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  • 1.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Little, Chelsea J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jagerbrand, Annika K.
    Molau, Ulf
    Dominance hierarchies, diversity and species richness of vascular plants in an alpine meadow: contrasting short and medium term responses to simulated global change2014In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 2, p. e406-Article in journal (Refereed)
    Abstract [en]

    We studied the impact of simulated global change on a high alpine meadow plant community. Specifically, we examined whether short-term (5 years) responses are good predictors for medium-term (7 years) changes in the system by applying a factorial warming and nutrient manipulation to 20 plots in Latnjajaure, subarctic Sweden. Seven years of experimental warming and nutrient enhancement caused dramatic shifts in dominance hierarchies in response to the nutrient and the combined warming and nutrient enhancement treatments. Dominance hierarchies in the meadow moved from a community being dominated by cushion plants, deciduous, and evergreen shrubs to a community being dominated by grasses, sedges, and forbs. Short-termresponses were shown to be inconsistent in their ability to predict medium-term responses for most functional groups, however, grasses showed a consistent and very substantial increase in response to nutrient addition over the seven years. The non-linear responses over time point out the importance of longer-term studies with repeated measurements to be able to better predict future changes. Forecasted changes to temperature and nutrient availability have implications for trophic interactions, and may ultimately influence the access to and palatability of the forage for grazers. Depending on what anthropogenic change will be most pronounced in the future (increase in nutrient deposits, warming, or a combination of them both), different shifts in community dominance hierarchies may occur. Generally, this study supports the productivity-diversity relationship found across arctic habitats, with community diversity peaking in mid-productivity systems and degrading as nutrient availability increases further. This is likely due the increasing competition in plant-plant interactions and the shifting dominance structure with grasses taking over the experimental plots, suggesting that global change could have high costs to biodiversity in the Arctic.

  • 2. Archer, Trevor
    et al.
    Garcia, Danilo
    Fredriksson, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Psychiatry, University Hospital.
    Restoration of MPTP-induced deficits by exercise and Milmed (R) co-treatment2014In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 2, p. e531-Article in journal (Refereed)
    Abstract [en]

    1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) induces permanent neurochemical and functional deficits. Following the administration of either two or four injections of the dopamine neurotoxin, MPTP, at a dose of 40 mg/kg, C57/BL6 mice were given access to running-wheels (30-min sessions, four times/week, Monday-Thursday) and treatment with the treated yeast, Milmed (R) (four times/week, Monday-Thursday), or simply running-wheel exercise by itself, over ten weeks. It was observed that the combination of physical exercise and Milmed (R) treatment, the MPTP + Exercise + Yeast (MC) group [MPTP + Exercise + Milmed (R) (MC)], restored spontaneous motor activity markedly by test day 10, restored completely subthreshold L-Dopa-induced activity, and dopamine concentration to 76% of control values, in the condition wherein two administrations of MPTP (2 x 40 mg/kg) were given prior to initiation of exercise and/or Milmed (R) treatment. Physical exercise by itself, MPTP + Exercise (MC) group, attenuated these deficits only partially. Administration of MPTP four times (i.e., 40 mg/kg, s.c., once weekly over four weeks for a total of 160 mg/kg, MPTP + Exercise + Yeast (MC) group [MPTP + Exercise + Milmed (R) (SC)] and MPTP + Exercise (SC), induced a lesioning effect that was far too severe for either exercise alone or the exercise + Milmed (R) combination to ameliorate. Nevertheless, these findings indicate a powerful effect of physical exercise reinforced by Milmed (R) treatment in restoring MPTP-induced deficits of motor function and dopamine neurochemistry in mice.

  • 3.
    Clement, Alice M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Flinders Univ S Australia, Sch Biol Sci, Adelaide, SA, Australia.;Museum Victoria, Dept Sci, Melbourne, Vic, Australia..
    Challands, Tom J.
    Univ Edinburgh, Sch Geosci, Edinburgh, Midlothian, Scotland..
    Long, John A.
    Flinders Univ S Australia, Sch Biol Sci, Adelaide, SA, Australia..
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The cranial endocast of Dipnorhynchus sussmilchi (Sarcopterygii: Dipnoi) and the interrelationships of stem-group lungfishes2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e2539Article in journal (Refereed)
    Abstract [en]

    The first virtual cranial endocast of a lungfish from the Early Devonian, Dipnorhynchus sussmilchi, is described. Dipnorhynchus, only the fourth Devonian lungfish for which a near complete cranial endocast is known, is a key taxon for clarifying primitive character states within the group. A ventrally-expanded telencephalic cavity is present in the endocast of Dipnorhynchus demonstrating that this is the primitive state for "true" Dipnoi. Dipnorhynchus also possesses a utricular recess differentiated from the sacculolagenar pouch like that seen in stratigraphically younger lungfish (Dipterus, Chirodipterus, Rhinodipterus), but absent from the dipnomorph Youngolepis. We do not find separate pineal and para-pineal canals in contrast to a reconstruction from previous authors. We conduct the first phylogenetic analysis of Dipnoi based purely on endocast characters, which supports a basal placement of Dipnorhynchus within the dipnoan stem group, in agreement with recent analyses. Our analysis demonstrates the value of endocast characters for inferring phylogenetic relationships.

  • 4.
    de Abreu, Murilo S.
    et al.
    Univ Fed Santa Maria, Programa Posgrad Farmacol, Santa Maria, RS, Brazil.
    Messias, Joao P. M.
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO, Porto, Portugal.
    Thörnqvist, Per-Ove
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
    Winberg, Svante
    Uppsala Univ, Dept Neurosci, Uppsala, Sweden.
    Soares, Marta C.
    Univ Porto, Ctr Invest Biodiversidade & Recursos Genet, CIBIO, Porto, Portugal.
    The variable monoaminergic outcomes of cleaner fish brains when facing different social and mutualistic contexts2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e4830Article in journal (Refereed)
    Abstract [en]

    The monoamines serotonin and dopamine are important neuromodulators present in the central nervous system, known to be active regulators of social behaviour in fish as in other vertebrates. Our aim was to investigate the region-specific brain monoaminergic differences arising when individual cleaners face a client (mutualistic context) compared to when they are introduced to another conspecific (conspecific context), and to understand the relevance of visual assessment compared to the impact of physical contact with any partner. We demonstrated that serotoninergic activity at the diencephalon responds mostly to the absence of physical contact with clients whereas cerebellar dopaminergic activity responds to actual cleaning engagement. We provide first insights on the brain's monoaminergic (region-specific) response variations, involved in the expression of cleaner fishes' mutualistic and conspecific behaviour. These results contribute to a better understanding of the monoaminergic activity in accordance to different socio-behavioural contexts.

