into the mesopsammon, pelagic, and coral-associated realms. In this revision of the Convolutida we provide revised synopses of its families - which we restrict to the Anaperidae, Convolutidae, and Sagittiferidae - and describe a new species, Polychoerus gordoni, from New Zealand. We transfer the genus Adenopea from the Antroposthiidae to the Convolutidae; Conaperta, Neochildia, and Oxyposthia from the Convolutidae to the Anaperidae; Paranaperus and Praeanaperus from the Anaperidae to the Haploposthiidae. Convoluta aegyptica is synonymized with Convoluta boehmigi, Convoluta lacazii with Convoluta sordida, and the genus Picola (Convolutidae) with Deuterogonaria (Haploposthiidae). Amphiscolops blumi, A. carvalhoi, and A. langerhansi, all of which possess a cellular seminal bursa, are transferred to the genus Heterochaerus. Convoluta elegans and Pseudanaperus tinctus are classified as nomina nuda. We use our findings on the ultrastructure of female genital organs and spermatozoa to show that sexual conflict plays a major role in the evolution of diversity of these structures and that the phylogeny of the Acoela would comprise early forms without female genital organs and hyper- or hypodermal transfer of sperm through advanced forms with ever longer and narrower bursal nozzles and sperm with axial microtubules. Moreover, our results show that the acquisition of endosymbiotic algae happened at least twice within the Acoela.

  • 7. Adem, Abdu
    et al.
    Madjid, Nather
    Stiedl, Oliver
    Bonito-Oliva, Alessandra
    Konradsson-Geuken, Åsa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi.
    Holst, Sarah
    Fisone, Gilberto
    Ögren, Sven Ove
    Atypical but not typical antipsychotic drugs ameliorate phencyclidine-induced emotional memory impairments in mice2019Ingår i: European Neuropsychopharmacology, ISSN 0924-977X, E-ISSN 1873-7862, Vol. 29, nr 5, s. 616-628, artikel-id S0924-977X(19)30195-6Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Schizophrenia is associated with cognitive impairments related to hypofunction in glutamatergic N-methyl-D-aspartate receptor (NMDAR) transmission. Phencyclidine (PCP), a non-competitive NMDAR antagonist, models schizophrenia-like behavioral symptoms including cognitive deficits in rodents. This study examined the effects of PCP on emotional memory function examined in the passive avoidance (PA) task in mice and the ability of typical and atypical antipsychotic drugs (APDs) to rectify the PCP-mediated impairment. Pre-training administration of PCP (0.5, 1, 2 or 3 mg/kg) dose-dependently interfered with memory consolidation in the PA task. In contrast, PCP was ineffective when administered after training, and immediately before the retention test indicating that NMDAR blockade interferes with memory encoding mechanisms. The typical APD haloperidol and the dopamine D2/3 receptor antagonist raclopride failed to block the PCP-induced PA impairment suggesting a negligible role of D2 receptors in the PCP impairment. In contrast, the memory impairment was blocked by the atypical APDs clozapine and olanzapine in a dose-dependent manner while risperidone was effective only at the highest dose tested (1 mg/kg). The PCP-induced impairment involves 5-HT1A receptor mechanisms since the antagonist NAD-299 blocked the memory impairment caused by PCP and the ability of clozapine to attenuate the impairment by PCP. These results indicate that atypical but not typical APDs can ameliorate NMDAR-mediated memory impairments and support the view that atypical APDs such as clozapine can modulate glutamatergic memory dysfunctions through 5-HT1A receptor mechanisms. These findings suggest that atypical APDs may improve cognitive impairments related to glutamatergic dysfunction relevant for emotional memories in schizophrenia.

  • 8.
    Adl, Sina M.
    et al.
    Univ Saskatchewan, Dept Soil Sci, Coll Agr & Bioresources, 51 Campus Dr, Saskatoon, SK S7N 5A8, Canada.
    Bass, David
    Nat Hist Museum, Dept Life Sci, Cromwell Rd, London SW7 5BD, England;CEFAS, Barrack Rd, Weymouth DT4 8UB, Dorset, England.
    Lane, Christopher E.
    Univ Rhode Isl, Dept Biol Sci, Kingston, RI 02881 USA.
    Lukes, Julius
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic;Univ South Bohemia, Fac Sci, Ceske Budejovice 37005, Czech Republic.
    Schoch, Conrad L.
    Natl Inst Biotechnol Informat, Natl Lib Med, NIH, Bethesda, MD 20892 USA.
    Smirnov, Alexey
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia.
    Agatha, Sabine
    Univ Salzburg, Dept Biosci, Hellbrunnerstr 34, A-5020 Salzburg, Austria.
    Berney, Cedric
    CNRS, UMR 7144 AD2M, Grp Evolut Protistes & Ecosyst Pelag, Stn Biol Roscoff, Pl Georges Teissier, F-29680 Roscoff, France.
    Brown, Matthew W.
    Mississippi State Univ, Dept Biol Sci, Starkville, MS 39762 USA;Mississippi State Univ, Inst Genom Biocomp & Biotechnol, Starkville, MS 39762 USA.
    Burki, Fabien
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Cárdenas, Paco
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Farmakognosi.
    Cepicka, Ivan
    Charles Univ Prague, Dept Zool, Fac Sci, Vinicna 7, CR-12844 Prague, Czech Republic.
    Chistyakova, Lyudmila
    St Petersburg State Univ, Core Facil Ctr Culture Collect Microorganisms, St Petersburg 198504, Russia.
    del Campo, Javier
    CSIC, Inst Ciencies Mar, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
    Dunthorn, Micah
    Univ Kaiserslautern, Dept Ecol, Erwin Schroedinger St, D-67663 Kaiserslautern, Germany;Univ Duisburg Essen, Dept Eukaryot Microbiol, Univ Str 5, D-45141 Essen, Germany.
    Edvardsen, Bente
    Univ Oslo, Dept Biosci, POB 1066 Blindern, N-0316 Oslo, Norway.
    Eglit, Yana
    Dalhousie Univ, Dept Biol, Halifax B3H 4R2, NS, Canada.
    Guillou, Laure
    Univ Paris 06, Sorbonne Univ, Paris 6, CNRS,UMR 7144 AD2M,Stn Biol Roscoff, Pl Georges Teissier,,CS90074, F-29688 Roscoff, France.
    Hampl, Vladimir
    Charles Univ Prague, Dept Parasitol, Fac Sci, BIOCEV, Prumyslov 595, Vestec 25242, Czech Republic.
    Heiss, Aaron A.
    Amer Museum Nat Hist, Dept Invertebrate Zool, New York, NY 10024 USA.
    Hoppenrath, Mona
    DZMB German Ctr Marine Biodivers Res, D-26382 Wilhelmshaven, Germany.
    James, Timothy Y.
    Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.
    Karnkowska, Anna
    Univ Warsaw, Dept Mol Phylogenet & Evolut, PL-02089 Warsaw, Poland.
    Karpov, Sergey
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia;RAS, Lab Parasit Worms & Protistol, Zool Inst, St Petersburg 199034, Russia.
    Kim, Eunsoo
    Amer Museum Nat Hist, Dept Invertebrate Zool, New York, NY 10024 USA.
    Kolisko, Martin
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic.
    Kudryavtsev, Alexander
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia;RAS, Lab Parasit Worms & Protistol, Zool Inst, St Petersburg 199034, Russia.
    Lahr, Daniel J. G.
    Univ Sao Paulo, Dept Zool, Inst Biosci, Matao Travessa 14 Cidade Univ, BR-05508090 Sao Paulo, SP, Brazil.
    Lara, Enrique
    Univ Neuchatel, Lab Soil Biodivers, Rue Emile Argand 11, CH-2000 Neuchatel, Switzerland;CSIC, Real Jardim Bot,Plaza Murillo 2, E-28014 Madrid, Spain.
    Le Gall, Line
    Sorbonne Univ, Museum Natl Hist Nat, Inst Systemat Evolut Biodiversit, 57 Rue Cuvier,CP 39, F-75005 Paris, France.
    Lynn, Denis H.
    Univ Guelph, Dept Integrat Biol, Summerlee Sci Complex, Guelph, ON N1G 2W1, Canada;Univ British Columbia, Dept Zool, 4200-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada.
    Mann, David G.
    Royal Bot Garden, Edinburgh EH3 5LR, Midlothian, Scotland;Inst Agrifood Res & Technol, C Poble Nou Km 5-5, E-43540 San Carlos de la Rapita, Spain.
    Massana, Ramon
    CSIC, Inst Ciencies Mar, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
    Mitchell, Edward A. D.
    Univ Neuchatel, Lab Soil Biodivers, Rue Emile Argand 11, CH-2000 Neuchatel, Switzerland;Jardin Bot Neuchatel,Chemin Perthuis du Salut 58, CH-2000 Neuchatel, Switzerland.
    Morrow, Christine
    Natl Museums Northern Ireland, Dept Nat Sci, 153 Bangor Rd, Holywood BT18 0EU, England.
    Park, Jong Soo
    Kyungpook Natl Univ, Sch Earth Syst Sci, Dept Oceanog, Daegu, South Korea;Kyungpook Natl Univ, Sch Earth Syst Sci, Kyungpook Inst Oceanog, Daegu, South Korea.
    Pawlowski, Jan W.
    Univ Geneva, Dept Genet & Evolut, CH-1211 Geneva 4, Switzerland.
    Powell, Martha J.
    Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA.
    Richter, Daniel J.
    Univ Pompeu Fabra, CSIC, Inst Biol Evolut, Passeig Maritim Barceloneta 37-49, Barcelona 08003, Spain.
    Rueckert, Sonja
    Edinburgh Napier Univ, Sch Appl Sci, Edinburgh EH11 4BN, Midlothian, Scotland.
    Shadwick, Lora
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA.
    Shimano, Satoshi
    Hosei Univ, Sci Res Ctr, Chiyoda Ku, 2-17-1 Fujimi, Tokyo, Japan.
    Spiegel, Frederick W.
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA.
    Torruella, Guifre
    Univ Paris XI, Lab Evolut & Systemat, F-91405 Orsay, France.
    Youssef, Noha
    Oklahoma State Univ, Dept Microbiol & Mol Genet, Stillwater, OK 74074 USA.
    Zlatogursky, Vasily V.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia.
    Zhang, Qianqian
    Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
    Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes2019Ingår i: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 66, nr 1, s. 4-119Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

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  • 9. Agerstrand, Marlene
    et al.
    Berg, Cecilia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Miljötoxikologi.
    Bjorlenius, Berndt
    Breitholtz, Magnus
    Brunström, Björn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Miljötoxikologi.
    Fick, Jerker
    Gunnarsson, Lina
    Larsson, D. G. Joakim
    Sumpter, John P.
    Tysklind, Mats
    Ruden, Christina
    Improving Environmental Risk Assessment of Human Pharmaceuticals2015Ingår i: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 49, nr 9, s. 5336-5345Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    This paper presents 10 recommendations for improving the European Medicines Agency's guidance for environmental risk assessment of human pharmaceutical products. The recommendations are based on up-to-date, available science in combination with experiences from other chemical frameworks such as the REACH-legislation for industrial chemicals. The recommendations concern: expanding the scope of the current guideline; requirements to assess the risk for development of antibiotic resistance; jointly performed assessments; refinement of the test proposal; mixture toxicity assessments on active pharmaceutical ingredients with similar modes of action; use of all available ecotoxicity studies; mandatory reviews; increased transparency; inclusion of emission data from production; and a risk management option. We believe that implementation of our recommendations would strengthen the protection of the environment and be beneficial to society. Legislation and guidance documents need to be updated at regular intervals in order to incorporate new knowledge from the scientific community. This is particularly important for regulatory documents concerning pharmaceuticals in the environment since this is a research field that has been growing substantially in the last decades.

