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Siddall A, Williams AA, Sanders J, Denton JA, Madden D, Schollar J, Bryk J. Unigems: plasmids and parts to facilitate teaching on assembly, gene expression control and logic in E. coli. Access Microbiol 2023; 5:000596.v3. [PMID: 37841098 PMCID: PMC10569648 DOI: 10.1099/acmi.0.000596.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/04/2023] [Indexed: 10/17/2023] Open
Abstract
Synthetic biology enables the creative combination of engineering and molecular biology for exploration of fundamental aspects of biological phenomena. However, there are limited resources available for such applications in the educational context, where straightforward setup, easily measurable phenotypes and extensibility are of particular importance. We developed unigems, a set of ten plasmids that enable classroom-based investigation of gene-expression control and biological logic gates to facilitate teaching synthetic biology and genetic engineering. It is built on a high-copy plasmid backbone and is easily extensible thanks to a common primer set that facilitates Gibson assembly of PCR-generated or synthesized DNA parts into the target vector. It includes two reporter genes with either two constitutive (high- or low-level) or two inducible (lactose- or arabinose-) promoters, as well as a single-plasmid implementation of an AND logic gate. The set can readily be employed in undergraduate teaching settings, during outreach events and for training of iGEM teams. All plasmids have been deposited in Addgene.
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Affiliation(s)
- Alex Siddall
- School of Applied Sciences, University of Huddersfield, Huddersfield, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Abbie Ann Williams
- School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Jason Sanders
- School of Art, Design and Architecture, University of Huddersfield, Huddersfield, UK
| | - Jai A. Denton
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Institute of Vector-borne Disease, Monash University, Clayton, Australia
| | - Dean Madden
- National Centre for Biotechnology Education, University of Reading, Reading, UK
| | - John Schollar
- National Centre for Biotechnology Education, University of Reading, Reading, UK
| | - Jarosław Bryk
- School of Applied Sciences, University of Huddersfield, Huddersfield, UK
- National Centre for Biotechnology Education, University of Reading, Reading, UK
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Martin Cerezo ML, Raval R, de Haro Reyes B, Kucka M, Chan FY, Bryk J. Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol. Mol Ecol Resour 2022; 22:2860-2870. [PMID: 35668693 PMCID: PMC9796921 DOI: 10.1111/1755-0998.13661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 01/07/2023]
Abstract
Highly multiplexed approaches have become common in genomic studies. They have improved the cost-effectiveness of genotyping hundreds of individuals using combinatorially barcoded adapters. These strategies, however, can potentially misassigned reads to incorrect samples. Here, we used a modified quaddRAD protocol to analyse the occurrence of index hopping and PCR chimeras in a series of experiments with up to 100 multiplexed samples per sequencing lane (639 samples in total). We created two types of sequencing libraries: four libraries of type A, where PCRs were run on individual samples before multiplexing, and three libraries of type B, where PCRs were run on pooled samples. We used fixed pairs of inner barcodes to identify chimeric reads. Type B libraries show a higher percentage of misassigned reads (1.15%) than type A libraries (0.65%). We also quantify the commonly undetectable chimeric sequences that occur whenever multiplexed groups of samples with different outer barcodes are sequenced together on a single flow cell. Our results suggest that these types of chimeric sequences represent up to 1.56% and 1.29% of reads in type A and B libraries, respectively. We also show that increasing the number of mismatches allowed for barcode rescue to above 2 dramatically increases the number of recovered chimeric reads. We provide recommendations for developing highly multiplexed RAD-seq protocols and analysing the resulting data to minimize the generation of chimeric sequences, allowing their quantification and a finer control on the number of PCR cycles necessary to generate enough input DNA for library preparation.
