385 results on '"Mendoza, Alex"'
Search Results
202. Acknowledgments
- Author
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Woodworth, Steven E., Lundberg, John R., Mendoza, Alexander, Powell, David, Rafuse, Ethan S., and Robertson, William G.
- Published
- 2010
203. Machinations in the Confederate High Command: Gen. Braxton Bragg and his Campaign to Discredit Lt. Gen. James Longstreet.
- Author
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Mendoza, Alex
- Abstract
The article discusses conflicts between Confederate general Braxton Bragg and Confederate lieutenant general James Longstreet during the U.S. Civil War. Bragg used his influence to hamper Longstreet's command due to Longstreet's opposition to Bragg following the battle of Chickamauga, Georgia. Longstreet's troops were transferred to Tennessee, where they received insufficient transportation and support to attack Knoxville, Tennessee. Longstreet later brought charges against generals Evander Law and Lafayette McLaws.
- Published
- 2009
204. Analysis of Membrane Proteins from Human Chronic Myelogenous Leukemia Cells: Comparison of Extraction Methods for Multidimensional LC−MS/MS
- Author
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C. Ruth, Mariah, M. Old, William, A. Emrick, Michelle, Meyer-Arendt, Karen, D. Aveline-Wolf, Lauren, G. Pierce, Kevin, M. Mendoza, Alex, R. Sevinsky, Joel, Hamady, Micah, D. Knight, Robin, A. Resing, Katheryn, and G. Ahn, Natalie
- Abstract
An important strategy for “shotgun proteomics” profiling involves solution proteolysis of proteins, followed by peptide separation using multidimensional liquid chromatography and automated sequencing by mass spectrometry (LC−MS/MS). Several protocols for extracting and handling membrane proteins for shotgun proteomics experiments have been reported, but few direct comparisons of different protocols have been reported. We compare four methods for preparing membrane proteins from human cells, using acid labile surfactants (ALS), urea, and mixed organic-aqueous solvents. These methods were compared with respect to their efficiency of protein solubilization and proteolysis, peptide and protein recovery, membrane protein enrichment, and peptide coverage of transmembrane proteins. Overall, ∼50−60% of proteins recovered were membrane-associated, identified from Gene Ontology annotations and transmembrane prediction software. Samples extracted with ALS, extracted with urea followed by dilution, or extracted with urea followed by desalting yielded comparable peptide recoveries and sequence coverage of transmembrane proteins. In contrast, suboptimal proteolysis was observed with organic solvent. Urea extraction followed by desalting may be a particularly useful approach, as it is less costly than ALS and yields satisfactory protein denaturation and proteolysis under conditions that minimize reactivity with urea-derived cyanate. Spectral counting was used to compare datasets of proteins from membrane samples with those of soluble proteins from K562 cells, and to estimate fold differences in protein abundances. Proteins most highly abundant in the membrane samples showed enrichment of integral membrane protein identifications, consistent with their isolation by differential centrifugation. Keywords: mass spectrometry • leukemia • membrane proteins • urea • acid labile surfactant
- Published
- 2006
- Full Text
- View/download PDF
205. “For Our Own Best Interests”: Nineteenth-Century Laredo Tejanos, Military Service, and the Development of American Nationalism
- Author
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Mendoza, Alexander
- Published
- 2011
- Full Text
- View/download PDF
206. DNA methylation enables recurrent endogenization of giant viruses in an animal relative.
- Author
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Sarre, Luke A., Kim, Iana V., Ovchinnikov, Vladimir, Olivetta, Marine, Hiroshi Suga, Dudin, Omaya, Sebé-Pedrós, Arnau, and de Mendoza, Alex
- Subjects
- *
DNA methylation , *EUKARYOTIC genomes , *VIRAL DNA , *GENETIC regulation , *METHYLCYTOSINE , *MICROSATELLITE repeats , *DNA insertion elements - Abstract
5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention and its genomic consequences are still poorly understood. Here, we show that the protist closely related to animals Amoebidium appalachense features both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. Unexpectedly, hypermethylated genomic regions in Amoebidium derive from viral insertions, including hundreds of endogenized giant viruses, contributing 14% of the proteome. Using a combination of inhibitors and genomic assays, we demonstrate that 5mC silences these giant virus insertions. Moreover, alternative Amoebidium isolates show polymorphic giant virus insertions, highlighting a dynamic process of infection, endogenization, and purging. Our results indicate that 5mC is critical for the controlled coexistence of newly acquired viral DNA into eukaryotic genomes, making Amoebidium a unique model to understand the hybrid origins of eukaryotic DNA. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
207. Lincoln's Tragic Admiral: The Life of Samuel Francis Du Pont (review)
- Author
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Mendoza, Alexander
- Published
- 2007
- Full Text
- View/download PDF
208. Modelo prolab: Enguan, una propuesta de solución para mejorar el servicio de transporte público en rutas cortas
- Author
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Bustamante Gongora, Josselyn, Longa Cruzado, Jens Hans, Paredes Bullon, David Eduardo, Nuñez Mendoza, Alex Manuel, Bustamante Gongora, Josselyn, Longa Cruzado, Jens Hans, Paredes Bullon, David Eduardo, and Nuñez Mendoza, Alex Manuel
- Abstract
Lima es una ciudad con problemas de transporte, y para revertir este escenario, las autoridades implementan mejoras tales como buses alimentadores, corredores, trenes, construcción de pistas, etc. Sin embargo, según la percepción de los pasajeros respecto al transporte público para rutas cortas, este les genera una mala experiencia de viaje debido a la inseguridad, informalidad, mal trato, desorden, suciedad e incomodidad. Por lo tanto, se identificó una oportunidad de mejora, es decir, una propuesta capaz de lograr que la experiencia de viaje del pasajero sea placentera. El proceso que se siguió para abordar la problemática fue un modelo de design thinking, iniciando por la fase de empatía que permitió conocer el dolor del pasajero al usar transporte público, y nos llevó a detectar una necesidad a resolver. La propuesta de solución fue planteada mediante iteraciones a partir de la construcción de un mapa de propuesta de valor centrado en el pasajero como usuario. Luego se validaron las hipótesis de deseabilidad obteniendo que casi el 70% si estuviera dispuesto a pagar la suscripción mensual, y que el 85% accedería al descuento de la membresía a cambio de llevar publicidad al interior de su unidad de transporte. En el caso de la factibilidad, dio como resultado una probabilidad de 85.68% de que el plan de marketing tenga éxito de lograr un ratio de 10.03, y una probabilidad del 73.56% de cumplir con un tiempo menor a 90 segundos para el proceso de solicitar una unidad de transporte. Enguan ofrece un servicio de transporte público para rutas cortas a través de un aplicativo móvil, que conectará a los pasajeros con los conductores de mototaxis, con el objetivo de mejorar el transporte público para rutas cortas en los conos de Lima. El IRS de Enguan es 80% a partir de los impactos en los ODS 9 y 11. Para la ejecución de la propuesta, se requiere de una inversión de 298,580.30 USD la misma que en un horizonte de 5 años, generará un VAN de 1,186,364.12 USD, un periodo de, Lima is a city with transportation problems, and to reverse this scenario, the authorities implement improvements such as feeder buses, corridors, trains, construction of tracks, etc. However, according to the perception of passengers regarding public transport for short routes, this generates a bad travel experience due to insecurity, informality, poor treatment, disorder, dirt and discomfort. Therefore, an opportunity for improvement was identified, that is, a proposal capable of making the passenger's travel experience a pleasant one. The process followed to address the problem was a design thinking model, starting with the empathy phase that allowed us to know the passenger's pain when using public transport, and led us to detect a need to solve. The solution proposal was proposed through iterations based on the construction of a value proposition map focused on the passenger as user. Then the desirability hypotheses were validated, obtaining that almost 70% if they were willing to pay the monthly subscription, and that 85% would access the membership discount in exchange for bringing advertising inside their transportation unit. In the case of feasibility, it resulted in an 85.68% probability that the marketing plan will be successful in achieving a ratio of 10.03, and a 73.56% probability of meeting a time of less than 90 seconds for the request process. a transport unit. Enguan offers a public transport service for short routes through a mobile application, which will connect passengers with motorcycle taxi drivers, with the aim of improving public transport for short routes in the cones of Lima. Enguan's IRS is 80% based on the impacts on SDG 9 and 11. For the execution of the proposal, an investment of USD 298,580.30 is required, the same as in a 5-year horizon, it will generate a NPV of USD 1,186,364.12, a payback period of 2.79 years and an average EBITDA of 34.47%. Enguan's social profitability is positive, due to its social NPV of 407.18 M USD.