  • 5.
    Derraik, Jose G. B.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health. A Better Start Natl Sci Challenge, Auckland, New Zealand;Univ Auckland, Liggins Inst, Auckland, New Zealand.
    Albert, Benjamin B.
    Univ Auckland, Liggins Inst, Auckland, New Zealand.
    de Bock, Martin
    Univ Otago, Dept Paediat, Christchurch, New Zealand;Univ Auckland, Liggins Inst, Auckland, New Zealand.
    Butler, Eadaoin M.
    A Better Start Natl Sci Challenge, Auckland, New Zealand;Univ Auckland, Liggins Inst, Auckland, New Zealand.
    Hofman, Paul L.
    Univ Auckland, Liggins Inst, Auckland, New Zealand.
    Cutfield, Wayne S.
    A Better Start Natl Sci Challenge, Auckland, New Zealand;Univ Auckland, Liggins Inst, Auckland, New Zealand.
    Socioeconomic status is not associated with health-related quality of life in a group of overweight middle-aged men2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e5193Article in journal (Refereed)
    Abstract [en]

    Socioeconomic status is a known determinant of health. In secondary data analyses, we assessed whether socioeconomic status affected health-related quality of life in a group of overweight (body mass index 25-30 kg/m(2)) middle-aged (45.9 +/- 5.4 years) men, recruited in Auckland (New Zealand). Health-related quality of life was assessed with SF-36v2 three times: at baseline, and 12 and 30 weeks later. Socioeconomic status was determined by geo-coded deprivation scores derived from current address using the New Zealand Index of Deprivation 2006 (NZDep2006), as well as capital value of residence. Univariable and multivariable analyses showed no associations between measures of socioeconomic status and any mental or physical health domains. Our findings may reflect the fact that these men are not currently experiencing comorbidities associated with overweight.

  • 6.
    Franzen, Oscar
    et al.
    Karolinska Inst, Integrated Cardio Metab Ctr, Huddinge, Sweden..
    Ermel, Raili
    Tartu Univ Hosp, Dept Cardiac Surg, Tartu, Estonia..
    Sukhavasi, Katyayani
    Univ Tartu, Inst Biomed & Translat Med, Dept Pathophysiol, Tartu, Estonia..
    Jain, Rajeev
    Univ Tartu, Inst Biomed & Translat Med, Dept Pathophysiol, Tartu, Estonia..
    Jain, Anamika
    Univ Tartu, Inst Biomed & Translat Med, Dept Pathophysiol, Tartu, Estonia..
    Betsholtz, Christer
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology. Karolinska Inst, Integrated Cardio Metab Ctr, Huddinge, Sweden.
    Giannarelli, Chiara
    Icahn Sch Med Mt Sinai, Cardiovasc Res Ctr, New York, NY 10029 USA.;Icahn Sch Med Mt Sinai, Inst Genom & Multiscale Biol, Dept Genet & Genom Sci, New York, NY 10029 USA..
    Kovacic, Jason C.
    Icahn Sch Med Mt Sinai, Cardiovasc Res Ctr, New York, NY 10029 USA..
    Ruusalepp, Arno
    Tartu Univ Hosp, Dept Cardiac Surg, Tartu, Estonia.;Univ Tartu, Inst Biomed & Translat Med, Dept Pathophysiol, Tartu, Estonia.;Clin Gene Networks AB, Stockholm, Sweden..
    Skogsberg, Josefin
    Karolinska Inst, Dept Med Biochem & Biophys, Solna, Sweden..
    Hao, Ke
    Icahn Sch Med Mt Sinai, Inst Genom & Multiscale Biol, Dept Genet & Genom Sci, New York, NY 10029 USA..
    Schadt, Eric E.
    Icahn Sch Med Mt Sinai, Inst Genom & Multiscale Biol, Dept Genet & Genom Sci, New York, NY 10029 USA.;Clin Gene Networks AB, Stockholm, Sweden..
    Bjoerkegren, Johan L. M.
    Karolinska Inst, Integrated Cardio Metab Ctr, Huddinge, Sweden.;Univ Tartu, Inst Biomed & Translat Med, Dept Pathophysiol, Tartu, Estonia.;Icahn Sch Med Mt Sinai, Inst Genom & Multiscale Biol, Dept Genet & Genom Sci, New York, NY 10029 USA.;Clin Gene Networks AB, Stockholm, Sweden..
    Global analysis of A-to-I RNA editing reveals association with common disease variants2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e4466Article in journal (Refereed)
    Abstract [en]

    RNA editing modifies transcripts and may alter their regulation or function. In humans, the most common modification is adenosine to inosine (A-to-I). We examined the global characteristics of RNA editing in 4,301 human tissue samples. More than 1.6 million A-to-I edits were identified in 62% of all protein-coding transcripts. mRNA recoding was extremely rare; only 11 novel recoding sites were uncovered. Thirty single nucleotide polymorphisms from genome-wide association studies were associated with RNA editing; one that influences type 2 diabetes (rs2028299) was associated with editing in ARPIN. Twenty-five genes, including LRP11 and PLIN5, had editing sites that were associated with plasma lipid levels. Our findings provide new insights into the genetic regulation of RNA editing and establish a rich catalogue for further exploration of this process.

