| 1. |
- Bengtsson-Palme, Johan, 1985, et al.
(författare)
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Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker
- 2018
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Ingår i: Bioinformatics (Oxford, England). - : Oxford University Press (OUP). - 1367-4811 .- 1367-4803. ; 34:23, s. 4027-4033
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Tidskriftsartikel (refereegranskat)abstract
- Correct taxonomic identification of DNA sequences is central to studies of biodiversity using both shotgun metagenomic and metabarcoding approaches. However, no genetic marker gives sufficient performance across all the biological kingdoms, hampering studies of taxonomic diversity in many groups of organisms. This has led to the adoption of a range of genetic markers for DNA metabarcoding. While many taxonomic classification software tools can be re-trained on these genetic markers, they are often designed with assumptions that impair their utility on genes other than the SSU and LSU rRNA. Here, we present an update to Metaxa2 that enables the use of any genetic marker for taxonomic classification of metagenome and amplicon sequence data.We evaluated the Metaxa2 Database Builder on eleven commonly used barcoding regions and found that while there are wide differences in performance between different genetic markers, our software performs satisfactorily provided that the input taxonomy and sequence data are of high quality.Freely available on the web as part of the Metaxa2 package at http://microbiology.se/software/metaxa2/.Supplementary data are available at Bioinformatics online.
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| 2. |
- Jafari, Gholamali, et al.
(författare)
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Genetics of extracellular matrix remodeling during organ growth using the Caenorhabditis elegans pharynx model.
- 2010
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Ingår i: Genetics. - : Oxford University Press (OUP). - 1943-2631. ; 186:3, s. 969-82
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Tidskriftsartikel (refereegranskat)abstract
- The organs of animal embryos are typically covered with an extracellular matrix (ECM) that must be carefully remodeled as these organs enlarge during post-embryonic growth; otherwise, their shape and functions may be compromised. We previously described the twisting of the Caenorhabditis elegans pharynx (here called the Twp phenotype) as a quantitative mutant phenotype that worsens as that organ enlarges during growth. Mutations previously known to cause pharyngeal twist affect membrane proteins with large extracellular domains (DIG-1 and SAX-7), as well as a C. elegans septin (UNC-61). Here we show that two novel alleles of the C. elegans papilin gene, mig-6(et4) and mig-6(sa580), can also cause the Twp phenotype. We also show that overexpression of the ADAMTS protease gene mig-17 can suppress the pharyngeal twist in mig-6 mutants and identify several alleles of other ECM-related genes that can cause or influence the Twp phenotype, including alleles of fibulin (fbl-1), perlecan (unc-52), collagens (cle-1, dpy-7), laminins (lam-1, lam-3), one ADAM protease (sup-17), and one ADAMTS protease (adt-1). The Twp phenotype in C. elegans is easily monitored using light microscopy, is quantitative via measurements of the torsion angle, and reveals that ECM components, metalloproteinases, and ECM attachment molecules are important for this organ to retain its correct shape during post-embryonic growth. The Twp phenotype is therefore a promising experimental system to study ECM remodeling and diseases.
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| 3. |
- Lebreton, Sebastien, et al.
(författare)
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A Drosophila female pheromone elicits species-specific long-range attraction via an olfactory channel with dual specificity for sex and food
- 2017
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Mate finding and recognition in animals evolves during niche adaptation and involves social signals and habitat cues. Drosophila melanogaster and related species are known to be attracted to fermenting fruit for feeding and egg-laying, which poses the question of whether species-specific fly odours contribute to long-range premating communication. Results: We have discovered an olfactory channel in D. melanogaster with a dual affinity to sex and food odorants. Female flies release a pheromone, (Z)-4-undecenal (Z4-11Al), that elicits flight attraction in both sexes. Its biosynthetic precursor is the cuticular hydrocarbon (Z,Z)-7,11-heptacosadiene (7,11-HD), which is known to afford reproductive isolation between the sibling species D. melanogaster and D. simulans during courtship. Twin olfactory receptors, Or69aB and Or69aA, are tuned to Z4-11Al and food odorants, respectively. They are co-expressed in the same olfactory sensory neurons, and feed into a neural circuit mediating species-specific, long-range communication; however, the close relative D. simulans, which shares food resources with D. melanogaster, does not respond to Z4-11Al. Conclusion: The Or69aA and Or69aB isoforms have adopted dual olfactory traits. The underlying gene yields a collaboration between natural and sexual selection, which has the potential to drive speciation.
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| 4. |
- Lind, Johan, 1972-, et al.
