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Fine-grained and mainly reddish color, compact and slightly breccious and vesicular pyrometamorphic rocks (natural clinker) are associated to the spontaneous combustion of coal seams of the Cerrejón Formation exploited by Carbones del Cerrejón Limited in La Guajira Peninsula (Caribbean Region of Colombia). These rocks constitute remaining inorganic materials derived from claystones, mudstones and sandstones originally associated with the coal and are essentially a complex mixture of various amorphous and crystalline inorganic constituents. In this paper, a petrographic characterization of natural clinker, aswell as the application of the X-ray diffraction (Rietveld method) by mean of quantitative analysis of its mineral phases were carried out. The RIQAS program was used for the refinement of X ray powder diffraction profiles, analyzing the importance of using the correct isostructural models for each of the existing phases, which were obtained from the Inorganic Crystal Structure Database (ICSD). The results obtained in this investigation show that the Rietveld method can be used as a powerful tool in the quantitative analysis of phases in polycrystalline samples, which has been a traditional problem in geology.

El presente artículo busca contribuir al desarrollo y consolidación de los estudios sobre la gourmetización y la gentrificación alimentaria, enfatizando los efectos que estos procesos tienen en ámbitos que exceden a la vida urbana. En ese marco, se propone recuperar los engranajes de la cadena de valor y sus localizaciones –desde los barrios gentrificados hasta las comunidades rurales agrícolas–, indicando los procesos de valorización y desvalorización y cómo estos afectan de forma desigual a los actores involucrados. Se enfatiza sobre este punto, estableciendo un diálogo interdisciplinar. A partir de una revisión bibliográfica, el artículo se basa en cuatro casos que se recuperan de fuentes secundarias y que ilustran la forma en la que operan estos procesos en distintos niveles, territorios y escalas: el café de autor en cuanto símbolo de distinción en los barrios gentrificados; la palta o aguacate a partir de su manifestación gastronómica en el avocado toast; el vino, desde la turistificación de su producción hasta las estrategias de valorización en su consumo urbano; y la quinoa desde el patentamiento de nuevas variedades hasta el desarrollo de mercados expulsivos de amplios sectores de población. Se concluye que el auge de estos alimentos tiene efectos de acumulación del capital por desposesión en los ámbitos rural y urbano al igual que en los procesos de producción y de consumo.

Understanding the evolutionary patterns and geographic spread of SARS-CoV-2 variants, particularly Omicron, is essential for effective public health responses. This study focused on the genomic analysis of the Omicron variant in Cordoba, Argentina from 2021 to 2022. Phylogenetic analysis revealed the dominant presence of BA.1 and BA.2 lineages, with BA.5 emerging earlier than BA.4, aligning with observations from other regions. Haplotype network analysis showed significant genetic divergence within Omicron samples, forming distinct clusters. In comparison to global datasets, we identified mutations in the Omicron genomes (A27S, Y145D, and L212I) situated within the NTD region of the Spike protein. These mutations, while not widespread globally, showed higher prevalence in our region. Of particular interest were the Y145D and L212I substitutions, previously unreported in Argentina. In silico analysis revealed that both mutations impact the binding affinity of T-cell epitopes to HLA type I and II alleles. Notably, these alleles are among the most common in the Argentinian population, with some associated with protection against and others with susceptibility to SARS-CoV-2 infection. These findings strongly suggest that these prevalent mutations likely influence the immunogenicity of the Spike protein and contribute to immune evasion mechanisms. This study provides valuable insights into the genomic dynamics of the Omicron variant in Cordoba, Argentina and highlights unique mutations with potential implications for COVID-19 vaccines.

Son bien conocidas las posibilidades didácticas del teatro, como demuestran su uso en el ámbito de la Enseñanza Primaria, las posibilidades de la dramatización y de otras técnicas teatrales para potenciar todo lo referente a la lectoescritura en el aula de Lengua y Literatura o para la enseñanza de lenguas extranjeras—en particular, la enseñanza del español como ELE—. El aprovechamiento del teatro en la enseñanza no es algo nuevo, pues ya ocurría en el Renacimiento con el empleo de colloquia y del teatro escolar para mejorar el conocimiento de la lengua latina, por ejemplo. En este artículo, después de repasar su empleo como herramienta propedéutica en estos ámbitos, articulamos toda una propuesta para el empleo de textos adaptados de La Orestíada de Esquilo, acompañados de un cuestionario, como complemento al estudio teórico de la tragedia dentro del temario de literatura griega de Bachillerato.

Este artículo aborda las resultantes de la apertura de actividades económicas a la participación de las mujeres en Argentina a partir del caso del transporte masivo de pasajeros terrestre y aerocomercial. Se estudia su participación en la actividad, trayectorias laborales y barreras percibidas para el año 2020. La metodología combina análisis estadístico de datos secundarios con entrevistas semi-estructuradas a trabajadoras. Las variables analizadas por género fueron cantidad de personas trabajadoras por modo de transporte, categoría ocupacional, antigüedad y edad. Las entrevistas exploran relaciones de género en los espacios de trabajo, demandas sociales a su desempeño y obstáculos percibidos para su desarrollo profesional. La evidencia empírica corrobora que el transporte constituye una actividad de dominación masculina en la que actúan procesos de segregación vertical y horizontal que relegan a las mujeres a los puestos de menor remuneración, jerarquía y calificación, apoyados en barreras culturales basadas en estereotipos de género.