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Affiliation(s)
- Maria Luisa Martin Cerezo
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK,IFM BiologyLinköping UniversityLinköpingSweden
| | - Rohan Raval
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
| | - Bernardo de Haro Reyes
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK,IFM BiologyLinköping UniversityLinköpingSweden
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | | | - Jarosław Bryk
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
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Miranda I, Giska I, Farelo L, Pimenta J, Zimova M, Bryk J, Dalén L, Mills LS, Zub K, Melo-Ferreira J. Museomics dissects the genetic basis for adaptive seasonal colouration in the least weasel. Mol Biol Evol 2021; 38:4388-4402. [PMID: 34157721 PMCID: PMC8476133 DOI: 10.1093/molbev/msab177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Dissecting the link between genetic variation and adaptive phenotypes provides outstanding opportunities to understand fundamental evolutionary processes. Here, we use a museomics approach to investigate the genetic basis and evolution of winter coat colouration morphs in least weasels (Mustela nivalis), a repeated adaptation for camouflage in mammals with seasonal pelage colour moults across regions with varying winter snow. Whole-genome sequence data was obtained from biological collections and mapped onto a newly assembled reference genome for the species. Sampling represented two replicate transition zones between nivalis and vulgaris colouration morphs in Europe, which typically develop white or brown winter coats, respectively. Population analyses showed that the morph distribution across transition zones is not a by-product of historical structure. Association scans linked a 200 kb genomic region to colouration morph, which was validated by genotyping museum specimens from inter-morph experimental crosses. Genotyping the wild populations narrowed down the association to pigmentation gene MC1R and pinpointed a candidate amino acid change co-segregating with colouration morph. This polymorphism replaces an ancestral leucine residue by lysine at the start of the first extracellular loop of the protein in the vulgaris morph. A selective sweep signature overlapped the association region in vulgaris, suggesting that past adaptation favoured winter-brown morphs and can anchor future adaptive responses to decreasing winter snow. Using biological collections as valuable resources to study natural adaptations, our study showed a new evolutionary route generating winter colour variation in mammals and that seasonal camouflage can be modulated by changes at single key genes.
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Affiliation(s)
- Inês Miranda
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, 4485-661, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, 4169-007, Portugal
| | - Iwona Giska
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, 4485-661, Portugal
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, 4485-661, Portugal
| | - João Pimenta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, 4485-661, Portugal
| | - Marketa Zimova
- School for Environment and Sustainability, University of Michigan, Dana Natural Resources Building, 440 Church St, Ann Arbor, MI, 49109, USA
| | - Jarosław Bryk
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, SE-10691, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm, SE-10405, Sweden
| | - L Scott Mills
- Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA.,Office of Research and Creative Scholarship, University of Montana, Missoula, MT, 59812, USA
| | - Karol Zub
- Mammal Research Institute, Polish Academy of Sciences, Stoczek 1, Białowieża 17-230, Poland
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, 4485-661, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, 4169-007, Portugal
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Martin Cerezo ML, Kucka M, Zub K, Chan YF, Bryk J. Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq. BMC Genomics 2020; 21:241. [PMID: 32183700 PMCID: PMC7079423 DOI: 10.1186/s12864-020-6603-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 02/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context. Results Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST<0.086. Conclusion Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.
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Affiliation(s)
- Maria Luisa Martin Cerezo
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.,AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, Linköping, Sweden
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Karol Zub
- The Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | | | - Jarosław Bryk
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.
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Bryk J, Reeves RG, Reed FA, Denton JA. Transcriptional effects of a positive feedback circuit in Drosophila melanogaster. BMC Genomics 2017; 18:990. [PMID: 29281970 PMCID: PMC5746007 DOI: 10.1186/s12864-017-4385-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/15/2017] [Indexed: 01/24/2023] Open
Abstract
Background Synthetic systems that use positive feedback have been developed to control human disease vectors and crop pests. The tTAV system, which has been deployed in several insect species, relies on a positive feedback circuit that can be inhibited via dietary tetracycline. Although insects carrying tTAV fail to survive until adulthood in the absence of tetracycline, the exact reason for its lethality, as well as the transcriptomic effects of an active positive feedback circuit, remain unknown. Results We engineered the tTAV system in Drosophila melanogaster and investigated the effects of tTAV genome integration locus on the whole fly transcriptome during larval and adult life stages in four transgenic fly strains using gene expression microarrays. We found that while there were widespread effects on the transcriptome, the gene expression differences after removal of tetracycline were not consistent between integration sites. No specific region of the genome was affected, no common set of genes or pathways, nor did the integration site affect the transcripts in cis. Conclusion Although the positive feedback tTAV system is effective at killing insect larvae regardless of where it is inserted in the genome, it does not exhibit a specific, consistent transcriptional signature. Instead, each insertion site is associated with broad, but different, transcriptional effects. Our results suggest that lethality may not be caused by a direct effect on transcription of a set of key genes or pathways. Instead, we propose that rather than a specific action of a tTAV protein, it is the stochastic transcriptional effects specific to each insertion site that contribute to the tTAV-induced mortality. Electronic supplementary material The online version of this article (10.1186/s12864-017-4385-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jarosław Bryk
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK
| | - R Guy Reeves
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Floyd A Reed
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Department of Biology, University of Hawai'i at Mānoa, Hawai'i, Honolulu, 96822, USA
| | - Jai A Denton
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany. .,Genomics & Regulatory Systems Unit, Okinawa Institute for Science & Technology Graduate University, Onna-son, Okinawa, Japan.
