| 1. |
- Davids, Wagied, et al.
(författare)
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Loss of gene function : Clues from expressed gene fragments in Rickettsia
- 2002
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Ingår i: Trends in Genetics. - 0168-9525 .- 1362-4555. ; 18:7, s. 331-334
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Tidskriftsartikel (refereegranskat)abstract
- Many obligate intracellular pathogens have small genomes with high fractions of pseudogenes. A recent analysis of gene expression patterns in Rickettsia conorii shows that short open reading frames inside deteriorating genes are occasionally transcribed into RNA. Here, we show that substitution frequencies at nonsynonymous sites are similar for expressed and unexpressed parts of the fragmented genes. We conclude that the observed expression is a temporary stage in the gene degradation process, suggesting that the expressed gene fragments are not functional.
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| 2. |
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| 3. |
- Behm, Mikaela, et al.
(författare)
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RNA Editing : A Contributor to Neuronal Dynamics in the Mammalian Brain
- 2016
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 32:3, s. 165-175
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Forskningsöversikt (refereegranskat)abstract
- Post-transcriptional RNA modification by adenosine to inosine (A-to-I) editing expands the functional output of many important neuronally expressed genes. The mechanism provides flexibility in the proteome by expanding the variety of isoforms, and is a requisite for neuronal function. Indeed, targets for editing include key mediators of synaptic transmission with an overall significant effect on neuronal signaling. In addition, editing influences splice-site choice and miRNA targeting capacity, and thereby regulates neuronal gene expression. Editing efficiency at most of these sites increases during neuronal differentiation and brain maturation in a spatiotemporal manner. This editing-induced dynamics in the transcriptome is essential for normal brain development, and we are only beginning to understand its role in neuronal function. In this review we discuss the impact of RNA editing in the brain, with special emphasis on the physiological consequences for neuronal development and plasticity.
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| 4. |
- Chen, Dan, et al.
(författare)
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Lessons and implications from association studies and post-GWAS analyses of cervical cancer
- 2015
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 31:1, s. 41-54
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Forskningsöversikt (refereegranskat)abstract
- Cervical cancer has a heritable genetic component. A large number of genetic associations with cervical cancer have been reported in hypothesis-driven candidate gene studies, but many of these results are either inconsistent or have failed to be independently replicated. Genome-wide association studies (GWAS) have identified additional susceptibility loci previously not implicated in cervical cancer development, highlighting the power of genome-wide unbiased association analyses. Post-GWAS analyses including pathway-based analysis and functional characterization of associated variants have provided new insights into the pathogenesis of cervical cancer. In this review we summarize findings from candidate gene association studies, GWAS, and post-GWAS analyses of cervical cancer. We also discuss gaps in our understanding, possible clinical implications of the findings, and lessons for studies of other complex diseases.
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| 5. |
- Darby, Alistair C., et al.
(författare)
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Intracellular pathogens go extreme: genome evolution in the Rickettsiales
- 2007
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 23:10, s. 511-520
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Forskningsöversikt (refereegranskat)abstract
- The Rickettsiales, a genetically diverse group of the α-Proteobacteria, include major mammalian pathogens, such as the agents of epidemic typhus, scrub typhus, ehrlichioses and heartwater disease. Sequenced genomes of this bacterial order have provided exciting insights into reductive genome evolution, antigenic variation and host cell manipulation. Recent results suggest that human pathogens emerged relatively late in the evolution of the Rickettsiales. Surprisingly, there is no association between pathogenicity and the acquisition of novel virulence genes. Here, we explore the genomic differences between members of the Rickettsiales and ask what are the changes that enable infectious agents to emerge from seemingly harmless bacteria.
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| 6. |
- Dussex, Nicolas, et al.
