| 1. |
- Drews, Anna, et al.
(författare)
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Expression and phylogenetic analyses reveal paralogous lineages of putatively classical and non-classical MHC-I genes in three sparrow species (Passer)
- 2017
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 17:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Major Histocompatibility Complex (MHC) plays a central role in immunity and has been given considerable attention by evolutionary ecologists due to its associations with fitness-related traits. Songbirds have unusually high numbers of MHC class I (MHC-I) genes, but it is not known whether all are expressed and equally important for immune function. Classical MHC-I genes are highly expressed, polymorphic and present peptides to T-cells whereas non-classical MHC-I genes have lower expression, are more monomorphic and do not present peptides to T-cells. To get a better understanding of the highly duplicated MHC genes in songbirds, we studied gene expression in a phylogenetic framework in three species of sparrows (house sparrow, tree sparrow and Spanish sparrow), using high-throughput sequencing. We hypothesize that sparrows could have classical and non-classical genes, as previously indicated though never tested using gene expression. Results: The phylogenetic analyses reveal two distinct types of MHC-I alleles among the three sparrow species, one with high and one with low level of polymorphism, thus resembling classical and non-classical genes, respectively. All individuals had both types of alleles, but there was copy number variation both within and among the sparrow species. However, the number of highly polymorphic alleles that were expressed did not vary between species, suggesting that the structural genomic variation is counterbalanced by conserved gene expression. Overall, 50% of the MHC-I alleles were expressed in sparrows. Expression of the highly polymorphic alleles was very variable, whereas the alleles with low polymorphism had uniformly low expression. Interestingly, within an individual only one or two alleles from the polymorphic genes were highly expressed, indicating that only a single copy of these is highly expressed. Conclusions: Taken together, the phylogenetic reconstruction and the analyses of expression suggest that sparrows have both classical and non-classical MHC-I genes, and that the evolutionary origin of these genes predate the split of the three investigated sparrow species 7 million years ago. Because only the classical MHC-I genes are involved in antigen presentation, the function of different MHC-I genes should be considered in future ecological and evolutionary studies of MHC-I in sparrows and other songbirds.
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| 2. |
- Ekholm, Kent, et al.
(författare)
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Ethanol-Diesel Fumigation in a Multi-Cylinder Engine
- 2008
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Ingår i: SAE technical paper 2008-01-0033.
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Konferensbidrag (refereegranskat)abstract
- Fumigation was studied in a 12 L six-cylinder heavy-duty engine. Port-injected ethanol was ignited with a small amount of diesel injected into the cylinder. The setup left much freedom for influencing the combustion process, and the aim of this study was to find operation modes that result in a combustion resembling that of a homogeneous charge compression ignition (HCCI) engine with high efficiency and low NOx emissions. Igniting the ethanol-air mixture using direct-injected diesel has attractive properties compared to traditional HCCI operation where the ethanol is ignited by pressure alone. No preheating of the mixture is required, and the amount of diesel injected can be used to control the heat release rate. The two fuel injection systems provide a larger flexibility in extending the HCCI operating range to low and high loads. It was shown that cylinder-to-cylinder variations present a considerable challenge for this type of combustion. By using closed-loop cylinder-individual control based on incylinder pressure sensors, combustion was successfully harmonized between the cylinders. Successful fumigation operation was verified up to 18.4 bar BMEP at a fixed engine speed of 1450 rpm. Two load points (4.6 bar BMEP and 9.2 bar BMEP) were studied in detail. Different diesel injection timings, diesel ratios, and EGR rates were investigated, and comparisons were drawn to pure diesel operation of the same engine. At medium load (9.2 bar BMEP), it was possible to obtain a stable HCCI-like combustion with low NOx emissions (0.1 g/kWh), reasonably high brake efficiency (37 %), and low pressure derivatives (5 bar/CAD). High load operation (18.4 bar BMEP) resulted in low pressure derivatives (5.5 bar/CAD), acceptable brake efficency (36 %), and relatively low NOx emissions (0.34 g/kWh).
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| 3. |
- Ekholm, Kent, et al.
(författare)
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Ethanol-Diesel Fumigation in a Multi-Cylinder Engine
- 2009
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Ingår i: SAE International Journal of Fuels and Lubricants. - 1946-3952. ; 1:1, s. 26-36
-
Tidskriftsartikel (refereegranskat)abstract
- Fumigation was studied in a 12 L six-cylinder heavy-duty engine. Port-injected ethanol was ignited with a small amount of diesel injected into the cylinder. The setup left much freedom for influencing the combustion process, and the aim of this study was to find operation modes that result in a combustion resembling that of a homogeneous charge compression ignition (HCCI) engine with high efficiency and low NOx emissions. Igniting the ethanol-air mixture using direct-injected diesel has attractive properties compared to traditional HCCI operation where the ethanol is ignited by pressure alone. No preheating of the mixture is required, and the amount of diesel injected can be used to control the heat release rate. The two fuel injection systems provide a larger flexibility in extending the HCCI operating range to low and high loads. It was shown that cylinder-to-cylinder variations present a challenge for this type of combustion. By using closed-loop cylinder-individual control of pressure derivatives and IMEP with the amounts of fuels injected, combustion was successfully harmonized between the cylinders. Successful fumigation operation was verified up to 18.4 bar BMEP at a fixed engine speed of 1450 rpm. Two load points (4.6 bar BMEP and 9.2 bar BMEP) were studied in detail. Different diesel injection timings, diesel ratios, and EGR rates were investigated, and comparisons were drawn to pure diesel operation of the same engine. At medium load (9.2 bar BMEP), it was possible to obtain a stable HCCI-like combustion with low NOx emissions (0.1 g/kWh), reasonably high brake efficiency (38 %), and low pressure derivatives (5 bar/CAD). High load operation (18.4 bar BMEP) resulted in low pressure derivatives (5.5 bar/CAD), acceptable brake efficency (38 %), and relatively low NOx emissions (0.34 g/kWh).
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| 4. |
- Gonzalez, Francisco, et al.
(författare)
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Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths
- 2020
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 10:14, s. 7334-7348
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Tidskriftsartikel (refereegranskat)abstract
- The search for mates and food is mediated by volatile chemicals. Insects sense food odorants and sex pheromones through odorant receptors (ORs) and pheromone receptors (PRs), which are expressed in olfactory sensory neurons. Molecular phylogenetics of ORs, informed by behavioral and functional data, generates sound hypotheses for the identification of semiochemicals driving olfactory behavior. Studying orthologous receptors and their ligands across taxa affords insights into the role of chemical communication in reproductive isolation and phylogenetic divergence. The female sex pheromone of green budworm mothHedya nubiferana(Lepidoptera, Totricidae) is a blend of two unsaturated acetates, only a blend of both elicits male attraction. Females produce in addition codlemone, which is the sex pheromone of another tortricid, codling mothCydia pomonella. Codlemone also attracts green budworm moth males. Concomitantly, green budworm and codling moth males are attracted to the host plant volatile pear ester. A congruent behavioral response to the same pheromone and plant volatile in two tortricid species suggests co-occurrence of dedicated olfactory channels. In codling moth, one PR is tuned to both compounds, the sex pheromone codlemone and the plant volatile pear ester. Our phylogenetic analysis finds that green budworm moth expresses an orthologous PR gene. Shared ancestry, and high levels of amino acid identity and sequence similarity, in codling and green budworm moth PRs offer an explanation for parallel attraction of both species to the same compounds. A conserved olfactory channel for a sex pheromone and a host plant volatile substantiates the alliance of social and habitat signals in insect chemical communication. Field attraction assays confirm that in silico investigations of ORs afford powerful predictions for an efficient identification of behavior-modifying semiochemicals, for an improved understanding of the mechanisms of host plant attraction in insect herbivores and for the further development of sustainable insect control.
