| 1. |
- Pathan, M., et al.
(författare)
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A novel community driven software for functional enrichment analysis of extracellular vesicles data
- 2017
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Ingår i: Journal of Extracellular Vesicles. - : Wiley. - 2001-3078. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture "what the community needs in a tool". Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes. Remarkably, with the enthusiastic participation of the community, we were able to implement 90% of the requested features. FunRich enables plugin for extracellular vesicles wherein users can download and analyse data from Vesiclepedia database. By involving researchers early through community needs software development, we believe that comprehensive analysis tools can be developed in various scientific disciplines.
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| 2. |
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| 3. |
- Fontal-Cazalla, F.M., Buffington, M., Nordlander, G., Liljeblad, J., Ros-Farré, P., Nieves-Aldrey, J.L., Pujade-Villar, J. & Ronquist, F.
(författare)
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Phylogeny of the Eucoilinae (Hymenoptera: Cynipoidea: Figitidae).
- 2002
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Ingår i: Cladistics. ; :18, s. 154-199
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Nickel, Katrin F., et al.
(författare)
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The polyphosphate-factor XII pathway drives coagulation in prostate cancer-associated thrombosis
- 2015
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Ingår i: Blood. - : American Society of Hematology. - 0006-4971 .- 1528-0020. ; 126:11, s. 1379-1389
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is a leading cause of thrombosis. We identify a new procoagulant mechanism that contributes to thromboembolism in prostate cancer and allows for safe anticoagulation therapy development. Prostate cancer-mediated procoagulant activity was reduced in plasma in the absence of factor XII or its substrate of the intrinsic coagulation pathway factor XI. Prostate cancer cells and secreted prostasomes expose long chain polyphosphate on their surface that colocalized with active factor XII and initiated coagulation in a factor XII-dependent manner. Polyphosphate content correlated with the procoagulant activity of prostasomes. Inherited deficiency in factor XI or XII or high-molecular-weight kininogen, but not plasma kallikrein, protected mice from prostasome-induced lethal pulmonary embolism. Targeting polyphosphate or factor XII conferred resistance to prostate cancer-driven thrombosis in mice, without increasing bleeding. Inhibition of factor XII with recombinant 3F7 antibody reduced the increased prostasome-mediated procoagulant activity in patient plasma. The data illustrate a critical role for polyphosphate/factor XII-triggered coagulation in prostate cancer-associated thrombosis with implications for anticoagulation without therapy-associated bleeding in malignancies.
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| 5. |
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| 6. |
- Ahlström, Katarina, 1966, et al.
(författare)
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Exogenous carbon monoxide does not affect cell membrane energy availability assessed by sarcolemmal calcium fluxes during myocardial ischaemia-reperfusion in the pig
- 2011
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Ingår i: European Journal of Anaesthesiology. - 0265-0215 .- 1365-2346. ; 28:5, s. 356-362
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Tidskriftsartikel (refereegranskat)abstract
- Carbon monoxide is thought to be cytoprotective and may hold therapeutic promise for mitigating ischaemic injury. The purpose of this study was to test low-dose carbon monoxide for protective effects in a porcine model of acute myocardial ischaemia and reperfusion. In acute open-thorax experiments in anaesthetised pigs, pretreatment with low-dose carbon monoxide (5% increase in carboxyhaemoglobin) was conducted for 120 min before localised ischaemia (45 min) and reperfusion (60 min) was performed using a coronary snare. Metabolic and injury markers were collected by microdialysis sampling in the ventricular wall. Recovery of radio-marked calcium delivered locally by microperfusate was measured to assess carbon monoxide treatment effects during ischaemia/reperfusion on the intracellular calcium pool. Coronary occlusion and ischaemia/reperfusion were analysed for 16 animals (eight in each group). Changes in glucose, lactate and pyruvate from the ischaemic area were observed during ischaemia and reperfusion interventions, though there was no difference between carbon monoxide-treated and control groups during ischaemia or reperfusion. Similar results were observed for glycerol and microdialysate Ca-45(2+) recovery. These findings show that a relatively low and clinically relevant dose of carbon monoxide did not seem to provide acute protection as indicated by metabolic, energy-related and injury markers in a porcine myocardial ischaemia/reperfusion experimental model. We conclude that protective effects of carbon monoxide related to ischaemia/reperfusion either require higher doses of carbon monoxide or occur later after reperfusion than the immediate time frame studied here. More study is needed to characterise the mechanism and time frame of carbon monoxide-related cytoprotection.
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| 15. |
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| 16. |
- Iwaszkiewicz-Eggebrecht, Elzbieta, et al.