(författare)
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The kākāpō (Strigops habroptilus)
- 2022
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Ingår i: Trends in Genetics. - : Elsevier. - 0168-9525 .- 1362-4555. ; 38:8
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Tidskriftsartikel (refereegranskat)
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| 7. |
- Ekwall, Karl
(författare)
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Genome-wide analysis of HDAC function
- 2005
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 21:11, s. 608-615
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Tidskriftsartikel (refereegranskat)abstract
- This article focuses on new developments in the genome-wide analysis of histone deacetylase (HDAC) function in yeast. HDACs are highly conserved in many organisms; therefore, their basic functions can be investigated using experimentally tractable model organisms, such as the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. New microarray techniques have enabled the systematic study of HDACs by identifying their direct and indirect gene targets in addition to their physiological functions and enzymatic specificity. These new approaches have already provided new surprising insights into the basic function of HDACs.
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| 8. |
- Ellegren, Hans
(författare)
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The different levels of genetic diversity in sex chromosomes and autosomes
- 2009
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 25:6, s. 278-284
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Forskningsöversikt (refereegranskat)abstract
- Sex chromosomes and autosomes differ in their effective population size, mutation and demography, all of which affect the relative level of genetic diversity within the genome. Moreover, natural selection acts differentially on the two chromosomal categories, for example, because recessive mutations are directly exposed to selection on the single X chromosome of males. Recent genome analyses reveal a heterogeneous picture of the sex-chromosome-to-autosome diversity ratio in different organisms. Reduced X chromosome diversity has been interpreted to reflect demographic features such as bottlenecks and male-biased dispersal, whereas more equal diversity in sex chromosomes and autosomes has been explained by polygynous mating systems.
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| 9. |
- Fortes-Lima, Cesar A., et al.
(författare)
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Closing the Gaps in Genomic Research
- 2021
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Ingår i: Trends in Genetics. - : Cell Press. - 0168-9525 .- 1362-4555. ; 37:2, s. 104-106
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Despite Africa's central role in the origin of our species, our knowledge of the genomic diversity in Africa is remarkably sparse. A recent publication by Choudhury et al. underscores the scientific imperative for a broader characterisation of African genomic diversity to better understand demographic history and improve global human health.
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| 10. |
- Fouché, Simone, et al.
(författare)
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A devil's bargain with transposable elements in plant pathogens
- 2022
-
Ingår i: Trends in Genetics. - : Elsevier. - 0168-9525 .- 1362-4555. ; 38:3, s. 222-230
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Forskningsöversikt (refereegranskat)abstract
- Transposable elements (TEs) spread in genomes through self-copying mecha-nisms and are a major cause of genome expansions. Plant pathogens have finely tuned the expression of virulence factors to rely on epigenetic control targeted at nearby TEs. Stress experienced during the plant infection process leads to de -repression of TEs and concurrently allows the expression of virulence factors. We argue that the derepression of TEs elements causes an evolutionary conflict by favoring TEs that can be reactivated. Active TEs and recent genome size expansions indicate that plant pathogens could face long-term consequences from the short-term benefit of fine-tuning the infection process. Hence, encoding key virulence factors close to TEs under epigenetic control constitutes a devil's bargain for pathogens.
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| 11. |
- Gilks, William P, et al.
(författare)
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Sex differences in disease genetics: evidence, evolution, and detection.
- 2014
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Ingår i: Trends in Genetics. - : Elsevier BV. - 1362-4555 .- 0168-9525. ; 30:10, s. 453-463
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Forskningsöversikt (refereegranskat)abstract
- Understanding the genetic architecture of disease is an enormous challenge, and should be guided by evolutionary principles. Recent studies in evolutionary genetics show that sexual selection can have a profound influence on the genetic architecture of complex traits. Here, we summarise data from heritability studies and genome-wide association studies (GWASs) showing that common genetic variation influences many diseases and medically relevant traits in a sex-dependent manner. In addition, we discuss how the discovery of sex-dependent effects in population samples is improved by joint interaction analysis (rather than separate-sex), as well as by recently developed software. Finally, we argue that although genetic variation that has sex-dependent effects on disease risk could be maintained by mutation-selection balance and genetic drift, recent evidence indicates that intra-locus sexual conflict could be a powerful influence on complex trait architecture, and maintain sex-dependent disease risk alleles in a population because they are beneficial to the opposite sex.
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| 12. |
- Hartfield, Matthew, et al.
