135 results on '"Farré, Marta"'
Search Results
102. Aportació al coneixement de la doctora Dolors Aleu i Riera, metgessa catalana (1857-1913)
- Author
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Camps i Lasa, Judith and Casasús i Farré, Marta
- Published
- 2000
103. Refuerzo de la clasificación de las muestras del Museo de Geología de la UTO
- Author
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Universitat Politècnica de Catalunya. Departament d'Enginyeria Minera i Recursos Naturals, Universitat Politècnica de Catalunya. Centre de Cooperació per al Desenvolupament, Mineria per al Desenvolupament, Universitat Politècnica de Catalunya. ERNMA - Enginyeria dels Recursos Naturals i Medi Ambient, Universidad Técnica de Oruro, Mata Perelló, Josep Maria, Torró Abat, Lisard, Ristol, Jordi, Sarri Tutusaus, Andrea, Parcerisa Duocastella, David, Sanz Balagué, Joaquim, Casarramona Farré, Marta, Alfonso Abella, María Pura, Llanque, M., Universitat Politècnica de Catalunya. Departament d'Enginyeria Minera i Recursos Naturals, Universitat Politècnica de Catalunya. Centre de Cooperació per al Desenvolupament, Mineria per al Desenvolupament, Universitat Politècnica de Catalunya. ERNMA - Enginyeria dels Recursos Naturals i Medi Ambient, Universidad Técnica de Oruro, Mata Perelló, Josep Maria, Torró Abat, Lisard, Ristol, Jordi, Sarri Tutusaus, Andrea, Parcerisa Duocastella, David, Sanz Balagué, Joaquim, Casarramona Farré, Marta, Alfonso Abella, María Pura, and Llanque, M.
- Abstract
Bolivia posee una de las mayores riquezas mineralógicas del mundo. Una buena representación de ellas se encuentra en el Museo Mineralógico de la Facultad de Minas de la UTO en Oruro. La trayectoria de más de 100 años de la colección había provocado que esta no se encontrara en su mejor situación. Por eso se decide una catalogación, inventariado y reordenación de las muestras mineralógicas que posee. Para ello se utilizan diversas técnicas de identificación mineral que van desde las clásicas de visu hasta el estudio petrográfico con lámina delgada o Difracción de RX. Se procede también a la renovación de las fichas identificatorias y al fotografiado de las más de 3500 muestras de que dispone., Postprint (published version)
- Published
- 2011
104. L'estudi del museu de geologia d'Oruro (Bolívia)
- Author
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Mineria per al Desenvolupament, Universitat Politècnica de Catalunya. Centre de Cooperació per al Desenvolupament, Universidad Técnica de Oruro, Torró Abat, Lisard, Ristol, Jordi, Sarri Tutusaus, Andrea, Parcerisa Duocastella, David, Sanz Balagué, Joaquim, Casarramona Farré, Marta, Alfonso Abella, María Pura, Llanque, M., Mata Perelló, Josep Maria, Mineria per al Desenvolupament, Universitat Politècnica de Catalunya. Centre de Cooperació per al Desenvolupament, Universidad Técnica de Oruro, Torró Abat, Lisard, Ristol, Jordi, Sarri Tutusaus, Andrea, Parcerisa Duocastella, David, Sanz Balagué, Joaquim, Casarramona Farré, Marta, Alfonso Abella, María Pura, Llanque, M., and Mata Perelló, Josep Maria
- Abstract
Bolívia compta amb una de les majors riqueses mineralògiques del món (Hyršl i Petrov, 2009). Una bona representació d’elles es troba al Museo Mineralógico de la Facultad de Minas de la UTO en Oruro (Llanque, 2006; Neumeier, 2009; Petrov, 2009). La trajectòria de més de cent anys de la col∙lecció però, havia provocat que aquesta no presentavà la seva millor situació. És per això que es decideix dur a terme una catalogació, inventariat i reordenació de les mostres mineralògiques de què disposa. Per fer-ho s'utilitzen diverses tècniques d'identificació mineral, que van des de les clàssiques de visu fins a mètodes més sofisticats com l'estudi petrogràfic amb làmina prima o amb Difracció de RX. Es procedeix també a la renovació de les fitxes identificatòries i al fotografiat de les més de 3500 mostres. Amb aquesta finalitat se signa el projecte de col∙laboració entre la Universitat Politècnica de Catalunya (U.P.C.) i la Universidad Técnica de Oruro (U.T.O.), en què es busca una sol∙lució als problemes mencionats durant l’any 2010., Peer Reviewed
- Published
- 2010
105. Enfoque de los proyectos de cooperación en la minería artesanal y pequeña minería
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Universitat Politècnica de Catalunya. Departament d'Enginyeria Minera, Industrial i TIC, Universitat Politècnica de Catalunya. Centre de Cooperació per al Desenvolupament, Mineria per al Desenvolupament, Universitat Politècnica de Catalunya. GREMS - Grup de Recerca en Mineria Sostenible, Mesa Vílchez, Claudia, Alfonso Abella, María Pura, Monterde Ruiz, Eva, Casarramona Farré, Marta, Santacreu, Maria Antonieta, Universitat Politècnica de Catalunya. Departament d'Enginyeria Minera, Industrial i TIC, Universitat Politècnica de Catalunya. Centre de Cooperació per al Desenvolupament, Mineria per al Desenvolupament, Universitat Politècnica de Catalunya. GREMS - Grup de Recerca en Mineria Sostenible, Mesa Vílchez, Claudia, Alfonso Abella, María Pura, Monterde Ruiz, Eva, Casarramona Farré, Marta, and Santacreu, Maria Antonieta
- Abstract
Desde hace cuatro años el departamento de Enginyeria Minera i Recursos Naturals realiza actividades de cooperación con la pequeña minería en diferentes países, especialmente de Latinoamérica. Esto ha llevado a la creación de la ONG Minería para el Desarrollo. En el marco de esta ONG se han realizado diversos proyectos de cooperación en Peru y uno en Angola, parcialmente financiados por el CCD (Centre de Cooperació per al Desenvolupament) de la Universitat Politècnica de Catalunya. La realización de los diferentes proyectos de cooperación en el campo de la minería artesanal y pequeña minería en diferentes emplazamientos geográficos ha dejado ver que los ámbitos de actuación de las ONGs vienen dados por el ciclo mismo de la explotación minera: por la importancia de la geología y minería durante las fases de exploración e investigación, así como para el cálculo de reservas según la ley de mercado y la ingeniería de minas para el óptimo diseño de la explotación, que minimice riesgos, maximice ganancias y sea más tolerable con el entorno. Estos proyectos se generan en el marco de programas de desarrollo social-organizativo, legal, técnico ambiental y empresarial. Para que se realicen con éxito deben crear mecanismos que permitan a la contraparte local expresar sus necesidades, crear condiciones que permitan salir a esta minería de la informalidad, abrir el camino para un crecimiento económico del sector e introducir correctas técnicas ambientales tolerantes con el entorno., Peer Reviewed, Postprint (published version)
