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  • 251.
    De Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Oslo, Nat Hist Museum, Oslo, Norway.;Naturalis Biodivers Ctr, Leiden, Netherlands..
    Cross, Hugh B.
    Norwegian Inst Bioecon Res, As, Norway..
    De Wilde, Willem J. J. O.
    Naturalis Biodivers Ctr, Leiden, Netherlands..
    Duyfjes, Brigitta E. E.
    Naturalis Biodivers Ctr, Leiden, Netherlands..
    Gravendeel, Barbara
    Naturalis Biodivers Ctr, Leiden, Netherlands.;Univ Appl Sci Leiden, Leiden, Netherlands..
    Molecular phylogenetic analyses of Cucurbitaceae tribe Benincaseae urge for merging of Pilogyne with Zehneria2015In: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 236, no 2, p. 173-183Article in journal (Refereed)
    Abstract [en]

    The tropical cucurbitaceous genus Zehneria as traditionally circumscribed displays much morphological diversity. Recent taxonomic revisions have resulted in its redefinition through both recognition and subsequent lumping of several additional genera. This study utilized plastid and nuclear DNA sequence data to reconstruct a molecular phylogeny of Zehneria and its close relatives in order to test whether these revisions reflected the molecular evolution in this group. The results suggest that Neoachmandra is monophyletic, and that Zehneria in a restricted sense and Neoachmandra accessions form a single monophyletic clade, whereas Pilogyne in its present understanding is polyphyletic. In the light of these results Pilogyne should be merged back into Zehneria from which it was split off earlier.

  • 252.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Oslo, Nat Hist Museum, Oslo, Norway.;Nat Biodivers Ctr, Leiden, Netherlands..
    Ghorbani, Abdolbaset
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Manzanilla, Vincent
    Univ Oslo, Nat Hist Museum, Oslo, Norway..
    Raclariu, Ancuta-Cristina
    Univ Oslo, Nat Hist Museum, Oslo, Norway.;NIRDBIS, Stejarul Res Ctr Biol Sci, Piatra Neamt, Romania..
    Kreziou, Anna
    Argonafton 30, Thessaloniki, Greece..
    Ounjai, Sarawut
    Chiang Mai Univ, Dept Biol, Chiang Mai, Thailand..
    Osathanunkul, Maslin
    Chiang Mai Univ, Dept Biol, Chiang Mai, Thailand..
    Gravendeel, Barbara
    Nat Biodivers Ctr, Leiden, Netherlands..
    DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1863, article id 20171182Article in journal (Refereed)
    Abstract [en]

    In eastern Mediterranean countries orchids continue to be collected from the wild for the production of salep, a beverage made of dried orchid tubers. In this study we used nrITS1 and nrITS2 DNA metabarcoding to identify orchid and other plant species present in 55 commercial salep products purchased in Iran, Turkey, Greece and Germany. Thirty samples yielded a total of 161 plant taxa, and 13 products (43%) contained orchid species and these belonged to 10 terrestrial species with tuberous roots. Another 70% contained the substitute ingredient Cyamopsis tetraganoloba (Guar). DNA metabarcoding using the barcoding markers nrITS1 and nrITS2 shows the potential of these markers and approach for identification of species used in salep products. The analysis of interspecific genetic distances between sequences of these markers for the most common salep orchid genera shows that species level identifications can be made with a high level of confidence. Understanding the species diversity and provenance of salep orchid tubers will enable the chain of commercialization of endangered species to be traced back to the harvesters and their natural habitats, and thus allow for targeted efforts to protect or sustainably use wild populations of these orchids.

  • 253.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ichim, Mihael C.
    Newmaster, Steven G.
    DNA Barcoding and Pharmacovigilance of Herbal Medicines2015In: Drug Safety, ISSN 0114-5916, E-ISSN 1179-1942, Vol. 38, no 7, p. 611-620Article in journal (Refereed)
    Abstract [en]

    Pharmacovigilance of herbal medicines relies on the product label information regarding the ingredients and the adherence to good manufacturing practices along the commercialisation chain. Several studies have shown that substitution of plant species occurs in herbal medicines, and this in turn poses a challenge to herbal pharmacovigilance as adverse reactions might be due to adulterated or added ingredients. Authentication of constituents in herbal medicines using analytical chemistry methods can help detect contaminants and toxins, but are often limited or incapable of detecting the source of the contamination. Recent developments in molecular plant identification using DNA sequence data enable accurate identification of plant species from herbal medicines using defined DNA markers. Identification of multiple constituent species from compound herbal medicines using amplicon metabarcoding enables verification of labelled ingredients and detection of substituted, adulterated and added species. DNA barcoding is proving to be a powerful method to assess species composition in herbal medicines and has the potential to be used as a standard method in herbal pharmacovigilance research of adverse reactions to specific products.

  • 254.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kool, Anneleen
    Identifying Medicinal Plant Roots in Trade: DNA barcoding in Morocco2014In: iBOL Barcode Bulletin, Vol. 5, no 1, p. 3-5Article in journal (Other (popular science, discussion, etc.))
  • 255.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kool, Anneleen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Björk, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Ethnobotanical research and teaching: A Case in Bulgaria2006In: Program of the Society for Economic Botany 47th Annual Meeting, 2006Conference paper (Other (popular science, discussion, etc.))
    Abstract [en]

    Introduction

    Bulgarian people in rural areas have a tradition of using herbal medicine as household remedies,

    due partly to the scarcity of pharmaceuticals during the Soviet era. As part of a fieldwork exercise

    in the ethnobotany course taught at Uppsala University students carried out ethnobotanical

    research in different areas in Bulgaria to study and describe these traditions.

    Objectives

    To study: Plants used to treat fevers and cold; plants used to treat wounds and for pain-relief;

    plants grown in home gardens; plants used for magical purposes; and awareness of endangerment

    of medicinally used plants.

    Methods

    Our group of 16 students was divided in groups of two-three students. Each group had written a

    project proposal focusing on one of the study objectives, and carried out this research with the help

    of a Bulgarian translator, who was knowledgeable about the local flora. Three field sites had been

    selected to spread the students throughout the country and to prevent informant fatigue. Interviews

    were semi-structured and if necessary, walks were made with the informants to point out plants and

    collect herbarium vouchers.

    Results

    The students as a whole managed to collect an enormous amount of data in a very short time, and

    some groups carried out as many as 18 interviews during the 8-day field period. Results were

    analyzed per group and presented during a one-day seminar at Ruse University, Bulgaria.

    Conclusion

    Bulgarian villagers, mainly ederly people, rely to a great extent on the use of medicinal plants to

    treat common and non-threatening chronic diseases. These plants are often grown in home

    gardens, and less so collected in the wild. Knowledge is often based on books, and less so on

    maternal or paternal transmission. The people living in Roussenski Lom national park experience

    that most medicinally used wild plants have stayed equal or increased in abundance over the last

    decennium. Carrying out ethnobotanical field research can be effective and efficiently done as part

    of a course training ethnobotany students.

  • 256.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lamxay, Vichith
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Plants used during pregnancy, childbirth and postpartum healthcare in Lao PDR: A comparative study of the Brou, Saek and Kry ethnic groups2009In: Journal of Ethnobiology and Ethnomedicine, ISSN 1746-4269, E-ISSN 1746-4269, Vol. 5, p. 25-Article in journal (Refereed)
    Abstract [en]

    Background

    In many Southeast Asian cultures the activities and diet during the postpartum period are culturally dictated and a period of confinement is observed. Plants play an important role in recovery during the postpartum period in diet, traditional medicine, steam bath and mother roasting (where mother and child placed on a bed above a brazier with charcoal embers on which aromatic plants are laid). This research focuses on the use of plants during pregnancy, parturition, postpartum recovery and infant healthcare among three ethnic groups, the Brou, Saek and Kry. It aims to identify culturally important traditions that may facilitate implementation of culturally appropriate healthcare.

    Methods

    Data were collected in 10 different villages in Khammouane province, Lao PDR, through group and individual interviews with women by female interviewers.

    Results

    A total of 55 different plant species are used in women's healthcare, of which over 90% are used in postpartum recovery. Consensus Analysis rejects the hypothesis that the three ethnic groups belong to a single culture for postpartum plant use, and multidimensional scaling reveals non-overlapping clusters per ethnic group.

    Conclusion

    Medicinal plant use is common among the Brou, Saek and Kry to facilitate childbirth, alleviate menstruation problems, assist recovery after miscarriage, mitigate postpartum haemorrhage, aid postpartum recovery, and for use in infant care. The wealth of novel insights into plant use and preparation will help to understand culturally important practices such as confinement, dietary restrictions, mother roasting and herbal steam baths and their incorporation into modern healthcare

  • 257.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lamxay, Vichith
    Björk, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Comparing medicinal plant knowledge using similarity indices: A case of the Brou, Saek and Kry in Lao PDR2012In: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 141, no 1, p. 481-500Article in journal (Refereed)
    Abstract [en]

    known traditional ecosystem services, as it provides primary healthcare, contributes to subsistence livelihoods, and for its potential value as a source of novel pharmaceuticals. People living in close contact with their surroundings for many generations are hypothesized to have developed, through trial-and-error, in-depth knowledge of ecosystems, biodiversity, and their management and utility. In the case of medicinal plant knowledge it could lead to an asymptotic climax or a constantly evolving equilibrium of cures with proven efficacy and those under assessment.Methods: An in-depth study of 97 plant species used in traditional medicine by the Brou, Saek and Kry ethnic groups in Lao PDR was made to test similarity in medicinal plant knowledge.Results: Medicinal plants were used in 99 different ways in 510 species-use combinations. Medicinal uses could be generalized into 12 use categories with 747 species-category combinations. Similarity indices show Brou and Saek plant use appears to be most similar (QS(BS): 60.0; JI(BS): 75.1) followed by Kry and Saek (QS(KS): 51.6; JI(KS): 53.4), and then Kry and Brou (QS(BK): 46.9; JI(BK): 44.1).Discussion: Intercultural similarities found are quite low, considering that all three groups share the same geographical and ecological area and have the same dependence on medicinal plants. Intercultural transmission is unimpeded but many treatments are likely to be ineffective. Comparison of the similarities found here with similarities computed from other data show that these results are homologous with other sympatric ethnic groups, and much higher than those for allopatrically living groups.Conclusion: Medicinal plant knowledge does not reach a stable climax, but appears to evolve continually by trial-and-error, as effective cures to many ailments are unavailable.