(författare)
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The Evolutionary Interplay between Adaptation and Self-Fertilization
- 2017
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 33:6, s. 420-431
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Forskningsöversikt (refereegranskat)abstract
- Genome-wide surveys of nucleotide polymorphisms, obtained from next-generation sequencing, have uncovered numerous examples of adaptation in self-fertilizing organisms, especially regarding changes to climate, geography, and reproductive systems. Yet existing models for inferring attributes of adaptive mutations often assume idealized outcrossing populations, which risks mis-characterizing properties of these variants. Recent theoretical work is emphasizing how various aspects of self-fertilization affects adaptation, yet empirical data on these properties are lacking. We review theoretical and empirical studies demonstrating how self-fertilization alters the process of adaptation, illustrated using examples from current sequencing projects. We propose ideas for how future research can more accurately quantify aspects of adaptation in self-fertilizers, including incorporating the effects of standing variation, demographic history, and polygenic adaptation.
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| 13. |
- Jern, Patric, et al.
(författare)
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Wildlife endogenous retroviruses : colonization, consequences, and cooption
- 2024
-
Ingår i: Trends in Genetics. - : Elsevier. - 0168-9525 .- 1362-4555. ; 40:2, s. 149-159
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Forskningsöversikt (refereegranskat)abstract
- A recent increase in the number of high-quality genome sequences and assemblies facilitates systematic screening of vertebrate DNA, better reflecting endogenous retrovirus (ERV) variability across wildlife and providing a means for evaluating historic and contemporary retrovirus transmission.In contrast to commonly studied laboratory and domestic animals, recent studies of wildlife ERVs and exogenous retroviruses (XRVs) offer insights into historic and contemporary retrovirus activities in hosts undergoing natural selection.Wildlife host populations under natural selection provide insights into ERV variation that segregates at various frequencies in host populations and highlight limitations of ERV detection relying on reference genome assemblies derived from one or a few individuals alone.Phylogenetic differences between ERVs and contemporary XRVs suggest that XRVs are prone to extinction over evolutionary timescales, while the ERV record persists, or that many retroviruses remain to be discovered.Large-scale phylogenomic screening for coopted ERV functions suggest that the frequency of coopted genes is underestimated.
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| 14. |
- Johannesson, Kerstin, 1955, et al.
(författare)
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Diverse pathways to speciation revealed by marine snails
- 2024
-
Ingår i: Trends in Genetics. - 0168-9525 .- 1362-4555.
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Forskningsöversikt (refereegranskat)abstract
- Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.
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| 15. |
- Jones, Eleanor P., et al.
(författare)
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Genetic tracking of mice and other bioproxies to infer human history
- 2013
-
Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 29:5, s. 298-308
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Forskningsöversikt (refereegranskat)abstract
- The long-distance movements made by humans through history are quickly erased by time but can be reconstructed by studying the genetic make-up of organisms that travelled with them. The phylogeography of the western house mouse (Mus musculus domesticus), whose current widespread distribution around the world has been caused directly by the movements of (primarily) European people, has proved particularly informative in a series of recent studies. The geographic distributions of genetic lineages in this commensal have been linked to the Iron Age movements within the Mediterranean region and Western Europe, the extensive maritime activities of the Vikings in the 9th to 11th centuries, and the colonisation of distant landmasses and islands by the Western European nations starting in the 15th century. We review here recent insights into human history based on phylogeographic studies of mice and other species that have travelled with humans, and discuss how emerging genomic methodologies will increase the precision of these inferences.
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| 16. |
- Naurin, Sara, et al.
(författare)
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Why does dosage compensation differ between XY and ZW taxa?
