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  • 1451. Westin, M A K
    et al.
    Hunt, M C
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för genetik, mikrobiologi och toxikologi. Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för genetik, mikrobiologi och toxikologi. Genetik.
    Alexson, S E H
    Short- and medium-chain carnitine acyltransferases and acyl-CoA thioesterases in mouse provide complementary systems for transport of beta-oxidation products out of peroxisomes.2008Inngår i: Cell Mol Life Sci, ISSN 1420-682X, Vol. 65, nr 6, s. 982-90Artikkel i tidsskrift (Fagfellevurdert)
  • 1452.
    Westman, Anna-Karin
    Mittuniversitetet, Fakulteten för naturvetenskap, teknik och medier, Institutionen för naturvetenskap, teknik och matematik.
    Investigation of Progress in Peer Discussions Regarding Genetic ConceptsManuskript (preprint) (Annet vitenskapelig)
  • 1453.
    Wetterbom, Anna
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    Sevov, Marie
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    Cavelier, Lucia
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi.
    Bergström, Tomas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för genetik och patologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Centrum för bioinformatik.
    Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution2006Inngår i: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 63, nr 5, s. 682-690Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sequence comparison of humans and chimpanzees is of interest to understand the mechanisms behind primate evolution. Here we present an independent analysis of human chromosome 21 and the high-quality BAC clone sequences of the homologous chimpanzee chromosome 22. In contrast to previous studies, we have used global alignment methods and Ensembl predictions of protein coding genes (n = 224) for the analysis. Divergence due to insertions and deletions (indels) along with substitutions was examined separately for different genomic features (coding, noncoding genic, and intergenic sequence). The major part of the genomic divergence could be attributed to indels (5.07%), while the nucleotide divergence was estimated as 1.52%. Thus the total divergence was estimated as 6.58%. When excluding repeats and low-complexity DNA the total divergence decreased to 2.37%. The chromosomal distribution of nucleotide substitutions and indel events was significantly correlated. To further examine the role of indels in primate evolution we focused on coding sequences. Indels were found within the coding sequence of 13% of the genes and approximately half of the indels have not been reported previously. In 5% of the chimpanzee genes, indels or substitutions caused premature stop codons that rendered the affected transcripts nonfunctional. Taken together, our findings demonstrate that indels comprise the majority of the genomic divergence. Furthermore, indels occur frequently in coding sequences. Our results thereby support the hypothesis that indels may have a key role in primate evolution.

  • 1454.
    Wheatcroft, David
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Qvarnström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Genetic divergence of early song discrimination between two young songbird species2017Inngår i: NATURE ECOLOGY & EVOLUTION, ISSN 2397-334X, Vol. 1, nr 7, artikkel-id UNSP 0192Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Juvenile songbirds express species-specific song discrimination from an early age, which focuses learning onto the songs of their parental species. However, it remains unknown whether this early song discrimination is influenced by early social experience or maternal effects or whether it is instead largely genetically determined. We manipulated early social experience by swapping young embryos between the nests of two co-occurring songbird species-pied and collared flycatchers. We show that nestlings are more active in response to playbacks of conspecific songs, even when raised by adults from the other species, thus enabling us to reject social experience as the main determinant of early song discrimination. We then crossed the two species in captivity and showed that the song responses of hybrid nestlings do not depend on social experience or maternal species, implying genetic divergence of early song discrimination. Our results provide conclusive evidence that early song discrimination has a largely genetic component, which can stabilize reproductive isolation by reducing song learning across closely related species.

  • 1455.
    Widell, Paulina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Genetiken bakom artbildning: fokus på Leptidea Sinapis2017Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Artbildning, det vill säga uppkomst av nya arter, är ett centralt ämne inom evolutionsbiologinoch en process som kan fortskrida på ett flertal olika sätt. Reproduktiva barriärer som är nödvändiga för artbildningsprocessen kan utvecklas mellan populationer och verkar antingen så att individer hindras från att para sig med varandra (prezygotisk isolering) eller så att överlevnad eller reproduktionsframgång hos avkomman är reducerad (postzygotisk isolering).Syftet men där här studien är att först beskriva dessa olika typer av isoleringar och sedan summera den aktuella kunskapen om hur själva artbildningsprocessen kan fortgå. Avslutningvis beskrivs ett exempelsystem med tre geografiskt separerade populationer avarten skogsvitsvinge (Leptidea sinapis). Skillnader i kromosomantal och ekologi mellan vissa av populationerna kan potentiellt vara faktorer som har lett till begränsat genflöde och som i slutänden kan leda till att fullständigt reproduktivt isolerade arter uppkommer.

    Fulltekst (pdf)
    fulltext
  • 1456.
    Wikström, P
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    O'Neill, E
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Ng, L C
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Shingler, V
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    The regulatory N-terminal region of the aromatic-responsive transcriptional activator DmpR constrains nucleotide-triggered multimerisation.2001Inngår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 314, nr 5Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The transcriptional promoting activity of DmpR is under the strict control of its aromatic effector ligands that are bound by its regulatory N-terminal domain. The positive control function of DmpR resides within the central C-domain that is highly conserved among activators of sigma(54)-RNA polymerase. The C-domain mediates ATP hydrolysis and interaction with sigma(54)-RNA polymerase that are essential for open-complex formation and thus initiation of transcription. Wild-type and loss-of-function derivatives of DmpR, which are defective in distinct steps in nucleotide catalysis, were used to address the consequences of nucleotide binding and hydrolysis with respect to the multimeric state of DmpR and its ability to promote in vitro transcription. Here, we show that DmpR derivatives deleted of the regulatory N-terminal domain undergo an aromatic-effector independent ATP-binding triggered multimerisation as detected by cross-linking. In the intact protein, however, aromatic effector activation is required before ATP-binding can trigger an apparent dimer-to-hexamer switch in subunit conformation. The data suggest a model in which the N-terminal domain controls the transcriptional promoting property of DmpR by constraining ATP-mediated changes in its oligomeric state. The results are discussed in the light of recent mechanistic insights from the AAA(+) superfamily of ATPases that utilise nucleotide hydrolysis to restructure their substrates.

  • 1457. Willems, Sara M.
    et al.
    Wright, Daniel J.
    Day, Felix R.
    Trajanoska, Katerina
    Joshi, Peter K.
    Morris, John A.
    Matteini, Amy M.
    Garton, Fleur C.
    Grarup, Niels
    Oskolkov, Nikolay
    Thalamuthu, Anbupalam
    Mangino, Massimo
    Liu, Jun
    Demirkan, Ayse
    Lek, Monkol
    Xu, Liwen
    Wang, Guan
    Oldmeadow, Christopher
    Gaulton, Kyle J.
    Lotta, Luca A.
    Miyamoto-Mikami, Eri
    Rivas, Manuel A.
    White, Tom
    Loh, Po-Ru
    Aadahl, Mette
    Amin, Najaf
    Attia, John R.
    Austin, Krista
    Benyamin, Beben
    Brage, Soren
    Cheng, Yu-Ching
    Cieszczyk, Pawel
    Derave, Wim
    Eriksson, Karl-Fredrik
    Eynon, Nir
    Linneberg, Allan
    Lucia, Alejandro
    Massidda, Myosotis
    Mitchell, Braxton D.
    Miyachi, Motohiko
    Murakami, Haruka
    Padmanabhan, Sandosh
    Pandey, Ashutosh
    Papadimitriou, Loannis
    Rajpal, Deepak K.
    Sale, Craig
    Schnurr, Theresia M.
    Sessa, Francesco
    Shrine, Nick
    Tobin, Martin D.
    Varley, Ian
    Wain, Louise V.
    Wray, Naomi R.
    Lindgren, Cecilia M.
    MacArthur, Daniel G.
    Waterworth, Dawn M.
    McCarthy, Mark I.
    Pedersen, Oluf
    Khaw, Kay-Tee
    Kie, Douglas P.
    Pitsiladis, Yannis
    Fuku, Noriyuki
    Franks, Paul W.
    Umeå universitet, Medicinska fakulteten, Institutionen för folkhälsa och klinisk medicin, Medicin. Umeå universitet, Medicinska fakulteten, Enheten för biobanksforskning. Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Skånes University Hospital, 222 41 Lund, Sweden.
    North, Kathryn N.
    van Duijn, Cornelia M.
    Mather, Karen A.
    Hansen, Torben
    Hansson, Ola
    Spector, Tim
    Murabito, Joanne M.
    Richards, J. Brent
    Rivadeneira, Fernando
    Langenberg, Claudia
    Perry, John R. B.
    Wareham, Nick J.
    Scott, Robert A.
    Large-scale GWAS identifies multiple loci for hand grip strength providing biological insights into muscular fitness2017Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, artikkel-id 16015Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Hand grip strength is a widely used proxy of muscular fitness, a marker of frailty, and predictor of a range of morbidities and all-cause mortality. To investigate the genetic determinants of variation in grip strength, we perform a large-scale genetic discovery analysis in a combined sample of 195,180 individuals and identify 16 loci associated with grip strength (P<5 x 10(-8)) in combined analyses. A number of these loci contain genes implicated in structure and function of skeletal muscle fibres (ACTG1), neuronal maintenance and signal transduction (PEX14, TGFA, SYT1), or monogenic syndromes with involvement of psychomotor impairment (PEX14, LRPPRC and KANSL1). Mendelian randomization analyses are consistent with a causal effect of higher genetically predicted grip strength on lower fracture risk. In conclusion, our findings provide new biological insight into the mechanistic underpinnings of grip strength and the causal role of muscular strength in age-related morbidities and mortality.

    Fulltekst (pdf)
    fulltext
  • 1458. Williams, Jessica S
    et al.
    Clausen, Anders R
    Nick McElhinny, Stephanie A
    Watts, Brian E
    Johansson, Erik
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Kunkel, Thomas A
    Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase ɛ.2012Inngår i: DNA Repair, ISSN 1568-7864, E-ISSN 1568-7856, Vol. 11, nr 8, s. 649-656Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have investigated the ability of the 3' exonuclease activity of Saccharomyces cerevisiae DNA polymerase ɛ (Pol ɛ) to proofread newly inserted ribonucleotides (rNMPs). During DNA synthesis in vitro, Pol ɛ proofreads ribonucleotides with apparent efficiencies that vary from none at some locations to more than 90% at others, with rA and rU being more efficiently proofread than rC and rG. Previous studies show that failure to repair ribonucleotides in the genome of rnh201Δ strains that lack RNase H2 activity elevates the rate of short deletions in tandem repeat sequences. Here we show that this rate is increased by 2-4-fold in pol2-4 rnh201Δ strains that are also defective in Pol ɛ proofreading. In comparison, defective proofreading in these same strains increases the rate of base substitutions by more than 100-fold. Collectively, the results indicate that although proofreading of an 'incorrect' sugar is less efficient than is proofreading of an incorrect base, Pol ɛ does proofread newly inserted rNMPs to enhance genome stability.