- Published
- 2009
106. Projecte de cooperació miner-ambiental per la millora de la qualitat de vida de Misky
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Universitat Politècnica de Catalunya. Centre de Cooperació per al Desenvolupament, Mineria per al Desenvolupament, Casarramona Farré, Marta, Universitat Politècnica de Catalunya. Centre de Cooperació per al Desenvolupament, Mineria per al Desenvolupament, and Casarramona Farré, Marta
- Abstract
Postprint (published version)
- Published
- 2008
107. Desenvolupament de les potencialitats de la mineria
- Author
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Universitat Politècnica de Catalunya. Centre de Cooperació per al Desenvolupament, Mineria per al Desenvolupament, Casarramona Farré, Marta, Universitat Politècnica de Catalunya. Centre de Cooperació per al Desenvolupament, Mineria per al Desenvolupament, and Casarramona Farré, Marta
- Abstract
Postprint (published version)
- Published
- 2007
108. Perspectives About Health Care Provision in Dementia Care in Spain.
- Author
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Risco, Ester, Cabrera, Esther, Farré, Marta, Alvira, Carme, Miguel, Susana, and Zabalegui, Adelaida
- Abstract
Background: The aim of this study is to identify the barriers and facilitators in dementia care with respect to information provision, communication, and collaboration from the perspectives of the person with dementia, family caregivers, and health care professionals over the course of the illness. Methods: A qualitative study using Focus-Group methodology was carried out in people with dementia, family caregivers, and health care providers. Results: The categories that emerged from the analysis were insufficient information provided, specific dementia care needs, and acceptance of long-term care institutionalization from the people with dementia and caregivers’ groups and insufficient communication between health care providers, differential information according to disease stage, and home care coordination from the health care providers’ groups. Conclusion: The family is a key element in successful care coordination during dementia care provision. New effective strategies including self-management and emergent roles, such as case managers, could bring great benefits to people with dementia, caregivers, and health care providers. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
109. Recombination Rates and Genomic Shuffling in Human and Chimpanzee—A New Twist in the Chromosomal Speciation Theory
- Author
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Farré, Marta, primary, Micheletti, Diego, additional, and Ruiz-Herrera, Aurora, additional
- Published
- 2012
- Full Text
- View/download PDF
110. Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Author
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Damas, Joana, O'Connor, Rebecca, Farré, Marta, Lenis, Vasileios Panagiotis E., Martell, Henry J., Mandawala, Anjali, Fowler, Katie, Joseph, Sunitha, Swain, Martin T., Griffin, Darren K., and Larkin, Denis M.
- Abstract
Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.
- Published
- 2017
- Full Text
- View/download PDF
111. Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great Apes
- Author
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Farré, Marta, primary, Bosch, Montserrat, additional, López-Giráldez, Francesc, additional, Ponsà, Montserrat, additional, and Ruiz-Herrera, Aurora, additional
- Published
- 2011
- Full Text
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112. Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa
- Author
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Wang, Zheng, Lopez-Giraldez, Francesc, Lehr, Nina, Farré, Marta, Common, Ralph, Trail, Frances, and Townsend, Jeffrey P.
- Abstract
ABSTRACTFungi can serve as highly tractable models for understanding genetic basis of sexual development in multicellular organisms. Applying a reverse-genetic approach to advance such a model, we used random and multitargeted primers to assay gene expression across perithecial development in Neurospora crassa. We found that functionally unclassified proteins accounted for most upregulated genes, whereas downregulated genes were enriched for diverse functions. Moreover, genes associated with developmental traits exhibited stage-specific peaks of expression. Expression increased significantly across sexual development for mating type gene mat a-1and for mat A-1specific pheromone precursor ccg-4. In addition, expression of a gene encoding a protein similar to zinc finger, stc1, was highly upregulated early in perithecial development, and a strain with a knockout of this gene exhibited arrest at the same developmental stage. A similar expression pattern was observed for genes in RNA silencing and signaling pathways, and strains with knockouts of these genes were also arrested at stages of perithecial development that paralleled their peak in expression. The observed stage specificity allowed us to correlate expression upregulation and developmental progression and to identify regulators of sexual development. Bayesian networks inferred from our expression data revealed previously known and new putative interactions between RNA silencing genes and pathways. Overall, our analysis provides a fine-scale transcriptomic landscape and novel inferences regarding the control of the multistage development process of sexual crossing and fruiting body development in N. crassa.
