المؤلفون: Miller-Lewis, LR, Lewis, TW, Tieman, J, Rawlings, D, Parker, D, Sanderson, CR

مصطلحات موضوعية: General Science & Technology, Humans, Death, Linear Models, Emotions, Ego, Time Factors, Vocabulary

الوصف: Understanding public attitudes towards death is needed to inform health policies to foster community death awareness and preparedness. Linguistic sentiment analysis of how people describe their feelings about death can add to knowledge gained from traditional self-reports. This study provided the first description of emotive attitudes expressed towards death utilising textual sentiment analysis for the dimensions of valence, arousal and dominance. A linguistic lexicon of sentiment norms was applied to activities conducted in an online course for the general-public designed to generate discussion about death. We analysed the sentiment of words people chose to describe feelings about death, for themselves, for perceptions of the feelings of ‘others’, and for longitudinal changes over the time-period of exposure to a course about death (n = 1491). The results demonstrated that sadness pervades affective responses to death, and that inevitability, peace, and fear were also frequent reactions. However, words chosen to represent perceptions of others’ feelings towards death suggested that participants perceived others as feeling more negative about death than they do themselves. Analysis of valence, arousal and dominance dimensions of sentiment pre-to-post course participation demonstrated that participants chose significantly happier (more positive) valence words, less arousing (calmer) words, and more dominant (in-control) words to express their feelings about death by the course end. This suggests that the course may have been helpful in participants becoming more emotionally accepting in their feelings and attitude towards death. Furthermore, the change over time appeared greater for younger participants, who showed more increase in the dominance (power/control) and pleasantness (valence) in words chosen at course completion. Sentiment analysis of words to describe death usefully extended our understanding of community death attitudes and emotions. Future application of sentiment analysis to other related areas of ...

وصف الملف: Electronic-eCollection; application/pdf

العلاقة: PLoS One; PLoS One, 2021, 16, (1); http://hdl.handle.net/10453/150584Test

الإتاحة: http://hdl.handle.net/10453/150584Test

المؤلفون: Collisson, Eric, Muzny, DM, Bainbridge, MN, Chang, K, Dinh, HH, Drummond, JA, Fowler, G, Kovar, CL, Lewis, LR, Morgan, MB, Newsham, IF

الوصف: To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) unde

الوصول الحر: https://escholarship.org/uc/item/4rk6f86tTest

المؤلفون: Bell, D, Berchuck, A, Birrer, M, Chien, J, Cramer, DW, Dao, F, Dhir, R, DiSaia, P, Gabra, H, Glenn, P, Godwin, AK, Gross, J, Hartmann, L, Huang, M, Huntsman, DG, Iacocca, M, Imielinski, M, Kalloger, S, Karlan, BY, Levine, DA, Mills, GB, Morrison, C, Mutch, D, Olvera, N, Orsulic, S, Park, K, Petrelli, N, Rabeno, B, Rader, JS, Sikic, BI, Smith-McCune, K, Sood, AK, Bowtell, D, Penny, R, Testa, JR, Chang, K, Creighton, CJ, Dinh, HH, Drummond, JA, Fowler, G, Gunaratne, P, Hawes, AC, Kovar, CL, Lewis, LR, Morgan, MB, Newsham, IF, Santibanez, J, Reid, JG, Trevino, LR, Wu, Y-Q, Wang, M, Muzny, DM, Wheeler, DA, Gibbs, RA, Getz, G, Lawrence, MS, Cibulskis, K, Sivachenko, AY, Sougnez, C, Voet, D, Wilkinson, J, Bloom, T, Ardlie, K, Fennell, T, Baldwin, J, Nichol, R, Fisher, S, Gabriel, S, Lander, ES, Ding, L, Fulton, RS, Koboldt, DC, McLellan, MD, Wylie, T, Walker, J, O’Laughlin, M, Dooling, DJ, Fulton, L, Abbott, R, Dees, ND, Zhang, Q, Kandoth, C, Wendl, M, Schierding, W, Shen, D, Harris, CC, Schmidt, H, Kalicki, J, Delehaunty, KD, Fronick, CC, Demeter, R, Cook, L, Wallis, JW, Lin, L, Magrini, VJ, Hodges, JS, Eldred, JM, Smith, SM, Pohl, CS, Vandin, F