  • 7. Govindarajan, Annette F.
    et al.
    Källström, Björn
    Selander, Erik
    Östman, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Dahlgren, Thomas G.
    The highly toxic and cryptogenic clinging jellyfish Gonionemus sp. (Hydrozoa, Limnomedusae) on the Swedish west coast2019In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 7, article id e6883Article in journal (Refereed)
    Abstract [en]

    The clinging jellyfish Gonionemus sp. is a small hydromedusa species known historically from the Swedish west coast but not reported in recent times. This species is thought to be native to the northwest Pacific where it is notorious for causing severe stings in humans and is considered invasive or cryptogenic elsewhere. This year, unlike in the past, severe stings in swimmers making contact with Gonionemus sp. medusae occurred in Swedish waters from a sheltered eelgrass bed in the inner Skagerrak archipelago. To the best of our knowledge, this is only the second sting record of Gonionemus sp. from the Northeast Atlantic—with the first record occurring off the Belgian coast in the 1970s. Stinging Gonionemus sp. medusae have also been recently reported from the northwestern Atlantic coast, where, like on the Swedish coast, stings were not reported in the past. We analyzed sea surface temperature data from the past 30 years and show that 2018 had an exceptionally cold spring followed by an exceptionally hot summer. It is suggested that the 2018 temperature anomalies contributed to the Swedish outbreak. An analysis of mitochondrial COI sequences showed that Swedish medusae belong to the same clade as those from toxic populations in the Sea of Japan and northwest Atlantic. Gonionemus sp. is particularly prone to human-mediated dispersal and we suggest that it is possible that this year’s outbreak is the result of anthropogenic factors either through a climate-driven northward range shift or an introduction via shipping activity. We examined medusa growth rates and details of medusa morphology including nematocysts. Two types of penetrating nematocysts: euryteles and b-mastigophores were observed, suggesting that Gonionemus sp. medusae are able to feed on hard-bodied organisms like copepods and cladocerans. Given the now-regular occurrence and regional spread of Gonionemus sp. in the northwest Atlantic, it seems likely that outbreaks in Sweden will continue. More information on its life cycle, dispersal mechanisms, and ecology are thus desirable.

  • 8.
    Harish, Ajith
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology. Uppsala Univ, Dept Cell & Mol Biol, Program Mol Biol, Uppsala, Sweden.
    What is an archaeon and are the Archaea really unique?2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e5770Article in journal (Refereed)
    Abstract [en]

    The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling of multi-locus datasets have resolved many recalcitrant branches of the ToL. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. These issues concern (i) the uniqueness (monophyly) of the Archaea, and (ii) the evolutionary relationships of the Archaea to the Bacteria and the Eukarya; both of these are relevant to the deep structure of the ToL. To explore the causes for this persistent ambiguity, I examine multiple datasets and different phylogenetic approaches that support contradicting conclusions. I find that the uncertainty is primarily due to a scarcity of information in standard datasets-universal core-genes datasets-to reliably resolve the conflicts. These conflicts can be resolved efficiently by comparing patterns of variation in the distribution of functional genomic signatures, which are less diffused unlike patterns of primary sequence variation. Relatively lower heterogeneity in distribution patterns minimizes uncertainties and supports statistically robust phylogenetic inferences, especially of the earliest divergences of life. This case study further highlights the limitations of primary sequence data in resolving difficult phylogenetic problems, and raises questions about evolutionary inferences drawn from the analyses of sequence alignments of a small set of core genes. In particular, the findings of this study corroborate the growing consensus that reversible substitution mutations may not be optimal phylogenetic markers for resolving early divergences in the ToL, nor for determining the polarity of evolutionary transitions across the ToL.

  • 9.
    Hart, Michael W.
    et al.
    Simon Fraser University, Department of Biological Science, Burnaby.
    Stover, Daryn A.
    Arizona State University Colleges at Lake Havasu City, School of Mathematical and Natural Sciences.
    Guerra, Vanessa
    Simon Fraser University, Department of Biological Science, Burnaby.
    Mozaffari, Sahar V.
    University of Chicago, Department of Human Genetics.
    Ober, Carole
    University of Chicago, Department of Human Genetics.
    Mugal, Carina F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kaj, Ingemar
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Analysis and Probability Theory.
    Positive selection on human gamete-recognition genes2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e4259Article in journal (Refereed)
    Abstract [en]

    Coevolution of genes that encode interacting proteins expressed on the surfaces of sperm and eggs can lead to variation in reproductive compatibility between mates and reproductive isolation between members of different species. Previous studies in mice and other mammals have focused in particular on evidence for positive or diversifying selection that shapes the evolution of genes that encode sperm-binding proteins expressed in the egg coat or zona pellucida (ZP). By fitting phylogenetic models of codon evolution to data from the 1000 Genomes Project, we identified candidate sites evolving under diversifying selection in the human genes ZP3 and ZP2. We also identified one candidate site under positive selection in C4BPA, which encodes a repetitive protein similar to the mouse protein ZP3R that is expressed in the sperm head and binds to the ZP at fertilization. Results from several additional analyses that applied population genetic models to the same data were consistent with the hypothesis of selection on those candidate sites leading to coevolution of sperm- and egg-expressed genes. By contrast, we found no candidate sites under selection in a fourth gene (ZP1) that encodes an egg coat structural protein not directly involved in sperm binding. Finally, we found that two of the candidate sites (in C4BPA and ZP2) were correlated with variation in family size and birth rate among Hutterite couples, and those two candidate sites were also in linkage disequilibrium in the same Hutterite study population. All of these lines of evidence are consistent with predictions from a previously proposed hypothesis of balancing selection on epistatic interactions between C4BPA and ZP3 at fertilization that lead to the evolution of co-adapted allele pairs. Such patterns also suggest specific molecular traits that may be associated with both natural reproductive variation and clinical infertility.