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| 5. |
- Hansson, Bengt, et al.
(författare)
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Contrasting results from GWAS and QTL mapping on wing length in great reed warblers
- 2018
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 18:4, s. 867-876
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Tidskriftsartikel (refereegranskat)abstract
- A major goal in evolutionary biology is to understand the genetic basis of adaptive traits. In migratory birds, wing morphology is such a trait. Our previous work on the great reed warbler (Acrocephalus arundinaceus) shows that wing length is highly heritable and under sexually antagonistic selection. Moreover, a quantitative trait locus (QTL) mapping analysis detected a pronounced QTL for wing length on chromosome 2, suggesting that wing morphology is partly controlled by genes with large effects. Here, we re-evaluate the genetic basis of wing length in great reed warblers using a genomewide association study (GWAS) approach based on restriction site-associated DNA sequencing (RADseq) data. We use GWAS models that account for relatedness between individuals and include covariates (sex, age and tarsus length). The resulting association landscape was flat with no peaks on chromosome 2 or elsewhere, which is in line with expectations for polygenic traits. Analysis of the distribution of p-values did not reveal biases, and the inflation factor was low. Effect sizes were however not uniformly distributed on some chromosomes, and the Z chromosome had weaker associations than autosomes. The level of linkage disequilibrium (LD) in the population decayed to background levels within c. 1 kbp. There could be several reasons to why our QTL study and GWAS gave contrasting results including differences in how associations are modelled (cosegregation in pedigree vs. LD associations), how covariates are accounted for in the models, type of marker used (multi- vs. biallelic), difference in power or a combination of these. Our study highlights that the genetic architecture even of highly heritable traits is difficult to characterize in wild populations.
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| 6. |
- Henningsson, Maria, et al.
(författare)
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Closed-Loop Control of Combustion Phasing in an HCCI Engine Using VVA and Variable EGR
- 2007. - 10
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Ingår i: 5th IFAC Symposium on Advances in Automotive Control. ; 40, s. 501-506
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Konferensbidrag (refereegranskat)abstract
- A homogeneous charge compression ignition (HCCI) engine requires closed-loop control of combustion phasing for reliable operation. Variable valve actuation (VVA) has previously been shown to enable cycle-to-cycle, cylinder-individual control with high precision, but suffers from a narrow operating range. Adding variable exhaust gas recirculation (EGR) to the closed-loop control structure can extend the operating range. A mid-ranging control structure is presented here for combined VVA and EGR actuations in a multi-cylinder engine. The control structure is simple to implement and preserves the fast, cylinder-individual, and precise actuation of the VVA system while extending the operating range. Experimental results verify the performance of the control structure.
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| 7. |
- Henningsson, Maria, et al.
(författare)
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Dynamic Mapping of Diesel Engine through System identification
- 2012
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Ingår i: Identification for Automotive Systems. - London : Springer London. - 0170-8643. ; LNCIS 418, s. 223-239
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Konferensbidrag (refereegranskat)abstract
- From a control design point of view, modern diesel engines are dynamic, nonlinear, MIMO systems. This paper presents a method to find low-complexity black-box dynamic models suitable for model predictive control (MPC) of NOx and soot emissions based on on-line emissions measurements. A four-input-five-output representation of the engine is considered, with fuel injection timing, fuel injection duration, exhaust gas recirculation (EGR) and variable geometry turbo (VGT) valve positions as inputs, and indicated mean effective pressure, combustion phasing, peak pressure derivative, NOx emissions, and soot emissions as outputs. Experimental data were collected on a six-cylinder heavy-duty engine at 30 operating points. The identification procedure starts by identifying local linear models at each operating point. To reduce the number of dynamic models necessary to describe the engine dynamics, Wiener models are introduced and a clustering algorithm is proposed. A resulting set of two to five dynamic models is shown to be able to predict all outputs at all operating points with good accuracy.
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| 8. |
- Henningsson, Maria, et al.
(författare)
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Dynamic Mapping of Diesel Engine through System Identification
- 2010
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Ingår i: Proceedings of the 2010 American Control Conference. - 2378-5861 .- 0743-1619. - 9781424474264 - 9781424474271 ; , s. 3015-3020
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Konferensbidrag (refereegranskat)abstract
- From a control design point of view, modern diesel engines are dynamic, nonlinear, MIMO systems. This paper presents a method to find low-complexity black-box dynamic models suitable for model predictive control (MPC) of NOx and soot emissions based on on-line emissions measurements. A four-input-five-output representation of the engine is considered, with fuel injection timing, fuel injection duration, exhaust gas recirculation (EGR) and variable geometry turbo (VGT) valve positions as inputs, and indicated mean effective pressure, combustion phasing, peak pressure derivative, NOx emissions, and soot emissions as outputs. Experimental data were collected on a six-cylinder heavy-duty engine at 30 operating points. The identification procedure starts by identifying local linear models at each operating point. To reduce the number of dynamic models necessary to describe the engine dynamics, Wiener models are introduced and a clustering algorithm is proposed. A resulting set of two to five dynamic models is shown to be able to predict all outputs at all operating points with good accuracy.
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| 9. |
- Henningsson, Maria, et al.
(författare)
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LQG Control for Minimization of Emissions in a Diesel Engine
- 2008
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Ingår i: 2008 IEEE International Conference on Control Applications, Vol1 and 2. - 1085-1992. - 9781424422227 ; , s. 303-308
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Konferensbidrag (refereegranskat)abstract
- The problem of minimizing emissions of NO. and soot in a diesel engine using fuel injection timings and exhaust gas recirculation (EGR) valve position in a low-pressure EGR system as control variables is addressed. Two feedback variables are computed from in-cylinder pressure sensor data, the crank angle degree of 50 % fuel burnt, and the ignition delay. Empirical maps of NO, and soot according to the feedback variables form the basis of a quadratic cost function in the feedback variables which is minimized by LQG control. For a multi-cylinder engine, the number of control variables will be less than the number of output variables to be controlled, and the consequences of this setup for the LQG controller is addressed. Experimental results verify the performance of the controller at a fixed operating point of a six-cylinder heavy-duty engine.
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| 10. |
- Henningsson, Maria, et al.