  • 1459. Wilsker, Deborah
    et al.
    Chung, Jon H.
    Pradilla, Ivan
    Petermann, Eva
    Helleday, Thomas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för genetik, mikrobiologi och toxikologi.
    Bunz, Fred
    Targeted Mutations in the ATR Pathway Define Agent-Specific Requirements for Cancer Cell Growth and Survival2012Inngår i: Molecular Cancer Therapeutics, ISSN 1535-7163, E-ISSN 1538-8514, Vol. 11, nr 1, s. 98-107Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many anticancer agents induce DNA strand breaks or cause the accumulation of DNA replication intermediates. The protein encoded by ataxia-telangiectasia mutated and Rad 3-related (ATR) generates signals in response to these altered DNA structures and activates cellular survival responses. Accordingly, ATR has drawn increased attention as a potential target for novel therapeutic strategies designed to potentiate the effects of existing drugs. In this study, we use a unique panel of genetically modified human cancer cells to unambiguously test the roles of upstream and downstream components of the ATR pathway in the responses to common therapeutic agents. Upstream, the S-phase-specific cyclin-dependent kinase (Cdk) 2 was required for robust activation of ATR in response to diverse chemotherapeutic agents. While Cdk2-mediated ATR activation promoted cell survival after treatment with many drugs, signaling from ATR directly to the checkpoint kinase Chk1 was required for survival responses to only a subset of the drugs tested. These results show that specifically inhibiting the Cdk2/ATR/Chk1 pathway via distinct regulators can differentially sensitize cancer cells to a wide range of therapeutic agents.

  • 1460. Wind, Julia J.
    et al.
    Peviani, Alessia
    Snel, Berend
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Smeekens, Sjef C.
    ABI4: versatile activator and repressor2013Inngår i: Trends in Plant Science, ISSN 1360-1385, E-ISSN 1878-4372, Vol. 18, nr 3, s. 125-132Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The ABSCISIC ACID INSENSITIVE4 (ABI4) gene was discovered to be an abscisic acid (ABA) signaling responsive transcription factor active during seed germination. The evolutionary history of the ABI4 gene supports its role as an ABA signaling intermediate in land plants. Investigating the ABI4 protein-cis element interaction supports the proposal that ABI4 binding to its known CE1 cis-element competes with transcription factor binding to the overlapping G-Box element. Recent publications report on ABI4 as a regulatory factor in diverse processes. In developing seedlings, ABI4 mediates sugar signaling, lipid breakdown, and plastid-to-nucleus signaling. Moreover, ABI4 is a regulator of rosette growth, redox signaling, cell wall metabolism and the effect of nitrate on lateral root development.

  • 1461.
    Wittenburg, Dörte
    et al.
    Institute for Genetics and Biometry, Unit Biomathematics and Bioinformatics, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany .
    Melzer, Nina
    Institute for Genetics and Biometry, Unit Biomathematics and Bioinformatics, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany .
    Willmitzer, Lothar
    Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany.
    Lisec, Jan
    Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany.
    Kesting, U
    Landeskontrollverband für Leistungs, Qualitätsprüfung Mecklenburg-Vorpommern e.V. (LKV), Güstrow, Germany .
    Reinsch, Norbert
    Institute for Genetics and Biometry, Unit Biomathematics and Bioinformatics, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany .
    Repsilber, Dirk
    Institute for Genetics and Biometry, Unit Biomathematics and Bioinformatics, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany .
    Milk metabolites and their genetic variability2013Inngår i: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 96, nr 4, s. 2557-69Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The composition of milk is crucial to evaluate milk performance and quality measures. Milk components partly contribute to breeding scores, and they can be assessed to judge metabolic and energy status of the cow as well as to serve as predictive markers for diseases. In addition to the milk composition measures (e.g., fat, protein, lactose) traditionally recorded during milk performance test via infrared spectroscopy, novel techniques, such as gas chromatography-mass spectrometry, allow for a further analysis of milk into its metabolic components. Gas chromatography-mass spectrometry is suitable for measuring several hundred metabolites with high throughput, and thus it is applicable to study sources of genetic and nongenetic variation of milk metabolites in dairy cows. Heritability and mode of inheritance of metabolite measurements were studied in a linear mixed model approach including expected (pedigree) and realized (genomic) relationship between animals. The genetic variability of 190 milk metabolite intensities was analyzed from 1,295 cows held on 18 farms in Mecklenburg-Western Pomerania, Germany. Besides extensive pedigree information, genotypic data comprising 37,180 single nucleotide polymorphism markers were available. Goodness of fit and significance of genetic variance components based on likelihood ratio tests were investigated with a full model, including marker- and pedigree-based genetic effects. Broad-sense heritability varied from zero to 0.699, with a median of 0.125. Significant additive genetic variance was observed for highly heritable metabolites, but dominance variance was not significantly present. As some metabolites are particularly favorable for human nutrition, for instance, future research should address the identification of locus-specific genetic effects and investigate metabolites as the molecular basis of traditional milk performance test traits.

  • 1462.
    Wolf, Jochen B. W.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Ludwig Maximilian Univ Munich, Dept Biol 2, Sect Evolutionary Biol, Grosshaderner Str 2, D-82152 Planegg Martinsried, Germany..
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Making sense of genomic islands of differentiation in light of speciation2017Inngår i: Nature reviews genetics, ISSN 1471-0056, E-ISSN 1471-0064, Vol. 18, nr 2, s. 87-100Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    As populations diverge, genetic differences accumulate across the genome. Spurred by rapid developments in sequencing technology, genome-wide population surveys of natural populations promise insights into the evolutionary processes and the genetic basis underlying speciation. Although genomic regions of elevated differentiation are the focus of searches for 'speciation genes', there is an increasing realization that such genomic signatures can also arise by alternative processes that are not related to population divergence, such as linked selection. In this Review, we explore methodological trends in speciation genomic studies, highlight the difficulty in separating processes related to speciation from those emerging from genome-wide properties that are not related to reproductive isolation, and provide a set of suggestions for future work in this area.

  • 1463. Wong, Gane Ka-Shu
    et al.
    Liu, Bin
    Wang, Jun
    Zhang, Yong
    Yang, Xu
    Zhang, Zengjin
    Meng, Qingshun
    Zhou, Jun
    Li, Dawei
    Zhang, Jingjing
    Ni, Peixiang
    Li, Songgang
    Ran, Longhua
    Li, Heng
    Zhang, Jianguo
    Li, Ruiqiang
    Li, Shengting
    Zheng, Hongkun
    Lin, Wei
    Li, Guangyuan
    Wang, Xiaoling
    Zhao, Wenming
    Li, Jun
    Ye, Chen
    Dai, Mingtao
    Ruan, Jue
    Zhou, Yan
    Li, Yuanzhe
    He, Ximiao
    Zhang, Yunze
    Wang, Jing
    Huang, Xiangang
    Tong, Wei
    Chen, Jie
    Ye, Jia
    Chen, Chen
    Wei, Ning
    Li, Guoqing
    Dong, Le
    Lan, Fengdi
    Sun, Yongqiao
    Zhang, Zhenpeng
    Yang, Zheng
    Yu, Yingpu
    Huang, Yanqing
    He, Dandan
    Xi, Yan
    Wei, Dong
    Qi, Qiuhui
    Li, Wenjie
    Shi, Jianping
    Wang, Miaoheng
    Xie, Fei
    Wang, Jianjun
    Zhang, Xiaowei
    Wang, Pei
    Zhao, Yiqiang
    Li, Ning
    Yang, Ning
    Dong, Wei
    Hu, Songnian
    Zeng, Changqing
    Zheng, Weimou
    Hao, Bailin
    Hillier, Ladeana W
    Yang, Shiaw-Pyng
    Warren, Wesley C
    Wilson, Richard K
    Brandström, Mikael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Institutionen för evolution, genomik och systematik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Institutionen för evolution, genomik och systematik, Evolutionsbiologi. Evolutionsbiologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Institutionen för evolution, genomik och systematik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Institutionen för evolution, genomik och systematik, Evolutionsbiologi. Evolutionsbiologi.
    Crooijmans, Richard P M A
    van der Poel, Jan J
    Bovenhuis, Henk
    Groenen, Martien A M
    Ovcharenko, Ivan
    Gordon, Laurie
    Stubbs, Lisa
    Lucas, Susan
    Glavina, Tijana
    Aerts, Andrea
    Kaiser, Pete
    Rothwell, Lisa
    Young, John R
    Rogers, Sally
    Walker, Brian A
    van Hateren, Andy
    Kaufman, Jim
    Bumstead, Nat
    Lamont, Susan J
    Zhou, Huaijun
    Hocking, Paul M
    Morrice, David
    de Koning, Dirk-Jan
    Law, Andy
    Bartley, Neil
    Burt, David W
    Hunt, Henry
    Cheng, Hans H
    Gunnarsson, Ulrika
    Medicinska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Institutionen för evolution, genomik och systematik, Evolutionsbiologi.
    Wahlberg, Per
    Medicinska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Institutionen för evolution, genomik och systematik, Evolutionsbiologi.
    Andersson, Leif
    Medicinska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Institutionen för evolution, genomik och systematik, Evolutionsbiologi.
    Kindlund, Ellen
    Tammi, Martti T
    Andersson, Björn
    Webber, Caleb
    Ponting, Chris P
    Overton, Ian M
    Boardman, Paul E
    Tang, Haizhou
    Hubbard, Simon J
    Wilson, Stuart A
    Yu, Jun
    Wang, Jian
    Yang, Huanming
    A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.2004Inngår i: Nature, ISSN 1476-4687, Vol. 432, nr 7018, s. 717-22Artikkel i tidsskrift (Fagfellevurdert)
  • 1464.
    Woronik, Alyssa
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Neethiraj, Ramprasad
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Lehmann, Philipp
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Maria, de la Paz Celorio Mancera
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Stefanescu, Constanti
    Hill, Jason
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Käkelä, Reijo
    Brattstrom, Oskar
    Wheat, Christopher
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    A transposable element insertion is associated with a female-limited, alternative life history strategyManuskript (preprint) (Annet vitenskapelig)
  • 1465. Wrzaczek, Michael
    et al.
    Vainonen, Julia P.
    Stael, Simon
    Tsiatsiani, Liana
    Help-Rinta-Rahko, Hanna
    Gauthier, Adrien
    Kaufholdt, David
    Bollhöner, Benjamin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Lamminmaki, Airi
    Staes, An
    Gevaert, Kris
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Van Breusegem, Frank
    Helariutta, Yka
    Kangasjarvi, Jaakko
    GRIM REAPER peptide binds to receptor kinase PRK5 to trigger cell death in Arabidopsis2015Inngår i: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 31, nr 1, s. 55-66Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recognition of extracellular peptides by plasma membrane-localized receptor proteins is commonly used in signal transduction. In plants, very little is known about how extracellular peptides are processed and activated in order to allow recognition by receptors. Here, we show that induction of cell death in planta by a secreted plant protein GRIM REAPER (GRI) is dependent on the activity of the type II metacaspase METACASPASE-9. GRI is cleaved by METACASPASE-9 in vitro resulting in the release of an 11 amino acid peptide. This peptide bound in vivo to the extracellular domain of the plasma membrane-localized, atypical leucine-rich repeat receptor-like kinase POLLEN-SPECIFIC RECEPTOR-LIKE KINASE 5 (PRK5) and was sufficient to induce oxidative stress/ROS-dependent cell death. This shows a signaling pathway in plants from processing and activation of an extracellular protein to recognition by its receptor.