209. Modelo prolab: Enguan, una propuesta de solución para mejorar el servicio de transporte público en rutas cortas
- Author
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Bustamante Gongora, Josselyn, Longa Cruzado, Jens Hans, Paredes Bullon, David Eduardo, Nuñez Mendoza, Alex Manuel, Bustamante Gongora, Josselyn, Longa Cruzado, Jens Hans, Paredes Bullon, David Eduardo, and Nuñez Mendoza, Alex Manuel
- Abstract
Lima es una ciudad con problemas de transporte, y para revertir este escenario, las autoridades implementan mejoras tales como buses alimentadores, corredores, trenes, construcción de pistas, etc. Sin embargo, según la percepción de los pasajeros respecto al transporte público para rutas cortas, este les genera una mala experiencia de viaje debido a la inseguridad, informalidad, mal trato, desorden, suciedad e incomodidad. Por lo tanto, se identificó una oportunidad de mejora, es decir, una propuesta capaz de lograr que la experiencia de viaje del pasajero sea placentera. El proceso que se siguió para abordar la problemática fue un modelo de design thinking, iniciando por la fase de empatía que permitió conocer el dolor del pasajero al usar transporte público, y nos llevó a detectar una necesidad a resolver. La propuesta de solución fue planteada mediante iteraciones a partir de la construcción de un mapa de propuesta de valor centrado en el pasajero como usuario. Luego se validaron las hipótesis de deseabilidad obteniendo que casi el 70% si estuviera dispuesto a pagar la suscripción mensual, y que el 85% accedería al descuento de la membresía a cambio de llevar publicidad al interior de su unidad de transporte. En el caso de la factibilidad, dio como resultado una probabilidad de 85.68% de que el plan de marketing tenga éxito de lograr un ratio de 10.03, y una probabilidad del 73.56% de cumplir con un tiempo menor a 90 segundos para el proceso de solicitar una unidad de transporte. Enguan ofrece un servicio de transporte público para rutas cortas a través de un aplicativo móvil, que conectará a los pasajeros con los conductores de mototaxis, con el objetivo de mejorar el transporte público para rutas cortas en los conos de Lima. El IRS de Enguan es 80% a partir de los impactos en los ODS 9 y 11. Para la ejecución de la propuesta, se requiere de una inversión de 298,580.30 USD la misma que en un horizonte de 5 años, generará un VAN de 1,186,364.12 USD, un periodo de, Lima is a city with transportation problems, and to reverse this scenario, the authorities implement improvements such as feeder buses, corridors, trains, construction of tracks, etc. However, according to the perception of passengers regarding public transport for short routes, this generates a bad travel experience due to insecurity, informality, poor treatment, disorder, dirt and discomfort. Therefore, an opportunity for improvement was identified, that is, a proposal capable of making the passenger's travel experience a pleasant one. The process followed to address the problem was a design thinking model, starting with the empathy phase that allowed us to know the passenger's pain when using public transport, and led us to detect a need to solve. The solution proposal was proposed through iterations based on the construction of a value proposition map focused on the passenger as user. Then the desirability hypotheses were validated, obtaining that almost 70% if they were willing to pay the monthly subscription, and that 85% would access the membership discount in exchange for bringing advertising inside their transportation unit. In the case of feasibility, it resulted in an 85.68% probability that the marketing plan will be successful in achieving a ratio of 10.03, and a 73.56% probability of meeting a time of less than 90 seconds for the request process. a transport unit. Enguan offers a public transport service for short routes through a mobile application, which will connect passengers with motorcycle taxi drivers, with the aim of improving public transport for short routes in the cones of Lima. Enguan's IRS is 80% based on the impacts on SDG 9 and 11. For the execution of the proposal, an investment of USD 298,580.30 is required, the same as in a 5-year horizon, it will generate a NPV of USD 1,186,364.12, a payback period of 2.79 years and an average EBITDA of 34.47%. Enguan's social profitability is positive, due to its social NPV of 407.18 M USD.
210. From Coveralls to Zoot Suits: The Lives of Mexican American Women on the World War II Home Front by Elizabeth R. Escobedo (review)
- Author
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Mendoza, Alexander
- Published
- 2014
- Full Text
- View/download PDF
211. Adenine DNA methylation associated to transcription is widespread across eukaryotes
- Author
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Mendoza, Alex de, primary, Charria, Pedro Romero, primary, Shabardina, Victoria, primary, and Casacuberta, Elena, primary
- Full Text
- View/download PDF
212. Fort Concho: A History and a Guide (review)
- Author
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Mendoza, Alexander
- Published
- 2006
- Full Text
- View/download PDF
213. Braxton Bragg: The Most Hated Man in the Confederacy.
- Author
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MENDOZA, ALEX
- Published
- 2017
214. Bowled Over: Big-Time College Football from the Sixties to the BCS Era.
- Author
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Mendoza, Alex
- Abstract
A review of the book "Bowled Over: Big-Time College Football From the Sixties to the BCS Era," by Michael Oriard is presented.
- Published
- 2011
215. Improving Sensitivity in Shotgun Proteomics Using a Peptide-Centric Database with Reduced Complexity: Protease Cleavage and SCX Elution Rules from Data Mining of MS/MS Spectra.
- Author
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Chia-Yu Yen, Russell, Steve, Mendoza, Alex M., Meyer-Arendt, Karen, Shaojun Sun, Cios, Krzysztof J., Ahn, Natalie G., and Resing, Katheryn A.
