Search

Your search keyword '"Ivask M"' showing total 15 results
Start Over Author "Ivask M" Publication Year Range Last 3 years
15 results on '"Ivask M"'

1. Genetic parameters for bull effects on in vitro embryo production (IVP) and relationship between semen quality traits and IVP performance

Author

Gebreyesus, G., Secher, J. B., Lund, M. S., Kupisiewicz, K., Ivask, M., Hallap, T., Pärn, P., Su, G., Gebreyesus, G., Secher, J. B., Lund, M. S., Kupisiewicz, K., Ivask, M., Hallap, T., Pärn, P., and Su, G.

Abstract

In vitro production of embryos (IVP) is increasingly applied in dairy cattle breeding and promises widespread use of females of superior genetic merits. One of the current challenges with implementation of IVP is the variability in blastocyst rates. Several factors contribute to these variabilities, among which is known to be the bull used for oocytes fertilization. The extent of genetic control of bulls’ effect on IVP performances is yet to be investigated. This study estimates genetic parameters for bull effects on IVP performance traits including blastocyst rate, hatching rate and an index trait combining Blastocyst rate, Kinetic Score, and Morphology score (BL_M_K). The IVP experiments were performed using oocytes aspirated from slaughterhouse ovaries from Holstein cows, fertilized with semen from 123 Holstein bulls. A total of 77 in vitro fertilization (IVF) experiments with 163 records (different IVF groups) were available for the analysis. The results indicate low to moderate heritability and moderate to high repeatability estimates for bull effects on IVP performance traits. Our study also showed that some semen quality traits had significant effects on IVP performance. This included strong genetic correlations between pre-cryopreservation sperm viability and blastocyst rate as well as BL_M_K score at days 7 and 8. Despite the generally weak bull effect correlations and the high standard errors of the estimates, our results provide initial evidence of a measurable genetic component in the bull's impact on IVP performance traits. However, the high standard errors underscore the need for further studies with a larger sample size.