  • 1466. Wu, Chenglin
    et al.
    Mignardi, Marco
    chen, lei
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi.
    Landegren, Ulf
    Nilsson, Mats
    Profiling and genotyping individual mRNA molecules through in situ sequencing of super rolling circle amplification productsManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    We have recently developed a technology for localized sequence library preparation with rolling-circle amplification (RCA) as an approach for in situ sequencing. This method involves generation of clonally amplified and specially confined substrates for next-generation sequencing within the preserved context of cells and tissues. Our approach combines padlock probing, RCA, and sequencing-by-ligation chemistry that can resolve expression profiles of sets of genes and mutations in tissues without loss of histological context. Like other fluorescence-based assays, it can be hindered by high level of background fluorescence. To achieve high signal-to-noise ratios, we now describe a method to boost the amplification generated by RCA of padlock probes in situ by super RCA (sRCA). In this technique, a second padlock probe is hybridized, ligated and amplified on the first RCA product for enhanced, localized amplification. We describe and compare different sRCA strategies where gap-fill ligation was showed to be most efficient. The sRCA products co-localize and have comparable sizes as RCA products but they display at least two fold higher signal intensity. This increase in signal to noise also proved to result in two folds increase in the number of sRCA products detected. By combining sRCA with in situ sequencing for highly multiplex detection in tissue a four-time increase was seen. In summary, we demonstrate that sRCA can significantly increase the performance of padlock-based in situ sequencing for gene expression profiling of tissue sections, enabling detection of low abundant transcripts and the analysis of also highly auto-fluorescent samples. 

  • 1467.
    Wu, Chi-Chih
    et al.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Klaesson, Axel
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Buskas, Julia
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Ranefall, Petter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för visuell information och interaktion. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Mirzazadeh, Reza
    Söderberg, Ola
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaceutisk biovetenskap.
    Wolf, Jochen B. W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation2019Inngår i: Journal of Experimental Biology, ISSN 0022-0949, E-ISSN 1477-9145, Vol. 222, nr 5Artikkel i tidsskrift (Fagfellevurdert)
  • 1468.
    Wu, Cuiyan
    et al.
    School of Public Health, Health Science Center of Xi'an Jiaotong University; Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission of the People's Republic of China, Xi'an, P.R. China.
    Liu, Huan
    School of Public Health, Health Science Center of Xi'an Jiaotong University; Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission of the People's Republic of China, Xi'an, P.R. China.
    Zhang, Feng'e
    School of Public Health, Health Science Center of Xi'an Jiaotong University; Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission of the People's Republic of China, Xi'an, P.R. China.
    Shao, Wanzhen
    School of Public Health, Health Science Center of Xi'an Jiaotong University; Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission of the People's Republic of China, Xi'an, P.R. China.
    Yang, Lei
    School of Public Health, Health Science Center of Xi'an Jiaotong University; Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission of the People's Republic of China, Xi'an, P.R. China.
    Ning, Yujie
    School of Public Health, Health Science Center of Xi'an Jiaotong University; Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission of the People's Republic of China, Xi'an, P.R. China.
    Wang, Sen
    School of Public Health, Health Science Center of Xi'an Jiaotong University; Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission of the People's Republic of China, Xi'an, P.R. China.
    Zhao, Guanghui
    Department of Knee Joint, Xi'an Hong Hui Hospital, Xi'an, P.R. China.
    Lee, Byeong Jae
    Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, Korea.
    Lammi, Mikko
    Umeå universitet, Medicinska fakulteten, Institutionen för integrativ medicinsk biologi (IMB).
    Guo, Xiong
    Long noncoding RNA expression profile reveals lncRNAs signature associated with extracellular matrix degradation in kashin-beck disease2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 17553Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Kashin-Beck disease (KBD) is a deformative, endemic osteochondropathy involving degeneration and necrosis of growth plates and articular cartilage. The pathogenesis of KBD is related to gene expression and regulation mechanisms, but long noncoding RNAs (lncRNAs) in KBD have not been investigated. In this study, we identified 316 up-regulated and 631 down-regulated lncRNAs (≥ 2-fold change) in KBD chondrocytes using microarray analysis, of which more than three-quarters were intergenic lncRNAs and antisense lncRNAs. We also identified 232 up-regulated and 427 down-regulated mRNAs (≥ 2-fold change). A lncRNA-mRNA correlation analysis combined 343 lncRNAs and 292 mRNAs to form 509 coding-noncoding gene co-expression networks (CNC networks). Eleven lncRNAs were predicted to have cis-regulated target genes, including NAV2 (neuron navigator 2), TOX (thymocyte selection-associated high mobility group box), LAMA4 (laminin, alpha 4), and DEPTOR (DEP domain containing mTOR-interacting protein). The differentially expressed mRNAs in KBD significantly contribute to biological events associated with the extracellular matrix. Meanwhile, 34 mRNAs and 55 co-expressed lncRNAs constituted a network that influences the extracellular matrix. In the network, FBLN1 and LAMA 4 were the core genes with the highest significance. These novel findings indicate that lncRNAs may play a role in extracellular matrix destruction in KBD.

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  • 1469.
    Wu, Sihan
    et al.
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA.
    Turner, Kristen M.
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA;Boundless Bio Inc, La Jolla, CA USA.
    Nguyen, Nam
    Raviram, Ramya
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA.
    Erb, Marcella
    Univ Calif San Diego, Dept Neurosci, UCSD Light Microscopy Core Facil, La Jolla, CA 92093 USA.
    Santini, Jennifer
    Univ Calif San Diego, Dept Neurosci, UCSD Light Microscopy Core Facil, La Jolla, CA 92093 USA.
    Luebeck, Jens
    Univ Calif San Diego, Bioinformat & Syst Biol Grad Program, La Jolla, CA 92093 USA.
    Rajkumar, Utkrisht
    Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA;Duke Univ, Sch Med, Dept Cell Biol, Regenerat Next Initiat, Durham, NC USA.
    Diao, Yarui
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA;Duke Univ, Sch Med, Dept Orthopaed Surg, Regenerat Next Initiat, Durham, NC USA.
    Li, Bin
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA.
    Zhang, Wenjing
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA.
    Jameson, Nathan
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA.
    Corces, M. Ryan
    Stanford Univ, Ctr Personal Dynam Regulomes, Stanford, CA 94305 USA.
    Granja, Jeffrey M.
    Stanford Univ, Ctr Personal Dynam Regulomes, Stanford, CA 94305 USA.
    Chen, Xingqi
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylära verktyg. Stanford Univ, Ctr Personal Dynam Regulomes, Stanford, CA 94305 USA.
    Coruh, Ceyda
    Salk Inst Biol Studies, Plant Mol & Cellular Biol Lab, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA.
    Abnousi, Armen
    Cleveland Clin Fdn, Lerner Res Inst, Dept Quantitat Hlth Sci, 9500 Euclid Ave, Cleveland, OH 44195 USA.
    Houston, Jack
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA.
    Ye, Zhen
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA.
    Hu, Rong
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA.
    Yu, Miao
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA.
    Kim, Hoon
    Jackson Lab Genom Med, Farmington, CT USA.
    Law, Julie A.
    Salk Inst Biol Studies, Plant Mol & Cellular Biol Lab, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA.
    Verhaak, Roel G. W.
    Jackson Lab Genom Med, Farmington, CT USA.
    Hu, Ming
    Cleveland Clin Fdn, Lerner Res Inst, Dept Quantitat Hlth Sci, 9500 Euclid Ave, Cleveland, OH 44195 USA.
    Furnari, Frank B.
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA.
    Chang, Howard Y.
    Stanford Univ, Ctr Personal Dynam Regulomes, Stanford, CA 94305 USA;Stanford Univ, Howard Hughes Med Inst, Stanford, CA 94305 USA.
    Ren, Bing
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA;Univ Calif San Diego, Ctr Epigen, Dept Cellular & Mol Med, La Jolla, CA 92093 USA;Univ Calif San Diego, Moores Canc Ctr, Inst Genom Med, La Jolla, CA 92093 USA.
    Bafna, Vineet
    Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA.
    Mischel, Paul S.
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA;Univ Calif San Diego, Moores Canc Ctr, La Jolla, CA 92093 USA;Univ Calif San Diego, Dept Pathol, La Jolla, CA 92093 USA.
    Circular ecDNA promotes accessible chromatin and high oncogene expression2019Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 575, nr 7784, s. 699-703Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer(1,2), but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultrastructural imaging, long-range optical mapping and computational analysis of whole-genome sequencing, we demonstrate the structure of circular ecDNA. Pan-cancer analyses reveal that oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of the tumours, linking increased copy number with high transcription levels. Quantitative assessment of the chromatin state reveals that although ecDNA is packaged into chromatin with intact domain structure, it lacks higher-order compaction that is typical of chromosomes and displays significantly enhanced chromatin accessibility. Furthermore, ecDNA is shown to have a significantly greater number of ultra-long-range interactions with active chromatin, which provides insight into how the structure of circular ecDNA affects oncogene function, and connects ecDNA biology with modern cancer genomics and epigenetics.

  • 1470. Wu, Xiaofen
    et al.
    Pedersen, Karsten
    Edlund, Johanna
    Eriksson, Lena
    Astrom, Mats
    Andersson, Anders F.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Bertilsson, Stefan
    Dopson, Mark
    Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters2017Inngår i: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 5, artikkel-id 37Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. Results: In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide-and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria. Conclusions: Populations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.

  • 1471.
    Wu, Xiushan
    Stockholms universitet.
    Transition of R- to I-type and the variation in the strength of R-reactivity and I-inductivity in inbred lines of Drosophila melanogaster1990Doktoravhandling, med artikler (Annet vitenskapelig)
  • 1472.
    Wuolikainen, Anna
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Medicinska fakulteten, Institutionen för farmakologi och klinisk neurovetenskap, Klinisk neurovetenskap.
    Moritz, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Marklund, Stefan L
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Klinisk kemi.
    Antti, Henrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Andersen, Peter M
    Umeå universitet, Medicinska fakulteten, Institutionen för farmakologi och klinisk neurovetenskap, Klinisk neurovetenskap.
    ALS patients with mutations in the SOD1 gene have an unique metabolomic profile in the cerebrospinal fluid compared with ALS patients without mutations2012Inngår i: Molecular Genetics and Metabolism, ISSN 1096-7192, E-ISSN 1096-7206, Vol. 105, nr 3, s. 472-478Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A specific biochemical marker for early diagnosing and for monitoring disease progression in amyotrophic lateral sclerosis (ALS) will have important clinical applications. ALS is a heterogeneous syndrome with multiple subtypes with ill-defined borders. A minority of patients carries mutations in the Cu/Zn-superoxide dismutase (SOD1) gene but the disease mechanism remains unknown for all types of ALS. Using a GC-TOFMS platform we studied the cerebrospinal fluid (CSF) metabolome in 16 ALS patients with six different mutations in the SOD1 gene and compared with ALS-patients without such mutations. OPLS-DA was used for classification modeling. We find that patients with a SOD1 mutation have a distinct metabolic profile in the CSF. In particular, the eight patients homozygous for the D90A SOD1 mutation showed a distinctively different signature when modeled against ALS patients with other SOD1 mutations and sporadic and familial ALS patients without a SOD1 gene mutation. This was found irrespective of medication with riluzole and survival time. Among the metabolites that contributed most to the CSF signature were arginine, lysine, ornithine, serine, threonine and pyroglutamic acid, all found to be reduced in patients carrying a D90A SOD1 mutation. ALS-patients with a SOD1 gene mutation appear as a distinct metabolic entity in the CSF, in particular in patients with the D90A mutation, the most frequently identified cause of ALS. The findings suggest that metabolomic profiling using GC-TOFMS and multivariate data analysis may be a future tool for diagnosing and monitoring disease progression, and may cast light on the disease mechanisms in ALS.

