270 results on '"Mitochondrial-Dna"'
Search Results
2. Sea snakes rarely venture far from home
- Author
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Lukoschek, Vimoksalehi and Shine, Richard
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Coral reefs ,demographic isolation ,live-bearing ,marine reptile ,philopatrygenetic differentiation measure ,great-barrier-reef ,emydocephalus-annulatus ,aipysurus-laevis ,population-structure ,northern australia ,mitochondrial-dna ,dispersal ,fish ,hydrophiidae - Published
- 2012
3. Asymmetrical Gene Flow in a Hybrid Zone of Hawaiian Schiedea (Caryophyllaceae) Species with Contrasting Mating Systems
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Wallace, Lisa E., Culley, Theresa M., Weller, Stephen G., Sakai, Ann K., Kuenzi, Ashley, Roy, Tilottama, Wagner, Warren L., and Nepokroeff, Molly
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adaptive radiation ,salicaria caryophyllaceae ,inbreeding depression ,phylogenetic analysis ,silversword alliance ,wind pollination ,interspecific hybridization ,natural-populations ,gynodioecious plant ,mitochondrial-dna - Abstract
Asymmetrical gene flow, which has frequently been documented in naturally occurring hybrid zones, can result from various genetic and demographic factors. Understanding these factors is important for determining the ecological conditions that permitted hybridization and the evolutionary potential inherent in hybrids. Here, we characterized morphological, nuclear, and chloroplast variation in a putative hybrid zone between Schiedea menziesii and S. salicaria, endemic Hawaiian species with contrasting breeding systems. Schiedea menziesii is hermaphroditic with moderate selfing; S. salicaria is gynodioecious and wind-pollinated, with partially selfing hermaphrodites and largely outcrossed females. We tested three hypotheses: 1) putative hybrids were derived from natural crosses between S. menziesii and S. salicaria, 2) gene flow via pollen is unidirectional from S. salicaria to S. menziesii and 3) in the hybrid zone, traits associated with wind pollination would be favored as a result of pollen-swamping by S. salicaria. Schiedea menziesii and S. salicaria have distinct morphologies and chloroplast genomes but are less differentiated at the nuclear loci. Hybrids are most similar to S. menziesii at chloroplast loci, exhibit nuclear allele frequencies in common with both parental species, and resemble S. salicaria in pollen production and pollen size, traits important to wind pollination. Additionally, unlike S. menziesii, the hybrid zone contains many females, suggesting that the nuclear gene responsible for male sterility in S. salicaria has been transferred to hybrid plants. Continued selection of nuclear genes in the hybrid zone may result in a population that resembles S. salicaria, but retains chloroplast lineage(s) of S. menziesii.
- Published
- 2011
4. Genetic Composition of Laboratory Stocks of the Self-Fertilizing Fish Kryptolebias marmoratus: A Valuable Resource for Experimental Research
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Tatarenkov, Andrey, Ring, Brian C., Elder, John F., Bechler, David L., and Avise, John C.
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rivulus-ocellatus-marmoratus ,hermaphroditic fish ,mangrove killifish ,oncogene expression ,sequence alignment ,mitochondrial-dna ,hepatic neoplasms ,acute toxicity ,air-exposure ,diethylnitrosamine - Abstract
The hermaphroditic Mangrove Killifish, Kryptolebias marmoratus, is the world's only vertebrate that routinely self-fertilizes. As such, highly inbred and presumably isogenic “clonal” lineages of this androdioecious species have long been maintained in several laboratories and used in a wide variety of experiments that require genetically uniform vertebrate specimens. Here we conduct a genetic inventory of essentially all laboratory stocks of the Mangrove Killifish held worldwide. At 32 microsatellite loci, these stocks proved to show extensive interline differentiation as well as some intraline variation, much of which can be attributed to post-origin de novo mutations and/or to the segregation of polymorphisms from wild progenitors. Our genetic findings also document that many of the surveyed laboratory strains are not what they have been labeled, apparently due to the rather frequent mishandling or unintended mixing of various laboratory stocks over the years. Our genetic inventory should help to clarify much of this confusion about the clonal identities and genetic relationships of laboratory lines, and thereby help to rejuvenate interest in K. marmoratus as a reliable vertebrate model for experimental research that requires or can capitalize upon “clonal” replicate specimens.
- Published
- 2010
5. Circular mitochondrial DNA: A Geant4-DNA user application for evaluating radiation-induced damage in circular mitochondrial DNA
- Author
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Mohammad Bagher Tavakoli, Habiballah Moradi, Hossein Khanahmad, and Mohsen Hosseini
- Subjects
Geant4 ,geometrical model ,mitochondrial-DNA ,Monte Carlo ,radiation ,Medical technology ,R855-855.5 - Abstract
Background: The aim of this study was to develop a nucleotide geometrical model of the circular mitochondrial DNA (mt-DNA) structure using Geant4-DNA toolkit to predict the radiation-induced damages such as single-strand breaks (SSB), double-strand breaks (DSB), and some other physical parameters. Methods: Our model covers the organization of a circular human mt genetic system. The current model includes all 16,659 base pairs of human mt-DNA. This new mt-DNA model has been preliminarily tested in this work by determining SSB and DSB DNA damage yields and site-hit probabilities due to the impact of proton particles. The accuracy of the geometry was determined by three-dimensional visualization in various ring element numbers. The hit locations were determined with respect to a reference coordinate system, and the corresponding base pairs were stored in the ROOT output file. Results: The coordinate determination according to the algorithm was consistent with the expected results. The output results contain the information about the energy transfers in the backbone region of the DNA double helix. The output file was analyzed by root analyzing tools. Estimation of SSBs and DSBs yielded similar results with the increment of incident particle linear energy transfer. In addition, these values seem to be consistent with the corresponding experimental determinations. Conclusions: This model can be used in numerical simulations of mt-DNA radiation interactions to perform realistic evaluations of DNA-free radical reactions. This work will be extended to supercoiled conformation in the near future.
- Published
- 2017
- Full Text
- View/download PDF
6. A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins
- Author
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Ingo Müller, Per Ericson, Filip Thörn, Knud Jønsson, Mozes Blom, and Martin Irestedt
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natural history collections ,SEQUENCES ,MITOCHONDRIAL-DNA ,genomic libraries ,COLLECTIONS ,PARADISE ,Museums ,High-Throughput Nucleotide Sequencing ,FORMAT ,Genomics ,Sequence Analysis, DNA ,museomics ,MUSEUM SPECIMENS ,Birds ,birds ,REVEALS ,HISTORY ,Genetics ,ANCIENT DNA ,RADIATION ,Animals ,Ecology, Evolution, Behavior and Systematics ,Biotechnology - Abstract
Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present-day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high-throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.
- Published
- 2022
7. Morphometric and Genetic Characterization of Honey Bees (Apis mellifera L.) From Thrace Region of Turkey
- Author
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Fulya Özdil, Devrim Oskay, Raziye Işık, Selen Yatkın, Abdurrahman Aydın, and Ahmet Güler
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Dna Sequencing ,4th Lineage ,Thrace Honey Bees ,Trna(Leu)-Cox2 Gene ,Turkish Honeybees ,Microsatellite ,Apidae Populations ,Phylogenetic-Relationships ,Molecular Characterization ,Plant Science ,Apis Mellifera ,Mitochondrial-Dna ,Insect Science ,Sequence ,Discrimination ,Carnica ,Morphometrics - Abstract
A detailed morphological and genetic characterization of honey bees from the Thrace and west Anatolian regions of Turkey was surveyed. A total of 1650 worker bee samples (110 colonies) were evaluated with the forty-one morphological characters and 217 honey bee samples were analyzed via DNA sequencing of the tRNA(leu)-cox2 region. In this study, three different populations, Thrace (Tekirdag, Kirklareli and Edirne provinces), Island Gokceada, and western Anatolia were formed based on morphometrics, since the Marmara Sea has taken a very strong barrier role in this formation. The morphological similarity of the Thrace population was supported by the genetic analysis. The sequencing of the tRNA(leu)-cox2 region revealed twenty-two different haplotypes, sixteen of which are novel. The C2d, macedonica-like haplotype, was the most widely found haplotype (48%) all around the Thrace region. Along with the C2d haplotype, previously published C2s, C2v, C2i, C2j, and C2h haplotypes, and the newly found haplotypes were also observed but less frequently. In this study, Thrace honey bees were found to more similar to A. m. macedonica through the mtDNA sequence analysis, whereas carnica-like honey bees were only found near the Istranca mountain ridges, Kirklareli province and macedonica-like honey bees all around the Thrace region. According to our results, some of the Thrace honey bee populations may be both A. m. carnica and A. m. macedonica but the assignment to the latter subspecies seems more likely due to its geographic range. Scientific and Technological Research Council of Turkey-TUBITAK [3001-TOVAG 114O883] The authors are deeply indebted to numerous people that have contributed to this study for providing honey bee reference samples; Ljubia Z. Stanisavljevi for providing A. m. carnica samples from Serbia and Leonidas Charistos for providing A. m. macedonica samples from Greece. Financial support for this research was provided by The Scientific and Technological Research Council of Turkey-TUBITAK through the Project 3001-TOVAG 114O883, Project Coordinator Fulya ozdil.
- Published
- 2022
8. Haematobium irritans and Haematobium titillans as potential vectors of Parabronema skrjabini in camels (Camelus bactrianus) in Inner Mongolia, China.
- Author
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Liu, Yang, Zhao, Zhiguo, Yang, Xiaoye, Yang, Lianru, Yang, Bo, Zheng, Wenqing, Li, Wensheng, Luo, Xiaoping, Wang, Rui, Gu, Wei, and Wang, Penglong
- Subjects
- *
CAMELS , *HORN fly , *ANIMAL culture , *CYTOCHROME oxidase , *LIFE history theory - Abstract
Parabronema skrjabini is one of the most harmful nematodes to camels and is responsible for economic losses in animal husbandry industry. There is an urgent need for in-depth studies of potential vectors of the nematode due to its scant regarding information. As previous studies indicated that flies may be the vectors of P. skrjabini, we captured flies in the main camel-producing areas of Inner Mongolia. After autopsy of the specimens of two species of horn flies, we observed the morphology of the suspected nematode larvae found in them. Internal transcribed spacer ribosomal-DNA gene sequences were considered the best candidate to confirm the species of the larvae found. Our results showed that the homology compared with P. skrjabini was 99.5% in GenBank. Subsequently, we preliminarily identified two species of horn flies through morphological observation and then sequenced the mitochondrial-DNA-gene cytochrome oxidase subunit I obtained from two species of horn flies, with 100 and 99.2% similarity to sequences deposited in GenBank, respectively. Thus, we identified Haematobia titillans and Haematobia irritans and provided evidence for their potential role as vectors of parabronemosis. Our study provides reference for future research on the life history of the nematode and the vectors of parabronemosis. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
9. Liquid biopsy
- Subjects
GENOMIC DNA ,MITOCHONDRIAL-DNA ,Biopsy ,circulating cells ,spent embryo culture medium ,cell-free DNA ,Artificial Intelligence ,Neoplasms ,NONINVASIVE PRENATAL-DIAGNOSIS ,Humans ,MATERNAL PLASMA ,GENE-EXPRESSION ,non-invasive prenatal testing ,next generation sequencing ,Tumor ,liquid biopsy ,INCIDENTAL DETECTION ,EMBRYO CULTURE-MEDIUM ,CIRCULATING TUMOR-CELLS ,Reproductive Medicine ,FREE FETAL DNA ,IVF ,preimplantation genetic testing ,Cell-Free Nucleic Acids ,Biomarkers ,ART - Abstract
Liquid biopsy is the process of sampling and analyzing body fluids, which enables non-invasive monitoring of complex biological systems in vivo. Liquid biopsy has myriad applications in health and disease as a wide variety of components, ranging from circulating cells to cell-free nucleic acid molecules, can be analyzed. Here, we review different components of liquid biopsy, survey state-of-the-art, non-invasive methods for detecting those components, demonstrate their clinical applications and discuss ethical considerations. Furthermore, we emphasize the importance of artificial intelligence in analyzing liquid biopsy data with the aim of developing ethically-responsible non-invasive technologies that can enhance individualized healthcare. While previous reviews have mainly focused on cancer, this review primarily highlights applications of liquid biopsy in reproductive medicine.
- Published
- 2021
10. Tetracycline-induced mitohormesis mediates disease tolerance against influenza
- Author
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Adrienne Mottis, Terytty Y. Li, Gaby El Alam, Alexis Rapin, Elena Katsyuba, David Liaskos, Davide D’Amico, Nicola L. Harris, Mark C. Grier, Laurent Mouchiroud, Mark L. Nelson, and Johan Auwerx
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r-package ,i interferon ,General Medicine ,Tetracycline ,Anti-Bacterial Agents ,Mice ,antibacterial ,Orthomyxoviridae Infections ,Tetracyclines ,Doxycycline ,mitochondrial-dna ,Influenza, Human ,derivatives ,Animals ,Humans ,stress-response ,protein ,genes ,innate immunity - Abstract
Mitohormesis defines the increase in fitness mediated by adaptive responses to mild mitochondrial stress. Tetracyclines inhibit not only bacterial but also mitochondrial translation, thus imposing a low level of mitochondrial stress on eukaryotic cells. We demonstrate in cell and germ-free mouse models that tetracyclines induce a mild adaptive mitochondrial stress response (MSR), involving both the ATF4-mediated integrative stress response and type I interferon (IFN) signaling. To overcome the interferences of tetracyclines with the host microbiome, we identify tetracycline derivatives that have minimal antimicrobial activity, yet retain full capacity to induce the MSR, such as the lead compound, 9-tert-butyl doxycycline (9-TB). The MSR induced by doxycycline (Dox) and 9-TB improves survival and disease tolerance against lethal influenza virus (IFV) infection when given preventively. 9-TB, unlike Dox, did not affect the gut microbiome and also showed encouraging results against IFV when given in a therapeutic setting. Tolerance to IFV infection is associated with the induction of genes involved in lung epithelial cell and cilia function, and with downregulation of inflammatory and immune gene sets in lungs, liver, and kidneys. Mitohormesis induced by non-antimicrobial tetracyclines and the ensuing IFN response may dampen excessive inflammation and tissue damage during viral infections, opening innovative therapeutic avenues.