(författare)
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Multiple-Input Multiple-Output Model Predictive Control of a Diesel Engine
- 2010
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Ingår i: IFAC Proceedings Volumes (IFAC-PapersOnline). - 2405-8963. ; 43:7, s. 131-136
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Tidskriftsartikel (refereegranskat)abstract
- Traditionally, diesel engine control has had to rely on indirect feedback variables and empirical open-loop maps because direct measurements of the variables representing high-level objectives, such as emissions, have not been available in production engines. With new sensors being developed, the opportunity opens to design the controller directly based on high-level objectives. In this paper, we propose to use model predictive control as a systematic way to go directly from high-level specifications to a control algorithm. The controller uses four actuator variables and five measured variables and is based on a model obtained through system identification. Experimental results on a six-cylinder heavy-duty engine around a fixed operating point demonstrate the potential of the control scheme.
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| 11. |
- Hersh, Evan, et al.
(författare)
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Sexual antagonism in the pistil varies among populations of a hermaphroditic mixed-mating plant.
- 2015
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Ingår i: Journal of evolutionary biology. - : Wiley. - 1420-9101 .- 1010-061X. ; 28:7, s. 1321-1334
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Tidskriftsartikel (refereegranskat)abstract
- Sexual conflicts and their evolutionary outcomes may be influenced by population-specific features such as mating system and ecological context; however, very few studies have investigated the link between sexual conflict and mating system. The self-compatible, mixed-mating hermaphrodite Collinsia heterophylla (Plantaginaceae) is thought to exhibit a sexual conflict over timing of stigma receptivity. This conflict involves 1) delayed stigma receptivity, which intensifies pollen competition, and 2) early fertilization forced by pollen, which reduces seed set. We investigated the potential for the conflict to occur under field conditions and performed greenhouse crosses within eight populations to assess its consistency across populations. Flowers were visited, and produced seeds after pollination, at all developmental stages, suggesting that the conflict can be of significance under natural conditions. In the greenhouse, early pollination imposed costs in all populations. Overall, the timing of first seed set was most strongly affected by the maternal parent, denoting stronger female than male ability to influence onset of stigma receptivity. Crosses also revealed a negative relationship between donor- and recipient-related onset of receptivity within individuals, a novel result hinting at trade-offs in sex-allocation or a history of antagonistic selection. Neither timing of stigma receptivity, timing of first seed set, nor pollen competitive ability covaried with population outcrossing rate. In conclusion, these results indicate that sexually antagonistic selection may be present in varying degrees in different populations of C. heterophylla, but this variation does not appear to be directly related to mating system variation. This article is protected by copyright. All rights reserved.
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| 12. |
- Höglund, Julia, et al.
(författare)
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Owls lack UV-sensitive cone opsin and red oil droplets, but see UV light at night : Retinal transcriptomes and ocular media transmittance
- 2019
-
Ingår i: Vision Research. - : Elsevier BV. - 0042-6989 .- 1878-5646. ; 158, s. 109-119
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Tidskriftsartikel (refereegranskat)abstract
- Most diurnal birds have cone-dominated retinae and tetrachromatic colour vision based on ultra-violet/violet-sensitive UV/V cones expressing short wavelength-sensitive opsin 1 (SWS1), S cones expressing short wavelength-sensitive opsin 2 (SWS2), M cones expressing medium wavelength-sensitive opsin (RH2) and L cones expressing long wavelength-sensitive opsin (LWS). Double cones (D) express LWS but do not contribute to colour vision. Each cone is equipped with an oil droplet, transparent in UV/V cones, but pigmented by carotenoids: galloxanthin in S, zeaxanthin in M, astaxanthin in L and a mixture in D cones. Owls (Strigiformes) are crepuscular or nocturnal birds with rod-dominated retinae and optical adaptations for high sensitivity. For eight species, the absence of functional SWS1 opsin has recently been documented, functional RH2 opsin was absent in three of these. Here we confirm the absence of SWS1 transcripts for the Long-eared owl (Asio otus) and demonstrate its absence for the Short-eared owl (Asio flammeus), Tawny owl (Strix aluco) and Boreal owl (Aegolius funereus). All four species had transcripts of RH2, albeit with low expression. All four species express all enzymes needed to produce galloxanthin, but lack CYP2J19 expression required to produce astaxanthin from dietary precursors. We also present ocular media transmittance of the Eurasian eagle owl (Bubo bubo) and Short-eared owl and predict spectral sensitivities of all photoreceptors of the Tawny owl. We conclude that owls, despite lacking UV/V cones, can detect UV light. This increases the sensitivity of their rod vision allowing them, for instance, to see UV-reflecting feathers as brighter signals at night.
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| 13. |
- Lankinen, Åsa, et al.
(författare)
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Can Sexual Selection Cause Divergence in Mating System-Related Floral Traits?
- 2019
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Ingår i: International journal of plant sciences. - : University of Chicago Press. - 1058-5893 .- 1537-5315. ; 180, s. 996-1003
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Tidskriftsartikel (refereegranskat)abstract
- Premise of research. The wide diversity of floral traits seen among plants is shaped by neutral and selective evolutionary processes. In outcrossing species, sexual selection from competing pollen donors is expected to be important for shaping mating system-related traits, but empirical evidence is scarce. In a previous evaluation of experimental evolution lines crossed with either one or two pollen donors (monogamous, M, or polyandrous, P, lines) at early floral stages in mixed-mating Collinsia heterophylla (Plantaginaceae), P evolved enhanced pollen competitive ability and reduced maternal seed set compared with M, in accordance with the sexually antagonistic evolution of pollen. Here, we asked whether the presence of sexual selection during pollen competition affects mating system-related floral traits in the same lines. Methodology. We compared flowering start, timing of anther-stigma contact (as an indication of timing of self-pollination), timing of stigma receptivity, and first seed set between M and P and with a source line, S (starting plants). The first three traits are later in outcrossers than in selfers of Collinsia. The last trait was expected to be earlier in P than in M, resulting from sexual selection for early seed siring of pollen. Pivotal results. Artificial polyandry for four generations resulted in later flowering start and later anther-stigma contact in P compared with M, and the latter trait was intermediate in S. Thus, P appeared more "outcrossing" than M. Timing of stigma receptivity did not differ between lines. First seed set was earlier in P than in M, as expected from sexual selection. Conclusions. Our results from the C. heterophylla experimental evolution lines suggest that a component of sexual selection during outcross pollination could enhance the patterns of floral divergence commonly found between outcrossers and selfers.
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| 14. |
- Lankinen, Åsa, et al.
(författare)
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Differential selection on pollen and pistil traits in relation to pollen competition in the context of a sexual conflict over timing of stigma receptivity
- 2016
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Ingår i: AoB Plants. - : Oxford University Press (OUP). - 2041-2851. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Sexual conflict and its evolutionary consequences are understudied in plants, but the theory of sexual conflict may help explain how selection generates and maintains variability. Here, we investigated selection on pollen and pistil traits when pollen arrives sequentially to partially receptive pistils in relation to pollen competition and a sexual conflict over timing of stigma receptivity in the mixed-mating annual Collinsia heterophylla (Plantaginaceae). In this species the conflict is generated by early fertilizing pollen that reduces seed production, which is counteracted by delaying receptivity in the recipient. We performed sequential two-donor pollinations at early floral developmental stages involving two pollen deposition schedules (with or without a time lag of 1 day), using only outcross or self and outcross pollen. We investigated pollen and pistil traits in relation to siring success (male fitness) and seed production (female fitness). In contrast to previous findings in receptive pistils in C. heterophylla and in other species, last arriving pollen donors showed highest siring success in partially receptive pistils. The last male advantage was weaker when self pollen was the first arriving donor. Two measures of germination rate (early and late) and pollen tube growth rate of first arriving donors were important for siring success in crosses with a time lag, while only late germination rate had an effect in contemporary crosses. Curiously, late stigma receptivity was negatively related to seed production in our contemporary crosses, which was opposite to expectation. Our results in combination with previous studies suggest that pollen and pistil traits in C. heterophylla are differentially advantageous depending on stage of floral development and varying pollen deposition schedules. Variation in success of these traits over floral development time may result from sexually antagonistic selection.
