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  • 1.
    Cavalcante, Larissa Lopes
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Barbolini, Natasha
    Department of Ecology, Environment and Plant Sciences and Bolin Centre for Climate Research, Stockholm University, SE-106 91 Stockholm, Sweden.
    Bacsik, Zoltán
    Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
    Vajda, Vivi
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Analysis of fossil plant cuticles using vibrational spectroscopy: A new preparation protocol2023Ingår i: Review of Palaeobotany and Palynology, ISSN 0034-6667, E-ISSN 1879-0615, Vol. 316, artikel-id 104944Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Analyses for organic “fingerprints” on fossilized plant cuticles and pollen hold valuable chemotaxonomic and palaeoclimatic information, and are thus becoming more utilized by palaeobotanists. Plant cuticle and pollen composition are generally analyzed after standard treatments with several chemical reagents for mineral and mesophyll removal. However, the potential alterations on the fossil composition caused by the different cleaning reagents used are still poorly understood. We tested the effects of commonly used palaeobotanical processing methods on the spectra of fossilized cuticles from successions of Late Triassic to Early Jurassic age, including the gymnosperms Lepidopteris, Ginkgoites, Podozamites, Ptilozamites and Pterophyllum astartense. Our study shows that standard chemical processing caused chemical alterations that might lead to erroneous interpretation of the infrared (IR) spectra. The difference in pH caused by HCl induces changes in the proportion between the two bands at ~1720 and 1600 cm 1 (carboxylate and C-C stretch of aromatic compounds) indicating that the band at ~1610 cm 1 at least partially corresponds to carboxylate instead of C-C stretch of aromatic compounds. Interestingly, despite being used in high concentration, HF did not cause changes in the chemical composition of the cuticles. The most alarming changes were caused by the use of Schulze ’s solution, which resulted in the addition of both NO2 and (O)NO2 compounds in the cuticle. Consequently, a new protocol using H2CO3, HF, and H2O2 for preparing fossil plant cuticles aimed for chemical analyses is proposed, which provides an effective substitute to the conventional methods. In particular, a less aggressive and more sustainable alternative to Schulze’s solution is shown to be hydrogen peroxide, which causes only minor alteration of the fossil cuticle ’s chemical composition. Future work should carefully follow protocols, having in mind the impacts of different solutions used to treat leaves and other palaeobotanical material such as palynomorphs with aims to enable the direct comparison of spectra obtained in different studies.

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    Cavalcante et al_2023_Analysis of fossil plant cuticles using vibrational spectroscopy
  • 2.
    Fedosov, Alexander
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi. Swedish Museum of Natural History.
    Tucci, Carmen Federica
    Kantor, Yuri
    Farhat, Sarah
    Puillandre, Nicolas
    Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production2023Ingår i: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 91, s. 837-853Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Venomous marine gastropods of the family Conidae are among the most diversifed predators in marine realm—in large due to their complex venoms. Besides being a valuable source of bioactive neuropeptides conotoxins, cone-snails venoms are an excellent model for molecular evolution studies, addressing origin of key innovations. However, these studies are handicapped by scarce current knowledge on the tissues involved in venom production, as it is generally assumed the sole prerogative of the venom gland (VG). The role of other secretory glands that are present in all Conus species (salivary gland, SG) or only in some species (accessory salivary gland, ASG) remains poorly understood. Here, for the frst time, we carry out a detailed analysis of the VG, SG, and ASG transcriptomes in the vermivorous Conus virgo. We detect multiple transcripts clusters in both the SG and ASG, whose annotations imply venom-related functions. Despite the subsets of transcripts highly-expressed in the VG, SG, and ASG being very distinct, SG expresses an L-, and ASG—Cerm08-, and MEFRR- superfamily conotoxins, all previously considered specifc for VG. We corroborate our results with the analysis of published SG and VG transcriptomes from unrelated fsh-hunting C. geographus, and C. striatus, possibly fsh-hunting C. rolani, and worm-hunting Conus quercinus. In spite of low expression levels of conotoxins, some other specifc clusters of putative venom-related peptides are present and may be highly expressed in the SG of these species. Further functional studies are necessary to determine the role that these peptides play in envenomation. In the meantime, our results show importance of routine multi-tissue sampling both for accurate interpretation of tissue-specifc venom composition in cone-snails, and for better understanding origin and evolution of venom peptides genes.

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    fulltext
  • 3.
    Gharibi, Hassan
    et al.
    Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
    Chernobrovkin, Alexey L.
    Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden;Pelago Bioscience, SE-171 48 Solna, Sweden.
    Eriksson, Gunilla
    Department of Archaeology and Classical Studies, Stockholm University, SE-114 19 Stockholm, Sweden.
    Saei, Amir Ata
    Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden;Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States.
    Timmons, Zena
    Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, U.K..
    Kitchener, Andrew C.
    Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, U.K..
    Kalthoff, Daniela C.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Lidén, Kerstin
    Department of Archaeology and Classical Studies, Stockholm University, SE-114 19 Stockholm, Sweden.
    Makarov, Alexander A.
    Thermo Fisher Scientific GmbH, 28199 Bremen, Germany.
    Zubarev, Roman A.
    Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden;Department of Pharmacological & Technological Chemistry, I. M. Sechenov First Moscow State Medical University, Moscow 119991, Russia;The National Medical Research Center for Endocrinology, Moscow 115478, Russia.
    Abnormal (Hydroxy)proline Deuterium Content Redefines Hydrogen Chemical Mass2022Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 144, nr 6, s. 2484-2487Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Analyzing the δ2H values in individual amino acids of proteins extracted from vertebrates, we unexpectedly found insome samples, notably bone collagen from seals, more than twice as much deuterium in proline and hydroxyproline residues than inseawater. This corresponds to at least 4 times higher δ2H than in any previously reported biogenic sample. We ruled out diet as aplausible mechanism for such anomalous enrichment. This finding puts into question the old adage that “you are what you eat”.