- Published
- 2022
11. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions
- Author
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Nijman, I. J., Rosen, B. D., Bardou, P., Faraut, T., Cumer, T., Daly, K. G., Zheng, Z., Cai, Y., Asadollahpour, H., Kul, B. C., Zhang, W. -Y., Guangxin, E., Ayin, A., Baird, H., Bakhtin, M., Balteanu, V. A., Barfield, D., Berger, B., Blichfeldt, T., Boink, G., Bugiwati, S. R. A., Cai, Z., Carolan, S., Clark, E., Cubric-Curik, V., Dagong, M. I. A., Dorji, T., Drew, L., Guo, J., Hallsson, J., Horvat, S., Kantanen, J., Kawaguchi, F., Kazymbet, P., Khayatzadeh, N., Kim, N., Shah, M. K., Liao, Y., Martinez, A., Masangkay, J., Masaoka, M., Mazza, R., Mcewan, J., Milanesi, M., Omar, F. M., Nomura, Y., Ouchene-Khelifi, N. -A., Pereira, F., Sahana, G., Salavati, M., Sasazaki, S., Da Silva, A., Simcic, M., Solkner, J., Sutherland, A., Tigchelaar, J., Zhang, H., Ajmone-Marsan, P., Bradley, D. G., Colli, L., Drogemuller, C., Jiang, Y., Lei, C., Mannen, H., Pompanon, F., Tosser-Klopp, G., Lenstra, J. A., Kijas, J., Guldbrandtsen, B., Denoyelle, L., Sarry, J., le Talouarn, E., Alberti, A., Orvain, C., Engelen, S., Duby, D., Martin, P., Danchin, C., Duclos, D., Allain, D., Arquet, R., Mandonnet, N., Naves, M., Palhiere, I., Rupp, R., Rezaei, H. R., Foran, M., Stella, A., Del Corvo, M., Crisa, A., Marletta, D., Crepaldi, P., Ottino, M., Randi, E., Mujibi, D. F., Gondwe, T., Benjelloun, B., Taela, M. D. G., Nash, O., Moaeen-ud-Din, M., Visser, C., Goyache, F., Alvarez, I., Amills, M., Sanchez, A., Capote, J., Jordana, J., Pons, A., Balears, I., Molina, A., Mruttu, H. A., Masiga, C. W., Van Tassell, C. P., Reecy, J., Luikart, G., Sikosana, J., Anila, H., Petrit, D., Roswitha, B., Philippe, B., Aziz, F., Christos, P., El-Barody, M. A. A., Pierre, T., Phillip, E., Gordon, L., Albano, B. -P., Stephanie, Z., Michel, T., Georg, E., Horst, B., Eveline, I. -A., Luhken, G., Krugmann, D., Eva-Maria, P., Shirin, L., Katja, G., Christina, P., Jutta, R., Marco, B., Andreas, G., Al Tarrayrah, J., Georgios, K., Olga, K., Katerina, K., Christina, L., Anton, I., Lazlo, F., Gabriele, C., Elisabetta, M., Marco, P., Antonello, C., Tiziana, S., Mario, C., Francesca, F., Stefano, G., Marta, M., Bordonaro, S., Giuseppe, D. U., Fabio, P., Mariasilvia, D. A., Alessio, V., Irene, C., Lorraine, P., Mahamoud, A. -S., Van Cann, L. M., Roman, N., Popielarczyk, D., Ewa, S., Augustin, V., Susana, D., Javier, C., Oscar, C., David, G., Regis, C., Gabriela, O. -R., Glowatzki, M. -L., Okan, E., Inci, T., Evren, K., Mike, B., Trinidad, P., Gabriela, J., Godfrey, H., Stella, D., Louise, W., Martin, T., Sam, J., and Riccardo, S.
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haplogroup ,introgresija ,domestication ,goat ,introgression ,migration ,phylogeography ,Y-chromosome ,Evolution ,MITOCHONDRIAL-DNA ,FLOW ,Haplotypes/genetics ,divje koze ,DNA, Mitochondrial ,DNA, Mitochondrial/genetics ,Behavior and Systematics ,BREEDS ,Y Chromosome ,Goats/genetics ,Genetics ,Animals ,domače koze ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,udc:575:636.39 ,kozorogi ,Ecology ,630 Agriculture ,Goats ,Genetic Variation ,NETWORKS ,DIFFERENTIATION ,genetika ,Haplotypes ,ORIGINS ,GENETIC DIVERSITY ,590 Animals (Zoology) ,570 Life sciences ,biology ,Y Chromosome/genetics - Abstract
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range.
- Published
- 2022
12. Ancient DNA provides insights into 4,000 years of resource economy across Greenland
- Author
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Seersholm, Frederik V., Harmsen, Hans, Gotfredsen, Anne Birgitte, Madsen, Christian K., Jensen, Jens F., Hollesen, Jørgen, Meldgaard, Morten, Bunce, Michael, Hansen, Anders J., Seersholm, Frederik V., Harmsen, Hans, Gotfredsen, Anne Birgitte, Madsen, Christian K., Jensen, Jens F., Hollesen, Jørgen, Meldgaard, Morten, Bunce, Michael, and Hansen, Anders J.
- Abstract
Seersholm et al. analysed permafrozen middens from Inuit and Viking settlements to uncover evidence of diet in prehistoric Greenland. Using ancient DNA, they identified 42 different species and found that whales were surprisingly common.The success and failure of past cultures across the Arctic was tightly coupled to the ability of past peoples to exploit the full range of resources available to them. There is substantial evidence for the hunting of birds, caribou and seals in prehistoric Greenland. However, the extent to which these communities relied on fish and cetaceans is understudied because of taphonomic processes that affect how these taxa are presented in the archaeological record. To address this, we analyse DNA from bulk bone samples from 12 archaeological middens across Greenland covering the Palaeo-Inuit, Norse and Neo-Inuit culture. We identify an assemblage of 42 species, including nine fish species and five whale species, of which the bowhead whale (Balaena mysticetus) was the most commonly detected. Furthermore, we identify a new haplotype in caribou (Rangifer tarandus), suggesting the presence of a distinct lineage of (now extinct) dwarfed caribou in Greenland 3,000 years ago.
- Published
- 2022
13. A guide to avian museomics:Insights gained from resequencing hundreds of avian study skins
- Author
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Irestedt, Martin, Thörn, Filip, Müller, Ingo A., Jønsson, Knud A., Ericson, Per G. P., Blom, Mozes P. K., Irestedt, Martin, Thörn, Filip, Müller, Ingo A., Jønsson, Knud A., Ericson, Per G. P., and Blom, Mozes P. K.
- Abstract
Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present-day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high-throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.
- Published
- 2022
14. Association of Oxidative Stress-Induced Nucleic Acid Damage With Psychiatric Disorders in Adults A Systematic Review and Meta-analysis
- Author
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Jorgensen, Anders, Baago, Ida Bendixen, Rygner, Zerlina, Jorgensen, Martin Balslev, Andersen, Per Kragh, Kessing, Lars Vedel, Poulsen, Henrik Enghusen, Jorgensen, Anders, Baago, Ida Bendixen, Rygner, Zerlina, Jorgensen, Martin Balslev, Andersen, Per Kragh, Kessing, Lars Vedel, and Poulsen, Henrik Enghusen
- Abstract
IMPORTANCE Nucleic acid damage from oxidative stress (NA-OXS) may be a molecular mechanism driving the severely increased morbidity and mortality from somatic causes in adults with psychiatric disorders.OBJECTIVE To systematically retrieve and analyze data on NA-OXS across the psychiatric disorder diagnostic spectrum.DATA SOURCES The PubMed, Embase, and PsycINFO databases were searched from inception to November 16, 2021. A hand search of reference lists of relevant articles was also performed.STUDY SELECTION Key study inclusion criteria in this meta-analysis were as follows: adult human study population, measurement of any marker of DNA or RNA damage from oxidative stress, and either a (1) cross-sectional design comparing patients with psychiatric disorders (any diagnosis) with a control group or (2) prospective intervention. Two authors screened the studies, and 2 senior authors read the relevant articles in full and assessed them for eligibility.DATA EXTRACTION AND SYNTHESIS The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines were followed. Two authors performed data extraction independently, and a senior coauthor was consulted in cases of disagreement. Data were synthesized with random-effects and multilevel meta-analyses.MAIN OUTCOMES AND MEASURES The predefined hypothesis was that individuals with psychiatric disorders have increased NA-OXS levels. The main outcome was the standardized mean differences (SMDs) among patients and controls in nucleic acid oxidation markers compared across diagnostic groups. Analyses were divided into combinations of biological matrices and nucleic acids.RESULTS Eighty-two studies fulfilled the inclusion criteria, comprising 205 patient vs control group comparisons and a total of 10 151 patient and 10 532 control observations. Overall, the data showed that patients with psychiatric disorders had higher NA-OXS levels vs controls across matrices and
- Published
- 2022
15. Distinctive mitogenomic lineages within populations of White-tailed Eagles:[Inkl. Corrigendum]
- Author
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Hansen, Charles Christian Riis, Baleka, Sina, Guðjónsdóttir, Sólveig Magnea, Rasmussen, Jacob Agerbo, Ballesteros, Jesus Adrian Chimal, Hallgrimsson, Gunnar Thor, Stefansson, Robert A., von Schmalensee, Menja, Skarphedinsson, Kristinn Haukur, Labansen, Aili Lage, Leivits, Madis, Skelmose, Kim, Sonne, Christian, Dietz, Rune, Boertmann, David, Eulaers, Igor, Martin, Michael D., Pálsson, Snæbjörn, Hansen, Charles Christian Riis, Baleka, Sina, Guðjónsdóttir, Sólveig Magnea, Rasmussen, Jacob Agerbo, Ballesteros, Jesus Adrian Chimal, Hallgrimsson, Gunnar Thor, Stefansson, Robert A., von Schmalensee, Menja, Skarphedinsson, Kristinn Haukur, Labansen, Aili Lage, Leivits, Madis, Skelmose, Kim, Sonne, Christian, Dietz, Rune, Boertmann, David, Eulaers, Igor, Martin, Michael D., and Pálsson, Snæbjörn
- Abstract
Using whole mitochondrial DNA sequences from 89 White-tailed Eagles (Haliaeetus albicilla) sampled from Iceland, Greenland, Norway, Denmark and Estonia between 1990 and 2018, we investigate the mitogenomic variation within and between countries. We show that there is a substantial population differentiation between the countries, reflecting similar major phylogeographic patterns obtained previously for the control region of the mitochondria, which suggested two main refugia during the last glacial period. Distinct mitogenomic lineages are observed within countries with divergence times exceeding the end of the last glacial period of the Ice Age. Deviations from neutrality indicate that these lineages have been maintained by natural selection and there is an excess of segregating amino acids in comparison with number of fixations suggesting a large load of deleterious mutations. The maintenance of the distinct mitogenic lineages within countries inflates our estimates of divergence times.Lay Summary center dot Whole mitochondrial genomes were used to examine the population genetics of White-tailed Eagles. center dot Large genetic differences potentially upheld by selection within populations were identified. center dot Potential time of population splits during the last Ice age were identified.
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- 2022
16. Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction
- Author
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M. Thomas P. Gilbert, Filipe G. Vieira, and José Alfredo Samaniego Castruita
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0106 biological sciences ,DNA damage ,MITOCHONDRIAL-DNA ,In silico ,Biology ,MISCODING LESIONS ,010603 evolutionary biology ,01 natural sciences ,Genome ,ancestral genome reconstruction ,DNA sequencing ,03 medical and health sciences ,symbols.namesake ,Mapping algorithm ,HISTORY ,ANCIENT DNA ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Nature and Landscape Conservation ,Sanger sequencing ,DAMAGE ,0303 health sciences ,Ecology ,SEQUENCES ,ORIGIN ,Hypotheses ,EVOLUTION ,INSIGHTS ,Ancient DNA ,paleogenomics ,Evolutionary biology ,symbols ,Evolutionary divergence - Abstract
Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome‐scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR‐based Sanger sequencing, following the dawn of the second‐generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained., A significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from the ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples.