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Bryk J, Tautz D. Copy number variants and selective sweeps in natural populations of the house mouse (Mus musculus domesticus). Front Genet 2014; 5:153. [PMID: 24917877 PMCID: PMC4042557 DOI: 10.3389/fgene.2014.00153] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/09/2014] [Indexed: 12/28/2022] Open
Abstract
Copy-number variants (CNVs) may play an important role in early adaptations, potentially facilitating rapid divergence of populations. We describe an approach to study this question by investigating CNVs present in natural populations of mice in the early stages of divergence and their involvement in selective sweeps. We have analyzed individuals from two recently diverged natural populations of the house mouse (Mus musculus domesticus) from Germany and France using custom, high-density, comparative genome hybridization arrays (CGH) that covered almost 164 Mb and 2444 genes. One thousand eight hundred and sixty one of those genes we previously identified as differentially expressed between these populations, while the expression of the remaining genes was invariant. In total, we identified 1868 CNVs across all 10 samples, 200 bp to 600 kb in size and affecting 424 genic regions. Roughly two thirds of all CNVs found were deletions. We found no enrichment of CNVs among the differentially expressed genes between the populations compared to the invariant ones, nor any meaningful correlation between CNVs and gene expression changes. Among the CNV genes, we found cellular component gene ontology categories of the synapse overrepresented among all the 2444 genes tested. To investigate potential adaptive significance of the CNV regions, we selected six that showed large differences in frequency of CNVs between the two populations and analyzed variation in at least two microsatellites surrounding the loci in a sample of 46 unrelated animals from the same populations collected in field trappings. We identified two loci with large differences in microsatellite heterozygosity (Sfi1 and Glo1/Dnahc8 regions) and one locus with low variation across the populations (Cmah), thus suggesting that these genomic regions might have recently undergone selective sweeps. Interestingly, the Glo1 CNV has previously been implicated in anxiety-like behavior in mice, suggesting a differential evolution of a behavioral trait.
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Affiliation(s)
- Jarosław Bryk
- Max Planck Institute for Evolutionary Biology Plön, Germany
| | - Diethard Tautz
- Max Planck Institute for Evolutionary Biology Plön, Germany
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Reeves RG, Bryk J, Altrock PM, Denton JA, Reed FA. First steps towards underdominant genetic transformation of insect populations. PLoS One 2014; 9:e97557. [PMID: 24844466 PMCID: PMC4028297 DOI: 10.1371/journal.pone.0097557] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 04/08/2014] [Indexed: 11/18/2022] Open
Abstract
The idea of introducing genetic modifications into wild populations of insects to stop them from spreading diseases is more than 40 years old. Synthetic disease refractory genes have been successfully generated for mosquito vectors of dengue fever and human malaria. Equally important is the development of population transformation systems to drive and maintain disease refractory genes at high frequency in populations. We demonstrate an underdominant population transformation system in Drosophila melanogaster that has the property of being both spatially self-limiting and reversible to the original genetic state. Both population transformation and its reversal can be largely achieved within as few as 5 generations. The described genetic construct {Ud} is composed of two genes; (1) a UAS-RpL14.dsRNA targeting RNAi to a haploinsufficient gene RpL14 and (2) an RNAi insensitive RpL14 rescue. In this proof-of-principle system the UAS-RpL14.dsRNA knock-down gene is placed under the control of an Actin5c-GAL4 driver located on a different chromosome to the {Ud} insert. This configuration would not be effective in wild populations without incorporating the Actin5c-GAL4 driver as part of the {Ud} construct (or replacing the UAS promoter with an appropriate direct promoter). It is however anticipated that the approach that underlies this underdominant system could potentially be applied to a number of species.