- Subjects
- *
PROTEOMICS , *MOLECULAR biology , *EUKARYOTIC cells , *PROTEINS , *PROTEOLYSIS , *LEUCINE aminopeptidase , *PEPTIDES , *CHROMATOGRAPHIC analysis , *ION exchange (Chemistry) - Abstract
Correct identification of a peptide sequence from MS/MS data is still a challenging research problem, particularly in proteomic analyses of higher eukaryotes where protein databases are large. The scoring methods of search programs often generate cases where incorrect peptide sequences score higher than correct peptide sequences (referred to as distraction). Because smaller databases yield less distraction and better discrimination between correct and incorrect assignments, we developed a method for editing a peptide-centric database (PC-DB) to remove unlikely sequences and strategies for enabling search programs to utilize this peptide database. Rules for unlikely missed cleavage and nontryptic proteolysis products were identified by data mining 11 849 high-confidence peptide assignments. We also evaluated ion exchange chromatographic behavior as an editing criterion to generate subset databases. When used to search a well- annotated test data set of MS/MS spectra, we found no loss of critical information using PC-DBs, validating the methods for generating and searching against the databases. On the other hand, improved confidence in peptide assignments was achieved for tryptic peptides, measured by changes in ΔCN and RSP. Decreased distraction was also achieved, consistent with the 3-9-fold decrease in database size. Data mining identified a major class of common nonspecific proteolytic products corresponding to leucine aminopeptidase (LAP) cleavages. Large improvements in identifying LAP products were achieved using the PC-DB approach when compared with conventional searches against protein databases. These results demonstrate that peptide properties can be used to reduce database size, yielding improved accuracy and information capture due to reduced distraction, but with little loss of information compared to conventional protein database searches. [ABSTRACT FROM AUTHOR]
- Published
- 2006
- Full Text
- View/download PDF
216. Fighting Stock: John S. "Rip" Ford of Texas.
- Author
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Mendoza, Alex
- Abstract
A review of the book "Fighting Stock: John S. "Rip" Ford of Texas," which is part of the Texas Biography Series, no. 3, by Richard B. McCaslin is presented.
- Published
- 2012
217. Texas Devils: Rangers and Regulators on the Lower Rio Grande, 1846-1861.
- Author
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Mendoza, Alex
- Subjects
- *
NONFICTION , *HISTORY - Abstract
The article reviews the book "Texas Devils: Rangers and Regulators on the Lower Rio Grande, 1846-1861" by Michael L. Collins.
- Published
- 2010
218. Audacity Personified: The Generalship of Robert E. Lee.
- Author
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Mendoza, Alex
- Subjects
- *
ARMY officers , *NONFICTION - Abstract
Reviews the book "Audacity Personified: The Generalship of Robert E. Lee," edited by Peter Carmichael.
- Published
- 2005
219. The Making of Robert E. Lee.
- Author
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Mendoza, Alex
- Subjects
- *
ARMY officers , *NONFICTION - Abstract
Reviews the book "The Making of Robert E. Lee," by Michael Fellman.
- Published
- 2005
220. Decided on the Battlefield: Grant, Sherman, Lincoln, and the Election of 1864.
- Author
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MENDOZA, ALEX
- Subjects
- *
NONFICTION ,UNITED States presidential election, 1864 - Abstract
The article reviews the book "Decided on the Battlefield: Grant, Sherman, Lincoln, and the Election of 1864," by David Alan Johnson.
- Published
- 2012
221. Talking about living and dying with the oldest old: public involvement in a study on end of life care in care homes.
- Author
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Goodman, Claire, Mathie, Elspeth, Cowe, Marion, Mendoza, Alex, Westwood, Daphne, Munday, Diane, Wilson, Patricia M, Crang, Clare, Foggatt, Katherine, Illiffe, Steve, Mathorpe, Jill, Gage, Heather, and Barclay, Stephen
- Published
- 2011
222. Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria.
- Author
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Guynes K, Sarre LA, Carrillo-Baltodano AM, Davies BE, Xu L, Liang Y, Martín-Zamora FM, Hurd PJ, de Mendoza A, and Martín-Durán JM
- Subjects
- Animals, Annelida genetics, Phylogeny, Epigenome, 5-Methylcytosine metabolism, DNA Transposable Elements, Evolution, Molecular, DNA Methylation, Epigenesis, Genetic, Aging genetics
- Abstract
Background: DNA methylation in the form of 5-methylcytosine (5mC) is the most abundant base modification in animals. However, 5mC levels vary widely across taxa. While vertebrate genomes are hypermethylated, in most invertebrates, 5mC concentrates on constantly and highly transcribed genes (gene body methylation; GbM) and, in some species, on transposable elements (TEs), a pattern known as "mosaic". Yet, the role and developmental dynamics of 5mC and how these explain interspecies differences in DNA methylation patterns remain poorly understood, especially in Spiralia, a large clade of invertebrates comprising nearly half of the animal phyla., Results: Here, we generate base-resolution methylomes for three species with distinct genomic features and phylogenetic positions in Annelida, a major spiralian phylum. All possible 5mC patterns occur in annelids, from typical invertebrate intermediate levels in a mosaic distribution to hypermethylation and methylation loss. GbM is common to annelids with 5mC, and methylation differences across species are explained by taxon-specific transcriptional dynamics or the presence of intronic TEs. Notably, the link between GbM and transcription decays during development, alongside a gradual and global, age-dependent demethylation in adult stages. Additionally, reducing 5mC levels with cytidine analogs during early development impairs normal embryogenesis and reactivates TEs in the annelid Owenia fusiformis., Conclusions: Our study indicates that global epigenetic erosion during development and aging is an ancestral feature of bilateral animals. However, the tight link between transcription and gene body methylation is likely more important in early embryonic stages, and 5mC-mediated TE silencing probably emerged convergently across animal lineages., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
223. Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons.
- Author
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Dossmann L, Emperle M, Dukatz M, de Mendoza A, Bashtrykov P, and Jeltsch A
- Subjects
- Animals, Mice, CpG Islands, DNA (Cytosine-5-)-Methyltransferases genetics, DNA (Cytosine-5-)-Methyltransferases metabolism, DNA Methylation, Retroelements genetics
- Abstract
The DNA methyltransferase DNMT3C appeared as a duplication of the DNMT3B gene in muroids and is required for silencing of young retrotransposons in the male germline. Using specialized assay systems, we investigate the flanking sequence preferences of DNMT3C and observe characteristic preferences for cytosine at the -2 and -1 flank that are unique among DNMT3 enzymes. We identify two amino acids in the catalytic domain of DNMT3C (C543 and V547) that are responsible for the DNMT3C-specific flanking sequence preferences and evolutionary conserved in muroids. Reanalysis of published data shows that DNMT3C flanking preferences are consistent with genome-wide methylation patterns in mouse ES cells only expressing DNMT3C. Strikingly, we show that CpG sites with the preferred flanking sequences of DNMT3C are enriched in murine retrotransposons that were previously identified as DNMT3C targets. Finally, we demonstrate experimentally that DNMT3C has elevated methylation activity on substrates derived from these biological targets. Our data show that DNMT3C flanking sequence preferences match the sequences of young murine retrotransposons which facilitates their methylation. By this, our data provide mechanistic insights into the molecular co-evolution of repeat elements and (epi)genetic defense systems dedicated to maintain genomic stability in mammals., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
224. Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.