- Published
- 2013
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113. Comparative Chromosome Mapping of Musk Ox and the X Chromosome among Some Bovidae Species.
- Author
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Proskuryakova, Anastasia A., Kulemzina, Anastasia I., Perelman, Polina L., Yudkin, Dmitry V., Lemskaya, Natalya A., Okhlopkov, Innokentii M., Kirillin, Egor V., Farré, Marta, Larkin, Denis M., Roelke-Parker, Melody E., O'Brien, Stephen J., Bush, Mitchell, and Graphodatsky, Alexander S.
- Subjects
X chromosome ,GENE mapping ,KARYOTYPES ,CHROMOSOME structure ,SPECIES ,ANTELOPES - Abstract
Bovidae, the largest family in Pecora infraorder, are characterized by a striking variability in diploid number of chromosomes between species and among individuals within a species. The bovid X chromosome is also remarkably variable, with several morphological types in the family. Here we built a detailed chromosome map of musk ox (Ovibos moschatus), a relic species originating from Pleistocene megafauna, with dromedary and human probes using chromosome painting. We trace chromosomal rearrangements during Bovidae evolution by comparing species already studied by chromosome painting. The musk ox karyotype differs from the ancestral pecoran karyotype by six fusions, one fission, and three inversions. We discuss changes in pecoran ancestral karyotype in the light of new painting data. Variations in the X chromosome structure of four bovid species nilgai bull (Boselaphus tragocamelus), saola (Pseudoryx nghetinhensis), gaur (Bos gaurus), and Kirk's Dikdik (Madoqua kirkii) were further analyzed using 26 cattle BAC-clones. We found the duplication on the X in saola. We show main rearrangements leading to the formation of four types of bovid X: Bovinae type with derived cattle subtype formed by centromere reposition and Antilopinae type with Caprini subtype formed by inversion in XSB1. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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114. near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert.
- Author
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Farré, Marta, Li, Qiye, Zhou, Yang, Damas, Joana, Chemnick, Leona G, Kim, Jaebum, Ryder, Oliver A, Ma, Jian, Zhang, Guojie, Larkin, Denis M, and Lewin, Harris A
- Subjects
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CHROMOSOMES , *GEMSBOK , *SPECIES diversity - Abstract
Background The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts. Findings Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to Benchmarking Universal Single-Copy Orthologs analysis. The Reference-Assisted Chromosome Assembly tool was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions. Conclusions Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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- View/download PDF
115. Tracing genome evolution : from ancestral karyotypes to current genomes in three mammalian clades
- Author
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Arias Sardá, Cristina and Farré, Marta
- Subjects
QH426 Genetics - Abstract
Mammals show a wide range of chromosomic diversity. Their karyotypes range from 2n=6/7 in the Indian muntjac (Ruminantia) to 2n=102 in the Viscacha rat (Rodentia). Although the mammalian genome size is round 3.5 Gb, the mammalian average chromosome size is highly variable, including species with a high number of small chromosomes such as cattle (a ruminant with 2n=60 and an average chromosome size of 87 Mb), and species with a low number of big chromosomes such as Tasmanian devil (a marsupial with 2n=14 and an average chromosome size of 440 Mb). Identifying and timing when and where gross genomic rearrangements occurred during evolution will help to explain changes in genome structure with functional consequences that might eventually lead to speciation. Here we used DESCHRAMBLER to reconstruct eight ancestral genomes from three different lineages: Ruminantia, Marsupialia and Afrotheria. We classified the rearrangement events occurring in each lineage and identified the Evolutionary Breakpoints Regions (EBRs) and Homologous Synteny Blocks (HSBs). Cattle and African elephant showed the same number of well-defined EBRs, 32, while Tasmanian devil only showed 19. Marsupial and ruminant genomes are characterised by inversions, while interchromosomal rearrangements are also important in the oldest ancestor of ruminants and are the main rearrangement force in the afrotherians. These EBRs are located in gene-rich regions of the genome, and in ruminants and afrotherians, they are also located in regions with a high density of transposable elements (TEs). Moreover, we identified signatures of convergent evolution in mammals with an extreme range of both, diploid numbers and chromosome sizes, using representative species of the three lineages and searching for positive selection in their orthologous genes. We found that some genes under convergent evolution and positive selection were related to processes such as chromatin structure or DNA repair, such as MSH6 or RNF123, that, at the same time, are related to causes and consequences of chromosome rearrangements (CRs). Overall, our results significantly expand knowledge of genome evolution and will facilitate greater understanding of the role of CRs in mammalian evolution.
- Published
- 2023
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116. Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Author
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Damas, Joana, O'Connor, Rebecca, Farré, Marta, Lenis, Vasileios Panagiotis E., Martell, Henry J., Mandawala, Anjali, Harvey, Katie, Joseph, Sunitha, Swain, Martin T., Griffin, Darren K., Larkin, Denis M., Damas, Joana, O'Connor, Rebecca, Farré, Marta, Lenis, Vasileios Panagiotis E., Martell, Henry J., Mandawala, Anjali, Harvey, Katie, Joseph, Sunitha, Swain, Martin T., Griffin, Darren K., and Larkin, Denis M.
- Abstract
Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.
117. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor
- Author
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Romanov, Michael N, Farré, Marta, Lithgow, Pamela E, Fowler, Katie E., Skinner, Benjamin M, O’Connor, Rebecca, Fonseka, Gothami, Backström, Niclas, Matsuda, Yoichi, Nishida, Chizuko, Houde, Peter, Jarvis, Erich D, Ellegren, Hans, Burt, David W, Larkin, Denis M, Griffin, Darren K, Romanov, Michael N, Farré, Marta, Lithgow, Pamela E, Fowler, Katie E., Skinner, Benjamin M, O’Connor, Rebecca, Fonseka, Gothami, Backström, Niclas, Matsuda, Yoichi, Nishida, Chizuko, Houde, Peter, Jarvis, Erich D, Ellegren, Hans, Burt, David W, Larkin, Denis M, and Griffin, Darren K
- Abstract
Background The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. Results Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species’ genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. Conclusions Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and b
118. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes.
- Author
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O'Connor, Rebecca E, Farré, Marta, Joseph, Sunitha, Damas, Joana, Kiazim, Lucas, Jennings, Rebecca, Bennett, Sophie, Slack, Eden A, Allanson, Emily, Larkin, Denis M, and Griffin, Darren K
- Published
- 2018
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119. syntenyPlotteR: a user-friendly R package to visualize genome synteny, ideal for both experienced and novice bioinformaticians.
- Author
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Quigley, Sarah, Damas, Joana, Larkin, Denis M, and Farré, Marta
- Subjects
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BIOINFORMATICS , *VISUALIZATION , *CHROMOSOMAL rearrangement , *COMPUTATIONAL biology , *BIOLOGICAL evolution - Abstract
Motivation The rapid increase in the number of chromosome-scale genome assemblies has renewed interest in chromosome evolution studies. The visualization of syntenic relationships between genomes is a crucial initial step in the study of chromosome rearrangements and evolution. There are few tools available that serve this purpose, and they can be difficult to learn. Moreover, these tools are limited in the number of species comparisons that can be visualized and the size of chromosome rearrangements identified. Thus, the development of novel visualization tools is in strong need. Results Here, we present syntenyPlotteR, an R package developed to visualize homologous synteny blocks in a pairwise or multispecies manner. This package contains three functions that allow users to generate publication-quality representations of syntenic relationships easily and quickly between genomes of interest. Availability and implementation SyntenyPlotteR can be installed from CRAN with the documentation found in https://farre-lab.github.io/syntenyPlotteR/. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
120. Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers.
- Author
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Darolti, Iulia, Wright, Alison E., Sandkam, Benjamin A., Morris, Jake, Bloch, Natasha I., Farré, Marta, Fuller, Rebecca C., Bourne, Godfrey R., Larkin, Denis M., Breden, Felix, and Mank, Judith E.
- Subjects
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SEX chromosomes , *Y chromosome , *SEX differentiation (Embryology) , *X chromosome , *GUPPIES - Abstract
Once recombination is halted between the X and Y chromosomes, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about the variation in sex chromosome differentiation within clades. Here, we combined whole-genome and transcriptome sequencing data to characterize the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged roughly 20 million years ago. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata and P. wingei are largely homomorphic, with recombination in the former persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely nonrecombining and strikingly heteromorphic. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of functional chromosome-wide dosage compensation in this species, which has not been previously observed in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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121. Identification of sequence changes in myosin II that adjust muscle contraction velocity
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Anthony J. Baines, Jonathan Walklate, Marta Farré, Michael A. Geeves, Carlos Vera, Mark N. Wass, Daniel P. Mulvihill, Jake E McGreig, Chloe A. Johnson, Martin S. Ridout, Leslie A. Leinwand, Sarah T. Jeanfavre, Johnson, Chloe A [0000-0003-0856-5041], Vera, Carlos D [0000-0003-1207-4878], Farré, Marta [0000-0001-9170-5767], Mulvihill, Daniel P [0000-0003-2502-5274], Wass, Mark N [0000-0001-5428-6479], Geeves, Michael A [0000-0002-9364-8898], and Apollo - University of Cambridge Repository
- Subjects