El objetivo del presente artículo es dar cuenta del proceso de construcción del sistema ferroviario de pasajeros de la Región Metropolitana de Buenos Aires (RMBA) como problema público en el período 2002-2015. Dicho análisis se aborda al estudiar la evolución que tuvieron los conflictos desarrollados en el interior del sistema y las controversias en torno a su problematización social en la arena pública, a partir del tratamiento dado a la temática en la prensa. Se implementa una estrategia metodológica cuantitativa y cualitativa que combina el uso de fuentes primarias y secundarias. Se sostiene que las perturbaciones del sistema (conflictos y accidentes) coadyuvaron progresivamente a madurar los debates en torno a la definición del problema ferroviario, hasta consolidarlo asociado a la cuestión de la corrupción.

El artículo trata sobre las construcciones del dolor infantil que realiza un equipo de Cuidados Paliativos Pediátrico de un hospital público especializado de la Ciudad Autónoma de Buenos Aires. Con un trabajo de campo etnográfico realizado durante el año 2015, se describen las dificultades al tratar el dolor como objeto de intervención/investigación. Se describen además, las indagaciones médicas para cualificar y explicar el origen del dolor y el uso de alegorías en esa labor. Se concluye que el dolor es un elemento de poder para estas paliativistas, el leitmotiv de su trabajo, su identidad y su expertise y sus definiciones no son ni simples ni acabadas.

La recuperación de empresas por sus trabajadores en la Argentina representa un proceso que a pesar de sus características disruptivas e innovadoras ha concitado una amplia legitimidad social. ¿Cuáles son las lógicas que fundan dicha legitimidad? ¿En qué medida esta valoración positiva se extiende a todos los atributos del proceso, aun los más disruptivos? ¿Cómo interactúan las lógicas operantes con los valores hegemónicos sobre los que se erige la sociedad capitalista? A través de la investigación por encuesta, realizamos una medición de la valoración social del proceso de recuperación de empresas en sus diferentes dimensiones e indagamos la configuración cultural que permite entender a la misma. Retomando los desarrollos teóricos en torno al concepto de economía moral, sostenemos que la legitimidad que concita el proceso se funda en la valoración que asume el trabajo como forma de reproducción social, material y simbólica en la sociedad argentina. Esta configuración cultural en torno al trabajo permite discriminar entre lo justo y lo injusto, promoviendo la acción colectiva y la tolerancia a la misma; planteando de este modo, límites a la mercantilización del trabajo.

El objetivo del artículo es abordar el rol que tuvo el sector editorial, los editores y los autores de libros de coyuntura en el tratamiento de los ferrocarriles de la Región Metropolitana de Buenos Aires (RMBA) como problema público. Se realiza una conceptualización teórica acerca de los problemas públicos y del rol del sistema de medios de comunicación y del sector editorial en la producción y reproducción de dichos problemas. Se da cuenta del estado de situación de la industria editorial para el período de análisis, haciendo énfasis en el comportamiento de los libros de no ficción que abordan la coyuntura política, específicamente los que trataron a la corrupción como tema central. Por último, se aborda el análisis de los libros especializados en la cuestión ferroviaria, ahondando en el estudio de dos casos representativos. A partir de una serie de datos de carácter cuantitativo (registro de libros de política publicados entre 2003 y 2015) y cualitativo (entrevistas, observaciones), se aborda el interrogante acerca de cómo opera el “efecto libro” en la configuración de un problema público y de especialistas o referentes en torno a este problema.

La trascendencia que adquiere el proceso de disolución de los patrimonios señoriales en la configuración de las actuales estructuras de propiedad de la tierra del antiguo Reino de Valencia -en función de la extensión del régimen señorial valenciano y de su vinculación con la enfiteusis como régimen de tenencia predominante- ha sido puesto de manifiesto por diversos autores (Gil Olcina, 1979; Gil Olcina y Canales Martínez, 1988; Romero González, 1983). Incidencia considerable ejerce, asimismo, este proceso iniciado tras la promulgación del decreto de 6-VIII-1811, en la comarca del Campo de Alicante, ámbito caracterizado tanto por la notoria implantación del régimen señorial como por la notable fragmentación jurisdiccional existente.

Background: Classical mutagenesis is a powerful tool that has allowed researchers to elucidate the molecular and genetic basis of a plethora of processes in many model species. The integration of these methods with modern massively parallel sequencing techniques, initially in model species but currently also in many crop species, is accelerating the identification of genes underlying a wide range of traits of agronomic interest., Results: We have developed MAPtools, an open-source Python3 application designed specifically for the analysis of genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments. We have extensively tested MAPtools using datasets published in recent literature., Conclusions: MAPtools gives users the flexibility to customize their bioinformatics pipeline with various commands for calculating allele count-based statistics, generating plots to pinpoint candidate regions, and annotating the effects of SNP and indel mutations. While extensively tested with plants, the program is versatile and applicable to any species for which a mapping population can be generated and a sequenced genome is available., Availability and Implementation: MAPtools is available under GPL v3.0 license and documented as a Python3 package at https://github.com/hcandela/MAPtools ., (© 2024. The Author(s).)