- Published
- 2020
17. Using urine to diagnose large‐scale mtDNA deletions in adult patients
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Anu Suomalainen, Kristin N. Varhaug, Gonzalo S. Nido, Charalampos Tzoulis, Pirjo Isohanni, Irenaeus F.M. de Coo, Laurence A. Bindoff, Per M. Knappskog, RS: MHeNs - R3 - Neuroscience, Klinische Genetica, HUS Children and Adolescents, Research Programs Unit, Anu Wartiovaara / Principal Investigator, Clinicum, Children's Hospital, STEMM - Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki University Hospital Area, HUSLAB, Department of Neurosciences, Neuroscience Center, and Helsinki Institute of Life Science HiLIFE
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Male ,0301 basic medicine ,Ophthalmoplegia, Chronic Progressive External ,MITOCHONDRIAL-DNA ,Urine ,Polymerase Chain Reaction ,3124 Neurology and psychiatry ,law.invention ,0302 clinical medicine ,law ,Medicine ,Research Articles ,Polymerase chain reaction ,Sequence Deletion ,Sanger sequencing ,medicine.diagnostic_test ,General Neuroscience ,Mitochondrial Myopathies ,Middle Aged ,Heteroplasmy ,READ ALIGNMENT ,3. Good health ,Real-time polymerase chain reaction ,SINGLE ,symbols ,DETECT ,Female ,Research Article ,RC321-571 ,Adult ,Mitochondrial DNA ,Adolescent ,DISORDERS ,Neurosciences. Biological psychiatry. Neuropsychiatry ,PHENOTYPES ,Urinalysis ,DNA, Mitochondrial ,Sensitivity and Specificity ,DNA sequencing ,03 medical and health sciences ,symbols.namesake ,Humans ,RC346-429 ,Muscle biopsy ,business.industry ,3112 Neurosciences ,Sequence Analysis, DNA ,Molecular biology ,030104 developmental biology ,Neurology. Diseases of the nervous system ,Neurology (clinical) ,business ,030217 neurology & neurosurgery - Abstract
Objective: The aim of this study was to evaluate if urinary sediment cells offered a robust alternative to muscle biopsy for the diagnosis of single mtDNA deletions. Methods: Eleven adult patients with progressive external ophthalmoplegia and a known single mtDNA deletion were investigated. Urinary sediment cells were used to isolate DNA, which was then subjected to long‐range polymerase chain reaction. Where available, the patient`s muscle DNA was studied in parallel. Breakpoint and thus deletion size were identified using both Sanger sequencing and next generation sequencing. The level of heteroplasmy was determined using quantitative polymerase chain reaction. Results: We identified the deletion in urine in 9 of 11 cases giving a sensitivity of 80%. Breakpoints and deletion size were readily detectable in DNA extracted from urine. Mean heteroplasmy level in urine was 38% ± 26 (range 8 ‐ 84%), and 57% ± 28 (range 12 – 94%) in muscle. While the heteroplasmy level in urinary sediment cells differed from that in muscle, we did find a statistically significant correlation between these two levels (R = 0.714, P = 0.031(Pearson correlation)). Interpretation: Our findings suggest that urine can be used to screen patients suspected clinically of having a single mtDNA deletion. Based on our data, the use of urine could considerably reduce the need for muscle biopsy in this patient group. publishedVersion
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- 2020
18. Population Connectivity Predicts Vulnerability to White-Nose Syndrome in the Chilean Myotis (Myotis chiloensis) - A Genomics Approach
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Anti Vasemägi, Anna S. Blomberg, David L. J. Vendrami, Joseph S. Johnson, Tiina Sävilammi, Veronica Yung, Gonzalo Ossa, Thomas M. Lilley, and Zoology
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TIERRA-DEL-FUEGO ,0106 biological sciences ,chiroptera ,MITOCHONDRIAL-DNA ,Population genetics ,GEOMYCES-DESTRUCTANS ,Population ,Species distribution ,TADARIDA-BRASILIENSIS ,Genomics ,Myotis myotis ,QH426-470 ,PSEUDOGYMNOASCUS-DESTRUCTANS ,010603 evolutionary biology ,01 natural sciences ,Gene flow ,Myotis chiloensis ,03 medical and health sciences ,Tadarida brasiliensis ,Genetics (medical genetics to be 30107 and agricultural genetics to be 40402) ,Geographical distance ,Pseudogymnoascus destructans ,GENE FLOW ,Genetics ,education ,Molecular Biology ,population connectivity ,1172 Environmental sciences ,Genetics (clinical) ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,CLIMATE-CHANGE ,biology ,Ecology ,disease spread ,1184 Genetics, developmental biology, physiology ,FREE-TAILED BAT ,Last Glacial Maximum ,population structure ,Torpor ,15. Life on land ,biology.organism_classification ,SPREAD - Abstract
Despite its peculiar distribution, the biology of the southernmost bat species in the world, the Chilean myotis (Myotis chiloensis), has garnered little attention so far. The species has a north-south distribution of c. 2800 km, mostly on the eastern side of the Andes mountain range. Use of extended torpor occurs in the southernmost portion of the range, putting the species at risk of bat white-nose syndrome, a fungal disease responsible for massive population declines in North American bats. Here, we examined how geographic distance and topology would be reflected in the population structure of M. chiloensis along the majority of its range using a double digestion RAD-seq method. We sampled 66 individuals across the species range and discovered pronounced isolation-by-distance. Furthermore, and surprisingly, we found higher degrees of heterozygosity in the southernmost populations compared to the north. A coalescence analysis revealed that our populations may still not have reached secondary contact after the Last Glacial Maximum. As for the potential spread of pathogens, such as the fungus causing WNS, connectivity among populations was noticeably low, especially between the southern hibernatory populations in the Magallanes and Tierra del Fuego, and more northerly populations. This suggests the probability of geographic spread of the disease from the north through bat-to-bat contact to susceptible populations is low. The study presents a rare case of defined population structure in a bat species and warrants further research on the underlying factors contributing to this. See the graphical abstract here. https://doi.org/10.25387/g3.12173385
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- 2020
19. Hybridization selects for prime‐numbered life cycles in Magicicada: An individual‐based simulation model of a structured periodical cicada population
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Jaakko Toivonen, Lutz Fromhage, and Department of Computer Science
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PRODOXIDAE ,0106 biological sciences ,structured population model ,MITOCHONDRIAL-DNA ,media_common.quotation_subject ,Population ,Biology ,010603 evolutionary biology ,01 natural sciences ,Magicicada ,Prime (order theory) ,Competition (biology) ,Predation ,HOMOPTERA-CICADIDAE ,13-YEAR ,03 medical and health sciences ,Individual based ,populaatiot ,lcsh:QH540-549.5 ,DIVERGENCE ,jälkeläiset ,education ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Nature and Landscape Conservation ,media_common ,Original Research ,suosinta ,0303 health sciences ,education.field_of_study ,Ecology ,kaskaat ,YUCCA MOTH ,alkuluvut ,Prime number ,prime numbers ,elinkaari ,lisääntyminen ,EVOLUTION ,LEPIDOPTERA ,17-YEAR CICADAS ,Evolutionary biology ,1181 Ecology, evolutionary biology ,individual‐based model ,lcsh:Ecology ,individual-based model - Abstract
We investigate competition between separate periodical cicada populations each possessing different life‐cycle lengths. We build an individual‐based model to simulate the cicada life cycle and allow random migrations to occur between patches inhabited by the different populations. We show that if hybridization between different cycle lengths produces offspring that have an intermediate life‐cycle length, then predation acts disproportionately to select against the hybrid offspring. This happens because they emerge in low densities without the safety‐in‐numbers provided by either parent population. Thus, prime‐numbered life cycles that can better avoid hybridization are favored. However, we find that this advantage of prime‐numbered cycles occurs only if there is some mechanism that can occasionally synchronize emergence between local populations in sufficiently many patches., We investigate competition between separate periodical cicada populations each possessing different life‐cycle lengths. We show that prime‐numbered life cycles are selected for when hybridization produces offspring with an intermediate life‐cycle length compared to their parents.
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- 2020
20. Clinical Heterogeneity in MT-ATP6 Pathogenic Variants: Same Genotype—Different Onset
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Sara Capiau, Joél Smet, Boel De Paepe, Yilmaz Yildiz, Mutluay Arslan, Olivier Stevens, Maxime Verschoore, Hedwig Stepman, Sara Seneca, Arnaud Vanlander, Medical Genetics, Clinical sciences, and Reproduction and Genetics
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CYTOCHROME-C-OXIDASE ,MITOCHONDRIAL-DNA ,QH301-705.5 ,ORGANIZATION ,genotype-phenotype correlation ,PHENOTYPE ,ELECTROPHORESIS ,C%22">NC_012920.1(MT-ATP6):m.9035T>C ,MT-ATP6 ,mitochondrial disorder ,Medicine and Health Sciences ,Biology (General) ,ATP-synthase ,complex V deficiency ,p.L170P ,C+[NC%5F012920%2E1%28MT-ATP6%29]%22">m.9035T>C [NC_012920.1(MT-ATP6)] ,ATP SYNTHASE ,IDENTIFICATION ,MUTATIONS ,Biology and Life Sciences ,General Medicine ,DEFICIENCY ,RESPIRATORY-CHAIN - Abstract
Human mitochondrial disease exhibits large variation of clinical phenotypes, even in patients with the same causative gene defect. We illustrate this heterogeneity by confronting clinical and biochemical data of two patients with the uncommon pathogenic homoplasmic NC_012920.1(MT-ATP6):m.9035T>C variant in MT-ATP6. Patient 1 presented as a toddler with severe motor and speech delay and spastic ataxia without extra-neurologic involvement. Patient 2 presented in adolescence with ataxia and ophthalmoplegia without cognitive or motor impairment. Respiratory chain complex activities were normal in cultured skin fibroblasts from both patients when calculated as ratios over citrate synthase activity. Native gels found presence of subcomplexes of complex V in fibroblast and/or skeletal muscle. Bioenergetic measurements in fibroblasts from both patients detected reduced spare respiratory capacities and altered extracellular acidification rates, revealing a switch from mitochondrial respiration to glycolysis to uphold ATP production. Thus, in contrast to the differing disease presentation, biochemical evidence of mitochondrial deficiency turned out quite similar. We conclude that biochemical analysis remains a valuable tool to confirm the genetic diagnosis of mitochondrial disease, especially in patients with new gene variants or atypical clinical presentation.
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- 2022
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21. Genetic diversity and selection in Puerto Rican horses
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Walter W. Wolfsberger, Nikole M. Ayala, Stephanie O. Castro-Marquez, Valerie M. Irizarry-Negron, Antoliy Potapchuk, Khrystyna Shchubelka, Ludvig Potish, Audrey J. Majeske, Luis Figueroa Oliver, Alondra Diaz Lameiro, Juan Carlos Martínez-Cruzado, Gabriella Lindgren, and Taras K. Oleksyk
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Agricultural genetics ,MITOCHONDRIAL-DNA ,Population genetics ,Evolution ,Science ,ANCESTRY ,Article ,Evolutionary genetics ,DMRT3 ,Animal and Dairy Science ,HISTORY ,Animals ,POPULATION-STRUCTURE ,Horses ,Animal breeding ,Multidisciplinary ,Science & Technology ,GAIT KEEPER MUTATION ,REVEAL ,Multidisciplinary Sciences ,DOMESTICATION ,ORIGINS ,Medicine ,Science & Technology - Other Topics ,INFERENCE - Abstract
Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the “Criollo”) horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the “gait-keeper” DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the “gait-keeper” DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant “gait-keeper” allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing the DMRT3 locus to this day. The lack of the detectable signature of selection associated with the DMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.
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- 2022
22. A new mouse model of radiation-induced liver disease reveals mitochondrial dysfunction as an underlying fibrotic stimulus
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Nicolas Melin, Tural Yarahmadov, Daniel Sanchez-Taltavull, Fabienne E. Birrer, Tess M. Brodie, Benoît Petit, Andrea Felser, Jean-Marc Nuoffer, Matteo Montani, Marie-Catherine Vozenin, Evelyn Herrmann, Daniel Candinas, Daniel M. Aebersold, and Deborah Stroka
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Hepatology ,Gastroenterology ,Internal Medicine ,Immunology and Allergy ,570 Life sciences ,biology ,610 Medicine & health ,4HNE, 4-hydroxynonenal ,CV, central vein ,ECM, extracellular matrix ,ETC, electron transfer chain ,GSH, reduced glutathione (glutathione) ,GSSG, oxidized glutathione (glutathione disulfide) ,HSCs, hepatic stellate cells ,IGRT, image-guided radiation therapy ,IHC, immunohistochemistry ,IMC, imaging mass cytometry ,MDA, malondialdehyde ,RILD, radiation-induced liver disease ,RNAseq, RNA sequencing ,ROS ,ROS, reactive oxygen species ,RT, radiation therapy ,SASP, senescence-associated secretory phenotype ,SNP, single nucleotide polymorphism ,SOS, sinusoidal obstruction syndrome ,fibrosis ,image guided radiation therapy (IGRT) ,mitochondrial dysfunction ,mitochondrial-DNA ,mouse model ,mtDNA, mitochondrial DNA ,mtROS, mitochondrial reactive oxygen species ,p53 ,radiation-induced liver disease (RILD) ,rcf, relative centrifuge force ,senescence ,sinusoidal obstruction syndrome - Abstract
Background & Aims High-dose irradiation is an essential tool to help control the growth of hepatic tumors, but it can cause radiation-induced liver disease (RILD). This life-threatening complication manifests itself months following radiation therapy and is characterized by fibrosis of the pericentral sinusoids. In this study, we aimed to establish a mouse model of RILD to investigate the underlying mechanism of radiation-induced liver fibrosis. Methods Using a small animal image-guided radiation therapy platform, an irradiation scheme delivering 50 Gy as a single dose to a focal point in mouse livers was designed. Tissues were analyzed 1 and 6 days, and 6 and 20 weeks post-irradiation. Irradiated livers were assessed by histology, immunohistochemistry, imaging mass cytometry and RNA sequencing. Mitochondrial function was assessed using high-resolution respirometry. Results At 6 and 20 weeks post-irradiation, pericentral fibrosis was visible in highly irradiated areas together with immune cell infiltration and extravasation of red blood cells. RNA sequencing analysis showed gene signatures associated with acute DNA damage, p53 activation, senescence and its associated secretory phenotype and fibrosis. Moreover, gene profiles of mitochondrial damage and an increase in mitochondrial DNA heteroplasmy were detected. Respirometry measurements of hepatocytes in vitro confirmed irradiation-induced mitochondrial dysfunction. Finally, the highly irradiated fibrotic areas showed markers of reactive oxygen species such as decreased glutathione and increased lipid peroxides and a senescence-like phenotype. Conclusions Based on our mouse model of RILD, we propose that irradiation-induced mitochondrial DNA instability contributes to the development of fibrosis via the generation of excessive reactive oxygen species, p53 pathway activation and a senescence-like phenotype. Lay summary Irradiation is an efficient cancer therapy, however, its applicability to the liver is limited by life-threatening radiation-induced hepatic fibrosis. We have developed a new mouse model of radiation-induced liver fibrosis, that recapitulates the human disease. Our model highlights the role of mitochondrial DNA instability in the development of irradiation-induced liver fibrosis. This new model and subsequent findings will help increase our understanding of the hepatic reaction to irradiation and to find strategies that protect the liver, enabling the expanded use of radiotherapy to treat hepatic tumors.
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- 2022
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23. Monocyte-derived macrophages aggravate pulmonary vasculitis via cGAS/STING/IFN-mediated nucleic acid sensing
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Nina Kessler, Susanne F. Viehmann, Calvin Krollmann, Karola Mai, Katharina M. Kirschner, Hella Luksch, Prasanti Kotagiri, Alexander M.C. Böhner, Dennis Huugen, Carina C. de Oliveira Mann, Simon Otten, Stefanie A.I. Weiss, Thomas Zillinger, Kristiyana Dobrikova, Dieter E. Jenne, Rayk Behrendt, Andrea Ablasser, Eva Bartok, Gunther Hartmann, Karl-Peter Hopfner, Paul A. Lyons, Peter Boor, Angela Rösen-Wolff, Lino L. Teichmann, Peter Heeringa, Christian Kurts, Natalio Garbi, Translational Immunology Groningen (TRIGR), and Groningen Kidney Center (GKC)
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Vasculitis ,Macrophages ,Immunology ,Membrane Proteins ,i interferon ,cytosolic dna ,Nucleotidyltransferases ,myeloperoxidase ,Mice ,cyclic gmp-amp ,neutrophils ,mitochondrial-dna ,Nucleic Acids ,Interferon Type I ,Animals ,Immunology and Allergy ,sting activation ,Membrane Proteins/metabolism ,dendritic cells ,Lung ,glomerulonephritis ,cgas - Abstract
Kessler et al. identify aberrant DNA recognition by cGAS/STING and IFN-I production by inflammatory macrophages as a driver of severe ANCA-associated vasculitis. Pharmacological interventions blocking this pathway ameliorate disease and accelerate recovery, identifying potential targets for therapeutic intervention in patients., Autoimmune vasculitis is a group of life-threatening diseases, whose underlying pathogenic mechanisms are incompletely understood, hampering development of targeted therapies. Here, we demonstrate that patients suffering from anti-neutrophil cytoplasmic antibodies (ANCA)-associated vasculitis (AAV) showed increased levels of cGAMP and enhanced IFN-I signature. To identify disease mechanisms and potential therapeutic targets, we developed a mouse model for pulmonary AAV that mimics severe disease in patients. Immunogenic DNA accumulated during disease onset, triggering cGAS/STING/IRF3-dependent IFN-I release that promoted endothelial damage, pulmonary hemorrhages, and lung dysfunction. Macrophage subsets played dichotomic roles in disease. While recruited monocyte-derived macrophages were major disease drivers by producing most IFN-beta, resident alveolar macrophages contributed to tissue homeostasis by clearing red blood cells and limiting infiltration of IFN-beta-producing macrophages. Moreover, pharmacological inhibition of STING, IFNAR-I, or its downstream JAK/STAT signaling reduced disease severity and accelerated recovery. Our study unveils the importance of STING/IFN-I axis in promoting pulmonary AAV progression and identifies cellular and molecular targets to ameliorate disease outcomes.