- 2010
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Ingår i: Trends in Genetics. - : Elsevier BV. - 1362-4555 .- 0168-9525. ; 26:1, s. 15-20
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies have demonstrated an extensive male bias in the gene expression on Z chromosomes in species with a ZW sex determination (e.g. birds), suggesting that ZW females have incomplete dosage compensation. We propose that the extensive male bias on Z chromosomes is caused by the functional properties of male-adapted genes, which make them unsuitable for high expression in females, and that ZW females are dosage-compensated to a point where they have achieved enough compensation to maintain the integrity of critical networks. In ZW systems, Z chromosomes spend two-thirds of their evolutionary time in males, and pronounced sexual selection in males and the male mutation bias can interact and affect levels of sexual antagonism, causing more extensive male bias in gene expression on Z-linked genes. These patterns and processes contrast with those acting on genes on the X chromosome in XY species, and might help explain the discrepancies in the degree of sex-biased gene expression and dosage compensation in XY and ZW systems.
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| 17. |
- Nelson, Ronald, et al.
(författare)
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A century after Fisher : time for a new paradigm in quantitative genetics.
- 2013
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 29:12
-
Tidskriftsartikel (refereegranskat)abstract
- Quantitative genetics traces its roots back through more than a century of theory, largely formed in the absence of directly observable genotype data, and has remained essentially unchanged for decades. By contrast, molecular genetics arose from direct observations and is currently undergoing rapid changes, making the amount of available data ever greater. Thus, the two disciplines are disparate both in their origins and their current states, yet they address the same fundamental question: how does the genotype affect the phenotype? The rapidly accumulating genomic data necessitate sophisticated analysis, but many of the current tools are adaptations of methods designed during the early days of quantitative genetics. We argue here that the present analysis paradigm in quantitative genetics is at its limits in regards to unraveling complex traits and it is necessary to re-evaluate the direction that genetic research is taking for the field to realize its full potential.
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| 18. |
- O'Connor, Emily, et al.
(författare)
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Immunity and lifespan: answering long-standing questions with comparative genomics
- 2022
-
Ingår i: Trends in Genetics. - : Elsevier BV. - 1362-4555 .- 0168-9525. ; 38:7, s. 650-661
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Tidskriftsartikel (refereegranskat)abstract
- Long life requires individuals to defend themselves against pathogens over prolonged periods of time whilst minimising damage to themselves. In vertebrates, pathogen defence is provided by two integrated systems, innate and adaptive immunity. Innate immunity is relatively nonspecific, resulting in collateral damage to hosts, and does not involve canonical immunological memory. In contrast, adaptive immunity is highly specific and confers long-lasting memory, which are features that are predicted to facilitate long life. However, there is long-standing debate over the general importance of adaptive immunity for the evolution of extended lifespans, partly because this is difficult to test. We highlight how recent improvements in whole genome assemblies open the door to immunogenomic comparative analyses that enable the coevolution of longevity and specific immune traits to be disentangled.
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| 19. |
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| 20. |
- Pinhasi, Ron, et al.
(författare)
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The genetic history of Europeans
- 2012
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 28:10, s. 496-505
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Forskningsöversikt (refereegranskat)abstract
- The evolutionary history of modern humans is characterized by numerous migrations driven by environmental change, population pressures, and cultural innovations. In Europe, the events most widely considered to have had a major impact on patterns of genetic diversity are the initial colonization of the continent by anatomically modern humans (AMH), the last glacial maximum, and the Neolithic transition. For some decades it was assumed that the geographical structuring of genetic diversity within Europe was mainly the result of gene flow during and soon after the Neolithic transition, but recent advances in next-generation sequencing (NGS) technologies, computer simulation modeling, and ancient DNA (aDNA) analyses are challenging this simplistic view. Here we review the current knowledge on the evolutionary history of humans in Europe based on archaeological and genetic data.
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| 21. |
- Piskur, Jure, et al.
(författare)
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Comparative genomics reveals novel biochemical pathways
- 2007
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Ingår i: Trends in Genetics. - : Elsevier BV. - 1362-4555 .- 0168-9525. ; 23:8, s. 369-372
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Tidskriftsartikel (refereegranskat)abstract
- How well do we understand which enzymes are involved in the primary metabolism of the cell? A recent study using comparative genomics and postgenomics approaches revealed a novel pathway in the most studied organism, Escherichia coli. The analysis of a new operon consisting of seven previously uncharacterized genes thought to be involved in the degradation of nucleic acid precursors showsthe impact of comparative genomics on the discovery of novel pathways and enzymes.