  • 10. Hastad, Olle
    et al.
    Ödeen, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    A vision physiological estimation of ultraviolet window marking visibility to birds2014In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 2, p. e621-Article in journal (Refereed)
    Abstract [en]

    Billions of birds are estimated to be killed in window collisions every year, worldwide. A popular solution to this problem may lie in marking the glass with ultraviolet reflective or absorbing patterns, which the birds, but not humans, would see. Elegant as this remedy may seem at first glance, few of its proponents have taken into consideration how stark the contrasts between ultraviolet and human visible light reflections or transmissions must be to be visible to a bird under natural conditions. Complicating matters is that diurnal birds differ strongly in how their photoreceptors absorb ultraviolet and to a lesser degree blue light. We have used a physiological model of avian colour vision to estimate the chromatic contrasts of ultraviolet markings against a natural scene reflected and transmitted by ordinary window glass. Ultraviolets markings may be clearly visible under a range of lighting conditions, but only to birds with a UVS type of ultraviolet vision, such as many passerines. To bird species with the common VS type of vision, ultraviolet markings should only be visible if they produce almost perfect ultraviolet contrasts and are viewed against a scene with low chromatic variation but high ultraviolet content.

  • 11.
    Hedberg Nyqvist, Kerstin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Rosenblad, Andreas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, Centre for Clinical Research, County of Västmanland. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Occupational and Environmental Medicine.
    Volgsten, Helena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences.
    Funkquist, Eva-Lotta
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Mattsson, Elisabet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Clinical Psychology in Healthcare.
    Early skin-to-skin contact between healthy late preterm infants and their parents: an observational cohort study2017In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5, article id e3949Article in journal (Refereed)
    Abstract [en]

    Background

    Skin-to-skin contact (SSC) is an important factor to consider in the care of late preterm infants (born between 34 0/7 and 36 6/7 completed weeks of gestation). The literature suggests that SSC between preterm infants and their mothers facilitates breastfeeding. However, more studies are needed to explore potential dose-response effects between SSC and breastfeeding as well as studies that explicitly investigate SSC by fathers among late preterm infants. The aim was to investigate the duration of healthy late preterm infants’ SSC with the mother and father, respectively, during the first 48 h after birth and the associations with breastfeeding (exclusive/partial at discharged), clinical and demographic variables.

    Methods

    This was an observational cohort study in which parents to healthy late preterm infants, born between 34 5/7 and 36 6/7 completed weeks of gestation, recorded duration of SSC provided by mother and father, respectively. Demographic and clinical variables were retrieved from the medical records and were used as predictors. Multiple linear regression analysis was used to assess the association between the predictors and the outcome, SSC (hours), separately for mothers and fathers.

    Results

    The mean (standard deviation [SD]) time per day spent with SSC with mothers (n = 64) and fathers (n = 64), was 14.7 (5.6) and 4.4 (3.3) hours during the first day (24 h) after birth and 9.2 (7.1) and 3.1 (3.3) hours during the second day (24 h), respectively. Regarding SSC with mothers, no variable was significantly associated with SSC during the first day, while the mean (95% confidence interval [CI]) time of SSC during the second day was 6.9 (1.4–12.4) hours shorter for each additional kg of birthweight (p = 0.014). Concerning SSC with fathers, the mean (95% CI) time of SSC during the first day was 2.1 (0.4–3.7) hours longer for infants born at night (p = 0.015), 1.7 (0.1–3.2) hours longer for boys (p = 0.033), 3.2 (1.2–5.2) hours longer for infants born by caesarean section (p = 0.003), and 1.6 (0.1–3.1) hours longer for infants exclusively breastfed at discharge (p = 0.040). During the second day, the mean (95% CI) time of SSC with fathers was 3.0 (0.6–5.4) hours shorter for each additional kg of birthweight (p = 0.014), 2.0 (0.5–3.6) hours longer for infants born during night-time (p = 0.011), 2.9 (1.4–4.4) hours longer if the mother was primipara (p < 0.001), and 1.9 (0.3–3.5) hours shorter if supplementary artificial milk feeds were given. None of the other predictors, i.e., mother’s age, gestational age, or induction of labor were significantly associated with infants’ SSC with mothers or fathers during any of the first two days after birth.

    Conclusion

    Future studies are warranted that investigate duration of SSC between late preterm infants and their parents separately and the associations with breastfeeding and other variables of clinical importance.

  • 12.
    Jerve, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Imperial Coll London, Dept Life Sci, Ascot, Berks, England.
    Qu, Qingming
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Univ Ottawa, Ctr Adv Res Environm Genom, Ottawa, ON, Canada.
    Sanchez, Sophie
    Uppsala University, Science for Life Laboratory, SciLifeLab. European Synchrotron Radiat Facil, Grenoble, France.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Three-dimensional paleohistology of the scale and median fin spine of Lophosteus superbus (Pander 1856)2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e2521Article in journal (Refereed)
    Abstract [en]

    Lophosteus superbus is one of only a handful of probable stem-group osteichthyans known from the fossil record. First collected and described in the late 19th century from the upper Silurian Saaremaa Cliff locality in Estonia, it is known from a wealth of disarticulated scales, fin spines, and bone fragments. In this study we provide the first description of the morphology and paleohistology of a fin spine and scale from Lophosteus using virtual thin sections and 3D reconstructions that were segmented using phase-contrast synchrotron X-ray microtomography. These data reveal that both structures have fully or partially buried odontodes, which retain fine morphological details in older generations, including sharp nodes and serrated ridgelets. The vascular architecture of the fin spine tip, which is composed of several layers of longitudinally directed bone vascular canals, is much more complex compared to the bulbous horizontal canals within the scale, but they both have distinctive networks of ascending canals within each individual odontode. Other histological characteristics that can be observed from the data are cell spaces and Sharpey's fibers that, when combined with the vascularization, could help to provide insights into the growth of the structure. The 3D data of the scales from Lophosteus superbus is similar to comparable data from other fossil osteichthyans, and the morphology of the reconstructed buried odontodes from this species is identical to scale material of Lophosteus ohesaarensis, casting doubt on the validity of that species. The 3D data presented in this paper is the first for fossil fin spines and so comparable data is not yet available. However, the overall morphology and histology seems to be similar to the structure of placoderm dermal plates. The 3D datasets presented here provide show that microtomography is a powerful tool for investigating the three-dimensional microstructure of fossils, which is difficult to study using traditional histological methods. These results also increase the utility of fin spines and scales suggest that these data are a potentially rich source of morphological data that could be used for studying questions relating to early vertebrate growth and evolution.