Published
2024

2. Global fine-resolution data on springtail abundance and community structure

Author

Potapov, A. M., Chen, T. -W., Striuchkova, A. V., Alatalo, J. M., Alexandre, D., Arbea, J., Ashton, T., Ashwood, F., Babenko, A. B., Bandyopadhyaya, I., Baretta, C. R. D. M., Baretta, D., Barnes, A. D., Bellini, B. C., Bendjaballah, M., Berg, M. P., Bernava, V., Bokhorst, S., Bokova, A. I., Bolger, T., Bouchard, M., Brito, R. A., Buchori, D., Castano-Meneses, G., Chauvat, M., Chomel, M., Chow, Y., Chown, S. L., Classen, A. T., Cortet, J., Cuchta, P., de la Pedrosa, A. M., De Lima, E. C. A., Deharveng, L. E., Doblas Miranda, E., Drescher, J., Eisenhauer, N., Ellers, J., Ferlian, O., Ferreira, S. S. D., Ferreira, A. S., Fiera, C., Filser, J., Franken, O., Fujii, S., Koudji, E. G., Gao, M., Gendreau-Berthiaume, B., Gers, C., Greve, M., Hamra-Kroua, S., Handa, I. T., Hasegawa, M., Heiniger, C., Hishi, T., Holmstrup, M., Homet, P., Hoye, T. T., Ivask, M., Jacques, B., Janion-Scheepers, C., Jochum, M., Joimel, S., Jorge, B. C. S., Jucevica, E., Kapinga, E. M., Kovac, L., Krab, E. J., Krogh, P. H., Kuu, A., Kuznetsova, N., Lam, W. N., Lin, D., Lindo, Z., Liu, A. W. P., Lu, J. -Z., Lucianez, M. J., Marx, M. T., Mawan, A., Mccary, M. A., Minor, M. A., Mitchell, G. I., Moreno, D., Nakamori, T., Negri, Ilaria, Nielsen, U. N., Ochoa-Hueso, R., Oliveira Filho, L. C. I., Palacios-Vargas, J. G., Pollierer, M. M., Ponge, J. -F., Potapov, M. B., Querner, P., Rai, B., Raschmanova, N., Rashid, M. I., Raymond-Leonard, L. J., Reis, A. S., Ross, G. M., Rousseau, L., Russell, D. J., Saifutdinov, R. A., Salmon, S., Santonja, M., Saraeva, A. K., Sayer, E. J., Scheunemann, N., Scholz, C., Seeber, J., Shaw, P., Shveenkova, Y. B., Slade, E. M., Stebaeva, S., Sterzynska, M., Sun, X., Susanti, W. I., Taskaeva, A. A., Tay, L. S., Thakur, M. P., Treasure, A. M., Tsiafouli, M., Twala, M. N., Uvarov, A. V., Venier, L. A., Widenfalk, L. A., Widyastuti, R., Winck, B., Winkler, D., Wu, D., Xie, Z., Yin, R., Zampaulo, R. A., Zeppelini, D., Zhang, B., Zoughailech, A., Ashford, O., Klauberg-Filho, O., Scheu, S., Negri I. (ORCID:0000-0001-5188-1408), Potapov, A. M., Chen, T. -W., Striuchkova, A. V., Alatalo, J. M., Alexandre, D., Arbea, J., Ashton, T., Ashwood, F., Babenko, A. B., Bandyopadhyaya, I., Baretta, C. R. D. M., Baretta, D., Barnes, A. D., Bellini, B. C., Bendjaballah, M., Berg, M. P., Bernava, V., Bokhorst, S., Bokova, A. I., Bolger, T., Bouchard, M., Brito, R. A., Buchori, D., Castano-Meneses, G., Chauvat, M., Chomel, M., Chow, Y., Chown, S. L., Classen, A. T., Cortet, J., Cuchta, P., de la Pedrosa, A. M., De Lima, E. C. A., Deharveng, L. E., Doblas Miranda, E., Drescher, J., Eisenhauer, N., Ellers, J., Ferlian, O., Ferreira, S. S. D., Ferreira, A. S., Fiera, C., Filser, J., Franken, O., Fujii, S., Koudji, E. G., Gao, M., Gendreau-Berthiaume, B., Gers, C., Greve, M., Hamra-Kroua, S., Handa, I. T., Hasegawa, M., Heiniger, C., Hishi, T., Holmstrup, M., Homet, P., Hoye, T. T., Ivask, M., Jacques, B., Janion-Scheepers, C., Jochum, M., Joimel, S., Jorge, B. C. S., Jucevica, E., Kapinga, E. M., Kovac, L., Krab, E. J., Krogh, P. H., Kuu, A., Kuznetsova, N., Lam, W. N., Lin, D., Lindo, Z., Liu, A. W. P., Lu, J. -Z., Lucianez, M. J., Marx, M. T., Mawan, A., Mccary, M. A., Minor, M. A., Mitchell, G. I., Moreno, D., Nakamori, T., Negri, Ilaria, Nielsen, U. N., Ochoa-Hueso, R., Oliveira Filho, L. C. I., Palacios-Vargas, J. G., Pollierer, M. M., Ponge, J. -F., Potapov, M. B., Querner, P., Rai, B., Raschmanova, N., Rashid, M. I., Raymond-Leonard, L. J., Reis, A. S., Ross, G. M., Rousseau, L., Russell, D. J., Saifutdinov, R. A., Salmon, S., Santonja, M., Saraeva, A. K., Sayer, E. J., Scheunemann, N., Scholz, C., Seeber, J., Shaw, P., Shveenkova, Y. B., Slade, E. M., Stebaeva, S., Sterzynska, M., Sun, X., Susanti, W. I., Taskaeva, A. A., Tay, L. S., Thakur, M. P., Treasure, A. M., Tsiafouli, M., Twala, M. N., Uvarov, A. V., Venier, L. A., Widenfalk, L. A., Widyastuti, R., Winck, B., Winkler, D., Wu, D., Xie, Z., Yin, R., Zampaulo, R. A., Zeppelini, D., Zhang, B., Zoughailech, A., Ashford, O., Klauberg-Filho, O., Scheu, S., and Negri I. (ORCID:0000-0001-5188-1408)

Abstract

Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.