المصدر: Nature. 474(7353)

مصطلحات موضوعية: Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Biotechnology, Rare Diseases, Human Genome, Ovarian Cancer, Cancer, Aged, Carcinoma, DNA Methylation, Female, Gene Dosage, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Genomics, Humans, MicroRNAs, Middle Aged, Mutation, Ovarian Neoplasms, RNA, Messenger, Cancer Genome Atlas Research Network, General Science & Technology

الوصف: A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/44b1h9tbTest

المؤلفون: Lewis LR, R. Rozzi & B. Goffinet.

الوصف: 11 ; 2015 ; Ecology ; Q1 ; 41

العلاقة: instname: Conicyt; reponame: Repositorio Digital RI2.0; info:eu-repo/grantAgreement/PIA/PFB23; https://doi.org/10.1111/jbi.12385Test; PFB23; WOS:000345328400016; https://hdl.handle.net/10533/148506Test

الإتاحة: https://doi.org/10.1111/jbi.12385Test
https://hdl.handle.net/10533/148506Test

المؤلفون: Simakov, O, Kawashima, T, Marletaz, F, Jenkins, J, Koyanagi, R, Mitros, T, Hisata, K, Bredeson, J, Shoguchi, E, Gyoja, F, Yue, J-X, Chen, Y-C, Freeman, RM, Sasaki, A, Hikosaka-Katayama, T, Sato, A, Fujie, M, Baughman, KW, Levine, J, Gonzalez, P, Cameron, C, Fritzenwanker, JH, Pani, AM, Goto, H, Kanda, M, Arakaki, N, Yamasaki, S, Qu, J, Cree, A, Ding, Y, Dinh, HH, Dugan, S, Holder, M, Jhangiani, SN, Kovar, CL, Lee, SL, Lewis, LR, Morton, D, Nazareth, LV, Okwuonu, G, Santibanez, J, Chen, R, Richards, S, Muzny, DM, Gillis, A, Peshkin, L, Wu, M, Humphreys, T, Su, Y-H, Putnam, NH, Schmutz, J, Fujiyama, A, Yu, J-K, Tagawa, K, Worley, KC, Gibbs, RA, Kirschner, MW, Lowe, CJ, Satoh, N, Rokhsar, DS, Gerhart, J

المصدر: Nature , 527 pp. 459-465. (2015)

الوصف: Acorn worms, also known as enteropneust (literally, ‘gut-breathing’) hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal ‘gill’ slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

وصف الملف: text

العلاقة: https://discovery.ucl.ac.uk/id/eprint/10097254/1/Marletaz_nature16150.pdfTest; https://discovery.ucl.ac.uk/id/eprint/10097254Test/

الإتاحة: https://discovery.ucl.ac.uk/id/eprint/10097254/1/Marletaz_nature16150.pdfTest
https://discovery.ucl.ac.uk/id/eprint/10097254Test/