  • 1473. Wärmländer, Sebastian
    Struktur och dynamik hos DNA studerad med KSR och optisk spektroskopi = Structure and dynamics of DNA studied by NMR and optical spectroscopy2003Doktoravhandling, med artikler (Annet vitenskapelig)
  • 1474. Xenikoudakis, G.
    et al.
    Ersmark, E.
    Tison, J. -L
    Waits, L.
    Kindberg, J.
    Swenson, J. E.
    Dalen, L.
    Consequences of a demographic bottleneck on geneticstructure and variation in the Scandinavian brown bear2015Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, nr 13, s. 3441-3454Artikkel i tidsskrift (Fagfellevurdert)
  • 1475. Xia, Hanhan
    et al.
    Wang, Baosheng
    Zhao, Wei
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Pan, Jin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Mao, Jian-Feng
    Wang, Xiao-Ru
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Combining mitochondrial and nuclear genome analyses to dissect the effects of colonization, environment, and geography on population structure in Pinus tabuliformis2018Inngår i: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 11, nr 10, s. 1931-1945Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The phylogeographic histories of plants in East Asia are complex and shaped by both past large‐scale climatic oscillations and dramatic tectonic events. The impact of these historic events, as well as ecological adaptation, on the distribution of biodiversity remains to be elucidated. Pinus tabuliformis is the dominant coniferous tree in northern China, with a large distribution across wide environmental gradients. We examined genetic variation in this species using genotyping‐by‐sequencing and mitochondrial (mt) DNA markers. We found population structure on both nuclear and mt genomes with a geographic pattern that corresponds well with the landscape of northern China. To understand the contributions of environment, geography, and colonization history to the observed population structure, we performed ecological niche modeling and partitioned the among‐population genomic variance into isolation by environment (IBE), isolation by distance (IBD), and isolation by colonization (IBC). We used mtDNA, which is transmitted by seeds in pine, to reflect colonization. We found little impact of IBE, IBD, and IBC on variation in neutral SNPs, but significant impact of IBE on a group of outlier loci. The lack of IBC illustrates that the maternal history can be quickly eroded from the nuclear genome by high rates of gene flow. Our results suggest that genomic variation in P. tabuliformis is largely affected by neutral and stochastic processes, and the signature of local adaptation is visible only at robust outlier loci. This study enriches our understanding on the complex evolutionary forces that shape the distribution of genetic variation in plant taxa in northern China, and guides breeding, conservation, and reforestation programs for P. tabuliformis.

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  • 1476.
    Xiao, Hui
    et al.
    Univ Cambridge, England.
    Bartoszek, Krzysztof
    Linköpings universitet, Institutionen för datavetenskap, Statistik och maskininlärning. Linköpings universitet, Filosofiska fakulteten.
    Lio, Pietro
    Univ Cambridge, England.
    Multi-omic analysis of signalling factors in inflammatory comorbidities2018Inngår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 19, artikkel-id 439Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    BackgroundInflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a long series of pathologic events that started years before. The systemic characteristics and related mechanisms could be investigated through the multi-omic comparative analysis of many inflammatory diseases. Therefore, it is important to use molecular data to study the genesis of the diseases. Here we propose a new methodology to study the relationships between inflammatory diseases and signalling molecules whose dysregulation at molecular levels could lead to systemic pathological events observed in inflammatory diseases.ResultsWe first perform an exploratory analysis of gene expression data of a number of diseases that involve a strong inflammatory component. The comparison of gene expression between disease and healthy samples reveals the importance of members of gene families coding for signalling factors. Next, we focus on interested signalling gene families and a subset of inflammation related diseases with multi-omic features including both gene expression and DNA methylation. We introduce a phylogenetic-based multi-omic method to study the relationships between multi-omic features of inflammation related diseases by integrating gene expression, DNA methylation through sequence based phylogeny of the signalling gene families. The models of adaptations between gene expression and DNA methylation can be inferred from pre-estimated evolutionary relationship of a gene family. Members of the gene family whose expression or methylation levels significantly deviate from the model are considered as the potential disease associated genes.ConclusionsApplying the methodology to four gene families (the chemokine receptor family, the TNF receptor family, the TGF- gene family, the IL-17 gene family) in nine inflammation related diseases, we identify disease associated genes which exhibit significant dysregulation in gene expression or DNA methylation in the inflammation related diseases, which provides clues for functional associations between the diseases.

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  • 1477. Xie, Peiwu
    et al.
    Tu, Tieyao
    Razafimandimbison, Sylvain G.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Naturvetenskapliga fakulteten, Bergianska botaniska trädgården (tills m Kungl. Vetenskapsakademien).
    Zhu, Chengjie
    Zhang, Dianxiang
    Phylogenetic position of Guihaiothamnus (Rubiaceae): Its evolutionary and ecological implications2014Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 78, s. 375-385Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Guihaiothamnus (Rubiaceae) is an enigmatic, monotypic genus endemic to southwestern China. Its generic status has never been doubted because it is morphologically unique by having rosette habit, showy, long-corolla-tubed flowers, and multi-seeded indehiscent berry-like fruits. The genus has been postulated to be a relict in the broad-leaved forests of China, and to be related to the genus Wendlandia, which was placed in the subfamily Cinchonoideae and recently classified in the tribe Augusteae of the subfamily Dialypetalanthoideae. Using combined evidence from palynology, cytology, and DNA sequences of nuclear ITS and four plastid markers (rps16, trnT-F, ndhF, rbcL), we assessed the phylogenetic position of Guihaiothamnus in Rubiaceae. Our molecular phylogenetic analyses placed the genus deeply nested within Wendlandia. This relationship is corroborated by evidence from palynology and cytology. Using a relaxed molecular clock method based on five fossil records, we dated the stem age of Wendlandia to be 17.46 my and, the split between G. acaulis and related Wendlandia species in southwestern China to be 2.11 mya. This young age, coupled with the derived position in Wendlandia, suggests an evolutionary derivation rather than an evolutionary relict of G. acaulis. Its rosette habit and large showy flowers, which are very distinctive from other Wendlandias, are interpreted as a result of recent rapid adaptation to rock and cliff habitats.

  • 1478. Xing, Fangqian
    et al.
    Mao, Jian-Feng
    Meng, Jingxiang
    Dai, Jianfeng
    Zhao, Wei
    Liu, Hao
    Xing, Zhen
    Zhang, Hua
    Wang, Xiao-Ru
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Li, Yue
    Needle morphological evidence of the homoploid hybrid origin of Pinus densata based on analysis of artificial hybrids and the putative parents, Pinus tabuliformis and Pinus yunnanensis2014Inngår i: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 4, nr 10, s. 1890-1902Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genetic analyses indicate that Pinus densata is a natural homoploid hybrid originating from Pinus tabuliformis and Pinus yunnanensis. Needle morphological and anatomical features show relative species stability and can be used to identify coniferous species. Comparative analyses of these needle characteristics and phenotypic differences between the artificial hybrids, P.densata, and parental species can be used to determine the genetic and phenotypic evolutionary consequences of natural hybridization. Twelve artificial hybrid families, the two parental species, and P.densata were seeded in a high-altitude habitat in Linzhi, Tibet. The needles of artificial hybrids and the three pine species were collected, and 24 needle morphological and anatomical traits were analyzed. Based on these results, variations in 10 needle traits among artificial hybrid families and 22 traits among species and artificial hybrids were predicted and found to be under moderate genetic control. Nineteen needle traits in artificial hybrids were similar to those in P.densata and between the two parental species, P.tabuliformis and P.yunnanensis. The ratio of plants with three needle clusters in artificial hybrids was 22.92%, which was very similar to P.densata. The eight needle traits (needle length, the mean number of stomata in sections 2mm in length of the convex and flat sides of the needle, mean stomatal density, mesophyll/vascular bundle area ratio, mesophyll/resin canal area ratio, mesophyll/(resin canals and vascular bundles) area ratio, vascular bundle/resin canal area ratio) relative to physiological adaptability were similar to the artificial hybrids and P.densata. The similar needle features between the artificial hybrids and P.densata could be used to verify the homoploid hybrid origin of P.densata and helps to better understand of the hybridization roles in adaptation and speciation in plants.