Published
2024

4. Globally invariant metabolism but density-diversity mismatch in springtails

Author

Potapov, A. M., Guerra, C. A., van den Hoogen, J., Babenko, A., Bellini, B. C., Berg, M. P., Chown, S. L., Deharveng, L., Kováč, Ľ., Kuznetsova, N. A., Ponge, J. F., Potapov, M. B., Russell, D. J., Alexandre, D., Alatalo, J. M., Arbea, J. I., Bandyopadhyaya, I., Bernava, V., Bokhorst, S., Bolger, T., Castaño-Meneses, G., Chauvat, M., Chen, T. W., Chomel, M., Classen, A. T., Cortet, J., Čuchta, P., Manuela de la Pedrosa, A., Ferreira, S. S. D., Fiera, C., Filser, J., Franken, O., Fujii, S., Koudji, E. G., Gao, M., Gendreau-Berthiaume, B., Gomez-Pamies, D. F., Greve, M., Tanya Handa, I., Heiniger, C., Holmstrup, M., Homet, P., Ivask, M., Janion-Scheepers, C., Jochum, M., Joimel, S., Claudia, S. Jorge B., Jucevica, E., Ferlian, O., Iuñes de Oliveira Filho, L. C., Klauberg-Filho, O., Baretta, D., Krab, E. J., Kuu, A., de Lima, E. C. A., Lin, D., Lindo, Z., Liu, A., Lu, J. Z., Luciañez, M. J., Marx, M. T., Mccary, M. A., Minor, M. A., Nakamori, T., Negri, Ilaria, Ochoa-Hueso, R., Palacios-Vargas, J. G., Pollierer, M. M., Querner, P., Raschmanová, N., Rashid, M. I., Raymond-Léonard, L. J., Rousseau, L., Saifutdinov, R. A., Salmon, S., Sayer, E. J., Scheunemann, N., Scholz, C., Seeber, J., Shveenkova, Y. B., Stebaeva, S. K., Sterzynska, M., Sun, X., Susanti, W. I., Taskaeva, A. A., Thakur, M. P., Tsiafouli, M. A., Turnbull, M. S., Twala, M. N., Uvarov, A. V., Venier, L. A., Widenfalk, L. A., Winck, B. R., Winkler, D., Wu, D., Xie, Z., Yin, R., Zeppelini, D., Crowther, T. W., Eisenhauer, N., Negri I. (ORCID:0000-0001-5188-1408), Potapov, A. M., Guerra, C. A., van den Hoogen, J., Babenko, A., Bellini, B. C., Berg, M. P., Chown, S. L., Deharveng, L., Kováč, Ľ., Kuznetsova, N. A., Ponge, J. F., Potapov, M. B., Russell, D. J., Alexandre, D., Alatalo, J. M., Arbea, J. I., Bandyopadhyaya, I., Bernava, V., Bokhorst, S., Bolger, T., Castaño-Meneses, G., Chauvat, M., Chen, T. W., Chomel, M., Classen, A. T., Cortet, J., Čuchta, P., Manuela de la Pedrosa, A., Ferreira, S. S. D., Fiera, C., Filser, J., Franken, O., Fujii, S., Koudji, E. G., Gao, M., Gendreau-Berthiaume, B., Gomez-Pamies, D. F., Greve, M., Tanya Handa, I., Heiniger, C., Holmstrup, M., Homet, P., Ivask, M., Janion-Scheepers, C., Jochum, M., Joimel, S., Claudia, S. Jorge B., Jucevica, E., Ferlian, O., Iuñes de Oliveira Filho, L. C., Klauberg-Filho, O., Baretta, D., Krab, E. J., Kuu, A., de Lima, E. C. A., Lin, D., Lindo, Z., Liu, A., Lu, J. Z., Luciañez, M. J., Marx, M. T., Mccary, M. A., Minor, M. A., Nakamori, T., Negri, Ilaria, Ochoa-Hueso, R., Palacios-Vargas, J. G., Pollierer, M. M., Querner, P., Raschmanová, N., Rashid, M. I., Raymond-Léonard, L. J., Rousseau, L., Saifutdinov, R. A., Salmon, S., Sayer, E. J., Scheunemann, N., Scholz, C., Seeber, J., Shveenkova, Y. B., Stebaeva, S. K., Sterzynska, M., Sun, X., Susanti, W. I., Taskaeva, A. A., Thakur, M. P., Tsiafouli, M. A., Turnbull, M. S., Twala, M. N., Uvarov, A. V., Venier, L. A., Widenfalk, L. A., Winck, B. R., Winkler, D., Wu, D., Xie, Z., Yin, R., Zeppelini, D., Crowther, T. W., Eisenhauer, N., and Negri I. (ORCID:0000-0001-5188-1408)

Abstract

Soil life supports the functioning and biodiversity of terrestrial ecosystems. Springtails (Collembola) are among the most abundant soil arthropods regulating soil fertility and flow of energy through above- and belowground food webs. However, the global distribution of springtail diversity and density, and how these relate to energy fluxes remains unknown. Here, using a global dataset representing 2470 sites, we estimate the total soil springtail biomass at 27.5 megatons carbon, which is threefold higher than wild terrestrial vertebrates, and record peak densities up to 2 million individuals per square meter in the tundra. Despite a 20-fold biomass difference between the tundra and the tropics, springtail energy use (community metabolism) remains similar across the latitudinal gradient, owing to the changes in temperature with latitude. Neither springtail density nor community metabolism is predicted by local species richness, which is high in the tropics, but comparably high in some temperate forests and even tundra. Changes in springtail activity may emerge from latitudinal gradients in temperature, predation and resource limitation in soil communities. Contrasting relationships of biomass, diversity and activity of springtail communities with temperature suggest that climate warming will alter fundamental soil biodiversity metrics in different directions, potentially restructuring terrestrial food webs and affecting soil functioning.