المؤلفون: Worley, KC, Warren, WC, Rogers, J, Locke, D, Muzny, DM, Mardis, ER, Weinstock, GM, Tardif, SD, Aagaard, KM, Archidiacono, N, Rayan, NA, Batzer, MA, Beal, K, Brejova, B, Capozzi, O, Capuano, SB, Casola, C, Chandrabose, MM, Cree, A, Dao, MD, de Jong, PJ, del Rosario, RC-H, Delehaunty, KD, Dinh, HH, Eichler, EE, Fitzgerald, S, Flicek, P, Fontenot, CC, Fowler, RG, Fronick, C, Fulton, LA, Fulton, RS, Gabisi, RA, Gerlach, D, Graves, TA, Gunaratne, PH, Hahn, MW, Haig, D, Han, Y, Harris, RA, Herrero, J, Hillier, LW, Hubley, R, Hughes, JF, Hume, J, Jhangiani, SN, Jorde, LB, Joshi, V, Karakor, E, Konkel, MK, Kosiol, C, Kovar, CL, Kriventseva, EV, Lee, SL, Lewis, LR, Liu, Y-S, Lopez, J, Lopez-Otin, C, Lorente-Galdos, B, Mansfield, KG, Marques-Bonet, T, Minx, P, Misceo, D, Moncrieff, JS, Morgan, MB, Nazareth, LV, Newsham, I, Ngoc, BN, Okwuonu, G, Prabhakar, S, Perales, L, Pu, L-L, Puente, XS, Quesada, V, Ranck, MC, Raney, BJ, Raveendran, M, Deiros, DR, Rocchi, M, Rodriguez, D, Ross, C, Ruffier, M, Ruiz, SJ, Sajjadian, S, Santibanez, J, Schrider, DR, Searle, S, Skaletsky, H, Soibam, B, Smit, AFA, Tennakoon, JB, Tomaska, L, Ullmer, B, Vejnar, CE, Ventura, M, Vilella, AJ, Vinar, T, Vogel, J-H, Walker, JA, Wang, Q, Warner, CM, Wildman, DE, Witherspoon, DJ, Wright, RA, Wu, Y, Xiao, W, Xing, J, Zdobnov, EM, Zhu, B, Gibbs, RA, Wilson, RK

المصدر: Nature Genetics , 46 (8) pp. 850-857. (2014)

مصطلحات موضوعية: Science & Technology, Life Sciences & Biomedicine, Genetics & Heredity, MULTILOCUS GENOTYPE DATA, INCREASED OVULATION RATE, SEGMENTAL DUPLICATIONS, GENE, GROWTH, MUTATIONS, VARIANTS, VERTEBRATES, CHIMPANZEE, CHIMERISM, Animal physiology, Genomics, Sequencing

الوصف: We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6×) and a whole-genome shotgun strategy. A first analysis has permitted comparison with the genomes of apes and Old World monkeys and the identification of specific features that might contribute to the unique biology of this diminutive primate, including genetic changes that may influence body size, frequent twinning and chimerism. We observed positive selection in growth hormone/insulin-like growth factor genes (growth pathways), respiratory complex I genes (metabolic pathways), and genes encoding immunobiological factors and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibited evidence of rapid sequence evolution. This genome sequence for a New World monkey enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application.

وصف الملف: text

العلاقة: https://discovery.ucl.ac.uk/id/eprint/1437020/1/Herrero_ng.3042.pdfTest; https://discovery.ucl.ac.uk/id/eprint/1437020Test/

الإتاحة: https://discovery.ucl.ac.uk/id/eprint/1437020/1/Herrero_ng.3042.pdfTest
https://discovery.ucl.ac.uk/id/eprint/1437020Test/