  • 13.
    Lindner, Philip
    et al.
    Stockholm Univ, Dept Psychol, S-10691 Stockholm, Sweden.;Karolinska Inst, Dept Clin Neurosci, Stockholm, Sweden..
    Carlbring, Per
    Stockholm Univ, Dept Psychol, S-10691 Stockholm, Sweden..
    Flodman, Erik
    Linkoping Univ, Dept Behav Sci & Learning, Linkoping, Sweden..
    Hebert, Amanda
    Linkoping Univ, Dept Behav Sci & Learning, Linkoping, Sweden..
    Poysti, Stephanie
    Linkoping Univ, Dept Behav Sci & Learning, Linkoping, Sweden..
    Hagkvist, Filip
    Norrbotten Cty Council, NeuroVux Clin, Lulea, Sweden..
    Johansson, Robert
    Karolinska Inst, Dept Clin Neurosci, Stockholm, Sweden.;Linkoping Univ, Dept Behav Sci & Learning, Linkoping, Sweden..
    Westin, Vendela Zetterqvist
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Psychiatry, University Hospital.
    Berger, Thomas
    Univ Bern, Dept Clin Psychol & Psychotherapy, Bern, Switzerland..
    Andersson, Gerhard
    Karolinska Inst, Dept Clin Neurosci, Stockholm, Sweden.;Linkoping Univ, Dept Behav Sci & Learning, Linkoping, Sweden..
    Does cognitive flexibility predict treatment gains in Internet-delivered psychological treatment of social anxiety disorder, depression, or tinnitus?2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e1934Article in journal (Refereed)
    Abstract [en]

    Little is known about the individual factors that predict outcomes in Internet-administered psychological treatments. We hypothesized that greater cognitive flexibility (i.e. the ability to simultaneously consider several concepts and tasks and switch effortlessly between them in response to changes in environmental contingencies) would provide a better foundation for learning and employing the cognitive restructuring techniques taught and exercised in therapy, leading to greater treatment gains. Participants in three trials featuring Internet-administered psychological treatments for depression (n = 36), social anxiety disorder (n = 115) and tinnitus (n = 53) completed the 64-card Wisconsin Card Sorting Test (WCST) prior to treatment. We found no significant associations between perseverative errors on the WCST and treatment gains in any group. We also found low accuracy in the classification of treatment responders. We conclude that lower cognitive flexibility, as captured by perseverative errors on the WCST, should not impede successful outcomes in Internet-delivered psychological treatments.

  • 14.
    Linz, Alexandra M.
    et al.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.
    He, Shaomei
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA;Univ Wisconsin, Dept Geosci, Madison, WI USA.
    Stevens, Sarah L. R.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.
    Anantharaman, Karthik
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA.
    Rohwer, Robin R.
    Univ Wisconsin, Environm Chem & Technol Program, Madison, WI USA.
    Malmstrom, Rex R.
    Joint Genome Inst, Dept Energy, Walnut Creek, CA USA.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    McMahon, Katherine D.
    Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA;Univ Wisconsin, Dept Civil & Environm Engn, Madison, WI 53706 USA.
    Freshwater carbon and nutrient cycles revealed through reconstructed population genomes2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e6075Article in journal (Refereed)
    Abstract [en]

    Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.

  • 15.
    Ljungman, Lisa
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Clinical Psychology in Healthcare.
    Cernvall, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Clinical Psychology in Healthcare.
    Ghaderi, Ata
    Division of Psychology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Ljungman, Gustaf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Neuropediatrics/Paediatric oncology.
    von Essen, Louise
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Clinical Psychology in Healthcare.
    Ljótsson, Brjánn
    Division of Psychology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    An open trial of individualized face-to-face cognitive behavior therapy for psychological distress in parents of children after end of treatment for childhood cancer including a cognitive behavioral conceptualization2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e4570Article in journal (Refereed)
    Abstract [en]

    Objective

    A subgroup of parents of children who have been treated for childhood cancer report high levels of psychological distress. To date there is no empirically supported psychological treatment targeting cancer-related psychological distress in this population. The aim of the current study was to test the feasibility and preliminarily evaluate the effect of individualized face-to-face cognitive behavior therapy (CBT) for parents of children after the end of treatment for childhood cancer. A secondary aim was to present a cognitive behavioral conceptualization of cancer-related distress for these parents.

    Methods

    An open trial was conducted where 15 parents of children who had completed successful treatment for cancer three months to five years earlier and who reported psychological distress related to a child’s previous cancer disease were provided CBT at a maximum of 15 sessions. Participants were assessed at baseline, post-intervention, and three-month follow-up using self-reported psychological distress (including posttraumatic stress symptoms (PTSS), depression, and anxiety) and the diagnostic Mini-International Neuropsychiatric Interview. Feasibility outcomes relating to recruitment, data collection, and delivery of the treatment were also examined. Individual case formulations for each participant guided the intervention and these were aggregated and presented in a conceptualization detailing core symptoms and their suggested maintenance mechanisms.

    Results

    A total of 93% of the participants completed the treatment and all of them completed the follow-up assessment. From baseline to post-assessment, parents reported significant improvements in PTSS, depression, and anxiety with medium to large effect sizes (Cohen’s d = 0.65–0.92). Results were maintained or improved at a three-month follow-up. At baseline, seven (47%) participants fulfilled the diagnostic criteria for major depressive disorder and four (29%) fulfilled the criteria for posttraumatic stress disorder, compared to none at a post-assessment and a follow-up assessment. The resulting cognitive behavioral conceptualization suggests traumatic stress and depression as the core features of distress, and avoidance and inactivity is suggested as the core maintenance mechanisms.

    Conclusion

    The treatment was feasible and acceptable to the participants. Significant improvements in distress were observed during the study. Overall, results suggest that the psychological treatment for parents of children after end of treatment for childhood cancer used in the current study is promising and should be tested and evaluated in future studies.