  • 258.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lamxay, Vichith
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Björk, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Steam sauna and mother roasting in Lao PDR: Practices and Chemical constituents of essential oils of plant species used in postpartum recovery2011In: BMC Complementary and Alternative Medicine, ISSN 1472-6882, E-ISSN 1472-6882, Vol. 11, p. 128-Article in journal (Refereed)
    Abstract [en]

    Background: Fundamental in traditional postpartum recovery in Lao PDR is the use of hotbeds, mother roasting, steam sauna and steam baths. During these treatments medicinal plants play a crucial role, but little has been published about how the treatments are carried out precisely, which species are used, the medicinal properties of these species, and the medicinal efficacy of their chemical constituents.

    Methods: Sixty-five interviews, in 15 rural villages, with women of 4 different ethnic groups were conducted to survey confinement rituals, and postpartum plant use and salience. Essential oils from the main species used were extracted using steam distillation and the main chemical constituents characterized using gas chromatography-mass spectrometry (GC-MS).

    Results: A total of 10 different species were used by three or more of the ethnic groups included in this study. All species were used in steam sauna and bath, but only 3 species were used in hotbed and mother roasting. Essential oils of Amomum villosum, Amomum microcarpum and Blumea balsamifera were found to contain significant amounts of the following terpenes: β-pinene, camphor, bornyl acetate, borneol, linalool, D-limonene, fenchone, terpinen-4-ol and α-terpinene.

    Conclusions: Many of these terpenes have documented antimicrobial and analgesic properties, and some have also synergistic interactions with other terpenes. The mode of application in hotbed and mother roasting differs from the documented mechanisms of action of these terpenes. Plants in these two practices are likely to serve mainly hygienic purposes, by segregating the mother from infection sources such as beds, mats, stools, cloth and towels. Steam sauna medicinal plant use through inhalation of essential oils vapors can possibly have medicinal efficacy, but is unlikely to alleviate the ailments commonly encountered during postpartum convalescence. Steam sauna medicinal plant use through dermal condensation of essential oils, and steam bath cleansing of the perineal area is possibly a pragmatic use of the reported medicinal plants, as terpene constituents have documented antimicrobial, analgesic and anti-inflammatory properties.

  • 259.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Meyboom, Ronald
    Ericsson, Jenny
    Farah, Mohamed
    Farmacovigilantie van fytotherapeutica door het Uppsala Monitoring Centre2004In: Nederlands Tijdschrift voor Fytotherapie, Vol. 17, no 4, p. 2-4Article in journal (Other academic)
  • 260.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Nat Biodivers Ctr, Leiden, Netherlands; Univ Oslo, Nat Hist Museum, Oslo, Norway.
    Ouarghidi, Abderrahim
    Cadi Ayyad Univ, Fac Sci Semlalia, Marrakech, Morocco; Global Div Fdn, Marrakech, Morocco.
    Martin, Gary
    Cadi Ayyad Univ, Fac Sci Semlalia, Marrakech, Morocco; Global Div Fdn, Marrakech, Morocco.
    Abbad, Abdelaziz
    Cadi Ayyad Univ, Fac Sci Semlalia, Marrakech, Morocco; Global Div Fdn, Marrakech, Morocco.
    Kool, Anneleen
    Univ Oslo, Nat Hist Museum, Oslo, Norway.
    DNA Barcoding Reveals Limited Accuracy of Identifications Based on Folk Taxonomy2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 1, article id e84291Article in journal (Refereed)
    Abstract [en]

    Background:

    The trade of plant roots as traditional medicine is an important source of income for many people around theworld. Destructive harvesting practices threaten the existence of some plant species. Harvesters of medicinal roots identifythe collected species according to their own folk taxonomies, but once the dried or powdered roots enter the chain ofcommercialization, accurate identification becomes more challenging.

    Methodology:

    A survey of morphological diversity among four root products traded in the medina of Marrakech wasconducted. Fifty-one root samples were selected for molecular identification using DNA barcoding using three markers,trnH-psbA, rpoC1, and ITS. Sequences were searched using BLAST against a tailored reference database of Moroccanmedicinal plants and their closest relatives submitted to NCBI GenBank.Principal Findings: Combining psbA-trnH, rpoC1, and ITS allowed the majority of the market samples to be identified tospecies level. Few of the species level barcoding identifications matched the scientific names given in the literature,including the most authoritative and widely cited pharmacopeia.

    Conclusions/Significance:

    The four root complexes selected from the medicinal plant products traded in Marrakech allcomprise more than one species, but not those previously asserted. The findings have major implications for the monitoringof trade in endangered plant species as morphology-based species identifications alone may not be accurate. As a result,trade in certain species may be overestimated, whereas the commercialization of other species may not be recorded at all.

  • 261.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Schaefer, Hanno
    Harvard University, Department of Organismic and Evolutionary Biology.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Renner, Susanne S.
    University of Munich (LMU), Systematic Botany and Mycology.
    Evolution and loss of long-fringed petals: A case study using a dated phylogeny of the snake gourds, Trichosanthes (Cucurbitaceae)2012In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 12, p. 108-Article in journal (Refereed)
    Abstract [en]

    Background

    The Cucurbitaceae genus Trichosanthes comprises 90–100 species that occur from India to Japan and southeast to Australia and Fiji. Most species have large white or pale yellow petals with conspicuously fringed margins, the fringes sometimes several cm long. Pollination is usually by hawkmoths. Previous molecular data for a small number of species suggested that a monophyletic Trichosanthes might include the Asian genera Gymnopetalum (four species, lacking long petal fringes) and Hodgsonia (two species with petals fringed). Here we test these groups’ relationships using a species sampling of c. 60% and 4759 nucleotides of nuclear and plastid DNA. To infer the time and direction of the geographic expansion of the Trichosanthes clade we employ molecular clock dating and statistical biogeographic reconstruction, and we also address the gain or loss of petal fringes.

    Results

    Trichosanthes is monophyletic as long as it includes Gymnopetalum, which itself is polyphyletic. The closest relative of Trichosanthes appears to be the sponge gourds, Luffa, while Hodgsonia is more distantly related. Of six morphology-based sections in Trichosanthes with more than one species, three are supported by the molecular results; two new sections appear warranted. Molecular dating and biogeographic analyses suggest an Oligocene origin of Trichosanthes in Eurasia or East Asia, followed by diversification and spread throughout the Malesian biogeographic region and into the Australian continent.

    Conclusions

    Long-fringed corollas evolved independently in Hodgsonia and Trichosanthes, followed by two losses in the latter coincident with shifts to other pollinators but not with long-distance dispersal events. Together with the Caribbean Linnaeosicyos, the Madagascan Ampelosicyos and the tropical African Telfairia, these cucurbit lineages represent an ideal system for more detailed studies of the evolution and function of petal fringes in plant-pollinator mutualisms.

  • 262.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Steffen, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Wendy, Cooper
    Sunda to Sahul dispersals in Trichosanthes (Cucurbitaceae): a dated phylogeny reveals five independent dispersal events to Australasia2015In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 42, no 3, p. 519-531Article in journal (Refereed)
    Abstract [en]

    AimThe Cucurbitaceae genus Trichosanthes is widespread in Asia and Australia, and previous studies have shown that the genus originated in Asia, and that three independent lineages dispersed through the Sunda archipelago to Australasia. The timing and routes of these three dispersals, as well as the dispersal of two widespread species found in Australia and New Guinea, were investigated. LocationSunda-Sahul dispersals with a focus on New Guinea and Australia. MethodsA combined dataset of nuclear ribosomal (ITS1-5.8S-ITS2) and plastid DNA (matK, ndhF, rpl20-rps12, rps16) was used for maximum likelihood and Bayesian phylogenetic analysis to infer the relationships of the studied taxa. A fossil-calibrated molecular dating was used to time the dispersal events, and a biogeographical analysis was used to study the origin and dispersal of the genus. ResultsThe two widespread species, T. pilosa and T. cucumerina, form monophyletic groups in Australia, suggesting single dispersals. Molecular dating analysis dates four of the dispersal events to the Miocene, and two to the Oligo-Miocene boundary and the initial Sahul shelf collision with the Philippine plate. Most known Sahul-Philippine dispersals concern species that migrated from the Sahul shelf, whereas dispersals south are fewer. Southward Miocene dispersals include species that were present on the Sunda shelf before the tectonic formation of the Makassar Straits. All lineages that dispersed to Australasia have undergone extensive diversification following dispersal. Lineages adapted to wet tropical climates have speciated mostly in New Guinea, and lineages adapted to monsoon tropical climates have speciated mostly in northern Australia. Main conclusionsDispersals in Trichosanthes pre-date human colonization of Australasia, suggesting natural long-distance dispersal and establishment of all lineages. Diversification within lineages found in both Australia and New Guinea is limited, corroborating frequent land connections between these areas during the Pleistocene. Sunda-Sahul dispersals are likely to have been more common through time than previously suggested, especially in genera with floating fruit such as Trichosanthes.