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  • 1479.
    Xochelli, Aliki
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Experimentell och klinisk onkologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. CERTH, Inst Appl Biosci, Thessaloniki, Greece.
    Baliakas, Panagiotis
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Experimentell och klinisk onkologi. ..
    Kavakiotis, Ioannis
    Aristotle Univ Thessaloniki, Dept Informat, Thessaloniki, Greece..
    Agathangelidis, Andreas
    CERTH, Inst Appl Biosci, Thessaloniki, Greece.;IRCCS San Raffaele Sci Inst, Div Expt Oncol, Milan, Italy.;IRCCS San Raffaele Sci Inst, Dept Oncohematol, Milan, Italy..
    Sutton, Lesley Ann
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden..
    Minga, Eva
    CERTH, Inst Appl Biosci, Thessaloniki, Greece..
    Ntoufa, Stavroula
    CERTH, Inst Appl Biosci, Thessaloniki, Greece..
    Tausch, Eugen
    Ulm Univ, Dept Internal Med 3, Ulm, Germany..
    Yan, Xiao-Jie
    Northwell Hlth, Feinstein Inst Med Res, Manhasset, NY USA..
    Shanafelt, Tait
    Mayo Clin, Dept Med, Dept Hematol, Rochester, MN USA..
    Plevova, Karla
    Masaryk Univ, Cent European Inst Technol, Brno, Czech Republic..
    Boudjogra, Myriam
    Hop La Pitie Salpetriere, Dept Hematol, Paris, France.;Univ Paris 06, Paris, France..
    Rossi, Davide
    Univ Piemonte Orientale, Dept Translat Med, Dept Haematol, Novara, Italy..
    Davis, Zadie
    Royal Bournemouth Hosp, Dept Haematol, Bournemouth, Dorset, England..
    Navarro, Alba
    Univ Barcelona, Inst Invest Biomed August Pi & Sunyer IDIBAPS, Hosp Clin, Barcelona, Spain..
    Sandberg, Yorick
    Univ Med Ctr Rotterdam, Erasmus MC, Dept Immunol, Rotterdam, Netherlands..
    Vojdeman, Fie Juhl
    Rigshosp, Dept Haematol, Copenhagen, Denmark..
    Scarfo, Lydia
    IRCCS San Raffaele Sci Inst, Div Expt Oncol, Milan, Italy.;IRCCS San Raffaele Sci Inst, Dept Oncohematol, Milan, Italy..
    Stavroyianni, Niki
    G Papanicolaou Hosp, Dept Hematol, Thessaloniki, Greece.;G Papanicolaou Hosp, HCT Unit, Thessaloniki, Greece..
    Sudarikov, Andrey
    Natl Res Ctr Hematol, Moscow, Russia..
    Veronese, Silvio
    Osped Niguarda Ca Granda, Mol Pathol Unit, Milan, Italy.;Osped Niguarda Ca Granda, Dept Haematol, Milan, Italy..
    Tzenou, Tatiana
    Univ Athens, Dept Propaedeut Med 1, Athens, Greece..
    Karan-Djurasevic, Teodora
    Univ Belgrade, Inst Mol Genet & Genet Engn, Belgrade, Serbia..
    Catherwood, Mark
    Belfast City Hosp, Dept Haematooncol, Belfast, Antrim, North Ireland..
    Kienle, Dirk
    Ulm Univ, Dept Internal Med 3, Ulm, Germany..
    Chatzouli, Maria
    Nikea Gen Hosp, Dept Hematol, Piraeus, Greece..
    Facco, Monica
    Univ Padua, Sch Med, Hematol & Clin Immunol Branch, Dept Med, Padua, Italy..
    Bahlo, Jasmin
    Univ Hosp Cologne, Dept Internal Med 1, Cologne, Germany.;Univ Hosp Cologne, Ctr Integrated Oncol, Cologne, Germany..
    Pott, Christiane
    Univ Hosp Schleswig Holstein, Med Dept 2, Campus Kiel, Kiel, Germany..
    Pedersen, Lone Bredo
    Rigshosp, Dept Haematol, Copenhagen, Denmark..
    Mansouri, Larry
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Experimentell och klinisk onkologi. Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden..
    Smedby, Karin E.
    Karolinska Inst, Clin Epidemiol Unit, Dept Med Solna, Stockholm, Sweden..
    Chu, Charles C.
    Northwell Hlth, Feinstein Inst Med Res, Manhasset, NY USA..
    Giudicelli, Veronique
    Univ Montpellier, CNRS, UPR 1142, IMGT,LIGM,IGH, Montpellier, France..
    Lefranc, Marie-Paule
    Univ Montpellier, CNRS, UPR 1142, IMGT,LIGM,IGH, Montpellier, France..
    Panagiotidis, Panagiotis
    Univ Athens, Dept Propaedeut Med 1, Athens, Greece..
    Juliusson, Gunnar
    Lund Univ, Lund, Sweden.;Lund Stem Cell Ctr, Hosp Dept Hematol, Lund, Sweden..
    Anagnostopoulos, Achilles
    G Papanicolaou Hosp, Dept Hematol, Thessaloniki, Greece.;G Papanicolaou Hosp, HCT Unit, Thessaloniki, Greece..
    Vlahavas, Ioannis
    Aristotle Univ Thessaloniki, Dept Informat, Thessaloniki, Greece..
    Antic, Darko
    Ctr Clin, Clin Hematol, Belgrade, Serbia.;Univ Belgrade, Fac Med, Belgrade, Serbia..
    Trentin, Livio
    Univ Padua, Sch Med, Hematol & Clin Immunol Branch, Dept Med, Padua, Italy..
    Montillo, Marco
    Osped Niguarda Ca Granda, Mol Pathol Unit, Milan, Italy.;Osped Niguarda Ca Granda, Dept Haematol, Milan, Italy..
    Niemann, Carsten
    Rigshosp, Dept Haematol, Copenhagen, Denmark..
    Doehner, Hartmut
    Ulm Univ, Dept Internal Med 3, Ulm, Germany..
    Langerak, Anton W.
    Univ Med Ctr Rotterdam, Erasmus MC, Dept Immunol, Rotterdam, Netherlands..
    Pospisilova, Sarka
    Masaryk Univ, Cent European Inst Technol, Brno, Czech Republic..
    Hallek, Michael
    Univ Hosp Cologne, Dept Internal Med 1, Cologne, Germany.;Univ Hosp Cologne, Ctr Integrated Oncol, Cologne, Germany..
    Campo, Elias
    Univ Barcelona, Inst Invest Biomed August Pi & Sunyer IDIBAPS, Hosp Clin, Barcelona, Spain..
    Chiorazzi, Nicholas
    Northwell Hlth, Feinstein Inst Med Res, Manhasset, NY USA..
    Maglaveras, Nikos
    Aristotle Univ Thessaloniki, Lab Med Informat, Thessaloniki, Greece..
    Oscier, David
    Royal Bournemouth Hosp, Dept Haematol, Bournemouth, Dorset, England..
    Gaidano, Gianluca
    Univ Piemonte Orientale, Dept Translat Med, Dept Haematol, Novara, Italy..
    Jelinek, Diane F.
    Mayo Clin, Dept Immunol, Rochester, MN USA..
    Stilgenbauer, Stephan
    Ulm Univ, Dept Internal Med 3, Ulm, Germany..
    Chouvarda, Ioanna
    Aristotle Univ Thessaloniki, Lab Med Informat, Thessaloniki, Greece..
    Darzentas, Nikos
    Masaryk Univ, Cent European Inst Technol, Brno, Czech Republic..
    Belessi, Chrysoula
    Nikea Gen Hosp, Dept Hematol, Piraeus, Greece..
    Davi, Frederic
    Hop La Pitie Salpetriere, Dept Hematol, Paris, France.;Univ Paris 06, Paris, France..
    Hadzidimitriou, Anastasia
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. CERTH, Inst Appl Biosci, Thessaloniki, Greece..
    Rosenquist, Richard
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Experimentell och klinisk onkologi. Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden..
    Ghia, Paolo
    IRCCS San Raffaele Sci Inst, Div Expt Oncol, Milan, Italy.;IRCCS San Raffaele Sci Inst, Dept Oncohematol, Milan, Italy.;Univ Vita Salute San Raffaele, Milan, Italy.;IRCCS Ist Sci San Raffaele, Milan, Italy..
    Stamatopoulos, Kostas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Experimentell och klinisk onkologi. CERTH, Inst Appl Biosci, Thessaloniki, Greece ;G Papanicolaou Hosp, Dept Hematol, Thessaloniki, Greece.;G Papanicolaou Hosp, HCT Unit, Thessaloniki, Greece..
    Chronic Lymphocytic Leukemia with Mutated IGHV4-34 Receptors: Shared and Distinct Immunogenetic Features and Clinical Outcomes2017Inngår i: Clinical Cancer Research, ISSN 1078-0432, E-ISSN 1557-3265, Vol. 23, nr 17, s. 5292-5301Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Purpose: We sought to investigate whether B cell receptor immunoglobulin (BcR IG) stereotypy is associated with particular clinicobiological features among chronic lymphocytic leukemia (CLL) patients expressing mutated BcR IG (M-CLL) encoded by the IGHV4-34 gene, and also ascertain whether these associations could refine prognostication. Experimental Design: In a series of 19,907 CLL cases with available immunogenetic information, we identified 339 IGHV4-34expressing cases assigned to one of the four largest stereotyped M-CLL subsets, namely subsets #4, #16, #29 and #201, and investigated in detail their clinicobiological characteristics and disease outcomes. Results: We identified shared and subset-specific patterns of somatic hypermutation (SHM) among patients assigned to these subsets. The greatest similarity was observed between subsets #4 and #16, both including IgG-switched cases (IgG-CLL). In contrast, the least similarity was detected between subsets #16 and #201, the latter concerning IgM/D-expressing CLL. Significant differences between subsets also involved disease stage at diagnosis and the presence of specific genomic aberrations. IgG subsets #4 and #16 emerged as particularly indolent with a significantly (P < 0.05) longer time-to-first-treatment (TTFT; median TTFT: not yet reached) compared with the IgM/D subsets #29 and #201 (median TTFT: 11 and 12 years, respectively). Conclusions: Our findings support the notion that BcR IG stereotypy further refines prognostication in CLL, superseding the immunogenetic distinction based solely on SHM load. In addition, the observed distinct genetic aberration landscapes and clinical heterogeneity suggest that not all M-CLL cases are equal, prompting further research into the underlying biological background with the ultimate aim of tailored patient management.  

  • 1480. Xu, Chao-Qun
    et al.
    Liu, Hui
    Zhou, Shan-Shan
    Zhang, Dong-Xu
    Zhao, Wei
    Wang, Sihai
    Chen, Fu
    Sun, Yan-Qiang
    Nie, Shuai
    Jia, Kai-Hua
    Jiao, Si-Qian
    Zhang, Ren-Gang
    Yun, Quan-Zheng
    Guan, Wenbin
    Wang, Xuewen
    Gao, Qiong
    Bennetzen, Jeffrey L.
    Maghuly, Fatemeh
    Porth, Ilga
    Van de Peer, Yves
    Wang, Xiao-Ru
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, School of Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
    Ma, Yongpeng
    Mao, Jian-Feng
    Genome sequence of Malania oleifera, a tree with great value for nervonic acid production2019Inngår i: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 8, nr 2, artikkel-id giy164Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. Conclusions Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.

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  • 1481.
    Xu, Dongqing
    et al.
    Peking Univ, Peking Tsinghua Ctr Life Sci, Sch Adv Agr Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China.;Peking Univ, Sch Life Sci, Beijing 100871, Peoples R China.;Gothenburg Univ, Dept Biol & Environm Sci, Gothenburg, Sweden..
    Lin, Fang
    Peking Univ, Peking Tsinghua Ctr Life Sci, Sch Adv Agr Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China.;Peking Univ, Sch Life Sci, Beijing 100871, Peoples R China..
    Jiang, Yan
    Peking Univ, Peking Tsinghua Ctr Life Sci, Sch Adv Agr Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China.;Peking Univ, Sch Life Sci, Beijing 100871, Peoples R China.;Gothenburg Univ, Dept Biol & Environm Sci, Gothenburg, Sweden..
    Ling, Junjie
    Peking Univ, Peking Tsinghua Ctr Life Sci, Sch Adv Agr Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China.;Peking Univ, Sch Life Sci, Beijing 100871, Peoples R China..
    Hettiarachchi, Chamari
    Univ Colombo, Dept Chem, Colombo, Sri Lanka..
    Tellgren-Roth, Christian
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi.
    Holm, Magnus
    Gothenburg Univ, Dept Biol & Environm Sci, Gothenburg, Sweden..
    Wei, Ning
    Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT USA..
    Deng, Xing Wang
    Peking Univ, Peking Tsinghua Ctr Life Sci, Sch Adv Agr Sci, State Key Lab Prot & Plant Gene Res, Beijing 100871, Peoples R China.;Peking Univ, Sch Life Sci, Beijing 100871, Peoples R China..
    Arabidopsis COP1 SUPPRESSOR 2 Represses COP1 E3 Ubiquitin Ligase Activity through Their Coiled-Coil Domains Association2015Inngår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 11, nr 12, artikkel-id e1005747Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) functions as an E3 ubiquitin ligase and mediates a variety of developmental processes in Arabidopsis by targeting a number of key regulators for ubiquitination and degradation. Here, we identify a novel COP1 interacting protein, COP1 SUPPRESSOR 2 (CSU2). Loss of function mutations in CSU2 suppress the constitutive photomorphogenic phenotype of cop1-6 in darkness. CSU2 directly interacts with COP1 via their coiled-coil domains and is recruited by COP1 into nuclear speckles in living plant cells. Furthermore, CSU2 inhibits COP1 E3 ubiquitin ligase activity in vitro, and represses COP1 mediated turnover of HY5 in cell-free extracts. We propose that in csu2 cop1-6 mutants, the lack of CSU2's repression of COP1 allows the low level of COP1 to exhibit higher activity that is sufficient to prevent accumulation of HY5 in the dark, thus restoring the etiolated phenotype. In addition, CSU2 is required for primary root development under normal light growth condition.