  • 10.
    Agnolin, Federico L.
    et al.
    Museo Argentino Ciencias Nat Bernardino Rivadavia, Lab Anat Comparada & Evoluc Vertebrados, Buenos Aires, DF, Argentina.; Univ Maimonides, CEBBAD, Dept Ciencias Nat & Antropol, Fundac Hist Nat Felix de Azara, Buenos Aires, DF, Argentina.
    Powell, Jaime E.
    Inst Miguel Lillo, RA-4000 San Miguel De Tucuman, Tucuman, Argentina.; Consejo Nacl Invest Cient & Tecn, RA-1033 Buenos Aires, DF, Argentina.
    Novas, Fernando E.
    Museo Argentino Ciencias Nat Bernardino Rivadavia, Lab Anat Comparada & Evoluc Vertebrados, Buenos Aires, DF, Argentina.; Consejo Nacl Invest Cient & Tecn, RA-1033 Buenos Aires, DF, Argentina.
    Kundrát, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    New alvarezsaurid (Dinosauria, Theropoda) from Latest Cretaceous of North-western Patagonia with associated eggs2012Ingår i: Cretaceous research (Print), ISSN 0195-6671, E-ISSN 1095-998X, Vol. 35, s. 33-56Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Alvarezsauridae represents a branch of peculiar basal coelurosaurs with an increasing representationof their Cretaceous radiation distributed worldwide. Here we describe a new member of the group, Bonapartenykus ultimus gen. et sp. nov. from Campanian-Maastrichtian strata of Northern Patagonia, Argentina. Bonapartenykus is represented by a single, incomplete postcranial skeleton. The morphologyof the known skeletal elements suggests close affinities with the previously described taxon from Patagonia, Patagonykus, and both conform to a new clade, here termed Patagonykinae nov. Two incomplete eggs have been discovered in association with the skeletal remains of Bonapartenykus, andseveral clusters of broken eggshells of the same identity were also found in a close proximity. These belong to the new ooparataxon Arriagadoolithus patagoniensis of the new oofamily Arriagadoolithidae, which provides first insights into unique shell microstructure and fungal contamination of eggs laid by alvarezsaurid theropods. The detailed study of the eggs sheds new light on the phylogenetic position of alvarezsaurids within the Theropoda, and the evolution of eggs among Coelurosauria. We suggest thatplesiomorphic alvarezsaurids survived in Patagonia until the latest Cretaceous, whereas these basal forms became extinct elsewhere.

  • 11.
    Agostinelli, Marta
    et al.
    Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Nguyen, Diem
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Witzell, Johanna
    Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Cleary, Michelle
    Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Mycobiome of Fraxinus excelsior With Different Phenotypic Susceptibility to Ash Dieback2021Ingår i: Frontiers in Forests and Global Change, E-ISSN 2624-893X, Vol. 4, artikel-id 580514Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    For the last two decades, large-scale population decline of European ash (Fraxinus excelsior) has occurred in Europe because of the introduction of the alien fungal pathogen, Hymenoscyphus fraxineus, from East Asia. Since European ash is a keystone species having critical importance for biodiversity, and only a small percentage of the ash population appears to show some tolerance against the pathogen, the loss of ash trees means that other associated organisms, especially those with high or obligate associations to ash, are at risk of further species declines. In this study, we used high throughput DNA sequencing and multivariate analysis to characterize: (i) the mycobiome in aerial tissues (i.e., leaf, bark, and xylem) of ash trees showing different phenotypic response to ash dieback, (ii) the temporal variation in fungal communities across the growing season, and (iii) the similarity in fungal community structure between ash and other common trees species that may serve as an ecological niche substitute for ash microfungi. Results showed that fungal communities differed among the three tissue types, susceptibility classes, in time and between sites. Trophic analysis of functional groups using the FUNGuild tool indicated a higher presence of pathotrophic fungi in leaves than in bark and xylem. The share of pathotrophic fungi increased along a gradient of low to high disease susceptibility in both bark and xylem tissue, while the proportion of symbiotrophic fungi correspondingly decreased in both tissue types. Neighboring, alternative host trees did not share all the fungal species found in ash, however, most microfungi uniquely associated to ash in this study are generalists and not strictly host specific. The progressive disappearance of ash trees on the landscape imposes a high risk for extinction of Red-listed macrofungal species, and breeding for resistance against ash dieback should help sustain important biodiversity associated to ash. Microfungal diversity though may be less prone to such demise since most ash-associated endophytes appear to occur on a broad range of host species. 

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  • 12.
    Agrillo, Caroline
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Miljötoxikologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    DNA methylation modifications in human mesenchymal stem cells  induced by exposure to endocrine disrupting plasticiser metabolites MBP, MEP, MBzP, MEHP and MINCH2022Självständigt arbete på avancerad nivå (masterexamen), 80 poäng / 120 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Endocrine disrupting chemicals (EDCs) are exogenous substances which can modify the function of the endocrine system and lead to adverse health effects. Humans experience daily uncontrolled exposure to EDC mixtures. Predicting mixture effects is complicated since the chemicals may produce different effects when combined together. EDCs may produce epigenetic effects such as alterations of the DNA methylation, which could modify the expression of the gene. Previously, 14 chemicals linked to metabolism (mixture G1) were reported to induce DNA methylation changes in an in vitro model. Mixture G1 were based on a Swedish longitudinal study which had identified the chemical burden of >2300 pregnant women. This project aimed to study single chemical driver effects of five individual chemicals from mixture G1, namely the four phthalate metabolites monobutyl phthalate (MBP), monoethyl phthalate (MEP), monobenzyl pthtalate (MBzP), mono-(2-ethylhexyl) phthalate (MEHP) and the non-phthalate plasticiser Bis(7-methyloctyl) Cyclohexane-1,2-dicarboxylate (DINCH) metabolite 2-4-methyl-7-oxyoctyl-oxycarbonyl-cyclohexane carboxylic acid (MINCH). Human mesenchymal stem cells (hMSCs) were exposed to the five compounds individually at the same concentrations as in mixture G1. After exposure, DNA methylation changes in four CpG sites within PGM1, MYOF and HCFC1 genes were analysed. While som chemicals did not show statistically significant effects, one chemical showed significant effects and thus could be a potential driver. The discrepancy between the observed DNA methylation alterations in the analysed genes and the alterations in mixture G1 highlights the need for comparing mixture to single chemical effects to identify drivers within mixes and for increased understanding of mixture effects.

    Publikationen är tillgänglig i fulltext från 2026-01-01 15:14
  • 13.
    Ahi, Ehsan Pashay
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi. Univ Helsinki, Organismal & Evolutionary Biol Res Programme, Helsinki, Finland..
    Brunel, Mathilde
    Swedish Univ Agr Sci, Dept Mol Sci, Uppsala, Sweden..
    Tsakoumis, Emmanouil
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Fysiologi och miljötoxikologi.
    Chen, Junyu
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi.
    Schmitz, Monika
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Fysiologi och miljötoxikologi.
    Appetite regulating genes in zebrafish gut; a gene expression study2022Ingår i: PLOS ONE, E-ISSN 1932-6203, Vol. 17, nr 7, artikel-id e0255201Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The underlying molecular pathophysiology of feeding disorders, particularly in peripheral organs, is still largely unknown. A range of molecular factors encoded by appetite-regulating genes are already described to control feeding behaviour in the brain. However, the important role of the gastrointestinal tract in the regulation of appetite and feeding in connection to the brain has gained more attention in the recent years. An example of such inter-organ connection can be the signals mediated by leptin, a key regulator of body weight, food intake and metabolism, with conserved anorexigenic effects in vertebrates. Leptin signals functions through its receptor (lepr) in multiple organs, including the brain and the gastrointestinal tract. So far, the regulatory connections between leptin signal and other appetite-regulating genes remain unclear, particularly in the gastrointestinal system. In this study, we used a zebrafish mutant with impaired function of leptin receptor to explore gut expression patterns of appetite-regulating genes, under different feeding conditions (normal feeding, 7-day fasting, 2 and 6-hours refeeding). We provide evidence that most appetite-regulating genes are expressed in the zebrafish gut. On one hand, we did not observed significant differences in the expression of orexigenic genes (except for hcrt) after changes in the feeding condition. On the other hand, we found 8 anorexigenic genes in wild-types (cart2, cart3, dbi, oxt, nmu, nucb2a, pacap and pomc), as well as 4 genes in lepr mutants (cart3, kiss1, kiss1r and nucb2a), to be differentially expressed in the zebrafish gut after changes in feeding conditions. Most of these genes also showed significant differences in their expression between wild-type and lepr mutant. Finally, we observed that impaired leptin signalling influences potential regulatory connections between anorexigenic genes in zebrafish gut. Altogether, these transcriptional changes propose a potential role of leptin signal in the regulation of feeding through changes in expression of certain anorexigenic genes in the gastrointestinal tract of zebrafish.

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  • 14.
    Ahi, Ehsan Pashay
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi.
    Brunel, Mathilde
    Swedish Univ Agr Sci, BioCentrum, Dept Mol Sci, Allmas Alle 5, SE-75007 Uppsala, Sweden.
    Tsakoumis, Emmanouil
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi.
    Schmitz, Monika
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi.
    Transcriptional study of appetite regulating genes in the brain of zebrafish (Danio rerio) with impaired leptin signalling2019Ingår i: Scientific Reports, E-ISSN 2045-2322, Vol. 9, artikel-id 20166Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The hormone leptin is a key regulator of body weight, food intake and metabolism. In mammals, leptin acts as an anorexigen and inhibits food intake centrally by affecting the appetite centres in the hypothalamus. In teleost fish, the regulatory connections between leptin and other appetite-regulating genes are largely unknown. In the present study, we used a zebrafish mutant with a loss of function leptin receptor to investigate brain expression patterns of 12 orexigenic and 24 anorexigenic genes under different feeding conditions (normal feeding, 7-day fasting, 2 and 6-hours refeeding). Expression patterns were compared to wild-type zebrafish, in order to identify leptin-dependent differentially expressed genes under different feeding conditions. We provide evidence that the transcription of certain orexigenic and anorexigenic genes is influenced by leptin signalling in the zebrafish brain. We found that the expression of orexigenic genes was not affected by impaired leptin signalling under normal feeding conditions; however, several orexigenic genes showed increased transcription during fasting and refeeding, including agrp, apln, galr1a and cnr1. This suggests an inhibitory effect of leptin signal on the transcription of these orexigenic genes during short-term fasting and refeeding in functional zebrafish. Most pronounced effects were observed in the group of anorexigenic genes, where the impairment of leptin signalling resulted in reduced gene expression in several genes, including cart family, crhb, gnrh2, mc4r, pomc and spx, in the control group. This suggests a stimulatory effect of leptin signal on the transcription of these anorexigenic genes under normal feeding condition. In addition, we found multiple gain and loss in expression correlations between the appetite-regulating genes, in zebrafish with impaired leptin signal, suggesting the presence of gene regulatory networks downstream of leptin signal in zebrafish brain. The results provide the first evidence for the effects of leptin signal on the transcription of various appetite-regulating genes in zebrafish brain, under different feeding conditions. Altogether, these transcriptional changes suggest an anorexigenic role for leptin signal, which is likely to be mediated through distinct set of appetite-regulating genes under different feeding conditions.