- Author
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Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Sato I, Wan W, Clark JW, Keating JN, Carlisle EM, Dearden RP, Giles S, Randle E, Sansom RS, Feuda R, Fleming JF, Sugahara F, Cummins C, Patricio M, Akanni W, D'Aniello S, Bertolucci C, Irie N, Alev C, Sheng G, de Mendoza A, Maeso I, Irimia M, Fromm B, Peterson KJ, Das S, Hirano M, Rast JP, Cooper MD, Paps J, Pisani D, Kuratani S, Martin FJ, Wang W, Donoghue PCJ, Zhang YE, and Pascual-Anaya J
- Subjects
- Animals, Phylogeny, Gene Duplication, Vertebrates genetics, Genome, Lampreys genetics, Hagfishes genetics
- Abstract
Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and 2R occurred in the gnathostome stem-lineage, maximally in the late Cambrian-earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced an additional independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only in the gnathostome but not in the cyclostome lineage, calling into question the general expectation that WGDs lead to leaps of bodyplan complexity., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
225. Vascular smooth muscle cell mechanotransduction through serum and glucocorticoid inducible kinase-1 promotes interleukin-6 production and macrophage accumulation in murine hypertension.
- Author
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Figueroa M, Hall S, Mattia V, Mendoza A, Brown A, Xiong Y, Mukherjee R, Jones JA, Richardson W, and Ruddy JM
- Abstract
Objective: The objective of this investigation was to demonstrate that in vivo induction of hypertension (HTN) and in vitro cyclic stretch of aortic vascular smooth muscle cells (VSMCs) can cause serum and glucocorticoid-inducible kinase (SGK-1)-dependent production of cytokines to promote macrophage accumulation that may promote vascular pathology., Methods: HTN was induced in C57Bl/6 mice with angiotensin II infusion (1.46 mg/kg/day × 21 days) with or without systemic infusion of EMD638683 (2.5 mg/kg/day × 21 days), a selective SGK-1 inhibitor. Systolic blood pressure was recorded. Abdominal aortas were harvested to quantify SGK-1 activity (pSGK-1/SGK-1) by immunoblot. Flow cytometry quantified the abundance of CD11b
+ /F480+ cells (macrophages). Plasma interleukin (IL)-6 and monocyte chemoattractant protein-1 (MCP-1) was assessed by enzyme-linked immunosorbent assay. Aortic VSMCs from wild-type mice were subjected to 12% biaxial cyclic stretch (Stretch) for 3 or 12 hours with or without EMD638683 (10 μM) and with or without SGK-1 small interfering RNA with subsequent quantitative polymerase chain reaction for IL-6 and MCP-1 expression. IL-6 and MCP-1 in culture media were analyzed by enzyme-linked immunosorbent assay. Aortic VSMCs from SGK-1flox+/+ mice were transfected with Cre-Adenovirus to knockdown SGK-1 (SGK-1KD VSMCs) and underwent parallel tension experimentation. Computational modeling was used to simulate VSMC signaling. Statistical analysis included analysis of variance with significance at a P value of <.05., Results: SGK-1 activity, abundance of CD11b+ /F4-80+ cells, and plasma IL-6 were increased in the abdominal aorta of mice with HTN and significantly reduced by treatment with EMD638683. This outcome mirrored the increased abundance of IL-6 in media from Stretch C57Bl/6 VSMCs and attenuation of the effect with EMD638683 or SGK-1 small interfering RNA. C57Bl/6 VSMCs also responded to Stretch with increased MCP-1 expression and secretion into the culture media. Further supporting the integral role of mechanical signaling through SGK-1, target gene expression and cytokine secretion was unchanged in SGK-1KD VSMCs with Stretch, and computer modeling confirmed SGK-1 as an intersecting node of signaling owing to mechanical strain and angiotensin II., Conclusions: Mechanical activation of SGK-1 in aortic VSMCs can promote inflammatory signaling and increased macrophage abundance, therefore this kinase warrants further exploration as a pharmacotherapeutic target to abrogate hypertensive vascular pathology., Competing Interests: J.M.R. is a surgical proctor for CVRx, outside the scope of the submitted work.- Published
- 2023
- Full Text
- View/download PDF
226. A mammalian DNA methylation landscape.
- Author
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de Mendoza A
- Subjects
- Animals, DNA Methylation, Mammals genetics, Longevity genetics
- Abstract
A study of 348 species offers clues into the diversity of mammalian life spans.
- Published
- 2023
- Full Text
- View/download PDF
227. Transient naive reprogramming corrects hiPS cells functionally and epigenetically.
- Author
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Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, Faulkner GJ, Nefzger CM, Polo JM, and Lister R
- Subjects
- Humans, Chromatin genetics, Chromatin metabolism, DNA Demethylation, DNA Methylation, DNA Transposable Elements, Human Embryonic Stem Cells cytology, Human Embryonic Stem Cells metabolism, Lamin Type B, Cellular Reprogramming, Epigenesis, Genetic, Induced Pluripotent Stem Cells cytology, Induced Pluripotent Stem Cells metabolism
- Abstract
Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function
1-8 . These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory., (© 2023. The Author(s).)- Published
- 2023
- Full Text
- View/download PDF
228. DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation.
- Author
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Dukatz M, Dittrich M, Stahl E, Adam S, de Mendoza A, Bashtrykov P, and Jeltsch A
- Subjects
- CpG Islands, DNA chemistry, DNA metabolism, DNA Modification Methylases genetics, Guanine, Mutation, DNA Methylation, DNA Methyltransferase 3A
- Abstract
Specific DNA methylation at CpG and non-CpG sites is essential for chromatin regulation. The DNA methyltransferase DNMT3A interacts with target sites surrounded by variable DNA sequences with its TRD and RD loops, but the functional necessity of these interactions is unclear. We investigated CpG and non-CpG methylation in a randomized sequence context using WT DNMT3A and several DNMT3A variants containing mutations at DNA-interacting residues. Our data revealed that the flanking sequence of target sites between the -2 and up to the +8 position modulates methylation rates >100-fold. Non-CpG methylation flanking preferences were even stronger and favor C(+1). R836 and N838 in concert mediate recognition of the CpG guanine. R836 changes its conformation in a flanking sequence-dependent manner and either contacts the CpG guanine or the +1/+2 flank, thereby coupling the interaction with both sequence elements. R836 suppresses activity at CNT sites but supports methylation of CAC substrates, the preferred target for non-CpG methylation of DNMT3A in cells. N838 helps to balance this effect and prevent the preference for C(+1) from becoming too strong. Surprisingly, we found L883 reduces DNMT3A activity despite being highly conserved in evolution. However, mutations at L883 disrupt the DNMT3A-specific DNA interactions of the RD loop, leading to altered flanking sequence preferences. Similar effects occur after the R882H mutation in cancer cells. Our data reveal that DNMT3A forms flexible and interdependent interaction networks with the CpG guanine and flanking residues that ensure recognition of the CpG and efficient methylation of the cytosine in contexts of variable flanking sequences., Competing Interests: Conflict of interest The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2022
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229. Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.
- Author
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de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, and Lister R
- Subjects
- Chromatin, CpG Islands, DNA metabolism, Humans, Promoter Regions, Genetic, Transcription Factors metabolism, DNA (Cytosine-5-)-Methyltransferases genetics, DNA (Cytosine-5-)-Methyltransferases metabolism, DNA Methylation
- Abstract
Background: Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA methylation on endogenous promoters; however, the downstream effects have not yet been comprehensively assessed., Results: Here, we simultaneously induce methylation at thousands of promoters in human cells using an engineered zinc finger-DNMT3A fusion protein, enabling us to test the effect of forced DNA methylation upon transcription, chromatin accessibility, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that transcriptional responses to DNA methylation are highly context-specific, including lack of repression, as well as cases of increased gene expression, which appears to be driven by the eviction of methyl-sensitive transcriptional repressors. Furthermore, we find that some regulatory networks can override DNA methylation and that promoter methylation can cause alternative promoter usage. DNA methylation deposited at promoter and distal regulatory regions is rapidly erased after removal of the zinc finger-DNMT3A fusion protein, in a process combining passive and TET-mediated demethylation. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II., Conclusions: These findings have important implications for epigenome engineering and demonstrate that the response of promoters to DNA methylation is more complex than previously appreciated., (© 2022. The Author(s).)