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- 2022
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24. Evidence for genetic hybridization between released and wild game birds: Phylogeography and genetic structure of chukar partridge, Alectoris chukar, in Turkey
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Tamer Albayrak, José Antonio Dávila García, Özlem Özmen, Filiz Karadas, Duygu Ateş, Michael Wink, and The Scientific and Technological Research Council of Turkey
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Red-Legged Partridge ,Markers ,Ecology ,Introgression ,Population genetics ,Evolution ,Climate ,Ecological Modeling ,Refugia ,Admixture ,Agricultural and Biological Sciences (miscellaneous) ,Population-Structure ,Mitochondrial-Dna ,Refugium ,population genetics ,evolution ,Anatolia ,refugium ,breeding station ,admixture ,Breeding station ,Rufa ,Software ,Demography ,Nature and Landscape Conservation - Abstract
This article belongs to the Section Biogeography and Macroecology., The Chukar Partridge (Alectoris chukar, Galliformes) is one of the most important game birds in its native range, spanning from the Balkans to eastern Asia, and the regions of Europe, North America and New Zealand where it was introduced. Previous studies found two main genetic lineages of the species forming an eastern and a western clade. Chukar Partridges are raised in game farms and released to supplement natural populations for shooting in the USA, Canada, Greece, and Turkey. To explore intraspecific genetic structure, phylogeography, and possible genetic admixture events of A. chukar in Turkey, we genotyped individuals from fourteen wild and five captive populations at two mitochondrial and ten microsatellite DNA loci in. Wild and farmed Chukar Partridge samples were analyzed together to investigate possible influences of intraspecific hybridizations. We found that the farmed chukars, which mainly (85%) cluster into the eastern clade, and wild ones were genetically distinct. The latter could be separated into six management units (MUs), with partridges from Gökçeada Island in the Aegean Sea forming the most divergent population. Intraspecific hybridization was detected between wild and captive populations. This phenomenon causes rampant introgression and homogenization. The phylogeographic analysis revealed admixture among wild populations; nevertheless, this did not impair pointing to Anatolia as likely having a “refugia-within-refugia” structure. We recommend that the genetic structure of Chukar Partridge and its MUs be taken into account when developing the policy of hunting, production, and release to preserve the genetic integrity of this species., This research was funded by TUBITAK, 117O580.
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- 2022
25. Pan-European phylogeography of the European roe deer (Capreolus capreolus)
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Kamila Plis, Magdalena Niedziałkowska, Tomasz Borowik, Johannes Lang, Mike Heddergott, Juha Tiainen, Aleksey Bunevich, Nikica Šprem, Ladislav Paule, Aleksey Danilkin, Marina Kholodova, Elena Zvychaynaya, Nadezhda Kashinina, Boštjan Pokorny, Katarina Flajšman, Algimantas Paulauskas, Mihajla Djan, Zoran Ristić, Luboš Novák, Szilvia Kusza, Christine Miller, Dimitris Tsaparis, Stoyan Stoyanov, Maryna Shkvyria, Franz Suchentrunk, Miroslav Kutal, Vukan Lavadinović, Dragana Šnjegota, Ana‐Maria Krapal, Gabriel Dănilă, Rauno Veeroja, Elżbieta Dulko, Bogumiła Jędrzejewska, Tomasz Borowik, Dragana Snjegota, Nikica Sprem, Елена Звычайная, Johannes Lang, Miroslav Kutal, Ana-Maria Krapal, Stoyan Stoyanov, Kamila Plis, Biosciences, Lammi Biological Station, Biological stations, and University of Helsinki
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COMMON VOLE ,PYGARGUS ,MITOCHONDRIAL-DNA ,DIVERSITY ,mitochondrial DNA ,GENETIC-STRUCTURE ,kvartalna zgodovina ,expansion ,mitohondrijska DNK ,the Quaternary history ,filogenetika ,udc:630*15 ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation ,Ecology ,POPULATION-GROWTH ,POSTGLACIAL COLONIZATION ,EASTERN-EUROPE ,humanities ,L ,Phylogenetics ,DIFFERENTIATION ,1181 Ecology, evolutionary biology ,Capreolus capreolus ,the Last Glacial Maximum refugia ,zadnja ledeniška maksimalna refugija - Abstract
To provide the most comprehensive picture of species phylogeny and phylogeography of European roe deer (Capreolus capreolus), we analyzed mtDNA control region (610 bp) of 1469 samples of roe deer from Central and Eastern Europe and included into the analyses additional 1541 mtDNA sequences from GenBank from other regions of the continent. We detected two mtDNA lineages of the species: European and Siberian (an introgression of C. pygargus mtDNA into C. capreolus). The Siberian lineage was most frequent in the eastern part of the continent and declined toward Central Europe. The European lineage contained three clades (Central, Eastern, and Western) composed of several haplogroups, many of which were separated in space. The Western clade appeared to have a discontinuous range from Portugal to Russia. Most of the haplogroups in the Central and the Eastern clades were under expansion during the Weichselian glacial period before the Last Glacial Maximum (LGM), while the expansion time of the Western clade overlapped with the Eemian interglacial. The high genetic diversity of extant roe deer is the result of their survival during the LGM probably in a large, contiguous range spanning from the Iberian Peninsula to the Caucasus Mts and in two northern refugia. © 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
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- 2022
26. Molecular evolution and radiation of dung beetles in Madagascar
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Ilkka Hanski, Helena Koivulehto, and Luisa Orsini
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0106 biological sciences ,Systematics ,coleoptera ,likelihood ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,missing data ,mitochondrial-dna ,phylogenetic inference ,substitution ,scarabaeidae ,Taxonomic rank ,Endemism ,Clade ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Scarabaeidae ,bees hymenoptera ,0303 health sciences ,biology ,Ecology ,15. Life on land ,biology.organism_classification ,Genetic divergence ,Taxon ,gene-sequences ,Taxonomy (biology) ,divergence - Abstract
Madagascar is the world's fourth largest island and has a wide range of climates and ecosystems. Environmental diversity combined with long history of isolation (160 Myr) has generated a high level of endemism at different taxonomic levels, making Madagascar one of the hotspots of global biodiversity. Dung beetles, represented by the two tribes of Canthonini and Helictopleurini, exemplify a large insect taxon. Helictopleurini are completely endemic to Madagascar while Canthonini are endemic at generic level. Using data from mitochondrial and nuclear genes, phylogenetic relationships were investigated in a sample of 44 species. The phylogeny for Canthonini consists of several distinct clades, possibly reflecting multiple colonization of Madagascar. The phylogeny does not support the current taxonomy for all genera. The phylogeny for Helictopleurini lacks statistical support at supra-specific level, and genetic divergence among the Helictopleurini species is comparable with that among species within genera in Canthonini. These results suggest that Helictopleurini has undergone rapid speciation and most likely more recently than Canthonini, consistent with the estimated radiation time based on mtDNA mutation rates in insects and with knowledge about the systematics and geographic distribution of dung beetles worldwide. A detailed analysis of sequence composition identified common patterns in Malagasy dung beetles and other insects. (c) The Willi Hennig Society 2007. ispartof: Cladistics vol:23 issue:2 pages:145-168 status: published
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- 2021
27. A Ten-Minute Bioassay to Test Metal Toxicity with the Freshwater Flagellate Euglena agilis
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Soyeon Choi, Hojun Lee, Min-Soo Lee, Joon Tae Park, Philippe M. Heynderickx, Di Wu, Stephen Depuydt, Jana Asselman, Colin Janssen, Donat P. Häder, Taejun Han, and Jihae Park
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GRACILIS ,General Immunology and Microbiology ,MITOCHONDRIAL-DNA ,GROWTH-RESPONSE ,PHOTOSYNTHESIS ,Biology and Life Sciences ,bioassays ,Euglena agilis ,end points ,heavy metals ,General Biochemistry, Genetics and Molecular Biology ,PHENOL TOXICITY ,CADMIUM ,HEAVY-METALS ,ddc:570 ,CELLS ,ALGAL ,FLUORESCENCE ,General Agricultural and Biological Sciences ,SIGN CHANGE - Abstract
Simple Summary Bioassays can offset the limitations of traditional chemical analyses (time constraints, high cost, and limited detection of interactions) in monitoring water pollution. Euglena, a flagellate green alga, is an attractive experimental model organism that has been used for toxicity testing for decades because it is easy to culture, grows rapidly, and responds quickly to environmental stresses. In the present study, we examined the effects of seven heavy metals in the native Korean E. agilis using six end points (motility, velocity, cell compactness, upward swimming, r-value, and orientation). The advantage of the ecotoxicity assay presented here is its rapidity. Unlike the usual 3-4 d of exposure time and work, this assay takes only 10 min to obtain results; moreover, it can be performed at room temperature under dark conditions. Therefore, this new method can be useful for the rapid toxicity screening of hazardous pollutants, as it may have operational advantages over test time. A chemical analysis of water quality cannot detect some toxicants due to time constraints, high costs, and limited interactions for detection. Bioassays would offer a complementary means to assess pollution levels in water. Euglena is a flagellate green alga and an excellent system for toxicity testing thanks to its ease of culture, rapid growth, and quick response to environmental stresses. Herein, we examined the sensitivity of E. agilis to seven heavy metals by analyzing six end-point parameters: motility, velocity, cell compactness, upward swimming, r-value, and alignment. Notably, the velocity of E. agilis was most sensitive to cadmium (96.28 mg center dot L-1), copper (6.51 mg center dot L-1), manganese (103.28 mg center dot L-1), lead (78.04 mg center dot L-1), and zinc (101.90 mg center dot L-1), while r-values were most sensitive to arsenic (12.84 mg center dot L-1) and mercury (4.26 mg center dot L-1). In this study, velocity and r-values are presented as useful biomarkers for the assessment of metal toxicity in Euglena. The metals As, Cd, Cu, and Pb were suitable for this test. The advantages of the ecotoxicity test are its rapidity: It takes 10 min to obtain results, as opposed to the typical 3-4 d of exposure time with intensive labor. Moreover, this test can be performed at room temperature under dark conditions.
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- 2022
28. Long-term spatiotemporal genetic structure of an accidental parasitoid introduction, and local changes in prevalence of its associated Wolbachia symbiont
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Toshka Nyman, Anne Duplouy, Abhilash Nair, Saskya van Nouhuys, University of Helsinki, Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Ecology and Evolutionary Biology, Organismal and Evolutionary Biology Research Programme, Biosciences, Insect Symbiosis Ecology and Evolution, Helsinki Institute of Life Science HiLIFE, and Ecology and Evolutionary Biology
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0106 biological sciences ,MITOCHONDRIAL-DNA ,Mesochorus stigmaticus ,Wasps ,Population ,Glanville fritillary ,DIVERSITY ,Zoology ,010603 evolutionary biology ,01 natural sciences ,Melitaea cinxia ,Parasitoid wasp ,trophic chain ,03 medical and health sciences ,Prevalence ,Genetics ,Animals ,Humans ,PROTECTION ,SPATIAL DYNAMICS ,METAPOPULATION ,education ,Ecology, Evolution, Behavior and Systematics ,POPULATION ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,endosymbiosis ,COMPLEXITY ,biology ,Host (biology) ,COEVOLUTION ,fungi ,biology.organism_classification ,Population bottleneck ,genotyping ,HABITAT FRAGMENTATION ,Genetic structure ,1181 Ecology, evolutionary biology ,1182 Biochemistry, cell and molecular biology ,Wolbachia ,gene flow ,Butterflies ,Aland Islands ,SYSTEM ,Microsatellite Repeats - Abstract
Population bottlenecks associated with founder events strongly impact the establishment and genetic makeup of populations. In addition to their genotype, founding individuals also bring along parasites, as well as symbionts that can manipulate the phenotype of their host, affecting the host population establishment, dynamics and evolution. Thus, to understand introduction, invasion, and spread, we should identify the roles played by accompanying symbionts. In 1991, the parasitoid wasp, Hyposoter horticola, and its associated hyperparasitoid were accidentally introduced from the main angstrom land islands, Finland, to an isolated island in the archipelago, along with their host, the Glanville fritillary butterfly. Though the receiving island was unoccupied, the butterfly was present on some of the small islands in the vicinity. The three introduced species have persisted locally ever since. A strain of the endosymbiotic bacterium Wolbachia has an intermediate prevalence in the parasitoid H. horticola across the main angstrom land population. The infection increases its susceptibility of to hyperparasitism. We investigated the establishment and spread of the parasitoid, along with patterns of prevalence of its symbiont using 323 specimens collected between 1992 and 2013, from five localities across angstrom land, including the source and introduced populations. Using 14 microsatellites and one mitochondrial marker, we suggest that the relatively diverse founding population and occasional migration between islands might have facilitated the persistence of all isolated populations, despite multiple local population crashes. We also show that where the hyperparasitoid is absent, and thus selection against infected wasp genotypes is relaxed, there is near-fixation of Wolbachia.