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Affiliation(s)
- R. Guy Reeves
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
| | - Jarosław Bryk
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Philipp M. Altrock
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jai A. Denton
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Floyd A. Reed
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Pozhitkov AE, Noble PA, Bryk J, Tautz D. A revised design for microarray experiments to account for experimental noise and uncertainty of probe response. PLoS One 2014; 9:e91295. [PMID: 24618910 PMCID: PMC3949741 DOI: 10.1371/journal.pone.0091295] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 02/11/2014] [Indexed: 11/18/2022] Open
Abstract
Background Although microarrays are analysis tools in biomedical research, they are known to yield noisy output that usually requires experimental confirmation. To tackle this problem, many studies have developed rules for optimizing probe design and devised complex statistical tools to analyze the output. However, less emphasis has been placed on systematically identifying the noise component as part of the experimental procedure. One source of noise is the variance in probe binding, which can be assessed by replicating array probes. The second source is poor probe performance, which can be assessed by calibrating the array based on a dilution series of target molecules. Using model experiments for copy number variation and gene expression measurements, we investigate here a revised design for microarray experiments that addresses both of these sources of variance. Results Two custom arrays were used to evaluate the revised design: one based on 25 mer probes from an Affymetrix design and the other based on 60 mer probes from an Agilent design. To assess experimental variance in probe binding, all probes were replicated ten times. To assess probe performance, the probes were calibrated using a dilution series of target molecules and the signal response was fitted to an adsorption model. We found that significant variance of the signal could be controlled by averaging across probes and removing probes that are nonresponsive or poorly responsive in the calibration experiment. Taking this into account, one can obtain a more reliable signal with the added option of obtaining absolute rather than relative measurements. Conclusion The assessment of technical variance within the experiments, combined with the calibration of probes allows to remove poorly responding probes and yields more reliable signals for the remaining ones. Once an array is properly calibrated, absolute quantification of signals becomes straight forward, alleviating the need for normalization and reference hybridizations.
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Affiliation(s)
- Alex E. Pozhitkov
- Max-Planck-Institut für Evolutionsbiologie, Plön, Germany
- Department of Periodontics, School of Dentistry, University of Washington, Seattle, Washington, United States of America
| | - Peter A. Noble
- Department of Periodontics, School of Dentistry, University of Washington, Seattle, Washington, United States of America
- Ph.D Microbiology Program, Department of Biological Sciences, Alabama State University, Montgomery, Alabama, United States of America
| | - Jarosław Bryk
- Max-Planck-Institut für Evolutionsbiologie, Plön, Germany
- National Centre for Biotechnology Education, University of Reading, Reading, United Kingdom
| | - Diethard Tautz
- Max-Planck-Institut für Evolutionsbiologie, Plön, Germany
- * E-mail:
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Bryk J, Somel M, Lorenc A, Teschke M. Early gene expression divergence between allopatric populations of the house mouse (Mus musculus domesticus). Ecol Evol 2013; 3:558-68. [PMID: 23532401 PMCID: PMC3605846 DOI: 10.1002/ece3.447] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 11/15/2012] [Accepted: 11/20/2012] [Indexed: 12/04/2022] Open
Abstract
Divergence of gene expression is known to contribute to the differentiation and separation of populations and species, although the dynamics of this process in early stages of population divergence remains unclear. We analyzed gene expression differences in three organs (brain, liver, and testis) between two natural populations of Mus musculus domesticus that have been separated for at most 3000 years. We used two different microarray platforms to corroborate the results at a large scale and identified hundreds of genes with significant expression differences between the populations. We find that although the three tissues have similar number of differentially expressed genes, brain and liver have more tissue–specific genes than testis. Most genes show changes in a single tissue only, even when expressed in all tissues, supporting the notion that tissue–specific enhancers act as separable targets of evolution. In terms of functional categories, in brain and to a smaller extent in liver, we find transcription factors and their targets to be particularly variable between populations, similar to previous findings in primates. Testis, however, has a different set of differently expressed genes, both with respect to functional categories and overall correlation with the other tissues, the latter indicating that gene expression divergence of potential importance might be present in other datasets where no differences in fraction of differentially expressed genes were reported. Our results show that a significant amount of gene expression divergence quickly accumulates between allopatric populations.