- Published
- 2022
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230. Reporting on patient and public involvement (PPI) in research publications: using the GRIPP2 checklists with lay co-researchers.
- Author
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Jones J, Cowe M, Marks S, McAllister T, Mendoza A, Ponniah C, Wythe H, and Mathie E
- Abstract
Background: Patient and public involvement (PPI) in health and social care research is considered important internationally, with increasing evidence that PPI improves the quality, relevance and outcomes of research. There has been a growth in research publications that describe PPI in the research process, but the frequency and detail of PPI reporting varies considerably. This paper reports on a collaborative study that aimed to describe the extent of PPI in publications from research funded by the Collaboration for Leadership in Applied Health Research and Care (CLAHRC) in the East of England (EoE), part of the National Institute of Health Research (NIHR) in England (2014-2019)., Methods: A descriptive study of all research publications (1st January 2014 to 31st October 2017) funded by the NIHR CLAHRC EoE. Members of the Public Involvement in Research group (PIRg), at the University of Hertfordshire, were actively involved, with four PIRg co-researchers. We used an internationally recognised reporting checklist for PPI called the GRIPP2 (Guidance for Reporting Involvement of Patients and the Public, Version 2) to guide the reviewing process., Results: Out of 148 research papers identified, 16 (14%) reported some aspect of PPI activity and were included for review. Ten of the publications (63%) acknowledged the contributions of PPI individuals and/or groups and five had PPI co-authors. There was considerable variation in the PPI reported in the publications, with some 'missed opportunities' to provide detail of PPI undertaken. The perspectives of the co-researchers shaped the reporting of the results from this study. The co-researchers found the GRIPP2-SF (short form) to be useful, but the GRIPP2-LF (long form) was considered over complicated and not user-friendly., Conclusions: This is one of the first studies to involve lay co-researchers in the review of PPI reporting using the GRIPP2 reporting checklists (GRIPP2-SF and GRIPP2-LF). We make recommendations for a revised version of the GRIPP2-SF, with clearer instructions and three additional sections to record whether PPI is reported in the abstract or key words, in the acknowledgements section, and whether there are PPI co-authors. We also recommend the provision of training and support for patient and public peer reviewers., (© 2021. The Author(s).)
- Published
- 2021
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231. The emergence of the brain non-CpG methylation system in vertebrates.
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de Mendoza A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustienes E, Gómez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, Venkatesh B, Bogdanovic O, and Lister R
- Subjects
- Animals, Brain metabolism, Genome, Vertebrates genetics, DNA Methylation, Methyl-CpG-Binding Protein 2 genetics, Methyl-CpG-Binding Protein 2 metabolism
- Abstract
Mammalian brains feature exceptionally high levels of non-CpG DNA methylation alongside the canonical form of CpG methylation. Non-CpG methylation plays a critical regulatory role in cognitive function, which is mediated by the binding of MeCP2, the transcriptional regulator that when mutated causes Rett syndrome. However, it is unclear whether the non-CpG neural methylation system is restricted to mammalian species with complex cognitive abilities or has deeper evolutionary origins. To test this, we investigated brain DNA methylation across 12 distantly related animal lineages, revealing that non-CpG methylation is restricted to vertebrates. We discovered that in vertebrates, non-CpG methylation is enriched within a highly conserved set of developmental genes transcriptionally repressed in adult brains, indicating that it demarcates a deeply conserved regulatory program. We also found that the writer of non-CpG methylation, DNMT3A, and the reader, MeCP2, originated at the onset of vertebrates as a result of the ancestral vertebrate whole-genome duplication. Together, we demonstrate how this novel layer of epigenetic information assembled at the root of vertebrates and gained new regulatory roles independent of the ancestral form of the canonical CpG methylation. This suggests that the emergence of non-CpG methylation may have fostered the evolution of sophisticated cognitive abilities found in the vertebrate lineage.
- Published
- 2021
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232. Developmental remodelling of non-CG methylation at satellite DNA repeats.
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Ross SE, Angeloni A, Geng FS, de Mendoza A, and Bogdanovic O
- Subjects
- Animals, Blastocyst metabolism, Embryonic Stem Cells metabolism, Heterochromatin, Histones genetics, Mosaicism, Repetitive Sequences, Nucleic Acid genetics, Zebrafish genetics, Zebrafish growth & development, DNA (Cytosine-5-)-Methyltransferases genetics, DNA Methylation genetics, DNA, Satellite genetics, Protein Processing, Post-Translational genetics, Zebrafish Proteins genetics
- Abstract
In vertebrates, DNA methylation predominantly occurs at CG dinucleotides however, widespread non-CG methylation (mCH) has been reported in mammalian embryonic stem cells and in the brain. In mammals, mCH is found at CAC trinucleotides in the nervous system, where it is associated with transcriptional repression, and at CAG trinucleotides in embryonic stem cells, where it positively correlates with transcription. Moreover, CAC methylation appears to be a conserved feature of adult vertebrate brains. Unlike any of those methylation signatures, here we describe a novel form of mCH that occurs in the TGCT context within zebrafish mosaic satellite repeats. TGCT methylation is inherited from both male and female gametes, remodelled during mid-blastula transition, and re-established during gastrulation in all embryonic layers. Moreover, we identify DNA methyltransferase 3ba (Dnmt3ba) as the primary enzyme responsible for the deposition of this mCH mark. Finally, we observe that TGCT-methylated repeats are specifically associated with H3K9me3-marked heterochromatin suggestive of a functional interplay between these two gene-regulatory marks. Altogether, this work provides insight into a novel form of vertebrate mCH and highlights the substrate diversity of vertebrate DNA methyltransferases., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2020
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233. Towards understanding the origin of animal development.
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Ruiz-Trillo I and de Mendoza A
- Subjects
- Animals, Choanoflagellata genetics, Gene Expression Regulation, Developmental genetics, Mammals genetics, Phylogeny, Zygote growth & development, Biological Evolution, Choanoflagellata growth & development, Embryonic Development genetics, Morphogenesis genetics
- Abstract
Almost all animals undergo embryonic development, going from a single-celled zygote to a complex multicellular adult. We know that the patterning and morphogenetic processes involved in development are deeply conserved within the animal kingdom. However, the origins of these developmental processes are just beginning to be unveiled. Here, we focus on how the protist lineages sister to animals are reshaping our view of animal development. Most intriguingly, many of these protistan lineages display transient multicellular structures, which are governed by similar morphogenetic and gene regulatory processes as animal development. We discuss here two potential alternative scenarios to explain the origin of animal embryonic development: either it originated concomitantly at the onset of animals or it evolved from morphogenetic processes already present in their unicellular ancestors. We propose that an integrative study of several unicellular taxa closely related to animals will allow a more refined picture of how the last common ancestor of animals underwent embryonic development., (© 2020. Published by The Company of Biologists Ltd.)
- Published
- 2020
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234. Author Correction: Enteric neurons increase maternal food intake during reproduction.