Contraction (grammar) ,Muscle Physiology ,Physiology ,Protein Sequencing ,Q1 ,Biochemistry ,Contractile Proteins ,Adenosine Triphosphate ,CrossBridge ,Myosin ,Medicine and Health Sciences ,Protein Isoforms ,Biology (General) ,Musculoskeletal System ,Conserved Sequence ,Phylogeny ,Data Management ,Mammals ,0303 health sciences ,General Neuroscience ,Muscles ,030302 biochemistry & molecular biology ,Cardiac muscle ,Eukaryota ,Phylogenetic Analysis ,Adaptation, Physiological ,Cell biology ,Phylogenetics ,Adenosine Diphosphate ,medicine.anatomical_structure ,Vertebrates ,Amino Acid Analysis ,medicine.symptom ,Anatomy ,General Agricultural and Biological Sciences ,Muscle contraction ,Research Article ,Muscle Contraction ,Gene isoform ,Computer and Information Sciences ,QH301-705.5 ,Motor Proteins ,Actin Motors ,Motility ,macromolecular substances ,Biology ,Myosins ,Research and Analysis Methods ,General Biochemistry, Genetics and Molecular Biology ,Cell Line ,03 medical and health sciences ,Protein Domains ,Molecular Motors ,medicine ,Animals ,Humans ,Evolutionary Systematics ,Amino Acid Sequence ,Molecular Biology Techniques ,Sequencing Techniques ,Molecular Biology ,030304 developmental biology ,Sequence (medicine) ,Taxonomy ,Cardiac Muscles ,Myosin Type II ,Evolutionary Biology ,Molecular Biology Assays and Analysis Techniques ,General Immunology and Microbiology ,Body Weight ,Organisms ,Biology and Life Sciences ,Proteins ,Cell Biology ,Rats ,Cytoskeletal Proteins ,Amniotes ,Zoology - Abstract
The speed of muscle contraction is related to body size; muscles in larger species contract at slower rates. Since contraction speed is a property of the myosin isoform expressed in a muscle, we investigated how sequence changes in a range of muscle myosin II isoforms enable this slower rate of muscle contraction. We considered 798 sequences from 13 mammalian myosin II isoforms to identify any adaptation to increasing body mass. We identified a correlation between body mass and sequence divergence for the motor domain of the 4 major adult myosin II isoforms (β/Type I, IIa, IIb, and IIx), suggesting that these isoforms have adapted to increasing body mass. In contrast, the non-muscle and developmental isoforms show no correlation of sequence divergence with body mass. Analysis of the motor domain sequence of β-myosin (predominant myosin in Type I/slow and cardiac muscle) from 67 mammals from 2 distinct clades identifies 16 sites, out of 800, associated with body mass (padj < 0.05) but not with the clade (padj > 0.05). Both clades change the same small set of amino acids, in the same order from small to large mammals, suggesting a limited number of ways in which contraction velocity can be successfully manipulated. To test this relationship, the 9 sites that differ between human and rat were mutated in the human β-myosin to match the rat sequence. Biochemical analysis revealed that the rat–human β-myosin chimera functioned like the native rat myosin with a 2-fold increase in both motility and in the rate of ADP release from the actin–myosin crossbridge (the step that limits contraction velocity). Thus, these sequence changes indicate adaptation of β-myosin as species mass increased to enable a reduced contraction velocity and heart rate., Heart and skeletal muscles of larger mammals contract more slowly than smaller ones. This study identifies amino acid changes in myosin isoforms that correlate with species size; mutating the residues in human β-myosin to match the rat sequence at these positions increased its in vitro velocity to that of the rat protein.
- Published
- 2021
122. Estratègies prèvies al sacrifici que poden afectar el benestar animal i la qualitat de la carn de porcs de diferent genotip RYRI
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Panella-Riera, Núria, Gil Farré, Marta, Oliver Pratsevall, Mª Àngels, Puigvert Colomer, Xavier, Universitat de Girona. Departament d'Enginyeria Química, Agrària i Tecnologia Agroalimentària, and Oliver Pratsevall, M. Àngels
- Subjects
Tesis i dissertacions acadèmiques ,636 - Explotació i cria d'animals. Cria del bestiar i d'animals domèstics ,Magnesi ,Fasting and lairage ,Feed intake ,Consumo de pienso ,Qualitat tecnològica de la carn ,Ayuno y espera ,food and beverages ,Triptophan ,Tratamiento ante mortem ,Triptòfan ,Triptófano ,Magnesio ,Cerdos ,Porcs ,Tractament ante mortem ,Technological meat quality ,Dejuni i espera ,Pigs ,Magnesium ,Calidad tecnológica de la carne ,Consum de pinso ,Ante mortem treatment - Abstract
The main objective of this thesis was to study (i) the effect of the fasting and lairage on carcass and technological meat quality and (ii) the inclusion of magnesium (MgCO3 and MgSO4) and/or tryptophan during 5 days before slaughtering pigs as a strategy to decrease stress levels and improve meat quality, with two different porcine RYR1 genotypes (NN and nn). An adequate combination of fasting and lairage period is recommended. A supplement of MgCO3 or Trp did not improve meat quality under minimal stressful ante mortem conditions; and MgSO4 had a laxative effect on pigs supplemented with it. When including nn pigs to the herd, it is recommended to consider the supplements’ combination of tryptophan and a source of Mg (avoiding MgSO4) to alleviate the negative effect of the stress and to improve technological meat quality., L’objectiu principal d’aquest treball fou estudiar (i) l’efecte del dejuni i el temps d’espera a l’escorxador i (ii) l’efecte de l’addició de suplements de magnesi (MgCO3 o MgSO4) i/o triptòfan a la dieta durant els 5 dies previs al sacrifici com a estratègia per disminuir els nivells d’estrès i millorar la qualitat de la carn, en dos genotips porcins diferents respecte el gen RYR1 (NN i nn). Es recomana combinar correctament el dejuni i l’espera per millorar el benestar i la qualitat de la carn. El MgCO3 o el Trp no va millorar la qualitat de la carn en condicions de mínim estrès; i el MgSO4 provocà problemes digestius. En el cas d’optar per la utilització de genètiques nn, es recomana considerar la utilització de suplements de L-Trp amb fonts de magnesi (excloent el MgSO4) per pal•liar les conseqüències negatives de l’estrès i millorar la qualitat tecnològica de la carn.
