| 1. |
- Abbasi, Rasha, et al.
(author)
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IceCube search for neutrinos from GRB 221009A
- 2023
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In: Proceedings of 38th International Cosmic Ray Conference (ICRC 2023). - : Sissa Medialab Srl.
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Conference paper (peer-reviewed)abstract
- GRB 221009A is the brightest Gamma Ray Burst (GRB) ever observed. The observed extremelyhigh flux of high and very-high-energy photons provide a unique opportunity to probe the predictedneutrino counterpart to the electromagnetic emission. We have used a variety of methods to searchfor neutrinos in coincidence with the GRB over several time windows during the precursor, promptand afterglow phases of the GRB. MeV scale neutrinos are studied using photo-multiplier ratescalers which are normally used to search for galactic core-collapse supernovae neutrinos. GeVneutrinos are searched starting with DeepCore triggers. These events don’t have directionallocalization, but instead can indicate an excess in the rate of events. 10 GeV - 1 TeV and >TeVneutrinos are searched using traditional neutrino point source methods which take into accountthe direction and time of events with DeepCore and the entire IceCube detector respectively. The>TeV results include both a fast-response analysis conducted by IceCube in real-time with timewindows of T0 − 1 to T0 + 2 hours and T0 ± 1 day around the time of GRB 221009A, as well asan offline analysis with 3 new time windows up to a time window of T0 − 1 to T0 + 14 days, thelongest time period we consider. The combination of observations by IceCube covers 9 ordersof magnitude in neutrino energy, from MeV to PeV, placing upper limits across the range forpredicted neutrino emission.
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| 2. |
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| 3. |
- Cuni-Sanchez, Aida, et al.
(author)
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High aboveground carbon stock of African tropical montane forests
- 2021
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 596:7873, s. 536-542
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Journal article (peer-reviewed)abstract
- Tropical forests store 40–50per cent of terrestrial vegetation carbon. However, spatial variations in aboveground live tree biomass carbon (AGC) stocks remain poorly understood, in particular in tropical montane forests. Owing to climatic and soil changes with increasing elevation, AGC stocks are lower in tropical montane forests compared with lowland forests. Here we assemble and analyse a dataset of structurally intact old-growth forests (AfriMont) spanning 44 montane sites in 12 African countries. We find that montane sites in the AfriMont plot network have a mean AGC stock of 149.4megagrams of carbon per hectare (95% confidence interval 137.1–164.2), which is comparable to lowland forests in the African Tropical Rainforest Observation Network4 and about 70per cent and 32per cent higher than averages from plot networks in montane and lowland forests in the Neotropics, respectively. Notably, our results are two-thirds higher than the Intergovernmental Panel on Climate Change default values for these forests in Africa8. We find that the low stem density and high abundance of large trees of African lowland forests is mirrored in the montane forests sampled. This carbon store is endangered: we estimate that 0.8 million hectares of old-growth African montane forest have been lost since 2000. We provide country-specific montane forest AGC stock estimates modelled from our plot network to helpto guide forest conservation and reforestation interventions. Our findings highlight the need for conserving these biodiverse and carbon-rich ecosystems.
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| 4. |
- Klimesova, Eva, et al.
(author)
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A multipurpose end-station for atomic, molecular and optical sciences and coherent diffractive imaging at ELI beamlines
- 2021
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In: The European Physical Journal Special Topics. - : Springer Nature. - 1951-6355 .- 1951-6401. ; 230:23, s. 4183-4194
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Journal article (peer-reviewed)abstract
- We report on the status of a users' end-station, MAC: a Multipurpose station for Atomic, molecular and optical sciences and Coherent diffractive imaging, designed for studies of structure and dynamics of matter in the femtosecond time-domain. MAC is located in the E1 experimental hall on the high harmonic generation (HHG) beamline of the ELI Beamlines facility. The extreme ultraviolet beam from the HHG beamline can be used at the MAC end-station together with a synchronized pump beam (which will cover the NIR/Vis/UV or THz range) for time-resolved experiments on different samples. Sample delivery systems at the MAC end-station include a molecular beam, a source for pure or doped clusters, ultrathin cylindrical or flat liquid jets, and focused beams of substrate-free nanoparticles produced by an electrospray or a gas dynamic virtual nozzle combined with an aerodynamic lens stack. We further present the available detectors: electron/ion time-of-flight and velocity map imaging spectrometers and an X-ray camera, and discuss future upgrades: a magnetic bottle electron spectrometer, production of doped nanodroplets and the planned developments of beam capabilities at the MAC end-station.