Published
2023

7. Wheat field earthworms under divergent farming systems across a European climate gradient.

Author

Nuutinen V, Briones MJI, Schrader S, Dekemati I, Grujić N, Hyvönen J, Ivask M, Lassen SB, Lloret E, Ollio I, Pérez-Rodríguez P, Simon B, Sutri M, de Sutter N, Brandt KK, Peltoniemi K, Shanskiy M, Waeyenberge L, Martínez-Martínez S, and Fernández-Calviño D

Subjects
Animals, Europe, Soil chemistry, Oligochaeta physiology, Triticum, Climate, Agriculture methods
Abstract

Earthworms are a key faunal group in agricultural soils, but little is known on how farming systems affect their communities across wide climatic gradients and how farming system choice might mediate earthworms' exposure to climate conditions. Here, we studied arable soil earthworm communities on wheat fields across a European climatic gradient, covering nine pedo-climatic zones, from Mediterranean to Boreal (S to N) and from Lusitanian to Pannonian (W to E). In each zone, 20-25 wheat fields under conventional or organic farming were sampled. Community metrics (total abundance, fresh mass, and species richness and composition) were combined with data on climate conditions, soil properties, and field management and analyzed with mixed models. There were no statistically discernible differences between organic and conventional farming for any of the community metrics. The effects of refined arable management factors were also not detected, except for an elevated proportion of subsurface-feeding earthworms when crop residues were incorporated. Soil properties were not significantly associated with earthworm community variations, which in the case of soil texture was likely due to low variation in the data. Pedo-climatic zone was an overridingly important factor in explaining the variation in community metrics. The Boreal zone had the highest mean total abundance (179 individuals m -2 ) and fresh mass (86 g m -2 ) of earthworms while the southernmost Mediterranean zones had the lowest metrics (<1 individual m -2 and <1 g m -2 ). Within each field, species richness was low across the zones, with the highest values being recorded at the Nemoral and North Atlantic zones (mean of 2-3 species per field) and declining from there toward north and south. No litter-dwelling species were found in the southernmost, Mediterranean zones. These regional trends were discernibly related to climate, with the community metrics declining with the increasing mean annual temperature. The current continent-wide warming of Europe and related increase of severe and rapid onsetting droughts will likely deteriorate the living conditions of earthworms, particularly in southern Europe. The lack of interaction between the pedo-climatic zone and the farming system in our data for any of the earthworm community metrics may indicate limited opportunities for alleviating the negative effects of a warming climate in cereal field soils of Europe., (© 2024 The Author(s). Ecological Applications published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)

Published
2025
Full Text
View/download PDF

8. Molecular cloning of PRD-like homeobox genes expressed in bovine oocytes and early IVF embryos.

Author

Yaşar B, Boskovic N, Ivask M, Weltner J, Jouhilahti EM, Vill P, Skoog T, Jaakma Ü, Kere J, Bürglin TR, Katayama S, Org T, and Kurg A

Subjects
Animals, Cattle, Gene Expression Regulation, Developmental, Embryonic Development genetics, Blastocyst metabolism, Transcription Factors genetics, Transcription Factors metabolism, Oocytes metabolism, Cloning, Molecular, Fertilization in Vitro, Homeodomain Proteins genetics, Homeodomain Proteins metabolism, Genes, Homeobox
Abstract