  • 16.
    Montero-Mendieta, Santiago
    et al.
    CSIC, Donana Biol Stn EBD, Dept Integrat Ecol, Conservat & Evolutionary Genet Grp, Seville, Spain..
    Grabherr, Manfred
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lantz, Henrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    De la Riva, Ignacio
    CSIC, Museo Nacl Ciencias Nat, Dept Biodivers & Evolutionary Biol, Madrid, Spain..
    Leonard, Jennifer A.
    CSIC, Donana Biol Stn EBD, Dept Integrat Ecol, Conservat & Evolutionary Genet Grp, Seville, Spain..
    Webster, Matthew Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vila, Carles
    CSIC, Donana Biol Stn EBD, Dept Integrat Ecol, Conservat & Evolutionary Genet Grp, Seville, Spain..
    A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog2017In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5, article id e3702Article in journal (Refereed)
    Abstract [en]

    Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. Weused RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github. com/biomendi/TRANSCRIPTOMEASSEMBLY- PIPELINE/wiki.

  • 17.
    Porter, Amy
    et al.
    Dian Fossey Gorilla Fund Int, Atlanta, GA 30315 USA.
    Eckardt, Winnie
    Dian Fossey Gorilla Fund Int, Atlanta, GA 30315 USA.
    Vecellio, Veronica
    Dian Fossey Gorilla Fund Int, Atlanta, GA 30315 USA.
    Guschanski, Katerina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Niehoff, Peter Philip
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ngobobo-As-Ibungu, Urbain
    Dian Fossey Gorilla Fund Int, Atlanta, GA 30315 USA.
    Pekeyake, Radar Nishuli
    Inst Congolais Conservat Nat, Kinshasa, DEM REP CONGO.
    Stoinski, Tara
    Dian Fossey Gorilla Fund Int, Atlanta, GA 30315 USA.
    Caillaud, Damien
    Dian Fossey Gorilla Fund Int, Atlanta, GA 30315 USA;Univ Calif Davis, Dept Anthropol, Davis, CA 95616 USA.
    Behavioral responses around conspecific corpses in adult eastern gorillas (Gorilla beringei spp.)2019In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 7, article id e6655Article in journal (Refereed)
    Abstract [en]

    Humans were once considered unique in having a concept of death but a growing number of observations of animal responses to dying and dead conspecifics suggests otherwise. Complex arrays of behaviors have been described ranging from corpse removal and burial among social insects to quiet attendance and caregiving among elephants and primates. Less frequently described, however, are behavioral responses of individuals from different age/sex classes or social position toward the death of conspecifics. We describe behavioral responses of mountain gorillas (Gorilla beringei beringei) to the deaths of a dominant silverback and a dominant adult female from the same social group in Volcanoes National Park in Rwanda and the responses of Grauer's gorillas (Gorilla b. graueri) to the corpse of an extra-group silverback in Kahuzi-Biega National Park, Democratic Republic of Congo. In gorillas, interactions between groups or with a lone silverback often result in avoidance or aggression. We predicted that: (i) more individuals should interact with the corpses of same-group members than with the corpse of the extra-group silverback; (ii) adult females with infants should avoid the corpse of the extra-group silverback; and (iii) in the mountain gorilla cases, individuals that shared close social relationships with the dead individual should spend more time with the corpse than other individuals in the group. We used a combination of detailed qualitative reports, photos, and videos to describe all occurrences of affiliative/investigative and agonistic behaviors observed at the corpses. We observed similar responses toward the corpses of group and extra-group individuals. Animals in all three cases showed a variety of affiliative/investigative and agonistic behaviors directed to the corpses. Animals of all age/sex classes interacted with the corpses in affiliative/investigative ways but there was a notable absence of all adult females at the corpse of the extra-group silverback. In all three cases, we observed only silverbacks and blackbacks being agonistic around and/or toward the corpses. In the mountain gorilla cases, the individuals who spent the most time with the corpses were animals who shared close social relationships with the deceased. We emphasize the similarity in the behavioral responses around the corpses of group and extra-group individuals, and suggest that the behavioral responses were influenced in part by close social relationships between the deceased and certain group members and by a general curiosity about death. We further discuss the implications close interactions with corpses have for disease transmission within and between gorilla social groups.

  • 18.
    Sachs, Sven
    et al.
    Nat Kundemuseum Bielefeld, Abt Geowissensch, Bielefeld, Germany..
    Hornung, Jahn J.
    Kear, Benjamin P.
    Uppsala University, Music and Museums, Museum of Evolution.
    Reappraisal of Europe's most complete Early Cretaceous plesiosaurian: Brancasaurus brancai Wegner, 1914 from the "Wealden facies" of Germany2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e2813Article in journal (Refereed)
    Abstract [en]

    The olotype of Brartcasaurus brancai is one of the most historically famous and anatomically complete Early Cretaceous plesiosaurian fossils. It derived from the Gerdernann & Co. brickworks clay pit near Gronau (Westfalen) in North Rhine-Westphalia, northwestern Germany. Stratigraphically this locality formed part of the classic European "Wealden facies," but is now more formally attributed to the upper most strata of the Buckeberg Group (upper Berriasian). Since its initial description in 1914, the type skeleton of B. brancai has suffered damage both during and after WWII. Sadly, these mishaps have resulted in the loss of substantial information, in particular an structures of the cranium and limb girdles, which are today only evidenced from published text and/or illustrations. This non-confirmable data has, however,. proven crucial for determining the relationships of B. brancai within Plesiosauna. either as an early long-necked elasmosaund, or a member of the controversial Early Cretaceous leptocleidid radiation. To evaluate these competing hypotheses and compile an undated osteological. compendium, we undertook a comprehensive examination of the holotype as it now preserved, and also assessed other Buckeberg Group plesiosaurian fossils to establish a morphological hypodigm. Phylogenetic simulations using the most species-rich datasets of Early Cretaceous plesiosaurians incorporating revised scores for B. brancai, together with a second recently named Backeberg Group plesiosaurian Granausaurus wegneri (Ham pc,. 2013), demonstrated that referral of these taxa to Leptocleididae was not unanimous, and that the topological stability, of this Glade is tenuous. In addition, the trait combinations manifested by B. brancai and G. wegneri were virtually identical. We therefore conclude that these monotypic individuals are ontogenetic morphs and G. wegneri is a junior synonym of B. brancai. Finally, anomalies detected in the diagnostic features for other "Wealden" plesiosaurians have prompted reconsiderations of interspecies homology versus intraspecific variability. We therefore propose that the still unresolved taxonomy of B. brancai should emphasize only those character states evident in the examinable fossil material, and specifically accommodate for growth-related modifications delimited via osteologically mature referred specimens.