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Affiliation(s)
- Jarosław Bryk
- Max Planck Institute for Evolutionary Biology August-Thienemann-Str. 2, 24306, Plön, Germany
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Chan Y, Jones F, McConnell E, Bryk J, Bünger L, Tautz D. Parallel Selection Mapping Using Artificially Selected Mice Reveals Body Weight Control Loci. Curr Biol 2012; 22:794-800. [DOI: 10.1016/j.cub.2012.03.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 02/17/2012] [Accepted: 03/05/2012] [Indexed: 12/21/2022]
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Wolf JB, Bryk J. General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq. BMC Genomics 2011; 12:91. [PMID: 21284834 PMCID: PMC3040151 DOI: 10.1186/1471-2164-12-91] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 02/01/2011] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Species with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic XX/XY systems suggest that dosage compensation mechanisms are in place to mitigate the detrimental effects of gene dose differences. However, recent genomic research on female heterogametic ZZ/ZW systems has generated surprising results. In two bird species and one lepidopteran no evidence for a global dosage compensating mechanism has been found. The recent advent of massively parallel RNA sequencing now opens up the possibility to gauge the generality of this observation with a broader phylogenetic sampling. It further allows assessing the validity of microarray-based inference on dosage compensation with a novel technology. RESULTS We here exemplify this approach using massively parallel sequencing on barcoded individuals of a bird species, the European crow (Corvus corone), where previously no genetic resources were available. Testing for Z-linkage with quantitative PCR (qPCR,) we first establish that orthology with distantly related species (chicken, zebra finch) can be used as a good predictor for chromosomal affiliation of a gene. We then use a digital measure of gene expression (RNA-seq) on brain transcriptome and confirm a global lack of dosage compensation on the Z chromosome. RNA-seq estimates of male-to-female (m:f) expression difference on the Z compare well to previous microarray-based estimates in birds and lepidopterans. The data further lends support that an up-regulation of female Z-linked genes conveys partial compensation and suggest a relationship between sex-bias and absolute expression level of a gene. Correlation of sex-biased gene expression on the Z chromosome across all three bird species further suggests that the degree of compensation has been partly conserved across 100 million years of avian evolution. CONCLUSIONS This work demonstrates that the study of dosage compensation has become amenable to species where previously no genetic resources were available. Massively parallele transcriptome sequencing allows re-assessing the degree of dosage compensation with a novel tool in well-studies species and, in addition, gain valuable insights into the generality of mechanisms across independent taxonomic group for both the XX/XY and ZZ/ZW system.
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Affiliation(s)
- Jochen Bw Wolf
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August-Thienemannstr, 2, 24306 Plön, Germany.
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Go K, Pribis J, Bryk J, Rominski S, Zhu X, Ochoa J. Prostaglandins Synergize to Increase Arginase Activity in Trauma-Induced Myeloid Derived Suppressor Cells (TI-MDSC). J Surg Res 2010. [DOI: 10.1016/j.jss.2009.11.766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pribis J, Follansbee C, Bryk J, Rominski S, Ochoa J. Effect of ß-Adrenergic Blockade on Myeloid Derived Suppressor Cell Response after Trauma. J Surg Res 2010. [DOI: 10.1016/j.jss.2009.11.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bryk J, Hardouin E, Pugach I, Hughes D, Strotmann R, Stoneking M, Myles S. Positive selection in East Asians for an EDAR allele that enhances NF-kappaB activation. PLoS One 2008; 3:e2209. [PMID: 18493316 PMCID: PMC2374902 DOI: 10.1371/journal.pone.0002209] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 04/07/2008] [Indexed: 12/18/2022] Open
Abstract
Genome-wide scans for positive selection in humans provide a promising approach to establish links between genetic variants and adaptive phenotypes. From this approach, lists of hundreds of candidate genomic regions for positive selection have been assembled. These candidate regions are expected to contain variants that contribute to adaptive phenotypes, but few of these regions have been associated with phenotypic effects. Here we present evidence that a derived nonsynonymous substitution (370A) in EDAR, a gene involved in ectodermal development, was driven to high frequency in East Asia by positive selection prior to 10,000 years ago. With an in vitro transfection assay, we demonstrate that 370A enhances NF-kappaB activity. Our results suggest that 370A is a positively selected functional genetic variant that underlies an adaptive human phenotype.