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- 2021
29. Wolbachia-driven selective sweep in a range expanding insect species
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Giacomo Assandri, Andrea Galimberti, Pallavi Chauhan, Erik I. Svensson, Junchen Deng, Lesley T. Lancaster, Yuma Takahashi, Anne Duplouy, Ryo Futahashi, Bengt Hansson, Deng, J, Assandri, G, Chauhan, P, Futahashi, R, Galimberti, A, Hansson, B, Lancaster, L, Takahashi, Y, Svensson, E, Duplouy, A, Insect Symbiosis Ecology and Evolution, and Organismal and Evolutionary Biology Research Programme
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0106 biological sciences ,Odonata ,Range (biology) ,MITOCHONDRIAL-DNA ,01 natural sciences ,Genetic diversity ,MOLECULAR EVIDENCE ,INFECTION ,CYTOPLASMIC INCOMPATIBILITY ,ENDOSYMBIONT ,QH540-549.5 ,Phylogeny ,0303 health sciences ,education.field_of_study ,Ecology ,General Medicine ,Mitochondria ,GENOME ,DROSOPHILA ,Phylogeography ,1181 Ecology, evolutionary biology ,Wolbachia ,Female ,Research Article ,Evolution ,Population ,Biology ,010603 evolutionary biology ,DNA, Mitochondrial ,03 medical and health sciences ,Genetic variation ,QH359-425 ,Animals ,Damselfly ,education ,Symbiosis ,030304 developmental biology ,MALE-KILLING WOLBACHIA ,Endosymbiosis ,Human evolutionary genetics ,Genetic Variation ,biology.organism_classification ,Ischnura ,Endosymbiosi ,13. Climate action ,Evolutionary biology ,Cyprus ,EVOLUTIONARY ,Selective sweep - Abstract
Background Evolutionary processes can cause strong spatial genetic signatures, such as local loss of genetic diversity, or conflicting histories from mitochondrial versus nuclear markers. Investigating these genetic patterns is important, as they may reveal obscured processes and players. The maternally inherited bacterium Wolbachia is among the most widespread symbionts in insects. Wolbachia typically spreads within host species by conferring direct fitness benefits, and/or by manipulating its host reproduction to favour infected over uninfected females. Under sufficient selective advantage, the mitochondrial haplotype associated with the favoured maternally-inherited symbiotic strains will spread (i.e. hitchhike), resulting in low mitochondrial genetic variation across the host species range. Method The common bluetail damselfly (Ischnura elegans: van der Linden, 1820) has recently emerged as a model organism for genetics and genomic signatures of range expansion during climate change. Although there is accumulating data on the consequences of such expansion on the genetics of I. elegans, no study has screened for Wolbachia in the damselfly genus Ischnura. Here, we present the biogeographic variation in Wolbachia prevalence and penetrance across Europe and Japan (including samples from 17 populations), and from close relatives in the Mediterranean area (i.e. I. genei: Rambur, 1842; and I. saharensis: Aguesse, 1958). Results Our data reveal (a) multiple Wolbachia-strains, (b) potential transfer of the symbiont through hybridization, (c) higher infection rates at higher latitudes, and (d) reduced mitochondrial diversity in the north-west populations, indicative of hitchhiking associated with the selective sweep of the most common strain. We found low mitochondrial haplotype diversity in the Wolbachia-infected north-western European populations (Sweden, Scotland, the Netherlands, Belgium, France and Italy) of I. elegans, and, conversely, higher mitochondrial diversity in populations with low penetrance of Wolbachia (Ukraine, Greece, Montenegro and Cyprus). The timing of the selective sweep associated with infected lineages was estimated between 20,000 and 44,000 years before present, which is consistent with the end of the last glacial period about 20,000 years. Conclusions Our findings provide an example of how endosymbiont infections can shape spatial variation in their host evolutionary genetics during postglacial expansion. These results also challenge population genetic studies that do not consider the prevalence of symbionts in many insects, which we show can impact geographic patterns of mitochondrial genetic diversity.
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- 2021
30. Invasive snails, parasite spillback, and potential parasite spillover drive parasitic diseases of Hippopotamus amphibius in artificial lakes of Zimbabwe
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Tine Huyse, Cyril Hammoud, Ruben Schols, Hans Carolus, Maxwell Barson, and Kudzai C Muzarabani
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Life Sciences & Biomedicine - Other Topics ,MITOCHONDRIAL-DNA ,Barcoding4 ,Physiology ,Bulinus truncatus ,Snails ,Plant Science ,Snail ,Conservation(9) ,Freshwater snail ,Structural Biology ,One Health3 ,KARIBA ,INFECTIOUS-DISEASES ,Biology (General) ,Taxonomic impediment(7) ,SCHISTOSOMIASIS ,Artiodactyla ,biology ,Anthropogenic Effects ,FRESH-WATER SNAILS ,Hippopotamus amphibius ,Biological invasions(10) ,Hippopotamus ,Trematodiasis(1) ,Xenomonitoring(2) ,General Agricultural and Biological Sciences ,Life Sciences & Biomedicine ,Research Article ,Biotechnology ,Zimbabwe ,QH301-705.5 ,Bulinus ,Artificial lake5 ,Pseudosuccinea columella ,Barcoding(4) ,Zoology ,NUCLEAR ,Parasitology(8) ,General Biochemistry, Genetics and Molecular Biology ,BIOLOGICAL INVASIONS ,Biomphalaria pfeifferi ,Xenomonitoring2 ,biology.animal ,parasitic diseases ,Parasitic Diseases ,Animals ,Hunting ,Integrative taxonomy(6) ,Parasites ,LIVER FLUKES ,Biology ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,Science & Technology ,FASCIOLA-HEPATICA ,Conservation9 ,IDENTIFICATION ,One Health(3) ,Cell Biology ,Trematodiasis1 ,biology.organism_classification ,Parasitology8 ,Lakes ,Integrative taxonomy6 ,Taxonomic impediment7 ,Artificial lake(5) ,Biological invasions10 ,Developmental Biology - Abstract
Background Humans impose a significant pressure on large herbivore populations, such as hippopotami, through hunting, poaching, and habitat destruction. Anthropogenic pressures can also occur indirectly, such as artificial lake creation and the subsequent introduction of invasive species that alter the ecosystem. These events can lead to drastic changes in parasite diversity and transmission, but generally receive little scientific attention. Results In order to document and identify trematode parasites of the common hippopotamus (Hippopotamus amphibius) in artificial water systems of Zimbabwe, we applied an integrative taxonomic approach, combining molecular diagnostics and morphometrics on archived and new samples. In doing so, we provide DNA reference sequences of the hippopotamus liver fluke Fasciola nyanzae, enabling us to construct the first complete Fasciola phylogeny. We describe parasite spillback of F. nyanzae by the invasive freshwater snail Pseudosuccinea columella, as a consequence of a cascade of biological invasions in Lake Kariba, one of the biggest artificial lakes in the world. Additionally, we report an unknown stomach fluke of the hippopotamus transmitted by the non-endemic snail Radix aff. plicatula, an Asian snail species that has not been found in Africa before, and the stomach fluke Carmyerius cruciformis transmitted by the native snail Bulinus truncatus. Finally, Biomphalaria pfeifferi and two Bulinus species were found as new snail hosts for the poorly documented hippopotamus blood fluke Schistosoma edwardiense. Conclusions Our findings indicate that artificial lakes are breeding grounds for endemic and non-endemic snails that transmit trematode parasites of the common hippopotamus. This has important implications, as existing research links trematode parasite infections combined with other stressors to declining wild herbivore populations. Therefore, we argue that monitoring the anthropogenic impact on parasite transmission should become an integral part of wildlife conservation efforts. Graphical abstract
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- 2021
31. Enhanced cGAS-STING–dependent interferon signaling associated with mutations in ATAD3A
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Stéphanie Chhun, Yanick J. Crow, Henna Tyynismaa, Bert Callewaert, Gillian I. Rice, Manju A Kurian, Christine Bodemer, Edwin Carter, Lien De Somer, Luis Seabra, Simon Holden, Hugh J. McMillan, Brigitte Bader-Meunier, Kristin Suetens, Timothy Wai, Lucy Grove, Sylvie Fraitag, Erika Della Mina, Ashish Dhir, Fran Faes, Marie Hully, Mathieu P Rodero, Pascale de Lonlay, Marie-Louise Frémond, Alice Lepelley, Daniela Buhas, David A. Dyment, Carine Wouters, Erika Van Nieuwenhove, Lise Waumans, STEMM - Stem Cells and Metabolism Research Program, Centre of Excellence in Stem Cell Metabolism, Staff Services, Henna Tyynismaa / Principal Investigator, Neuroscience Center, Helsinki Institute of Life Science HiLIFE, Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), University Hospitals Leuven [Leuven], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Centre national de Référence (CNR) des Hantavirus [UZ Leuven, Belgium], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), University of Manchester [Manchester], University of Edinburgh, McGill University Health Center [Montreal] (MUHC), McGill University = Université McGill [Montréal, Canada], Ghent University Hospital, Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), Children's Hospital of Eastern Ontario [Ottawa, Canada], West Suffolk Hospital Foundation Trust [Bury St Edmunds, UK] (WSHFT), Addenbrooke's Hospital, Cambridge University NHS Trust, University College of London [London] (UCL), University of Ottawa [Ottawa], University of Helsinki, Université Paris Descartes - Paris 5 (UPD5), Biologie mitochondriale – Mitochondrial biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), Y.J. Crow acknowledges that this project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement 786142), a state subsidy managed by the National Research Agency (France) under the 'Investments for the Future' program bearing the reference ANR-10-IAHU-01, and the National Institute for Health Research UK Rare Genetic Disease Research Consortium. The project was supported by MSDAVENIR (Devo-Decode Project). E. Van Nieuwenhove acknowledges the Research Foundation Flanders (Fonds voor Wetenschappelijk Onderzoek Vlaanderen, grant 1S22716N). B. Callewaert is a Senior Clinical Investigator of the Research Foundation Flanders. Ghent University Hospital, University Hospital Leuven, and Hôpital Universitaire, ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), European Project: 786142,ERC-2017-ADG,E-T1IFNs(2018), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut Pasteur [Paris]-Université de Paris (UP)-Centre National de la Recherche Scientifique (CNRS), Lepelley, alice, Instituts Hospitalo-Universitaires - Institut Hospitalo-Universitaire Imagine - - Imagine2010 - ANR-10-IAHU-0001 - IAHU - VALID, and Elaboration of the type I interferonopathies - E-T1IFNs - - ERC-2017-ADG2018-11-01 - 2023-10-31 - 786142 - VALID
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Male ,MITOCHONDRIAL-DNA ,THP-1 Cells ,[SDV]Life Sciences [q-bio] ,medicine.disease_cause ,DNA, Mitochondrial/genetics ,0302 clinical medicine ,Interferon ,DUPLICATIONS ,Medicine and Health Sciences ,Immunology and Allergy ,Child ,Genes, Dominant ,AICARDI-GOUTIERES SYNDROME ,0303 health sciences ,Mutation ,Gene knockdown ,I INTERFERON ,MEMBRANE-PROTEIN ,CHOLESTEROL ,INDUCTION ,Scleroderma, Systemic/genetics ,Nucleotidyltransferases ,3. Good health ,[SDV] Life Sciences [q-bio] ,Stimulator of interferon genes ,Child, Preschool ,Mitochondrial Proteins/genetics ,Female ,Signal transduction ,RNASEH2B ,medicine.drug ,RECURRENT DE-NOVO ,Signal Transduction ,Mitochondrial DNA ,Interferons/genetics ,Mitochondrial disease ,Immunology ,Biology ,DNA, Mitochondrial ,ATPases Associated with Diverse Cellular Activities/genetics ,Mitochondrial Proteins ,03 medical and health sciences ,Young Adult ,medicine ,Humans ,Membrane Proteins/genetics ,Gene ,030304 developmental biology ,Scleroderma, Systemic ,Membrane Proteins ,medicine.disease ,Molecular biology ,DYSFUNCTION ,Nucleotidyltransferases/genetics ,ATPases Associated with Diverse Cellular Activities ,Interferons ,3111 Biomedicine ,030217 neurology & neurosurgery - Abstract
Mitochondrial DNA (mtDNA) has been suggested to drive immune system activation, but the induction of interferon signaling by mtDNA has not been demonstrated in a Mendelian mitochondrial disease. We initially ascertained two patients, one with a purely neurological phenotype and one with features suggestive of systemic sclerosis in a syndromic context, and found them both to demonstrate enhanced interferon-stimulated gene (ISG) expression in blood. We determined each to harbor a previously described de novo dominant-negative heterozygous mutation in ATAD3A, encoding ATPase family AAA domain-containing protein 3A (ATAD3A). We identified five further patients with mutations in ATAD3A and recorded up-regulated ISG expression and interferon α protein in four of them. Knockdown of ATAD3A in THP-1 cells resulted in increased interferon signaling, mediated by cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING). Enhanced interferon signaling was abrogated in THP-1 cells and patient fibroblasts depleted of mtDNA. Thus, mutations in the mitochondrial membrane protein ATAD3A define a novel type I interferonopathy. ispartof: JOURNAL OF EXPERIMENTAL MEDICINE vol:218 issue:10 ispartof: location:United States status: published
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- 2021
32. Role of the cystathionine β-synthase / H2S pathway in the development of cellular metabolic dysfunction and pseudohypoxia in down syndrome
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Theodora Panagaki, Laszlo Pecze, Elisa B. Randi, Anni I. Nieminen, Csaba Szabo, and Institute for Molecular Medicine Finland
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trisomy ,down syndrome ,Organic Chemistry ,Clinical Biochemistry ,oxidative phosphorylation ,hydrogen sulfide ,deficit ,glycolysis ,bioenergetics ,Biochemistry ,hydrogen-sulfide ,mitochondrial-dna ,generation ,expression ,1182 Biochemistry, cell and molecular biology ,cells ,gene ,metabolism ,3-mercaptopyruvate sulfurtransferase - Abstract
Background: Overexpression of the transsulfuration enzyme cystathionine-beta-synthase (CBS), and overproduction of its product, hydrogen sulfide (H2S) are recognized as potential pathogenetic factors in Down syndrome (DS). The purpose of the study was to determine how the mitochondrial function and core metabolic pathways are affected by DS and how pharmacological inhibition of CBS affects these parameters., Methods: 8 human control and 8 human DS fibroblast cell lines have been subjected to bioenergetic and fluxomic and proteomic analysis with and without treatment with a pharmacological inhibitor of CBS., Results: DS cells exhibited a significantly higher CBS expression than control cells, and produced more H2S. They also exhibited suppressed mitochondrial electron transport and oxygen consumption and suppressed Complex IV activity, impaired cell proliferation and increased ROS generation. Inhibition of H2S biosynthesis with aminooxyacetic acid reduced cellular H2S, improved cellular bioenergetics, attenuated ROS and improved proliferation. C-13 glucose fluxomic analysis revealed that DS cells exhibit a suppression of the Krebs cycle activity with a compensatory increase in glycolysis. CBS inhibition restored the flux from glycolysis to the Krebs cycle and reactivated oxidative phosphorylation. Proteomic analysis revealed no CBS-dependent alterations in the expression level of the enzymes involved in glycolysis, oxidative phosphorylation and the pentose phosphate pathway. DS was associated with the dysregulation of several components of the autophagy network; CBS inhibition normalized several of these parameters., Conclusions: Increased H2S generation in DS promotes pseudohypoxia and contributes to cellular metabolic dysfunction by causing a shift from oxidative phosphorylation to glycolysis.
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- 2022
33. Genetic and morphological characterization of the freshwater mussel clubshell species complex (Pleurobema clava and Pleurobema oviforme) to inform conservation planning
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Morrison, Cheryl L., Johnson, Nathan A., Jones, Jess W., Eackles, Michael S., Aunins, Aaron W., Fitzgerald, Daniel B., Hallerman, Eric M., King, Tim L., Morrison, Cheryl L., Johnson, Nathan A., Jones, Jess W., Eackles, Michael S., Aunins, Aaron W., Fitzgerald, Daniel B., Hallerman, Eric M., and King, Tim L.