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| 22. |
- Piskur, Jure, et al.
(författare)
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How did Saccharomyces evolve to become a good brewer?
- 2006
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Ingår i: Trends in Genetics. - : Elsevier BV. - 1362-4555 .- 0168-9525. ; 22:4, s. 183-186
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Tidskriftsartikel (refereegranskat)abstract
- Brewing and wine production are among the oldest technologies and their products are almost indispensable in our lives. The central biological agents of beer and wine fermentation are yeasts belonging to the genus Saccharomyces, which can accumulate ethanol. Recent advances in comparative genomics and bioinformatics have made it possible to elucidate when and why yeasts produce ethanol in high concentrations, and how this remarkable trait originated and developed during their evolutionary history. Two research groups have shed light on the origin of the genes encoding alcohol dehydrogenase and the process of ethanol accumulation in Saccharomyces cerevisiae.
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| 23. |
- Tegnér, Jesper, et al.
(författare)
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Perturbations to uncover gene networks
- 2007
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 23:1, s. 34-41
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Forskningsöversikt (refereegranskat)abstract
- After the major achievements of the DNA sequencing projects, an equally important challenge now is to uncover the functional relationships among genes (i.e. gene networks). It has become increasingly clear that computational algorithms are crucial for extracting meaningful information from the massive amount of data generated by high-throughput genome-wide technologies. Here, we summarise how systems identification algorithms, originating from physics and control theory, have been adapted for use in biology. We also explain how experimental perturbations combined with genome-wide measurements are being used to uncover gene networks. Perturbation techniques could pave the way for identifying gene networks in more complex settings such as multifactorial diseases and for improving the efficacy of drug evaluation. © 2006 Elsevier Ltd. All rights reserved.
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| 24. |
- Theissinger, Kathrin, et al.
(författare)
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How genomics can help biodiversity conservation
- 2023
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Ingår i: Trends in Genetics. - : Elsevier. - 0168-9525 .- 1362-4555. ; 39:7, s. 545-559
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Forskningsöversikt (refereegranskat)abstract
- The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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| 25. |
- van de Lagemaat, LN, et al.
(författare)
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Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions
- 2003
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Ingår i: Trends in Genetics. - : Elsevier BV. - 1362-4555 .- 0168-9525. ; 19:10, s. 530-536
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Tidskriftsartikel (refereegranskat)abstract
- Nearly half of mammalian genomes are derived from ancient transposable elements (TEs). We analyzed the prevalence of TEs in untranslated regions of human and mouse mRNAs and found evidence suggesting that TEs affect the expression of many genes through the donation of transcriptional regulatory signals. Furthermore, we found that recently expanded gene classes, such as those involved in immunity or response to external stimuli, have transcripts enriched in TEs, whereas TEs are excluded from mRNAs of highly conserved genes with basic functions in development or metabolism. These results support the view that TEs have played a significant role in the diversification and evolution of mammalian genes.
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| 26. |
- Vihinen, Mauno
(författare)
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Muddled genetic terms miss and mess the message.
- 2015
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Ingår i: Trends in Genetics. - : Elsevier BV. - 1362-4555 .- 0168-9525. ; 31:8, s. 423-425
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Tidskriftsartikel (refereegranskat)abstract
- A critical aspect of science is the clear communication of complicated matters. However, language is often ambiguous, and the message can get lost in the telling. In particular, genetic terms can have different meanings for different people. Here, I discuss this problem and suggest remedies to clarify the message.
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| 27. |
- Wagner, Gerhart E. H., et al.
(författare)
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Antisense RNAs everywhere?
- 2002
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Ingår i: Trends in Genetics. - 0168-9525 .- 1362-4555. ; 18:5, s. 223-226
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In recent years, systematic searches of both prokaryote and eukaryote genomes have identified a staggering number of small RNAs, the biological functions of which remain unknown. Small RNA-based regulators are well known from bacterial plasmids. They act on target RNAs by sequence complementarity; that is, they are antisense RNAs. Recent findings suggest that many of the novel orphan RNAs encoded by bacterial and eukaryotic chromosomes might also belong to a ubiquitous, heterogeneous class of antisense regulators of gene expression.