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| 15. |
- Lankinen, Åsa, et al.
(författare)
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Sexually antagonistic evolution caused by male-male competition in the pistil
- 2017
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 71:10, s. 2359-2369
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Tidskriftsartikel (refereegranskat)abstract
- Although sexual selection and sexual conflict are important evolutionary forces in animals, their significance in plants is uncertain. In hermaphroditic organisms, such as many plants, sexual conflict may occur both between mating partners (interlocus conflict) and between male and female sex roles within an individual (intralocus conflict). We performed experimental evolution, involving lines that were crossed with either one or two pollen donors (monogamous or polyandrous lines), in the hermaphroditic plant (Collinsia heterophylla) where early fertilizations are associated with female fitness costs (reduced seed set). Artificial polyandry for four generations resulted in enhanced pollen performance and increased female fitness costs compared to the monogamous and source (starting material) lines. Female fitness was also reduced in the monogamous line, indicating a possible trade-off between sex roles, resulting from early pollination. We performed a second experiment to investigate a potential harming effect of pollen performance on seed set. We found that high siring success of early arriving pollen competing with later-arriving pollen was associated with high female fitness costs, consistent with an interlocus sexual conflict. Our study provides evidence for the importance of sexual selection in shaping evolution of plant reproductive strategies, but also pinpoints the complexity of sexual conflict in hermaphroditic species.
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| 16. |
- Leclaire, Sarah, et al.
(författare)
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Odour-based discrimination of similarity at the major histocompatibility complex in birds
- 2017
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Ingår i: Proceedings of the Royal Society B: Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 284:1846
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Tidskriftsartikel (refereegranskat)abstract
- Many animals are known to preferentially mate with partners that are dissimilar at the major histocompatibility complex (MHC) in order to maximize the antigen binding repertoire (or disease resistance) in their offspring. Although several mammals, fish or lizards use odour cues to assessMHCsimilarity with potential partners, the ability of birds to assessMHC similarity using olfactory cues has not yet been explored. Here we used a behavioural binary choice test and high-throughput-sequencing of MHC class IIB to determine whether blue petrels can discriminate MHC similarity based on odour cues alone. Blue petrels are seabirds with particularly good sense of smell, they have a reciprocal mate choice and are known to preferentially mate withMHC-dissimilar partners. Incubating males preferentially approached the odour of the more MHC-dissimilar female, whereas incubating females showed opposite preferences. Given their mating pattern, females were, however, expected to show preference for the odour of the more MHC-dissimilar male. Further studies are needed to determine whether, as in women and female mice, the preference varies with the reproductive cycle in blue petrel females. Our results provide the first evidence that birds can use odour cues only to assess MHC dissimilarity
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| 17. |
- Leclaire, Sarah, et al.
(författare)
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Plumage microbiota covaries with the major histocompatibility complex in blue petrels
- 2018
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X.
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Tidskriftsartikel (refereegranskat)abstract
- To increase fitness, a wide range of vertebrates preferentially mate with partners that are dissimilar at the major histocompatibility complex (MHC) or that have high MHC diversity. Although MHC often can be assessed through olfactory cues, the mechanism by which MHC genes influence odour remains largely unclear. MHC class IIB molecules, which enable recognition and elimination of extracellular bacteria, have been suggested to influence odour indirectly by shaping odour-producing microbiota, i.e. bacterial communities. However, there is little evidence of the predicted covariation between an animal's MHC genotype and its bacterial communities in scent-producing body surfaces. Here, using high-throughput sequencing, we tested the covariation between MHC class IIB genotypes and feather microbiota in the blue petrel (Halobaena caerulea), a seabird with highly developed olfaction that has been suggested to rely on oduor cues during an MHC-based mate choice. First, we show that individuals with similar MHC class IIB profiles also have similar bacterial assemblages in their feathers. Then, we show that individuals with high MHC diversity have less diverse feather microbiota and also a reduced abundance of a bacterium of the genus Arsenophonus, a genus in which some species are symbionts of avian ectoparasites. Our results, showing that feather microbiota covary with MHC, are consistent with the hypothesis that individual MHC genotype may shape the semiochemical-producing microbiota in birds.
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| 18. |
- Liénard, Marjorie, et al.
(författare)
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Key biosynthetic gene subfamily recruited for pheromone production prior to the extensive radiation of Lepidoptera
- 2008
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8:270
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Tidskriftsartikel (refereegranskat)abstract
- Background Moths have evolved highly successful mating systems, relying on species-specific mixtures of sex pheromone components for long-distance mate communication. Acyl-CoA desaturases are key enzymes in the biosynthesis of these compounds and to a large extent they account for the great diversity of pheromone structures in Lepidoptera. A novel desaturase gene subfamily that displays Δ11 catalytic activities has been highlighted to account for most of the unique pheromone signatures of the taxonomically advanced ditrysian species. To assess the mechanisms driving pheromone evolution, information is needed about the signalling machinery of primitive moths. The currant shoot borer, Lampronia capitella, is the sole reported primitive non-ditrysian moth known to use unsaturated fatty-acid derivatives as sex-pheromone. By combining biochemical and molecular approaches we elucidated the biosynthesis paths of its main pheromone component, the (Z,Z)-9,11-tetradecadien-1-ol and bring new insights into the time point of the recruitment of the key Δ11-desaturase gene subfamily in moth pheromone biosynthesis. Results The reconstructed evolutionary tree of desaturases evidenced two ditrysian-specific lineages (the Δ11 and Δ9 (18C>16C)) to have orthologs in the primitive moth L. capitella despite being absent in Diptera and other insect genomes. Four acyl-CoA desaturase cDNAs were isolated from the pheromone gland, three of which are related to Δ9-desaturases whereas the fourth cDNA clusters with Δ11-desaturases. We demonstrated that this transcript (Lca-KPVQ) exclusively accounts for both steps of desaturation involved in pheromone biosynthesis. This enzyme possesses a Z11-desaturase activity that allows transforming the palmitate precursor (C16:0) into (Z)-11-hexadecenoic acid and the (Z)-9-tetradecenoic acid into the conjugated intermediate (Z,Z)-9,11-tetradecadienoic acid. Conclusion The involvement of a single Z11-desaturase in pheromone biosynthesis of a non-ditrysian moth species, supports that the duplication event leading to the origin of the Lepidoptera-specific Δ11-desaturase gene subfamily took place before radiation of ditrysian moths and their divergence from other heteroneuran lineages. Our findings uncover that this novel class of enzymes affords complex combinations of unique unsaturated fatty acyl-moieties of variable chain-lengths, regio- and stereo-specificities since early in moth history and contributes a notable innovation in the early evolution of moth-pheromones.