  • 263.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Synopsis of Trichosanthes (Cucurbitaceae) based on recent molecular phylogenetic data2012In: PhytoKeys, ISSN 1314-2011, E-ISSN 1314-2003, Vol. 12, p. 23-33Article in journal (Refereed)
    Abstract [en]

    The snake gourd genus, Trichosanthes, is the largest genus in the Cucurbitaceae family, with over 90 species. Recent molecular phylogenetic data have indicated that the genus Gymnopetalum is to be merged with Trichosanthes to maintain monophyly. A revised infrageneric classification of Trichosanthes including Gymnopetalum is proposed with two subgenera, (I) subg. Scotanthus comb. nov. and (II) subg. Trichosanthes, eleven sections, (i) sect. Asterospermae, (ii) sect. Cucumeroides, (iii) sect. Edulis, (iv) sect. Foliobracteola, (v) sect. Gymnopetalum, (vi) sect. Involucraria, (vii) sect. Pseudovariifera sect. nov., (viii) sect. Villosae star. nov., (ix) sect. Trichosanthes, (x) sect. Tripodanthera, and (xi) sect. Truncata. A synopsis of Trichosanthes with the 91 species recognized here is presented, including four new combinations, Trichosanthes orientalis, Trichosanthes tubiflora, Trichosanthes scabra var. pectinata, Trichosanthes scabra var. penicaudii, and a clarified nomenclature of Trichosanthes costata and Trichosanthes scabra.

  • 264.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Virapongse, Arika
    Workshop: Student Network: Society for Economic Botany Annual Meeting2006Conference paper (Other (popular science, discussion, etc.))
    Abstract [en]

    Student members of the SEB hold a networking mixer each year in order to meet each other and to become acquainted with a variety of educational programs and faculty advisors. Faculty members who are part of training programs are encouraged to join the mixer to meet and talk with students.

  • 265.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Vongsombath, Chanda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Käfer, Jos
    A Fly in the Ointment: Evaluation of Traditional Use of Plants to Repel and Kill Blowfly Larvae in Fermented Fish2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 12, article id e29521Article in journal (Refereed)
    Abstract [en]

    Introduction: In rural areas in Laos, fly larvae infestations are common in fermenting fish. Blowflies (Chrysomyamegacephala, Diptera: Calliphoridae) are attracted to oviposit (and/or larviposit) onto fermenting fish which results ininfestations with fly larvae. Knowledge of traditional use of plants to repel larvae during the production of fermented fish iscommon and widespread in Lao PDR.

    Research Questions: How effective are the most salient species in repelling, and killing fly larvae in fermenting fish?

    Material and Methods: The three plant species most frequently reported to repel fly larvae during an ethnobotanical surveythroughout Lao PDR were tested for repellence and larvicidal activity of fly larvae infesting fermented fish. The lethality andrepellence of Tadehagi triquetrum (L.) H. Ohashi (Fabaceae), Uraria crinita (L.) Desv. ex DC. (Fabaceae) and Bambusa multiplex(Lour.) Raeusch. ex Schult. & Schult. f. (Poaceae) were tested in an experimental design using fermenting fish in Vientiane,Lao PDR.

    Results: The repellent effect of fresh material of T. triquetrum and U. crinita, and the larvicidal effect of fresh B. multiplex, issignificantly more effective than that of dried material of the same species, and the total effect (repellence and larvicidaleffect combined) for each of the three species was significantly more effective for fresh than for dry material. Fresh materialof T. triquetrum, U. crinita, or B. multiplex added on top of the fermenting fish repelled 50%, 54%, 37%, and killed 22%, 28%,and 40% of fly larvae. The total effect was not significantly different per species at 72%, 82%, and 77%, respectively.

    Discussion and Conclusions: The three most salient species are effective in repelling and killing fly larvae in the productionof fermented fish, and may be essential to augment food safety during traditional fermentation in open jars.

  • 266.
    de Boer, Hugo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Oslo, Nat Hist Museum, POB 1172 Blindern, Oslo, Norway.
    Newman, Mark
    Royal Bot Garden Edinburgh, Edinburgh, Midlothian, Scotland.
    Poulsen, Axel Dalberg
    Univ Oslo, Nat Hist Museum, POB 1172 Blindern, Oslo, Norway; Royal Bot Garden Edinburgh, Edinburgh, Midlothian, Scotland.
    Droop, A. Jane
    Royal Bot Garden Edinburgh, Edinburgh, Midlothian, Scotland.
    Fer, Tomas
    Charles Univ Prague, Fac Sci, Dept Bot, Prague, Czech Republic.
    Hien, Le Thi Thu
    Vietnam Acad Sci & Technol, Inst Genome Res, Hanoi, Vietnam.
    Hlavata, Kristyna
    Charles Univ Prague, Fac Sci, Dept Bot, Prague, Czech Republic.
    Lamxay, Vichith
    Natl Univ Laos, Fac Nat Sci, Dept Biol, Dong Dok, Vientiane, Laos.
    Richardson, James E.
    Royal Bot Garden Edinburgh, Edinburgh, Midlothian, Scotland; Univ Rosario, Programa Biol, Carrera, Bogota, Colombia.
    Steffen, Karin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Leong-Skornickova, Jana
    Singapore Bot Gardens, Natl Parks Board, Herbarium, Singapore, Singapore.
    Convergent morphology in Alpinieae (Zingiberaceae): Recircumscribing Amomum as a monophyletic genus2018In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 67, no 1, p. 6-36Article in journal (Refereed)
    Abstract [en]

    The tropical ginger genus Amomum (Zingiberaceae) has always posed challenges for classification based on morphological characters. Previous molecular phylogenetic studies showed Amomum to be paraphyletic but limited sampling and absence of the data of the type Amomum subulatum made it impossible to resolve the paraphyly and make nomenclatural changes. Here, Amomum is further investigated in a multi-marker phylogenetic framework using matK and nrITS including multiple accessions of the type, the genus Elettaria and additional accessions of Amomum, Alpinia, Elettariopsis, Geocharis, Geostachys and Hornstedtia. Amomum is shown to consist of nine clades and Alpinia of six. The genera Elettaria, Elettariopsis, Plagiostachys, and species in Hornstedtia are nested within these clades. Morphological studies of species previously subsumed in Amomum support recognition of new genera that correspond to well-delimited clades in the phylogenetic framework presented here. Recircumscription of the paraphyletic genus Amomum facilitates identification and creates nomenclatural stability. Three genera, Conamomum, Meistera and Wurfbainia, are resurrected, and three new genera Epiamomum, Lanxangia and Sundamomum are described, together with a key to the genera and a nomenclatural synopsis placing 384 specific names (incl. all synonyms) into the new generic framework. Of these 129 represent new combinations and 3 are replacement names. Types of Geocharis and Geostachys are designated. Further studies and specific sampling will be needed to resolve other branches of Alpinioideae containing other polyphyletic genera.

  • 267. de Vries, Jan
    et al.
    Fischer, Angela Melanie
    Roettger, Mayo
    Rommel, Sophie
    Schluepmann, Henriette
    Bräutigam, Andrea
    Carlsbecker, Annelie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    Gould, Sven Bernhard
    Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots.2016In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 209, no 2, p. 705-720Article in journal (Refereed)
    Abstract [en]

    The phytohormones cytokinin and auxin orchestrate the root meristem development in angiosperms by determining embryonic bipolarity. Ferns, having the most basal euphyllophyte root, form neither bipolar embryos nor permanent embryonic primary roots but rather an adventitious root system. This raises the questions of how auxin and cytokinin govern fern root system architecture and whether this can tell us something about the origin of that root. Using Azolla filiculoides, we characterized the influence of IAA and zeatin on adventitious fern root meristems and vasculature by Nomarski microscopy. Simultaneously, RNAseq analyses, yielding 36 091 contigs, were used to uncover how the phytohormones affect root tip gene expression. We show that auxin restricts Azolla root meristem development, while cytokinin promotes it; it is the opposite effect of what is observed in Arabidopsis. Global gene expression profiling uncovered 145 genes significantly regulated by cytokinin or auxin, including cell wall modulators, cell division regulators and lateral root formation coordinators. Our data illuminate both evolution and development of fern roots. Promotion of meristem size through cytokinin supports the idea that root meristems of euphyllophytes evolved from shoot meristems. The foundation of these roots was laid in a postembryonically branching shoot system.

  • 268.
    Debiais-Thibaud, Melanie
    et al.
    Univ Montpellier, EPHE, CNRS, ISEM,IRD, Montpellier, France.
    Simion, Paul
    Univ Montpellier, EPHE, CNRS, ISEM,IRD, Montpellier, France.
    Venteo, Stephanie
    Univ Montpellier, St Eloi Hosp, Neurosci Inst Montpellier, Inserm UMR1051, Montpellier, France.
    Munoz, David
    Univ Concepcion, Fac Biol Sci, Dept Cell Biol, Concepcion, Chile.
    Marcellini, Sylvain
    Univ Concepcion, Fac Biol Sci, Dept Cell Biol, Concepcion, Chile.
    Mazan, Sylvie
    UPMC, Observ Oceanol, Sorbonne Univ, CNRS,UMR7232 Biol Integrat Organismes Marins, Banyuls Sur Mer, France.
    Haitina, Tatjana
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Skeletal Mineralization in Association with Type X Collagen Expression Is an Ancestral Feature for Jawed Vertebrates2019In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 10, p. 2265-2276Article in journal (Refereed)
    Abstract [en]

    In order to characterize the molecular bases of mineralizing cell evolution, we targeted type X collagen, a nonfibrillar network forming collagen encoded by the Col10a1 gene. It is involved in the process of endochondral ossification in ray-finned fishes and tetrapods (Osteichthyes), but until now unknown in cartilaginous fishes (Chondrichthyes). We show that holocephalans and elasmobranchs have respectively five and six tandemly duplicated Col10a1 gene copies that display conserved genomic synteny with osteichthyan Col10a1 genes. All Col10a1 genes in the catshark Scyliorhinus canicula are expressed in ameloblasts and/or odontoblasts of teeth and scales, during the stages of extracellular matrix protein secretion and mineralization. Only one duplicate is expressed in the endoskeletal (vertebral) mineralizing tissues. We also show that the expression of type X collagen is present in teeth of two osteichthyans, the zebrafish Danio rerio and the western clawed frog Xenopus tropicalis, indicating an ancestral jawed vertebrate involvement of type X collagen in odontode formation. Our findings push the origin of Col10a1 gene prior to the divergence of osteichthyans and chondrichthyans, and demonstrate its ancestral association with mineralization of both the odontode skeleton and the endoskeleton.