المؤلفون: Renfree, MB, Papenfuss, AT, Deakin, JE, Lindsay, J, Heider, T, Belov, K, Rens, W, Waters, PD, Pharo, EA, Shaw, G, Wong, ESW, Lefèvre, CM, Nicholas, KR, Kuroki, Y, Wakefield, MJ, Zenger, KR, Wang, C, Ferguson-Smith, M, Nicholas, FW, Hickford, D, Yu, H, Short, KR, Siddle, HV, Frankenberg, SR, Chew, KY, Menzies, BR, Stringer, JM, Suzuki, S, Hore, TA, Delbridge, ML, Mohammadi, A, Schneider, NY, Hu, Y, O'Hara, W, Al Nadaf, S, Wu, C, Feng, ZP, Cocks, BG, Wang, J, Flicek, P, Searle, SMJ, Fairley, S, Beal, K, Herrero, J, Carone, DM, Suzuki, Y, Sugano, S, Toyoda, A, Sakaki, Y, Kondo, S, Nishida, Y, Tatsumoto, S, Mandiou, I, Hsu, A, McColl, KA, Lansdell, B, Weinstock, G, Kuczek, E, McGrath, A, Wilson, P, Men, A, Hazar-Rethinam, M, Hall, A, Davis, J, Wood, D, Williams, S, Sundaravadanam, Y, Muzny, DM, Jhangiani, SN, Lewis, LR, Morgan, MB, Okwuonu, GO, Ruiz, SJ, Santibanez, J, Nazareth, L, Cree, A, Fowler, G, Kovar, CL, Dinh, HH, Joshi, V, Jing, C, Lara, F, Thornton, R, Chen, L, Deng, J, Liu, Y, Shen, JY, Song, XZ, Edson, J, Troon, C, Thomas, D, Stephens, A, Yapa, L, Levchenko, T, Gibbs, RA, Cooper, DW, Speed, TP, Fujiyama, A, M Graves, JA, O'Neill, RJ

المصدر: urn:ISSN:1474-7596 ; urn:ISSN:1474-760X ; Genome Biology, 12, 8, 414

مصطلحات موضوعية: Biotechnology, Human Genome, Genetics, 1 Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Australia, Biological Evolution, Chromosome Mapping, Chromosomes, Mammalian, Female, Gene Expression Regulation, Genome, Genomic Imprinting, In Situ Hybridization, Fluorescence, Macropodidae, MicroRNAs, Molecular Sequence Data, Reproduction, Sequence Alignment, Sequence Analysis, DNA, Transcriptome, anzsrc-for: 05 Environmental Sciences, anzsrc-for: 06 Biological Sciences, anzsrc-for: 08 Information and Computing Sciences

الوصف: Background: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development.Results: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements.Conclusions: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution. © 2011 Renfree et al.; licensee BioMed Central Ltd.

وصف الملف: application/pdf

العلاقة: http://hdl.handle.net/1959.4/unsworks_72959Test; https://unsworks.unsw.edu.au/bitstreams/4bd0b9c4-3a7b-488a-884a-82a9f600db7b/downloadTest; https://doi.org/10.1186/gb-2011-12-8-r81Test

الإتاحة: https://doi.org/10.1186/gb-2011-12-8-r81Test
http://hdl.handle.net/1959.4/unsworks_72959Test
https://unsworks.unsw.edu.au/bitstreams/4bd0b9c4-3a7b-488a-884a-82a9f600db7b/downloadTest

المؤلفون: Worley KC, Warren WC, Rogers J, Locke D, Muzny DM, Mardis ER, Weinstock GM, Tardif SD, Aagaard KM, ARCHIDIACONO, Nicoletta, Rayan NA, Batzer MA, Beal K, Brejova B, CAPOZZI, ORONZO, Capuano SB, Casola C, Chandrabose MM, Cree A, Dao MD, d.e. Jong PJ, Cruz Herrera del Rosario R, Delehaunty KD, Dinh HH, Eichler EE, Fitzgerald S, Flicek P, Fontenot CC, Fowler RG, Fronick C, Fulton LA, Fulton RS, Gabisi RA, Gerlach D, Graves TA, Gunaratne PH, Hahn MW, Haig D, Han Y, Harris RA, Herrero J, Hillier LW, Hubley R, Hughes JF, Hume J, Jhangiani SN, Jorde LB, Joshi V, Karakor E, Konkel MK, Kosiol C, Kovar CL, Kriventseva EV, Lee SL, Lewis LR, Liu Y, Lopez J, Lopez Otin C, Lorente Galdos B, Mansfield KG, Marques Bonet T, Minx P, Misceo D, Moncrieff JS, Morgan MB, Nazareth LV, Newsham I, Nguyen NB, Okwuonu GO, Prabhakar S, Perales L, Pu L. L, Puente XS, Quesada V, Ranck MC, Raney BJ, Raveendran M, Deiros DR, ROCCHI, Mariano, Rodriguez D, Ross C, Ruffier M, Ruiz SJ, Sajjadian S, Santibanez J, Schrider DR, Searle S, Skaletsky H, Soibam B, Smit AFA, Tennakoon JB, Tomaska L, Ullmer B, Vejnar CE, VENTURA, MARIO, Vilella AJ, Vinar T, Vogel J. H, Walker JA, Wang Q, Warner CM, Wildman DE, Witherspoon DJ, Wright RA, Wu Y, Xiao W, Xing J, Zdobnov EM, Zhu B, Gibbs RA, Wilson RK

