Biology subjects

Pacheco, E.

Publications and source records attributed to Pacheco, E..

4 recordsLinked to original sources

bioRxiv2025

A high-quality genome assembly and integrative data portal (Phabase) for the Mesoamerican black bean (Phaseolus vulgaris cv. Negro Jamapa)

Common bean (Phaseolus vulgaris L.) is one of the major legume crops worldwide, constituting a fundamental part of the diet in several countries. In central and south Mexico, the Mesoamerican Negro Jamapa variety is the one of most widely consumed cultivar, and it has notably served as a working model for functional genomics to address the molecular responses to stresses and during the nitrogen-fixing symbiosis with rhizobia. Despite this, the genome sequence of this landrace is not yet available, and the transcriptomic data generated by different research groups on this species are scattered. This prompted us to carry out a de novo sequencing, assembly and gene prediction for Negro Jamapa genome, using Hi-Fi PacBio technology and advanced genomic tools, respectively. Herein, we present a high-quality genome assembly for Negro Jamapa at chromosome level. The assembled genome is 522 Mb length, with an N50 of 45Mb, 89X coverage and BUSCO completeness of 98.4%, parameters that are considerably better than the available Mesoamerican reference genome. In parallel, we built an expression atlas of P. vulgaris from various tissues and growth conditions, by re-mapping publicly available RNA-seq and small RNA-seq data produced in recent years by distinct research groups. This analysis is available for the scientific community in the new user-friendly portal developed in this study, Phabase (https://phabase.ccg.unam.mx/). This portal includes several tools such as BLAST, gene and microRNA expression atlas, JBrowse, download section and integration with other Phaseolus spp. genomes. Significance statementIn this study we report the first genome sequence of Phaseolus vulgaris Negro Jamapa, one of the most widely consumed bean varieties and a key experimental model for multiple research groups. We also developed Phabase (Phabase), an integrated database hosting this genome together with BLAST, JBrowse, and a comprehensive expression atlas. This resource enables functional genomics, comparative analyses, and accelerated breeding of common bean.

plant biology↗

bioRxiv2025

PHYSICOCHEMICAL PROPERTIES OF ENHANCED AND RECOVERED VENEZUELAN CRUDE OIL TREATED WITH BIOCOMPATIBLE PHARMACEUTICAL FORMULATION: SIMULATION OF THE ROLE OF WATER AND IONIC CONTENT.

In this work, the hydrogen bonding interaction of water and ethanol with Polysorbate 80 (P-80, Tween 80) is simulated, in relation to its role in oil upgrading and recovery, using real theoretical and experimental studies. The theoretical physicochemical results obtained were compared with other experimental results derived from the treatment of improved and recovered oil after mixing Biocompatible Pharmaceutical Formulations (BPF) of these three compounds and oil produced in Venezuela. The Spartan 16 program was used to build the molecular structures and simulate the interactions with the semi-empirical PM3 method, to compare them with two real experiments. These two experiments were performed as follows: in the first, the mixture consists of a surfactant, (Z)-Sorbitan mono-9-octadecenoate poly(oxy-1,2-ethanediyl) or polyoxoethylene (20) sorbitan mono-oleate (Polysorbate 80), which is mixed with the hydrocarbon, and then completely fluidized with the addition of ethyl alcohol or ethanol.Water and ions (<100 ppm) present in this experiment are contained in oil and ethanol as contaminants (approximately 1.73-1.30% of total water). In the second experiment, the BPF ratios were 10:5:0.1:0.01 for oil:water with 17,800 ppm NaCl:P-80:ethanol (approximately 33.09% of total water and 1.78% w/v NaCl). The simulations were performed taking into account both real experiments. The simulated interactive products were characterized by the following parameters: energy, minimum conformational energy, solvation energy, aqueous energy, HOMO energy, LUMO energy, {Delta}E, dipole moment, polarizability, electrostatic potential map (EPM) and electron density.A theoretical parametric relationship (sio Index, "stability in oil Index") is developed to evaluate the stability of the molecular forms generated within the hydrocarbon. The following theoretical experiments were performed: First, successive interactions of water with P-80 from position 1 to position 21. Second, successive interactions from position 1 to position 21 of P-80 of water and ethanol, 1 to 1. Third, successive interactions with P-80 of 21 ethanol molecules on the final product of the first experiment. These theoretical results were compared with some experimental results obtained using Oil Mixtures. The results obtained and compared in both experimental series (theoretical and real) allow to distinguish the role of P-80, Ethanol, Water and ions for the improvement and recovery of the treated oil. It is concluded that the formulation that does not contain added water and sodium chloride is supposed to use the contaminating water present in the petroleum and the water contained in the ethanol (<5%).This formulation has very little effect on the resulting Density of the improved Oil, but it greatly decreases the resulting Viscosity in the Crude Oil. The formulation that contains more than 30% added Water decreases the Density while the Viscosity of the Crude Oil responds proportionally to the Water retained in it. This difference in the results could be interpreted as a different proportion and chemical composition as a consequence of a different structural relationship between these components and a different conformation of the nanoparticle generated within the Oil, in each case. In this sense, the hypothesis is established that there would be an intermediate molecular form that could improve both Viscosity and Density.