(författare)
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A test of memory for stimulus sequences in great apes
- 2023
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 18:9
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Tidskriftsartikel (refereegranskat)abstract
- Identifying cognitive capacities underlying the human evolutionary transition is challenging, and many hypotheses exist for what makes humans capable of, for example, producing and understanding language, preparing meals, and having culture on a grand scale. Instead of describing processes whereby information is processed, recent studies have suggested that there are key differences between humans and other animals in how information is recognized and remembered. Such constraints may act as a bottleneck for subsequent information processing and behavior, proving important for understanding differences between humans and other animals. We briefly discuss different sequential aspects of cognition and behavior and the importance of distinguishing between simultaneous and sequential input, and conclude that explicit tests on non-human great apes have been lacking. Here, we test the memory for stimulus sequences-hypothesis by carrying out three tests on bonobos and one test on humans. Our results show that bonobos’ general working memory decays rapidly and that they fail to learn the difference between the order of two stimuli even after more than 2,000 trials, corroborating earlier findings in other animals. However, as expected, humans solve the same sequence discrimination almost immediately. The explicit test on whether bonobos represent stimulus sequences as an unstructured collection of memory traces was not informative as no differences were found between responses to the different probe tests. However, overall, this first empirical study of sequence discrimination on non-human great apes supports the idea that non-human animals, including the closest relatives to humans, lack a memory for stimulus sequences. This may be an ability that sets humans apart from other animals and could be one reason behind the origin of human culture.
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| 5. |
- Arshamian, Artin, et al.
(författare)
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A mammalian blood odor component serves as an approach-avoidance cue across phylum border - from flies to humans
- 2017
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Chemosignals are used by predators to localize prey and by prey to avoid predators. These cues vary between species, but the odor of blood seems to be an exception and suggests the presence of an evolutionarily conserved chemosensory cue within the blood odor mixture. A blood odor component, E2D, has been shown to trigger approach responses identical to those triggered by the full blood odor in mammalian carnivores and as such, is a key candidate as a food/alarm cue in blood. Using a multidisciplinary approach, we demonstrate that E2D holds the dual function of affecting both approach and avoidance behavior in a predator-prey predicted manner. E2D evokes approach responses in two taxonomically distant blood-seeking predators, Stable fly and Wolf, while evoking avoidance responses in the prey species Mouse. We extend this by demonstrating that this chemical cue is preserved in humans as well; E2D induces postural avoidance, increases physiological arousal, and enhances visual perception of affective stimuli. This is the first demonstration of a single chemical cue with the dual function of guiding both approach and avoidance in a predator-prey predicted manner across taxonomically distant species, as well as the first known chemosignal that affects both human and non-human animals alike.
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| 6. |
- Vinken, Vera, et al.
(författare)
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Models of conditioned reinforcement and abnormal behaviour in captive animals
- 2023
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Ingår i: Behavioural Processes. - 0376-6357 .- 1872-8308. ; 210
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Tidskriftsartikel (refereegranskat)abstract
- Abnormal behaviours are common in captive animals, and despite a lot of research, the development, maintenance and alleviation of these behaviours are not fully understood. Here, we suggest that conditioned reinforcement can induce sequential dependencies in behaviour that are difficult to infer from direct observation. We develop this hypothesis using recent models of associative learning that include conditioned reinforcement and inborn facets of behaviour, such as predisposed responses and motivational systems. We explore three scenarios in which abnormal behaviour emerges from a combination of associative learning and a mismatch between the captive environment and inborn predispositions. The first model considers how abnormal behaviours, such as locomotor stereotypies, may arise from certain spatial locations acquiring conditioned reinforcement value. The second model shows that conditioned reinforcement can give rise to abnormal behaviour in response to stimuli that regularly precede food or other reinforcers. The third model shows that abnormal behaviour can result from motivational systems being adapted to natural environments that have different temporal structures than the captive environment. We conclude that models including conditioned reinforcement offer an important theoretical insight regarding the complex relationships between captive environments, inborn predispositions, and learning. In the future, this general framework could allow us to further understand and possibly alleviate abnormal behaviours.
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| 7. |
- Balk, Lennart, et al.