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| 28. |
- Webster, Matthew Thomas
(författare)
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Apis mellifera
- 2019
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Ingår i: Trends in Genetics. - : Elsevier. - 0168-9525 .- 1362-4555. ; 35:11, s. 880-881
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 29. |
- Webster, Matthew T., et al.
(författare)
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Direct and indirect consequences of meiotic recombination : implications for genome evolution
- 2012
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 28:3, s. 101-109
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Forskningsöversikt (refereegranskat)abstract
- There is considerable variation within eukaryotic genomes in the local rate of crossing over. Why is this and what effect does it have on genome evolution? On the genome scale, it is known that by shuffling alleles, recombination increases the efficacy of selection. By contrast, the extent to which differences in the recombination rate modulate the efficacy of selection between genomic regions is unclear. Recombination also has direct consequences on the origin and fate of mutations: biased gene conversion and other forms of meiotic drive promote the fixation of mutations in a similar way to selection, and recombination itself may be mutagenic. Consideration of both the direct and indirect effects of recombination is necessary to understand why its rate is so variable and for correct interpretation of patterns of genome evolution.
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| 30. |
- Webster, Matthew Thomas, et al.
(författare)
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Fixation biases affecting human SNPs?
- 2004
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 20:3, s. 122-126
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Tidskriftsartikel (refereegranskat)abstract
- Under neutrality all classes of mutation have an equal probability of becoming fixed in a population. In this article, we describe our analysis of the frequency distributions of >5000 human SNPs and provide evident of biases in the process of fixation of certain classes of point mutation that are most likely to be attributable to biased gene conversion. The results indicate an increased fixation probability of mutations that result in the incorporation of a GC base pair. Furthermore, in transcribed regions this process exhibits strand asymmetry, and is biased towards preserving a G base on the coding strand. Biased gene conversion has the potential to explain both existence of isochores and the compositional asymmetry in mammalian transcribed regions.
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| 31. |
- Wellenreuther, Maren, et al.
(författare)
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Detecting Polygenic Evolution: Problems, Pitfalls, and Promises.
- 2016
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Ingår i: Trends in Genetics. - : Elsevier BV. - 1362-4555 .- 0168-9525.
-
Forskningsöversikt (refereegranskat)abstract
- Unraveling the genetic basis of organismal form and function remains one of the major goals of evolutionary biology. Theory has long supported a model of polygenic evolution in which quantitative traits are underpinned by many genes of small effect, but empirical methods have lacked the power to detect causative loci when effect sizes are small or moderate. We (i) review traditional approaches used for identifying the molecular basis of phenotypic traits, to highlight the inherent problems and pitfalls that bias them towards the detection of large-effect loci. We then (ii) outline the promises of recent statistical frameworks to detect polygenic signatures of trait evolution, and discuss some of the first studies in evolutionary biology employing these approaches. Lastly, we (iii) outline future directions and point to areas that still need development.
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| 32. |
- Williams, Tom A, et al.
(författare)
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Two chaperonin systems in bacterial genomes with distinct ecological roles
- 2010
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525 .- 1362-4555. ; 26:2, s. 47-51
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial chaperonins are essential to cell viability and have a role in endosymbiosis, which leads to increased biological complexity. However, the extent to which chaperonins promote ecological innovation is unknown. We screened 622 bacterial genomes for genes encoding chaperonins, and found archaeal-like chaperonins in bacteria that inhabit archaeal ecological niches. We found that chaperonins encoded in pathogenic bacteria are the most functionally divergent. We identified the molecular basis of the dramatic structural changes in mitochondrial GROEL, a highly derived chaperonin gene. Our analysis suggests that chaperonins are important capacitors of evolutionary and ecological change.
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| 33. |
- Brookes, AJ
(författare)
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HGBASE--a unified human SNP database
- 2001
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Ingår i: Trends in genetics : TIG. - 0168-9525. ; 17:4, s. 229-229
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 34. |
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| 35. |
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| 36. |
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| 37. |
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| 38. |
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| 39. |
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| 40. |
- Bouwman, BAM, et al.