Background: Embryonic genome activation (EGA) is a critical step in early embryonic development, as it marks the transition from relying on maternal factors to the initiation of transcription from embryo's own genome. The factors associated with EGA are not well understood and need further investigation. PRD-like (PRDL) homeodomain transcription factors (TFs) are considered to play crucial roles in this early event during development but these TFs have evolved differently, even within mammalian lineages. Different numbers of PRDL TFs have been predicted in bovine (Bos taurus); however, their divergent evolution requires species-specific confirmation and functional investigations., Results: In this study, we conducted molecular cloning of mRNAs for the PRDL TFs ARGFX, DUXA, LEUTX, NOBOX, TPRX1, TPRX2, and TPRX3 in bovine oocytes or in vitro fertilized (IVF) preimplantation embryos. Our results confirmed the expression of PRDL TF genes in early bovine development at the cDNA level and uncovered their structures. For each investigated PRDL TF gene, we isolated at least one homeodomain-encoding cDNA fragment, indicative of DNA binding and thus potential role in transcriptional regulation in developing bovine embryos. Additionally, our cDNA cloning approach allowed us to reveal breed-related differences in bovine, as evidenced by the identification of a high number of single nucleotide variants (SNVs) across the PRDL class homeobox genes. Subsequently, we observed the prediction of the 9aa transactivation domain (9aaTAD) motif in the putative protein sequence of TPRX3 leading us to conduct functional analysis of this gene. We demonstrated that the TPRX3 overexpression in bovine fibroblast induces not only protein-coding genes but also short noncoding RNAs involved in splicing and RNA editing. We supported this finding by identifying a shared set of genes between our and published bovine early embryo development datasets., Conclusions: Providing full-length cDNA evidence for previously predicted homeobox genes that belong to PRDL class improves the annotation of the bovine genome. Updating the annotation with seven developmentally-important genes will enhance the accuracy of RNAseq analysis with datasets derived from bovine preimplantation embryos. In addition, the absence of TPRX3 in humans highlights the species-specific and TF-specific regulation of biological processes during early embryo development., (© 2024. The Author(s).)

Published
2024
Full Text
View/download PDF

9. Investigating the impact of vitrification on bovine ovarian tissue morphology, follicle survival, and transcriptomic signature.

Author

Deligiannis SP, Kask K, Modhukur V, Boskovic N, Ivask M, Jaakma Ü, Damdimopoulou P, Tuuri T, Velthut-Meikas A, and Salumets A

Subjects
Animals, Female, Cattle, Fertility Preservation methods, Cell Proliferation genetics, DNA Damage genetics, Vitrification, Ovarian Follicle growth & development, Ovarian Follicle metabolism, Cryopreservation methods, Transcriptome genetics, Ovary metabolism
Abstract

Purpose: Ovarian tissue cryopreservation is vital for fertility preservation, yet its effect on ovarian tissue follicle survival and transcriptomic signature requires further investigation. This study delves into the effects of vitrification on tissue morphology, function, and transcriptomic changes, helping to find possibilities for vitrification protocol improvements., Methods: Ovarian cortex from 19 bovine animals were used to conduct pre- and post-vitrification culture followed by histological assessment, immunohistochemistry, and TUNEL assay. Follicles' functionality was assessed for viability and growth within the tissue and in isolated cultures. RNA-sequencing of ovarian tissue was used to explore the transcriptomic alterations caused by vitrification., Results: Follicle density, cell proliferation, and DNA damage in ovarian stroma were unaffected by vitrification. However, vitrified cultured tissue exhibited reduced follicle density of primordial/primary and antral follicles, while freshly cultured tissue manifested reduction of antral follicles. Increased stromal cell proliferation and DNA damage occurred in both groups post-culture. Isolated follicles from vitrified tissue exhibited similar viability to fresh follicles until day 4, after which the survival dropped. RNA-sequencing revealed minor effects of vitrification on transcriptomic signatures, while culture induced significant gene expression changes in both groups. The altered expression of WNT and hormonal regulation pathway genes post-vitrification suggests the molecular targets for vitrification protocol refinement., Conclusion: Vitrification minimally affects tissue morphology, follicle density, and transcriptomic signature post-thawing. However, culture revealed notable changes in vitrified tissue samples, including reduced follicle density, decreased isolated follicle survival, and alteration in WNT signalling and ovarian hormonal regulation pathways, highlighted them as possible limitations of the current vitrification protocol., (© 2024. The Author(s).)

Published
2024
Full Text
View/download PDF

10. Compliance with Pregnancy Prevention Recommendations for Isotretinoin Following the Amendment of the European Union Pregnancy Prevention Program: A Repeat Study in Estonia.