In diploid organisms, haploinsufficiency can be defined as the requirement for more than one fully functional copy of a gene. In contrast to most genes, whose loss-of-function alleles are recessive, loss-of-function alleles of haploinsufficient genes are dominant. However, forward and reverse genetic screens are biased toward obtaining recessive, loss-of-function mutations, and therefore, dominant mutations of all types are underrepresented in mutant collections. Despite this underrepresentation, haploinsufficient loci have intriguing implications for studies of genome evolution, gene dosage, stability of protein complexes, genetic redundancy, and gene expression. Here we review examples of haploinsufficiency in flowering plants and describe the underlying molecular mechanisms and evolutionary forces driving haploinsufficiency. Finally, we discuss the masking of haploinsufficiency by genetic redundancy, a widespread phenomenon among angiosperms., Competing Interests: Declaration of interests The authors have no interests to declare., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Nanotechnology is a very disruptive twenty-first-century revolution that will allow social and economic welfare to increase although it also involves a significant human exposure to nanoparticles. The aim of the present study was to contribute to the elucidation on whether metallic nanoparticles have a potential to induce fertility impairments. Regulatory studies that observed official OECD guidelines 415, 416 and 422 have failed to detect any fertility alterations caused by nanoparticle exposure. However, the scientific literature provides evidence that some nanoparticles may cause gonad impairments although the actual impact on fertility remains uncertain. This aim of the present study is to revisit the previously published RNAseq studies by analyzing the effects of several nanoparticles on the transcriptome of T98G human glioblastoma cells given that glial cells are known to play a pivotal role in the regulation of gonadotropin releasing hormone neurons. We found evidence that nanoparticles impair the gonadotropin releasing hormone receptor pathway and several related biological process like, among others, the cellular response to follicular stimulating hormone, cellular response to gonadotropin stimulus, cellular response to hormone stimulus, response to steroid hormone, ovulation cycle and response to estradiol. We propose that nanoparticles interfere with the ability of glial cells to regulate gonadotropin-releasing hormone neurons and, subsequently, the hypothalamic-pituitary-gonadal axis, potentially leading to fertility impairments. To our knowledge, this is the first proposal of a mode of action based on endocrine disruption for explaining the possible effects of nanoparticles on fertility. Whether these finding can be extended to other types of nanoparticles requires further investigation.

Garlic is cultivated worldwide for the value of its bulbs, but its cultivation is challenged by the infertility of commercial cultivars and the accumulation of pathogens over time, which occurs as a consequence of vegetative (clonal) propagation. In this review, we summarize the state of the art of garlic genetics and genomics, highlighting recent developments that will lead to its development as a modern crop, including the restoration of sexual reproduction in some garlic strains. The set of tools available to the breeder currently includes a chromosome-scale assembly of the garlic genome and multiple transcriptome assemblies that are furthering our understanding of the molecular processes underlying important traits like the infertility, the induction of flowering and bulbing, the organoleptic properties and resistance to various pathogens.

We report the molecular characterization of an ethyl methanesulfonate (EMS)-induced mutation that causes albinism and lethality at the seedling stage in Arabidopsis thaliana . We identified the mutation using a mapping-by-sequencing approach that uses Fisher's exact tests to detect changes in allele frequencies among the seedlings of an F 2 mapping population, which had been pooled according to their phenotypes (wild-type or mutant). After purifying genomic DNA from the plants of both pools, the two samples were sequenced using the Illumina HiSeq 2500 next-generation sequencing platform. The bioinformatic analysis allowed us to identify a point mutation that damages a conserved residue at the acceptor site of an intron of the At2g04030 gene, which encodes the chloroplast-localized AtHsp90.5 protein, a member of the HSP90 family of heat shock proteins. Our RNA-seq analysis demonstrates that the new allele alters the splicing of At2g04030 transcripts in multiple ways, leading to massive deregulation of genes encoding plastid-localized proteins. A search for protein-protein interactions using the yeast two-hybrid method allowed us to identify two members of the GrpE superfamily as potential interactors of AtHsp90.5, as has previously been reported for green algae.

The selection of plant genotypes with improved productivity and tolerance to environmental constraints has always been a major concern in plant breeding. Classical approaches based on the generation of variability and selection of better phenotypes from large variant collections have improved their efficacy and processivity due to the implementation of molecular biology techniques, particularly genomics, Next Generation Sequencing and other omics such as proteomics and metabolomics. In this regard, the identification of interesting variants before they develop the phenotype trait of interest with molecular markers has advanced the breeding process of new varieties. Moreover, the correlation of phenotype or biochemical traits with gene expression or protein abundance has boosted the identification of potential new regulators of the traits of interest, using a relatively low number of variants. These important breakthrough technologies, built on top of classical approaches, will be improved in the future by including the spatial variable, allowing the identification of gene(s) involved in key processes at the tissue and cell levels.

ATP-Binding Cassette E (ABCE) proteins dissociate cytoplasmic ribosomes after translation terminates, and contribute to ribosome recycling, thus linking translation termination to initiation. This function has been demonstrated to be essential in animals, fungi, and archaea, but remains unexplored in plants. In most species, ABCE is encoded by a single-copy gene; by contrast, Arabidopsis thaliana has two ABCE paralogs, of which ABCE2 seems to conserve the ancestral function. We isolated apiculata7-1 ( api7-1 ), the first viable, hypomorphic allele of ABCE2 , which has a pleiotropic morphological phenotype reminiscent of mutations affecting ribosome biogenesis factors and ribosomal proteins. We also studied api7-2 , a null, recessive lethal allele of ABCE2 . Co-immunoprecipitation experiments showed that ABCE2 physically interacts with components of the translation machinery. An RNA-seq study of the api7-1 mutant showed increased responses to iron and sulfur starvation. We also found increased transcript levels of genes related to auxin signaling and metabolism. Our results support for the first time a conserved role for ABCE proteins in translation in plants, as previously shown for the animal, fungal, and archaeal lineages. In Arabidopsis, the ABCE2 protein seems important for general growth and vascular development, likely due to an indirect effect through auxin metabolism., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Navarro-Quiles, Mateo-Bonmatí, Candela, Robles, Martínez-Laborda, Fernández, Šimura, Ljung, Rubio, Ponce and Micol.)