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| 5. |
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| 6. |
- Lisovski, Simeon, et al.
(author)
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The Indo-European flyway : Opportunities and constraints reflected by Common Rosefinches breeding across Europe
- 2021
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In: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 48:6, s. 1255-1266
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Journal article (peer-reviewed)abstract
- Aim: The configuration of the earth's landmasses influences global weather systems and spatiotemporal resource availability, thereby shaping biogeographical patterns and migratory routes of animals. Here, we aim to identify potential migratory barriers and corridors, as well as general migration strategies within the understudied Indo-European flyway. Location Europe, Central Asia. Major taxon studied Common rosefinches.Methods: We used a combination of theoretical optimization modelling and empirical tracking of Common Rosefinches (Carpodacus erythrinus) breeding across a large latitudinal gradient in Europe. First, we identified optimal migration routes driven by wind and resource availability along the Indo-European flyway. Second, we tracked rosefinches from five breeding populations using light-level geolocators. Finally, we compared to what extent empirical tracks overlapped with the modelled optimal routes.Results: In autumn, theoretical wind driven migration routes formed a broad-front corridor connecting Europe and the Indian Subcontinent while the theoretical resource driven routes formed a distinct north-south divide. The latter pattern also reflected the rosefinch tracks with all but the most southerly breeding birds making a northern detour towards non-breeding sites in Pakistan and India. In spring, the resource availability model predicted a similar migratory divide, however, the southern route seemed relatively more favourable and closely matched with the optimal wind driven migration routes. Spring tracking data showed larger overlap with the modelled wind driven migration routes compared to the resource driven routes.Main conclusions: Optimal wind and resource driven migration routes along the Indo-European flyway are seasonally specific and to a large extend do not overlap with one another. Under these conditions, migratory birds adopt seasonally distinct migration strategies following energy minimization strategy in autumn, driven by resource availability, and time minimizing strategy in spring, driven by wind conditions. Our optimal migration models can be applied worldwide and used to validate against empirical data to explain large-scale biogeographic pattern of migratory animals.
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| 7. |
- Mueller, Jakob C., et al.
(author)
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Micro Germline-Restricted Chromosome in Blue Tits : Evidence for Meiotic Functions
- 2023
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In: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 40:5
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Journal article (peer-reviewed)abstract
- The germline-restricted chromosome (GRC) is likely present in all songbird species but differs widely in size and gene content. This extra chromosome has been described as either a microchromosome with only limited basic gene content or a macrochromosome with enriched gene functions related to female gonad and embryo development. Here, we assembled, annotated, and characterized the first micro-GRC in the blue tit (Cyanistes caeruleus) using high-fidelity long-read sequencing data. Although some genes on the blue tit GRC show signals of pseudogenization, others potentially have important functions, either currently or in the past. We highlight the GRC gene paralog BMP15, which is among the highest expressed GRC genes both in blue tits and in zebra finches (Taeniopygia guttata) and is known to play a role in oocyte and follicular maturation in other vertebrates. The GRC genes of the blue tit are further enriched for functions related to the synaptonemal complex. We found a similar functional enrichment when analyzing published data on GRC genes from two nightingale species (Luscinia spp.). We hypothesize that these genes play a role in maintaining standard maternal inheritance or in recombining maternal and paternal GRCs during potential episodes of biparental inheritance.
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| 8. |
- Promerova, Marta, et al.