  • 269.
    Defourny, Jean
    et al.
    Univ Liege, Unit Cell & Tissue Biol, GIGA Neurosci, CHU B36, B-4000 Liege, Belgium;Univ Liege, Dev Neurobiol Unit, GIGA Neurosci, CHU B36, B-4000 Liege, Belgium.
    Peuckert, Christiane
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Kullander, Klas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Malgrange, Brigitte
    Univ Liege, Dev Neurobiol Unit, GIGA Neurosci, CHU B36, B-4000 Liege, Belgium.
    EphA4-ADAM10 Interplay Patterns the Cochlear Sensory Epithelium through Local Disruption of Adherens Junctions2019In: ISCIENCE, ISSN 2589-0042, Vol. 11, p. 246-257Article in journal (Refereed)
    Abstract [en]

    The cochlear sensory epithelium contains a functionally important triangular fluid-filled space between adjacent pillar cells referred to as the tunnel of Corti. However, the molecular mechanisms leading to local cell-cell separation during development remain elusive. Here we show that EphA4 associates with ADAM10 to promote the destruction of E-cadherin-based adhesions between adjacent pillar cells. These cells fail to separate from each other, and E-cadherin abnormally persists at the pillar cell junction in EphA4 forward-signaling-deficient mice, as well as in the presence of ADAM10 inhibitor. Using immunolabeling and an in situ proximity ligation assay, we found that EphA4 forms a complex with E-cadherin and its sheddase ADAM10, which could be activated by ephrin-B2 across the pillar cell junction to trigger the cleavage of E-cadherin. Altogether, our findings provide a new molecular insight into the regulation of adherens junctions, which might be extended to a variety of physiological or pathological processes.

  • 270. Delgado-Salinas, Alfonso
    et al.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Pasquet, Rémy
    Weeden, Norm
    Lavin, Matt
    Vigna (Leguminosae) sensu lato: The names and identities of the American segregate2011In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 98, no 10, p. 1694-1715Article in journal (Refereed)
    Abstract [en]

    Premise of study: The legume genus Vigna and close relatives have highly elaborated floral morphologies that involve the coiling, bending, and intricate connection of flower parts. Banners, levers, platforms, and pumps have evolved that attract pollinators and then manipulate their movement. Given this three-dimensional floral complexity, the taxonomy of Vigna and relatives has been confounded by the study of mostly two-dimensional museum specimens. A molecular phylogenetic analysis was undertaken in the effort to resolve long-standing taxonomic questions centered on floral morphology.

    Methods: The phylogenetic analysis included cpDNA trnK and nuclear ribosomal ITS/5.8S (ITS) sequence variation. The American species were comprehensively sampled and outgroups included Old World relatives.

    Key results: The trnK and ITS data analyses concurred in resolving six well-supported clades of American Vigna that are most closely related to other American genera: Dolichopsis, Macroptilium, Mysanthus, Oryxis, Oxyrhynchus, Phaseolus, Ramirezella, and Strophostyles. These 14 American clades ranked here as genera are resolved as sister to a clade comprising the mainly Old World species of Vigna.

    Conclusions: American Vigna clades were reassigned to the genera Ancistrotropis, Cochliasanthus, Condylostylis, Leptospron, Sigmoidotropis, and the newly described Helicotropis. Vigna sensu stricto in the Americas now includes relatively few and mostly pantropical species. Elaborate floral asymmetries are readily used to apomorphically diagnose nearly all of the American genera. The age estimates of the extant diversification of the American and its Old World sister clade are approximately coeval at ca. 6–7 million yr, which belies much greater floral variation in the Americas.

  • 271. Delgado-Salinas, Alfonso
    et al.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Pasquet, Rémy
    Weeden, Norm
    Lavin, Matt
    Vigna (Leguminosae) sensu lato: The names and identities of the American segregate genera2011In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 98, no 10, p. 1694-1715Article in journal (Refereed)
    Abstract [en]

    Premise of study: The legume genus Vigna and close relatives have highly elaborated floral morphologies that involve the coiling, bending, and intricate connection of flower parts. Banners, levers, platforms, and pumps have evolved that attract pollinators and then manipulate their movement. Given this three-dimensional floral complexity, the taxonomy of Vigna and relatives has been confounded by the study of mostly two-dimensional museum specimens. A molecular phylogenetic analysis was undertaken in the effort to resolve long-standing taxonomic questions centered on floral morphology. Methods: The phylogenetic analysis included cpDNA trnK and nuclear ribosomal ITS/5.8S (ITS) sequence variation. The American species were comprehensively sampled and outgroups included Old World relatives. Key results: The trnK and ITS data analyses concurred in resolving six well-supported clades of American Vigna that are most closely related to other American genera: Dolichopsis, Macroptilium, Mysanthus, Oryxis, Oxyrhynchus, Phaseolus, Ramirezella, and Strophostyles. These 14 American clades ranked here as genera are resolved as sister to a clade comprising the mainly Old World species of Vigna. Conclusions: American Vigna clades were reassigned to the genera Ancistrotropis, Cochliasanthus, Condylostylis, Leptospron, Sigmoidotropis, and the newly described Helicotropis. Vigna sensu stricto in the Americas now includes relatively few and mostly pantropical species. Elaborate floral asymmetries are readily used to apomorphically diagnose nearly all of the American genera. The age estimates of the extant diversification of the American and its Old World sister clade are approximately coeval at ca. 6-7 million yr, which belies much greater floral variation in the Americas.

  • 272.
    Den Boer, Wendy
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Swedish Nat Hist Museum, Dept Palaeobiol, S-10405 Stockholm, Sweden.
    Campione, Nicolás E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Univ New England, Palaeosci Res Ctr, Sch Environm & Rural Sci, Armidale, NSW 2531, Australia.
    Kear, Benjamin P.
    Uppsala University, Music and Museums, Museum of Evolution.
    Climbing adaptations, locomotory disparity and ecological convergence in ancient stem 'kangaroos'2019In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 6, no 2, article id 181617Article in journal (Refereed)
    Abstract [en]

    Living kangaroos, wallabies and rat-kangaroos (Macropodoidea) constitute the most ecologically diverse radiation of Australasian marsupials. Indeed, even their hallmark bipedal hopping gait has been variously modified for bounding, walking and climbing. However, the origins of this locomotory adaptability are uncertain because skeletons of the most ancient macropodoids are exceptionally rare. Some of the stratigraphically oldest fossils have been attributed to Balbaridae-a clade of potentially quadrupedal stem macropodoids that became extinct during the late Miocene. Here we undertake the first assessment of balbarid locomotion using two-dimensional geometric morphometrics and a correlative multivariate analysis of linear measurements. We selected the astragalus and pedal digit IV ungual as proxies for primary gait because these elements are preserved in the only articulated balbarid skeleton, as well as some unusual early Miocene balbarid-like remains that resemble the bones of modern tree-kangaroos. Our results show that these fossils manifest character states indicative of contrasting locomotory capabilities. Furthermore, predictive modelling reveals similarities with extant macropodoids that employ either bipedal saltation and/or climbing. We interpret this as evidence for archetypal gait versatility, which probably integrated higher-speed hopping with slower-speed quadrupedal progression and varying degrees of scansoriality as independent specializations for life in forest and woodland settings.

  • 273.
    Deng, Pan
    et al.
    Huazhong Univ Sci & Technol, State Key Lab Digital Mfg Equipment & Technol, Wuhan, Hubei, Peoples R China.
    Fu, Cheng-Jie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Wu, Zhigang
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Microsystems Technology. Huazhong Univ Sci & Technol, State Key Lab Digital Mfg Equipment & Technol, Wuhan, Hubei, Peoples R China.
    High purity and viability cell separation of a bacterivorous jakobid flagellate based on a steep velocity gradient induced soft inertial force2018In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 8, no 62, p. 35512-35520Article in journal (Refereed)
    Abstract [en]

    Cell separation is one of the key limiting factors for precise analysis of non-axenic microbial lab cultures or environmental samples, and it remains a challenge to isolate target cells with high purity and viability via high-throughput cell sorting. During the past decade, hydrodynamic microfluidic platforms have attracted great attention in cell preparation for their high efficiency, robust performance and low cost. Here, we employ the use of a low-velocity sheath flow with high viscosity near the wall and a high-velocity sheath flow with low viscosity on the other side of the sample flow in a soft inertial separation chip. This not only prevents hard interactions between cells and chip walls but, in comparison to previous inertial separation methods, generates a significant increase in deflection of large cells while keeping the small ones in the original flow. We first conducted experiments on a mixture of small and large fluorescent particles (1.0 and 9.9 m, respectively) and removed over 99% of the small particles. The separation efficiency was then tested on a culture of a bacterivorous jakobid flagellate, Seculamonas ecuadoriensis fed on the live bacterium, Klebsiella sp. Using our microfluidic chip, over 94% of live bacteria were removed while maintaining high jakobid cell viability. For comparison, we also conducted size-based cell sorting of the same culture using flow cytometry, which is widely used as a rapid and automated separation tool. Compared with the latter, our chip showed more than 40% higher separation efficiency. Thus, our device provides high purity and viability for cell separation of a sensitive cell sample (jakobid cells). Potentially, the method can be further used for applications in diagnostics, biological analyses and environmental assessment of mixed microbial samples.