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Affiliation(s)
- Jarosław Bryk
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Emilie Hardouin
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David Hughes
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rainer Strotmann
- Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sean Myles
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- * E-mail:
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15
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Lorenc A, Bryk J, Golik P, Kupryjańczyk J, Ostrowski J, Pronicki M, Semczuk A, Szołkowska M, Bartnik E. Homoplasmic MELAS A3243G mtDNA mutation in a colon cancer sample. Mitochondrion 2005; 3:119-24. [PMID: 16120350 DOI: 10.1016/s1567-7249(03)00106-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Revised: 07/24/2003] [Accepted: 07/29/2003] [Indexed: 10/27/2022]
Abstract
We have analyzed mtDNA variation in various cancer samples, comparing them with normal tissue controls, and identified mutations and polymorphisms, both known and novel, in mitochondrial tRNA, rRNA and protein genes. Most remarkably, in a colon cancer sample we have found the A3243G mutation in the homoplasmic state. This mutation is known to cause severe mitochondrial dysfunction and, until now, has not been found in cancer cells, nor in the homoplasmic state in living subjects. The mutation was absent from normal tissue, suggesting that mtDNA mutation and resulting respiratory deficiency played a role in carcinogenesis.
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Affiliation(s)
- Anna Lorenc
- Postgraduate School of Molecular Medicine, ul. Chalubinskiego 5, 02-004 Warsaw, Poland
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16
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Urbanska K, Romanowska-Dixon B, Elas M, Pajak S, Paziewski E, Bryk J, Kukielczak B, Slominski A, Zygulska-Mach H, Lukiewicz S. Experimental ruthenium plaque therapy of amelanotic and melanotic melanomas in the hamster eye. Melanoma Res 2000; 10:26-35. [PMID: 10711637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The effects of beta-radiation on melanoma implanted into the hamster's eye were investigated. Two Bomirski hamster melanomas (BHMs), differing in their melanin content, were compared with regard to their radiosensitivity to ruthenium-106 (106Ru) radiation. Tumours growing in the iris were irradiated with 3, 6 or 10 Gy of 106Ru given as a single dose or in four fractions at 24 h Intervals. Tumour growth kinetics and distant metastases were studied, and the eyeballs were examined histologically. Dose-dependent delay of tumour growth was observed in both melanomas. After treatment with a dose of 6 Gy, the Ab amelanotic tumours grew 2.6 times slower, and the Ma melanotic tumours 1.4 times slower than untreated ones. The location of metastases differed in the two tested lines--pigmented metastases were found mainly in the lungs, while unpigmented metastases were found mainly in the kidneys. Histopathological analysis showed signs of blood vessel damage such as endothelial cells swelling, erythrocyte extravasation and tumour necrosis. This last finding increased with the rising dose of beta-radiation. Pigmented tumours were found to be two times more resistant to beta-radiation than amelanotic ones. The pattern of metastases of BHMs is determined by the type of melanoma (Ab or Ma). Exposure to beta-radiation from 106Ru did not significantly affect either the number or size of metastases except at a dose of 10 Gy. This dose caused a statistically significant decrease in the number of metastases in the Ma melanotic subline.
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Affiliation(s)
- K Urbanska
- Institute of Molecular Biology, Jagiellonian University, Kraków, Poland.