Author

Ivask M, Kurvits K, Uusküla M, Juppo A, Laius O, and Siven M

Abstract

Background: Isotretinoin, indicated for severe acne, is a potent teratogen and therefore contraindicated in pregnancy. Thus, the pregnancy prevention program (PPP) for isotretinoin has been introduced., Objectives: The aim of this study was to assess the concomitant use of isotretinoin and effective contraception and the rate of potential isotretinoin-exposed pregnancies in females of childbearing age in 2017-2020 in Estonia. In addition, we aimed to evaluate whether compliance with the PPP has improved compared with the previous study conducted in Estonia covering the period of 2012-2016., Methods: This retrospective, nationwide study using prescription and healthcare claims data included 2575 females aged 15-45 years who started using isotretinoin between 2017 and 2020., Results: For 64.7% of females of childbearing age, no concurrent use of an effective contraceptive was detected while using isotretinoin. A moderately higher contraceptive coverage (35.3%) was observed compared with the previous study (29.7%) (p < 0.001). Complete contraception coverage was highest in females aged 30-39 years with an adjusted OR of 12.8 (p < 0.001) compared with the age group 15-19 years and 2.47 (p < 0.001) compared with the age group 20-29 years. 17 pregnancies coincided with the isotretinoin treatment-related period. The risk for potential isotretinoin-exposed pregnancy was 6.6 (95% CI 3.9-10.5) per 1000 treated females of childbearing age over the 4-year observation period. The risk for potential isotretinoin-exposed pregnancies per 1000 treated females was 1.0 in females aged 15-19 years, 11.6 in females aged 20-29 years, 8.8 in females aged 30-39 years, and 7.4 in females aged 40-45 years (p = 0.009)., Conclusion: A slight improvement in complete contraceptive coverage during isotretinoin use has not resulted in a decrease in the risk of isotretinoin-exposed pregnancies. The contraceptive usage and risk for pregnancy vary greatly across age groups, suggesting the need for a more targeted approach to improve the effectiveness of the PPP., (© 2023. The Author(s).)

Published
2024
Full Text
View/download PDF

11. Global fine-resolution data on springtail abundance and community structure.

Author

Potapov AM, Chen TW, Striuchkova AV, Alatalo JM, Alexandre D, Arbea J, Ashton T, Ashwood F, Babenko AB, Bandyopadhyaya I, Baretta CRDM, Baretta D, Barnes AD, Bellini BC, Bendjaballah M, Berg MP, Bernava V, Bokhorst S, Bokova AI, Bolger T, Bouchard M, Brito RA, Buchori D, Castaño-Meneses G, Chauvat M, Chomel M, Chow Y, Chown SL, Classen AT, Cortet J, Čuchta P, de la Pedrosa AM, De Lima ECA, Deharveng LE, Doblas Miranda E, Drescher J, Eisenhauer N, Ellers J, Ferlian O, Ferreira SSD, Ferreira AS, Fiera C, Filser J, Franken O, Fujii S, Koudji EG, Gao M, Gendreau-Berthiaume B, Gers C, Greve M, Hamra-Kroua S, Handa IT, Hasegawa M, Heiniger C, Hishi T, Holmstrup M, Homet P, Høye TT, Ivask M, Jacques B, Janion-Scheepers C, Jochum M, Joimel S, Jorge BCS, Juceviča E, Kapinga EM, Kováč Ľ, Krab EJ, Krogh PH, Kuu A, Kuznetsova N, Lam WN, Lin D, Lindo Z, Liu AWP, Lu JZ, Luciáñez MJ, Marx MT, Mawan A, McCary MA, Minor MA, Mitchell GI, Moreno D, Nakamori T, Negri I, Nielsen UN, Ochoa-Hueso R, Oliveira Filho LCI, Palacios-Vargas JG, Pollierer MM, Ponge JF, Potapov MB, Querner P, Rai B, Raschmanová N, Rashid MI, Raymond-Léonard LJ, Reis AS, Ross GM, Rousseau L, Russell DJ, Saifutdinov RA, Salmon S, Santonja M, Saraeva AK, Sayer EJ, Scheunemann N, Scholz C, Seeber J, Shaw P, Shveenkova YB, Slade EM, Stebaeva S, Sterzynska M, Sun X, Susanti WI, Taskaeva AA, Tay LS, Thakur MP, Treasure AM, Tsiafouli M, Twala MN, Uvarov AV, Venier LA, Widenfalk LA, Widyastuti R, Winck B, Winkler D, Wu D, Xie Z, Yin R, Zampaulo RA, Zeppelini D, Zhang B, Zoughailech A, Ashford O, Klauberg-Filho O, and Scheu S

Subjects
Animals, Ecosystem, Forests, Seasons, Soil, Arthropods
Abstract

Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data., (© 2024. The Author(s).)