  • 274.
    Dhillon, Sundeep S.
    et al.
    Univ Birmingham, Coll Med & Dent Sci, Sch Clin & Expt Med, Birmingham, W Midlands, England.
    Torell, Frida
    Umea Univ, Dept Chem, Computat Life Sci Cluster CLiC, Umea, Sweden;Karlsruhe Inst Technol, Accelerator Lab ACL, Karlsruhe, Germany;AcureOmics, Umea, Sweden.
    Donten, Magdalena
    AcureOmics, Umea, Sweden.
    Lundstedt-Enkel, Katrin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology. AcureOmics, Umea, Sweden.
    Bennett, Kate
    AcureOmics, Umea, Sweden.
    Raennar, Stefan
    AcureOmics, Umea, Sweden;Sartorius AG, Corp Res, Gottingen, Germany.
    Trygg, Johan
    Umea Univ, Dept Chem, Computat Life Sci Cluster CLiC, Umea, Sweden;Sartorius AG, Corp Res, Gottingen, Germany.
    Lundstedt, Torbjörn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. AcureOmics, Umea, Sweden.
    Metabolic profiling of zebrafish embryo development from blastula period to early larval stages2019In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, no 5, article id e0213661Article in journal (Refereed)
    Abstract [en]

    The zebrafish embryo is a popular model for drug screening, disease modelling and molecular genetics. In this study, samples were obtained from zebrafish at different developmental stages. The stages that were chosen were 3/4, 4/5, 24, 48, 72 and 96 hours post fertilization (hpf). Each sample included fifty embryos. The samples were analysed using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). Principle component analysis (PCA) was applied to get an overview of the data and orthogonal projection to latent structure discriminant analysis (OPLS-DA) was utilised to discriminate between the developmental stages. In this way, changes in metabolite profiles during vertebrate development could be identified. Using a GC-TOF-MS metabolomics approach it was found that nucleotides and metabolic fuel (glucose) were elevated at early stages of embryogenesis, whereas at later stages amino acids and intermediates in the Krebs cycle were abundant. This agrees with zebrafish developmental biology, as organs such as the liver and pancreas develop at later stages. Thus, metabolomics of zebrafish embryos offers a unique opportunity to investigate large scale changes in metabolic processes during important developmental stages in vertebrate development. In terms of stability of the metabolic profile and viability of the embryos, it was concluded at 72 hpf was a suitable time point for the use of zebrafish as a model system in numerous scientific applications.

  • 275.
    Di Paolo, Antonello
    et al.
    Univ Pisa, Sect Pharmacol, Dept Clin & Expt Med, Via Roma 55, I-56126 Pisa, Italy.
    Sarkozy, Francois
    FSNB Hlth & Care, Carenity, Paris, France.
    Ryll, Bettina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Melanoma Patient Network Europe.
    Siebert, Uwe
    UMIT Univ Hlth Sci Med Informat & Technol, Dept Publ Hlth Hlth Serv Res & Hlth Technol Asses, Hall In Tirol, Austria.;ONCOTYROL Ctr Personalized Canc Med, Area Hlth Technol Assessment, Innsbruck, Austria..
    Personalized medicine in Europe: not yet personal enough?2017In: BMC Health Services Research, ISSN 1472-6963, E-ISSN 1472-6963, Vol. 17, article id 289Article in journal (Refereed)
    Abstract [en]

    Background: Personalized medicine has the potential to allow patients to receive drugs specific to their individual disease, and to increase the efficiency of the healthcare system. There is currently no comprehensive overview of personalized medicine, and this research aims to provide an overview of the concept and definition of personalized medicine in nine European countries. Methods: A targeted literature review of selected health databases and grey literature was conducted to collate information regarding the definition, process, use, funding, impact and challenges associated with personalized medicine. In-depth qualitative interviews were carried out with experts with health technology assessment, clinical provisioning, payer, academic, economic and industry experience, and with patient organizations. Results: We identified a wide range of definitions of personalized medicine, with most studies referring to the use of diagnostics and individual biological information such as genetics and biomarkers. Few studies mentioned patients' needs, beliefs, behaviour, values, wishes, utilities, environment and circumstances, and there was little evidence in the literature for formal incorporation of patient preferences into the evaluation of new medicines. Most interviewees described approaches to stratification and segmentation of patients based on genetic markers or diagnostics, and few mentioned health-related quality of life. Conclusions: The published literature on personalized medicine is predominantly focused on patient stratification according to individual biological information. Although these approaches are important, incorporation of environmental factors and patients' preferences in decision making is also needed. In future, personalized medicine should move from treating diseases to managing patients, taking into account all individual factors.

  • 276. Diao, Yupu
    et al.
    Lu, Anrui
    Yang, Bing
    Hu, Wenli
    Peng, Qing
    Ling, Qing-Zhi
    Beerntsen, Brenda T.
    Söderhäll, Kenneth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology.
    Ling, Erjun
    Existence of Prophenoloxidase in Wing Discs: A Source of Plasma Prophenoloxidase in the Silkworm, Bombyx mori2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 7, p. e41416-Article in journal (Refereed)
    Abstract [en]

    In insects, hemocytes are considered as the only source of plasma prophenoloxidase (PPO). PPO also exists in the hemocytes of the hematopoietic organ that is connected to the wing disc of Bombyx mori. It is unknown whether there are other cells or tissues that can produce PPO and release it into the hemolymph besides circulating hemocytes. In this study, we use the silkworm as a model to explore this possibility. Through tissue staining and biochemical assays, we found that wing discs contain PPO that can be released into the culture medium in vitro. An in situ assay showed that some cells in the cavity of wing discs have PPO1 and PPO2 mRNA. We conclude that the hematopoietic organ may wrongly release hemocytes into wing discs since they are connected through many tubes as repost in previous paper. In wing discs, the infiltrating hemocytes produce and release PPO probably through cell lysis and the PPO is later transported into hemolymph. Therefore, this might be another source of plasma PPO in the silkworm: some infiltrated hemocytes sourced from the hematopoietic organ release PPO via wing discs.

  • 277.
    Dierker, Tabea
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Shao, Chun
    Boston Univ, Dept Biochem, Ctr Biomed Mass Spectrometry, Med Campus, Boston, MA 02215 USA..
    Haitina, Tatjana
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zaia, Joseph
    Boston Univ, Dept Biochem, Ctr Biomed Mass Spectrometry, Med Campus, Boston, MA 02215 USA..
    Hinas, Andrea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Kjellén, Lena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Nematodes join the family of chondroitin sulfate-synthesizing organisms: Identification of an active chondroitin sulfotransferase in Caenorhabditis elegans2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 34662Article in journal (Refereed)
    Abstract [en]

    Proteoglycans are proteins that carry sulfated glycosaminoglycans (GAGs). They help form and maintain morphogen gradients, guiding cell migration and differentiation during animal development. While no sulfated GAGs have been found in marine sponges, chondroitin sulfate (CS) and heparan sulfate (HS) have been identified in Cnidarians, Lophotrocozoans and Ecdysozoans. The general view that nematodes such as Caenorhabditis elegans, which belong to Ecdysozoa, produce HS but only chondroitin without sulfation has therefore been puzzling. We have analyzed GAGs in C. elegans using reversed-phase ion-pairing HPLC, mass spectrometry and immunohistochemistry. Our analyses included wild type C. elegans but also a mutant lacking two HS sulfotransferases (hst-6 hst-2), as we suspected that the altered HS structure could boost CS sulfation. We could indeed detect sulfated CS in both wild type and mutant nematodes. While 4-O-sulfation of galactosamine dominated, we also detected 6-O-sulfated galactosamine residues. Finally, we identified the product of the gene C41C4.1 as a C. elegans CS-sulfotransferase and renamed it chst-1 (CarboHydrate SulfoTransferase) based on loss of CS-4-O-sulfation in a C41C4.1 mutant and in vitro sulfotransferase activity of recombinant C41C4.1 protein. We conclude that C. elegans indeed manufactures CS, making this widely used nematode an interesting model for developmental studies involving CS.

  • 278. Dillman, Karen L.
    et al.
    Ahti, Teuvo
    Bjoerk, Curtis R.
    Clerc, Philippe
    Ekman, Stefan
    Uppsala University, Music and Museums, Museum of Evolution.
    Goward, Trevor
    Hafellner, Josef
    Perez-Ortega, Sergio
    Printzen, Christian
    Savic, Sanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Schultz, Matthias
    Svensson, Mans
    Thor, Goran
    Tonsberg, Tor
    Vitikainen, Orvo
    Westberg, Martin
    Spribille, Toby
    New records, range extensions and nomenclatural innovations for lichens and lichenicolous fungi from Alaska, USA2012In: Herzogia, ISSN 0018-0971, Vol. 25, no 2, p. 177-210Article in journal (Refereed)
    Abstract [en]

    New records, range extensions and nomenclatural innovations for lichens and lichenicolous fungi from Alaska, U.S.A. - Herzogia 25: 177-210. Surveys of lichens and lichenicolous fungi have been taking place in the U.S. state of Alaska for more than 160 years, but until now assessing the full extent of their diversity has been hampered by the lack of a comprehensive and synonymized baseline inventory. In this paper we will begin to redress this by resolving outstanding nomenclatural issues and providing voucher data for a forthcoming catalog of Alaskan lichens, specifically: 1) synonymization,and/or resolution of status of species previously reported from Alaska, with emphasis on Alaskan types; 2) species new to the Alaska lichen biota; and 3) biogeographically significant new records from within Alaska. We report 91 species new to the flora of Alaska, including 65 lichens, three saprophytic calicioid fungi and 23 lichenicolous fungi. Of these, we report thirteen species, Biatora sphaeroidiza, Biatorella conspurcans, Chaenothecopsis arthoniae, Collemopsidium foveolatum, Dactylospora frigida, Halospora discrepans, Lecanora bryopsora, Opegrapha geographicola, Peltigera lyngei, Petractis clausa, Protoblastenia cyclospora, Thelocarpon impressellum and Usnea cylindrica as new to North America. In addition, Arthonia pruinata and Flavocetraria minuscula are new to Canada and Adelococcus alpestris new to the United States. We further place the following five names into synonymy: Lecania disceptans (Nyl.) Lynge [= Halecania alpivaga (Th.Fr.) M.Mayrhofer], Lecidea pallidella Nyl. [= Lecania subfuscula (Nyl.) S.Ekman], Lempholemma triptodes (Nyl.) Zahlbr. Leciophysma finmarkicum Th.Fr.), Polyblastia obtenta (Nyl.) Lynge [= Sporodictyon terrestre (Th.Fr.) S.Savic & Tibell], and Verrucaria pernigrata Nyl. [= Protothelenella sphinctrinoides (Nyl.) H.Mayrhofer & Poelt]. We propose restoring the long overlooked taxon Polyblastia exalbida (Nyl.) Zahlbr., currently known only from Alaska, to the North American lichen checklist. Finally, we propose the new combination Puttea caesia (Fr.) M.Svensson & T.Sprib. to replace Lecidea symmictella Nyl., which becomes a synonym.