المساهمون: Worley, Kc, Warren, Wc, Rogers, J, Locke, D, Muzny, Dm, Mardis, Er, Weinstock, Gm, Tardif, Sd, Aagaard, Km, Archidiacono, Nicoletta, Rayan, Na, Batzer, Ma, Beal, K, Brejova, B, Capozzi, Oronzo, Capuano, Sb, Casola, C, Chandrabose, Mm, Cree, A, Dao, Md, Jong PJ, d. e., Cruz Herrera del Rosario, R, Delehaunty, Kd, Dinh, Hh, Eichler, Ee, Fitzgerald, S, Flicek, P, Fontenot, Cc, Fowler, Rg, Fronick, C, Fulton, La, Fulton, R, Gabisi, Ra, Gerlach, D, Graves, Ta, Gunaratne, Ph, Hahn, Mw, Haig, D, Han, Y, Harris, Ra, Herrero, J, Hillier, Lw, Hubley, R, Hughes, Jf, Hume, J, Jhangiani, Sn, Jorde, Lb, Joshi, V, Karakor, E, Konkel, Mk, Kosiol, C, Kovar, Cl, Kriventseva, Ev, Lee, Sl, Lewis, Lr, Liu, Y, Lopez, J, Lopez Otin, C, Lorente Galdos, B, Mansfield, Kg, Marques Bonet, T, Minx, P, Misceo, D, Moncrieff, J, Morgan, Mb, Nazareth, Lv, Newsham, I, Nguyen, Nb, Okwuonu, Go, Prabhakar, S, Perales, L, Pu, L. L., Puente, X, Quesada, V, Ranck, Mc, Raney, Bj, Raveendran, M, Deiros, Dr, Rocchi, Mariano, Rodriguez, D, Ross, C, Ruffier, M, Ruiz, Sj, Sajjadian, S, Santibanez, J, Schrider, Dr, Searle, S, Skaletsky, H, Soibam, B, Smit, Afa, Tennakoon, Jb, Tomaska, L, Ullmer, B, Vejnar, Ce, Ventura, Mario, Vilella, Aj, Vinar, T, Vogel, J. H., Walker, Ja, Wang, Q

الوصف: We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6[times]) and a whole-genome shotgun strategy. A first analysis has permitted comparison with the genomes of apes and Old World monkeys and the identification of specific features that might contribute to the unique biology of this diminutive primate, including genetic changes that may influence body size, frequent twinning and chimerism. We observed positive selection in growth hormone/insulin-like growth factor genes (growth pathways), respiratory complex I genes (metabolic pathways), and genes encoding immunobiological factors and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibited evidence of rapid sequence evolution. This genome sequence for a New World monkey enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application.

