Repositorio Nacional

Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the “diversity arrays technology sequencing,” while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled.

Bacterial Community Structure DArT-Seq Bacterial Community Functionality Genes Involved in N Cycling CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA AGRICULTURAL PRACTICES MAIZE RHIZOSPHERE STEMS NITROGEN FERTILIZERS

Evaluación de la acumulación mitocondrial de estrógenos sintéticos mito-dirigidos en un modelo in vitro

Evaluation of mitochondrial accumulation of mito-targeted synthetic estrogens on in vitro model

Magdiel Orozco Valdivia (2023, [Tesis de maestría])

La mitocondria es un organelo que cumple funciones esenciales en el mantenimiento de las células eucariotas y su disfunción está asociada a la progresión de enfermedades neurodegenerativas, metabólicas y cardiovasculares. Por lo anterior es necesario encontrar tratamientos que mejoren la función mitocondrial. Los estrógenos son hormonas que tienen diversos efectos benéficos sobre las células. Entre estos efectos, se ha observado que las hormonas inciden en la función mitocondrial, por lo que son un potencial tratamiento para las enfermedades asociadas a la disfunción mitocondrial. Una alternativa es mediante los compuestos mito-dirigidos, moléculas con actividad biológica que son acoplados a cationes lipofílicos con la capacidad de acumularse a mayor concentración en la mitocondria respecto a las sustancias no mito-dirigidas. Por lo tanto, se plantea conferir la propiedad acumulativa a los estrógenos mediante el acoplamiento de trifenilfosfonio, un catión lipofílico recurrentemente usado para la generación de mito-dirigidos. Para el presente trabajo se sintetizaron dos estrógenos mito-dirigidos. Este proyecto evalúa la acumulación mitocondrial de los estrógenos mito-dirigidos después de una exposición de estos en un modelo in vitro sensible a estrógenos, comparando su acumulación con la del estrógeno no mito-dirigido. Los resultados indican que los estrógenos mito-dirigidos se acumulan más en las mitocondrias que el estrógeno no mito-dirigido y demuestra que los estrógenos mito-dirigidos tienen capacidad acumulativa, esto permite sentar las bases de un tratamiento hormonal dirigido a las mitocondrias que se pueda aplicar a enfermedades asociadas a la disfunción mitocondrial.

Mitochondria are essential organelles of eukaryotic cells, and their dysfunction is associated with the onset and development of neurodegenerative, metabolic, and cardiovascular diseases. Thus, it is important to develop treatments to improve mitochondrial function. One of the options are estrogens, these hormones have a protective role in cellular function by participating in the regulation of mitochondrial function, making estrogens candidates to be a potential treatment for diseases related to mitochondrial dysfunction. One of the alternative treatments are mito-targeted molecules, which are biologically active molecules conjugated with lipophilic cations. These mito-targeted molecules can accumulate inside mitochondria more than non-targeted molecules. This project aims to synthesize mito-targeted estrogens by conjugating a lipophilic cation, triphenylphosphonium, to a parent estrogenic compound. Our hypothesis is that these novel molecules will accumulate in the interior of the mitochondria and will have more biological activity than the non-targeted estrogen. We synthesized two mito-targeted estrogens for this project and evaluated the mitochondrial accumulation in an estrogen-sensitive in vitro model, comparing their accumulation to non-targeted estrogens. The results indicate mito-targeted estrogens accumulate in mitochondria more than the non-targeted estrogens, showing that mito-targeted estrogens have an accumulation capacity. This insight will make new treatments for diseases related to mitochondrial dysfunction.

estrógenos, mito-dirigido, disfunción mitocondrial, acumulación, mitocondria estrogens, mitochondria, mito-targeted, accumulation, mitochondrial dysfunction BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA HUMANA HORMONAS HORMONAS

De Novo assembly and annotation of the Pacific calico scallop (Argopecten ventricosus) transcriptome for immune-related gene discovery

RUTH ESCAMILLA MONTES GENARO DIARTE PLATA GABRIELA BERENICE MENDOZA MALDONADO Aarón Barraza Celis Carlos Eliud Angulo Valadez Seyed Hossein Hoseinifar Jesús Arturo Fierro Coronado ANTONIO LUNA GONZALEZ (2022, [Artículo])

"Invertebrates' immune defense mechanisms play a critical role in pathogen recognition and elimination. De novo assembly and annotation of the Argopecten ventricosus transcriptome were performed for the immune-related gene identification. Scallops (height: 4.4 cm) were challenged with inactivated Vibrio parahaemolyticus IPNGS16. The RNA from different tissues was pooled for a single cDNA library construction sequenced by NextSeq 500 platform 2×75 paired‐end chemistry. Before de novo assembling with Trinity, reads were analyzed with FastQC, Trimmomatic, and Prinseq. Assembled sequences were analyzed by CD-HIT-EST and TransDecoder. The corresponding annotation was performed against NCBI-nr, RefSeq protein, and KAAS (KEGG) databases. The Trinity assembly yielded 107,516 contigs. TransDecoder yielded 25,285 sequences as CDSs of which, 16,123 were annotated against the NCBI-nr protein, most of them scored with Crassostrea gigas data. Gene ontology mapped sequences (15,262) were classified in molecular functions (~13,000), cellular components (~11,000), and biological processes (~13,000). The KAAS analysis showed biological categories for metabolism (13%), cellular processes (12%), genetic information processing (10%), organismal systems (19%), environmental information (13%), and human diseases (33 %). Within the organismal systems, 467 immune-related genes (KO) were identified. Sixty-four immune-related genes were annotated/blasted against the NCBI-nr and RefSeq protein databases. An RT-qPCR was performed to analyze the expression level of immune-related genes obtained in the transcriptome analysis in scallops (height 4.5 cm) treated with probiotic bacilli added to culture water. Bacilli significantly increased the expression of the HSP70 and PGRP genes. The gene transcripts analysis of A. ventricosus will better understand its immune response against pathogens in culture systems."

Argopecten ventricosus, calico scallop, transcriptome, bivalve, immune genes BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) INMUNOLOGÍA INMUNOLOGÍA

Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis

ELIANA VALENCIA LOZANO LISSET HERRERA ISIDRON Osiel Salvador Recoder-Meléndez Aarón Barraza Celis JOSE LUIS CABRERA PONCE (2022, [Artículo])

"Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein–protein interaction (PPI) network analyses performed in the STRING database (v11.5), we found 299 genes tightly associated in 14 clusters. Two major clusters of up-regulated proteins fundamental for life growth and development were found: 29 ribosomal proteins (RPs) interacting with 6 PEBP family members and 117 cell cycle (CC) proteins. The PPI network of up-regulated transcription factors (TFs) revealed that at least six TFs–MYB43, TSF, bZIP27, bZIP43, HAT4 and WOX9–may be involved during MTs development. The PPI network of down-regulated genes revealed a cluster of 83 proteins involved in light and photosynthesis, 110 in response to hormone, 74 in hormone mediate signaling pathway and 22 related to aging."

transcriptome-wide analysis, microtubers, potato, Solanum tuberosum, darkness, cell cycle, ribosomal proteins, PEBP family genes, cytokinin BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA MOLECULAR DE PLANTAS GENÉTICA MOLECULAR DE PLANTAS