(författare)
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The era of 3D and spatial genomics
- 2022
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Ingår i: Trends in genetics : TIG. - : Elsevier BV. - 0168-9525. ; 38:10, s. 1062-1075
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Tidskriftsartikel (refereegranskat)
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| 41. |
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| 42. |
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| 43. |
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| 44. |
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| 45. |
- Hofvander, Per, et al.
(författare)
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Potato trait development going fast-forward with genome editing
- 2022
-
Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525. ; 38, s. 218-221
-
Tidskriftsartikel (refereegranskat)abstract
- Implementations and improvements of genome editing techniques used in plant science have increased exponentially. For some crops, such as potato, the use of transcription activator-like effector nucleases (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR) has moved to the next step of trait development and field trials, and should soon be applied to commercial cultivation.
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| 46. |
- Jönsson, Marie E., et al.
(författare)
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Transposable Elements : A Common Feature of Neurodevelopmental and Neurodegenerative Disorders
- 2020
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525. ; 36:8, s. 610-623
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Forskningsöversikt (refereegranskat)abstract
- The etiology of most neurological disorders is poorly understood and current treatments are largely ineffective. New ideas and concepts are therefore vitally important for future research in this area. This review explores the concept that dysregulation of transposable elements (TEs) contributes to the appearance and pathology of neurodevelopmental and neurodegenerative disorders. Despite TEs making up at least half of the human genome, they are vastly understudied in relation to brain disorders. However, recent advances in sequencing technologies and gene editing approaches are now starting to unravel the pathological role of TEs. Aberrant activation of TEs has been found in many neurological disorders; the resulting pathogenic effects, which include alterations of gene expression, neuroinflammation, and direct neurotoxicity, are starting to be resolved. An increased understanding of the relationship between TEs and pathological processes in the brain improves the potential for novel diagnostics and interventions for brain disorders.
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| 47. |
- Köhler, Claudia
(författare)
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Helitrons: genomic parasites that generate developmental novelties
- 2024
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Ingår i: Trends in Genetics. - 0168-9525. ; 40, s. 437-448
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Forskningsöversikt (refereegranskat)abstract
- Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as 'peel-and-paste elements'. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for host genomes. This review discusses the current understanding of Helitrons, exploring their origins, transposition mechanism, and the extensive repercussions of their activity on genome structure and function. We also explore the evolutionary conflicts stemming from Helitron-transposed gene fragments and elucidate their domestication for regulating responses to environmental challenges. Looking ahead, further research in this evolving field promises to bring interesting discoveries on the role of Helitrons in shaping genomic landscapes.
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| 48. |
- Lehmann, Ordan J, et al.
(författare)
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Fox's in development and disease.
- 2003
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Ingår i: Trends in genetics : TIG. - 0168-9525. ; 19:6, s. 339-44
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Forskningsöversikt (refereegranskat)abstract
- Since the first forkhead (Fox) gene was identified, the importance of this family of transcription factors has increased steadily with the discoveries of the diverse range of developmental processes that they regulate in eukaryotes. Among other processes, the Fox factors are important in the establishment of the body axis and the development of tissues from all three germ layers. In this article, we present some of the recent data on this gene family with reference to selected phenotypes observed in patients and model organisms, and the sensitivity of developmental processes to alterations in forkhead gene dosage.
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| 49. |
- Lindqvist, Anna-Karin, et al.
(författare)
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Mouse models for rheumatoid arthritis
- 2002
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Ingår i: Trends in Genetics. - 1362-4555. ; 18:6, s. 7-13
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Tidskriftsartikel (refereegranskat)abstract
- Rheumatoid arthritis (RA) affects millions of people world wide causing considerable human suffering and large socioeconomic costs. Increased knowledge of pathological pathways involved in RA will enable development of modern drugs, with reduced side effects. The mouse models offer an attractive approach to dissect the genetic and molecular mechanisms of RA.
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| 50. |
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