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Hadjieconomou D, King G, Gaspar P, Mineo A, Blackie L, Ameku T, Studd C, de Mendoza A, Diao F, White BH, Brown AEX, Plaçais PY, Préat T, and Miguel-Aliaga I
- Published
- 2020
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235. Enteric neurons increase maternal food intake during reproduction.
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Hadjieconomou D, King G, Gaspar P, Mineo A, Blackie L, Ameku T, Studd C, de Mendoza A, Diao F, White BH, Brown AEX, Plaçais PY, Préat T, and Miguel-Aliaga I
- Subjects
- Animal Structures cytology, Animal Structures innervation, Animal Structures metabolism, Animals, Appetite Regulation physiology, Female, Hyperphagia metabolism, Male, Neuropeptides metabolism, Drosophila melanogaster cytology, Drosophila melanogaster physiology, Eating physiology, Energy Intake physiology, Mothers, Neurons metabolism, Reproduction physiology
- Abstract
Reproduction induces increased food intake across females of many animal species
1-4 , providing a physiologically relevant paradigm for the exploration of appetite regulation. Here, by examining the diversity of enteric neurons in Drosophila melanogaster, we identify a key role for gut-innervating neurons with sex- and reproductive state-specific activity in sustaining the increased food intake of mothers during reproduction. Steroid and enteroendocrine hormones functionally remodel these neurons, which leads to the release of their neuropeptide onto the muscles of the crop-a stomach-like organ-after mating. Neuropeptide release changes the dynamics of crop enlargement, resulting in increased food intake, and preventing the post-mating remodelling of enteric neurons reduces both reproductive hyperphagia and reproductive fitness. The plasticity of enteric neurons is therefore key to reproductive success. Our findings provide a mechanism to attain the positive energy balance that sustains gestation, dysregulation of which could contribute to infertility or weight gain.- Published
- 2020
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236. Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri.
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Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderón LA, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, Riesgo A, and Leys SP
- Subjects
- Adaptation, Physiological genetics, Animals, Epigenesis, Genetic, Fresh Water, Gene Expression Regulation, Developmental, Molecular Sequence Annotation, Phylogeny, Porifera growth & development, RNA-Seq, Sequence Analysis, DNA, Synteny, Chromosome Mapping, Chromosomes genetics, Evolution, Molecular, Porifera genetics
- Abstract
The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits, such as nervous systems, arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here, we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system which, with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range, allows exploration of genomic changes both within sponges and in early animal evolution.
- Published
- 2020
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237. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings.
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Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marlétaz F, Firbas PN, Feuda R, Masiero G, Medina P, Alcaina-Caro A, Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Vargas-Chavez C, Davie K, Misof B, González J, Aerts S, Lister R, Paps J, Rozas J, Sánchez-Gracia A, Irimia M, Maeso I, and Casares F
- Subjects
- Animals, Ephemeroptera classification, Ephemeroptera growth & development, Female, Gene Expression Regulation, Developmental, Genes, Insect genetics, Genome, Insect genetics, Gills, Insecta classification, Insecta genetics, Life Cycle Stages genetics, Male, Phylogeny, Adaptation, Physiological genetics, Ephemeroptera genetics, Evolution, Molecular, Wings, Animal
- Abstract
The evolution of winged insects revolutionized terrestrial ecosystems and led to the largest animal radiation on Earth. However, we still have an incomplete picture of the genomic changes that underlay this diversification. Mayflies, as one of the sister groups of all other winged insects, are key to understanding this radiation. Here, we describe the genome of the mayfly Cloeon dipterum and its gene expression throughout its aquatic and aerial life cycle and specific organs. We discover an expansion of odorant-binding-protein genes, some expressed specifically in breathing gills of aquatic nymphs, suggesting a novel sensory role for this organ. In contrast, flying adults use an enlarged opsin set in a sexually dimorphic manner, with some expressed only in males. Finally, we identify a set of wing-associated genes deeply conserved in the pterygote insects and find transcriptomic similarities between gills and wings, suggesting a common genetic program. Globally, this comprehensive genomic and transcriptomic study uncovers the genetic basis of key evolutionary adaptations in mayflies and winged insects.
- Published
- 2020
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238. Evolution of DNA Methylome Diversity in Eukaryotes.
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de Mendoza A, Lister R, and Bogdanovic O
- Abstract
Cytosine DNA methylation (5mC) is a widespread base modification in eukaryotic genomes with critical roles in transcriptional regulation. In recent years, our understanding of 5mC has changed because of advances in 5mC detection techniques that allow mapping of this mark on the whole genome scale. Profiling DNA methylomes from organisms across the eukaryotic tree of life has reshaped our views on the evolution of 5mC. In this review, we explore the macroevolution of 5mC in major eukaryotic groups, and then focus on recent advances made in animals. Genomic 5mC patterns as well as the mechanisms of 5mC deposition tend to be evolutionary labile across large phylogenetic distances; however, some common patterns are starting to emerge. Within the animal kingdom, 5mC diversity has proven to be much greater than anticipated. For example, a previously held common view that genome hypermethylation is a trait exclusive to vertebrates has recently been challenged. Also, data from genome-wide studies are starting to yield insights into the potential roles of 5mC in invertebrate cis regulation. Here we provide an evolutionary perspective of both the well-known and enigmatic roles of 5mC across the eukaryotic tree of life., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2020
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239. Origin and evolution of eukaryotic transcription factors.
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de Mendoza A and Sebé-Pedrós A
- Subjects
- DNA-Binding Proteins metabolism, Eukaryota metabolism, Genomics, Models, Genetic, Phylogeny, Protein Domains genetics, Transcription Factors metabolism, DNA-Binding Proteins genetics, Eukaryota genetics, Evolution, Molecular, Transcription Factors genetics
- Abstract
Transcription factors (TFs) have a central role in genome regulation directing gene transcription through binding specific DNA sequences. Eukaryotic genomes encode a large diversity of TF classes, each defined by unique DNA-interaction domains. Recent advances in genome sequencing and phylogenetic placement of diverse eukaryotic and archaeal species are re-defining the evolutionary history of eukaryotic TFs. The emerging view from a comparative genomics perspective is that the Last Eukaryotic Common Ancestor (LECA) had an extensive repertoire of TFs, most of which represent eukaryotic evolutionary novelties. This burst of TF innovation coincides with the emergence of genomic nuclear segregation and complex chromatin organization., (Copyright © 2019 Elsevier Ltd. All rights reserved.)
- Published
- 2019
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240. Convergent evolution of a vertebrate-like methylome in a marine sponge.
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de Mendoza A, Hatleberg WL, Pang K, Leininger S, Bogdanovic O, Pflueger J, Buckberry S, Technau U, Hejnol A, Adamska M, Degnan BM, Degnan SM, and Lister R
- Subjects
- Animals, DNA Methylation, Invertebrates, Vertebrates, Epigenome, Porifera
- Abstract
Vertebrates have highly methylated genomes at CpG positions, whereas invertebrates have sparsely methylated genomes. This increase in methylation content is considered a major regulatory innovation of vertebrate genomes. However, here we report that a sponge, proposed as the potential sister group to the rest of animals, has a highly methylated genome. Despite major differences in genome size and architecture, we find similarities between the independent acquisitions of the hypermethylated state. Both lineages show genome-wide CpG depletion, conserved strong transcription factor methyl-sensitivity and developmental methylation dynamics at 5-hydroxymethylcytosine enriched regions. Together, our findings trace back patterns associated with DNA methylation in vertebrates to the early steps of animal evolution. Thus, the sponge methylome challenges previous hypotheses concerning the uniqueness of vertebrate genome hypermethylation and its implications for regulatory complexity.