  • 19.
    Simeon, Saw
    et al.
    Mahidol Univ, Fac Med Technol, Ctr Data Min & Biomed Informat, Bangkok, Thailand..
    Anuwongcharoen, Nuttapat
    Mahidol Univ, Fac Med Technol, Ctr Data Min & Biomed Informat, Bangkok, Thailand..
    Shoombuatong, Watshara
    Mahidol Univ, Fac Med Technol, Ctr Data Min & Biomed Informat, Bangkok, Thailand..
    Malik, Aijaz Ahmad
    Mahidol Univ, Fac Med Technol, Ctr Data Min & Biomed Informat, Bangkok, Thailand..
    Prachayasittikul, Virapong
    Mahidol Univ, Fac Med Technol, Dept Clin Microbiol & Appl Technol, Bangkok, Thailand..
    Wikberg, Jarl E. S.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Nantasenamat, Chanin
    Mahidol Univ, Fac Med Technol, Ctr Data Min & Biomed Informat, Bangkok, Thailand..
    Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e2322Article in journal (Refereed)
    Abstract [en]

    Alzheimer's disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential Ifor cognition arid memory. A large non-redundant data set of 2,570 compounds with reported IC50 values against AChE was obtained frorn ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive rnodels were constructed from 100 different data splits using random forest. Generated models afforded R-2, Q(cv)(2) and Q(Ext)(2) values in ranges of 0.66-0.93, 0.55-0.79 and 0.56-0.81 for the training set, 10-fold cross-validated set and lexternal set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it afforded R-2, Q(CV)(2) and Q(Ext)(2) values of 0.92 +/- 0.01, 0.78 +/- 0.06 and 018 +/- 0.05, respectively. Furthermore, IT-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover Kennard Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing both hydrogen bonding and van der Waals interaction. Molecular docking revealed that compounds 13, 5 and 28 exhibited the lowest binding energies of -12.2, -12.0 and -12.0 kcal/mol, respectively, against human AChE, which is modulated by, hydrogen bonding, pi-pi stacking and hydrophobic interaction inside the binding pocket. These information may be used as guidelines for the design of novel and robust AChE inhibitors.

  • 20. Simeon, Saw
    et al.
    Spjuth, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lapins, Maris
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Nabu, Sunanta
    Anuwongcharoen, Nuttapat
    Prachayasittikul, Virapong
    Wikberg, Jarl E. S.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Nantasenamat, Chanin
    Origin of aromatase inhibitory activity via proteochemometric modeling2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e1979Article in journal (Refereed)
    Abstract [en]

    Aromatase, the rate-limiting enzyme that catalyzes the conversion of androgen to estrogen, plays an essential role in the development of estrogen-dependent breast cancer. Side effects due to aromatase inhibitors (AIs) necessitate the pursuit of novel inhibitor candidates with high selectivity, lower toxicity and increased potency. Designing a novel therapeutic agent against aromatase could be achieved computationally by means of ligand-based and structure-based methods. For over a decade, we have utilized both approaches to design potential AIs for which quantitative structure-activity relationships and molecular docking were used to explore inhibitory mechanisms of AIs towards aromatase. However, such approaches do not consider the effects that aromatase variants have on different AIs. In this study, proteochemometrics modeling was applied to analyze the interaction space between AIs and aromatase variants as a function of their substructural and amino acid features. Good predictive performance was achieved, as rigorously verified by 10-fold cross-validation, external validation, leave-one-compound-out cross-validation, leave-one-protein-out cross-validation and Y-scrambling tests. The investigations presented herein provide important insights into the mechanisms of aromatase inhibitory activity that could aid in the design of novel potent AIs as breast cancer therapeutic agents.

  • 21.
    Sinclair, Lucas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Ijaz, Umer Z.
    Univ Glasgow, Sch Engn, Infrastruct & Environm Res Div, Glasgow, Lanark, Scotland..
    Jensen, Lars Juhl
    Univ Copenhagen, Fac Hlth & Med Sci, Novo Nordisk Fdn Ctr Prot Res, Copenhagen, Denmark..
    Coolen, Marco J. L.
    Curtin Univ Technol, Dept Chem, WA OIGC, Bentley, WA, Australia..
    Gubry-Rangin, Cecile
    Univ Aberdeen, Inst Biol & Environm Sci, Aberdeen, Scotland..
    Chronakova, Alica
    Acad Sci Czech Republic, Ctr Biol, Inst Soil Biol, Ceske Budejovice, Czech Republic..
    Oulas, Anastasis
    Cyprus Inst Neurol & Genet, Bioinformat Grp, Nicosia, Cyprus.;Hellen Ctr Marine Res, Inst Marine Biol Biotechnol & Aquaculture IMBBC, Iraklion, Greece..
    Pavloudi, Christina
    Hellen Ctr Marine Res, Inst Marine Biol Biotechnol & Aquaculture IMBBC, Iraklion, Greece..
    Schnetzer, Julia
    Max Planck Inst Marine Microbiol, Microbial Genom & Bioinformat Grp, Dept Mol Ecol, Bremen, Germany..
    Weimann, Aaron
    Helmholtz Ctr Infect Res, Computat Biol Infect Res, Braunschweig, Germany..
    Ijaz, Ali
    Univ Western Sydney, Hawkesbury Inst Environm, Sydney, NSW, Australia..
    Eiler, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Quince, Christopher
    Univ Warwick, Warwick Med Sch, Warwick, England..
    Pafilis, Evangelos
    Hellen Ctr Marine Res, Inst Marine Biol Biotechnol & Aquaculture IMBBC, Iraklion, Greece..
    Seqenv: linking sequences to environments through text mining2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e2690Article in journal (Refereed)
    Abstract [en]

    Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the "nt" nucleotide database provided by NCBI and, out of every hit, extracts if it is available the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, n turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and s of microbial biogeography.

