Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum

<p>Abstract</p> <p>Background</p> <p><it>Physarum polycephalum </it>is a free-living amoebozoan protist displaying a complex life cycle, including alternation between single- and multinucleate stages through sporulation, a simple form of cell differentiation. Sporulation in <it>Physarum </it>can be experimentally induced by several external factors, and <it>Physarum </it>displays many biochemical features typical for metazoan cells, including metazoan-type signaling pathways, which makes this organism a model to study cell cycle, cell differentiation and cellular reprogramming.</p> <p>Results</p> <p>In order to identify the genes associated to the light-induced sporulation in <it>Physarum</it>, especially those related to signal transduction, we isolated RNA before and after photoinduction from sporulation- competent cells, and used these RNAs to synthesize cDNAs, which were then analyzed using the 454 sequencing technology. We obtained 16,669 cDNAs that were annotated at every computational level. 13,169 transcripts included hit count data, from which 2,772 displayed significant differential expression (upregulated: 1,623; downregulated: 1,149). Transcripts with valid annotations and significant differential expression were later integrated into putative networks using interaction information from orthologs.</p> <p>Conclusions</p> <p>Gene ontology analysis suggested that most significantly downregulated genes are linked to DNA repair, cell division, inhibition of cell migration, and calcium release, while highly upregulated genes were involved in cell death, cell polarization, maintenance of integrity, and differentiation. In addition, cell death- associated transcripts were overrepresented between the upregulated transcripts. These changes are associated to a network of actin-binding proteins encoded by genes that are differentially regulated before and after light induction.</p

Nanopore-based complete genome sequence of a Sri Lankan cassava mosaic virus (Geminivirus) strain from Thailand

Sri Lankan cassava mosaic virus is an emerging pathogen in Southeast Asia. Here, we report the complete genome of a Thai isolate obtained using Nanopore technology. The isolate was collected in 2019 from the northeastern province of Surin, soon after disease eradication was reported in the country

Edición y comentario de los ‘títulos’ Amicitia, Amor y Gloria del florilegio temático contenido en el ms. 246 de la Biblioteca de Santa Cruz de Valladolid

The present work focuses on the critical edition of the three ‘titles’ – Amicitia, Amor and Gloria– belonging to the thematic florilegium conserved in the ms. 246 the Old Fund of Valladolid University (Santa Cruz Library), whose probable author is Don Cristóbal García Guillén de la Paz (17th century). The text offers two commentaries: the first one consists on a commentary of works, authors and original texts; the second is a philological commentary on the florilegium. Finally, the philological commentary studies the existence of false attributions and auctores incerti

Modelo prolab: De un plan alternativo para el tratamiento paliativo en pacientes con patologías neoplásicas y otras enfermedades crónicas no transmisibles

En los últimos años, el mercado de productos derivados de cannábicos se ha incrementado considerablemente. Perú no escapa de este fenómeno, ya que, a finales del 2017, el Congreso de la República del Perú aprobó el Proyecto de Ley N° 30681, que regula el uso medicinal y terapéutico del cannabis y sus derivados. Entonces, se identifica un problema relevante desde el punto de vista social, pues, la forma en que ha sido abordada la comercialización de estos productos, deja virtualmente excluidos a quienes residen fuera de Lima y, especialmente a quienes no disponen de recursos económicos para sufragar los costos del tratamiento, además los asociados a traslados y manutención en Lima para recibir la medicación y aliviar así las dolencias y colaterales que se derivan del padecimiento de patologías neoplásica y otras enfermedades crónicas no transmisibles. Por ello, se realizó una investigación para proponer una solución que resultara viable desde el punto de vista económico y social y favorecer así a quienes resultan excluidos, atentando contra el principio de salud universal. La solución propuesta, contempla la creación de un Centro Integral de Salud, basado en el uso de la terapia de cannabis medicinal, virtualmente. Se trata de crear una comunidad donde los pacientes no solo adquieran el medicamento, sino que se beneficien de una serie de actividades complementarias y colaterales que contribuyan a mejorar su calidad de vida, más allá del alivio de sus dolencias. El modelo de negocio es factible y viable bajo los indicadores de un VAN de S/ 4,612,939.53 frente a S/3,697,635.87 de la inversión inicial y una TIR de 53% frente al 15% de tasa de interés que fijaron los accionistas, convirtiéndolo en un proyecto de negocio que además de cumplir con los ODS de la agenda 2030 de las Naciones Unidas es sostenible en el tiempo.In recent years, the market for products based on cannabis derivatives has increased considerably. Peru does not escape this phenomenon, since, at the end of 2017, the Congress of the Republic of Peru approved Bill No. 30681, a Law that regulates the medicinal and therapeutic use of cannabis and its derivatives. Then, a relevant problem from the social point of view is identified, since the way in which the commercialization of these products has been approached, leaves those who reside outside of Lima virtually excluded and, especially, those who do not have economic resources to cover the costs of the treatment, in addition to those associated with transfers and maintenance in Lima to receive the medication and thus alleviate the ailments and collaterals that derive from the suffering of neoplastic pathologies and other chronic non-communicable diseases. For this reason, an investigation was carried out to propose a solution that would be viable from the economic and social point of view and thus favor those who are excluded, violating the principle of universal health. The proposed solution contemplates the creation of a Comprehensive Health Center, based on the use of medicinal cannabis therapy, but in a virtual way. It is about creating a community where patients not only acquire the medicine, but also benefit from a series of complementary and collateral activities that contribute to improving their quality of life beyond alleviating their ailments. The business model is feasible and viable under the indicators of a NPV of S/ 4,612,939.53 compared to S/ 3,697,635.87 of the initial investment and an IRR of 53% compared to the 15% interest rate set by the shareholders, making it a project of business that, in addition to complying with the SDGs of the United Nations 2030 agenda, is sustainable over time