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  • 1482.
    Xu, Feifei
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Jerlström-Hultqvist, Jon
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Einarsson, Elin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Astvaldsson, Asgeir
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Svärd, Staffan G
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Andersson, Jan O
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments2014Inngår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 10, nr 2, s. e1004053-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Spironucleus salmonicida causes systemic infections in salmonid fish. It belongs to the group diplomonads, binucleated heterotrophic flagellates adapted to micro-aerobic environments. Recently we identified energy-producing hydrogenosomes in S. salmonicida. Here we present a genome analysis of the fish parasite with a focus on the comparison to the more studied diplomonad Giardia intestinalis. We annotated 8067 protein coding genes in the ∼12.9 Mbp S. salmonicida genome. Unlike G. intestinalis, promoter-like motifs were found upstream of genes which are correlated with gene expression, suggesting a more elaborate transcriptional regulation. S. salmonicida can utilise more carbohydrates as energy sources, has an extended amino acid and sulfur metabolism, and more enzymes involved in scavenging of reactive oxygen species compared to G. intestinalis. Both genomes have large families of cysteine-rich membrane proteins. A cluster analysis indicated large divergence of these families in the two diplomonads. Nevertheless, one of S. salmonicida cysteine-rich proteins was localised to the plasma membrane similar to G. intestinalis variant-surface proteins. We identified S. salmonicida homologs to cyst wall proteins and showed that one of these is functional when expressed in Giardia. This suggests that the fish parasite is transmitted as a cyst between hosts. The extended metabolic repertoire and more extensive gene regulation compared to G. intestinalis suggest that the fish parasite is more adapted to cope with environmental fluctuations. Our genome analyses indicate that S. salmonicida is a well-adapted pathogen that can colonize different sites in the host.

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  • 1483.
    Xu, Fu
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Factors modulating tRNA biogenesis and function in Saccharomyces cerevisiae2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Transfer RNA (tRNA) genes are transcribed by RNA polymerase III as precursors that undergo multiple processing steps to form mature tRNAs. These steps include processing of the 5’ leader and 3’ trailer sequences, addition of a 3’ CCA tail, removal of introns, and formation of modified nucleosides. The mature tRNAs carry amino acids to the ribosome where proteins are synthesized. The aim of this thesis is to identify and characterize factors that influence tRNA biogenesis and function in Saccharomyces cerevisiae.

    Nonsense suppressor tRNAs are encoded by mutated tRNA genes and able to read stop codons. The SUP4 gene encodes such a suppressor tRNA that base-pairs with UAA stop codons. By screening for mutations that impair the nonsense suppression of the SUP4-encoded tRNA, we identified a loss-of-function mutation in the YPK9 gene. Inactivation of Ypk9p causes a reduction in the readthrough of UAA stop codon. We found that phenotypes of ypk9Δ cells including decreased UAA readthrough and sensitivity to Mn2+ are counteracted by increasing the cellular levels of putrescine, one type of polyamine. Importantly, cells lacking Ypk9p show reduced levels of putrescine. Our results suggest that the YPK9 gene product influences the cellular levels of putrescine, which plays a role in maintaining the fidelity of translation termination.

    The Elongator complex, consisting of Elp1p-Elp6p six proteins, catalyzes the formation of U34 modifications in the anticodon region of 11 tRNA species. Elongator mutants display pleiotropic phenotypes that are caused by decreased tRNA functionality. We found that the genetic background, largely due to a polymorphism at the SSD1 locus, influences the pleiotropic phenotypes of Elongator mutants.

    In a genetic screen for factors that are essential for the survival of cells encoding a destabilized tRNASerCGA, several gene products were identified. We demonstrate that mutations in these genes result in reduced levels of the destabilized tRNASerCGA, suggesting a role for these gene products in tRNASerCGA biosynthesis.

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  • 1484.
    Xu, Fu
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Byström, Anders
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Johansson, Marcus J. O.
    Umeå universitet, Medicinska fakulteten, Institutionen för odontologi.
    SSD1 modifies phenotypes of Elongator mutants2019Inngår i: Current Genetics, ISSN 0172-8083, E-ISSN 1432-0983Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The translational decoding properties of tRNAs are influenced by post-transcriptional modification of nucleosides in their anticodon region. The Elongator complex promotes the first step in the formation of 5-methoxycarbonylmethyl (mcm(5)), 5-methoxycarbonylhydroxymethyl (mchm(5)), and 5-carbamoylmethyl (ncm(5)) groups on wobble uridine residues in eukaryotic cytosolic tRNAs. Elongator mutants in yeast, worms, plants, mice, and humans not only show a tRNA modification defect, but also a diverse range of additional phenotypes. Even though the phenotypes are almost certainly caused by the reduced functionality of the hypomodified tRNAs in translation, the basis for specific phenotypes is not well understood. Here, we discuss the recent finding that the phenotypes of Saccharomyces cerevisiae Elongator mutants are modulated by the genetic background. This background-effect is largely due to the allelic variation at the SSD1 locus, which encodes an mRNA-binding protein involved in post-transcriptional regulation of gene expression. A nonsense ssd1 allele is found in several wild-type laboratory strains and the presence of this allele aggravates the stress-induced phenotypes of Elongator mutants. Moreover, other phenotypes, such as the histone acetylation and telomeric gene silencing defects, are dependent on the mutant ssd1 allele. Thus, SSD1 is a genetic modifier of the phenotypes of Elongator-deficient yeast cells.

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  • 1485.
    Xu, Luohao
    et al.
    Zhejiang Univ, MOE Lab Biosyst Homeostasis & Protect, Life Sci Inst, Hangzhou, Zhejiang, Peoples R China;Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Auer, Gabriel
    Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Peona, Valentina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Suh, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Deng, Yuan
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;BGI Shenzhen, Shenzhen, Peoples R China.
    Feng, Shaohong
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;BGI Shenzhen, Shenzhen, Peoples R China.
    Zhang, Guojie
    BGI Shenzhen, China Natl Genebank, Shenzhen, Peoples R China;Chinese Acad Sci, State Key Lab Genet Resources & Evolut, Kunming Inst Zool, Kunming, Yunnan, Peoples R China;Univ Copenhagen, Sect Ecol & Evolut, Dept Biol, Copenhagen, Denmark.
    Blom, Mozes P. K.
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden;Leibniz Inst Evolut & Biodiversitatsforsch, Museum Naturkunde, Berlin, Germany.
    Christidis, Les
    Southern Cross Univ, Natl Marin Sci Ctr, Coffs Harbour, NSW, Australia;Univ Melbourne, Sch Biosci, Victoria, Australia.
    Prost, Stefan
    Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA;Senckenberg, LOEWE Ctr Translat Biodivers Genom, Frankfurt, Germany.
    Irestedt, Martin
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.
    Zhou, Qi
    Zhejiang Univ, MOE Lab Biosyst Homeostasis & Protect, Life Sci Inst, Hangzhou, Zhejiang, Peoples R China;Univ Vienna, Dept Mol Evolut & Dev, Vienna, Austria.
    Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds2019Inngår i: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 3, nr 5, s. 834-844Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.

  • 1486. Xue, Weiya
    et al.
    Ruprecht, Colin
    Street, Nathaniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Hematy, Kian
    Chang, Christine
    Frommer, Wolf B
    Persson, Staffan
    Niittyla, Totte
    Paramutation-like interaction of T-DNA loci in arabidopsis2012Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, nr 12, s. e51651-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In paramutation, epigenetic information is transferred from one allele to another to create a gene expression state which is stably inherited over generations. Typically, paramutation describes a phenomenon where one allele of a gene down-regulates the expression of another allele. Paramutation has been described in several eukaryotes and is best understood in plants. Here we describe an unexpected paramutation-like trans SALK T-DNA interaction in Arabidopsis. Unlike most of the previously described paramutations, which led to gene silencing, the trans SALK T-DNA interaction caused an increase in the transcript levels of the endogenous gene (COBRA) where the T-DNA was inserted. This increased COBRA expression state was stably inherited for several generations and led to the partial suppression of the cobra phenotype. DNA methylation was implicated in this trans SALK T-DNA interaction since mutation of the DNA methyltransferase 1 in the suppressed cobra caused a reversal of the suppression. In addition, null mutants of the DNA demethylase ROS1 caused a similar COBRA transcript increase in the cobra SALK T-DNA mutant as the trans T-DNA interaction. Our results provide a new example of a paramutation-like trans T-DNA interaction in Arabidopsis, and establish a convenient hypocotyl elongation assay to study this phenomenon. The results also alert to the possibility of unexpected endogenous transcript increase when two T-DNAs are combined in the same genetic background. Citation: Xue W, Ruprecht C, Street N, Hematy K, Chang C, et al. (2012) Paramutation-Like Interaction of T-DNA Loci in Arabidopsis. PLoS ONE 7(12): e51651. doi:10.1371/journal.pone.0051651

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  • 1487.
    Xue-Franzen, Yongtao
    et al.
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Kjaerulff, Soren
    University of Copenhagen, Copenhagen, Denmark.
    Holmberg, Christian
    University of Copenhagen, Copenhagen, Denmark.
    Wright, Anthony
    Södertörns högskola, Institutionen för livsvetenskaper. Karolinska Institutet.
    Nielsen, Olaf
    University of Copenhagen, Copenhagen, Denmark.
    Genomewide identification of pheromone-targeted transcription in fission yeast2006Inngår i: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 7, s. 303-, artikkel-id 303Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Fission yeast cells undergo sexual differentiation in response to nitrogen starvation. In this process haploid M and P cells first mate to form diploid zygotes, which then enter meiosis and sporulate. Prior to mating, M and P cells communicate with diffusible mating pheromones that activate a signal transduction pathway in the opposite cell type. The pheromone signalling orchestrates mating and is also required for entry into meiosis. Results: Here we use DNA microarrays to identify genes that are induced by M-factor in P cells and by P-factor in M-cells. The use of a cyr1 genetic background allowed us to study pheromone signalling independently of nitrogen starvation. We identified a total of 163 genes that were consistently induced more than two-fold by pheromone stimulation. Gene disruption experiments demonstrated the involvement of newly discovered pheromone-induced genes in the differentiation process. We have mapped Gene Ontology ( GO) categories specifically associated with pheromone induction. A direct comparison of the M- and P-factor induced expression pattern allowed us to identify cell-type specific transcripts, including three new M- specific genes and one new P-specific gene. Conclusion: We found that the pheromone response was very similar in M and P cells. Surprisingly, pheromone control extended to genes fulfilling their function well beyond the point of entry into meiosis, including numerous genes required for meiotic recombination. Our results suggest that the SteII transcription factor is responsible for the majority of pheromone-induced transcription. Finally, most cell-type specific genes now appear to be identified in fission yeast.