  • 22.
    Svensson, Brita M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Carlsson, Bengt Å.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Melillo, Jerry M.
    Marine Biol Lab, Ecosyst Ctr, Woods Hole, MA 02543 USA.
    Changes in species abundance after seven years of elevated atmospheric CO2 and warming in a Subarctic birch forest understorey, as modified by rodent and moth outbreaks2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e4843Article in journal (Refereed)
    Abstract [en]

    A seven-year long, two-factorial experiment using elevated temperatures (5 degrees C) and CO2 (concentration doubled compared to ambient conditions) designed to test the effects of global climate change on plant community composition was set up in a Subarctic ecosystem in northernmost Sweden. Using point-frequency analyses in permanent plots, an increased abundance of the deciduous Vaccinium myrtillus, the evergreens V. vitis-idaea and Empetrum nigrum ssp. hermaphroditum and the grass Avenella flexuosa was found in plots with elevated temperatures. We also observed a possibly transient community shift in the warmed plots, from the vegetation being dominated by the deciduous V. myrtillus to the evergreen V. vitis-idaea. This happened as a combined effect of V. myrtillus being heavily grazed during two events of herbivore attack-one vole outbreak (Clethrionomys rufocanus) followed by a more severe moth (.Epirrita autumnata) outbreak that lasted for two growing seasons-producing a window of opportunity for V. vitis-idaea to utilize the extra light available as the abundance of V. myrtillus decreased, while at the same time benefitting from the increased growth in the warmed plots. Even though the effect of the herbivore attacks did not differ between treatments they may have obscured any additional treatment effects. This long-term study highlights that also the effects of stochastic herbivory events need to be accounted for when predicting future plant community changes.

  • 23.
    Tahir, Aisha
    et al.
    Univ Agr Faisalabad, Fac Sci, Dept Biochem, Faisalabad, Pakistan..
    Hussain, Fatma
    Univ Agr Faisalabad, Fac Sci, Dept Biochem, Faisalabad, Pakistan..
    Ahmed, Nisar
    Univ Agr Faisalabad, Ctr Agr Biochem & Biotechnol, Faisalabad, Pakistan..
    Ghorbani, Abdolbaset
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Jamil, Amer
    Univ Agr Faisalabad, Fac Sci, Dept Biochem, Faisalabad, Pakistan..
    Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e4499Article in journal (Refereed)
    Abstract [en]

    In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK-krbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2H-matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmacovigilance, trade of medicinal plants and biodiversity conservation.

  • 24.
    Tusso, Sergio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Morcinek, Kerstin
    Vogler, Catherine
    Schupp, Peter J.
    Caballes, Ciemon F.
    Vargas, Sergio
    Wörheide, Gert
    Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4Article in journal (Refereed)
    Abstract [en]

    Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster ‘planci’ L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific.

  • 25.
    Yi-Ting, Lin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular epidemiology. Kaohsiung Med Univ, Kaohsiung Med Univ Hosp, Dept Family Med, Kaohsiung, Taiwan.
    Chou, Mei-Chuan
    Kaohsiung Med Univ, Kaohsiung Med Univ Hosp, Dept Neurol, Kaohsiung, Taiwan;Kaohsiung Med Univ, Kaohsiung Municipal Ta Tung Hosp, Dept Neurol, Kaohsiung, Taiwan.
    Wu, Shyh-Jong
    Kaohsiung Med Univ, Dept Med Lab Sci & Biotechnol, Kaohsiung, Taiwan.
    Yang, Yuan-Han
    Kaohsiung Med Univ, Kaohsiung Med Univ Hosp, Dept Neurol, Kaohsiung, Taiwan;Kaohsiung Med Univ, Kaohsiung Municipal Ta Tung Hosp, Dept Neurol, Kaohsiung, Taiwan;Kaohsiung Med Univ, Fac Med, Dept Neurol, Kaohsiung, Taiwan;Kaohsiung Med Univ, Fac Med, Masters Program Neurol, Kaohsiung, Taiwan;Kaohsiung Med Univ, Neurosci Res Ctr, Kaohsiung, Taiwan.
    Galantamine plasma concentration and cognitive response in Alzheimer's disease2019In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 7, article id e6887Article in journal (Refereed)
    Abstract [en]

    Background

    Galantamine has been approved for the treatment of Alzheimer's disease (AD). However, there are few studies which have reported the association between cognitive responses and galantamine plasma concentration. The aim of this study was to determine the correlation between galantamine plasma concentration and the subsequent cognitive response following treatment in AD patients.

    Methods

    ADsufferers who continuously took 8 mg/d galantamine for at least 6 months without previous exposure to other kinds of AChEI such as donepezil, rivastigmine, or memantine were included in this cohort study. The assessments included the Mini Mental Status Examination (MMSE), Clinical Dementia Rating Scale (CDR) and the Cognitive Assessment Screening Instrument (CASI). Each subdomain of the CASI assessment was conducted at baseline and after 6 months of galantamine. The plasma concentrations of galantamine were measured by capillary electrophoresis after 6 months of the treatment. Logistic regression was performed to adjust for age, gender, apolipoprotein E epsilon 4 genotype status, and baseline score to investigate the association between galantamine plasma concentrations and the cognitive response.

    Results

    The total sample consisted of 33 clinically diagnosed AD patients taking galantamine 8 mg/d for 6 months. There was no linear correlation between galantamine concentration and cognitive response in patients. However, 22 patients were responsive to the treatment in the long-term memory domain. In CASI subset domain, concentration improved during the 6 months follow up.

    Conclusions

    In the limited samples study, galantamine mostly benefitted the cognitive domain of long-term memory. The benefits were not related to the galantamine plasma concentration. Objective intra-individual evaluation of therapeutic response should be encouraged.

  • 26.
    Östman, Carina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Govindarajan, Annette
    Källström, Björn
    Selander, Erik
    Dahlgren, Thomas
    The highly toxic and cryptogenic clinging jellyfish Gonionemus sp. (Hydrozoa, Limnomedusae) on the Swedish west coast2019In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, p. 1-18Article in journal (Refereed)
1 - 26 of 26
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