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  • 15.
    Ahi, Ehsan Pashay
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi. Karl Franzens Univ Graz, Inst Biol, Graz, Austria.
    Duenser, Anna
    Karl Franzens Univ Graz, Inst Biol, Graz, Austria.
    Singh, Pooja
    Karl Franzens Univ Graz, Inst Biol, Graz, Austria;Univ Calgary, Inst Biol Sci, Calgary, AB, Canada.
    Gessl, Wolfgang
    Karl Franzens Univ Graz, Inst Biol, Graz, Austria.
    Sturmbauer, Christian
    Karl Franzens Univ Graz, Inst Biol, Graz, Austria.
    Appetite regulating genes may contribute to herbivory versus carnivory trophic divergence in haplochromine cichlids2020Ingår i: PeerJ, E-ISSN 2167-8359, Vol. 8, artikel-id e8375Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Feeding is a complex behaviour comprised of satiety control, foraging, ingestion and subsequent digestion. Cichlids from the East African Great Lakes are renowned for their diverse trophic specializations, largely predicated on highly variable jaw morphologies. Thus, most research has focused on dissecting the genetic, morphological and regulatory basis of jaw and teeth development in these species. Here for the first time we explore another aspect of feeding, the regulation of appetite related genes that are expressed in the brain and control satiety in cichlid fishes. Using qPCR analysis, we first validate stably expressed reference genes in the brain of six haplochromine cichlid species at the end of larval development prior to foraging. We next evaluate the expression of 16 appetite related genes in herbivorous and carnivorous species from the parallel radiations of Lake Tanganyika, Malawi and Victoria. Interestingly, we find increased expression of two appetite-regulating genes (anorodgenic genes), cart and npy2r, in the brain of carnivorous species in all the three lakes. This supports the notion that appetite gene regulation might play a part in determining trophic niche specialization in divergent cichlid species, already prior to exposure to different diets. Our study contributes to the limited body of knowledge on the neurological circuitry that controls feeding transitions and adaptations in cichlids and other teleosts.

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  • 16.
    Ahi, Ehsan Pashay
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Lecaudey, Laurene A.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria;Norwegian Univ Sci & Technol, NTNU Univ Museum, Dept Nat Hist, NO-7491 Trondheim, Norway.
    Ziegelbecker, Angelika
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Steiner, Oliver
    Karl Franzens Univ Graz, Inst Chem, Univ Pl 1, A-8010 Graz, Austria.
    Glabonjat, Ronald
    Karl Franzens Univ Graz, Inst Chem, Univ Pl 1, A-8010 Graz, Austria.
    Goessler, Walter
    Karl Franzens Univ Graz, Inst Chem, Univ Pl 1, A-8010 Graz, Austria.
    Hois, Victoria
    Karl Franzens Univ Graz, Inst Mol Biosci, Heinrichstr 31-2, A-8010 Graz, Austria.
    Wagner, Carina
    Karl Franzens Univ Graz, Inst Mol Biosci, Heinrichstr 31-2, A-8010 Graz, Austria.
    Lass, Achim
    Karl Franzens Univ Graz, Inst Mol Biosci, Heinrichstr 31-2, A-8010 Graz, Austria;BioTechMed Graz, A-8010 Graz, Austria.
    Sefc, Kristina M.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Comparative transcriptomics reveals candidate carotenoid color genes in an East African cichlid fish2020Ingår i: BMC Genomics, E-ISSN 1471-2164, Vol. 21, artikel-id 54Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Carotenoids contribute significantly to animal body coloration, including the spectacular color pattern diversity among fishes. Fish, as other animals, derive carotenoids from their diet. Following uptake, transport and metabolic conversion, carotenoids allocated to body coloration are deposited in the chromatophore cells of the integument. The genes involved in these processes are largely unknown. Using RNA-Sequencing, we tested for differential gene expression between carotenoid-colored and white skin regions of a cichlid fish, Tropheus duboisi "Maswa", to identify genes associated with carotenoid-based integumentary coloration. To control for positional gene expression differences that were independent of the presence/absence of carotenoid coloration, we conducted the same analyses in a closely related population, in which both body regions are white.

    Results: A larger number of genes (n = 50) showed higher expression in the yellow compared to the white skin tissue than vice versa (n = 9). Of particular interest was the elevated expression level of bco2a in the white skin samples, as the enzyme encoded by this gene catalyzes the cleavage of carotenoids into colorless derivatives. The set of genes with higher expression levels in the yellow region included genes involved in xanthophore formation (e.g., pax7 and sox10), intracellular pigment mobilization (e.g., tubb, vim, kif5b), as well as uptake (e.g., scarb1) and storage (e.g., plin6) of carotenoids, and metabolic conversion of lipids and retinoids (e.g., dgat2, pnpla2, akr1b1, dhrs). Triglyceride concentrations were similar in the yellow and white skin regions. Extracts of integumentary carotenoids contained zeaxanthin, lutein and beta-cryptoxanthin as well as unidentified carotenoid structures.

    Conclusion: Our results suggest a role of carotenoid cleavage by Bco2 in fish integumentary coloration, analogous to previous findings in birds. The elevated expression of genes in carotenoid-rich skin regions with functions in retinol and lipid metabolism supports hypotheses concerning analogies and shared mechanisms between these metabolic pathways. Overlaps in the sets of differentially expressed genes (including dgat2, bscl2, faxdc2 and retsatl) between the present study and previous, comparable studies in other fish species provide useful hints to potential carotenoid color candidate genes.

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  • 17.
    Ahi, Ehsan Pashay
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Lecaudey, Laurène A.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria; Norwegian Univ Sci & Technol, NTNU Univ Museum, Dept Nat Hist, NO-7491 Trondheim, Norway.
    Ziegelbecker, Angelika
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Steiner, Oliver
    Graz Univ, Inst Chem, Univ Pl 1, A-8010 Graz, Austria.
    Goessler, Walter
    Graz Univ, Inst Chem, Univ Pl 1, A-8010 Graz, Austria.
    Sefc, Kristina M.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Expression levels of the tetratricopeptide repeat protein gene ttc39b covary with carotenoid-based skin colour in cichlid fish2020Ingår i: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 16, nr 11, artikel-id 20200629Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Carotenoid pigments play a major role in animal body colouration, generating strong interest in the genes involved in the metabolic processes that lead from their dietary uptake to their storage in the integument. Here, we used RNA sequencing (RNA-Seq) to test for differentially expressed genes in a taxonomically replicated design using three pairs of related cichlid fish taxa from the genera Tropheus and Aulonocara. Within each pair, taxa differed in terms of red and yellow body colouration, and high‐performance liquid chromatography (HPLC) analyses of skin extracts revealed different carotenoid profiles and concentrations across the studied taxa. Five genes were differentially expressed in all three yellow–red skin contrasts (dhrsx, nlrc3, tcaf2, urah and ttc39b), but only the tetratricopeptide repeat protein-coding gene ttc39b, whose gene product is linked to mammalian lipid metabolism, was consistently expressed more highly in the red skin samples. The RNA-Seq results were confirmed by quantitative PCR. We propose ttc39b as a compelling candidate gene for variation in animal carotenoid colouration. Since differential expression of ttc39b was correlated with the presence/absence of yellow carotenoids in a previous study, we suggest that ttc39b is more likely associated with the concentration of total carotenoids than with the metabolic formation of red carotenoids.

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  • 18.
    Ahi, Ehsan Pashay
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Richter, Florian
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Lecaudey, Laurene Alicia
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Sefc, Kristina M.
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Gene expression profiling suggests differences in molecular mechanisms of fin elongation between cichlid species2019Ingår i: Scientific Reports, E-ISSN 2045-2322, Vol. 9, artikel-id 9052Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Comparative analyses of gene regulation inform about the molecular basis of phenotypic trait evolution. Here, we address a fin shape phenotype that evolved multiple times independently across teleost fish, including several species within the family Cichlidae. In a previous study, we proposed a gene regulatory network (GRN) involved in the formation and regeneration of conspicuous filamentous elongations adorning the unpaired fins of the Neolamprologus brichardi. Here, we tested the members of this network in the blockhead cichlid, Steatocranus casuarius, which displays conspicuously elongated dorsal and moderately elongated anal fins. Our study provided evidence for differences in the anatomy of fin elongation and suggested gene regulatory divergence between the two cichlid species. Only a subset of the 20 genes tested in S. casuarius showed the qPCR expression patterns predicted from the GRN identified in N. brichardi, and several of the gene-by-gene expression correlations differed between the two cichlid species. In comparison to N. brichardi, gene expression patterns in S. casuarius were in better (but not full) agreement with gene regulatory interactions inferred in zebrafish. Within S. casuarius, the dorsoventral asymmetry in ornament expression was accompanied by differences in gene expression patterns, including potential regulatory differentiation, between the anal and dorsal fin.

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  • 19.
    Ahi, Ehsan Pashay
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Singh, Pooja
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Duenser, Anna
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Gessl, Wolfgang
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Sturmbauer, Christian
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging2019Ingår i: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 19, artikel-id 150Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    BackgroundUnderstanding how variation in gene expression contributes to morphological diversity is a major goal in evolutionary biology. Cichlid fishes from the East African Great lakes exhibit striking diversity in trophic adaptations predicated on the functional modularity of their two sets of jaws (oral and pharyngeal). However, the transcriptional basis of this modularity is not so well understood, as no studies thus far have directly compared the expression of genes in the oral and pharyngeal jaws. Nor is it well understood how gene expression may have contributed to the parallel evolution of trophic morphologies across the replicate cichlid adaptive radiations in Lake Tanganyika, Malawi and Victoria.ResultsWe set out to investigate the role of gene expression divergence in cichlid fishes from these three lakes adapted to herbivorous and carnivorous trophic niches. We focused on the development stage prior to the onset of exogenous feeding that is critical for understanding patterns of gene expression after oral and pharyngeal jaw skeletogenesis, anticipating environmental cues. This framework permitted us for the first time to test for signatures of gene expression underlying jaw modularity in convergent eco-morphologies across three independent adaptive radiations. We validated a set of reference genes, with stable expression between the two jaw types and across species, which can be important for future studies of gene expression in cichlid jaws. Next we found evidence of modular and non-modular gene expression between the two jaws, across different trophic niches and lakes. For instance, prdm1a, a skeletogenic gene with modular anterior-posterior expression, displayed higher pharyngeal jaw expression and modular expression pattern only in carnivorous species. Furthermore, we found the expression of genes in cichlids jaws from the youngest Lake Victoria to exhibit low modularity compared to the older lakes.ConclusionOverall, our results provide cross-species transcriptional comparisons of modularly-regulated skeletogenic genes in the two jaw types, implicating expression differences which might contribute to the formation of divergent trophic morphologies at the stage of larval independence prior to foraging.

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  • 20.
    Ahi, Ehsan Pashay
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi. Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Singh, Pooja
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Lecaudey, Laurene Alicia
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Gessl, Wolfgang
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Sturmbauer, Christian
    Karl Franzens Univ Graz, Inst Biol, Univ Pl 2, A-8010 Graz, Austria.
    Maternal mRNA input of growth and stress-response-related genes in cichlids in relation to egg size and trophic specialization2018Ingår i: EvoDevo, E-ISSN 2041-9139, Vol. 9, artikel-id 23Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Egg size represents an important form of maternal effect determined by a complex interplay of long-term adaptation and short-term plasticity balancing egg size with brood size. Haplochromine cichlids are maternal mouthbrooders showing differential parental investment in different species, manifested in great variation in egg size, brood size and duration of maternal care. Little is known about maternally determined molecular characters of eggs in fishes and their relation to egg size and trophic specialization. Here we investigate maternal mRNA inputs of selected growth- and stress-related genes in eggs of mouthbrooding cichlid fishes adapted to different trophic niches from Lake Tanganyika, Lake Malawi, Lake Victoria and compare them to their riverine allies.