(författare)
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FAVIS : Fast and versatile protocol for nondestructive metabarcoding of bulk insect samples
- 2023
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 18:7, s. e0286272-
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Tidskriftsartikel (refereegranskat)abstract
- Insects are diverse and sustain essential ecosystem functions, yet remain understudied. Recent reports about declines in insect abundance and diversity have highlighted a pressing need for comprehensive large-scale monitoring. Metabarcoding (high-throughput bulk sequencing of marker gene amplicons) offers a cost-effective and relatively fast method for characterizing insect community samples. However, the methodology applied varies greatly among studies, thus complicating the design of large-scale and repeatable monitoring schemes. Here we describe a non-destructive metabarcoding protocol that is optimized for high-throughput processing of Malaise trap samples and other bulk insect samples. The protocol details the process from obtaining bulk samples up to submitting libraries for sequencing. It is divided into four sections: 1) Laboratory workspace preparation; 2) Sample processing-decanting ethanol, measuring the wet-weight biomass and the concentration of the preservative ethanol, performing non-destructive lysis and preserving the insect material for future work; 3) DNA extraction and purification; and 4) Library preparation and sequencing. The protocol relies on readily available reagents and materials. For steps that require expensive infrastructure, such as the DNA purification robots, we suggest alternative low-cost solutions. The use of this protocol yields a comprehensive assessment of the number of species present in a given sample, their relative read abundances and the overall insect biomass. To date, we have successfully applied the protocol to more than 7000 Malaise trap samples obtained from Sweden and Madagascar. We demonstrate the data yield from the protocol using a small subset of these samples.
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| 17. |
- Iwaszkiewicz-Eggebrecht, Elzbieta, et al.
(författare)
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Optimizing insect metabarcoding using replicated mock communities
- 2023
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Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 14:4, s. 1130-1146
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Tidskriftsartikel (refereegranskat)abstract
- Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms of presence-absence, abundance and biomass. Here we use mock community experiments and a simple probabilistic model to evaluate the effect of different DNA extraction protocols on metabarcoding performance. Specifically, we ask four questions: (Q1) How consistent are the recovered community profiles across replicate mock communities?; (Q2) How does the choice of lysis buffer affect the recovery of the original community?; (Q3) How are community estimates affected by differing lysis times and homogenization? and (Q4) Is it possible to obtain adequate species abundance estimates through the use of biological spike-ins? We show that estimates are quite variable across community replicates. In general, a mild lysis protocol is better at reconstructing species lists and approximate counts, while homogenization is better at retrieving biomass composition. Small insects are more likely to be detected in lysates, while some tough species require homogenization to be detected. Results are less consistent across biological replicates for lysates than for homogenates. Some species are associated with strong PCR amplification bias, which complicates the reconstruction of species counts. Yet, with adequate spike-in data, species abundance can be determined with roughly 40% standard error for homogenates, and with roughly 50% standard error for lysates, under ideal conditions. In the latter case, however, this often requires species-specific reference data, while spike-in data generalize better across species for homogenates. We conclude that a non-destructive, mild lysis approach shows the highest promise for the presence/absence description of the community, while also allowing future morphological or molecular work on the material. However, homogenization protocols perform better for characterizing community composition, in particular in terms of biomass.
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| 18. |
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| 19. |
- Liljeblad, J, et al.
(författare)
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A phylogenetic analysis of higher-level gall wasp relationships (Hymenoptera : Cynipidae)
- 1998
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Ingår i: SYSTEMATIC ENTOMOLOGY. - : BLACKWELL SCIENCE LTD. - 0307-6970. ; 23:3, s. 229-252
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- We present the most comprehensive analysis of higher-level relationships in gall wasps conducted thus far. The analysis was based on detailed study of the skeletal morphology of adults, resulting in 164 phylogenetically informative characters, complemente
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| 20. |
- Marquina, Daniel, et al.
(författare)
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New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods
- 2019
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 19:1, s. 90-104
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Tidskriftsartikel (refereegranskat)abstract
- Insect metabarcoding has been mainly based on PCR amplification of short fragments within the barcoding region of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein-coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon-based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.
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| 21. |
- Mitroiu, Mircea-Dan, et al.
(författare)
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Fauna Europaea: Hymenoptera - Apocrita (excl. Ichneumonoidea).
- 2015
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Ingår i: Biodiversity data journal. - 1314-2828 .- 1314-2836. ; :3
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Tidskriftsartikel (refereegranskat)abstract
- Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Hymenoptera is one of the four largest orders of insects, with about 130,000 described species. In the Fauna Europaea database, 'Hymenoptera - Apocrita (excluding Ichneumonoidea)' comprises 13 superfamilies, 52 families, 91 subfamilies, 38 tribes and 13,211 species. The paper includes a complete list of taxa dealt with, the number of species in each and the name of the specialist responsible for data acquisition. As a general conclusion about the European fauna of Hymenoptera, the best known countries in terms of recorded species are those from northwestern Europe, with the least known fauna probably in the more eastern and southeastern parts of Europe.