We report the first complete genome sequence of an isolate of Passiflora chlorosis virus (PaCV), a member of the Potyviridae family, identified in passion fruit ( Passiflora edulis Sims) plants grown in Israel. The assembled genome is 9672 nucleotides long and encodes a 3084 amino acids polyprotein that is predicted to be proteolytically cleaved into 10 mature peptides. Our analysis of the genome sequence shows that PaCV is a distinct species, sharing 68.5% nucleotide sequence identity and 71.5% amino acid sequence identity with isolates of the bean common mosaic necrosis virus (BCMNV), the most closely related virus classified within the genus Potyvirus . Using quantitative PCR, we detected the virus in RNA samples from leaves exhibiting symptoms of infection, with higher levels in clearly chlorotic leaves, but not in those from healthy leaves.

Quantum dots are nanoparticles with very promising biomedical applications. However, before these applications can be authorized, a complete toxicological assessment of quantum dots toxicity is needed. This work studied the effects of cadmium-selenium quantum dots on the transcriptome of T98G human glioblastoma cells. It was found that 72-h exposure to 40 µg/mL (a dose that reduces cell viability by less than 10%) alters the transcriptome of these cells in biological processes and molecular pathways, which address mainly neuroinflammation and hormonal control of hypothalamus via the gonadotropin-releasing hormone receptor. The biological significance of neuroinflammation alterations is still to be determined because, unlike studies performed with other nanomaterials, the expression of the genes encoding pro-inflammatory interleukins is down-regulated rather than up-regulated. The hormonal control alterations of the hypothalamus pose a new concern about a potential adverse effect of quantum dots on fertility. In any case, more studies are needed to clarify the biological relevance of these findings, and especially to assess the real risk of toxicity derived from quantum dots exposure appearing in physiologically relevant scenarios.

Soil flooding is a compound abiotic stress that alters soil properties and limits atmospheric gas diffusion (O 2 and CO 2 ) to the roots. The involvement of abscisic acid (ABA) in the regulation of soil flooding-specific genetic and metabolic responses has been scarcely studied despite its key importance as regulator in other abiotic stress conditions. To attain this objective, wild type and ABA-deficient tomatoes were subjected to short-term (24 h) soil waterlogging. After this period, gas exchange parameters were reduced in the wild type but not in ABA-deficient plants that always had higher E and g s . Transcript and metabolite alterations were more intense in waterlogged tissues, with genotype-specific variations. Waterlogging reduced the ABA levels in the roots while inducing PYR/PYL/RCAR ABA receptors and ABA-dependent transcription factor transcripts, of which induction was less pronounced in the ABA-deficient genotype. Ethylene/O 2 -dependent genetic responses (ERFVIIs, plant anoxia survival responses, and genes involved in the N-degron pathway) were induced in hypoxic tissues independently of the genotype. Interestingly, genes encoding a nitrate reductase and a phytoglobin involved in NO biosynthesis and scavenging and ERFVII stability were induced in waterlogged tissues, but to a lower extent in ABA-deficient tomato. At the metabolic level, flooding-induced accumulation of Ala was enhanced in ABA-deficient lines following a differential accumulation of Glu and Asp in both hypoxic and aerated tissues, supporting their involvement as sources of oxalacetate to feed the tricarboxylic acid cycle in waterlogged tissues and constituting a potential advantage upon long periods of soil waterlogging. The promoter analysis of upregulated genes indicated that the production of oxalacetate from Asp via Asp oxidase, energy processes such as acetyl-CoA, ATP, and starch biosynthesis, and the lignification process were likely subjected to ABA regulation. Taken together, these data indicate that ABA depletion in waterlogged tissues acts as a positive signal, inducing several specific genetic and metabolic responses to soil flooding., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 De Ollas, González-Guzmán, Pitarch, Matus, Candela, Rambla, Granell, Gómez-Cadenas and Arbona.)

Titanium dioxide and zinc oxide are two of the most widely used nanomaterials. We assessed the effects of noncytotoxic doses of both nanomaterials on T98G human glioblastoma cells by omic approaches. Surprisingly, no effects on the transcriptome of T98G cells was detected after exposure to 5 µg/mL of zinc oxide nanoparticles during 72 h. Conversely, the transcriptome of the cells exposed to 20 µg/mL of titanium dioxide nanoparticles during 72 h revealed alterations in lots of biological processes and molecular pathways. Alterations to the transcriptome suggests that exposure to titanium dioxide nanoparticles might, potentially, compromise the integrity of the blood brain barrier integrity and cause neuroinflammation. The latter issue was further confirmed phenotypically with a proteomic analysis and by recording the release of interleukin 8. Titanium dioxide also caused autophagy, which was demonstrated through the increase in the expression of the autophagy-related 3 and microtubule associated protein 1 light chain 3 alpha genes. The proteomic analysis revealed that titanium dioxide nanoparticles might have anticancerigen properties by downregulating genes involved in the detoxication of anthracyclines. A risk assessment resulting from titanium dioxide exposure, focusing on the central nervous system as a potential target of toxicity, is necessary.