- Published
- 2011
123. Características bioquímicas del músculo, calidad de la carne y de la grasa de conejos seleccionados por velocidad de crecimiento
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Ramírez Télles, Jorge Alberto, Oliver Pratsevall, Mª Àngels, Gil Farré, Marta, and Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments
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663/664 ,Miosina ,Textura ,Conejo ,Ciències de la Salut - Published
- 2004
124. La raça bovina Bruna dels Pirineus: qualitat de la canal i de la carn. Característiques bioquímiques del múscul longissimus thoracis en set races autòctones
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Serra i Dalmau, Xavier, Gil Farré, Marta, Oliver Pratsevall, Mª Àngels, and Universitat Autònoma de Barcelona. Departament de Bioquímica i Biologia Molecular
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Ciències Experimentals ,vacum de carn ,qualitat de carn ,bioquímica del múscul - Abstract
L'objectiu principal d'aquesta tesi és la caracterització de la raça bovina Bruna dels Pirineus per tal de conèixer, per una banda, la variabilitat de la raça en relació a la qualitat de la canal, la qualitat de la carn i les característiques bioquímiques del múscul longissimus thoracis (pigments hemo, percentatge de miosina MHC I mitjançant ELISA i activitats enzimàtiques lactat deshidrogenasa i isocitrat deshidrogenasa) i, per l'altra, l'estudi de les seves relacions amb les variables o atributs de l'anàlisi sensorial (olor de vedella, olor de fetge, flavor de vedella, flavor de fetge, tendresa i sucositat), a fi de poder avaluar objectivament el potencial d'aquesta raça.Un total de 74 vedells mascles de la raça Bruna dels Pirineus (provinents de 22 ramaders i engreixats al llarg dels anys 1996-98) van ser deslletats als 7 mesos de mitjana d'edat i amb un pes mitjà de 268 kg. L'alimentació del període d'engreix (171 dies de mitjana) va ser ad libitum, amb una dieta exclusivament vegetal, a base de pinso concentrat i suplementada amb farratge. El pes viu de sacrifici dels animals fou de 541,3 ±29,6 kg, amb una edat mitjana de 380,6 ±34,4 dies.A més a més, també s'estudia l'efecte raça-sistema de producció sobre el color i les característiques bioquímiques del múscul longissimus thoracis (LT) en set races autòctones espanyoles de vacum de carn amb un total de 478 vedells mascles repartits de la manera següent: 70 de l' Asturiana de los Valles (AV), 70 de l' Asturiana de la Montaña (AM), 55 de la Pirenaica (PI), 74 de la Bruna dels Pirineus (BP), 71 de l' Avileña-Negra Ibérica (A-NI), 70 de la Morucha (MO) i 68 de la Retinta (RE). Els vedells es van criar amb les mares en sistema extensiu fins a l'inici del període d'engreix (entre 5 i 7 mesos), el qual va consistir en una alimentació ad libitum i d'acord amb el sistema de producció característic de cada raça. La mitjana d'edat de sacrifici de les diferents races va oscil·lar entre els 363 i els 541dies, mentre que el pes canal es va moure entre els 250 i 334,5 kg. S'observà un efecte significatiu del raça-sistema de producció sobre el color i les característiques bioquímiques del múscul LT., The main objective of this study was the characterisation of the Bruna dels Pirineus cattle breed in relation to carcass quality, meat quality and longissimus thoracis (LT) biochemical characteristics variability (haem pigments, myosin MHC I percentage, lactate dehydrogenase and isocitrate dehydrogenase activities), and furthermore, to examine their relationships with the sensory analysis variables (beef and livery odour intensity, beef and livery flavour intensity, tenderness and juiciness), in order to evaluate the potential of this breed.A total of 74 young bulls of the Bruna dels Pirineus Breed (from 22 herds and reared along 1996-98) were used. Calves were weaned at about 7 months old, with an average weaning-weight of 286 kg, and fed ad libitum with an exclusively vegetal diet (concentrate and supplemented with hay) during 171 days, on average. Live weight at sacrifice was 541.3 ±29.6 kg, with an average age of 380.6 ±34.4 days. Additionally, the effect of the breed-production system on the colour and the biochemical characteristics of LT muscle in seven local Spanish beef cattle breeds was studied (478 young bulls): 70 from Asturiana de los Valles (AV), 70 from Asturiana de la Montaña (AM), 55 from Pirenaica (PI), 74 from Bruna dels Pirineus (BP), 71 from Avileña-Negra Ibérica (A-NI), 70 from Morucha (MO) and 68 from Retinta (RE). Calves were reared in an extensive regime together with their mothers and started fattening at about 5 to 7 months old. They were fed a breed-specific diet ad libitum. The ingredients always had a vegetable origin. Age at slaughter was between 363 and 541 days; and carcass weight between 250 and 334.5 kg. Significant differences between breed-production systems were found for all the traits evaluated.
- Published
- 2001
125. Evolution of the ancestral mammalian karyotype and syntenic regions.
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Damas J, Corbo M, Kim J, Turner-Maier J, Farré M, Larkin DM, Ryder OA, Steiner C, Houck ML, Hall S, Shiue L, Thomas S, Swale T, Daly M, Korlach J, Uliano-Silva M, Mazzoni CJ, Birren BW, Genereux DP, Johnson J, Lindblad-Toh K, Karlsson EK, Nweeia MT, Johnson RN, and Lewin HA
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- Animals, Cattle genetics, Chromosomes, Mammalian genetics, Eutheria genetics, Humans, Phylogeny, Sloths genetics, Evolution, Molecular, Karyotype, Mammals genetics, Synteny genetics
- Abstract
Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.
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- 2022
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126. 3D chromatin remodelling in the germ line modulates genome evolutionary plasticity.