العلاقة: info:eu-repo/semantics/altIdentifier/wos/WOS:000339704400013; volume:46; issue:8; firstpage:850; lastpage:857; numberofpages:8; journal:NATURE GENETICS; http://hdl.handle.net/11586/131193Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84905588751; http://www.nature.com/ng/journal/v46/n8/full/ng.3042.htmlTest

الإتاحة: https://doi.org/10.1038/ng.3042Test
http://hdl.handle.net/11586/131193Test
http://www.nature.com/ng/journal/v46/n8/full/ng.3042.htmlTest

المؤلفون: Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs R.A., ARCHIDIACONO, Nicoletta, ROCCHI, Mariano, VENTURA, MARIO

المساهمون: Carbone, L, Harris, Ra, Gnerre, S, Veeramah, Kr, Lorente Galdos, B, Huddleston, J, Meyer, Tj, Herrero, J, Roos, C, Aken, B, Anaclerio, F, Archidiacono, Nicoletta, Baker, C, Barrell, D, Batzer, Ma, Beal, K, Blancher, A, Bohrson, Cl, Brameier, M, Campbell, M, Capozzi, O, Casola, C, Chiatante, G, Cree, A, Damert, A, de Jong, Pj, Dumas, L, Fernandez Callejo, M, Flicek, P, Fuchs, Nv, Gut, I, Gut, M, Hahn, Mw, Hernandez Rodriguez, J, Hillier, Lw, Hubley, R, Ianc, B, Izsvák, Z, Jablonski, Ng, Johnstone, Lm, Karimpour Fard, A, Konkel, Mk, Kostka, D, Lazar, Nh, Lee, Sl, Lewis, Lr, Liu, Y, Locke, Dp, Mallick, S, Mendez, Fl, Muffato, M, Nazareth, Lv, Nevonen, Ka, O'Bleness, M, Ochis, C, Odom, Dt, Pollard, K, Quilez, J, Reich, D, Rocchi, Mariano, Schumann, Gg, Searle, S, Sikela, Jm, Skollar, G, Smit, A, Sonmez, K, ten Hallers, B, Terhune, E, Thomas, Gw, Ullmer, B, Ventura, Mario, Walker, Ja, Wall, Jd, Walter, L, Ward, Mc, Wheelan, Sj, Whelan, Cw, White, S, Wilhelm, Lj, Woerner, Ae, Yandell, M, Zhu, B, Hammer, Mf, Marques Bonet, T, Eichler, Ee, Fulton, L, Fronick, C, Muzny, Dm, Warren, Wc, Worley, Kc, Rogers, J, Wilson, Rk, Gibbs, R. A.

مصطلحات موضوعية: gibbon, evolution, genomes

الوصف: Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy akey nodeinthe primate phylogeny between OldWorldmonkeys andgreat apes.Herewepresent the assembly andanalysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation 5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally,weidentify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat.

العلاقة: info:eu-repo/semantics/altIdentifier/wos/WOS:000341362800043; volume:513; firstpage:195; lastpage:201; numberofpages:7; journal:NATURE; http://hdl.handle.net/11586/131200Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84907284157

الإتاحة: https://doi.org/10.1038/nature13679Test
http://hdl.handle.net/11586/131200Test