Nanotechnology has been well developed in recent decades because it provides social progress and welfare. Consequently, exposure of population is increasing and further increases in the near future are forecasted. Therefore, assessing the safety of applications involving nanoparticles is strongly advisable. We assessed the effects of silver nanoparticles at a non-cytotoxic concentration on the performance of T98G human glioblastoma cells mainly by an omic approach. We found that silver nanoparticles are able to alter several molecular pathways related to inflammation. Cellular repair and regeneration were also affected by alterations to the fibroblast growth factor pathways operating mainly via mitogen-activated protein kinase cascades. It was concluded that, given the relevant role of glia on central nervous system maintenance homeostasis, exposure to silver nanoparticles could eventually lead to severe toxicity in the central nervous system, although current exposure levels do not pose a significant risk., Competing Interests: Declaration of Competing Interest All the authors declare no financial and personal relationships with other people or organizations that could inappropriately influence (bias) this work., (Copyright © 2020 Elsevier Inc. All rights reserved.)

We report the complete nucleotide sequence of a new member of the Potyviridae family isolated from passion fruit plants grown in Israel, called Passiflora edulis symptomless virus (PeSV). The PeSV genome is 9,928 nucleotides long and encodes a 3,173 amino acids polyprotein that is predicted to be proteolytically cleaved into 10 mature peptides. Our phylogenetic analysis shows that PeSV represents a new species, and is most closely related to rose yellow mosaic virus (RoYMV). According to currently accepted criteria for genus demarcation, both viruses should be assigned as representative isolates of new species in the recently approved genus, Roymovirus, in the Potyviridae family.

All critical developmental and physiological events in a plant's life cycle depend on the proper activation and repression of specific gene sets, and this often involves epigenetic mechanisms. Some Arabidopsis thaliana mutants with disorders of the epigenetic machinery exhibit pleiotropic defects, including incurved leaves and early flowering, due to the ectopic and heterochronic derepression of developmental regulators. Here, we studied one such mutant class, the incurvata11 ( icu11 ) loss-of-function mutants. We have identified ICU11 as the founding member of a small gene family that we have named CUPULIFORMIS ( CP ). This family is part of the 2-oxoglutarate/Fe(II)-dependent dioxygenase superfamily. ICU11 and its closest paralog, CP2, have unequally redundant functions: although cp2 mutants are phenotypically wild type, icu11 cp2 double mutants skip vegetative development and flower upon germination. This phenotype is reminiscent of loss-of-function mutants of the Polycomb-group genes EMBRYONIC FLOWER1 ( EMF1 ) and EMF2 Double mutants harboring icu11 alleles and loss-of-function alleles of genes encoding components of the epigenetic machinery exhibit synergistic, severe phenotypes, and some are similar to those of emf mutants. Hundreds of genes are misexpressed in icu11 plants, including SEPALLATA3 ( SEP3 ), and derepression of SEP3 causes the leaf phenotype of icu11 ICU11 and CP2 are nucleoplasmic proteins that act as epigenetic repressors through an unknown mechanism involving histone modification, but not DNA methylation., (© 2018 American Society of Plant Biologists. All rights reserved.)

Ovules are fundamental for plant reproduction and crop yield as they are the precursors of seeds. Therefore, ovule specification is a critical developmental program. In Arabidopsis thaliana, ovule identity is redundantly conferred by the homeotic D-class genes SHATTERPROOF1 (SHP1), SHP2 and SEEDSTICK (STK), phylogenetically related to the MADS-domain regulatory gene AGAMOUS (AG), essential in floral organ specification. Previous studies have shown that the HUA-PEP activity, comprised of a suite of RNA-binding protein (RBP) encoding genes, regulates AG pre-mRNA processing and thus flower patterning and organ identity. Here, we report that the HUA-PEP activity additionally governs ovule morphogenesis. Accordingly, in severe hua-pep backgrounds ovules transform into flower organ-like structures. These homeotic transformations are most likely due to the dramatic reduction in SHP1, SHP2 and STK activity. Our molecular and genome-wide profiling strategies revealed the accumulation of prematurely terminated transcripts of D-class genes in hua-pep mutants and reduced amounts of their respective functional messengers, which points to pre-mRNA processing misregulation as the origin of the ovule developmental defects in such backgrounds. RNA processing and transcription are coordinated by the RNA polymerase II (RNAPII) carboxyl-terminal domain (CTD). Our results show that HUA-PEP activity members can interact with the CTD regulator C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 (CPL1), supporting a co-transcriptional mode of action for the HUA-PEP activity. Our findings expand the portfolio of reproductive developmental programs in which HUA-PEP activity participates, and further substantiates the importance of RNA regulatory mechanisms (pre-mRNA co-transcriptional regulation) for correct gene expression during plant morphogenesis.

Several hundred genes are required for embryonic and gametophytic development in the model plant Arabidopsis thaliana, as inferred from the lethality of their mutations. Despite many of these genes are expressed throughout the plant life cycle, the corresponding mutants arrest at early stages, preventing the study of their post-embryonic functions by conventional methods. Clonal analysis represents an effective solution to this problem by uncovering the effects of embryo-lethal mutations in sectors of mutant cells within an otherwise normal adult plant. In this pilot study, we have evaluated the suitability of two sector induction methods for the large-scale study of the post-embryonic effects of embryo-lethal (emb) mutations in Arabidopsis. In line with the interests of our laboratory, we selected 24 emb mutations that damage genes that are expressed in wild-type vegetative leaves but whose effects on leaf development remain unknown. For the induction of mutant sectors in adult plants, we followed one approach based on the X-ray irradiation of 'cell autonomy' (CAUT) lines, and another based on the site-specific excision of transgenes mediated by Cre recombinase. We conclude that both methods are time-consuming and difficult to scale up, being better suited for the study of emb mutations on a case-by-case basis.