    Results: We first identified two reference genes, atf7ip and mid1ip1, to be suitable for cross-species quantification of mRNA abundance via qRT-PCR in the cichlid eggs. Using these reference genes, we found substantial variation in maternal mRNA input for a set of candidate genes related to growth and stress response across species and lakes. We observed negative correlation of mRNA abundance between two of growth hormone receptor paralogs (ghr1 and ghr2) across all haplochromine cichlid species which also differentiate the species in the two younger lakes, Malawi and Lake Victoria, from those in Lake Tanganyika and ancestral riverine species. Furthermore, we found correlations between egg size and maternal mRNA abundance of two growth-related genes igf2 and ghr2 across the haplochromine cichlids as well as distinct clustering of the species based on their trophic specialization using maternal mRNA abundance of five genes (ghr1, ghr2, igf2, gr and sgk1).

    Conclusions: These findings indicate that variations in egg size in closely related cichlid species can be linked to differences in maternal RNA deposition of key growth-related genes. In addition, the cichlid species with contrasting trophic specialization deposit different levels of maternal mRNAs in their eggs for particular growth-related genes; however, it is unclear whether such differences contribute to differential morphogenesis at later stages of development. Our results provide first insights into this aspect of gene activation, as a basis for future studies targeting their role during ecomorphological specialization and adaptive radiation.

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  • 21.
    Ahi, Ehsan Pashay
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi. University of Helsinki.
    Tsakoumis, Emmanouil
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi.
    Brunel, Mathilde
    Department of Molecular Sciences, Swedish University of Agricultural Sciences, Allmas Allé 5, SE-750 07, Uppsala, Sweden.
    Schmitz, Monika
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi.
    Transcriptional study reveals a potential leptin-dependent gene regulatory network in zebrafish brain2021Ingår i: Fish Physiology & Biochemistry, ISSN 0920-1742, E-ISSN 1573-5168, Vol. 47, nr 4, s. 1283-1298Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The signal mediated by leptin hormone and its receptor is a major regulator of body weight, food intake and metabolism. In mammals and many teleost fish species, leptin has an anorexigenic role and inhibits food intake by influencing the appetite centres in the hypothalamus. However, the regulatory connections between leptin and downstream genes mediating its appetite-regulating effects are still not fully explored in teleost fish. In this study, we used a loss of function leptin receptor zebrafish mutant and real-time quantitative PCR to assess brain expression patterns of several previously identified anorexigenic genes downstream of leptin signal under different feeding conditions (normal feeding, 7-day fasting, 2 and 6-h refeeding). These downstream factors include members of cart genes, crhb and gnrh2, as well as selected genes co-expressed with them based on a zebrafish co-expression database. Here, we found a potential gene expression network (GRN) comprising the abovementioned genes by a stepwise approach of identifying co-expression modules and predicting their upstream regulators. Among the transcription factors (TFs) predicted as potential upstream regulators of this GRN, we found expression pattern of sp3a to be correlated with transcriptional changes of the downstream gene network. Interestingly, the expression and transcriptional activity of Sp3 orthologous gene in mammals have already been implicated to be under the influence of leptin signal. These findings suggest a potentially conserved regulatory connection between leptin and sp3a, which is predicted to act as a transcriptional driver of a downstream gene network in the zebrafish brain.

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    Ahi et al. 2019
  • 22.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    A comparative genomic framework for the fish-tetrapod transition2021Ingår i: Science China Life Sciences, ISSN 1674-7305, E-ISSN 1869-1889, Vol. 64, nr 4, s. 664-666Artikel i tidskrift (Övrigt vetenskapligt)
  • 23.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Follow the footprints and mind the gaps: a new look at the origin of tetrapods2019Ingår i: Earth and environmental science transactions of the Royal Society of Edinburgh, ISSN 1755-6910, E-ISSN 1755-6929, Vol. 109, nr 1-2, s. 115-137Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The hypothesis that tetrapods evolved from elpistostegids during the Frasnian, in a predominantly aquatic context, has been challenged by the discovery of Middle Devonian tetrapod trackways predating the earliest body fossils of both elpistostegids and tetrapods. Here I present a new hypothesis based on an overview of the trace fossil and body fossil evidence. The trace fossils demonstrate that tetrapods were capable of performing subaerial lateral sequence walks before the end of the Middle Devonian. The derived morphological characters of elpistostegids and Devonian tetrapods are related to substrate locomotion, weight support and aerial vision, and thus to terrestrial competence, but the retention of lateral-line canals, gills and fin rays shows that they remained closely tied to the water. Elpistostegids and tetrapods both evolved no later than the beginning of the Middle Devonian. The earliest tetrapod records come from inland river basins, sabkha plains and ephemeral coastal lakes that preserve few, if any, body fossils; contemporary elpistostegids occur in deltas and the lower reaches of permanent rivers where body fossils are preserved. During the Frasnian, elpistostegids disappear and these riverine-deltaic environments are colonised by tetrapods. This replacement has, in the past, been misinterpreted as the origin of tetrapods.

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  • 24.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Jennifer Clack (1947–2020): Palaeontologist who described how vertebrates moved from water to land2020Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 580, nr 7805, s. 587-587Artikel i tidskrift (Övrig (populärvetenskap, debatt, mm))
  • 25.
    Ahlberg, Per
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Beznosov, P. A.
    Russian Acad Sci, Inst Geol, FRC Komi Sci Ctr, Ural Branch, Syktyvkar 167982, Russia..
    The Significance of the Devonian Tetrapods of Timan2022Ingår i: Paleontological journal, ISSN 0031-0301, E-ISSN 1555-6174, Vol. 56, s. 1029-1031Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Brief information on the recently described Parmastega and newly discovered unpublished tetrapod material from the Devonian sequence of Timan is given. The significance of these discoveries is discussed.

  • 26.
    Ahlberg, Per
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Beznosov, Pavel
    Luksevics, Ervins
    Clack, Jennifer
    A very primitive tetrapod from the earliest Famennian of South Timan, Russia2011Ingår i: Program and Abstracts: 71st Annual Meeting Society of Vertebrate Paleontology, Paris Las Vegas, Las Vegas, Nevada USA, November 2—5, 2011, Philadelphia: Society of Vertebrate Paleontology , 2011, s. 60-60Konferensbidrag (Övrigt vetenskapligt)
  • 27.
    Ahlberg, Per E.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Clack, Jennifer A.
    Univ Museum Zool Cambridge, Downing St, Cambridge CB2 3EJ, England..
    The smallest known Devonian tetrapod shows unexpectedly derived features2020Ingår i: Royal Society Open Science, E-ISSN 2054-5703, Vol. 7, nr 4, artikel-id 192117Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A new genus and species of Devonian tetrapod, Brittagnathus minutus gen. et sp. nov., is described from a single complete right lower jaw ramus recovered from the Acanthostega mass-death deposit in the upper part of the Britta Dal Formation (upper Famennian) of Stensio Bjerg, Gauss Peninsula, East Greenland. Visualization by propagation phase contrast synchrotron microtomography allows a complete digital dissection of the specimen. With a total jaw ramus length of 44.8 mm, Brittagnathus is by far the smallest Devonian tetrapod described to date. It differs from all previously known Devonian tetrapods in having only a fang pair without a tooth row on the anterior coronoid and a large posterior process on the posterior coronoid. The presence of an incipient surangular crest and a concave prearticular margin to the adductor fossa together cause the fossa to face somewhat mesially, reminiscent of the condition in Carboniferous tetrapods. A phylogenetic analysis places Brittagnathus crownward to other Devonian tetrapods, adjacent to the Tournaisian genus Pederpes. Together with other recent discoveries, it suggests that diversification of 'Carboniferous-grade' tetrapods had already begun before the end of the Devonian and that the group was not greatly affected by the end-Devonian mass extinction.

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  • 28.
    Ahlberg, Per Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Humeral homology and the origin of the tetrapod elbow: a reinterpretation of the enigmatic specimens ANSP 21350 and GSM 1045362011Ingår i: Studies on fossil tetrapods / [ed] P. M. Barrett, A. R. Milner, London: The Palaeontological Association , 2011, s. 17-29Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Two putative tetrapod humeri of Devonian age, ANSP 21350 from the late Famennian of Pennsylvania and GSM 104536 from the late Frasnian of Scat Craig, Scotland, are reinterpreted in the light of more recent discoveries. The morphology of ANSP 21350 can be more fully homologized with those of elpistostegids and early tetrapods than previously recognized. Unique features include distally displaced dorsal muscle attachments and a ventrally rotated distal face of the bone. This suggests that a weight-bearing ventrally directed forearm was created, not by means of a flexed elbow as in other tetrapods, but by distorting the humerus. The olecranon process on the ulna was probably poorly developed or absent. Primitive characters that are absent in other tetrapods add support to the contention that ANSP 21350 is the least crownward of known tetrapod humeri. Contrary to previous claims, Acanthostega has a characteristic tetrapod ulnar morphology with an olecranon process; it does not resemble an elpistostegid ulna and is not uniquely primitive for tetrapods. This suggests that the flexed tetrapod elbow with ulnar extensor muscles attached to the olecranon evolved simultaneously with the large rectangular entepicondyle typical for early tetrapods, probably as part of a single functional complex. GSM 104536 is denfinitely not a primitive tetrapod humerus, nor a sarcopterygian branchial bone, but cannot be positively identified at present.    

  • 29.
    Ahlberg, Per
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Haitina, Tatjana
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Chapter 8 Neural Crest in Fossil Vertebrates:: What, If Anything, Can We Know?2020Ingår i: Evolving Neural Crest Cells / [ed] Brian Frank Eames, Daniel Meulemans Medeiros, Igor Adameyko, Taylor & Francis Group, 2020, 1, s. 1-294Kapitel i bok, del av antologi (Refereegranskat)
  • 30.
    Ahmerkamp, Soeren
    et al.
    Max Planck Inst Marine Microbiol, D-28359 Bremen, Germany..
    Jalaluddin, Farooq Moin
    Max Planck Inst Marine Microbiol, D-28359 Bremen, Germany..
    Cui, Yuan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Fysiologi och miljötoxikologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Brumley, Douglas R.
    Univ Melbourne, Sch Math & Stat, Parkville, Vic 3010, Australia..
    Pacherres, Cesar O.
    Alfred Wegener Inst, Helmholtz Ctr Polar & Marine Res, Bremerhaven, Germany.;Univ Copenhagen, Dept Biol, Copenhagen, Denmark..
    Berg, Jasmine S.
    Univ Lausanne, Inst Earth Surface Dynam, CH-1015 Lausanne, Switzerland..
    Stocker, Roman
    Swiss Fed Inst Technol, Dept Civil Environm & Geomat Engn, Inst Environm Engn, CH-8093 Zurich, Switzerland..
    Kuypers, Marcel M. M.
    Max Planck Inst Marine Microbiol, D-28359 Bremen, Germany..
    Koren, Klaus
    Aarhus Univ, Ctr Water Technol, Dept Biol, DK-8000 Aarhus, Denmark..
    Behrendt, Lars
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Fysiologi och miljötoxikologi.
    Simultaneous visualization of flow fields and oxygen concentrations to unravel transport and metabolic processes in biological systems2022Ingår i: CELL REPORTS METHODS, ISSN 2667-2375, Vol. 2, nr 5, artikel-id 100216Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    From individual cells to whole organisms, O-2 transport unfolds across micrometer- tomillimeter-length scales and can change within milliseconds in response to fluid flows and organismal behavior. The spatiotemporal complexity of these processes makes the accurate assessment of O-2 dynamics via currently availablemethods difficult or unreliable. Here, we present "sensPIV,'' a method to simultaneously measure O-2 concentrations and flow fields. By tracking O-2-sensitive microparticles in flow using imaging technologies that allow for instantaneous referencing, wemeasuredO(2) transportwithin (1) microfluidic devices, (2) sinkingmodel aggregates, and (3) complex colony-forming corals. Through the use of sensPIV, we find that corals use ciliarymovement to link zones of photosynthetic O-2 production to zones of O-2 consumption. SensPIV can potentially be extendable to study flow-organism interactions across many life-science and engineering applications.