Published
2024
Full Text
View/download PDF

12. Uterine Fluid Extracellular Vesicles Proteome Is Altered During the Estrous Cycle.

Author

Piibor J, Waldmann A, Dissanayake K, Andronowska A, Ivask M, Prasadani M, Kavak A, Kodithuwakku S, and Fazeli A

Subjects
Female, Animals, Cattle, Uterus, Estrous Cycle metabolism, Embryonic Development, Proteome metabolism, Extracellular Vesicles metabolism
Abstract

Uterine environment is tightly and finely regulated via various signaling pathways mediated through endocrine, exocrine, autocrine, juxtacrine, and paracrine mechanisms. In utero signaling processes are paramount for normal and abnormal physiology which involves cell to cell, cells to gametes, cells to embryo, and even interkingdom communications due to presence of uterine microbiota. Extracellular vesicles (EVs) in the uterine fluid (UF) and their cargo components are known to be mediators of in utero signaling and communications. Interestingly, the changes in UF-EV proteome during the bovine estrous cycle and the effects of these differentially enriched proteins on embryo development are yet to be fully discovered. In this study, shotgun quantitative proteomics-based mass spectrometry was employed to compare UF-EV proteomes at day 0, 7, and 16 of the estrous cycle to understand the estrous cycle-dependent dynamics. Furthermore, different phase UF-EVs were supplemented in embryo cultures to evaluate their impact on embryo development. One hundred fifty-nine UF-EV proteins were differentially enriched at different time points indicating the UF-EV proteome is cycle-dependent. Overall, many identified pathways are important for normal uterine functions, early embryo development, and its nutritional needs, such as antioxidant activity, cell morphology and cycle, cellular homeostasis, cell adhesion, and carbohydrate metabolic process. Furthermore, the luteal phase UF-EVs supplementation increased in vitro blastocyst rates from 25.0 ± 5.9% to 41.0 ± 4.0% (p ≤ 0.05). Our findings highlight the importance of bovine UF-EV in uterine communications throughout the estrous cycle. Interestingly, comparison of hormone-synchronized EV proteomes to natural cycle UF-EVs indicated shift of signaling. Finally, UF-EVs can be used to improve embryo production in vitro., Competing Interests: Conflict of interest The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2023
Full Text
View/download PDF

13. Detecting Embryo Developmental Potential by Single Blastomere RNA-Seq.

Author

Nõmm M, Ivask M, Pärn P, Reimann E, Kõks S, and Jaakma Ü

Subjects
Pregnancy, Female, Animals, Cattle, RNA-Seq, Fertilization in Vitro methods, Embryonic Development genetics, RNA, Messenger, Blastomeres, Preimplantation Diagnosis methods
Abstract

Recent advances in preimplantation embryo diagnostics enable a wide range of applications using single cell biopsy and molecular-based selection techniques without compromising embryo production. This study was conducted to develop a single cell embryo biopsy technique and gene expression analysis method with a very low input volume to ensure normal embryo development and to see if there are differences in gene expression profiles between day-5 biopsied bovine embryos that developed into blastocysts and embryos arrested at morula stage. Out of the 65 biopsied morulae, 32 developed to blastocysts (49.2%). Out of the 13,580 successfully annotated genes, 1204 showed a difference in mRNA expression level. Out of these, 155 genes were expressed in embryos developing to blastocysts. The pathway enrichment analysis revealed significant enrichment in "organelle biogenesis and maintenance", "mRNA splicing" and "mitochondrial translation" pathways. These findings suggest principal differences in gene expression patterns and functional networks of embryos able to reach the blastocyst stage compared to embryos arrested in development. Our preliminary data suggest that single blastomere biopsy and selected gene expression profiles at morula stage could offer additional possibilities for early preimplantation embryo selection before transfer.

Published
2023
Full Text
View/download PDF

14. Globally invariant metabolism but density-diversity mismatch in springtails.

Author

Potapov AM, Guerra CA, van den Hoogen J, Babenko A, Bellini BC, Berg MP, Chown SL, Deharveng L, Kováč Ľ, Kuznetsova NA, Ponge JF, Potapov MB, Russell DJ, Alexandre D, Alatalo JM, Arbea JI, Bandyopadhyaya I, Bernava V, Bokhorst S, Bolger T, Castaño-Meneses G, Chauvat M, Chen TW, Chomel M, Classen AT, Cortet J, Čuchta P, Manuela de la Pedrosa A, Ferreira SSD, Fiera C, Filser J, Franken O, Fujii S, Koudji EG, Gao M, Gendreau-Berthiaume B, Gomez-Pamies DF, Greve M, Tanya Handa I, Heiniger C, Holmstrup M, Homet P, Ivask M, Janion-Scheepers C, Jochum M, Joimel S, Claudia S Jorge B, Jucevica E, Ferlian O, Iuñes de Oliveira Filho LC, Klauberg-Filho O, Baretta D, Krab EJ, Kuu A, de Lima ECA, Lin D, Lindo Z, Liu A, Lu JZ, Luciañez MJ, Marx MT, McCary MA, Minor MA, Nakamori T, Negri I, Ochoa-Hueso R, Palacios-Vargas JG, Pollierer MM, Querner P, Raschmanová N, Rashid MI, Raymond-Léonard LJ, Rousseau L, Saifutdinov RA, Salmon S, Sayer EJ, Scheunemann N, Scholz C, Seeber J, Shveenkova YB, Stebaeva SK, Sterzynska M, Sun X, Susanti WI, Taskaeva AA, Thakur MP, Tsiafouli MA, Turnbull MS, Twala MN, Uvarov AV, Venier LA, Widenfalk LA, Winck BR, Winkler D, Wu D, Xie Z, Yin R, Zeppelini D, Crowther TW, Eisenhauer N, and Scheu S