biophysics↗

bioRxiv2023

Highlighting fibroblast plasticity in lung fibrosis: the WI-38 cell line as a model for investigating the myofibroblast and lipofibroblast switch

BackgroundMyofibroblasts (MYFs) are generally considered the principal culprits in excessive extracellular matrix deposition and scar formation in the pathogenesis of lung fibrosis. Lipofibroblasts (LIFs), on the other hand, are defined by their lipid-storing capacity and are predominantly found in the alveolar regions of the lung. They have been proposed to play a protective role in lung fibrosis. We previously reported that a LIF to MYF reversible differentiation switch occurred during fibrosis formation and resolution. In this study, we tested whether WI-38 cells, a human embryonic lung fibroblast cell line, could be used to study fibroblast differentiation towards the LIF or MYF phenotype and whether this could be relevant for idiopathic pulmonary fibrosis (IPF). Methodsusing WI-38 cells, MYF differentiation was triggered using TGF-{beta}1 treatment and LIF differentiation using Metformin treatment. We analyzed the LIF to MYF and MYF to LIF differentiation by pre-treating the WI-38 cells with TGF-{beta}1 or Metformin first, followed by treatment with Metformin and TGF-{beta}1, respectively. We used IF, qPCR and bulk RNA-Seq to analyze the phenotypic and transcriptomic changes in the cells. We correlated our in vitro transcriptome data from WI-38 cells (obtained via bulk RNA sequencing) with the transcriptomic signature of LIFs and MYFs derived from the IPF cell atlas as well as with our own single-cell transcriptomic data from IFP patients-derived lung fibroblasts (LF-IPF) cultured in vitro. We also carried out alveolosphere assays to evaluate the ability of the proposed LIF and MYF cells to support the growth of alveolar epithelial type 2 cells. ResultsWI-38 and LF-IPF display similar phenotypical and gene expression responses to TGF-{beta}1 and Metformin treatment. Bulk RNA-Seq analysis of WI-38 and LF-IPF treated with TGF-{beta}1, or Metformin indicate similar transcriptomic changes. We also show the partial conservation of the LIF and MYF signature extracted from the Habermann et al. scRNA-seq dataset in WI-38 cells treated with Metformin or TGF-{beta}1, respectively. Alveolosphere assays indicate that LIFs enhance organoid growth, while MYFs inhibit organoid growth. Finally, we provide evidence supporting the LIF to MYF reversible switch using WI-38 cells. ConclusionsWI-38 cells represent a versatile and reliable model to study the intricate dynamics of fibroblast differentiation towards the MYF or LIF phenotype associated with lung fibrosis formation and resolution, providing valuable insights to drive future research. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/572972v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@9a5c19org.highwire.dtl.DTLVardef@149edborg.highwire.dtl.DTLVardef@1c9579aorg.highwire.dtl.DTLVardef@1964167_HPS_FORMAT_FIGEXP M_FIG in vitro approach using WI-38 cells as a versatile and reliable model to study the MYF or LIF phenotype associated with lung fibrosis formation and resolution observed in vivo. WI-38 are providing valuable insights to drive future research on lung fibrosis. C_FIG

cell biology↗

bioRxiv2018

The genetic prehistory of the Andean highlands 7,000 Years BP though European contact

The peopling of the Andean highlands above 2500m in elevation was a complex process that included cultural, biological and genetic adaptations. Here we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7,000 calendar years before present (BP), and compare them to 64 new genome-wide genetic variation datasets from both high and lowland populations. We infer three significant features: a split between low and high elevation populations that occurred between 9200-8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. Importantly, we do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.\n\nOne Sentence SummaryAncient DNA from the Andes reveals a complex picture of human adaptation from early settlement to the colonial period.

genomics↗