Biomass production requires the coordination between growth and metabolism. In a large-scale screen for mutants affected in leaf morphology, we isolated the orbiculata1 (orb1) mutants, which exhibit a pale green phenotype and reduced growth. The combination of map-based cloning and next-generation sequencing allowed us to establish that ORB1 encodes the GLUTAMATE SYNTHASE 1 (GLU1) enzyme, also known as FERREDOXIN-DEPENDENT GLUTAMINE OXOGLUTARATE AMINOTRANSFERASE 1 (Fd-GOGAT1). We performed an RNA-seq analysis to identify global gene expression changes in the orb1-3 mutant. We found altered expression levels of genes encoding enzymes involved in nitrogen assimilation and amino acid biosynthesis, such as glutamine synthetases, asparagine synthetases and glutamate dehydrogenases, showing that the expression of these genes depends on the levels of glutamine and/or glutamate. In addition, we observed a concerted upregulation of genes encoding subunits of the cytosolic ribosome. A gene ontology (GO) analysis of the differentially expressed genes between Ler and orb1-3 showed that the most enriched GO terms were 'translation', 'cytosolic ribosome' and 'structural constituent of ribosome'. The upregulation of ribosome-related functions might reflect an attempt to keep protein synthesis at optimal levels even when the pool of glutamate is reduced.

The characterization of mutants with altered leaf shape and pigmentation has previously allowed the identification of nuclear genes that encode plastid-localized proteins that perform essential functions in leaf growth and development. A large-scale screen previously allowed us to isolate ethyl methanesulfonate-induced mutants with small rosettes and pale green leaves with prominent marginal teeth, which were assigned to a phenotypic class that we dubbed Angulata. The molecular characterization of the 12 genes assigned to this phenotypic class should help us to advance our understanding of the still poorly understood relationship between chloroplast biogenesis and leaf morphogenesis. In this article, we report the phenotypic and molecular characterization of the angulata7-1 (anu7-1) mutant of Arabidopsis thaliana, which we found to be a hypomorphic allele of the EMB2737 gene, which was previously known only for its embryonic-lethal mutations. ANU7 encodes a plant-specific protein that contains a domain similar to the central cysteine-rich domain of DnaJ proteins. The observed genetic interaction of anu7-1 with a loss-of-function allele of GENOMES UNCOUPLED1 suggests that the anu7-1 mutation triggers a retrograde signal that leads to changes in the expression of many genes that normally function in the chloroplasts. Many such genes are expressed at higher levels in anu7-1 rosettes, with a significant overrepresentation of those required for the expression of plastid genome genes. Like in other mutants with altered expression of plastid-encoded genes, we found that anu7-1 exhibits defects in the arrangement of thylakoidal membranes, which appear locally unappressed., (© 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.)

Multiple epidemiological and experimental studies have demonstrated that exposure to organophosphorus compounds (OPs) is associated with a variety of neurological disorders. Some of these exposure symptoms cannot be precisely correlated with known molecular targets and mechanisms of toxicity. Most of the known molecular targets of OPs fall in the protein family of serine esterases. We have shown that three esterase components in the soluble fraction of chicken brain (an animal model frequently used in OP neurotoxicity assays) can be kinetically distinguished using paraoxon, mipafox and phenylmethyl sulfonyl fluoride as inhibitors, and phenyl valerate as a substrate; we termed them Eα, Eβ and Eγ. The Eα-component, which is highly sensitive to paraoxon and mipafox and resistant to PMSF, has shown sensitivity to the substrate acetylthiocholine, and to ethopropazine and iso-OMPA (specific inhibitors of butyrylcholinesterase; BChE) but not to BW 284C51 (a specific inhibitor of acetylcholinesterase; AChE). In this work, we employed a large-scale proteomic analysis B with a LC/MS/MS TripleTOF system; 259 proteins were identified in a chromatographic fractionated sample enriched in Eα activity of the chicken brain soluble fraction. Bioinformatics analysis revealed that BChE is the only candidate protein identified to be responsible for almost all the Eα activity. This study demonstrates the potential information to be gained from combining kinetic dissection with large-scale proteomics and bioinformatics analyses for identification of proteins that are targets of OP toxicity and may be involved in detoxification of phosphoryl and carbonyl esters.

The shoot apical meristem (SAM) of angiosperm plants is a small, highly organized structure that gives rise to all above-ground organs. The SAM is divided into three functional domains: the central zone (CZ) at the SAM tip harbors the self-renewing pluripotent stem cells and the organizing center, providing daughter cells that are continuously displaced into the interior rib zone (RZ) or the surrounding peripheral zone (PZ), from which organ primordia are initiated. Despite the constant flow of cells from the CZ into the RZ or PZ, and cell recruitment for primordium formation, a stable balance is maintained between the distinct cell populations in the SAM. Here we combined an in-depth phenotypic analysis with a comparative RNA-Seq approach to characterize meristems from selected combinations of clavata3 (clv3), jabba-1D (jba-1D) and erecta (er) mutants of Arabidopsis thaliana We demonstrate that CLV3 restricts meristem expansion along the apical-basal axis, whereas class III HD-ZIP and ER pathways restrict meristem expansion laterally, but in distinct and possibly perpendicular orientations. Our k-means analysis reveals that clv3, jba-1D/+ and er lead to meristem enlargement by affecting different aspects of meristem function; for example, clv3 displays an increase in the stem cell population, whereas jba-1D/+ er exhibits an increase in mitotic activity and in the meristematic cell population. Our analyses demonstrate that a combined genetic and mRNA-Seq comparative approach provides a precise and sensitive method to identify cell type-specific transcriptomes in a small structure, such as the SAM., (© 2016. Published by The Company of Biologists Ltd.)