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| 22. |
- Nordlander, G, et al.
(författare)
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Phylogeny and historical biogeography of the cynipoid wasp family Ibaliidae (Hymenoptera)
- 1996
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Ingår i: SYSTEMATIC ENTOMOLOGY. - : BLACKWELL SCIENCE LTD. - 0307-6970. ; 21:2, s. 151-165
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The Ibaliidae are a small family of cynipoid wasps, the members of which parasitize woodboring siricid larvae in hardwoods and conifers. The 19 currently recognized extant species occur mainly in the Northern Hemisphere. No fossils are known despite the p
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| 23. |
- Nylin, S., Nyblom, K., Ronquist, F., Janz, N., Belicek, J. & Källersjö, M.
(författare)
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Phylogeny of Polygonia, Nymphalis and related butterflies (Lepidoptera: Nymphalidae): a total-evidence analysis.
- 2001
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Ingår i: Zoological Journal fo the Linnean Society. ; :132, s. 441-468
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Tidskriftsartikel (refereegranskat)
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| 24. |
- Prager, Maria, et al.
(författare)
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ASV portal : an interface to DNA-based biodiversity data in the Living Atlas
- 2023
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Ingår i: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited func-tionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Ampli-con Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.Results: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. Conclusion: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.
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| 25. |
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| 26. |
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| 27. |
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| 28. |
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| 29. |
- Ronquist, F
(författare)
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Dispersal-vicariance analysis: A new approach to the quantification of historical biogeography
- 1997
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Ingår i: SYSTEMATIC BIOLOGY. - : SOC SYSTEMATIC BIOLOGISTS. - 1063-5157. ; 46:1, s. 195-203
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Quantification in historical biogeography has usually been based on the search for a single branching relationship among areas of endemism. Unlike organisms, however, areas rarely have a unique hierarchical history. Dispersal barriers appear and disappear
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| 30. |
- Ronquist, F
(författare)
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Fast Fitch-parsimony algorithms for large data sets
- 1998
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Ingår i: CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY. - : ACADEMIC PRESS LTD. - 0748-3007. ; 14:4, s. 387-400
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The speed of analytical algorithms becomes increasingly important as systematists accumulate larger data sets. In this paper I discuss several time-saving modifications to published Fitch-parsimony tree search algorithms, including shortcuts that allow ra
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| 31. |
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| 32. |
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| 33. |
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| 34. |
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| 35. |
- Ronquist, F
(författare)
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Phylogenetic approaches in coevolution and biogeography
- 1997
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Ingår i: ZOOLOGICA SCRIPTA. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0300-3256. ; 26:4, s. 313-322
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- I review phylogenetic approaches to problems in coevolution and biogeography, illustrating with case studies. In coevolution, genealogical trees are essential in differentiating between ancient and recent associations, in identifying cospeciation events,
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| 36. |
- RONQUIST, F
(författare)
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PHYLOGENY AND CLASSIFICATION OF THE LIOPTERIDAE, AN ARCHAIC GROUP OF CYNIPOID WASPS (HYMENOPTERA)
- 1995
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Ingår i: ENTOMOLOGICA SCANDINAVICA. - : ENTOMOL SCANDINAVICA. - 0013-8711. ; , s. 3-74
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The world fauna of the Liopteridae, a mainly tropical to subtropical group of cynipoid parasitoids of wood-boring insect larvae, was revised at the generic level based on the largest material of the family ever collated, including type specimens of most d
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| 37. |
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| 38. |
- Ronquist, F, et al.
(författare)
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Phylogeny of the Hymenoptera: A cladistic reanalysis of Rasnitsyn's (1988) data
- 1999
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Ingår i: ZOOLOGICA SCRIPTA. - : BLACKWELL SCIENCE LTD. - 0300-3256. ; 28:1-2, s. 13-50
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The hypothesis of higher-level relationships among extinct and extant hymenopterans presented by Rasnitsyn in 1988 is widely cited but the evidence has never been presented in the form of a character matric. or analysed cladistically. We review Rasnitsyn'
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| 39. |
- Ronquist, F
(författare)
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Phylogeny of the Hymenoptera (Insecta): The state of the art
- 1999
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Ingår i: ZOOLOGICA SCRIPTA. - : BLACKWELL SCIENCE LTD. - 0300-3256. ; 28:1-2, s. 3-11
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The Hymenoptera form one of the major insect orders in terms of species diversity and they are also of great ecological and economic importance, notably as pollinators and natural enemies of pests. Phylogenies provide an essential framework for systematic
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| 40. |
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| 41. |
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| 42. |
- Ronquist, F
(författare)
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Three-dimensional cost-matrix optimization and maximum cospeciation
- 1998
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Ingår i: CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY. - : ACADEMIC PRESS LTD. - 0748-3007. ; 14:2, s. 167-172
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In recent years, event-based approaches have been gaining ground in coevolutionary and biogeographical inference. Unlike pattern-based methods, event-based protocols deal directly with evolutionary events, such as dispersals and host switches. Three proto
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| 43. |
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| 44. |
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| 45. |
- Sanmartin, I, et al.