- Published
- 2019
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241. Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family.
- Author
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de Mendoza A, Pflueger J, and Lister R
- Subjects
- Amino Acid Sequence, Animals, Arthropods classification, Arthropods metabolism, Cytosine metabolism, DNA Methylation, DNA-Binding Proteins metabolism, Phylogeny, Protein Domains, Sequence Alignment, Sequence Homology, Amino Acid, Species Specificity, Arthropods genetics, CpG Islands, DNA-Binding Proteins genetics, Genome, Retroelements
- Abstract
The repressive capacity of cytosine DNA methylation is mediated by recruitment of silencing complexes by methyl-CpG binding domain (MBD) proteins. Despite MBD proteins being associated with silencing, we discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD. We functionally show how retrotransposon-encoded MBDs preferentially bind to CpG-dense methylated regions, which correspond to transposable element regions of the host genome, in the myriapod Strigamia maritima Consistently, young MBD-encoding Copia retrotransposons (CopiaMBD) accumulate in regions with higher CpG densities than other LTR-retrotransposons also present in the genome. This would suggest that retrotransposons use MBDs to integrate into heterochromatic regions in Strigamia , avoiding potentially harmful insertions into host genes. In contrast, CopiaMBD insertions in the spider Stegodyphus dumicola genome disproportionately accumulate in methylated gene bodies compared with other spider LTR-retrotransposons. Given that transposons are not actively targeted by DNA methylation in the spider genome, this distribution bias would also support a role for MBDs in the integration process. Together, these data show that retrotransposons can co-opt host-derived epigenome readers, potentially harnessing the host epigenome landscape to advantageously tune the retrotransposition process., (© 2019 de Mendoza et al.; Published by Cold Spring Harbor Laboratory Press.)
- Published
- 2019
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242. Author Correction: Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.
- Author
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de Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Li H, Yang F, Li L, Hori K, Pflueger J, Buckberry S, Ohta H, Rosic N, Lesage P, Lin S, and Lister R
- Abstract
The original version of this Article contained an error in the spelling of the author Hongfei Li, which was incorrectly given as Fei Hong. This has now been corrected in both the PDF and HTML versions of the Article.
- Published
- 2018
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243. Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.
- Author
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de Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Li H, Yang F, Li L, Hori K, Pflueger J, Buckberry S, Ohta H, Rosic N, Lesage P, Lin S, and Lister R
- Subjects
- DNA Methylation genetics, Epigenesis, Genetic, Evolution, Molecular, Gene Silencing, Phylogeny, Charophyceae enzymology, Charophyceae genetics, DNA (Cytosine-5-)-Methyltransferases genetics, DNA (Cytosine-5-)-Methyltransferases metabolism, Dinoflagellida enzymology, Dinoflagellida genetics, Retroelements
- Abstract
Transposable elements are in a constant arms race with the silencing mechanisms of their host genomes. One silencing mechanism commonly used by many eukaryotes is dependent on cytosine methylation, a covalent modification of DNA deposited by C5 cytosine methyltransferases (DNMTs). Here, we report how two distantly related eukaryotic lineages, dinoflagellates and charophytes, have independently incorporated DNMTs into the coding regions of distinct retrotransposon classes. Concomitantly, we show that dinoflagellates of the genus Symbiodinium have evolved cytosine methylation patterns unlike any other eukaryote, with most of the genome methylated at CG dinucleotides. Finally, we demonstrate the ability of retrotransposon DNMTs to methylate CGs de novo, suggesting that retrotransposons could self-methylate retrotranscribed DNA. Together, this is an example of how retrotransposons incorporate host-derived genes involved in DNA methylation. In some cases, this event could have implications for the composition and regulation of the host epigenomic environment.
- Published
- 2018
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244. Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming.
- Author
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Knaupp AS, Buckberry S, Pflueger J, Lim SM, Ford E, Larcombe MR, Rossello FJ, de Mendoza A, Alaei S, Firas J, Holmes ML, Nair SS, Clark SJ, Nefzger CM, Lister R, and Polo JM
- Subjects
- Animals, Chromatin genetics, Female, Induced Pluripotent Stem Cells cytology, Mice, Mice, Inbred NOD, Mice, SCID, Transcription Factors genetics, Cellular Reprogramming genetics, Chromatin metabolism, Induced Pluripotent Stem Cells metabolism, Transcription Factors metabolism
- Abstract
Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) induces changes in genome architecture reflective of the embryonic stem cell (ESC) state. However, only a small minority of cells typically transition to pluripotency, which has limited our understanding of the process. Here, we characterize the DNA regulatory landscape during reprogramming by time-course profiling of isolated sub-populations of intermediates poised to become iPSCs. Widespread reconfiguration of chromatin states and transcription factor (TF) occupancy occurs early during reprogramming, and cells that fail to reprogram partially retain their original chromatin states. A second wave of reconfiguration occurs just prior to pluripotency acquisition, where a majority of early changes revert to the somatic cell state and many of the changes that define the pluripotent state become established. Our comprehensive characterization of reprogramming-associated molecular changes broadens our understanding of this process and sheds light on how TFs access and change the chromatin during cell-fate transitions., (Copyright © 2017 Elsevier Inc. All rights reserved.)
- Published
- 2017
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245. Sterol and genomic analyses validate the sponge biomarker hypothesis.
- Author
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Gold DA, Grabenstatter J, de Mendoza A, Riesgo A, Ruiz-Trillo I, and Summons RE
- Subjects
- Animals, Biomarkers chemistry, Dehydrocholesterols analysis, Dehydrocholesterols chemistry, Dehydrocholesterols metabolism, Evolution, Molecular, Gene Duplication, Methyltransferases chemistry, Methyltransferases genetics, Methyltransferases metabolism, Models, Molecular, Molecular Structure, Phylogeny, Porifera classification, Porifera metabolism, Protein Structure, Secondary, Protein Structure, Tertiary, Species Specificity, Sterols analysis, Sterols chemistry, Time Factors, Biomarkers metabolism, Genomics methods, Porifera genetics, Sterols biosynthesis
- Abstract
Molecular fossils (or biomarkers) are key to unraveling the deep history of eukaryotes, especially in the absence of traditional fossils. In this regard, the sterane 24-isopropylcholestane has been proposed as a molecular fossil for sponges, and could represent the oldest evidence for animal life. The sterane is found in rocks ∼650-540 million y old, and its sterol precursor (24-isopropylcholesterol, or 24-ipc) is synthesized today by certain sea sponges. However, 24-ipc is also produced in trace amounts by distantly related pelagophyte algae, whereas only a few close relatives of sponges have been assayed for sterols. In this study, we analyzed the sterol and gene repertoires of four taxa (Salpingoeca rosetta, Capsaspora owczarzaki, Sphaeroforma arctica, and Creolimax fragrantissima), which collectively represent the major living animal outgroups. We discovered that all four taxa lack C30 sterols, including 24-ipc. By building phylogenetic trees for key enzymes in 24-ipc biosynthesis, we identified a candidate gene (carbon-24/28 sterol methyltransferase, or SMT) responsible for 24-ipc production. Our results suggest that pelagophytes and sponges independently evolved C30 sterol biosynthesis through clade-specific SMT duplications. Using a molecular clock approach, we demonstrate that the relevant sponge SMT duplication event overlapped with the appearance of 24-isopropylcholestanes in the Neoproterozoic, but that the algal SMT duplication event occurred later in the Phanerozoic. Subsequently, pelagophyte algae and their relatives are an unlikely alternative to sponges as a source of Neoproterozoic 24-isopropylcholestanes, consistent with growing evidence that sponges evolved long before the Cambrian explosion ∼542 million y ago.