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  • 4. Granquist, Sandra M
    et al.
    Esparza-Salas, Rodrigo
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Hauksson, Erlingur
    Karlsson, Olle
    Naturhistoriska riksmuseet, Enheten för miljöforskning och övervakning.
    Angerbjörn, Anders
    Fish consumption of harbour seals (Phoca vitulina) in north western Iceland assessed by DNA metabarcoding and morphological analysis2018Ingår i: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056Artikel i tidskrift (Refereegranskat)
  • 5.
    Ivarsson, Magnus
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Schnürer, Anna
    Swedish University of Agricultural Sciences.
    Bengtson, Stefan
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Neubeck, Anna
    Naturhistoriska riksmuseet, Enheten för paleobiologi. Stockholm University.
    Anaerobic fungi: a potential source of biological H2 in the oceanic crust.2016Ingår i: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 7, nr 674, s. 1-8Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The recent recognition of fungi in the oceanic igneous crust challenges the understanding of this environment as being exclusively prokaryotic and forces reconsiderations of the ecology of the deep biosphere. Anoxic provinces in the igneous crust are abundant and increase with age and depth of the crust. The presence of anaerobic fungi in deep-sea sediments and on the seafloor introduces a type of organism with attributes of geobiological significance not previously accounted for. Anaerobic fungi are best known from the rumen of herbivores where they produce molecular hydrogen, which in turn stimulates the growth of methanogens. The symbiotic cooperation between anaerobic fungi and methanogens in the rumen enhance the metabolic rate and growth of both. Methanogens and other hydrogen-consuming anaerobic archaea are known from subseafloor basalt; however, the abiotic production of hydrogen is questioned to be sufficient to support such communities. Alternatively, biologically produced hydrogen could serve as a continuous source. Here, we propose anaerobic fungi as a source of bioavailable hydrogen in the oceanic crust, and a close interplay between anaerobic fungi and hydrogen-driven prokaryotes.

  • 6.
    Vajda, Vivi
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi. Department of Geology, Lund University, Sweden.
    Pucetaite, Milda
    Centre for Environmental and Climate Science, Lund University.
    Steinthorsdottir, Margret
    Naturhistoriska riksmuseet, Enheten för paleobiologi. Bolin Centre for Climate Research, Stockholm University.
    Geochemical Fingerprints of Ginkgoales Across the Triassic-Jurassic Boundary of Greenland2021Ingår i: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 182, nr 7, s. 649-662Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Premise of research. Geochemical fingerprinting of fossil plants is a relatively new research field complementing morphological analyses and providing information for paleoenvironmental interpretations. Ginkgoales contains a single extant species but was diverse through the Mesozoic and is an excellent target for biochemical analyses.

    Methodology. Cuticles derived from fresh and fallen autumn leaves of extant Ginkgo biloba and seven fossil gink- goalean leaf taxa, one seed fern taxon, and two taxa with bennettitalean affinity were analyzed by infrared (IR) microspec- troscopy at the D7 beamline in the MAX IV synchrotron laboratory, Sweden. The fossil material derives from Triassic and Jurassic successions of Greenland. Spectral data sets were compared and evaluated by hierarchical cluster analysis (HCA) and principal component analysis performed on vector-normalized, first-derivative IR absorption spectra.

    Pivotal results. The IR absorption spectra of the fossil leaves all reveal signatures that clearly indicate the pres- ence of organic compounds. Spectra of the extant G. biloba leaves reveal the presence of aliphatic chains, aromatic and ester carbonyl functional groups from polymer cutin and other waxy compounds, and polysaccharides. Inter- estingly, both the extant autumn leaves and the fossil specimens reveal the presence of carboxyl/ketone molecules, suggesting that chemical alterations during the initial stages of decomposition are preserved through fossilization. Two major subclusters were identified through HCA of the fossil spectra.

    Conclusions. Consistent chemical IR signatures, specific for each fossil taxon are present in cuticles, and suf- ficient molecular content is preserved in key regions to reflect the plants’ original chemical signatures. The alter- ations of the organic compounds are initiated as soon as the leaves are shed, with loss of proteins and increased ester and carboxyl/ketone compound production in the fallen leaves. We further show that the groupings of taxa reflect a combination of phylogeny and environmental conditions related to the end-Triassic event.

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  • 7. Verschut, Vasiliki
    et al.
    Strandmark, Alma
    Esparza-Salas, Rodrigo
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Hambäck, Peter
    Seasonally varying marine influences on the coastal ecosystem detected through molecular gut analysis2018Ingår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArtikel i tidskrift (Refereegranskat)
1 - 7 av 7
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