(författare)
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Widespread episodic thiamine deficiency in Northern Hemisphere wildlife
- 2016
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Many wildlife populations are declining at rates higher than can be explained by known threats to biodiversity. Recently, thiamine (vitamin B-1) deficiency has emerged as a possible contributing cause. Here, thiamine status was systematically investigated in three animal classes: bivalves, ray-finned fishes, and birds. Thiamine diphosphate is required as a cofactor in at least five life-sustaining enzymes that are required for basic cellular metabolism. Analysis of different phosphorylated forms of thiamine, as well as of activities and amount of holoenzyme and apoenzyme forms of thiaminedependent enzymes, revealed episodically occurring thiamine deficiency in all three animal classes. These biochemical effects were also linked to secondary effects on growth, condition, liver size, blood chemistry and composition, histopathology, swimming behaviour and endurance, parasite infestation, and reproduction. It is unlikely that the thiamine deficiency is caused by impaired phosphorylation within the cells. Rather, the results point towards insufficient amounts of thiamine in the food. By investigating a large geographic area, by extending the focus from lethal to sublethal thiamine deficiency, and by linking biochemical alterations to secondary effects, we demonstrate that the problem of thiamine deficiency is considerably more widespread and severe than previously reported.
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| 8. |
- Boss, John, et al.
(författare)
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Gene expression in the brain of a migratory songbird during breeding and migration
- 2016
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Ingår i: Movement Ecology. - : Springer Science and Business Media LLC. - 2051-3933. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: We still have limited knowledge about the underlying genetic mechanisms that enable migrating species of birds to navigate the globe. Here we make an attempt to get insight into the genetic architecture controlling this complex innate behaviour. We contrast the gene expression profiles of two closely related songbird subspecies with divergent migratory phenotypes. In addition to comparing differences in migratory strategy we include a temporal component and contrast patterns between breeding adults and autumn migrating juvenile birds of both subspecies. The two willow warbler subspecies, Phylloscopus trochilus trochilus and P. t. acredula, are remarkably similar both in phenotype and genotype and have a narrow contact zone in central Scandinavia. Here we used a microarray gene chip representing 23,136 expressed sequence tags (ESTs) from the zebra finch Taeniopygia guttata to identify mRNA level differences in willow warbler brain tissue in relation to subspecies and season.RESULTS: Out of the 22,109 EST probe sets that remained after filtering poorly binding probes, we found 11,898 (51.8 %) probe sets that could be reliably and uniquely matched to a total of 6,758 orthologous zebra finch genes. The two subspecies showed very similar levels of gene expression with less than 0.1 % of the probe sets being significantly differentially expressed. In contrast, 3,045 (13.8 %) probe sets were found to be differently regulated between samples collected from breeding adults and autumn migrating juvenile birds. The genes found to be differentially expressed between seasons appeared to be enriched for functional roles in neuronal firing and neuronal synapse formation.CONCLUSIONS: Our results show that only few genes are differentially expressed between the subspecies. This suggests that the different migration strategies of the subspecies might be governed by few genes, or that the expression patterns of those genes are time-structured or tissue-specific in ways, which our approach fails to uncover. Our findings will be useful in the planning of new experiments designed to unravel the genes involved in the migratory program of birds.
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| 9. |
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| 10. |
- Krupenko, Darya, et al.
(författare)
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Polymorphic parasitic larvae cooperate to build swimming colonies luring hosts
- 2023
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Ingår i: Current Biology. - : Cell Press. - 0960-9822 .- 1879-0445. ; 33:20, s. 4524-4531
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Tidskriftsartikel (refereegranskat)abstract
- Parasites have evolved a variety of astonishing strategies to survive within their hosts, yet the most chal-lenging event in their personal chronicles is the passage from one host to another. It becomes even more complex when a parasite needs to pass through the external environment. Therefore, the free-living stages of parasites present a wide range of adaptations for transmission. Parasitic flatworms from the group Di-genea (flukes) have free-living larvae, cercariae, which are remarkably diverse in structure and behavior. One of the cercariae transmission strategies is to attain a prey-like appearance for the host. This can be done through the formation of a swimming aggregate of several cercariae adjoined together by their tails. Through the use of live observations and light, electron, and confocal microscopy, we described such a supposedly prey-mimetic colony comprising cercariae of two distinct morphotypes. They are functionally specialized: larger morphotype (sailors) enable motility, and smaller morphotype (passengers) presumably facilitate infection. The analysis of local read alignments between the two samples reveals that both cercaria types have identical 18S, 28S, and 5.8S rRNA genes. Further phylogenetic analysis of these ribo-somal sequences indicates that our specimen belongs to the digenean family Acanthocolpidae, likely genus Pleorchis. This discovery provides a unique example and a novel insight into how morphologically and functionally heterogeneous individuals of the same species cooperate to build colonial organisms for the purpose of infection. This strategy bears resemblance to the cooperating castes of the same species found among insects.
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