Translational regulation, exerted by the cytosolic ribosome, has been shown to participate in the establishment of abaxial-adaxial polarity in Arabidopsis thaliana: many hypomorphic and null alleles of genes encoding proteins of the cytosolic ribosome enhance the leaf polarity defects of asymmetric leaves1 (as1) and as2 mutants. Here, we report the identification of the SCABRA1 (SCA1) nuclear gene, whose loss-of-function mutations also enhance the polarity defects of the as2 mutants. In striking contrast to other previously known enhancers of the phenotypes caused by the as1 and as2 mutations, we found that SCA1 encodes a plastid-type ribosomal protein that functions as a structural component of the 70S plastid ribosome and, therefore, its role in abaxial-adaxial patterning was not expected.

Plants exhibit high capacity to regenerate in three alternative pathways: tissue repair, somatic embryogenesis and de novo organogenesis. For most plants, de novo organ initiation can be easily achieved in tissue culture by exposing explants to auxin and/or cytokinin, yet the competence to regenerate varies among species and within tissues from the same plant. In Arabidopsis, root explants incubated directly on cytokinin-rich shoot inducing medium (SIM-direct), are incapable of regenerating shoots, and a pre-incubation step on auxin-rich callus inducing medium (CIM) is required to acquire competency to regenerate on the SIM. However the mechanism underlying competency acquisition still remains elusive. Here we show that the chromomethylase 3 (cmt3) mutant which exhibits significant reduction in CHG methylation, shows high capacity to regenerate on SIM-direct and that regeneration occurs via direct organogenesis. In WT, WUSCHEL (WUS) promoter, an essential gene for shoot formation, is highly methylated, and its expression on SIM requires pre-incubation on CIM. However, in cmt3, WUS expression induced by SIM-direct. We propose that pre-incubation on CIM is required for the re-activation of cell division. Following the transfer of roots to SIM, the intensive cell division activity continues, and in the presence of cytokinin leads to a dilution in DNA methylation that allows certain genes required for shoot regeneration to respond to SIM, thereby advancing shoot formation., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)

Next-generation sequencing (NGS) technologies allow the cost-effective sequencing of whole genomes and have expanded the scope of genomics to novel applications, such as the genome-wide characterization of intraspecific polymorphisms and the rapid mapping and identification of point mutations. Next-generation sequencing platforms, such as the Illumina HiSeq2000 platform, are now commercially available at affordable prices and routinely produce an enormous amount of sequence data, but their wide use is often hindered by a lack of knowledge on how to manipulate and process the information produced. In this review, we focus on the strategies that are available to geneticists who wish to incorporate these novel approaches into their research but who are not familiar with the necessary bioinformatic concepts and computational tools. In particular, we comprehensively summarize case studies where the use of NGS technologies has led to the identification of point mutations, a strategy that has been dubbed "mapping-by-sequencing", and review examples from plants and other model species such as Caenorhabditis elegans, Saccharomyces cerevisiae, and Drosophila melanogaster. As these technologies are becoming cheaper and more powerful, their use is also expanding to allow mutation identification in species with larger genomes, such as many crop plants., (© 2014 Institute of Botany, Chinese Academy of Sciences.)

Maize leaves have distinct tissues that serve specific purposes. The blade tilts back to photosynthesize and the sheath wraps around the stem to provide structural support and protect young leaves. At the junction between blade and sheath are the ligule and auricles, both of which are absent in the recessive liguleless1 (lg1) mutant. Using an antibody against LG1, we reveal LG1 accumulation at the site of ligule formation and in the axil of developing tassel branches. The dominant mutant Wavy auricle in blade1 (Wab1-R) produces ectopic auricle tissue in the blade and increases the domain of LG1 accumulation. We determined that wab1 encodes a TCP transcription factor by positional cloning and revertant analysis. Tassel branches are few and upright in the wab1 revertant tassel and have an increased branch angle in the dominant mutant. wab1 mRNA is expressed at the base of branches in the inflorescence and is necessary for LG1 expression. wab1 is not expressed in leaves, except in the dominant mutant. The domain of wab1 expression in the Wab1-R leaf closely mirrors the accumulation of LG1. Although wab1 is not needed to induce lg1 expression in the leaf, LG1 is needed to counteract the severe phenotype of the dominant Wab1-R mutant. The regulatory interaction of LG1 and WAB1 reveals a link between leaf shape and tassel architecture, and suggests the ligule is a boundary similar to that at the base of lateral organs., (© 2014. Published by The Company of Biologists Ltd.)

Map-based (positional) cloning has traditionally been the preferred strategy for identifying the causal genes underlying the phenotypes of mutants isolated in forward genetic screens. Massively parallel sequencing technologies are enabling the rapid cloning of genes identified in such screens. We have used a combination of linkage mapping and whole-genome re-sequencing to identify the causal mutations in four loss-of-function angulata (anu) mutants. These mutants were isolated in a screen for mutants with defects in leaf shape and leaf pigmentation. Our results show that the anu1-1, anu4-1, anu9-1 and anu12-1 mutants carry new alleles of the previously characterized SECA2, TRANSLOCON AT THE OUTER MEMBRANE OF CHLOROPLASTS 33 (TOC33), NON-INTRINSIC ABC PROTEIN 14 (NAP14) and CLP PROTEASE PROTEOLYTIC SUBUNIT 1 (CLPR1) genes. Re-sequencing the genomes of fine mapped mutants is a feasible approach that has allowed us to identify a moderate number of candidate mutations, including the one that causes the mutant phenotype, in a nonstandard genetic background. Our results indicate that anu mutations specifically affect plastid-localized proteins involved in diverse processes, such as the movement of peptides through chloroplast membranes (ANU1 and ANU4), metal homeostasis (ANU9) and protein degradation (ANU12).