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  • 31.
    Aignon, Hyppolite L.
    et al.
    Univ Parakou, Res Unit Trop Mycol & Plant Soil Fungi Interact, Fac Agron, 03 BP 125, Parakou, Benin..
    Jabeen, Sana
    Univ Educ, Dept Bot, Div Sci & Technol, Lahore, Pakistan..
    Naseer, Arooj
    Univ Punjab, Dept Bot, Quaid E Azam Campus, Lahore 54590, Pakistan..
    Yorou, Nourou S.
    Univ Parakou, Res Unit Trop Mycol & Plant Soil Fungi Interact, Fac Agron, 03 BP 125, Parakou, Benin..
    Ryberg, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Three new species of Inosperma (Agaricales, Inocybaceae) from Tropical Africa2021Ingår i: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, nr 77, s. 97-116Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Here, we describe three new species of Inosperma from Tropical Africa: Inosperma africanum, I. bulhomarginatum and I. flavobrunneum. Morphological and molecular data show that these species have not been described before, hence need to be described as new. The phylogenetic placements of these species were inferred, based on molecular evidence from sequences of 28S and RPB2. Additional analysis using ITS dataset shows interspecific variation between each species. Phylogenetic analyses resolve I. flavobrunneum in Old World Tropical lade I with weak support, I. bulbomarginatum is sister of Old World Tropical clack 1 and I. africanum is indicated as sister to the rest of Inosperma. Complete description and illustrations, including photographs and line drawings, are presented for each species. A new combination of Inocybe shawarensis into Inosperma is also proposed.

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  • 32.
    Aignon, Hyppolite L.
    et al.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Plant Soil Fungi Interact, 03 BP 125, Parakou, Benin..
    Naseer, Arooj
    Univ Punjab, Dept Bot, Quaid E Azam Campus, Lahore 54590, Pakistan..
    Matheny, Brandon P.
    Univ Tennessee, Dept Ecol & Evolutionary Biol, Knoxville, TN 37996 USA..
    Yorou, Nourou S.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Plant Soil Fungi Interact, 03 BP 125, Parakou, Benin..
    Ryberg, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Mallocybe africana (Inocybaceae, Fungi), the first species of Mallocybe described from Africa2021Ingår i: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 478, nr 1, s. 49-60Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The family Inocybaceae has been poorly studied in Africa. Here we describe the first species of the genus Mallocybe from West African and Zambian woodlands dominated by ectomycorrhizal trees of Fabaceae and Phyllanthaceae. The new species M. africana is characterized by orange-brown fruitbodies, a fibrillose pileus, a stipe tapered towards the base and large ellipsoid basidiospores. It resembles many north and south temperate species of Mallocybe but is most closely related to the southeast Asian tropical species, M. errata. M. africana is widely distributed in West Africa (Benin, Togo, Burkina Faso and Ivory Coast) extending to South-eastern Africa in Zambia. Phylogenetic analyses based on 5.8S rDNA, nLSU and RPB2 sequence data confirm that M. africana is nested within Mallocybe. A complete morphological description and illustrations, including photographs and line drawings, are presented.

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    fulltext
  • 33.
    Ajawatanawong, Pravech
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Mine the Gaps: Evolution of Eukaryotic Protein Indels and their Application for Testing Deep Phylogeny2014Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Insertions/deletions (indels) are potentially powerful evolutionary markers, but little is known about their evolution and few tools exist to effectively study them. To address this, I developed SeqFIRE, a tool for automated identification and extraction of indels from protein multiple sequence alignments. The program also extracts conserved alignment blocks, thus covering all major steps in preparing multiple sequence alignments for phylogenetic analysis.

    I then used SeqFIRE to build an indel database, using 299 single copy proteins from a broad taxonomic sampling of mainly multicellular eukaryotes. A total of 4,707 indels were extracted, of which 901 are simple (one genetic event) and 3,806 are complex (multiple events). The most abundant indels are single amino acid simple indels. Indel frequency decreases exponentially with length and shows a linear relationship with host protein size. Singleton indels reveal a strong bias towards insertions (2.31 x deletions on average). These analyses also identify 43 indels marking major clades in Plantae and Fungi (clade defining indels or CDIs), but none for Metazoa.

    In order to study the 3806 complex indels they were first classified by number of states. Analysis of the 2-state complex and simple indels combined (“bi-state indels”) confirms that insertions are over 2.5 times as frequent as deletions. Three-quarters of the complex indels had three-nine states (“slightly complex indels”). A tree-assisted search method was developed allowing me to identify 1,010 potential CDIs supporting all examined major branches of Plantae and Fungi.

    Forty-two proteins were also found to host complex indel CDIs for the deepest branches of Metazoa. After expanding the taxon set for these proteins, I identified a total of 49 non-bilaterian specific CDIs. Parsimony analysis of these indels places Ctenophora as sister taxon to all other Metazoa including Porifera. Six CDIs were also found placing Placozoa as sister to Bilateria. I conclude that slightly complex indels are a rich source of CDIs, and my tree-assisted search strategy could be automated and implemented in the program SeqFIRE to facilitate their discovery. This will have important implications for mining the phylogenomic content of the vast resource of protist genome data soon to become available.

    Delarbeten
    1. SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
    Öppna denna publikation i ny flik eller fönster >>SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
    Visa övriga...
    2012 (Engelska)Ingår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, nr W1, s. W340-W347Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.

    Nyckelord
    Indels, Alignment, Conserved blocks
    Nationell ämneskategori
    Bioinformatik (beräkningsbiologi) Bioinformatik och systembiologi
    Identifikatorer
    urn:nbn:se:uu:diva-179937 (URN)10.1093/nar/gks561 (DOI)000306670900056 ()
    Tillgänglig från: 2012-08-27 Skapad: 2012-08-27 Senast uppdaterad: 2019-08-28Bibliografiskt granskad
    2. Evolution of protein indels in plants, animals and fungi
    Öppna denna publikation i ny flik eller fönster >>Evolution of protein indels in plants, animals and fungi
    2013 (Engelska)Ingår i: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 13, s. 140-Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Background: Insertions/deletions (indels) in protein sequences are useful as drug targets, protein structure predictors, species diagnostics and evolutionary markers. However there is limited understanding of indel evolutionary patterns. We sought to characterize indel patterns focusing first on the major groups of multicellular eukaryotes. Results: Comparisons of complete proteomes from a taxonically broad set of primarily Metazoa, Fungi and Viridiplantae yielded 299 substantial (>250aa) universal, single-copy (in-paralog only) proteins, from which 901 simple (present/absent) and 3,806 complex (multistate) indels were extracted. Simple indels are mostly small (1-7aa) with a most frequent size class of 1aa. However, even these simple looking indels show a surprisingly high level of hidden homoplasy (multiple independent origins). Among the apparently homoplasy-free simple indels, we identify 69 potential clade-defining indels (CDIs) that may warrant closer examination. CDIs show a very uneven taxonomic distribution among Viridiplante (13 CDIs), Fungi (40 CDIs), and Metazoa (0 CDIs). An examination of singleton indels shows an excess of insertions over deletions in nearly all examined taxa. This excess averages 2.31 overall, with a maximum observed value of 7.5 fold. Conclusions: We find considerable potential for identifying taxon-marker indels using an automated pipeline. However, it appears that simple indels in universal proteins are too rare and homoplasy-rich to be used for pure indel-based phylogeny. The excess of insertions over deletions seen in nearly every genome and major group examined maybe useful in defining more realistic gap penalties for sequence alignment. This bias also suggests that insertions in highly conserved proteins experience less purifying selection than do deletions.

    Nyckelord
    Indels, Rare genomic changes, Phylogeny, Insertion/deletion, Multiple sequence alignment, Eukaryote evolution, Indel profiles
    Nationell ämneskategori
    Naturvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-204971 (URN)10.1186/1471-2148-13-140 (DOI)000321461800001 ()
    Tillgänglig från: 2013-08-16 Skapad: 2013-08-13 Senast uppdaterad: 2024-01-17Bibliografiskt granskad
    3. An automatable method for high throughput analysis of evolutionary patterns in slightly complex indels and its application to the deep phylogeny of Metazoa
    Öppna denna publikation i ny flik eller fönster >>An automatable method for high throughput analysis of evolutionary patterns in slightly complex indels and its application to the deep phylogeny of Metazoa
    2014 (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Insertions/deletions (indels) in protein sequences are potential powerful evolutionary markers. However, these characters have rarely been explored systematically at deep phylogenetic levels. Previous analyses of simple (2-state) clade defining indels (CDIs) in universal eukaryotic proteins found none to support any major animal clade. We hypothesized that CDIs might still be found in the remaining population of indels, which we term complex indels. Here, we propose a method for analyzing the simplest class of complex indels the “slightly complex indels”, and use these to investigate deep branches in animal phylogeny. Complex indels with two states, called bi-state indels, show similar evolutionary patterns to singleton simple indels and confirms that insertion mutations are more common than deletions. Exploration of CDIs in 2- to 9-state complex indels shows strong support for all examined branches of fungi and Archaeplastida. Surprisingly, we also found CDIs supporting major branches in animals, particular in vertebrates. We then expanded the search to non-bilaterial animals (Porifera, Cnidaria and Ctenophora). The phylogenetic tree reconstructed by CDIs places the Ctenophore Mnemiopsis leidyi as the deepest branch of animals with 6 CDIs support. Trichoplax adhaerens is closely related to the Bilateria. Moreover, the indel phylogeny shows Nematostella vectensis and Hydra magnipapillata are paraphyletic group and position of Cnidarian branches seems to be problematic in the indel phylogeny because of homoplasy. This might be solved if we discover CDIs from animal specific proteins, which emerged after the universal orthologous proteins.Evolutionary Patterns in Slightly Complex Protein Insertions/Deletions (Indels) and Their Application to the Study of Deep Phylogeny in Metazoa

    Nationell ämneskategori
    Annan biologi
    Identifikatorer
    urn:nbn:se:uu:diva-216842 (URN)
    Tillgänglig från: 2014-01-27 Skapad: 2014-01-27 Senast uppdaterad: 2024-04-03Bibliografiskt granskad
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  • 34.
    Ajawatanawong, Pravech
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Atkinson, Gemma C.
    Watson-Haigh, Nathan S.
    MacKenzie, Bryony
    Baldauf, Sandra L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments2012Ingår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, nr W1, s. W340-W347Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.