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The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme
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- 2021
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34. Biomarkers of nucleic acid oxidation:A summary state-of-the-art
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Chao, Mu-Rong, Evans, Mark D., Hu, Chiung-Wen, Ji, Yunhee, Møller, Peter, Rossner, Pavel, Cooke, Marcus S., Chao, Mu-Rong, Evans, Mark D., Hu, Chiung-Wen, Ji, Yunhee, Møller, Peter, Rossner, Pavel, and Cooke, Marcus S.
- Abstract
Oxidatively generated damage to DNA has been implicated in the pathogenesis of a wide variety of diseases. Increasingly, interest is also focusing upon the effects of damage to the other nucleic acids, RNA and the (2?deoxy-)ribonucleotide pools, and evidence is growing that these too may have an important role in disease. LCMS/MS has the ability to provide absolute quantification of specific biomarkers, such as 8-oxo-7,8-dihydro-2?deoxyGuo (8-oxodG), in both nuclear and mitochondrial DNA, and 8-oxoGuo in RNA. However, significant quantities of tissue are needed, limiting its use in human biomonitoring studies. In contrast, the comet assay requires much less material, and as little as 5 ?L of blood may be used, offering a minimally invasive means of assessing oxidative stress in vivo, but this is restricted to nuclear DNA damage only. Urine is an ideal matrix in which to non-invasively study nucleic acid-derived biomarkers of oxidative stress, and considerable progress has been made towards robustly validating these measurements, not least through the efforts of the European Standards Committee on Urinary (DNA) Lesion Analysis. For urine, LC-MS/MS is considered the gold standard approach, and although there have been improvements to the ELISA methodology, this is largely limited to 8oxodG. Emerging DNA adductomics approaches, which either comprehensively assess the totality of adducts in DNA, or map DNA damage across the nuclear and mitochondrial genomes, offer the potential to considerably advance our understanding of the mechanistic role of oxidatively damaged nucleic acids in disease.
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- 2021
35. Pleistocene origins, western ghost lineages, and the emerging phylogeographic history of the red wolf and coyote
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Sacks, Benjamin N., Mitchell, Kieren J., Quinn, Cate B., Hennelly, Lauren M., Sinding, Mikkel-Holger S., Statham, Mark J., Preckler-Quisquater, Sophie, Fain, Steven R., Kistler, Logan, Vanderzwan, Stevi L., Meachen, Julie A., Ostrander, Elaine A., Frantz, Laurent A. F., Sacks, Benjamin N., Mitchell, Kieren J., Quinn, Cate B., Hennelly, Lauren M., Sinding, Mikkel-Holger S., Statham, Mark J., Preckler-Quisquater, Sophie, Fain, Steven R., Kistler, Logan, Vanderzwan, Stevi L., Meachen, Julie A., Ostrander, Elaine A., and Frantz, Laurent A. F.
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The red wolf (Canis rufus) of the eastern US was driven to near-extinction by colonial-era persecution and habitat conversion, which facilitated coyote (C. latrans) range expansion and widespread hybridization with red wolves. The observation of some grey wolf (C. lupus) ancestry within red wolves sparked controversy over whether it was historically a subspecies of grey wolf with its predominant "coyote-like" ancestry obtained from post-colonial coyote hybridization (2-species hypothesis) versus a distinct species closely related to the coyote that hybridized with grey wolf (3-species hypothesis). We analysed mitogenomes sourced from before the 20th century bottleneck and coyote invasion, along with hundreds of modern amplicons, which led us to reject the 2-species model and to investigate a broader phylogeographic 3-species model suggested by the fossil record. Our findings broadly support this model, in which red wolves ranged the width of the American continent prior to arrival of the grey wolf to the mid-continent 60-80 ka; red wolves subsequently disappeared from the mid-continent, relegated to California and the eastern forests, which ushered in emergence of the coyote in their place (50-30 ka); by the early Holocene (12-10 ka), coyotes had expanded into California, where they admixed with and phenotypically replaced western red wolves in a process analogous to the 20th century coyote invasion of the eastern forests. Findings indicate that the red wolf pre-dated not only European colonization but human, and possibly coyote, presence in North America. These findings highlight the urgency of expanding conservation efforts for the red wolf.
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- 2021
36. Unraveling elephant-shrews:Phylogenetic relationships and unexpected introgression among giant sengis
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Lawson, Lucinda P., Castruita, Jose Alfredo Samaniego, Haile, James S., Vernesi, Cristiano, Rovero, Francesco, Lorenzen, Eline D., Lawson, Lucinda P., Castruita, Jose Alfredo Samaniego, Haile, James S., Vernesi, Cristiano, Rovero, Francesco, and Lorenzen, Eline D.
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Giant sengis, or elephant-shrews (Macroscelidea; Macroscelididae; Rhynchocyon), are small-bodied mammals found in central and eastern African forests. Studies have provided contrasting views of the extent and direction of introgression among species. We generated full mitochondrial genomes, and compiled publically available mtDNA 12S and nuclear vWF sequences from Rhynchocyon cirnei, R. petersi and R. udzungwensis that had not previously been analyzed in concert, to elucidate the phylogenetic and population-specific context of potential introgression. Our spatially and phylogenetically broad sampling across species revealed substantial, unidirectional mitochondrial introgression of the R. petersi lineage into R. cirnei reichardi and R. udzungwensis, and from R. udzungwensis into R. c. reichardi. All introgression was highly localized and found only in the eastern Udzungwa Mountains forests in Tanzania. The nuclear data showed another pattern, with R. petersi haplotypes in R. cirnei cirnei and R. c. reichardi. No individuals showed both mitochondrial and nuclear introgression. Our results suggest higher levels of hybridization among giant sengi species than previously recognized, but also highlight the need for further genome-wide analysis and increased spatial sampling to clarify the many aspects of diversification and introgression in this group.
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- 2021
37. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe
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Marie-France Deguilloux, Agata Hałuszko, Maïté Rivollat, Sandra Penske, J. S. Díaz, Michal Ernée, Eirini Skourtanioti, Miroslav Dobeš, Cosimo Posth, Mario Küßner, Stéphane Rottier, Gunnar U. Neumann, Emmanuel Ghesquière, Susanne Friederich, Yılmaz Selim Erdal, Adam Ben Rohrlach, Rana Özbal, Svend Hansen, Marcella Frangipane, Marcello A. Mannino, Ainash Childebayeva, Consuelo Roca de Togores Muñoz, Sabine Reinhold, Murat Akar, Wolfgang Haak, Alexander Herbig, Luka Papac, Yavor Boyadzhiev, Domingo C. Salazar-García, Vanessa Villalba-Mouco, Kamen Boyadzhiev, Johannes Krause, K. Aslıhan Yener, Mirosław Furmanek, Marieke Sophia van de Loosdrecht, Philipp W. Stockhammer, European Commission, Max Planck Institute for the Science of Human History (MPI-SHH), Max-Planck-Gesellschaft, University of Adelaide, De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Spanish National Research Council (CSIC), Mustafa Kemal University, Bulgarian Academy of Sciences (BAS), Czech Academy of Sciences [Prague] (CAS), Hacettepe University = Hacettepe Üniversitesi, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], University of Wrocław [Poland] (UWr), State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Institut national de recherches archéologiques préventives (Inrap), Centre de Recherche en Archéologie, Archéosciences, Histoire (CReAAH), Le Mans Université (UM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC)-Nantes Université (NU), German Archaeological Institute (DAI), Aarhus University [Aarhus], Koç University, Basque Foundation for Science (Ikerbasque), University of Cape Town, Departamento de Inteligencia Artificial [UPM, Spain] (DIA), Universidad Politécnica de Madrid (UPM), Universitat de València (UV), Medizinische Klinik und Poliklinik III [Bonn, Germany], Universitätsklinikum Bonn (UKB), MARQ - Museo Arqueológico Provincial de Alicante (MARQ), Ludwig Maximilian University [Munich] (LMU), New York University [New York] (NYU), NYU System (NYU), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, University of South Australia [Adelaide], Max Planck Society Foundation CELLEX, French (ANR) French National Research Agency (ANR), German (DFG) Research Foundations under the INTERACT project German Research Foundation (DFG) [ANR17-FRAL-0010, DFG-HA-5407/4-1], European Research Council (ERC) under the European Union European Research Council (ERC) [771234-PALEoRIDER], Czech Academy of Sciences Czech Academy of Sciences, Institute of Archaeology of the Czech Academy of Sciences, Prague Czech Academy of Sciences [RVO 67985912], Projekt DEAL, ANR-17-FRAL-0010,INTERACT,Interactions entre groupes humains en Europe de l'Ouest durant la transition Mésolithique-Néolithique: la double perspective des échanges biologiques et culturels(2017), Özbal, Rana (ORCID 0000-0001-6765-2765 & YÖK ID 55583), Rohrlach, A.B., Papac, L., Childebayeva, A., Rivollat, M., Villalba Mouco, V., Neumann, G.U., Penske, S., Skourtanioti, E., van de Loosdrecht, M., Akar, M., Boyadzhiev, K., Boyadzhiev, Y., Deguilloux, M.F., Dobes, M., Erdal, Y.S., Ernée, M., Frangipane, M., Furmanek, M., Friederich, S., Ghesquière, E., Ha?uszko, A., Hansen, S., Küßner, M., Mannino, M., Reinhold, S., Rottier, S., Salazar García, D.C., Diaz, J.S., Stockhammer, P.W., de Togores Muñoz, C.R., Yener, K.A., Posth, C., Krause, J., Herbig, A., Haak, W., College of Social Sciences and Humanities, Department of Archeology and History of Art, Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Université de Nantes (UN)-Le Mans Université (UM)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR Histoire, Histoire de l'Art et Archéologie (UFR HHAA), Université de Nantes (UN)-Université de Nantes (UN)-Ministère de la Culture (MC), Max Planck Society, Agence Nationale de la Recherche (France), German Research Foundation, European Research Council, Academy of Sciences of the Czech Republic, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Le Mans Université (UM)-Université de Rennes (UR)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Université de Nantes - UFR Histoire, Histoire de l'Art et Archéologie (UFR HHAA), and Ikerbasque - Basque Foundation for Science
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Czech ,SELECTION ,Population genetics ,MITOCHONDRIAL-DNA ,early farmers ,DIVERSITY ,mitochondrial DNA ,shotgun sequencing ,Prehistòria ,Haplogroup ,German ,0302 clinical medicine ,Medicine and Health Sciences ,DNA sequencing ,Science and technology ,media_common ,0303 health sciences ,Multidisciplinary ,Horizon (archaeology) ,Critical event ,Shotgun sequencing ,chromosomal haplogroups ,European research ,STEPPE ,Western europe ,language ,Medicine ,Genetic Markers ,Mitochondrial DNA ,[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory ,uniparentally-inherited markers ,Science ,Library science ,Biology ,Y chromosome ,DNA, Mitochondrial ,Polymorphism, Single Nucleotide ,Target enrichment ,Article ,03 medical and health sciences ,Political science ,Humans ,media_common.cataloged_instance ,ANCIENT DNA ,Genetic Testing ,European union ,Alleles ,030304 developmental biology ,MUTATION-RATE ,Chromosomes, Human, Y ,Saturation (genetic) ,History and Archaeology ,Y-mappable capture assay ,Ancient DNA ,Neanderthals ,Anatomically modern humans ,language.human_language ,Neolithic transition ,Genetics, Population ,Haplotypes ,Evolutionary biology ,GENOMIC HISTORY ,030217 neurology & neurosurgery - Abstract
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe., Open Access funding enabled and organized by Projekt DEAL. This study was funded by the Max Planck Society, the French (ANR) and German (DFG) Research Foundations under the INTERACT project (ANR-17-FRAL-0010, DFG-HA-5407/4-1, 2018-2021) to M.R. and W.H., the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program under Grant agreement no. 771234-PALEoRIDER to W.H., the award Praemium Academiae of the Czech Academy of Sciences to M.E. and the project RVO 67985912 of the Institute of Archaeology of the Czech Academy of Sciences, Prague to M.S.