  • 279.
    Dirks-Mulder, Anita
    et al.
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Butot, Roland
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands..
    van Schaik, Peter
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Wijnands, Jan Willem P. M.
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    van den Berg, Roel
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Krol, Louie
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Doebar, Sadhana
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    van Kooperen, Kelly
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Oslo, Nat Hist Museum, POB 1172 Blindern, N-0318 Oslo, Norway..
    Kramer, Elena M.
    Harvard Univ, Dept Organism & Evolutionary Biol, 16 Div Ave, Cambridge, MA 02138 USA..
    Smets, Erik F.
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Katholieke Univ Leuven, Ecol Evolut & Biodivers Conservat cluster, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium..
    Vos, Rutger A.
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Amsterdam, Inst Biodivers & Ecosyst Dynam, Sci Pk 904, NL-1098 XH Amsterdam, Netherlands..
    Vrijdaghs, Alexander
    Katholieke Univ Leuven, Ecol Evolut & Biodivers Conservat cluster, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium..
    Gravendeel, Barbara
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands.;Leiden Univ, Inst Biol, Sylviusweg 72, NL-2333 BF Leiden, Netherlands..
    Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 89Article in journal (Refereed)
    Abstract [en]

    Background: Thousands of flowering plant species attract pollinators without offering rewards, but the evolution of this deceit is poorly understood. Rewardless flowers of the orchid Erycina pusilla have an enlarged median sepal and incised median petal ('lip') to attract oil-collecting bees. These bees also forage on similar looking but rewarding Malpighiaceae flowers that have five unequally sized petals and gland-carrying sepals. The lip of E. pusilla has a 'callus' that, together with winged 'stelidia', mimics these glands. Different hypotheses exist about the evolutionary origin of the median sepal, callus and stelidia of orchid flowers. Results: The evolutionary origin of these organs was investigated using a combination of morphological, molecular and phylogenetic techniques to a developmental series of floral buds of E. pusilla. The vascular bundle of the median sepal indicates it is a first whorl organ but its convex epidermal cells reflect convergence of petaloid features. Expression of AGL6 EpMADS4 and APETALA3 EpMADS14 is low in the median sepal, possibly correlating with its petaloid appearance. A vascular bundle indicating second whorl derivation leads to the lip. AGL6 EpMADS5 and APETALA3 EpMADS13 are most highly expressed in lip and callus, consistent with current models for lip identity. Six vascular bundles, indicating a stamen-derived origin, lead to the callus, stelidia and stamen. AGAMOUS is not expressed in the callus, consistent with its sterilization. Out of three copies of AGAMOUS and four copies of SEPALLATA, EpMADS22 and EpMADS6 are most highly expressed in the stamen. Another copy of AGAMOUS, EpMADS20, and the single copy of SEEDSTICK, EpMADS23, are most highly expressed in the stelidia, suggesting EpMADS22 may be required for fertile stamens. Conclusions: The median sepal, callus and stelidia of E. pusilla appear to be derived from a sepal, a stamen that gained petal identity, and stamens, respectively. Duplications, diversifying selection and changes in spatial expression of different MADS-box genes shaped these organs, enabling the rewardless flowers of E. pusilla to mimic an unrelated rewarding flower for pollinator attraction. These genetic changes are not incorporated in current models and urge for a rethinking of the evolution of deceptive flowers.

  • 280.
    Donpudsa, Suchao
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology.
    Rimphanitchayakit, Vichien
    Tassanakajon, Anchalee
    Söderhäll, Irene
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology.
    Söderhäll, Kenneth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Comparative Physiology.
    Characterization of two crustin antimicrobial peptides from the freshwater crayfish Pacifastacus leniusculus2010In: Journal of Invertebrate Pathology, ISSN 0022-2011, E-ISSN 1096-0805, Vol. 104, no 3, p. 234-238Article in journal (Refereed)
    Abstract [en]

    The two bacteria-induced crustin genes, Plcrustin1 and Plcrustin2, previously found in the hemocyte cDNA library of Pacifastacus leniusculus, contain the open reading frames of 357 bp encoding a putative protein of 118 amino acid residues and 330 bp encoding a putative protein of 109 amino acid residues, respectively. The carboxyl-terminal part of the two crustins possesses, respectively, 7 and 8 conserved cysteine residues representation of a WAP domain that is found in carcinins and crustins in other several crustaceans. The amino acid sequences of Plcrustin1 and Plcrustin2 show that they belong to type I crustins. In order to characterize their properties and biological activities, the two recombinant crustin proteins were produced in the Escherichia coil expression system. Antimicrobial assays showed that the growth of only one Gram-positive bacterium, Micrococcus luteus M1 11, was inhibited by the recombinant Plcrustin1 and Plcrustin2 with MIC of about 0.07-0.27 mu M and 3.5-8 mu M, respectively. In addition, the study of inhibition mechanism revealed that the antimicrobial activity of the two recombinant crustin proteins was a result of bactericidal effect. However, the two crustins did not exhibit the inhibitory activities against trypsin, chymotrypsin, elastase and subtilisin A.

  • 281.
    Donpudsa, Suchao
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Comparative Physiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Söderhäll, Irene
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Comparative Physiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Rimphanitchayakit, Vichien
    Cerenius, Lage
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Comparative Physiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Tassanakajon, Anchalee
    Söderhäll, Kenneth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Comparative Physiology.
    Proteinase inhibitory activities of two two-domain Kazal proteinase inhibitors from the freshwater crayfish Pacifastacus leniusculus and the importance of the P2 position in proteinase inhibitory activity2010In: Fish and Shellfish Immunology, ISSN 1050-4648, E-ISSN 1095-9947, Vol. 29, no 5, p. 716-723Article in journal (Refereed)
    Abstract [en]

    Serine proteinase inhibitors are found ubiquitously in living organisms and involved in homeostasis of processes using proteinases as well as innate immune defense. Two two-domain Kazal-type serine proteinase inhibitors (KPIs), KPI2 and KPI8, have been identified from the hemocyte cDNA library of the crayfish Pacifastacus leniusculus. Unlike other KPIs from P. leniusculus, they are found specific to the hernocytes and contain an uncommon P-2 amino acid residue, Gly. To unveil their inhibitory activities, the two KPIs and their domains were over-expressed. By testing against subtilisin, trypsin, chymotrypsin and elastase, the KPI2 was found to inhibit strongly against subtilisin and weakly against trypsin, while the KPI8 was strongly active against only trypsin. With their P-1 Set and Lys residues, the KPI2_domain2 and KPI8_domain2 were responsible for strong inhibition against subtilisin and trypsin, respectively. Mutagenesis of KPI8_domain1 at P-2 amino acid residue from Gly to Pro, mimicking the P-2 residue of KPI8_domain2, rendered the KPI8_domain1 strongly active against trypsin, indicating the important role of P-2 residue in inhibitory activities of the Kazal-type serine proteinase inhibitors. Only the KPI2 was found to inhibit against the extracellular serine proteinases from the pathogenic oomycete of the freshwater crayfish, Aphanomyces astaci.