  • 1488. Xun, Wei Wei
    et al.
    Brennan, Paul
    Tjonneland, Anne
    Vogel, Ulla
    Overvad, Kim
    Kaaks, Rudolf
    Canzian, Federico
    Boeing, Heiner
    Trichopoulou, Antonia
    Oustoglou, Erifili
    Giotaki, Zoi
    Johansson, Mattias
    Palli, Domenico
    Agnoli, Claudia
    Tumino, Rosario
    Sacerdote, Carlotta
    Panico, Salvatore
    Bueno-de-Mesquita, H Bas
    Peeters, Petra H M
    Lund, Eiliv
    Kumle, Merethe
    Rodríguez, Laudina
    Agudo, Antonio
    Sánchez, Maria-José
    Arriola, Larraitz
    Chirlaque, María-Dolores
    Barricarte, Aurelio
    Hallmans, Göran
    Umeå universitet, Medicinska fakulteten, Institutionen för folkhälsa och klinisk medicin, Näringsforskning.
    Rasmuson, Torgny
    Umeå universitet, Medicinska fakulteten, Institutionen för strålningsvetenskaper, Onkologi.
    Khaw, Kay-Tee
    Wareham, Nicholas
    Key, Tim
    Riboli, Elio
    Vineis, Paolo
    Single-nucleotide polymorphisms (5p15.33, 15q25.1, 6p22.1, 6q27 and 7p15.3) and lung cancer survival in the European Prospective Investigation into Cancer and Nutrition (EPIC).2011Inngår i: Mutagenesis, ISSN 0267-8357, E-ISSN 1464-3804, Vol. 26, nr 5, s. 657-666Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The single-nucleotide polymorphisms (SNPs) rs402710 (5p15.33), rs16969968 and rs8034191 (15q25.1) have been consistently identified by genome-wide association studies (GWAS) as significant predictors of lung cancer risk, while rs4324798 (6p22.1) was previously found to influence survival time in small-cell lung cancer (SCLC) patients. Using the same population of one of the original GWAS, we investigated whether the selected SNPs and 31 others (also identified in GWAS) influence survival time, assuming an additive model. The effect of each polymorphism on all cause survival was estimated in 1094 lung cancer patients, and lung cancer-specific survival in 763 patients, using Cox regression adjusted for a priori confounders and competing causes of death where appropriate. Overall, after 1558 person-years of post-diagnostic follow-up, 874 deaths occurred from all causes, including 690 from lung cancer. In the lung cancer-specific survival analysis (1102 person-years), only rs7452888 (6q27) and rs2710994 (7p15.3) modified survival, with adjusted hazard ratios of 1.19 (P = 0.009) and 1.32 (P = 0.011) respectively, taking competing risks into account. Some weak associations were identified in subgroup analysis for rs16969968 and rs8034191 (15q25.1) and rs4324798 (6p22.1) and survival in never-smokers, as well as for rs402710 in current smokers and SCLC patients. In conclusion, rs402710 (5p15.33), rs16969968 and rs8034191 (both 15q25.1) and rs4324798 (6p22.1) were found to be unrelated to survival times in this large cohort of lung cancer patients, regardless of whether the cause of death was from lung cancer or not. However, rs7452888 (6q27) was identified as a possible candidate SNP to influence lung cancer survival, while stratified analysis hinted at a possible role for rs8034191, rs16969968 (15q25.1) and rs4324798 (6p22.1) in influencing survival time in lung cancer patients who were never-smokers, based on a small sample.

  • 1489.
    Yazdi, Homa Papoli
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik.
    The evolution of sex chromosomes and sex-linked sequences in birds2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Identifying the processes involved in the evolution of suppressed recombination between sex chromosomes and understanding their consequences for the evolutionary dynamics of sex-linked loci have been major topics of research during the last century. In this thesis, I used the avian ZW system, where females are the heterogametic sex, to investigate the underlying processes in sex chromosome evolution in birds. I identified the gametologous genes between the largely recombining Z and W chromosomes of ostrich and dated the timing of the cessation of recombination to prior to the split of modern birds. I then constructed a genetic map of the ostrich Z chromosome and corrected its assembly in order to obtain the ancestral organization of the Z chromosome in a basal clade of birds. By analyzing the inversion events across the avian phylogeny, I concluded that a combination of Z- and possibly W-linked inversions might have been responsible for the evolution of suppressed recombination in avian sex chromosomes. To understand the determinants of levels of genetic diversity on Z chromosome compared to autosomes, I calculated Z to autosome (Z:A) genetic diversity across 32 avian species. This revealed a broad range of Z:A genetic diversity, between 0.278 – 1.27. Lineage-specific estimates of the nonsynonymous to synonymous substitution rate ratio (dN:dS) for autosomal and Z-linked genes further revealed a Fast-Z effect in the majority of birds. The lack of a significant correlation between Z:A dN:dS and Z:A genetic diversity indicated that genetic drift might not be sufficient to explain faster evolution of Z-linked genes, suggesting that positive selection might also contribute to the observed values. Finally, I calculated genetic diversity and linkage disequilibrium (LD) along the pseudoautosomal region (PAR) of the Z chromosome using population genomics data of ostrich. In contrast to theoretical expectation, levels of diversity on the PAR were not significantly higher close to the sex-determining region (SDR) compared to autosomal values. Additionally, I observed a lower level of LD on the PAR compared to the average for the Z chromosome and no significant level of LD across the PAR boundary was detected, indicating recombination allows the boundary-proximal region of PAR to behave independently of SDR. Considered together with a higher level of recombination rate in females in the proximity of the SDR, this observation might help explain the maintenance of a long PAR in ostriches and other ratites. Altogether, the results of this thesis make a modest contribution to our understanding of sex chromosome evolution in birds.

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  • 1490.
    Yazdi, Homa Papoli
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution2018Inngår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 10, nr 8, s. 2049-2060Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae. We therefore developed a high-density genetic linkage map of the ostrich Z chromosome and used this to correct an existing assembly, including correction of a large chimeric superscaffold and the order and orientation of other superscaffolds. We identified the pseudoautosomal region as a 52 Mb segment (approximate to 60% of the Z chromosome) where recombination occurred in both sexes. By comparing the order and location of genes on the ostrich Z chromosome with that of six bird species from the other major Glade of birds (Neognathae), and of reptilian outgroup species, 25 Z-linked inversions were inferred in the avian lineages. We defined Z chromosome organization in an early avian ancestor and identified inversions spanning the candidate sex-determining DMRT1 gene in this ancestor, which could potentially have triggered the onset of avian sex chromosome evolution. We conclude that avian sex chromosome evolution has been characterized by a complex process of probably both Z-linked and W-linked inversions (and/or other processes). This study illustrates the need for validated chromosome-level assemblies for inference of genome evolution.

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  • 1491.
    Yazdi, Homa Papoli
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Old but Not (So) Degenerated-Slow Evolution of Largely Homomorphic Sex Chromosomes in Ratites2014Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, nr 6, s. 1444-1453Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Degeneration of the nonrecombining chromosome is a common feature of sex chromosome evolution, readily evident by the presence of a pair of largely heteromorphic chromosomes, like in eutherian mammals and birds. However, in ratites (order Palaeognathae, including, e.g., ostrich), the Z and W chromosomes are similar in size and largely undifferentiated, despite avian sex chromosome evolution was initiated > 130 Ma. To better understand what may limit sex chromosome evolution, we performed ostrich transcriptome sequencing and studied genes from the nonrecombining region of the W chromosome. Fourteen gametologous gene pairs present on the W chromosome and Z chromosome were identified, with synonymous sequence divergence of 0.027-0.177. The location of these genes on the Z chromosome was consistent with a sequential increase in divergence, starting 110-157 and ending 24-30 Ma. On the basis of the occurrence of Z-linked genes hemizygous in females, we estimate that about one-third of the Z chromosome does not recombine with the W chromosome in female meiosis. Pairwise d(N)/d(S) between gametologs decreased with age, suggesting strong evolutionary constraint in old gametologs. Lineage-specific d(N)/d(S) was consistently higher in W-linked genes, in accordance with the lower efficacy of selection expected in nonrecombining chromosomes. A higher ratio of GC > AT:AT > GC substitutions in W-linked genes supports a role for GC-biased gene conversion in differentially driving base composition on the two sex chromosomes. A male-to-female (M:F) expression ratio of close to one for recombining genes and close to two for Z-linked genes lacking a W copy show that dosage compensation is essentially absent. Some gametologous genes have retained active expression of the W copy in females (giving a M:F ratio of 1 for the gametologous gene pair), whereas for others W expression has become severely reduced resulting in a M:F ratio of close to 2. These observations resemble the patterns of sex chromosome evolution seen in other avian and mammalian lineages, suggesting similar underlying evolutionary processes, although the rate of sex chromosome differentiation has been atypically low. Lack of dosage compensation may be a factor hindering sex chromosome evolution in this lineage.

  • 1492.
    Yildirim, Yeserin
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Tinnert, Jon
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Forsman, Anders
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Contrasting patterns of neutral and functional genetic diversity in stable and disturbed environments2018Inngår i: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, nr 23, s. 12073-12089Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genetic structure among and diversity within natural populations is influenced by acombination of ecological and evolutionary processes. These processes can differentlyinfluence neutral and functional genetic diversity and also vary according toenvironmental settings. To investigate the roles of interacting processes as drivers ofpopulation‐level genetic diversity in the wild, we compared neutral and functionalstructure and diversity between 20 Tetrix undulata pygmy grasshopper populations indisturbed and stable habitats. Genetic differentiation was evident among the differentpopulations, but there was no genetic separation between stable and disturbedenvironments. The incidence of long‐winged phenotypes was higher in disturbedhabitats, indicating that these populations were recently established by flight‐capablecolonizers. Color morph diversity and dispersion of outlier genetic diversity, estimatedusing AFLP markers, were higher in disturbed than in stable environments,likely reflecting that color polymorphism and variation in other functionally importanttraits increase establishment success. Neutral genetic diversity estimated usingAFLP markers was lower in disturbed habitats, indicating stronger eroding effects onneutral diversity of genetic drift associated with founding events in disturbed comparedto stable habitats. Functional diversity and neutral diversity were negativelycorrelated across populations, highlighting the utility of outlier loci in genetics studiesand reinforcing that estimates of genetic diversity based on neutral markers donot infer evolutionary potential and the ability of populations and species to copewith environmental change.