    Ladda ner fulltext (pdf)
    fulltext
  • 35.
    Ajawatanawong, Pravech
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Baldauf, Sandra
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    An automatable method for high throughput analysis of evolutionary patterns in slightly complex indels and its application to the deep phylogeny of Metazoa2014Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Insertions/deletions (indels) in protein sequences are potential powerful evolutionary markers. However, these characters have rarely been explored systematically at deep phylogenetic levels. Previous analyses of simple (2-state) clade defining indels (CDIs) in universal eukaryotic proteins found none to support any major animal clade. We hypothesized that CDIs might still be found in the remaining population of indels, which we term complex indels. Here, we propose a method for analyzing the simplest class of complex indels the “slightly complex indels”, and use these to investigate deep branches in animal phylogeny. Complex indels with two states, called bi-state indels, show similar evolutionary patterns to singleton simple indels and confirms that insertion mutations are more common than deletions. Exploration of CDIs in 2- to 9-state complex indels shows strong support for all examined branches of fungi and Archaeplastida. Surprisingly, we also found CDIs supporting major branches in animals, particular in vertebrates. We then expanded the search to non-bilaterial animals (Porifera, Cnidaria and Ctenophora). The phylogenetic tree reconstructed by CDIs places the Ctenophore Mnemiopsis leidyi as the deepest branch of animals with 6 CDIs support. Trichoplax adhaerens is closely related to the Bilateria. Moreover, the indel phylogeny shows Nematostella vectensis and Hydra magnipapillata are paraphyletic group and position of Cnidarian branches seems to be problematic in the indel phylogeny because of homoplasy. This might be solved if we discover CDIs from animal specific proteins, which emerged after the universal orthologous proteins.Evolutionary Patterns in Slightly Complex Protein Insertions/Deletions (Indels) and Their Application to the Study of Deep Phylogeny in Metazoa

  • 36.
    Ajawatanawong, Pravech
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Baldauf, Sandra L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Evolution of protein indels in plants, animals and fungi2013Ingår i: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 13, s. 140-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Insertions/deletions (indels) in protein sequences are useful as drug targets, protein structure predictors, species diagnostics and evolutionary markers. However there is limited understanding of indel evolutionary patterns. We sought to characterize indel patterns focusing first on the major groups of multicellular eukaryotes. Results: Comparisons of complete proteomes from a taxonically broad set of primarily Metazoa, Fungi and Viridiplantae yielded 299 substantial (>250aa) universal, single-copy (in-paralog only) proteins, from which 901 simple (present/absent) and 3,806 complex (multistate) indels were extracted. Simple indels are mostly small (1-7aa) with a most frequent size class of 1aa. However, even these simple looking indels show a surprisingly high level of hidden homoplasy (multiple independent origins). Among the apparently homoplasy-free simple indels, we identify 69 potential clade-defining indels (CDIs) that may warrant closer examination. CDIs show a very uneven taxonomic distribution among Viridiplante (13 CDIs), Fungi (40 CDIs), and Metazoa (0 CDIs). An examination of singleton indels shows an excess of insertions over deletions in nearly all examined taxa. This excess averages 2.31 overall, with a maximum observed value of 7.5 fold. Conclusions: We find considerable potential for identifying taxon-marker indels using an automated pipeline. However, it appears that simple indels in universal proteins are too rare and homoplasy-rich to be used for pure indel-based phylogeny. The excess of insertions over deletions seen in nearly every genome and major group examined maybe useful in defining more realistic gap penalties for sequence alignment. This bias also suggests that insertions in highly conserved proteins experience less purifying selection than do deletions.

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  • 37.
    Akgül, Özge
    et al.
    Izmir Democracy Univ, Fac Arts & Sci, Dept Psychol, Izmir, Turkiye..
    Fide, Ezgi
    Dokuz Eylul Univ, Dept Neurosci, Izmir, Turkiye..
    Özel, Fatih
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Fysiologi och miljötoxikologi.
    Alptekin, Köksal
    Dokuz Eylul Univ, Dept Neurosci, Izmir, Turkiye.;Dokuz Eylul Univ, Fac Med, Dept Psychiat, Izmir, Turkiye..
    Bora, Emre
    Dokuz Eylul Univ, Dept Neurosci, Izmir, Turkiye.;Dokuz Eylul Univ, Fac Med, Dept Psychiat, Izmir, Turkiye..
    Akdede, Berna Binnur
    Dokuz Eylul Univ, Dept Neurosci, Izmir, Turkiye.;Dokuz Eylul Univ, Fac Med, Dept Psychiat, Izmir, Turkiye..
    Yener, Görsev
    Dokuz Eylul Univ, Brain Dynam Multidisciplinary Res Ctr, Izmir, Turkiye.;Izmir Univ Econ, Fac Med, Dept Neurol, Izmir, Turkiye.;Dokuz Eylul Univ, Izmir Int Biomed & Genome Inst, Izmir, Turkiye.;Izmir Univ Econ, Fac Med, Dept Neurol, TR-35340 Izmir, Turkiye..
    Enhanced Punishment Responses in Patients With Schizophrenia: An Event-Related Potential Study2024Ingår i: Clinical EEG and Neuroscience, ISSN 1550-0594, E-ISSN 2169-5202, Vol. 55, nr 2, s. 219-229Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    It is well known that abnormal reward processing is a characteristic feature of various psychopathologies including schizophrenia. Reduced reward anticipation has been suggested as a core symptom of schizophrenia. The Monetary Incentive Delay Task (MID) is frequently used to detect reward anticipation. The present study aims to evaluate the amplitude and latency of event-related potential (ERP) P300 in patients with schizophrenia (SCH) compared to healthy controls during the MID task. Twenty patients with SCH and 21 demographically matched healthy controls (HC) were included in the study. ERP P300 amplitude and latency values were compared between groups using an MID task in which reward and loss cues were presented. Relations between P300 and clinical facets were investigated in the patient group. SCH group had enhanced mean P300 amplitudes and delayed peak latency in the punishment condition compared with HC. These higher responses were also associated with negative symptoms. SCH group showed altered reward processing as being more sensitive to loss of reward conditions as firstly evidenced by electrophysiological methods, possibly due to abnormality in various systems including social withdrawal, social defeat, and behavioral inhibition system.

  • 38.
    Akgül, Özge
    et al.
    Izmir Democracy Univ, Dept Psychol, Fac Arts & Sci, Izmir, Turkiye..
    Fide, Ezgi
    Dokuz Eylul Univ, Dept Neurosci, Izmir, Turkiye..
    Özel, Fatih
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Fysiologi och miljötoxikologi.
    Alptekin, Köksal
    Dokuz Eylul Univ, Dept Neurosci, Izmir, Turkiye.;Dokuz Eylul Univ, Fac Med, Dept Psychiat, Izmir, Turkiye..
    Bora, Emre
    Dokuz Eylul Univ, Dept Neurosci, Izmir, Turkiye.;Dokuz Eylul Univ, Fac Med, Dept Psychiat, Izmir, Turkiye..
    Akdede, Berna Binnur
    Dokuz Eylul Univ, Dept Neurosci, Izmir, Turkiye.;Dokuz Eylul Univ, Fac Med, Dept Psychiat, Izmir, Turkiye..
    Yener, Görsev
    Dokuz Eylul Univ, Dept Neurosci, Izmir, Turkiye.;Izmir Univ Econ, Fac Med, Dept Anat, Izmir, Turkiye.;Izmir Int Biomed & Genome Inst, Izmir, Turkiye..
    Reduced Reward Processing in Schizophrenia: A Comprehensive EEG Event-Related Oscillation Study2024Ingår i: Brain Topography, ISSN 0896-0267, E-ISSN 1573-6792, Vol. 37, nr 1, s. 126-137Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    It is well known that abnormal reward processing is a characteristic feature of various psychopathologies including schizophrenia (SZ). Reduced reward anticipation has been suggested as a core symptom of SZ. The present study aims to evaluate the event-related oscillations (EROs) delta, theta, alpha, beta, and gamma in patients with SZ during the Monetary Incentive Delay (MID) task, which elicits the neural activity of reward processing. Twenty-one patients with SZ and twenty-two demographically matched healthy controls were included in the study. EROs were compared between groups and correlation analyses were conducted to determine a possible relationship between clinical scores and ERO values. Compared with healthy controls, the SZ group had reduced (1) delta and theta amplitudes in the reward condition (2) total beta and non-incentive cue-related beta amplitudes, and (3) incentive cue-related frontal gamma amplitudes. These reductions can be interpreted as impaired dopaminergic neurotransmission and disrupted cognitive functioning in the reward processing of SZ. In contrast, SZ patients showed higher incentive cue-related theta and occipital gamma amplitudes compared to controls. These increments may reflect negative symptoms in SZ. Moreover, theta amplitudes showed a negative correlation with Calgary Depression Scale for Schizophrenia scores and a positive correlation with attentional impulsivity. This is the first study showing the impairments of SZ patients in EROs from delta to gamma frequency bands compared with healthy controls during reward anticipation. Being the first comprehensive study, our results can be interpreted as providing evidence for disrupted brain dynamics in the reward processing of SZ studied by EROs. It may become possible to help patients' wellness by improving our understanding of reward processing in schizophrenia and developing innovative rehabilitation treatments based on these findings.

  • 39.
    Al Jewari, Caesar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Resolving deep nodes of eukaryote phylogeny2022Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    My thesis aims to solve deep nodes in the eukaryote tree of life (eToL), by developing new data sets and new approaches to analysing them. In paper I, I described a dataset of 76 universal eukaryotic proteins of bacterial descent (euBacs), in order to test the relations among the three main divisions of mitochondriate eukaryotes (Amorphea, Diaphretickes and Discoba). I developed two protocols to identify problematic data. The conJac protocol analyzes data by jackknifing to detect outlier sequences, while conWin uses a sliding window to find sequence fragments of potentially foreign origin. Phylogenetic analyses of the 76 euBacs, with and without conWin or conJac filtering place Discoba as the sister group to Amorphea and Diaphretickes. The results are largely consistent and highly supported under various evolutionary models except for highly complex CAT models. In paper II, I describe a dataset of 198 universal eukaryote proteins of archaeal ancestry (euArcs), which includes the remaining eukaryotes, informally referred to as amitochondriate excavate. These were excluded from the previous study because they lack euBacs. Phylogenetic analyses of the euArc dataset place the amitochondriate excavate as the first three branches of eToL, followed by Discoba, the only mitochondriate excavates, which appear as a sister group to the remaining eukaryotes. I also developed a protocol using predicted protein structures to increase the fitness of the model without inflating the parameter space, allowing me to conduct a series of control analyses and further support the multi-excavate root. In Paper III, I describe a new application of reciprocal-rooting using concatenated sequences, which I then use to test the euArc root. I also developed two sampling protocols unique to this kind of data. The protocols confirm the multi-excavate euArc root, which indicates that eukaryotes arose from an excavate ancestor. Paper IV describes a follow-up on the ConWin results from Paper I. These show moderate to strong support for mosaicism in 16 euBac proteins from diverse metabolic pathways and donor lineages. In summary, this thesis presents a novel root for the eukaryote tree of life. The new root requires revision of fundamental theories of eukaryote evolution including the source and timing of mitochondrial origins. The methods I have developed are applicable to many different kinds of phylogenetic studies, and the new protein structure model should make these analyses faster, more flexible, and more widely available.

    Delarbeten
    1. Conflict over the Eukaryote Root Resides in Strong Outliers, Mosaics and Missing Data Sensitivity of Site-Specific (CAT) Mixture Models
    Öppna denna publikation i ny flik eller fönster >>Conflict over the Eukaryote Root Resides in Strong Outliers, Mosaics and Missing Data Sensitivity of Site-Specific (CAT) Mixture Models
    2022 (Engelska)Ingår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836XArtikel i tidskrift (Refereegranskat) Epub ahead of print
    Abstract [en]

    Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees. However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artifacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, whereas ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi, and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in undersampled lineages, whereas ConWin analyses of Discoba, the most undersampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa.