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- 2021
38. Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data
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Paulo A. V. Borges, Sara E. Silva, Selçuk Yurtsever, Maria Teresa Rebelo, Octávio S. Paulo, Michael R. Wilson, Chris D. Jiggins, Eduardo Marabuto, Vinton Thompson, Antti Halkka, Ana Carina Neto, Sofia G. Seabra, Jose Alberto Quartau, Francisco Pina-Martins, Ana S. B. Rodrigues, Repositório da Universidade de Lisboa, Jiggins, Chris [0000-0002-7809-062X], Apollo - University of Cambridge Repository, and Faculty of Biological and Environmental Sciences
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0106 biological sciences ,Species Divergence ,GLASSY-WINGED SHARPSHOOTER ,MITOCHONDRIAL-DNA ,Range (biology) ,Local adaptation ,Population ,Aedeagus ,Philaenus spumarius ,RAD sequencing ,Biology ,010603 evolutionary biology ,01 natural sciences ,DNA barcoding ,General Biochemistry, Genetics and Molecular Biology ,Gene flow ,Species divergence ,Population genomics ,03 medical and health sciences ,GENUS ,Local Adaptation ,RAD Sequencing ,XYLELLA-FASTIDIOSA ,WOLBACHIA INFECTION ,education ,SELECTIVE SWEEPS ,SPECIATION ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,education.field_of_study ,CLIMATE-CHANGE ,General Neuroscience ,General Medicine ,15. Life on land ,biology.organism_classification ,EVOLUTION ,Aphrophoridae ,Population Genomics ,DIFFERENTIATION ,Evolutionary biology ,1181 Ecology, evolutionary biology ,Medicine ,General Agricultural and Biological Sciences - Abstract
Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation. This work was financially supported by Portuguese national funds through FCT-Fundacao para a Ciencia e a Tecnologia, I.P., Portugal: Project PTDC/BIA-BEC/098783/2008; Project FCTPTDC/BIA-BEC/100182/2008; Grant SFRH/BPD/26365/2006 (to Sofia G Seabra); Grant SFRH/BD/73879/2010 (to Ana SB Rodrigues); Contrato de Trabalho Norma Transitoria - DL57/2016/CP1479/(to Sofia G Seabra); cE3c Unit FCT funding in the frame of the project UIDB/00329/2020; CESAM funding UIDP/50017/2020 + UIDB/50017/2020-POCI-01-0145-FEDER-007638; PIDDAC; co-funding by the FEDER, within the PT2020 Partnership Agreement and Compete 2020. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. info:eu-repo/semantics/publishedVersion
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- 2021
39. Evolutionary Relationships of Ljungan Virus Variants Circulating in Multi-Host Systems across Europe
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Heikki Henttonen, Birger Hörnfeldt, Gert E. Olsson, Rainer G. Ulrich, Frauke Ecke, Chiara Rossi, René Kallies, Heidi C. Hauffe, Anne J. Jääskeläinen, Magnus Magnusson, Mária Kazimírová, Cristina Fevola, Nicola Zadra, Department of Virology, Faculty of Medicine, and University of Helsinki
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0301 basic medicine ,VOLES MYODES-GLAREOLUS ,Picornavirus ,MITOCHONDRIAL-DNA ,Parechovirus ,Picornaviridae ,Zoonosis ,Settore BIO/05 - ZOOLOGIA ,Genotype ,Small mammals ,MOLECULAR CHARACTERIZATION ,MAXIMUM-LIKELIHOOD ,Phylogeny ,11832 Microbiology and virology ,Mammals ,biology ,Bank vole ,LYMPHOCYTIC CHORIOMENINGITIS ,CLINICAL-SAMPLES ,QR1-502 ,Europe ,Infectious Diseases ,Ljungan virus ,Rodent-borne virus ,PUBLIC-HEALTH ,SEROLOGICAL SURVEY ,030106 microbiology ,Microbiology ,Article ,Host Specificity ,Evolution, Molecular ,03 medical and health sciences ,Genetic drift ,Phylogenetics ,Virology ,Animals ,Ljungan virus isolates ,Microtus ,HUMAN PARECHOVIRUSES ,Genetic diversity ,Evolutionary Biology ,Picornaviridae Infections ,Genetic Variation ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,PUUMALA VIRUSES ,3111 Biomedicine ,5' Untranslated Regions ,Parechovirus B - Abstract
The picornavirus named ‘Ljungan virus’ (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe, but detailed information on its genetic diversity and host specificity is lacking. Here, we analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 region (encoding the capsid protein and associated with LV serotype) and the 3Dpol region (encoding the RNA polymerase) from 24 LV RNA-positive animals and a fragment of the 5′ untranslated region (UTR) sequence (used for defining strains) in sympatric small mammals. We define three new VP1 genotypes: two in bank voles (Myodes glareolus) (genotype 8 from Finland, Sweden, France, and Italy, and genotype 9 from France and Italy) and one in field voles (Microtus arvalis) (genotype 7 from Finland). There are several other indications that LV variants are host-specific, at least in parts of their range. Our results suggest that LV evolution is rapid, ongoing and affected by genetic drift, purifying selection, spillover and host evolutionary history. Although recent studies suggest that LV does not have zoonotic potential, its widespread geographical and host distribution in natural populations of well-characterized small mammals could make it useful as a model for studying RNA virus evolution and transmission.
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- 2021
40. A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius
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Bohao Fang, Baocheng Guo, Alexandra Yu. Kravchenko, Paolo Momigliano, Cui Wang, Takahito Shikano, Juha Merilä, Organismal and Evolutionary Biology Research Programme, Ecological Genetics Research Unit, Helsinki Institute of Urban and Regional Studies (Urbaria), Biosciences, and Ecology and Evolutionary Biology
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0106 biological sciences ,0301 basic medicine ,NINESPINE STICKLEBACKS ,Time Factors ,MITOCHONDRIAL-DNA ,01 natural sciences ,RAD-seq ,Phylogenomics ,Convergent evolution ,Phylogeny ,Likelihood Functions ,INTROGRESSIVE HYBRIDIZATION ,FRESH-WATER ,Geography ,phylogenomics ,Smegmamorpha ,Mitochondria ,SEX-DETERMINATION ,1181 Ecology, evolutionary biology ,Female ,Taxonomy (biology) ,Gene Flow ,Mitochondrial DNA ,Species complex ,introgression ,Introgression ,Biology ,010603 evolutionary biology ,GENETIC ARCHITECTURE ,SPECIES DELIMITATION ,PELVIC REDUCTION ,03 medical and health sciences ,Pungitius ,Species Specificity ,Phylogenetics ,Genetics ,Animals ,POPULATION-STRUCTURE ,biogeography ,Ecology, Evolution, Behavior and Systematics ,Cell Nucleus ,Genetic Variation ,15. Life on land ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,PARALLEL EVOLUTION ,Gasterosteidae ,1182 Biochemistry, cell and molecular biology ,Hybridization, Genetic - Abstract
Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome-anchored single nucleotide polymorphisms and de novo assembled RAD-tag loci were constructed with RAD-seq data. Both data sets yielded topologically identical and well-supported species trees. Incongruence between nuclear and mitochondrial DNA-based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology-based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius-complex, including suggestion of several trans-Arctic invasions of Europe from the Northern Pacific. The well-resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.
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- 2019
41. Biomolecular Consequences of Platelet Pathogen Inactivation Methods
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Hendrik B. Feys, Britt Van Aelst, and Veerle Compernolle
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MITOCHONDRIAL-DNA ,Riboflavin ,Clinical Biochemistry ,REDUCTION TECHNOLOGY TREATMENT ,Signal transduction ,030204 cardiovascular system & hematology ,THROMBUS FORMATION KINETICS ,0302 clinical medicine ,Furocoumarins ,Neoplasms ,Nucleic Acids ,Medicine and Health Sciences ,Platelet ,PLASMA ,Membrane ,Transfusion medicine ,Hematology ,Pathogen inactivation ,Blood Banks ,Cell damage ,MESSENGER-RNA ,ULTRAVIOLET-LIGHT TREATMENT ,Signal Transduction ,Blood Platelets ,Platelets ,medicine.medical_specialty ,Ultraviolet Rays ,Platelet Transfusion ,RIBOFLAVIN ,03 medical and health sciences ,TRANSFUSION ,medicine ,Humans ,Blood Transfusion ,Hemostasis ,business.industry ,COMPONENTS ,PSORALEN ,Biochemistry (medical) ,Biology and Life Sciences ,medicine.disease ,Thrombocytopenia ,Metabolism ,Blood Preservation ,Immunology ,Nucleic acid ,business ,Function (biology) ,030215 immunology - Abstract
Pathogen inactivation (PI) for platelet concentrates (PC) is a fairly recent development in transfusion medicine that is intended to decrease infectious disease transmission from the donor to the receiving patient. Effective inactivation of viruses, bacteria and eukaryotic parasites adds a layer of safety, protecting the blood supply against customary and emerging pathogens. Three PI methods have been described for platelets. These are based on photochemical damage of nucleic acids which prevents replication of most infectious pathogens and contaminating donor leukocytes. Because platelets do not replicate, the collateral damage to platelet function is considered low to non-existing. This is disputable however because photochemistry is not specific for nucleic acids and significantly affects platelet biomolecules as well. The impact of these biomolecular changes on platelet function and hemostasis is not well understood, but is increasingly being studied. The results of these studies can help explain current and future clinical observations with PI platelets, including the impact on transfusion yield and bleeding. This review summarizes the biomolecular effects of PI treatment on platelets. We conclude that despite a comparable principle of photochemical inactivation, all three methods affect platelets in different ways. This knowledge can help blood banks and transfusion specialists to guide their choice when considering the implementation or clinical use of PI treated platelets.
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- 2019
42. Asymmetric inheritance of RNA toxicity in C. elegans expressing CTG repeats
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Braun, Maya, Shoshani, Shachar, Teixeira, Joana, Shtern, Anna Mellul, Miller, Maya, Granot, Zvi, Fischer, Sylvia E. J., Garcia, Susana M. D. A., Tabach, Yuval, Institute of Biotechnology, and Helsinki Institute of Life Science HiLIFE
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INTERFERENCE ,EPIGENETIC MEMORY ,Multidisciplinary ,IDENTIFICATION ,MITOCHONDRIAL-DNA ,TRIPLET REPEAT ,1182 Biochemistry, cell and molecular biology ,DOUBLE-STRANDED-RNA ,TRINUCLEOTIDE-REPEAT ,MYOTONIC-DYSTROPHY PATIENTS ,CAENORHABDITIS-ELEGANS ,GENE - Abstract
Nucleotide repeat expansions are a hallmark of over 40 neurodegenerative diseases and cause RNA toxicity and multisystemic symptoms that worsen with age. Through an unclear mechanism, RNA toxicity can trigger severe disease manifestation in infants if the repeats are inherited from their mother. Here we use Caenorhabditis elegans bearing expanded CUG repeats to show that this asymmetric intergenerational inheritance of toxicity contributes to disease pathogenesis. In addition, we show that this mechanism is dependent on small RNA pathways with maternal repeat-derived small RNAs causing transcriptomic changes in the offspring, reduced motility, and shortened lifespan. We rescued the toxicity phenotypes in the offspring by perturbing the RNAi machinery in the affected hermaphrodites. This points to a novel mechanism linking maternal bias and the RNAi machinery and suggests that toxic RNA is transmitted to offspring, causing disease phenotypes through intergenerational epigenetic inheritance.
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- 2022
43. Population Dynamics in Italian Canids between the Late Pleistocene and Bronze Age
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Koupadi, Kyriaki, Fontani, Francesco, Ciucani, Marta Maria, Maini, Elena, De Fanti, Sara, Cattani, Maurizio, Curci, Antonio, Nenzioni, Gabriele, Reggiani, Paolo, Andrews, Adam J., Sarno, Stefania, Bini, Carla, Pelotti, Susi, Caniglia, Romolo, Luiselli, Donata, Cilli, Elisabetta, Koupadi, Kyriaki, Fontani, Francesco, Ciucani, Marta Maria, Maini, Elena, De Fanti, Sara, Cattani, Maurizio, Curci, Antonio, Nenzioni, Gabriele, Reggiani, Paolo, Andrews, Adam J., Sarno, Stefania, Bini, Carla, Pelotti, Susi, Caniglia, Romolo, Luiselli, Donata, and Cilli, Elisabetta
- Abstract
Dog domestication is still largely unresolved due to time-gaps in the sampling of regions. Ancient Italian canids are particularly understudied, currently represented by only a few specimens. In the present study, we sampled 27 canid remains from Northern Italy dated between the Late Pleistocene and Bronze Age to assess their genetic variability, and thus add context to dog domestication dynamics. They were targeted at four DNA fragments of the hypervariable region 1 of mitochondrial DNA. A total of 11 samples had good DNA preservation and were used for phylogenetic analyses. The dog samples were assigned to dog haplogroups A, C and D, and a Late Pleistocene wolf was set into wolf haplogroup 2. We present our data in the landscape of ancient and modern dog genetic variability, with a particular focus on the ancient Italian samples published thus far. Our results suggest there is high genetic variability within ancient Italian canids, where close relationships were evident between both a similar to 24,700 years old Italian canid, and Iberian and Bulgarian ancient dogs. These findings emphasize that disentangling dog domestication dynamics benefits from the analysis of specimens from Southern European regions.
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- 2020
44. Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction
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Vieira, Filipe Garrett, Castruita, Jose Alfredo Samaniego, Gilbert, M. Thomas P., Vieira, Filipe Garrett, Castruita, Jose Alfredo Samaniego, and Gilbert, M. Thomas P.
- Abstract
Paleogenomics is the nascent discipline concerned with sequencing and analysis of genome-scale information from historic, ancient, and even extinct samples. While once inconceivable due to the challenges of DNA damage, contamination, and the technical limitations of PCR-based Sanger sequencing, following the dawn of the second-generation sequencing revolution, it has rapidly become a reality. However, a significant challenge facing ancient DNA studies on extinct species is the lack of closely related reference genomes against which to map the sequencing reads from ancient samples. Although bioinformatic efforts to improve the assemblies have focused mainly in mapping algorithms, in this article we explore the potential of an alternative approach, namely using reconstructed ancestral genome as reference for mapping DNA sequences of ancient samples. Specifically, we present a preliminary proof of concept for a general framework and demonstrate how under certain evolutionary divergence thresholds, considerable mapping improvements can be easily obtained.
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- 2020
45. Liquid biopsy: state of reproductive medicine and beyond
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Gaby Schobers, Arthur van den Wijngaard, Guido de Wert, Han G. Brunner, Merryn V. E. Macville, Servi J. C. Stevens, Dominique Pellaers, Masoud Zamani Esteki, Christine E. M. de Die-Smulders, Aimee D C Paulussen, Rebekka Koeck, and Edith Coonen
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medicine.medical_specialty ,GENOMIC DNA ,MITOCHONDRIAL-DNA ,Biopsy ,Mini Review ,Reproductive medicine ,circulating cells ,spent embryo culture medium ,cell-free DNA ,Neoplasms ,NONINVASIVE PRENATAL-DIAGNOSIS ,Biomarkers, Tumor ,Medicine ,Humans ,Sampling (medicine) ,Medical physics ,Liquid biopsy ,MATERNAL PLASMA ,GENE-EXPRESSION ,non-invasive prenatal testing ,next generation sequencing ,Tumor ,Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7] ,liquid biopsy ,business.industry ,Rehabilitation ,INCIDENTAL DETECTION ,Obstetrics and Gynecology ,EMBRYO CULTURE-MEDIUM ,artificial intelligence ,AcademicSubjects/MED00905 ,CIRCULATING TUMOR-CELLS ,FREE FETAL DNA ,Reproductive Medicine ,IVF ,business ,preimplantation genetic testing ,Cell-Free Nucleic Acids ,Biomarkers ,ART - Abstract
Contains fulltext : 244031.pdf (Publisher’s version ) (Open Access) Liquid biopsy is the process of sampling and analyzing body fluids, which enables non-invasive monitoring of complex biological systems in vivo. Liquid biopsy has myriad applications in health and disease as a wide variety of components, ranging from circulating cells to cell-free nucleic acid molecules, can be analyzed. Here, we review different components of liquid biopsy, survey state-of-the-art, non-invasive methods for detecting those components, demonstrate their clinical applications and discuss ethical considerations. Furthermore, we emphasize the importance of artificial intelligence in analyzing liquid biopsy data with the aim of developing ethically-responsible non-invasive technologies that can enhance individualized healthcare. While previous reviews have mainly focused on cancer, this review primarily highlights applications of liquid biopsy in reproductive medicine.