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Álvarez-González L, Burden F, Doddamani D, Malinverni R, Leach E, Marín-García C, Marín-Gual L, Gubern A, Vara C, Paytuví-Gallart A, Buschbeck M, Ellis PJI, Farré M, and Ruiz-Herrera A
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- Animals, Chromatin genetics, DNA Breaks, Double-Stranded, Genome, Male, Meiosis genetics, Mice, Spermatogenesis genetics, Chromatin Assembly and Disassembly genetics, Germ Cells
- Abstract
Chromosome folding has profound impacts on gene regulation, whose evolutionary consequences are far from being understood. Here we explore the relationship between 3D chromatin remodelling in mouse germ cells and evolutionary changes in genome structure. Using a comprehensive integrative computational analysis, we (i) reconstruct seven ancestral rodent genomes analysing whole-genome sequences of 14 species representatives of the major phylogroups, (ii) detect lineage-specific chromosome rearrangements and (iii) identify the dynamics of the structural and epigenetic properties of evolutionary breakpoint regions (EBRs) throughout mouse spermatogenesis. Our results show that EBRs are devoid of programmed meiotic DNA double-strand breaks (DSBs) and meiotic cohesins in primary spermatocytes, but are associated in post-meiotic cells with sites of DNA damage and functional long-range interaction regions that recapitulate ancestral chromosomal configurations. Overall, we propose a model that integrates evolutionary genome reshuffling with DNA damage response mechanisms and the dynamic spatial genome organisation of germ cells., (© 2022. The Author(s).)
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- 2022
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127. The Plasticity of Genome Architecture.
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Farré M and Ruiz-Herrera A
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- Adaptation, Physiological genetics, Animals, Chromosomes ultrastructure, DNA, Satellite genetics, Female, Humans, Invertebrates genetics, Male, Sex Determination Processes, Species Specificity, Vertebrates genetics, Chromosomes genetics, Evolution, Molecular, Genetic Speciation, Genome
- Abstract
Understanding the origin of species and their adaptability to new environments is one of the main questions in biology [...].
- Published
- 2020
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128. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi).
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Farré M, Li Q, Darolti I, Zhou Y, Damas J, Proskuryakova AA, Kulemzina AI, Chemnick LG, Kim J, Ryder OA, Ma J, Graphodatsky AS, Zhang G, Larkin DM, and Lewin HA
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- Animals, Computational Biology methods, Evolution, Molecular, High-Throughput Nucleotide Sequencing, Karyotyping, Molecular Sequence Annotation, Phylogeny, Chromosomes, Mammalian, Genome, Genomics methods, Giraffes genetics
- Abstract
Background: The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes., Findings: Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions., Conclusions: We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population size has declined by 52% in recent years., (© The Author(s) 2019. Published by Oxford University Press.)
- Published
- 2019
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129. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.
- Author
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Farré M, Kim J, Proskuryakova AA, Zhang Y, Kulemzina AI, Li Q, Zhou Y, Xiong Y, Johnson JL, Perelman PL, Johnson WE, Warren WC, Kukekova AV, Zhang G, O'Brien SJ, Ryder OA, Graphodatsky AS, Ma J, Lewin HA, and Larkin DM
- Subjects
- Animals, DNA Transposable Elements, Enhancer Elements, Genetic, Karyotype, Protein Binding, Selection, Genetic, Transcription Factors metabolism, Chromosome Breakpoints, Evolution, Molecular, Ruminants genetics, Synteny
- Abstract
The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution., (© 2019 Farré et al.; Published by Cold Spring Harbor Laboratory Press.)
- Published
- 2019
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130. A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert.
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Farré M, Li Q, Zhou Y, Damas J, Chemnick LG, Kim J, Ryder OA, Ma J, Zhang G, Larkin DM, and Lewin HA
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- Animals, Female, Genomics, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Phylogeny, Sequence Analysis, DNA, Antelopes genetics, Genome
- Abstract
Background: The gemsbok (Oryx gazella) is one of the largest antelopes in Africa. Gemsbok are heterothermic and thus highly adapted to live in the desert, changing their feeding behavior when faced with extreme drought and heat. A high-quality genome sequence of this species will assist efforts to elucidate these and other important traits of gemsbok and facilitate research on conservation efforts., Findings: Using 180 Gbp of Illumina paired-end and mate-pair reads, a 2.9 Gbp assembly with scaffold N50 of 1.48 Mbp was generated using SOAPdenovo. Scaffolds were extended using Chicago library sequencing, which yielded an additional 114.7 Gbp of DNA sequence. The HiRise assembly using SOAPdenovo + Chicago library sequencing produced a scaffold N50 of 47 Mbp and a final genome size of 2.9 Gbp, representing 90.6% of the estimated genome size and including 93.2% of expected genes according to Benchmarking Universal Single-Copy Orthologs analysis. The Reference-Assisted Chromosome Assembly tool was used to generate a final set of 47 predicted chromosome fragments with N50 of 86.25 Mbp and containing 93.8% of expected genes. A total of 23,125 protein-coding genes and 1.14 Gbp of repetitive sequences were annotated using de novo and homology-based predictions., Conclusions: Our results provide the first high-quality, chromosome-scale genome sequence assembly for gemsbok, which will be a valuable resource for studying adaptive evolution of this species and other ruminants.
- Published
- 2019
- Full Text
- View/download PDF
131. Costs and Burden Associated With Loss of Labor Productivity in Informal Caregivers of People With Dementia: Results From Spain.
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Farré M, Kostov B, Haro JM, Cabrera E, Risco E, Alvira M, Miguel S, and Zabalegui A
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- Absenteeism, Aged, Aged, 80 and over, Cohort Studies, Humans, Middle Aged, Spain, Surveys and Questionnaires, Caregivers psychology, Cost of Illness, Dementia, Home Care Agencies, Nursing Homes, Work Performance
- Abstract
Aims: We analyzed indirect costs related to loss of labor productivity (LLP) in informal caregivers (ICs) of people with dementia (PwD) and the associated caregiver burden and patients' clinical variables., Methods: Multicenter cohort study of PwD and their ICs (n = 287) focused on two groups: (1) home care and (2) institutional long-term care. The costs of LLP were assessed using the Resource Utilization Dementia instrument and a human capital approach., Results: The cost for LLP was 378&OV0556;/month or 4.536&OV0556;/year. Greater disease severity increased the likelihood of reducing working hours and missing a working day. There was a significant association between partial absenteeism and burden in employed informal caregiver in both the home and institutional setting., Conclusion: Cognitive impairment contributes to the cost of LLP in IC especially in home-care. LLP has a negative impact on IC burden.