    Nationell ämneskategori
    Biologisk systematik
    Identifikatorer
    urn:nbn:se:uu:diva-484535 (URN)10.1093/sysbio/syac029 (DOI)000804041500001 ()35412616 (PubMedID)
    Forskningsfinansiär
    Vetenskapsrådet, 2017-04351
    Tillgänglig från: 2022-09-13 Skapad: 2022-09-13 Senast uppdaterad: 2022-10-18
    2. An excavate root for the eukaryote tree of life
    Öppna denna publikation i ny flik eller fönster >>An excavate root for the eukaryote tree of life
    2023 (Engelska)Ingår i: Science Advances, ISSN 2375-2548, Vol. 9, nr 17, artikel-id eade4973Artikel i tidskrift (Övrigt vetenskapligt) Published
    Abstract [en]

    Much of the higher-order phylogeny of eukaryotes is well resolved, but the root remains elusive. We assembled a dataset of 183 eukaryotic proteins of archaeal ancestry to test this root. The resulting phylogeny identifies four lineages of eukaryotes currently classified as “Excavata” branching separately at the base of the tree. Thus, Parabasalia appear as the first major branch of eukaryotes followed sequentially by Fornicata, Preaxostyla, and Discoba. All four excavate branch points receive full statistical support from analyses with commonly used evolutionary models, a protein structure partition model that we introduce here, and various controls for deep phylogeny artifacts. The absence of aerobic mitochondria in Parabasalia, Fornicata, and Preaxostyla suggests that modern eukaryotes arose under anoxic conditions, probably much earlier than expected, and without the benefit of mitochondrial respiration.

    Ort, förlag, år, upplaga, sidor
    American Association for the Advancement of Science (AAAS), 2023
    Nationell ämneskategori
    Biologisk systematik Ekologi Evolutionsbiologi
    Identifikatorer
    urn:nbn:se:uu:diva-484543 (URN)10.1126/sciadv.ade4973 (DOI)000989268500015 ()37115919 (PubMedID)
    Forskningsfinansiär
    Vetenskapsrådet, 2017-04351Forskningsrådet FormasForte, Forskningsrådet för hälsa, arbetsliv och välfärd, 2017-04351
    Tillgänglig från: 2022-09-13 Skapad: 2022-09-13 Senast uppdaterad: 2023-10-04Bibliografiskt granskad
    3. Reciprocal rooting with concatenation supports the multi-excavate root
    Öppna denna publikation i ny flik eller fönster >>Reciprocal rooting with concatenation supports the multi-excavate root
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Biologisk systematik
    Forskningsämne
    Biologi med inriktning mot systematik
    Identifikatorer
    urn:nbn:se:uu:diva-484545 (URN)
    Tillgänglig från: 2022-09-13 Skapad: 2022-09-13 Senast uppdaterad: 2022-09-13
    4. Widespread mosaicism in eukaryotic genes of bacterial ancestry
    Öppna denna publikation i ny flik eller fönster >>Widespread mosaicism in eukaryotic genes of bacterial ancestry
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Biologisk systematik
    Forskningsämne
    Biologi med inriktning mot systematik
    Identifikatorer
    urn:nbn:se:uu:diva-484571 (URN)
    Forskningsfinansiär
    Vetenskapsrådet, 2017-04351
    Tillgänglig från: 2022-09-13 Skapad: 2022-09-13 Senast uppdaterad: 2022-09-13
    Ladda ner fulltext (pdf)
    UUThesis_Al Jewari,C-2022
    Ladda ner (jpg)
    presentationsbild
  • 40.
    Al Jewari, Caesar
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Baldauf, Sandra L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    An excavate root for the eukaryote tree of life2023Ingår i: Science Advances, ISSN 2375-2548, Vol. 9, nr 17, artikel-id eade4973Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    Much of the higher-order phylogeny of eukaryotes is well resolved, but the root remains elusive. We assembled a dataset of 183 eukaryotic proteins of archaeal ancestry to test this root. The resulting phylogeny identifies four lineages of eukaryotes currently classified as “Excavata” branching separately at the base of the tree. Thus, Parabasalia appear as the first major branch of eukaryotes followed sequentially by Fornicata, Preaxostyla, and Discoba. All four excavate branch points receive full statistical support from analyses with commonly used evolutionary models, a protein structure partition model that we introduce here, and various controls for deep phylogeny artifacts. The absence of aerobic mitochondria in Parabasalia, Fornicata, and Preaxostyla suggests that modern eukaryotes arose under anoxic conditions, probably much earlier than expected, and without the benefit of mitochondrial respiration.

    Ladda ner fulltext (pdf)
    fulltext
  • 41.
    Al Jewari, Caesar
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Baldauf, Sandra L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Conflict over the Eukaryote Root Resides in Strong Outliers, Mosaics and Missing Data Sensitivity of Site-Specific (CAT) Mixture Models2022Ingår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836XArtikel i tidskrift (Refereegranskat)
    Abstract [en]

    Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees. However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artifacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, whereas ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi, and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in undersampled lineages, whereas ConWin analyses of Discoba, the most undersampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa.

  • 42.
    Alcolombri, Uria
    et al.
    Swiss Fed Inst Technol, Dept Civil Environm & Geomat Engn, Inst Environm Engn, Zurich, Switzerland..
    Peaudecerf, Francois J.
    Swiss Fed Inst Technol, Dept Civil Environm & Geomat Engn, Inst Environm Engn, Zurich, Switzerland..
    Fernandez, Vicente I.
    Swiss Fed Inst Technol, Dept Civil Environm & Geomat Engn, Inst Environm Engn, Zurich, Switzerland..
    Behrendt, Lars
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Miljötoxikologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Swiss Fed Inst Technol, Dept Civil Environm & Geomat Engn, Inst Environm Engn, Zurich, Switzerland.
    Lee, Kang Soo
    Swiss Fed Inst Technol, Dept Civil Environm & Geomat Engn, Inst Environm Engn, Zurich, Switzerland..
    Stocker, Roman
    Swiss Fed Inst Technol, Dept Civil Environm & Geomat Engn, Inst Environm Engn, Zurich, Switzerland..
    Sinking enhances the degradation of organic particles by marine bacteria2021Ingår i: Nature Geoscience, ISSN 1752-0894, E-ISSN 1752-0908, Vol. 14, nr 10, s. 775-780Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The sinking of organic particles in the ocean and their degradation by marine microorganisms is one of the main drivers of the biological pump. Yet, the mechanisms determining the magnitude of the pump remain poorly understood, limiting our ability to predict this carbon flux in future ocean scenarios. Current ocean models assume that the biological pump is governed by the competition between sinking speed and degradation rate, with the two processes independent from one another. Contrary to this paradigm, we show that sinking itself is a primary determinant of the rate at which bacteria degrade particles. Heterotrophic bacterial degradation rates were obtained from a laboratory study on model surface-colonized particles at atmospheric pressure under a range of flow speeds to mimic different sinking velocities. We find that even modest sinking speeds of 8 m day−1 enhance degradation rates more than 10-fold compared with degradation rates of non-sinking particles. We discovered that the molecular mechanism underlying this sinking-enhanced degradation is the flow-induced removal from the particles of the oligomeric breakdown products, which otherwise compete for enzymatic activity. This mechanism applies across several substrates and bacterial strains, suggesting its potentially broad occurrence under natural marine conditions. Integrating our findings into a mathematical model of particulate carbon flux, we propose that the coupling of sinking and degradation may contribute, in conjunction with other processes, to determining the magnitude of the vertical carbon flux in the ocean.

  • 43.
    Aleix-Mata, Gael
    et al.
    Univ Jaen, Dept Biol Expt, Area Genet, Campus Las Lagunillas S-N, Jaen 23071, Spain.;Univ Jaen, Dept Biol Anim Biol Vegetal & Ecol, Campus Las Lagunillas S-N, Jaen 23071, Spain..
    Gutierrez, Juana
    Univ Jaen, Dept Biol Expt, Area Genet, Campus Las Lagunillas S-N, Jaen 23071, Spain..
    Ruiz-Ruano, Francisco J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Lorite, Pedro
    Univ Jaen, Dept Biol Expt, Area Genet, Campus Las Lagunillas S-N, Jaen 23071, Spain..
    Marchal, Juan A.
    Univ Jaen, Dept Biol Expt, Area Genet, Campus Las Lagunillas S-N, Jaen 23071, Spain..
    Sanchez, Antonio
    Univ Jaen, Dept Biol Expt, Area Genet, Campus Las Lagunillas S-N, Jaen 23071, Spain..
    The complete mitochondrial genome of Talpa aquitania (Talpidae; Insectivora), a mole species endemic to northern Spain and southern France2020Ingår i: Molecular Biology Reports, ISSN 0301-4851, E-ISSN 1573-4978, Vol. 47, nr 3, s. 2397-2403Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The complete mitogenome sequence of Talpa aquitania, a recently described Talpa species, was assembled using whole-genome sequencing data. It varies in length from 16,776 to 16,846 bp, contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L-strand replication, and a control region. In the control region, which varied from 1320 to 1390 bp, we identified the extended termination-associated sequence (ETAS-1 and ETAS-2) and the conserved sequence blocks (CSB-1, 2, 3, B, C, D, E, F). In addition, this region includes a 10 bp tandem repeat DNA sequence, with a variable number of repeats that suggest the existence of heteroplasmy. Phylogeny reconstructions based on Maximum Likelihood, Neighbor-joining and Bayesian inference analyses yielded phylogenies with similar topologies demonstrating that T. aquitania and T. occidentalis are sister species.

  • 44.
    Alejandro Zamora-Briseno, Jesus
    et al.
    Inst Politecn Nacl, Unidad Merida, Ctr Invest & Estudios Avanzados, Lab Inmunol & Biol Mol,Dept Recursos Mar, Merida, Yucatan, Mexico..
    Ruiz-May, Eliel
    Cluster Cientif & Tecnol BioMimic, Inst Ecol, Red Estudios Mol Avanzados, Xalapa, Veracruz, Mexico..
    Miguel Elizalde-Contreras, Jose
    Cluster Cientif & Tecnol BioMimic, Inst Ecol, Red Estudios Mol Avanzados, Xalapa, Veracruz, Mexico..
    Margarita Hernandez-Velazquez, Ioreni
    Inst Politecn Nacl, Unidad Merida, Ctr Invest & Estudios Avanzados, Lab Inmunol & Biol Mol,Dept Recursos Mar, Merida, Yucatan, Mexico..
    Hernandez-Perez, Ariadne
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Jämförande fysiologi.
    Guadalupe Fuentes-Garcia, Ana
    Inst Politecn Nacl, Unidad Merida, Ctr Invest & Estudios Avanzados, Lab Inmunol & Biol Mol,Dept Recursos Mar, Merida, Yucatan, Mexico..
    Herrera-Salvatierra, Nancy
    Inst Politecn Nacl, Unidad Merida, Ctr Invest & Estudios Avanzados, Lab Inmunol & Biol Mol,Dept Recursos Mar, Merida, Yucatan, Mexico..
    Briones-Fourzan, Patricia
    Univ Nacl Autonoma Mexico, Isnt Ciencias Mar & Limnol, Unidad Acad Sistemas Arrecifales, Puerto Morelos, Mexico..
    Pascual-Jimenez, Cristina
    Univ Nacl Autonoma Mexico, Unidad Multidisciplinaria Docencia & Invest, Fac Ciencias, Sisal, Mexico..
    Lozano-Alvarez, Enrique
    Univ Nacl Autonoma Mexico, Isnt Ciencias Mar & Limnol, Unidad Acad Sistemas Arrecifales, Puerto Morelos, Mexico..
    Rodriguez-Canul, Rossanna
    Inst Politecn Nacl, Unidad Merida, Ctr Invest & Estudios Avanzados, Lab Inmunol & Biol Mol,Dept Recursos Mar, Merida, Yucatan, Mexico..
    iTRAQ-Based Proteomic Profile Analysis of the Hepatopancreas of Caribbean Spiny Lobsters Infected WithPanulirus argusVirus 1: Metabolic and Physiological Implications2020Ingår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 11, artikel-id 1084Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Caribbean spiny lobsterPanulirus argus(Latreille, 1084) sustains economically valuable fisheries throughout the wider Caribbean region. This species is currently affected by the pathogenic virusPanulirus argusVirus 1 (PaV1) that causes a systemic and chronic-degenerative infection in juvenile spiny lobstersP. argus. To date, there is no available information regarding the host alterations induced by this pathogen at the molecular level. In the present study, comparative proteomic analyses of the changes in the hepatopancreas between infected and non-infected juvenile lobsters were analyzed by isobaric tags for relative and absolute quantitation (iTRAQ) coupled to synchronous precursor selection (SPS)-based MS3. We identified a total of 636 proteins, being 68 down-regulated and 71 up-regulated proteins. Among the down-regulated proteins, we identified several enzymes involved in the metabolism of hormones and lipids, digestive proteases and glycosidases, while proteins associated with the histone core, protein synthesis, immune response and RNA regulation were up-regulated. Several misregulated enzymes involved in the regulation of neuromodulators were also identified. RT-qPCR assays were used to validate the expression of transcripts encoding for selected differential proteins that were in concordance to proteomic data, as well as the tendency observed in the enzymatic activities of trypsin, chymotrypsin, and glycosidase. In a similar way, we observed glycogen reduction in muscle, and an increase in plasma acylglycerides and glucose, which may be explained by proteomic data. This study provides the first insight into the molecular changes in the hepatopancreas of Caribbean spiny lobsters associated to PaV1 infection. Data provided herein would help to clarify the origin of the molecular misregulations observed at macroscopic level in this host-pathogen interaction.