The chloroplasts of land plants contain internal membrane systems, the thylakoids, which are arranged in stacks called grana. Because grana have not been found in Cyanobacteria, the evolutionary origin of genes controlling the structural and functional diversification of thylakoidal membranes in land plants remains unclear. The angulata10-1 (anu10-1) mutant, which exhibits pale-green rosettes, reduced growth, and deficient leaf lateral expansion, resulting in the presence of prominent marginal teeth, was isolated. Palisade cells in anu10-1 are larger and less packed than in the wild type, giving rise to large intercellular spaces. The ANU10 gene encodes a protein of unknown function that localizes to both chloroplasts and amyloplasts. In chloroplasts, ANU10 associates with thylakoidal membranes. Mutant anu10-1 chloroplasts accumulate H2O2, and have reduced levels of chlorophyll and carotenoids. Moreover, these chloroplasts are small and abnormally shaped, thylakoidal membranes are less abundant, and their grana are absent due to impaired thylakoid stacking in the anu10-1 mutant. Because the trimeric light-harvesting complex II (LHCII) has been reported to be required for thylakoid stacking, its levels were determined in anu10-1 thylakoids and they were found to be reduced. Together, the data point to a requirement for ANU10 for chloroplast and mesophyll development., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

The body architectures of most multicellular organisms consistently display both symmetry and asymmetry. Here, we discuss some of the available knowledge and open questions on how symmetry and asymmetry appear in several conspicuous plant cells and tissues. We focus, where possible, on the role of genes that participate in the maintenance or the breaking of symmetry and that are directly or indirectly related to the cell cycle, under an organ-centric point of view and with an emphasis on the leaf., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Whole-genome duplication events have driven to a large degree the evolution of angiosperm genomes. Although the majority of redundant gene copies after a genome duplication are lost, subfunctionalization or gene balance account for the retention of gene copies. The Arabidopsis 80S ribosome represents an excellent model to test the gene balance hypothesis as it consists of 80 ribosomal proteins, all of them encoded by genes belonging to small gene families. Here, we present the isolation of mutant alleles of the APICULATA2 (API2) and RPL36aA paralogous genes, which encode identical ribosomal proteins but share a similarity of 89% in their coding sequences. RPL36aA was found expressed at a higher level than API2 in the wild type. The loss-of-function api2 and rpl36aa mutations are recessive and affect leaf development in a similar way. Their double mutant combinations with asymmetric leaves2-1 (as2-1) caused leaf polarity defects that were stronger in rpl36aa as2-1 than in api2 as2-1. Our results highlight the role of combined haploinsufficiency and purifying selection in the retention of these paralogous genes in the Arabidopsis genome.

How cells acquire competence to differentiate according to position is an essential question in developmental biology. Maize leaves provide a unique opportunity to study positional information. In the developing leaf primordium, a line is drawn across a field of seemingly identical cells. Above the line, the cells become blade, below the line the cells become sheath and at the line, the cells differentiate into the specialized tissues of ligule and auricle. We identified a new mutation, Liguleless narrow (Lgn), that affects this patterning and shows striking defects in lateral growth as well, thus linking proximal-distal patterning to medial-lateral growth. In characterizing the defect we discovered that both the auxin transport protein ZmPIN1a and the squamosa promoter-binding protein LIGULELESS1 are expressed precisely at this positionally cued line and are disrupted by Lgn. Positional cloning and a transposon-derived allele demonstrate that LGN is a kinase. These results suggest that LGN participates in setting up positional information through a signaling cascade. Interestingly, LGN has a paralog that is upregulated in the mutant, suggesting an important feedback mechanism involved in setting the positional boundary.

Ribosomes play a basic housekeeping role in global translation. However, a number of ribosomal-protein-defective mutants show common and rare developmental phenotypes including growth defects, changes in leaf development, and auxin-related phenotypes. This suggests that translational regulation may be occurring during development. In addition, proteomic and bioinformatic analyses have demonstrated a high heterogeneity in ribosome composition. Although this might be a sign of unequal roles of individual ribosomal proteins, it does not explain every ribosomal-protein-defective phenotype. Moreover, comprehensive interpretations concerning the relationship between ribosomal-protein-defective phenotypes and molecular changes in ribosome status are lacking. In this review, we address these phenotypes based on three models, ribosome insufficiency, heterogeneity, and aberrancy, to consider how ribosomes play developmental roles. We propose that the three models are not mutually exclusive, and ribosomal-protein-defective phenotypes can be explained with one or more of these models. The three models with reference to genetic, biochemical, and bioinformatic knowledge will serve as a foundation for future studies of translational regulation., (Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.)

We isolated Arabidopsis thaliana mutants with incurved vegetative leaves. Positional cloning of incurvata8 (icu8), icu9 and icu15 has identified them as new loss-of-function alleles of the HYPONASTIC LEAVES1 (HYL1), ARGONAUTE1 (AGO1) and HUA ENHANCER1 (HEN1) genes, respectively, which encode known components of the microRNA pathway. The morphological and histological characterization of these mutants and of dicer-like1-9 indicates that small RNAs participate in the proximal-distal and adaxial-abaxial patterning of leaves, as well as in stomatal number establishment. The abnormal vasculature of ago1 and hyl1 leaves also suggests a role for AGO1 and HYL1 in venation patterning. Our mutants expand the allelic series of AGO1, HYL1 and HEN1, and might help to understand the developmental and cellular significance of miRNA-mediated posttranscriptional regulation.