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| 19. |
- Lukasch, Barbara, et al.
(författare)
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Genes of the major histocompatibility complex highlight interactions of the innate and adaptive immune system
- 2017
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: A well-functioning immune defence is crucial for fitness, but our knowledge about the immune system and its complex interactions is still limited. Major histocompatibility complex (MHC) molecules are involved in T-cell mediated adaptive immune responses, but MHC is also highly upregulated during the initial innate immune response. The aim of our study was therefore to determine to what extent the highly polymorphic MHC is involved in interactions of the innate and adaptive immune defence and if specific functional MHC alleles (FA) or heterozygosity at the MHC are more important.METHODS: To do this we used captive house sparrows (Passer domesticus) to survey MHC diversity and immune function controlling for several environmental factors. MHC class I alleles were identified using parallel amplicon sequencing and to mirror immune function, several immunological tests that correspond to the innate and adaptive immunity were conducted.RESULTS: Our results reveal that MHC was linked to all immune tests, highlighting its importance for the immune defence. While all innate responses were associated with one single FA, adaptive responses (cell-mediated and humoral) were associated with several different alleles.DISCUSSION: We found that repeated injections of an antibody in nestlings and adults were linked to different FA and hence might affect different areas of the immune system. Also, individuals with a higher number of different FA produced a smaller secondary response, indicating a disadvantage of having numerous MHC alleles. These results demonstrate the complexity of the immune system in relation to the MHC and lay the foundation for other studies to further investigate this topic.
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| 20. |
- O'Connor, Emily, et al.
(författare)
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The Evolution of Highly Variable Immunity Genes Across a Passerine Bird Radiation
- 2016
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083.
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Tidskriftsartikel (refereegranskat)abstract
- In order to survive, individuals must be able to recognise and eliminate pathogens. The genes of the Major Histocompatibility Complex (MHC) play an essential role in this process in vertebrates as their diversity affects the repertoire of pathogens that can be recognised by the immune system. Emerging evidence suggests that birds within the parvorder Passerida possess an exceptionally high number of MHC genes. However, this has yet to be directly investigated using a consistent framework, and the question of how this MHC diversity has evolved has not been addressed. We used next generation sequencing to investigate how MHC class I gene copy number and sequence diversity varies across the Passerida radiation using twelve species chosen to represent the phylogenetic range of this group. Additionally, we performed phylogenetic analyses on this data to identify, for the first time, the evolutionary model that best describes how MHC class I gene diversity has evolved within Passerida. We found evidence of multiple MHC class I genes in every family tested, with an extremely broad range in gene copy number across Passerida. There was a strong phylogenetic signal in MHC gene copy number and diversity, and these traits appear to have evolved through a process of Brownian Motion in the species studied, i.e. following the pattern of genetic drift or fluctuating selection, as opposed to towards a single optimal value or through evolutionary ‘bursts’. By characterising MHC class I gene diversity across Passerida in a systematic framework, this study provides a first step towards understanding this huge variation.
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| 21. |
- Richter, Anne, et al.
(författare)
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Implementing School-Based Mental Health Services : A Scoping Review of the Literature Summarizing the Factors That Affect Implementation
- 2022
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Ingår i: International Journal of Environmental Research and Public Health. - : MDPI AG. - 1661-7827 .- 1660-4601. ; 19:6
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Forskningsöversikt (refereegranskat)abstract
- BACKGROUND: Mental illness in children and youths has become an increasing problem. School-based mental health services (SBMHS) are an attempt to increase accessibility to mental health services. The effects of these services seem positive, with some mixed results. To date, little is known about the implementation process of SBMHS. Therefore, this scoping review synthesizes the literature on factors that affect the implementation of SBMHS.METHODS: A scoping review based on four stages: (a) identifying relevant studies; (b) study selection; (c) charting the data; and (d) collating, summarizing, and reporting the results was performed. From the searches (4414 citations), 360 were include in the full-text screen and 38 in the review.RESULTS: Implementation-related factors were found in all five domains of the Consolidated Framework for Implementation Research. However, certain subfactors were mentioned more often (e.g., the adaptability of the programs, communication, or engagement of key stakeholders).CONCLUSIONS: Even though SBMHS differed in their goals and way they were conducted, certain common implementation factors were highlighted more frequently. To minimize the challenges associated with these types of interventions, learning about the implementation of SBMHS and using this knowledge in practice when introducing SBMHS is essential to achieving the best possible effects with SMBHSs.
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| 22. |
- Romare Strandh, Maria, et al.
(författare)
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Psychosocial interventions targeting parenting distress among parents with cancer : A systematic review and narrative synthesis of available interventions
- 2023
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Ingår i: Critical reviews in oncology/hematology. - : Elsevier. - 1040-8428 .- 1879-0461. ; 191
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Forskningsöversikt (refereegranskat)abstract
- BackgroundBalancing having cancer and parenting a major stressor, and may result in parenting distress, negatively affecting the whole family. To provide adequate support, knowledge of existing psychosocial interventions are crucial to guide future interventions. This study aimed to describe available psychosocial interventions for parents with cancer and dependent children (<18 years).MethodWe conducted a systematic review, and four databases were searched from January 2000 to March 2023.ResultsThirty studies were included, reporting on 22 psychosocial interventions for parents with cancer. They aimed to improve different aspects of parenting distress, and included psychoeducation and communication strategies. Interventions were beneficial to and acceptable among parents, but only a few had been evaluated. The study quality was, overall, assessed as moderate.ConclusionsThe results of this review highlight the diversity of available psychosocial interventions for parents with cancer and the outcomes on parenting distress, as well as methodological challenges.
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| 23. |
- Romare Strandh, Maria, et al.
(författare)
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The Complexity of Being a Parent in the Hospital and a Patient at Home : A Qualitative Study on Parenting Concerns and Challenges Among Parents With Cancer
- 2023
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Ingår i: Cancer Nursing. - 0162-220X .- 1538-9804.
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Tidskriftsartikel (refereegranskat)abstract
- Background Parents given a diagnosis of cancer must balance the demands of their illness and caregiving responsibilities. This can result in parental stress and have a negative impact on the well-being of the whole family. A greater understanding of the experiences of parents with cancer is necessary to provide adequate support.Objective The aim of this study was to explore parenting concerns and challenges among parents with cancer who were caring for dependent children younger than 18 years.Methods Semistructured interviews were carried out with 22 parents with cancer. Interviews were audio-recorded, transcribed, and analyzed using thematic analysis.Results Parental concerns and challenges affected parents in their parental role and their everyday family life. Three overarching themes described the struggles in balancing life as a parent and as a patient: navigating dual roles as a parent with cancer, impact of cancer on parenting, and impact on family life. Parents’ primary focus was on their children’s well-being, and they struggled to manage their own expectations of parenting and the demands on their role in the family.Conclusion The results highlight the complexity of being a parent with cancer while caring for dependent children. To support parents during the cancer journey, it is important to understand the consequences of their illness on their parental role and the family.Implications for Practice Supporting parents to feel secure in their parental role and providing support to them during their cancer journey should be integrated into routine cancer care, where parenting concerns and challenges are addressed.