(author)
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MHC Class IIB Exon 2 Polymorphism in the Grey Partridge (Perdix perdix) Is Shaped by Selection, Recombination and Gene Conversion
- 2013
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:7, s. e69135-
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Journal article (peer-reviewed)abstract
- Among bird species, the most studied major histocompatibility complex (MHC) is the chicken MHC. Although the number of studies on MHC in free-ranging species is increasing, the knowledge on MHC variation in species closely related to chicken is required to understand the peculiarities of bird MHC evolution. Here we describe the variation of MHC class IIB (MHCIIB) exon 2 in a population of the Grey partridge (Perdix perdix), a species of high conservation concern throughout Europe and an emerging galliform model in studies of sexual selection. We found 12 alleles in 108 individuals, but in comparison to other birds surprisingly many sites show signatures of historical positive selection. Individuals displayed between two to four alleles both on genomic and complementary DNA, suggesting the presence of two functional MHCIIB loci. Recombination and gene conversion appear to be involved in generating MHCIIB diversity in the Grey partridge; two recombination breakpoints and several gene conversion events were detected. In phylogenetic analysis of galliform MHCIIB, the Grey partridge alleles do not cluster together, but are scattered through the tree instead. Thus, our results indicate that the Grey partridge MHCIIB is comparable to most other galliforms in terms of copy number and population polymorphism.
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| 9. |
- Rymesova, Dana, et al.
(author)
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Mate choice for major histocompatibility complex complementarity in a strictly monogamous bird, the grey partridge (Perdix perdix)
- 2017
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In: Frontiers in Zoology. - : Springer Science and Business Media LLC. - 1742-9994. ; 14
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Journal article (peer-reviewed)abstract
- Background: Sexual selection has been hypothesised as favouring mate choice resulting in production of viable offspring with genotypes providing high pathogen resistance. Specific pathogen recognition is mediated by genes of the major histocompatibility complex (MHC) encoding proteins fundamental for adaptive immune response in jawed vertebrates. MHC genes may also play a role in odour-based individual recognition and mate choice, aimed at avoiding inbreeding. MHC genes are known to be involved in mate choice in a number of species, with 'good genes' (absolute criteria) and 'complementary genes' (self-referential criteria) being used to explain MHC-based mating. Here, we focus on the effect of morphological traits and variation and genetic similarity between individuals in MHC class IIB (MHCIIB) exon 2 on mating in a free-living population of a monogamous bird, the grey partridge. Results: We found no evidence for absolute mate choice criteria as regards grey partridge MHCIIB genotypes, i.e., number and occurrence of amino acid variants, though red chroma of the spot behind eyes was positively associated with male pairing success. On the other hand, mate choice at MHCIIB was based on relative criteria as females preferentially paired with more dissimilar males having a lower number of shared amino acid variants. This observation supports the 'inbreeding avoidance' and 'complementary genes' hypotheses. Conclusions: Our study provides one of the first pieces of evidence for MHC-based mate choice for genetic complementarity in a strictly monogamous bird. The statistical approach employed can be recommended for testing mating preferences in cases where availability of potential mates (recorded with an appropriate method such as radiotracking) shows considerable temporal variation. Additional genetic analyses using neutral markers may detect whether MHC-based mate choice for complementarity emerges as a by-product of general inbreeding avoidance in grey partridges.
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| 10. |
- Schlebusch, Stephen A., et al.
(author)
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Rapid gene content turnover on the germline-restricted chromosome in songbirds
- 2023
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Journal article (peer-reviewed)abstract
- Songbirds have an extra chromosome with unknown function found only in their germline. This study assembles and compares this chromosome in two closely related nightingale species, finding large differences in genetic content and only one conserved gene with probable essential function. The germline-restricted chromosome (GRC) of songbirds represents a taxonomically widespread example of programmed DNA elimination. Despite its apparent indispensability, we still know very little about the GRC's genetic composition, function, and evolutionary significance. Here we assemble the GRC in two closely related species, the common and thrush nightingale. In total we identify 192 genes across the two GRCs, with many of them present in multiple copies. Interestingly, the GRC appears to be under little selective pressure, with the genetic content differing dramatically between the two species and many GRC genes appearing to be pseudogenized fragments. Only one gene, cpeb1, has a complete coding region in all examined individuals of the two species and shows no copy number variation. The acquisition of this gene by the GRC corresponds with the earliest estimates of the GRC origin, making it a good candidate for the functional indispensability of the GRC in songbirds.