(författare)
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Patterns of animal dispersal, vicariance and diversification in the Holarctic
- 2001
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Ingår i: BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY. - : ACADEMIC PRESS LTD. ; 73:4, s. 345-390
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Recension (övrigt vetenskapligt/konstnärligt)abstract
- We analysed patterns of animal dispersal, vicariance and diversification in the Holarctic based on complete phylogenies of 57 extant non-marine taxa, together comprising 170 species, documenting biogeographic events from the Late Mesozoic to the present.
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| 46. |
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| 47. |
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| 48. |
- Shalchian-Tabrizi, Kamran, et al.
(författare)
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Heterotachy processes in rhodophyte-derived secondhand plastid genes : Implications for addressing the origin and evolution of dinoflagellate plastids
- 2006
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 23:8, s. 1504-1515
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Tidskriftsartikel (refereegranskat)abstract
- Serial transfer of plastids from one eukaryotic host to another is the key process involved in evolution of secondhand plastids. Such transfers drastically change the environment of the plastids and hence the selection regimes, presumably leading to changes over time in the characteristics of plastid gene evolution and to misleading phylogenetic inferences. About half of the dinoflagellate protists species are photosynthetic and unique in harboring a diversity of plastids acquired from a wide range of eukaryotic algae. They are therefore ideal for studying evolutionary processes of plastids gained through secondary and tertiary endosymbioses. In the light of these processes, we have evaluated the origin of 2 types of dinoflagellate plastids, containing the peridinin or 19'-hexanoyloxyfucoxanthin (19'-HNOF) pigments, by inferring the phylogeny using "covarion" evolutionary models allowing the pattern of among-site rate variation to change over time. Our investigations of genes from secondary and tertiary plastids derived from the rhodophyte plastid lineage clearly reveal "heterotachy" processes characterized as stationary covarion substitution patterns and changes in proportion of variable sites across sequences. Failure to accommodate covarion-like substitution patterns can have strong effects on the plastid tree topology. Importantly, multigene analyses performed with probabilistic methods using among-site rate and covarion models of evolution conflict with proposed single origin of the peridinin- and 19'-HNOF-containin- plastids, suggesting that analysis of secondhand plastids can be hampered by convergence in the evolutionary signature of the plastid DNA sequences. Another type of sequence convergence was detected at protein level involving the psaA gene. Excluding the psaA sequence from a concatenated protein alignment grouped the peridinin plastid with haptophytes, congruent with all DNA trees. Altogether, taking account of complex processes involved in the evolution of dinoflagellate plastid sequences (both at the DNA and amino acid level), we demonstrate the difficulty of excluding independent, tertiary origin for both the peridinin and 19'-HNOF plastids involving engulfment of haptophyte-like algae. In addition, the refined topologies suggest the red algal order, Porphyridales, as the endosymbiont ancestor of the secondary plastids in cryptophytes, haptophytes, and heterokonts.
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| 49. |
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| 50. |
- van Dijk, Laura J.A., et al.
(författare)
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Temperature and water availability drive insect seasonality across a temperate and a tropical region
- 2024
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 291:2025
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Tidskriftsartikel (refereegranskat)abstract
- The more insects there are, the more food there is for insectivores and the higher the likelihood for insect-associated ecosystem services. Yet, we lack insights into the drivers of insect biomass over space and seasons, for both tropical and temperate zones. We used 245 Malaise traps, managed by 191 volunteers and park guards, to characterize year-round flying insect biomass in a temperate (Sweden) and a tropical (Madagascar) country. Surprisingly, we found that local insect biomass was similar across zones. In Sweden, local insect biomass increased with accumulated heat and varied across habitats, while biomass in Madagascar was unrelated to the environmental predictors measured. Drivers behind seasonality partly converged: In both countries, the seasonality of insect biomass differed between warmer and colder sites, and wetter and drier sites. In Sweden, short-term deviations from expected season-specific biomass were explained by week-to-week fluctuations in accumulated heat, rainfall and soil moisture, whereas in Madagascar, weeks with higher soil moisture had higher insect biomass. Overall, our study identifies key drivers of the seasonal distribution of flying insect biomass in a temperate and a tropical climate. This knowledge is key to understanding the spatial and seasonal availability of insects-as well as predicting future scenarios of insect biomass change.
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