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| 24. |
- Råberg, Lars, et al.
(författare)
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MHC class II genotype-by-pathogen genotype interaction for infection prevalence in a natural rodent-Borrelia system
- 2022
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 76:9, s. 2067-2075
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Tidskriftsartikel (refereegranskat)abstract
- MHC genes are extraordinarily polymorphic in most taxa. Host-pathogen coevolution driven by negative frequency-dependent selection (NFDS) is one of the main hypotheses for the maintenance of such immunogenetic variation. Here, we test a critical but rarely tested assumption of this hypothesis—that MHC alleles affect resistance/susceptibility to a pathogen in a strain-specific way, that is, there is a host genotype-by-pathogen genotype interaction. In a field study of bank voles naturally infected with the tick-transmitted bacterium Borrelia afzelii, we tested for MHC class II (DQB) genotype-by-B. afzelii strain interactions for infection prevalence between 10 DQB alleles and seven strains. One allele (DQB*37) showed an interaction, such that voles carrying DQB*37 had higher prevalence of two strains and lower prevalence of one strain than individuals without the allele. These findings were corroborated by analyses of strain composition of infections, which revealed an effect of DQB*37 in the form of lower β diversity among infections in voles carrying the allele. Taken together, these results provide rare support at the molecular genetic level for a key assumption of models of antagonistic coevolution through NFDS.
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| 25. |
- Sigeman, Hanna, et al.
(författare)
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Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration
- 2021
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 38:12, s. 5275-5291
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Tidskriftsartikel (refereegranskat)abstract
- How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (My) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event similar to 24 Ma formed "neo-sex chromosomes" consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and whereas the added-Z has retained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for nonrandom maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex linkage.
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| 26. |
- Strandh, Maria, et al.
(författare)
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Characterization of MHC class I and II genes in a subantarctic seabird, the blue petrel, Halobaena caerulea (Procellariiformes)
- 2011
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Ingår i: Immunogenetics. - : Springer Science and Business Media LLC. - 1432-1211 .- 0093-7711. ; 63:10, s. 653-666
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Tidskriftsartikel (refereegranskat)abstract
- The great polymorphism observed in the major histocompatibility complex (MHC) genes is thought to be maintained by pathogen-mediated selection possibly combined with MHC-disassortative mating, guided by MHC-determined olfactory cues. Here, we partly characterize the MHC class I and II B of the blue petrel, Halobaena caerulea (Procellariiformes), a bird with significant olfactory abilities that lives under presumably low pathogen burdens in Subantarctica. Blue petrels are long-lived, monogamous birds which suggest the necessity of an accurate mate choice process. The species is ancestral to songbirds (Passeriformes; many MHC loci), although not to gamefowls (Galliformes; few MHC loci). Considering the phylogenetic relationships and the low subantarctic pathogen burden, we expected few rather than many MHC loci in the blue petrel. However, when we analysed partial MHC class I and class II B cDNA and gDNA sequences we found evidence for as many as at least eight MHC class I loci and at least two class II B loci. These class I and II B sequences showed classical MHC characteristics, e.g. high nucleotide diversity, especially in putative peptide-binding regions where signatures of positive selection was detected. Trans-species polymorphism was found between MHC class II B sequences of the blue petrel and those of thin-billed prion, Pachyptila belcheri, two species that diverged similar to 25 MYA. The observed MHC allele richness in the blue petrel may well serve as a basis for mate choice, especially since olfactory discrimination of MHC types may be possible in this species.
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| 27. |
- Strandh, Maria, et al.
(författare)
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Global transcriptional analysis of pheromone biosynthesis-related genes in the female turnip moth, Agrotis segetum (Noctuidae) using a custom-made cDNA microarray.
- 2009
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Ingår i: Insect Biochemistry and Molecular Biology. - : Elsevier BV. - 1879-0240 .- 0965-1748. ; 39, s. 484-489
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Tidskriftsartikel (refereegranskat)abstract
- Using a custom-made cDNA microarray, global transcriptional analyses were conducted to identify genes differentially regulated in the pheromone gland as compared to the remaining insect tissue of the moth Agrotis segetum (Noctuidae). A two-fold or larger difference in relative expression levels was found for 227 of 864 genes investigated comparing the two tissues. Unexpectedly, an antennal binding protein homologue, containing a pheromone-binding/general odorant-binding protein PFAM domain, was expressed at a 56-fold higher level in the pheromone gland. Relatively higher expression levels in the pheromone gland were also found for other gene representatives putatively encoding odorant-binding proteins and chemosensory proteins, as well as a number of gene representatives putatively encoding proteins involved in juvenile hormone interactions. The largest relative up-regulation (84-fold) in the pheromone gland was found for a gene encoding a Delta11-desaturase homologue implicated in desaturation of pheromone precursors. For three gene representatives, the expression patterns were independently verified by quantitative real-time PCR (qPCR). Additionally the expression pattern in the pheromone gland for the Delta11-desaturase homologue was shown by qPCR to follow the previously known pattern of pheromone production in female A. segetum, both with respect to age and circadian rhythm, whereas the expression of a Delta9-desaturase and a chemosensory protein homologue did not share this pattern.
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| 28. |
- Strandh, Maria, et al.
(författare)
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Major histocompatibility complex class II compatibility, but not class I, predicts mate choice in a bird with highly developed olfaction.
- 2012
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Ingår i: Proceedings of the Royal Society B: Biological Sciences. - : The Royal Society. - 1471-2954 .- 0962-8452. ; 279:1746, s. 4457-4463
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Tidskriftsartikel (refereegranskat)abstract
- Mate choice for major histocompatibility complex (MHC) compatibility has been found in several taxa, although rarely in birds. MHC is a crucial component in adaptive immunity and by choosing an MHC-dissimilar partner, heterozygosity and potentially broad pathogen resistance is maximized in the offspring. The MHC genotype influences odour cues and preferences in mammals and fish and hence olfactory-based mate choice can occur. We tested whether blue petrels, Halobaena caerulea, choose partners based on MHC compatibility. This bird is long-lived, monogamous and can discriminate between individual odours using olfaction, which makes it exceptionally well suited for this analysis. We screened MHC class I and II B alleles in blue petrels using 454-pyrosequencing and quantified the phylogenetic, functional and allele-sharing similarity between individuals. Partners were functionally more dissimilar at the MHC class II B loci than expected from random mating (p = 0.033), whereas there was no such difference at the MHC class I loci. Phylogenetic and non-sequence-based MHC allele-sharing measures detected no MHC dissimilarity between partners for either MHC class I or II B. Our study provides evidence of mate choice for MHC compatibility in a bird with a high dependency on odour cues, suggesting that MHC odour-mediated mate choice occurs in birds.
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| 29. |
- Strandh, Maria, et al.