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    FULLTEXT01
  • 45.
    Alfjorden, Anders
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Brännström, Ioana Onut
    Wengström, Niklas
    Jamy, Mahwash
    Kristmundson, Arni
    Jansson, Eva
    Burki, Fabien
    Identification of a new gregarine parasite [Apicomplexa, Alveolata] in mass mortality events of freshwater pearl mussels (Margaritifera margaritifera)Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    The freshwater pearl mussel (FPM) Margaritifera margaritifera is a Holarctic species with key roles in river ecosystems. Although of highly ecological importance the species is globally threatened and reaching nearing extinction in Europe. FPM is particularly vulnerable to fluctuations of environmental conditions, being entirely dependent of highly oxygenated streams with clear running water. Therefore anthropogenic activities resulting in habitat loss or affecting water quality such as sedimentation, eutrophication, or acidification of streams have been viewed as important causes of the mass mortality events in FPM.  However, in many of these investigations, possible infections from protist parasites were never considered. Here report on a novel parasite associated with several population losses in Swedish rivers. Phylogenetic analysis of the first molecular data for this parasite (18S rDNA gene) revealed that it is related to a terrestrial group of gregarines (Apicomplexa), specifically to parasites of tadpoles belonging to the genus Nematopsis. Further investigations of environmental data revealed the presence of this parasite in Canadian peat bogs and Swedish lakes. We describe the parasite using histology, in-situ hybridization, and transmission electron microscopy and propose a tentative life cycle within the FPM host. Together, our results identify for the first time a pathogenic agent that maybe responsible for the steady decline of a critical animal species in freshwater ecosystems worldwide.

  • 46.
    Alfsnes, Kristian
    et al.
    Norwegian Inst Publ Hlth, Infect Dis Control & Environm Hlth, Oslo, Norway..
    Eldholm, Vegard
    Norwegian Inst Publ Hlth, Infect Dis Control & Environm Hlth, Oslo, Norway..
    Gaunt, Michael W.
    London Sch Hyg & Trop Med, Keppel St, London WC1E 7HT, England..
    de Lamballerie, Xavier
    Aix Marseille Univ, UMR Unite Virus Emergents, IRD 190 Inserm 1207 IHU Mediterranee Infect, Marseille, France.;Inst Hosp Univ Mediterranee Infect, APHM Publ Hosp Marseille, Marseille, France..
    Gould, Ernest A.
    Aix Marseille Univ, UMR Unite Virus Emergents, IRD 190 Inserm 1207 IHU Mediterranee Infect, Marseille, France..
    Pettersson, John
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Publ Hlth Agcy Sweden, Solna, Sweden.;Univ Sydney, Sch Life & Environm Sci, Sydney Inst Infect Dis, Sydney, NSW, Australia.;Univ Sydney, Sch Med Sci, Sydney, NSW, Australia..
    Tracing and tracking the emergence, epidemiology and dispersal of dengue virus to Africa during the 20th century2021Ingår i: One Health, ISSN 2352-7714, Vol. 13, artikel-id 100337Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The four mosquito-borne dengue virus serotypes (DENV1-DENV4) cause a high burden of disease throughout the tropical and sub-tropical regions of the world. Nevertheless, their precise epidemiological history in Africa, including when and where they originated and were distributed during the 20th century, remains unclear stressing the need for One Health focused research. Accordingly, we conducted a time-scaled molecular epide-miological reconstruction using publicly available and newly sequenced dengue virus genomes of African origin representing all four serotypes to deduce the most likely temporal and spatial transmission routes of each DENV serotype from their ancestral regions to, within and from Africa. Our analyses suggest that during the 20th century, serotypes DENV1-DENV3 were introduced to Africa from South East Asia on multiple occasions. The earliest evidence recorded indicates introduction of DENV2 during the early-1940s and of DENV1 during the mid-1940s to Western Africa from South East Asia. The analysis also implies an early introduction of DENV4 during the mid-1940s to Western Africa, alongside DENV1, probably originating in South East Asia. Establishment of DENV3 in Africa appears to have occurred later in the 1960s, apparently originating from South East Asia. However, with the re-establishment of DENV in the Americas, following the cessation of the PAHO mosquito control programme during the mid-20th century, evidence of introductions of DENV1 and DENV2 from the Americas to Western Africa was also observed. The data also identify intra-regional circulation of DENV, but also inter-regional dispersal of all four serotypes within Africa, which has led to a high degree of geographical overlap among serotypes. It is also noteworthy that DENV from both Eastern and Western Africa, have been introduced into Central Africa but there is no support for the converse relationship. For serotypes DENV1-DENV3, we observed probable exports from within established African DENV clusters (>= 2 sequences) primarily to Eastern and Southern Asia. Collectively, our findings support the view that all DENV serotypes, apart from DENV4, have been introduced on multiple occasions to Africa, primarily originating from South East Asia, and subsequently to neighbouring regions within Africa.

    Ladda ner fulltext (pdf)
    fulltext
  • 47.
    Allen, Marie
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Medicinsk genetik och genomik. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Bjerke, Mia
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Karolinska Inst, Dept Lab Med, SE-14186 Stockholm, Sweden..
    Edlund, Hanna
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Nelander, Sven
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Neuroonkologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Westermark, Bengt
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Neuroonkologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Origin of the U87MG glioma cell line: Good news and bad news2016Ingår i: Science Translational Medicine, ISSN 1946-6234, E-ISSN 1946-6242, Vol. 8, nr 354, artikel-id 354re3Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Human tumor-derived cell lines are indispensable tools for basic and translational oncology. They have an infinite life span and are easy to handle and scalable, and results can be obtained with high reproducibility. However, a tumor-derived cell line may not be authentic to the tumor of origin. Two major questions emerge: Have the identity of the donor and the actual tumor origin of the cell line been accurately determined? To what extent does the cell line reflect the phenotype of the tumor type of origin? The importance of these questions is greatest in translational research. We have examined these questions using genetic profiling and transcriptome analysis in human glioma cell lines. We find that the DNA profile of the widely used glioma cell line U87MG is different from that of the original cells and that it is likely to be a bona fide human glioblastoma cell line of unknown origin.

  • 48. Allorent, Guillaume
    et al.
    Petroutsos, Dimitris
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Fysiologi och miljötoxikologi.
    Photoreceptor-dependent regulation of photoprotection2017Ingår i: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 37, s. 102-108Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In photosynthetic organisms, proteins in the light-harvesting complex (LHC) harvest light energy to fuel photosynthesis, whereas photoreceptor proteins are activated by the different wavelengths of the light spectrum to regulate cellular functions. Under conditions of excess light, blue-light photoreceptors activate chloroplast avoidance movements in sessile plants, and blue- and green-light photoreceptors cause motile algae to swim away from intense light. Simultaneously, LHCs switch from light-harvesting mode to energy-dissipation mode, which was thought to be independent of photoreceptor-signaling up until recently. Recent advances, however, indicate that energy dissipation in green algae is controlled by photoreceptors activated by blue and UV-B light, and new molecular links have been established between photoreception and photoprotection.

  • 49. Alstrup, Vagn
    et al.
    Aptroot, Andre
    Divakar, Pradeep K.
    LaGreca, Scott
    Tibell, Leif
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Lichens from Tanzania and Kenya III: Macrolichens and calicioid lichens2010Ingår i: Cryptogamie Mycologie, ISSN 0181-1584, E-ISSN 1776-100X, Vol. 31, nr 3, s. 333-351Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    156 species of macrolichens and calicioid lichens are reported from Tanzania and Kenya. 28 species are new for Tanzania and 2 for Kenya. New for Africa are Hypotrachyna novella, H. physcioides, Melanelia panniformis, Physcidia squamulosa, and Xanthoparmelia microspora.

  • 50.
    Alva, Omar
    et al.
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Leroy, Anais
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Heiske, Margit
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Pereda-Loth, Veronica
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Tisseyre, Lenka
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Boland, Anne
    Ctr Natl Genotypage, Inst Genom, Commissariat Energie Atom, F-91000 Evry, France..
    Deleuze, Jean-Francois
    Ctr Natl Genotypage, Inst Genom, Commissariat Energie Atom, F-91000 Evry, France..
    Rocha, Jorge
    Univ Porto, InBIO Lab Associado, Ctr Invest Biodiversidade & Recursos, CIBIO, Campus Vairao, P-4485661 Vairao, Portugal.;Univ Porto, Fac Ciencias, Dept Biol, P-4099002 Porto, Portugal.;CIBIO, BIOPOLIS Program Genom Biodivers & Land Planning, Campus Vairao, P-4485661 Vairao, Portugal..
    Schlebusch, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Fortes-Lima, Cesar A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Stoneking, Mark
    Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, D-04103 Leipzig, Germany.;Univ Lyon 1, Lab Biometrie & Biol Evolut, CNRS, UMR 5558, Villeurbanne, France..
    Radimilahy, Chantal
    Univ Antananarivo, Musee Art & Archeol, Antananarivo, Madagascar..
    Rakotoarisoa, Jean-Aime
    Univ Antananarivo, Musee Art & Archeol, Antananarivo, Madagascar..
    Letellier, Thierry
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    Pierron, Denis
    Univ Toulouse III, EVOLSAN Fac Chirurg Dent, Equipe Med Evolut, Toulouse, France..
    The loss of biodiversity in Madagascar is contemporaneous with major demographic events2022Ingår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 32, nr 23, s. 4997-+Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Only 400 km off the coast of East Africa, the island of Madagascar is one of the last large land masses to have been colonized by humans. While many questions surround the human occupation of Madagascar, recent studies raise the question of human impact on endemic biodiversity and landscape transformation. Previous genetic and linguistic analyses have shown that the Malagasy population has emerged from an admixture that happened during the last millennium, between Bantu-speaking African populations and Austronesian-speaking Asian populations. By studying the sharing of chromosome segments between individuals (IBD determination), local ancestry information, and simulated genetic data, we inferred that the Malagasy ancestral Asian population was isolated for more than 1,000 years with an effective size of just a few hundred individuals. This isolation ended around 1,000 years before present (BP) by admixture with a small African population. Around the admixture time, there was a rapid demographic expansion due to intrinsic population growth of the newly admixed population, which coincides with extensive changes in Madagascar's landscape and the extinction of all endemic large- bodied vertebrates. Therefore, our approach can provide new insights into past human demography and associated impacts on ecosystems.

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