المؤلفون: Biankin, Av, Waddell, N, Kassahn, Ks, Gingras, Mc, Muthuswamy, Lb, Johns, Al, Miller, Dk, Wilson, Pj, Patch, Am, Wu, J, Chang, Dk, Cowley, Mj, Gardiner, Bb, Song, S, Harliwong, I, Idrisoglu, S, Nourse, C, Nourbakhsh, E, Manning, S, Wani, S, Gongora, M, Pajic, M, Scarlett, Cj, Gill, Aj, Pinho, Av, Rooman, I, Anderson, M, Holmes, O, Leonard, C, Taylor, D, Wood, S, Xu, Q, Nones, K, Fink, Jl, Christ, A, Bruxner, T, Cloonan, N, Kolle, G, Newell, F, Pinese, M, Mead, Rs, Humphris, Jl, Kaplan, W, Jones, Md, Colvin, Ek, Nagrial, Am, Humphrey, Es, Chou, A, Chin, Vt, Chantrill, La, Mawson, A, Samra, Js, Kench, Jg, Lovell, Ja, Daly, Rj, Merrett, Nd, Toon, C, Epari, K, Nguyen, Nq, Barbour, A, Zeps, N, Kakkar, N, Zhao, F, Wu, Yq, Wang, M, Muzny, Dm, Fisher, We, Brunicardi, Fc, Hodges, Se, Reid, Jg, Drummond, J, Chang, K, Han, Y, Lewis, Lr, Dinh, H, Buhay, Cj, Beck, T, Timms, L, Sam, M, Begley, K, Brown, A, Pai, D, Panchal, A, Buchner, N, De Borja, R, Denroche, Re, Yung, Ck, Serra, S, Onetto, N, Mukhopadhyay, D, Tsao, Ms, Shaw, Pa, Petersen, Gm, Gallinger, S, Hruban, Rh, Maitra, A, Iacobuzio Donahue, Ca, Schulick, Rd, Wolfgang, Cl, Morgan, Ra, Capelli, P, Scardoni, M, Tempero, Ma, Mann, Km, Jenkins, Na, Perez Mancera, Pa, Adams, Dj, Largaespada, Da, Wessels, Lf, Rust, Ag, Stein, Ld, Tuveson, Da, Copeland, Ng, Musgrove, Ea, Eshleman, Jr, Hudson, Tj, Sutherland, Rl, Wheeler, Da, Pearson, Jv, Mcpherson, Jd, Gibbs, Ra, LAWLOR, Rita Teresa, CORBO, Vincenzo, TORTORA, GIAMPAOLO, SCARPA, Aldo

المساهمون: Biankin, Av, Waddell, N, Kassahn, K, Gingras, Mc, Muthuswamy, Lb, Johns, Al, Miller, Dk, Wilson, Pj, Patch, Am, Wu, J, Chang, Dk, Cowley, Mj, Gardiner, Bb, Song, S, Harliwong, I, Idrisoglu, S, Nourse, C, Nourbakhsh, E, Manning, S, Wani, S, Gongora, M, Pajic, M, Scarlett, Cj, Gill, Aj, Pinho, Av, Rooman, I, Anderson, M, Holmes, O, Leonard, C, Taylor, D, Wood, S, Xu, Q, Nones, K, Fink, Jl, Christ, A, Bruxner, T, Cloonan, N, Kolle, G, Newell, F, Pinese, M, Mead, R, Humphris, Jl, Kaplan, W, Jones, Md, Colvin, Ek, Nagrial, Am, Humphrey, E, Chou, A, Chin, Vt, Chantrill, La, Mawson, A, Samra, J, Kench, Jg, Lovell, Ja, Daly, Rj, Merrett, Nd, Toon, C, Epari, K, Nguyen, Nq, Barbour, A, Zeps, N, Kakkar, N, Zhao, F, Wu, Yq, Wang, M, Muzny, Dm, Fisher, We, Brunicardi, Fc, Hodges, Se, Reid, Jg, Drummond, J, Chang, K, Han, Y, Lewis, Lr, Dinh, H, Buhay, Cj, Beck, T, Timms, L, Sam, M, Begley, K, Brown, A, Pai, D, Panchal, A, Buchner, N, De Borja, R, Denroche, Re, Yung, Ck, Serra, S, Onetto, N, Mukhopadhyay, D, Tsao, M, Shaw, Pa, Petersen, Gm, Gallinger, S, Hruban, Rh, Maitra, A, Iacobuzio Donahue, Ca, Schulick, Rd, Wolfgang, Cl, Morgan, Ra

مصطلحات موضوعية: PDAC, KRAS, Exome sequencing

الوصف: Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.

وصف الملف: STAMPA

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/23103869; info:eu-repo/semantics/altIdentifier/wos/WOS:000311031600037; volume:491; issue:7424; firstpage:399; lastpage:405; numberofpages:7; journal:NATURE; http://hdl.handle.net/11562/492954Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84869091997

الإتاحة: https://doi.org/10.1038/nature11547Test
http://hdl.handle.net/11562/492954Test