Subjects
Humans, Animals, Biodiversity, Tundra, Soil, Ecosystem, Arthropods
Abstract

Soil life supports the functioning and biodiversity of terrestrial ecosystems. Springtails (Collembola) are among the most abundant soil arthropods regulating soil fertility and flow of energy through above- and belowground food webs. However, the global distribution of springtail diversity and density, and how these relate to energy fluxes remains unknown. Here, using a global dataset representing 2470 sites, we estimate the total soil springtail biomass at 27.5 megatons carbon, which is threefold higher than wild terrestrial vertebrates, and record peak densities up to 2 million individuals per square meter in the tundra. Despite a 20-fold biomass difference between the tundra and the tropics, springtail energy use (community metabolism) remains similar across the latitudinal gradient, owing to the changes in temperature with latitude. Neither springtail density nor community metabolism is predicted by local species richness, which is high in the tropics, but comparably high in some temperate forests and even tundra. Changes in springtail activity may emerge from latitudinal gradients in temperature, predation and resource limitation in soil communities. Contrasting relationships of biomass, diversity and activity of springtail communities with temperature suggest that climate warming will alter fundamental soil biodiversity metrics in different directions, potentially restructuring terrestrial food webs and affecting soil functioning., (© 2023. The Author(s).)

Published
2023
Full Text
View/download PDF

15. Reduced Corneal Sensitivity With Neuronal Degeneration is a Novel Clinical Feature in Wolfram Syndrome.

Author

Waszczykowska A, Zmysłowska A, Bartosiewicz K, Studzian M, Pułaski Ł, Braun M, Ivask M, Koks S, Jurowski P, and Młynarski W

Subjects
Animals, Cornea innervation, Humans, Mice, Microscopy, Confocal methods, Nerve Fibers, Tomography, Optical Coherence methods, Corneal Dystrophies, Hereditary, Diabetes Mellitus, Type 1, Wolfram Syndrome diagnosis, Wolfram Syndrome genetics
Abstract

Purpose: To evaluate corneal sensitivity and corneal nerve morphology among patients with Wolfram syndrome (WFS)., Design: An observational clinical case series with confirmatory experiments., Methods: We included a group of 12 patients with biallelic mutations in the WFS1 gene and a control group composed of 30 individuals with type 1 diabetes (T1D). All participants (n = 42) underwent a complete ophthalmic examination, esthesiometry, and retinal nerve fiber layer assessment using optical coherence tomography. Morphologic assessment of corneal neuropathy by in vivo corneal confocal microscopy was conducted in 11 patients with WFS (both eyes) and 1 WFS patient (1 eye) as well as in 24 patients with T1D (both eyes in 6 patients and 1 eye in 18 patients). Additionally, corneas from Wfs1KO mice and their wild-type littermates were subjected to laser scanning confocal microscopy., Results: Corneal sensitivity was significantly reduced in patients with WFS compared with patients with T1D (4.50 cm [interquartile range, 3.50-5.50 cm] vs 6.00 cm [interquartile range, 6.00-6.00 cm]; P < 10 -5 ). Additionally, corneal nerve fiber and branch density as well as nerve fiber length were low among patients with WFS. Corneal sensitivity correlated with macular average thickness (R = 0.6928; P = .039) and best-corrected visual acuity (R = -0.61; P = .002) in the WFS group. Similarly, Wfs1 knockout mice also presented corneal neurodegeneration changes when corneal nerve fiber density and length were measured using laser scanning confocal microscopy., Conclusions: Decreased corneal sensitivity and corneal nerve degeneration are observed in WFS. Corneal sensitivity is linked with the degree of disease progression as measured by visual acuity and retinal thinning., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Published
2022
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results