- Published
- 2016
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246. Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division.
- Author
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Desvoyes B, de Mendoza A, Ruiz-Trillo I, and Gutierrez C
- Subjects
- Arabidopsis Proteins genetics, Cell Cycle, Gene Expression Regulation, Plant, Plant Cells, Arabidopsis Proteins physiology, Cell Division, Cell Proliferation, Plants metabolism
- Abstract
The retinoblastoma (Rb) protein was identified as a human tumour suppressor protein that controls various stages of cell proliferation through the interaction with members of the E2F family of transcription factors. It was originally thought to be specific to animals but plants contain homologues of Rb, called RETINOBLASTOMA-RELATED (RBR). In fact, the Rb-E2F module seems to be a very early acquisition of eukaryotes. The activity of RBR depends on phosphorylation of certain amino acid residues, which in most cases are well conserved between plant and animal proteins. In addition to its role in cell-cycle progression, RBR has been shown to participate in various cellular processes such as endoreplication, transcriptional regulation, chromatin remodelling, cell growth, stem cell biology, and differentiation. Here, we discuss the most recent advances to define the role of RBR in cell proliferation and asymmetric cell division. These and other reports clearly support the idea that RBR is used as a landing platform of a plethora of cellular proteins and complexes to control various aspects of cell physiology and plant development., (© The Author 2013. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
- Published
- 2014
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247. Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages.
- Author
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de Mendoza A, Sebé-Pedrós A, Šestak MS, Matejcic M, Torruella G, Domazet-Loso T, and Ruiz-Trillo I
- Subjects
- Computational Biology, Genomics methods, Statistics, Nonparametric, Cell Differentiation genetics, Embryonic Development genetics, Eukaryota genetics, Evolution, Molecular, Gene Expression Regulation, Developmental genetics, Transcription Factors genetics
- Abstract
Transcription factors (TFs) are the main players in transcriptional regulation in eukaryotes. However, it remains unclear what role TFs played in the origin of all of the different eukaryotic multicellular lineages. In this paper, we explore how the origin of TF repertoires shaped eukaryotic evolution and, in particular, their role into the emergence of multicellular lineages. We traced the origin and expansion of all known TFs through the eukaryotic tree of life, using the broadest possible taxon sampling and an updated phylogenetic background. Our results show that the most complex multicellular lineages (i.e., those with embryonic development, Metazoa and Embryophyta) have the most complex TF repertoires, and that these repertoires were assembled in a stepwise manner. We also show that a significant part of the metazoan and embryophyte TF toolkits evolved earlier, in their respective unicellular ancestors. To gain insights into the role of TFs in the development of both embryophytes and metazoans, we analyzed TF expression patterns throughout their ontogeny. The expression patterns observed in both groups recapitulate those of the whole transcriptome, but reveal some important differences. Our comparative genomics and expression data reshape our view on how TFs contributed to eukaryotic evolution and reveal the importance of TFs to the origins of multicellularity and embryonic development.
- Published
- 2013
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248. New genomes, new taxa and deep questions in the eukaryotic tree of life: a meeting report on the EMBO comparative genomics conference.
- Author
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de Mendoza A and Ruiz-Trillo I
- Abstract
A report on the meeting Comparative Genomics of Eukaryotic Microorganisms: understanding the complexity of diversity. Sant Feliu de Guíxols, Spain. October 15-20, 2011.
- Published
- 2011
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249. The mysterious evolutionary origin for the GNE gene and the root of bilateria.
- Author
-
de Mendoza A and Ruiz-Trillo I
- Subjects
- Animals, Carbohydrate Epimerases biosynthesis, Carbohydrate Epimerases genetics, Likelihood Functions, Models, Genetic, Evolution, Molecular, Gene Transfer, Horizontal genetics, Invertebrates genetics, Phylogeny
- Abstract
Phylogenomic analyses have revealed several important metazoan clades, such as the Ecdysozoa and the Lophotrochozoa. However, the phylogenetic positions of a few taxa, such as ctenophores, chaetognaths, acoelomorphs, and Xenoturbella, remain contentious. Thus, the findings of qualitative markers or "rare genomic changes" seem ideal to independently test previous phylogenetic hypotheses. We here describe a rare genomic change, the presence of the gene UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase (GNE). We show that GNE is encoded in the genomes of deuterostomes, acoelomorphs and Xenoturbella, whereas it is absent in protostomes and nonbilaterians. Moreover, the GNE has a complex evolutionary origin involving unique lateral gene transfer events and/or extensive hidden paralogy for each protein domain. However, rather than using GNE as a phylogenetic character, we argue that rare genomic changes such as the one presented here should be used with caution.
- Published
- 2011
- Full Text
- View/download PDF
250. Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: protease cleavage and SCX elution rules from data mining of MS/MS spectra.
- Author
-
Yen CY, Russell S, Mendoza AM, Meyer-Arendt K, Sun S, Cios KJ, Ahn NG, and Resing KA
- Subjects
- Amino Acid Sequence, Humans, Hydrolysis, Mass Spectrometry, Molecular Sequence Data, Sensitivity and Specificity, Databases, Protein, Information Storage and Retrieval, Peptide Hydrolases metabolism, Peptides chemistry, Proteomics
- Abstract
Correct identification of a peptide sequence from MS/MS data is still a challenging research problem, particularly in proteomic analyses of higher eukaryotes where protein databases are large. The scoring methods of search programs often generate cases where incorrect peptide sequences score higher than correct peptide sequences (referred to as distraction). Because smaller databases yield less distraction and better discrimination between correct and incorrect assignments, we developed a method for editing a peptide-centric database (PC-DB) to remove unlikely sequences and strategies for enabling search programs to utilize this peptide database. Rules for unlikely missed cleavage and nontryptic proteolysis products were identified by data mining 11 849 high-confidence peptide assignments. We also evaluated ion exchange chromatographic behavior as an editing criterion to generate subset databases. When used to search a well-annotated test data set of MS/MS spectra, we found no loss of critical information using PC-DBs, validating the methods for generating and searching against the databases. On the other hand, improved confidence in peptide assignments was achieved for tryptic peptides, measured by changes in DeltaCN and RSP. Decreased distraction was also achieved, consistent with the 3-9-fold decrease in database size. Data mining identified a major class of common nonspecific proteolytic products corresponding to leucine aminopeptidase (LAP) cleavages. Large improvements in identifying LAP products were achieved using the PC-DB approach when compared with conventional searches against protein databases. These results demonstrate that peptide properties can be used to reduce database size, yielding improved accuracy and information capture due to reduced distraction, but with little loss of information compared to conventional protein database searches.
- Published
- 2006
- Full Text
- View/download PDF
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