  • 282.
    Drakvik, Elina
    et al.
    Karolinska Inst, Inst Environm Med, Nobels Vag 13, SE-17177 Stockholm, Sweden;Stockholm Univ, ACES, SE-10691 Stockholm, Sweden.
    Altenburger, Rolf
    UFZ Helmholtz Ctr Environm Res, Permoserstr 15, D-04318 Leipzig, Germany.
    Aoki, Yasunobu
    Natl Inst Environm Studies, 16-2 Onogawa, Tsukuba, Ibaraki 3058506, Japan.
    Backhaus, Thomas
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, SE-40530 Gothenburg, Sweden.
    Bahadori, Tina
    US EPA, 1200 Penn Ave NW,MC 8201R, Washington, DC 20460 USA.
    Barouki, Robert
    Univ Paris, Inserm Unit 1124, 45 Rue St Peres, F-75006 Paris, France.
    Brack, Werner
    UFZ Helmholtz Ctr Environm Res, Permoserstr 15, D-04318 Leipzig, Germany;Rhein Westfal TH Aachen, Inst Environm Res, ABBt Aachen Biol, Worringerweg 1, D-52074 Aachen, Germany.
    Cronin, Mark T. D.
    Liverpool John Moores Univ, Sch Pharm & Biomol Sci, Byrom St, Liverpool L3 3AF, Merseyside, England.
    Demeneix, Barbara
    CNRS, MNHN, UMR 7221, 7 Rue Cuvier, F-75005 Paris, France.
    Bennekou, Susanne Hougaard
    Danish Tech Univ, FOOD, Kemitorvet 201, DK-2800 Lyngby, Denmark.
    van Klaveren, Jacob
    Natl Inst Publ Hlth & Environm RIVM, POB 1, NL-3720 BA Bilthoven, Netherlands.
    Kneuer, Carsten
    German Fed Inst Risk Assessment, Pesticide Safety, Max Dohrn Str 8-10, D-10589 Berlin, Germany.
    Kolossa-Gehring, Marike
    German Environm Agcy UBA, Correnspl 1, D-14195 Berlin, Germany.
    Lebret, Erik
    Natl Inst Publ Hlth & Environm RIVM, POB 1, NL-3720 BA Bilthoven, Netherlands;Univ Utrecht, IRAS, Yalelaan 2, NL-3584 CM Utrecht, Netherlands.
    Posthuma, Leo
    Natl Inst Publ Hlth & Environm RIVM, POB 1, NL-3720 BA Bilthoven, Netherlands;Radboud Univ Nijmegen, Dept Environm Sci, Inst Water & Wetland Res, Nijmegen, Netherlands.
    Reiber, Lena
    German Environm Agcy UBA, Correnspl 1, D-14195 Berlin, Germany.
    Rider, Cynthia
    NIEHS, Natl Toxicol Program, 111 TW Alexander Dr,POB 12233,MD K2-12, Res Triangle Pk, NC 27709 USA.
    Ruegg, Joëlle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Environmental toxicology. Karolinska Inst, Inst Environm Med, Nobels Vag 13, SE-17177 Stockholm, Sweden.
    Testa, Giuseppe
    Univ Milan, Dept Oncol, Via S Sofia 9-1, I-20122 Milan, Italy;IEO, Via Adamello 16, I-20139 Milan, Italy.
    van der Burg, Bart
    BioDetect Syst, Sci Pk 406, NL-1098 XH Amsterdam, Netherlands.
    van der Voet, Hilko
    Wageningen Univ & Res, Droevendaalsesteeg 1, NL-6708 PB Wageningen, Netherlands.
    Warhurst, A. Michael
    CHEM Trust, 34b York Way, London N1 9AB, England.
    van de Water, Bob
    Leiden Univ, Leiden Acad Ctr Drug Res, POB 9502, NL-2300 RA Leiden, Netherlands.
    Yamazaki, Kunihiko
    Minist Environm Japan, Chiyoda Ku, 1-2-2 Kasumigaseki, Tokyo 1008975, Japan.
    Oberg, Mattias
    Karolinska Inst, Inst Environm Med, Nobels Vag 13, SE-17177 Stockholm, Sweden.
    Bergman, Ake
    Stockholm Univ, ACES, SE-10691 Stockholm, Sweden;Orebro Univ, Dept Sci & Technol, SE-70182 Orebro, Sweden;Tongji Univ, Coll Environm Sci & Engn, State Key Lab Pollut Control & Resource Reuse, Shanghai 200092, Peoples R China.
    Statement on advancing the assessment of chemical mixtures and their risks for human health and the environment2020In: Environment International, ISSN 0160-4120, E-ISSN 1873-6750, Vol. 134, article id UNSP 105267Article in journal (Other academic)
    Abstract [en]

    The number of anthropogenic chemicals, manufactured, by-products, metabolites and abiotically formed transformation products, counts to hundreds of thousands, at present. Thus, humans and wildlife are exposed to complex mixtures, never one chemical at a time and rarely with only one dominating effect. Hence there is an urgent need to develop strategies on how exposure to multiple hazardous chemicals and the combination of their effects can be assessed. A workshop, "Advancing the Assessment of Chemical Mixtures and their Risks for Human Health and the Environment" was organized in May 2018 together with Joint Research Center in Ispra, EUfunded research projects and Commission Services and relevant EU agencies. This forum for researchers and policy-makers was created to discuss and identify gaps in risk assessment and governance of chemical mixtures as well as to discuss state of the art science and future research needs. Based on the presentations and discussions at this workshop we want to bring forward the following Key Messages: We are at a turning point: multiple exposures and their combined effects require better management to protect public health and the environment from hazardous chemical mixtures. Regulatory initiatives should be launched to investigate the opportunities for all relevant regulatory frameworks to include prospective mixture risk assessment and consider combined exposures to (real-life) chemical mixtures to humans and wildlife, across sectors. Precautionary approaches and intermediate measures (e.g. Mixture Assessment Factor) can already be applied, although, definitive mixture risk assessments cannot be routinely conducted due to significant knowledge and data gaps. A European strategy needs to be set, through stakeholder engagement, for the governance of combined exposure to multiple chemicals and mixtures. The strategy would include research aimed at scientific advancement in mechanistic understanding and modelling techniques, as well as research to address regulatory and policy needs. Without such a clear strategy, specific objectives and common priorities, research, and policies to address mixtures will likely remain scattered and insufficient.

  • 283.
    Dupret, Vincent
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Evolution and Developmental Biology.
    Revision of the genus Kujdanowiaspis Stensiö, 1942 (Placodermi, Arthrodira, "Actinolepida") from the Lower Devonian of Podolia (Ukraine)2010In: Geodiversitas, ISSN 1280-9659, E-ISSN 1638-9395, Vol. 32, p. 5-63Article in journal (Refereed)
    Abstract [en]

    The genus Kujdanowiaspis Stensiö, 1942 has long been considered as the archetype of placoderms; hence, it has been often used as outgroup in phylogenetic analyses involving placoderms, or used as a representative of all the placoderms for all early vertebrate works. Nevertheless, there has been no real work on the taxonomy of this genus since Denison (1978). Here we propose a revision of the material of Kujdanowiaspis from the Old Red Sandstone of Podolia (including neurocrania, skull roofs and thoracic armours), together with the description of unpublished specimens of the genus Heightingtonaspis White, 1969. Among the available Podolian material, three species are considered valid: Kujdanowiaspis buczacziensis (Brotzen, 1934), K. podolica (Brotzen, 1934) and Erikaspis zychi (Stensiö, 1945) (K. podolica and K. buczacziensis only differ in size and in the density and size of the tuberculated ornamentation; the dermal plate pattern of E. zychi differs from that of the genus Kujdanowiaspis). The axillar area of the scapulocoracoid of K. podolica is compared with those of an osteostracan “agnathan” and of a non-tetrapod sarcopterygian. In the three cases, the articulation of the pectoral fin is of the monobasal type. An analogy with the embryonic development of the pectoral fin of the actinopterygian Danio rerio (Hamilton, 1822) suggests that the monobasal articulation would correspond to the plesiomorphic condition compared with the multibasal one of the adult actinopterygians and some derived brachythoracid placoderms. The suprasynarcual is a newly identified, chondrified element of the vertebral column, supposed to respond to the height of the median dorsal plate in Kujdanowiaspis podolica.

  • 284.
    Dupret, Vincent
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Carls, Peter
    Martinez-Perez, Carlos
    Botella, Hector
    First Perigondwanan record of actinolepids (Vertebrata: Placodermi: Arthrodira) from the Lochkovian (Early Devonian) of Spain and its palaeobiogeographic significance2011In: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 310, no 3-4, p. 273-282Article in journal (Refereed)
    Abstract [en]

    Different palaeogeographic models have been proposed for the position of Laurussia ( including Baltica) and Gondwana-derived microcontinents ( including Ibero-Armorica) during Ordovician to Late Carboniferous times. Principal differences concern the presence and duration of a large ocean, the Rheic Ocean, acting as a faunal barrier between these areas. The timing of the collision of Laurussia with Gondwana and/or Gondwana-derived terranes continues to be debated. Here we present new faunal data revealing close biogeographical relations between Ibero-Armorica ("Perigondwanan" or Gondwanan derivate terranes) and Podolia (SE margin of Baltica, in Laurussia). The placoderm assemblage found in the mid-late Lochkovian (Lower Devonian) of Celtiberia (north-central Spain), consisting of the 'actinolepid' species Kujdanowiaspis podolica, Erikaspis zychi and the acanthothoracid Palaeacanthaspis aff. P. vasta, is similar, both in terms of taxonomy and stratigraphic record, to that encountered in the Lochkovian of Podolia (Ukraine; Laurussia) and until now considered as endemic to this region. Moreover, vertebrate faunal links between Podolia and Celtiberia are also extended to the chondrichthyan scale-based species Seretolepis elegans and Altholepis composita previously documented exclusively from Laurussian localities (Podolia and Mackenzie Mountains in Canada), which occur together with the placoderm remains described herein. These evidences support the hypothesis that intermittent shallow neritic migration paths between Podolia (as well as "Avalonia") and Iberia existed in the late Lochkovian, agreeing with a palaeogeographic reconstruction showing close proximity between peri-Gondwanan or Gondwana-derived terranes and Laurussia. It supports the palaeogeographic model of the non-oceanic Variscan Mobile Crustal Field and it corroborates the arguments against wide oceans, acting as biogeographical relevant barriers, between Baltica and Gondwana in early Devonian times. The distribution patterns of heavy-shelled ostracods, turbidicolous brachiopods, and Rhenish trilobites also support these conclusions.

  • 285.
    Dupret, Vincent
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Martinez-Perez, Carlos
    University of Valencia, Spain.
    Botella, Hector
    University of Valencia.
    Carls, Peter
    Technische Universität Braunschweig, Germany.
    Blieck, Alain
    Université des Sciences et Technologies Lille 1, France.
    Vertebrate macroremains as stratigraphic markers: the case of the Lower Devonian “Kujdanowiaspis assemblage” from Podolia (Ukraine) and Celtiberia (Spain)2010Conference paper (Other academic)
    Abstract [en]

    The vertebrate fauna, including chondrichthyan microremains and osteostracan and placoderm macroremains encountered in the Lower Devonian (i.e. Lochkovian and Pragian) deposits from Podolia (Ukraine; see list in Voichyshyn, 2001) was considered as unique. Unfortunately, because of the Old Red Sandstone facies, the stratigraphic boundaries were very difficult to determine. Until recently, most of the units were lithologic. The occurrence of the arthrodire placoderm Kujdanowiaspis buczacziensis has since been proposed to mark the beginning of the Pragian, owing to a number of correlations between fossil distributions (i.e. the pteraspidiform Althaspis) in Western Europe and Podolia (Dupret and Blieck, 2009).

    Recently, the long time “unique” placoderm and chondrichthyan faunal assemblage from Podolia has been found in Spain (Martinez-Pérez et al., in press; Dupret et al., submitted). The absence of K. buczacziensis, nevertheless, leads us to consider an age older than Pragian, i.e. late Lochkovian. This dating confirms previous works mainly based on invertebrates and conodonts. These “double check” processes confirm the possibility of using macrovertebrate remains for stratigraphic purposes.