Complete genome sequence of the plant pathogen Ralstonia solanacearum strain ciat-078, isolated in Colombia, obtained using Oxford Nanopore Technology

Moko is one of the main diseases affecting banana and plantain in Colombia. Here, we report the genome sequence of the causal agent, the bacterium Ralstonia solanacearum (Smith) strain CIAT-078, collected in 2004 from affected plantains in central-west Colombia. The assembled genome was obtained using Oxford Nanopore Technology

The 2‐methylpropene degradation pathway in Mycobacteriaceae family strains

Mycolicibacterium gadium IBE100 and Mycobacterium paragordonae IBE200 are aerobic, chemoorganoheterotrophic bacteria isolated from activated sludge from a wastewater treatment plant. They use 2‐methylpropene (isobutene, 2‐MP) as the sole source of carbon and energy. Here, we postulate a degradation pathway of 2‐methylpropene derived from whole genome sequencing, differential expression analysis and peptide‐mass fingerprinting. Key genes identified are coding for a 4‐component soluble diiron monooxygenase with epoxidase activity, an epoxide hydrolase, and a 2‐hydroxyisobutyryl‐CoA mutase. In both strains, involved genes are arranged in clusters of 61.0 and 58.5 kbp, respectively, which also contain the genes coding for parts of the aerobic pathway of adenosylcobalamin synthesis. This vitamin is essential for the carbon rearrangement reaction catalysed by the mutase. These findings provide data for the identification of potential 2‐methylpropene degraders

The transcriptomic networks controlling the sporulation in Physarum polycephalum

von Walter Israel Barrantes Bunstinz

Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany

Potash tailing piles located in Germany represent extremely hypersaline locations that negatively affect neighbouring environments and limit the development of higher vegetation. However, biocrusts, as cryptogamic covers, inhabit some of these areas and provide essential ecological functions, but, nevertheless, they remain poorly described. Here, we applied high-throughput sequencing (HTS) and targeted four groups of microorganisms: bacteria, cyanobacteria, fungi and other eukaryotes. The sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Cyanobacteria and Actinobacteria. Additionally, we applied yanobacteria-specific primers for a detailed assessment of the cyanobacterial community, which was dominated by members of the filamentous orders Synechococcales and Oscillatoriales. Furthermore, the majority of reads in the studied biocrusts obtained by sequencing of the 18S rRNA gene belonged to eukaryotic microalgae. In addition, sequencing of the internal rDNA transcribed spacer region (ITS) showed the dominance of Ascomycota within the fungal community. Overall, these molecular data provided the first detailed overview of microorganisms associated with biocrusts inhabiting highly saline potash tailing piles and showed the dissimilarities in microbial diversity among the samples

Microbial Diversity in Subarctic Biocrusts from West Iceland following an Elevation Gradient

Biological soil crusts (biocrusts) are essential communities of organisms in the Icelandic soil ecosystem, as they prevent erosion and cryoturbation and provide nutrients to vascular plants. However, biocrust microbial composition in Iceland remains understudied. To address this gap in knowledge, we applied high-throughput sequencing to study microbial community composition in biocrusts collected along an elevation gradient (11–157 m a.s.l.) stretching away perpendicular to the marine coast. Four groups of organisms were targeted: bacteria and cyanobacteria (16S rRNA gene), fungi (transcribed spacer region), and other eukaryotes (18S rRNA gene). The amplicon sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Bacteroidetes, and Actinobacteria. Within the cyanobacteria, filamentous forms from the orders Synechococcales and Oscillatoriales prevailed. Furthermore, fungi in the biocrusts were dominated by Ascomycota, while the majority of reads obtained from sequencing of the 18S rRNA gene belonged to Archaeplastida. In addition, microbial photoautotrophs isolated from the biocrusts were assigned to the cyanobacterial genera Phormidesmis, Microcoleus, Wilmottia, and Oscillatoria and to two microalgal phyla Chlorophyta and Charophyta. In general, the taxonomic diversity of microorganisms in the biocrusts increased following the elevation gradient and community composition differed among the sites, suggesting that microclimatic and soil parameters might shape biocrust microbiota

Microbial Diversity in Subarctic Biocrusts from West Iceland following an Elevation Gradient

Biological soil crusts (biocrusts) are essential communities of organisms in the Icelandic soil ecosystem, as they prevent erosion and cryoturbation and provide nutrients to vascular plants. However, biocrust microbial composition in Iceland remains understudied. To address this gap in knowledge, we applied high-throughput sequencing to study microbial community composition in biocrusts collected along an elevation gradient (11–157 m a.s.l.) stretching away perpendicular to the marine coast. Four groups of organisms were targeted: bacteria and cyanobacteria (16S rRNA gene), fungi (transcribed spacer region), and other eukaryotes (18S rRNA gene). The amplicon sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Bacteroidetes, and Actinobacteria. Within the cyanobacteria, filamentous forms from the orders Synechococcales and Oscillatoriales prevailed. Furthermore, fungi in the biocrusts were dominated by Ascomycota, while the majority of reads obtained from sequencing of the 18S rRNA gene belonged to Archaeplastida. In addition, microbial photoautotrophs isolated from the biocrusts were assigned to the cyanobacterial genera Phormidesmis, Microcoleus, Wilmottia, and Oscillatoria and to two microalgal phyla Chlorophyta and Charophyta. In general, the taxonomic diversity of microorganisms in the biocrusts increased following the elevation gradient and community composition differed among the sites, suggesting that microclimatic and soil parameters might shape biocrust microbiota