(författare)
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Natural selection acts on floral traits associated with selfing rate among populations of Mixed-Mating collinsia heterophylla (Plantaginaceae)
- 2017
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Ingår i: International Journal of Plant Sciences. - : University of Chicago Press. - 1058-5893 .- 1537-5315. ; 178:8, s. 594-606
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Tidskriftsartikel (refereegranskat)abstract
- Premise of research. A major aim in plant research is to understand the micro-and macroevolutionary processes generating the great diversity of mating systems and floral traits found in flowering plants. Using Collinsia heterophylla, a mixed-mating species in a genus with described variation in selfing rate and associated floral traits among species, we investigated (i) intraspecific selfing rate variation in relation to variation in environmental factors and floral traits and (ii) whether selection or genetic drift determine floral trait variation. Methodology. We estimated selfing rate in 21 Californian populations by means of microsatellite markers and investigated its relationship with sampling region, altitude, population ground cover, stage of stigma receptivity, stage of anther-stigma contact (indicating stage of self-pollination), flower size, and start of flowering. Phenotypic floral trait differentiation (PST) for the floral traits was contrasted with neutral genetic differentiation (FST). Pivotal results. The population selfing rate ranged between 0.16 and 0.71 and differed between regions, but it did not correlate with environmental factors. The best predictor of high selfing rate was early stigma receptivity. Stage of anther-stigma contact showed a nonlinear quadratic relation with selfing rate. PST was substantially higher than FST in the four traits, suggesting that variation in mating-related floral traits is shaped by natural selection. Conclusions. The importance of stage of stigma receptivity for predicting selfing rate in C. heterophylla is in line with the pattern found among Collinsia species, potentially indicating that microevolutionary processes in mixed mating influence macroevolutionary processes. The detected effect of natural selection acting on stage of stigma receptivity, in combination with previously detected genetic influence on this trait, gives support to the hypothesis that variability in mating system is adaptive.
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| 30. |
- Strandh, Maria
(författare)
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Pheromones, genes & transcriptomes. A molecular analysis of moth sex pheromone production.
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Female moths emit sex pheromones to lure a mate. In this thesis I examined the transcriptomes of female moth pheromone glands in order to identify genes encoding proteins involved in pheromone production. Two cDNA-libraries were constructed from Agrotis segetum (Noctuidae) pheromone glands and the remaining body tissue, respectively. The libraries were sampled and sequenced. A total of 707 unigenes was identified. One third of the unigenes were exclusively found in the gland library. Transcripts more abundantly found in the pheromone gland and with a putative function in pheromone biosynthesis, included homologs of the following genes: a Δ11-desaturase, a G-protein subunit, a chemosensory protein and a juvenile hormone binding protein. The unigene set identified in A. segetum was used to construct a cDNA microarray. Differential gene expression in the A. segetum pheromone gland versus the remaining body tissue was studied by comparative hybridization of RNA-derived cDNA targets from the two tissues. Of the gene reporters, 65% were differentially expressed in the pheromone gland compared to the body tissue, with approximately half of these reporters expressed at higher levels in the respective tissue. The highest gene expression levels in the pheromone gland were detected for a Δ11-desaturase homolog and an antennal binding protein homolog. The up-regulation of several chemosensory proteins and proteins involved in juvenile hormone interactions in the pheromone glands is also reported. Agrotis ipsilon is closely related to A. segetum. The two species have different pheromone blends but some pheromone components are in common. A cross-species hybridization experiment was performed between A. ipsilon and A. segetum pheromone glands on the microarray platform derived from A. segetum. We identified transcriptional differences in the two species that could account for the differences in pheromone blends. Candidates for the pheromone differences included two different reductases that were expressed more highly in the respective species. Desaturase-encoding transcripts of the primitive moth Lampronia capitella (Incurvariodea, Prodoxidae) were characterized and functionally expressed in yeast. A Δ11-desaturase, that arose from a gene duplication event, is present and most likely responsible for the conjugated diene pheromone of L. capitella. The presence of an active Δ11-desaturase in the pheromone gland of this primitive species implies that the gene duplication took place before the split of the ditrysian
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| 31. |
- Strandh, Maria, et al.
(författare)
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Transcriptional analysis of the pheromone gland of the turnip moth, Agrotis segetum (Noctuidae), reveals candidate genes involved in pheromone production.
- 2008
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Ingår i: Insect Molecular Biology. - : Wiley. - 1365-2583 .- 0962-1075. ; 17:1, s. 73-85
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Tidskriftsartikel (refereegranskat)abstract
- Moths generally rely on pheromone communication for mate finding. The pheromone components of most moths are produced by a common pathway of fatty-acid biosynthesis coupled with species-specific modifications of the final products. Some genes involved in moth pheromone production have previously been described, whereas others remain to be characterized and thus the molecular mechanisms accounting for the production of species-specific blends are far from understood. The turnip moth, Agrotis segetum, has a multicomponent pheromone, consisting of at least four components derived from palmitic and stearic acid. Different populations produce and respond to different pheromone blends, which makes this species an excellent model for research on genes and molecular mechanisms involved in moth pheromone production. For this purpose, we performed an expressed sequence tag (EST) analysis of two cDNA libraries, one representing the female pheromone gland and the other representing the remainder of the insect body. Among 2285 ESTs analysed altogether, we identified a unigene set of 707 putative gene representatives. The comparative distribution of those in the two libraries showed the transcriptomes of the tissues to be clearly different. One third of the gene representatives were exclusively found in the pheromone gland. From sequence homology to public database information we assigned putative functional roles for a majority of the unigenes and then compared functional profiles of the two tissues. In the set of ESTs more abundant in the pheromone gland library, we found homologues of an acyl-CoA Delta11-desaturase, a G-protein subunit, a chemosensory protein as well as a juvenile hormone binding protein.
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| 32. |
- Strandh, Maria, et al.
(författare)
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Within-host competition between Borrelia afzelii ospC strains in wild hosts as revealed by massively parallel amplicon sequencing.
- 2015
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Ingår i: Philosophical Transactions of the Royal Society B: Biological Sciences. - : The Royal Society. - 1471-2970 .- 0962-8436. ; 370:1675
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Tidskriftsartikel (refereegranskat)abstract
- Infections frequently consist of more than one strain of a given pathogen. Experiments have shown that co-infecting strains often compete, so that the infection intensity of each strain in mixed infections is lower than in single strain infections. Such within-host competition can have important epidemiological and evolutionary consequences. However, the extent of competition has rarely been investigated in wild, naturally infected hosts, where there is noise in the form of varying inoculation doses, asynchronous infections and host heterogeneity, which can potentially alleviate or eliminate competition. Here, we investigated the extent of competition between Borrelia afzelii strains (as determined by ospC genotype) in three host species sampled in the wild. For this purpose, we developed a protocol for 454 amplicon sequencing of ospC, which allows both detection and quantification of each individual strain in an infection. Each host individual was infected with one to six ospC strains. The infection intensity of each strain was lower in mixed infections than in single ones, showing that there was competition. Rank-abundance plots revealed that there was typically one dominant strain, but that the evenness of the relative infection intensity of the different strains in an infection increased with the multiplicity of infection. We conclude that within-host competition can play an important role under natural conditions despite many potential sources of noise, and that quantification by next-generation amplicon sequencing offers new possibilities to dissect within-host interactions in naturally infected hosts.
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| 33. |
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| 34. |
- Videvall, Elin, et al.