    The occurence of the same fauna during the Late Lochkovian in Podolia (southern margin of Laurussia) and in Spain (Armorican ”block”, part of northern margin of Gondwana or independant component), leads us to favour palaeogeographic reconstructions showing a proximity between both palaeo-provinces, allowing for the formation of, at least, punctual migratory paths. Moreover, the Old Red Sandstones have long been considered as non-marine deposits, especially in Podolia, despite the discovery of seldom brachiopod (lingulid) fragments. The similar faunal composition between Podolia and Celtiberia (the latter being clearly marine) challenges the non-marine status of the Podolian deposits.

  • 286.
    Dupret, Vincent
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Phuong, Ta Hoa
    Department of Geology, Vietnam National University, Ha Noi City.
    Thanh, Tong-Dzuy
    Department of Geology, Vietnam National University, Ha Noi City.
    Phong, Nguyen Duc
    Vietnam Institute of Geosciences and Mineral Resources.
    Janvier, Philippe
    Muséum National d'Histoire Naturelle, Paris, France.
    Clément, Gaël
    Muséum National d'Histoire Naturelle, Paris, France.
    The skull of Hagiangella goujeti Janvier, 2005, a high-crested acanthothoracid (Vertebrata, Placodermi) from the Lower Devonian of northern Vietnam2011In: Journal of Vertebrate Paleontology, ISSN 0272-4634, E-ISSN 1937-2809, Vol. 31, no 3, p. 531-538Article in journal (Refereed)
    Abstract [en]

    The acanthothoracid Hagiangella goujeti Janvier, 2005, has been described exclusively on the basis of isolatedthoracic plates from the Lochkovian (Lower Devonian) Khao Loc Formation of Tung Vai, Ha Giang Province, northernVietnam. It is characterized by a very high, triangular median crest on the median dorsal plate, and has been referred to theAcanthothoraci on the basis of the morphology of its fused anterolateral, spinal and anterior ventrolateral plates, and thecharacteristic stellate ornamentation of the group. Isolated plates of H. goujeti are relatively abundant at Tung Vai and noother placoderm taxon from this locality seems to share the same type of ornamentation. However, the skull of this speciesremained elusive. Here we report two well-preserved skull roofs from Tung Vai, which we refer to H. goujeti. They display thesame stellate ornamentation and small size as the previously described plates of the thoracic armor of this species. This newmaterial shows that the head of H. goujeti is surprisingly short (i.e., possibly lacking dermal rostral and pineal elements), incontrast to the elongate and narrow skull of all other acanthothoracids. The combination of unique characters (e.g., presenceof two pairs of posterior pit lines, two pairs of central and paranuchal plates, etc.) suggests a possible sister group relationshipto the placoderm assemblage Petalichthyida + Ptyctodontida + Arthrodira.

  • 287.
    Dupret, Vincent
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Australian Natl Univ, Dept Appl Math, Res Sch Phys & Engn, Canberra, ACT, Australia..
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. European Synchrotron Radiat Facil, Grenoble, France..
    Goujet, Daniel
    UPMC Paris 6, CNRS, MNHN, CR2P UMR 7207,Sorbonne Univ,Museum Natl Hist Nat, Paris, France..
    Ahlberg, Per Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The internal cranial anatomy of Romundina stellina Orvig, 1975 (Vertebrata, Placodermi, Acanthothoraci) and the origin of jawed vertebrates: Anatomical atlas of a primitive gnathostome2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 2, article id e0171241Article in journal (Refereed)
    Abstract [en]

    Placoderms are considered as the first jawed vertebrates and constitute a paraphyletic group in the stem-gnathostome grade. The acanthothoracid placoderms are among the phylogenetically most basal and morphologically primitive gnathostomes, but their neurocranial anatomy is poorly understood. Here we present a near-complete three-dimensional skull of Romundina stellina, a small Early Devonian acanthothoracid from the Canadian Arctic Archipelago, scanned with propagation phase contrast microtomography at a 7.46 mu m isotropic voxel size at the European Synchrotron Radiation Facility, Grenoble, France. This is the first model of an early gnathostome skull produced using this technique, and as such represents a major advance in objectivity compared to past descriptions of placoderm neurocrania on the basis of grinding series. Despite some loss of material along an oblique crack, most of the internal structures are remarkably preserved, and most of the missing structures can be reconstructed by symmetry. This virtual approach offers the possibility to connect with certainty all the external foramina to the blood and nerve canals and the central structures, and thus identify accurate homologies without destroying the specimen. The high level of detail enables description of the main arterial, venous and nerve canals of the skull, and other perichondrally ossified endocranial structures such as the palatoquadrate articulations, the endocranial cavity and the inner ear cavities. The braincase morphology appears less extreme than that of Brindabellaspis, and is in some respects more reminiscent of a basal arthrodire such as Kujdanowiaspis.

  • 288.
    Dupret, Vincent
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Goujet, Daniel
    Muséum National D'Histoire Naturelle, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Being Romundina stellina Ørvig, 1975 (Vertebrate, Placodermi, Acanthothoraci): itracranial anatomy of one of the deepest gnathostomes revealed by synchrotron tomograpy in phase contrast protocole2012In: / [ed] Malvesy, T., Gauthrot, M., Fuchs, C., Berthoz, A., Blieck, A., Becker, D., Buffetaut, E., Mazin, J. -M.,, Montbéliard, 2012, p. 19-19Conference paper (Refereed)
    Abstract [en]

    Dans la peau de Romundina stellina Ørvig, 1975 (Vertebrata, Placodermi, Acanthothoraci)

    Anatomie crânienne d'un des premiers gnathostomes révélée par tomographie synchrotron en contraste de phase

     Being Romundina stellina Ørvig, 1975  (Vertebrata, Placodermi, Acanthothoraci)

    Intracranial anatomy of one of the deepest gnathostomes revealed by synchrotron tomography in phase contrast protocole

     

     

    The acanthothoracid placoderms (armored fishes) are the most basal and primitive gnathostomes (jawed vertebrates; 1). However, their endocranial morphology is poorly understood, and only one genus (Brindabellaspis) has been described thoroughly (2).

    Here we present the 3D reconstruction of a subcomplete skull of Romundina stellina Ørvig, 3, from the Lochkovian of Prince of Wales Island, Canadian Arctic Archipelago. The specimen was imaged in 3D with propagation phase contrast microtomography (4) on the ID19 beamline of the ESRF, using a 7.45 µm isotropic voxel size.

    Most features are properly preserved and most of the missing structures can be virtually rebuilt by symmetry. Another advantage of this virtual approach is the possibility of connecting with certainty all the external foramina to the blood and nerve canals and the central/internal structures, and hence to identify accurate homologies without destroying the specimen. Ørvig’s original assumptions can now be checked with confidence.

    The vasculature of the dermal bones, rendered in detail, allowed a better understanding of plate growth. It permits the visualization of dermal bone establishment over perichondral bone (5).

    The high level of details of this model reveals that between the trigeminal and vagus nerve (and the inner ears), the perichondral bone wrapping the endocranial cavity shows a “lace” pattern, unknown so far in vertebrates (presumably because of the lack of data). The significance of this character is unclear, but it is definitely not an artifact of taphonomy or scanning.

     

    References

    1          Janvier, P. Early Vertebrates. Clarendon Press edn, Vol. 1 (Oxford Science Publications, 1996).

    2          Young, G. C. A new Early Devonian placoderm from New South Wales, Australia, with a discussion of placoderm phylogeny. Palaeontographica (A) 167, 10–76 (1980).

    3          Ørvig, T. Description, with special reference to the dermal skeleton, of a new Radotinid arthrodire from the Gedinnian of Arctic Canada. Extrait des Colloques internationaux du Centre National de la Recherche Scientifique - Problèmes actuels de Paléontologie - Evolution des Vertébrés 218, 41–71 (1975).

    4          Tafforeau, P. et al. Applications of X-ray synchrotron microtomography for non-destructive 3D studies of paleontological specimens. Applied Physics A - Materials Science & Processing 83, 195–202 (2006).

    5          Dupret, V., Sanchez, S., Goujet, D., Tafforeau, P. & Ahlberg, P. Bone vascularization and growth in placoderms (Vertebrata): the example of the premedian plate of Romundina stellina Ørvig, 1975 Comptes Rendus Palevol 9, 369–375 (2010).

     

     

  • 289.
    Dupret, Vincent
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Goujet, Daniel
    Muséum National D'Histoire Naturelle, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Fossil early vertebrates shed lights on the origin of the gnathostome face2013In: Program and Abstracts of the 10th International Congress of Vertebrate Morphology, Barcelona, Spain, 2013, p. 245-245Conference paper (Refereed)
    Abstract [en]

    Jawless cyclostomes and jawed gnathostomes show very different face patterns. Cyclostomes have a single median nasohypophysial duct, an anterior hypophysis and a short telencephalon, while gnathostomes have a pair of nasal sacs opening externally, a more posterior separate hypophysis open in the palate and a longer telencephalon.

    Embryonic processes differ as well. In cyclostomes, premandibular crest cells migrate forwards either side of the nasohypophysial placode to form the upper lip; in gnathostomes they migrate between the hypophysial and nasal placodes to form the trabecular region. Supraoptic neural crest remains posterior to the nasohypophysial duct in cyclostomes; it moves forward to create the nasal capsules in gnathostomes.

    Some fossil forms illustrate a transition between these two patterns.

    The jawless galeaspid Shuyu (-430 Ma) has a nasohypophysial duct, short telencephalon, and anteriorly oriented hypophysis, but the paired nasal sacs and hypophysis are separated by a rudimentary trabecula.

    The jawed primitive placoderm Romundina (-415 Ma) shows a cranial cavity reminiscent of that of Shuyu (anteriorly dir