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| 11. |
- Viitaniemi, Heidi M., et al.
(author)
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Impact of Z chromosome inversions on gene expression in testis and liver tissues in the zebra finch
- 2023
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In: Molecular Ecology. - 0962-1083 .- 1365-294X.
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Journal article (peer-reviewed)abstract
- Chromosomal inversions have been identified in many natural populations and can be responsible for novel traits and rapid adaptation. In zebra finch, a large region on the Z chromosome has been subject to multiple inversions, which have pleiotropic effects on multiple traits but especially on sperm phenotypes, such as midpiece and flagellum length. To understand the effect, the Z inversion has on these traits, we examined testis and liver transcriptomes of young males at different maturation times. We compared gene expression differences among three inversion karyotypes: AA, B*B* and AB*, where B* denotes the inverted regions on Z with respect to A. In testis, 794 differentially expressed genes were found and most of them were located on chromosome Z. They were functionally enriched for sperm-related traits. We also identified clusters of co-expressed genes that matched with the inversion-related sperm phenotypes. In liver, there were some enriched functions and some overrepresentation on chromosome Z with similar location as in testis. In both tissues, the overrepresented genes were located near the distal end of Z but also in the middle of the chromosome. For the heterokaryotype, we observed several genes with one allele being dominantly expressed, similar to expression patterns in one or the other homokaryotype. This was confirmed with SNPs for three genes, and interestingly one gene, DMGDH, had allele-specific expression originating mainly from one inversion haplotype in the testis, yet both inversion haplotypes were expressed equally in the liver. This karyotype-specific difference in tissue-specific expression suggests a pleiotropic effect of the inversion and thus suggests a mechanism for divergent phenotypic effects resulting from an inversion.
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| 12. |
- Westberg, Emelie, et al.
(author)
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Conditions for sample preparation and quantitative HPLC/MS-MS analysis of bulky adducts to serum albumin with diolepoxides of polycyclic aromatic hydrocarbons as models
- 2014
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In: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 406:5, s. 1519-1530
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Journal article (peer-reviewed)abstract
- Stable adducts to serum albumin (SA) from electrophilic and genotoxic compounds/metabolites can be used as biomarkers for quantification of the corresponding in vivo dose. In the present study, conditions for specific analysis of stable adducts to SA formed from carcinogenic polycyclic aromatic hydrocarbons (PAH) were evaluated in order to achieve a sensitive and reproducible quantitative method. Bulky adducts from diolepoxides (DE) of PAH, primarily DE of benzo[a]pyrene (BPDE) and also DE of dibenzo[a,l]pyrene (DBPDE) and dibenzo[a,h]anthracene (DBADE), were used as model compounds. The alkylated peptides obtained after enzymatic hydrolysis of human SA modified with the different PAHDE were principally PAHDE-His-Pro, PAHDE-His-Pro-Tyr and PAHDE-Lys. Alkaline hydrolysis under optimised conditions gave the BPDE-His as the single analyte of alkylated His, but also indicated degradation of this adduct. It was not possible to obtain the BPDE-His as one analyte from BPDE-alkylated SA through modifications of the enzymatic hydrolysis. The BPDE-His adduct was shown to be stable during the weak acidic conditions used in the isolation of SA. Enrichment by HPLC or SPE, but not butanol extraction, gave good recovery, using Protein LoBind tubes. A simple internal standard (IS) approach using SA modified with other PAHDE as IS was shown to be applicable. A robust analytical procedure based on digestion with pronase, enrichment by HPLC or SPE, and analysis with HPLC/MS-MS electrospray ionisation was achieved. A good reproducibility (coefficient of variation (CV) 11 %) was obtained, and the achieved limit of detection for the studied PAHDE, using standard instrumentation, was approximately 1 fmol adduct/mg SA analysing extract from 5 mg SA.
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| 13. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 14. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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