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17
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Mirkiewicz-Sieradzka B, Zygulska-Mach H, Romanowska B, Bryk J, Heitzman J, Ksiezyk M. [Attempts of orbit irradiation after enucleation of the eye with malignant choroidal melanoma. Part I]. Klin Oczna 1999; 101:287-90. [PMID: 10581897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
PURPOSE The problem of orbit irradiation after enucleation of the eye with choroidal melanoma is controversial. We have decided to analyse our own material in order to estimate the effectiveness of this method. MATERIAL AND METHODS The clinical material comprised 202 patients, 97 women and 105 men, in the age of 15-84 years, whose eyeballs were enucleated because of choroidal melanoma. In 72 patients the orbit was irradiated after enucleation with 60Co applicator (CKA4). The dose was about 50 Gy, 5 mm deep. The height of tumour, its location, histological type, infiltration of the sclera or beyond the eyeball and the treatment of tumour before enucleation were analysed. The follow-up time was 5-20 years. RESULTS AND CONCLUSIONS The survival time of patients in the age below 30 years (p < 0.05) and of patients with choroidal melanoma of the height above 3 mm (p < 0.01) was significantly longer when the orbit was irradiated. Also the survival time of patients with scleral infiltration and with spindle-cell type of tumour was longer (but statistically not significantly) in those, whose orbits were irradiated after enucleation. Exenteration of the orbit was necessary in 4 cases not irradiated after enucleation, only in 1 case after irradiation. The probability of survival after irradiation of the orbit was significantly higher than in cases not irradiated (0.6971 vs. 0.6219). The estimated mean survival time (in months) was longer, but not significantly, in patients after irradiation of the orbit (197.017 vs. 181.409). We conclude that irradiation of the orbit after enucleation of the eye with choroidal melanoma should be recommended. Further investigations will be continued with collaboration of Institute of Oncology in Cracow.
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Abstract
The purpose of this study was to evaluate the effects of cobalt-60 gamma-radiation and argon laser irradiation using injected merocyanine (MC540) as a photosensitizer on pigmented and non-pigmented Bomirski hamster melanomas growing in the eye. The animals were treated with one of four regimens, receiving gamma-irradiation only, photosensitization only, a combination of gamma-irradiation and photosensitization, or a combined time-fractionated treatment. Tumours were exposed to laser light 24 h after injection, when the photosensitizing dye concentration was highest. The degree of tissue damage was evaluated by observation of the area for necrosis, interruption of blood circulation, and the shape and dissemination of the tumour cells. Additionally, tumour growth was monitored through the measurement of tumour volume and also calculated from histological cross sections on the assumption that the tumour morphology is hemi-ellipsoidal. A single treatment of tumours by a combination of photodynamic therapy and ionizing radiation resulted in an additive effect, inhibiting tumour growth for 2-4 days. A time-fractionated treatment, given four times every 24 h, markedly delayed tumour growth for up to 6 weeks. The results indicate that MC540-mediated photodynamic treatment in combination with gamma-radiation exerts a significant therapeutic effect on a rapidly growing melanoma.
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Affiliation(s)
- B Kukielczak
- Department of Radiospectroscopy and Radiobiology of Cancer, Institute of Molecular Biology, Jagiellonian University, Krakow, Poland.
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Romanowska B, Kukiełczak B, Bryk J, Mirkiewicz-Sieradzka B, Heitzmann J, Lukiewicz S. [New technique for implanting Bomirski melanoma into the anterior chamber of Syrian hamster eyes]. Klin Oczna 1995; 97:324-7. [PMID: 8622289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
PURPOSE To describe a newly elaborated ocular tumor model, obtained by implanting Bomirski melanoma into the anterior chamber of the eye in Syrian hamsters (Mesocricetus auratus). MATERIAL AND METHODS The experiments were carried out using pigmented and non-pigmented lines of the tumor. Attempted injections of suspension of malignant melanoma cells in physiological salt solution to the anterior chamber with an infusion pump did not give the expected results. The growth of the tumor occurred only in 8% of eyes. The research material contained 132 adult pigmented hamsters. Tumor fragments of the size of 0,4-1,0 mm were implanted to the anterior chamber of the eyes. Melanotic cells were implanted in 71 hamsters, amelanotic ones in 61 hamsters. Hamsters were anesthetized with intravisceral vetbutal. The examination was carried out in 24 hour intervals. RESULTS During the first 2 to 3 days the disappearance of the cells were observed, and then iris tumors appeared, in the cases of amelanotic cells after 4-6 days, and in the cases of melanotic cells after 8-10 days. Enucleated eye-balls were examined histopathologically. In all cases confirmation of the growth of melanoma in the iris was obtained.
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Affiliation(s)
- B Romanowska
- Katedry i Kliniki Okulistyki Collegium Medicum Uniwersytetu Jagiellońskiego w Krakowie
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Parks SC, Schiller MR, Bryk J. Investment in our future--the role of science and scholarship in developing knowledge for dietetics practice. J Am Diet Assoc 1994; 94:1159-61. [PMID: 7930324 DOI: 10.1016/0002-8223(94)91140-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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