- Published
- 2018
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132. [Application of the Balance of Care model in decision-making regarding the best care for patients with dementia].
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Risco E, Zabalegui A, Miguel S, Farré M, Alvira C, and Cabrera E
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- Aged, Aged, 80 and over, Cost-Benefit Analysis, Female, Home Care Services economics, Humans, Institutionalization economics, Male, Mental Status and Dementia Tests, Patient Care Team, Decision Making, Dementia therapy, Models, Theoretical
- Abstract
Objective: To describe the implementation of the Balance of Care model in decision-making regarding the best care for patients with dementia in Spain., Methods: The Balance of Care model was used, which consists of (1) describing the profile of the typical cases of people with dementia and their caregivers, (2) identifying the most suitable care setting for each of the cases (home-care or long-term care institution), (3) designing specific care plans for each case, and (4) evaluating the cost of the proposed care plans., Results: A total of 1,641 people with dementia and their caregivers from eight European countries were used in the case design. The evaluation of cases was conducted by 20 experts in different medical fields of dementia. In Spain, the results indicated that initially the most suitable placement to take care of people with dementia was the home, however in cases with higher dependency in activities of daily living, the long-term care setting was the best option. For the best care plan, the following resources were chosen: professional help to perform basic activities; day center; multidisciplinary home care team; financial support; community nurse; and social worker., Discussion: The Balance of Care method allows us to assess the most appropriate place of care for people with dementia systematically, objectively and with a multidisciplinary team. Other cost-effective interventions should be integrated in patients with dementia care in order to improve home care., (Copyright © 2016 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.)
- Published
- 2017
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133. Reconstruction and evolutionary history of eutherian chromosomes.
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Kim J, Farré M, Auvil L, Capitanu B, Larkin DM, Ma J, and Lewin HA
- Subjects
- Algorithms, Animals, Cell Lineage, Chromosome Breakpoints, Computational Biology methods, Gene Rearrangement, Genome, Genome, Human, Humans, In Situ Hybridization, Fluorescence, Phylogeny, Software, Synteny, Chromosomes ultrastructure, Eutheria genetics, Evolution, Molecular
- Abstract
Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. For ancestral chromosome reconstructions, we developed an algorithm (DESCHRAMBLER) that probabilistically determines the adjacencies of syntenic fragments using chromosome-scale and fragmented genome assemblies. The reconstructed chromosomes of the eutherian, boreoeutherian, and euarchontoglires ancestor each included >80% of the entire length of the human genome, whereas reconstructed chromosomes of the most recent common ancestor of simians, catarrhini, great apes, and humans and chimpanzees included >90% of human genome sequence. These high-coverage reconstructions permitted reliable identification of chromosomal rearrangements over ∼105 My of eutherian evolution. Orangutan was found to have eight chromosomes that were completely conserved in homologous sequence order and orientation with the eutherian ancestor, the largest number for any species. Ruminant artiodactyls had the highest frequency of intrachromosomal rearrangements, and interchromosomal rearrangements dominated in murid rodents. A total of 162 chromosomal breakpoints in evolution of the eutherian ancestral genome to the human genome were identified; however, the rate of rearrangements was significantly lower (0.80/My) during the first ∼60 My of eutherian evolution, then increased to greater than 2.0/My along the five primate lineages studied. Our results significantly expand knowledge of eutherian genome evolution and will facilitate greater understanding of the role of chromosome rearrangements in adaptation, speciation, and the etiology of inherited and spontaneously occurring diseases., Competing Interests: The authors declare no conflict of interest.
- Published
- 2017
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134. Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax.
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Fang X, Nevo E, Han L, Levanon EY, Zhao J, Avivi A, Larkin D, Jiang X, Feranchuk S, Zhu Y, Fishman A, Feng Y, Sher N, Xiong Z, Hankeln T, Huang Z, Gorbunova V, Zhang L, Zhao W, Wildman DE, Xiong Y, Gudkov A, Zheng Q, Rechavi G, Liu S, Bazak L, Chen J, Knisbacher BA, Lu Y, Shams I, Gajda K, Farré M, Kim J, Lewin HA, Ma J, Band M, Bicker A, Kranz A, Mattheus T, Schmidt H, Seluanov A, Azpurua J, McGowen MR, Ben Jacob E, Li K, Peng S, Zhu X, Liao X, Li S, Krogh A, Zhou X, Brodsky L, and Wang J
- Published
- 2015
- Full Text
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135. Comparative genomics reveals insights into avian genome evolution and adaptation.
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Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Jarvis ED, Gilbert MT, and Wang J
- Subjects
- Adaptation, Physiological, Animals, Biodiversity, Birds classification, Birds physiology, Conserved Sequence, Diet, Female, Flight, Animal, Genes, Genetic Variation, Genomics, Male, Molecular Sequence Annotation, Phylogeny, Reproduction genetics, Selection, Genetic, Sequence Analysis, DNA, Synteny, Vision, Ocular genetics, Vocalization, Animal, Biological Evolution, Birds genetics, Evolution, Molecular, Genome
- Abstract
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits., (Copyright © 2014, American Association for the Advancement of Science.)
- Published
- 2014
- Full Text
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