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- 2021
46. Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication
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Yasin Gökhan Çakan, Yılmaz Selim Erdal, Füsun Özer, Anders Götherström, Eren Yüncü, Erhan Biçakçi, Pedro Morell Miranda, Mohammad Foad Abazari, Çiğdem Atakuman, Vendela Kempe Lagerholm, Sevgi Yorulmaz, N. Ezgi Altınışık, C. Can Bilgin, Özlem Çevik, Maja Krzewińska, Mustafa Özkan, Ali Akbaba, Torsten Günther, Ayshin Ghalichi, Douglas Baird, Johannes A. Lenstra, Louise Martin, İnci Togan, Fokke Gerritsen, Nihan Dilşad Dağtaş, Gözde Atağ, Javad Hoseinzadeh, Evangelia Pişkin, Mehmet Somel, Can Yumni Gündem, Ekin Sağlıcan, Onur Özer, Sinan Can Açan, Gülşah Merve Kılınç, Dilek Koptekin, Erinç Yurtman, Kıvılcım Başak Vural, Reyhan Yaka, Rana Özbal, Damla Kaptan, Müge Şevketoğlu, Elif Surer, Art and Culture, History, Antiquity, CLUE+, Özbal, Rana (ORCID 0000-0001-6765-2765 & YÖK ID 55583), Yurtman, Erinç, Özer, Onur, Yüncü, Eren, Dağtaş, Nihan Dilşad, Koptekin, Dilek, Çakan, Yasin Gökhan, Özkan, Mustafa, Akbaba, Ali, Kaptan, Damla, Atağ, Gözde, Vural, Kıvılcım Başak, Gündem, Can Yümni, Martin, Louise, Kılınç, Gülşah Merve, Ghalichi, Ayshin, Açan, Sinan Can, Yaka, Reyhan, Sağlıcan, Ekin, Lagerholm, Vendela Kempe, Krzewinska, Maja, Gunther, Torsten, Miranda, Pedro Morell, Pişkin, Evangelia, Sevketoğlu, Müge, Bilgin, C. Can, Atakuman, Ciğdem, Erdal, Yılmaz Selim, Sürer, Elif, Altınışık, N. Ezgi, Lenstra, Johannes A., Yorulmaz, Sevgi, Abazari, Mohammad Foad, Hoseinzadeh, Javad, Baird, Douglas, Bıcakcı, Erhan, Çevik, Özlem, Gerritsen, Fokke, Gotherstrom, Anders, Somel, Mehmet, Togan, İnci, Özer, Füsun, College of Social Sciences and Humanities, Department of Archeology and History of Art, and One Health Toxicologie
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Turkey ,QH301-705.5 ,Population genetics ,Demographic history ,Medicine (miscellaneous) ,Introgression ,Zoology ,Biochemistry ,DNA, Mitochondrial ,Mitochondrial-DNA ,Ancient DNA ,Origins ,Sequence ,Genomes ,Agriculture ,Management ,Emergence ,Lineages ,Farmers ,Article ,Evolutionary genetics ,General Biochemistry, Genetics and Molecular Biology ,Evolutionsbiologi ,Domestication ,Bronze Age ,Genetics ,Animals ,Biology (General) ,Genetik ,DNA, Ancient ,Innovation ,Sheep, Domestic ,Demography ,Cell Nucleus ,Evolutionary Biology ,Polymorphism, Genetic ,Epipaleolithic ,Agricultural and Biological Sciences(all) ,Biochemistry, Genetics and Molecular Biology(all) ,Genomics ,Archaeology ,Genetic structure ,and Infrastructure ,SDG 9 - Industry, Innovation, and Infrastructure ,General Agricultural and Biological Sciences ,SDG 9 - Industry ,Genetics and Molecular Biology(all) ,Biology ,Multidisciplinary sciences ,Life sciences ,Biomedicine ,Science and technology ,Human mitochondrial DNA haplogroup - Abstract
Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic., Yurtman, Özer, Yüncü et al. provide an ancient DNA data set to demonstrate the impact of human activity on the demographic history of domestic sheep. The authors demonstrate that there may have been multiple domestication events with notable changes to the gene pool of European and Anatolian sheep since the Neolithic.
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- 2021
47. Pleistocene origins, western ghost lineages, and the emerging phylogeographic history of the red wolf and coyote
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Sophie Preckler-Quisquater, Logan Kistler, Julie Meachen, Cate B. Quinn, Lauren M. Hennelly, Laurent A. F. Frantz, Stevi Lee Vanderzwan, Steven R. Fain, Benjamin N. Sacks, Mark J. Statham, Mikkel-Holger S. Sinding, Elaine A. Ostrander, and Kieren J. Mitchell
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0106 biological sciences ,Pleistocene ,Range (biology) ,MITOCHONDRIAL-DNA ,CANIS-LATRANS ,Subspecies ,phylogeography ,Coyotes ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,WOLVES ,REVEALS ,Genetics ,Animals ,hybridization ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,Holocene ,030304 developmental biology ,0303 health sciences ,red wolf ,Wolves ,US ,biology ,mitogenome ,Ecology ,15. Life on land ,biology.organism_classification ,EVOLUTION ,GENOME ,Phylogeography ,Canis ,Habitat ,Hybridization, Genetic ,POPULATIONS ,Canis rufus - Abstract
The red wolf (Canis rufus) of the eastern US was driven to near-extinction by colonial-era persecution and habitat conversion, which facilitated coyote (C. latrans) range expansion and widespread hybridization with red wolves. The observation of some grey wolf (C. lupus) ancestry within red wolves sparked controversy over whether it was historically a subspecies of grey wolf with its predominant "coyote-like" ancestry obtained from post-colonial coyote hybridization (2-species hypothesis) versus a distinct species closely related to the coyote that hybridized with grey wolf (3-species hypothesis). We analysed mitogenomes sourced from before the 20th century bottleneck and coyote invasion, along with hundreds of modern amplicons, which led us to reject the 2-species model and to investigate a broader phylogeographic 3-species model suggested by the fossil record. Our findings broadly support this model, in which red wolves ranged the width of the American continent prior to arrival of the grey wolf to the mid-continent 60-80 ka; red wolves subsequently disappeared from the mid-continent, relegated to California and the eastern forests, which ushered in emergence of the coyote in their place (50-30 ka); by the early Holocene (12-10 ka), coyotes had expanded into California, where they admixed with and phenotypically replaced western red wolves in a process analogous to the 20th century coyote invasion of the eastern forests. Findings indicate that the red wolf pre-dated not only European colonization but human, and possibly coyote, presence in North America. These findings highlight the urgency of expanding conservation efforts for the red wolf.
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- 2021
48. Biomarkers of nucleic acid oxidation:A summary state-of-the-art
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Pavel Rossner, Chiung-Wen Hu, Mark D. Evans, Peter Møller, Yunhee Ji, Marcus S. Cooke, and Mu-Rong Chao
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0301 basic medicine ,Mitochondrial DNA ,Medicine (General) ,COMET ASSAY ,DNA repair ,DNA damage ,QH301-705.5 ,MITOCHONDRIAL-DNA ,HUMAN URINE ,Clinical Biochemistry ,IN-VITRO REPAIR ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,R5-920 ,Tandem Mass Spectrometry ,Nucleic Acids ,Nucleotide pool ,Humans ,Biology (General) ,TANDEM MASS-SPECTROMETRY ,LINKED-IMMUNOSORBENT-ASSAY ,GINGIVAL CREVICULAR FLUID ,Chemistry ,Organic Chemistry ,Articles from the Special Issue on Oxidative stress in retina and retinal pigment epithelium in health and disease ,Edited by Dr. Vera Bonilha ,Deoxyguanosine ,DNA ,ENDOGENOUS DNA ADDUCT ,PERFORMANCE LIQUID-CHROMATOGRAPHY ,Nuclear DNA ,Comet assay ,Oxidative Stress ,030104 developmental biology ,Adductomics ,NUCLEOTIDE EXCISION-REPAIR ,8-Hydroxy-2'-Deoxyguanosine ,Oxidative stress ,Nucleic acid ,RNA ,030217 neurology & neurosurgery ,Biomarkers ,Chromatography, Liquid ,DNA Damage - Abstract
Oxidatively generated damage to DNA has been implicated in the pathogenesis of a wide variety of diseases. Increasingly, interest is also focusing upon the effects of damage to the other nucleic acids, RNA and the (2′-deoxy-)ribonucleotide pools, and evidence is growing that these too may have an important role in disease. LC-MS/MS has the ability to provide absolute quantification of specific biomarkers, such as 8-oxo-7,8-dihydro-2′-deoxyGuo (8-oxodG), in both nuclear and mitochondrial DNA, and 8-oxoGuo in RNA. However, significant quantities of tissue are needed, limiting its use in human biomonitoring studies. In contrast, the comet assay requires much less material, and as little as 5 μL of blood may be used, offering a minimally invasive means of assessing oxidative stress in vivo, but this is restricted to nuclear DNA damage only. Urine is an ideal matrix in which to non-invasively study nucleic acid-derived biomarkers of oxidative stress, and considerable progress has been made towards robustly validating these measurements, not least through the efforts of the European Standards Committee on Urinary (DNA) Lesion Analysis. For urine, LC-MS/MS is considered the gold standard approach, and although there have been improvements to the ELISA methodology, this is largely limited to 8-oxodG. Emerging DNA adductomics approaches, which either comprehensively assess the totality of adducts in DNA, or map DNA damage across the nuclear and mitochondrial genomes, offer the potential to considerably advance our understanding of the mechanistic role of oxidatively damaged nucleic acids in disease., Graphical abstract Image 1, Highlights • Oxidatively damaged nucleic acids are implicated in the pathogenesis of disease. • LC-MS/MS, comet assay and ELISA are often used to study oxidatively damaged DNA. • Urinary oxidatively damaged nucleic acids non-invasively reflect oxidative stress. • DNA adductomics will aid understanding the role of ROS damaged DNA in disease.
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- 2021
49. Profibrotic epithelial TGF-β1 signaling involves NOX4-mitochondria cross talk and redox-mediated activation of the tyrosine kinase FYN
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Marc A. Schneider, Aida Habibovic, Milena Hristova, John E. McDonough, Bart M. Vanaudenaerde, Nicolas Kahn, Frederik J. van Schooten, Christopher M. Dustin, Agnes W. Boots, Karamatullah Danyal, Albert van der Vliet, Michael Kreuter, Carmen Veith, Farmacologie en Toxicologie, and RS: NUTRIM - R3 - Respiratory & Age-related Health
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0301 basic medicine ,Pulmonary and Respiratory Medicine ,Mitochondrial ROS ,Physiology ,MITOCHONDRIAL-DNA ,MIGRATION ,MYOFIBROBLAST DIFFERENTIATION ,Cellular homeostasis ,Bronchi ,Proto-Oncogene Proteins c-fyn ,NOX4 ,Transforming Growth Factor beta1 ,03 medical and health sciences ,0302 clinical medicine ,FYN ,Physiology (medical) ,Pulmonary fibrosis ,TGF beta signaling pathway ,medicine ,Humans ,SRC KINASE ,OXIDATIVE STRESS ,redox signaling ,Chemistry ,NADPH-OXIDASE ,TGF-BETA ,Epithelial Cells ,Cell Biology ,LUNG FIBROSIS ,respiratory system ,medicine.disease ,Idiopathic Pulmonary Fibrosis ,Cell biology ,Mitochondria ,030104 developmental biology ,NADPH Oxidase 4 ,030220 oncology & carcinogenesis ,IDIOPATHIC PULMONARY-FIBROSIS ,Reactive Oxygen Species ,Tyrosine kinase ,Oxidation-Reduction ,Proto-oncogene tyrosine-protein kinase Src ,SRC ,Signal Transduction ,Research Article - Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by a disturbed redox balance and increased production of reactive oxygen species (ROS), which is believed to contribute to epithelial injury and fibrotic lung scarring. The main pulmonary sources of ROS include mitochondria and NADPH oxidases (NOXs), of which the NOX4 isoform has been implicated in IPF. Non-receptor SRC tyrosine kinases (SFK) are important for cellular homeostasis and are often dysregulated in lung diseases. SFK activation by the profibrotic transforming growth factor-beta (TGF-beta) is thought to contribute to pulmonary fibrosis, but the relevant SFK isoform and its relationship to NOX4 and/or mitochondrial ROS in the context of profibrotic TGF-beta signaling is not known. Here, we demonstrate that TGF-beta 1 can rapidly activate the SRC kinase FYN in human bronchial epithelial cells, which subsequently induces mitochondrial ROS (mtROS) production, genetic damage shown by the DNA damage marker 7H2AX, and increased expression of profibrotic genes. Moreover, TGF-beta 1-induced activation of FYN involves initial activation of NOX4 and direct cysteine oxidation of FYN, and both FYN and mtROS contribute to TGF-beta 1-induced induction of NOX4. NOX4 expression in lung tissues of IPF patients is positively correlated with disease severity, although FYN expression is down-regulated in IPF and does not correlate with disease severity. Collectively, our findings highlight a critical role for FYN in TGF-beta 1-induced mtROS production, DNA damage response, and induction of profibrotic genes in bronchial epithelial cells, and suggest that altered expression and activation of NOX4 and FYN may contribute to the pathogenesis of pulmonary fibrosis.
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- 2020
50. Evaluation of Molecular and Phenotypic Markers for Phylogeographic Analysis of the Black-Sea Turbot Scophthalmus maeoticus (Pallas, 1814) (Actinopterygii: Scophthalmidae)
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Karan, Serpil, Turan, Cemal, Deniz Bilimleri ve Teknolojisi Fakültesi -- Deniz Bilimleri Bölümü, Karan, Serpil, and Turan, Cemal
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Phenotypic markers ,Identification ,Diversity ,Scophthalmus maeoticus ,Population genetics ,Polymorphic microsatellite markers ,Psetta-maxima ,Otolith shape ,Molecular markers ,Determine stock structure ,Trachurus ,Mitochondrial-dna ,Genetics ,Population-structure ,Zoology ,Black Sea turbot - Abstract
WOS: 000521828400016, Molecular genetics and phenotypic markers were evaluated for detecting phylogeographic difference in the populations of the Black-Sea turbot Scophthalmus maeoticus occurring in the Black Sea and the Marmara Sea. Microsatellites of nuclear DNA and the COIII region of mitochondrial DNA (mtDNA) were used for the genetic analyses. Morphometrics, meristics, otolith shape and otolith chemistry were applied for the phenotypic analyses. The mean number of alleles was 14.4, using five polymorphic microsatellite loci; the lowest genetic distance (0.19549) was observed between the Marmara (MS) and the West Black Sea (BS2) populations; the highest genetic distance (0.21755) was observed between the Marmara Sea population and East Black Sea (BS1) population. MIDNA analysis revealed an overall genetic diversity of 0.00148. The smallest (0.001416) genetic distance was observed between BS2 and BS1 and the highest (0.001593) was the genetic distance between BSI and MS populations. Discriminant function analysis of morphometric and meristic characters discriminated only BS1 population from the other populations, which overlapped with one another. The otolith shape analysis also supported the morphometric and meristic analyses that the BS1 population was differentiated from the other two populations., Scientific and Technological Research of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [112O920], We are grateful to the Scientific and Technological Research of Turkey for their financial support (Project No. 112O920). The present study is the MSc thesis of S. Karan, in which COI was given instead of COIII by mistake.
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- 2020
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