  • 1493.
    Ytterborn, Karl H.
    Stockholms universitet.
    Autosomal recessive lethals, germinal selection, and fitness of lethal heterozygotes in experimental populations of Drosophila melanogaster.1968Doktoravhandling, med artikler (Annet vitenskapelig)
  • 1494.
    Yurova Axelsson, Ekaterina
    Linnéuniversitetet, Fakulteten för teknik (FTK), Institutionen för matematik (MA).
    On the representation of the genetic code by the attractors of 2-adic function2015Inngår i: Physica scripta. T, ISSN 0281-1847, Vol. 2015, nr T 165, artikkel-id 014043Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The genetic code is a map which gives the correspondence between codons in DNA and amino acids. As a continuation of the study made by Khrennikov and Kozyrev on the genetic code, we consider a construction, where amino acids are associated to the attractors of some two-adic function. In this paper, we give an explicit form of representations for the standard nuclear and vertebrate mitochondrial genetics codes. To set these functions we use a van der Put representation. The usage of the van der Put series reduces the complexity of computation for explicit form of the functions for the genetic codes.

  • 1495.
    Zajitschek, Felix
    et al.
    Monash Univ, Australia; Uppsala Univ, Sweden.
    Georgolopoulos, Grigorios
    Uppsala Univ, Sweden.
    Vourlou, Anna
    Uppsala Univ, Sweden.
    Ericsson, Maja
    Uppsala Univ, Sweden.
    Zajitschek, Susanne R. K.
    Monash Univ, Australia; CSIC, Spain; Uppsala Univ, Sweden.
    Friberg, Urban
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Uppsala Univ, Sweden.
    Maklakov, Alexei A.
    Uppsala Univ, Sweden; Univ East Anglia, England.
    Evolution Under Dietary Restriction Decouples Survival From Fecundity in Drosophila melanogaster Females2019Inngår i: The journals of gerontology. Series A, Biological sciences and medical sciences, ISSN 1079-5006, E-ISSN 1758-535X, Vol. 74, nr 10, s. 1542-1548Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    One of the key tenets of life-history theory is that reproduction and survival are linked and that they trade-off with each other. When dietary resources are limited, reduced reproduction with a concomitant increase in survival is commonly observed. It is often hypothesized that this dietary restriction effect results from strategically reduced investment in reproduction in favor of somatic maintenance to survive starvation periods until resources become plentiful again. We used experimental evolution to test this "waiting-for-the-good-times" hypothesis, which predicts that selection under sustained dietary restriction will favor increased investment in reproduction at the cost of survival because "good-times" never come. We assayed fecundity and survival of female Drosophila melanogaster fruit flies that had evolved for 50 generations on three different diets varying in protein content-low (classic dietary restriction diet), standard, and high-in a full-factorial design. High-diet females evolved overall increased fecundity but showed reduced survival on low and standard diets. Low-diet females evolved reduced survival on low diet without corresponding increase in reproduction. In general, there was little correspondence between the evolution of survival and fecundity across all dietary regimes. Our results contradict the hypothesis that resource reallocation between fecundity and somatic maintenance underpins life span extension under dietary restriction.

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  • 1496.
    Zajitschek, Felix
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Jin, Tuo
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Colchero, Fernando
    Maklakov, Alexei A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Aging Differently: Diet- and Sex-Dependent Late-Life Mortality Patterns in Drosophila melanogaster2014Inngår i: The journals of gerontology. Series A, Biological sciences and medical sciences, ISSN 1079-5006, E-ISSN 1758-535X, Vol. 69, nr 6, s. 666-674Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Diet effects on age-dependent mortality patterns are well documented in a large number of animal species, but studies that look at the effects of nutrient availability on late-life mortality plateaus are lacking. Here, we focus on the effect of dietary protein content (low, intermediate, and high) on mortality trajectories in late life in the fruit fly Drosophila melanogaster. According to the two theories that are mainly implicated in explaining the deceleration of mortality rate in late life (the heterogeneity/frailty theory and the Hamiltonian theory), we predict, in general, the occurrence of late-life mortality deceleration under most circumstances, independent of sex and dietary regime. However, the heterogeneity theory of late life is more flexible in allowing no mortality deceleration to occur under certain circumstances compared with the Hamiltonian theory. We applied a novel statistical approach based on Bayesian inference of age-specific mortality rates and found a deceleration of late-life mortality rates on all diets in males but only on the intermediate (standard) diet in females. The difference in mortality rate deceleration between males and females on extreme diets suggests that the existence of mortality plateaus in late life is sex and diet dependent and, therefore, not a universal characteristic of large enough cohorts.

  • 1497.
    Zajitschek, Felix
    et al.
    Department of Animal Ecology, Ageing Research Group, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Zajitschek, Susanne R. K.
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Friberg, Urban
    Department of Evolutionary Biology, Ageing Research Group, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Maklakov, Alexei A.
    Department of Animal Ecology, Ageing Research Group, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Interactive effects of sex, social environment, dietary restriction, and methionine on survival and reproduction in fruit flies2013Inngår i: Age (Omaha), ISSN 0161-9152, E-ISSN 1574-4647, Vol. 35, nr 4, s. 1193-1204Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    For the evolution of life histories, the trade-off between survival and reproduction is fundamental. Because sexes optimize fitness in different ways, this trade-off is expected to be resolved differently by males and females. Consequently, the sexes are predicted to respond differently to changes in resource availability. In fruit flies, research on dietary restriction has focused largely on females maintained in the absence of males, thereby neglecting sexual interactions that affect reproductive behavior of both sexes under more natural conditions. Here, we tested for the interactive effects of diet (40, 60, 100, and 300 % of standard yeast concentrations) and social environment (separate-sex vs. mixed-sex groups) on male and female Drosophila melanogaster life histories. Additionally, we evaluated the essential amino acid methionine as an agent that can uncouple the survival-reproduction trade-off. We show sex differences in the effect of social environment on survival patterns, but not on reproductive fitness. In females, yeast had a positive effect on reproduction and a negative effect on survival. In males, yeast had a negative effect on reproduction and the effect on survival depended on the social environment. Methionine reduced survival, but had no effect on reproduction. Our findings highlight the need to include both sexes and to vary social environments in research programs aimed at lifespan extension and call for further evaluation of the fecundity-restoring effect of methionine.

  • 1498.
    Zallar, L J
    et al.
    Section on Clinical Psychoneuroendocrinology and Neuropsychopharmacology, National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research and National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Bethesda, MD, USA; Neurobiology of Addiction Section, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
    Tunstall, B J
    Neurobiology of Addiction Section, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
    Richie, C T
    Genetic Engineering and Viral Vector Core, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
    Zhang, Y J
    Genetic Engineering and Viral Vector Core, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, USA; National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research, Rockville, MD, USA.
    You, Z B
    Neuropsychopharmacology Section, Molecular Targets and Medications Discover Branch, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
    Gardner, E L
    Neuropsychopharmacology Section, Molecular Targets and Medications Discover Branch, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
    Heilig, Markus
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Centrum för social och affektiv neurovetenskap. Linköpings universitet, Medicinska fakulteten. Region Östergötland, Närsjukvården i centrala Östergötland, Psykiatriska kliniken inkl beroendekliniken.
    Pickel, J
    Transgenic Core Facility, National Institute of Mental Health Intramural Research Program, Bethesda, MD, USA.
    Koob, G F
    Neurobiology of Addiction Section, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
    Vendruscolo, L F
    Neurobiology of Addiction Section, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.
    Harvey, B K
    Molecular Mechanisms of Cellular Stress and Inflammation Unit, National Institute on Drug Abuse Intramural Research Program, Baltimore, MD, USA.
    Leggio, L-
    Section on Clinical Psychoneuroendocrinology and Neuropsychopharmacology, National Institute on Alcohol Abuse and Alcoholism Division of Intramural Clinical and Biological Research and National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Bethesda, MD, USA. lorenzo.leggio@nih.gov; Center for Alcohol and Addiction Studies, Department of Behavioral and Social Sciences, Brown University, Providence, RI, USA.
    Development and initial characterization of a novel ghrelin receptor CRISPR/Cas9 knockout wistar rat model2019Inngår i: International Journal of Obesity, ISSN 0307-0565, E-ISSN 1476-5497, Vol. 43, nr 2, s. 344-354Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ghrelin, a stomach-derived hormone implicated in numerous behaviors including feeding, reward, stress, and addictive behaviors, acts by binding to the growth hormone secretagogue receptor (GHSR). Here, we present the development, verification, and initial characterization of a novel GHSR knockout (KO) Wistar rat model created with CRISPR genome editing.

  • 1499.
    Zan, Yanjun
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Carlborg, Örjan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    A multi-locus association analysis method integrating phenotype and expression data reveals multiple novel associations to flowering time variation in wild-collected Arabidopsis thaliana.2018Inngår i: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 18, nr 4Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The adaptation to a new habitat often results in a confounding between genome-wide genotype and beneficial alleles. When the confounding is strong, or the allelic effects weak, it is a major statistical challenge to detect the adaptive polymorphisms. We describe a novel approach to dissect polygenic traits in natural populations. First, candidate adaptive loci are identified by screening for loci directly associated with the adaptive trait or the expression of genes known to affect it. Then, a multi-locus genetic architecture is inferred using a backward elimination association analysis across all candidate loci with an adaptive false discovery rate based threshold. Effects of population stratification are controlled by accounting for genomic kinship in both steps of the analysis and also by simultaneously testing all candidate loci in the multi locus model. We illustrate the method by exploring the polygenic basis of an important adaptive trait, flowering time in Arabidopsis thaliana, using public data from the 1,001 genomes project. We revealed associations between 33 (29) loci and flowering time at 10 (16)°C in this collection of natural accessions, where standard genome wide association analysis methods detected 5 (3) loci. The 33 (29) loci explained approximately 55.1 (48.7)% of the total phenotypic variance of the respective traits. Our work illustrates how the genetic basis of highly polygenic adaptive traits in natural populations can be explored in much greater detail by using new multi-locus mapping approaches taking advantage of prior biological information, genome and transcriptome data.

  • 1500.
    Zan, Yanjun
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Carlborg, Örjan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    A polygenic genetic architecture of flowering time in the worldwide Arabidopsis thaliana population.2019Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, nr 1, s. 141-154Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Here, we report an empirical study of the polygenic basis underlying the evolution of complex traits. Flowering time variation measured at 10 and 16 °C in the 1,001-genomes Arabidopsis thaliana collection of natural accessions were used as a model. The polygenic architecture of flowering time was defined as the 48 loci that were significantly associated with flowering time - at 10 and/or 16 °C and/or their difference - in this population. Contributions from alleles at flowering time associated loci to global and local adaptation were explored by evaluating their distribution across genetically and geographically defined subpopulations across the native range of the species. The dynamics in the genetic architecture of flowering time in response to temperature was evaluated by estimating how the effects of these loci on flowering changed with growth temperature. Overall, the genetic basis of flowering time was stable - about 2/3 of the flowering time loci had similar effects at 10 °C and 16 °C - but many loci were involved in gene by temperature interactions. Globally present alleles, mostly of moderate effect, contributed to the differences in flowering times between the subpopulations via subtle changes in allele-frequencies. More extreme local adaptations were, on several occasions, due to regional alleles with relatively large effects, and their LD-patterns suggest co-evolution of functionally connected alleles within local populations. Overall, these findings provide a significant contribution to our understanding about the possible modes of global and local evolution of a complex adaptive trait in Arabidopsis thaliana.

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