(författare)
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Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
- 2017
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Ingår i: mSystems. - 2379-5077. ; 2:6
-
Tidskriftsartikel (refereegranskat)abstract
- The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples (rs > 0.7) but had low repeatability for cloacal (rs = 0.39) and ileal (rs = -0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S rRNA data, which can aid future gut microbiome studies. IMPORTANCE The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.
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| 35. |
- Videvall, Elin, et al.
(författare)
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Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
- 2017
-
Ingår i: mSystems. - : American Society for Microbiology. - 2379-5077. ; 2:6
-
Tidskriftsartikel (refereegranskat)abstract
- The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.
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| 36. |
- Videvall, Elin, et al.
(författare)
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Early-life gut dysbiosis linked to juvenile mortality in ostriches
- 2020
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 8:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbiosis, and if particular gut regions or specific time periods during ontogeny are more susceptible. We also know very little of this process in non-model organisms, despite an increasing realization of the general importance of gut microbiota for health. Methods: Here, we examine the changes that occur in the microbiome during dysbiosis in different parts of the gastrointestinal tract in a long-lived bird with high juvenile mortality, the ostrich (Struthio camelus). We evaluated the 16S rRNA gene composition of the ileum, cecum, and colon of 68 individuals that died of suspected enterocolitis during the first 3 months of life (diseased individuals), and of 50 healthy individuals that were euthanized as age-matched controls. We combined these data with longitudinal environmental and fecal sampling to identify potential sources of pathogenic bacteria and to unravel at which stage of development dysbiosis-associated bacteria emerge. Results: Diseased individuals had drastically lower microbial alpha diversity and differed substantially in their microbial beta diversity from control individuals in all three regions of the gastrointestinal tract. The clear relationship between low diversity and disease was consistent across all ages in the ileum, but decreased with age in the cecum and colon. Several taxa were associated with mortality (Enterobacteriaceae, Peptostreptococcaceae, Porphyromonadaceae, Clostridium), while others were associated with health (Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, Turicibacter, Roseburia). Environmental samples showed no evidence of dysbiosis-associated bacteria being present in either the food, water, or soil substrate. Instead, the repeated fecal sampling showed that pathobionts were already present shortly after hatching and proliferated in individuals with low microbial diversity, resulting in high mortality several weeks later. Conclusions: Identifying the origins of pathobionts in neonates and the factors that subsequently influence the establishment of diverse gut microbiota may be key to understanding dysbiosis and host development. [MediaObject not available: See fulltext.]
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| 37. |
- Videvall, Elin, et al.
(författare)
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Major shifts in gut microbiota during development and its relationship to growth in ostriches
- 2019
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 28:10, s. 2653-2667
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Tidskriftsartikel (refereegranskat)abstract
- The development of gut microbiota during ontogeny is emerging as an important process influencing physiology, immunity and fitness in vertebrates. However, knowledge of how bacteria colonize the juvenile gut, how this is influenced by changes in the diversity of gut bacteria and to what extent this influences host fitness, particularly in nonmodel organisms, is lacking. Here we used 16S rRNA gene sequencing to describe the successional development of the faecal microbiome in ostriches (Struthio camelus, n = 66, repeatedly sampled) over the first 3 months of life and its relationship to growth. We found a gradual increase in microbial diversity with age that involved multiple colonization and extinction events and a major taxonomic shift in bacteria that coincided with the cessation of yolk absorption. Comparisons with the microbiota of adults (n = 5) revealed that the chicks became more similar in their microbial diversity and composition to adults as they aged. There was a five-fold difference in juvenile growth during development, and growth during the first week of age was strongly positively correlated with the abundance of the genus Bacteroides and negatively correlated with Akkermansia. After the first week, the abundances of six phylogenetically diverse families (Peptococcaceae, S24-7, Verrucomicrobiae, Anaeroplasmataceae, Streptococcaceae, Methanobacteriaceae) were associated with subsequent reductions in chick growth in an age-specific and transient manner. These results have broad implications for our understanding of the development of gut microbiota and its associations with animal growth.
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| 38. |
- Videvall, Elin, et al.
(författare)
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Measuring the gut microbiome in birds : Comparison of faecal and cloacal sampling
- 2018
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 18:3, s. 424-434
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Tidskriftsartikel (refereegranskat)abstract
- The gut microbiomes of birds and other animals are increasingly being studied in ecological and evolutionary contexts. Numerous studies on birds and reptiles have made inferences about gut microbiota using cloacal sampling; however, it is not known whether the bacterial community of the cloaca provides an accurate representation of the gut microbiome. We examined the accuracy with which cloacal swabs and faecal samples measure the microbiota in three different parts of the gastrointestinal tract (ileum, caecum, and colon) using a case study on juvenile ostriches, Struthio camelus, and high-throughput 16S rRNA sequencing. We found that faeces were significantly better than cloacal swabs in representing the bacterial community of the colon. Cloacal samples had a higher abundance of Gammaproteobacteria and fewer Clostridia relative to the gut and faecal samples. However, both faecal and cloacal samples were poor representatives of the microbial communities in the caecum and ileum. Furthermore, the accuracy of each sampling method in measuring the abundance of different bacterial taxa was highly variable: Bacteroidetes was the most highly correlated phylum between all three gut sections and both methods, whereas Actinobacteria, for example, was only strongly correlated between faecal and colon samples. Based on our results, we recommend sampling faeces, whenever possible, as this sample type provides the most accurate assessment of the colon microbiome. The fact that neither sampling technique accurately portrayed the bacterial community of the ileum nor the caecum illustrates the difficulty in noninvasively monitoring gut bacteria located further up in the gastrointestinal tract. These results have important implications for the interpretation of avian gut microbiome studies.
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- Westerdahl, Helena, et al.
(författare)
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The genomic architecture of the passerine MHC region : high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes
- 2022
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 22:6, s. 2379-2395
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Tidskriftsartikel (refereegranskat)abstract
- The major histocompatibility complex (MHC) is of central importance to the immune system, and an optimal MHC diversity is believed to maximize pathogen elimination. Birds show substantial variation in MHC diversity, ranging from few genes in most bird orders to very many genes in passerines. Our understanding of the evolutionary trajectories of the MHC in passerines is hampered by lack of data on genomic organization. Therefore, we assembled and annotated the MHC genomic region of the great reed warbler (Acrocephalus arundinaceus), using long-read sequencing and optical mapping. The MHC region is large (>5.5 Mb), characterized by structural changes compared to hitherto investigated bird orders and shows higher repeat content than the genome average. These features were supported by analyses in three additional passerines. MHC genes in passerines are found in two different chromosomal arrangements, either as single copy MHC genes located among non-MHC genes, or as tandemly duplicated tightly linked MHC genes. Some single copy MHC genes are old and putative orthologues among species. In contrast tandemly duplicated MHC genes are monophyletic within species and have evolved by simultaneous gene duplication of several MHC genes. Structural differences in the MHC genomic region among bird orders seem substantial compared to mammals and have possibly been fuelled by clade-specific immune system adaptations. Our study provides methodological guidance in characterizing complex genomic regions, constitutes a resource for MHC research in birds, and calls for a revision of the general belief that avian MHC has a conserved gene order and small size compared to mammals.
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