Biology subjects

Perdomo, C.

Publications and source records attributed to Perdomo, C..

3 recordsLinked to original sources

bioRxiv2022

Comparison of B values obtained by two methodologies that use soil as a substrate and their influence on the estimation of the proportion of nitrogen fixed by legumes

The B value is required to quantify the nitrogen derived from the atmosphere (%Ndfa) in the Rhizobium-legume symbiosis using the 15N natural abundance method. When the B value of a particular specie is not known, one possibility Is to use as a proxy the B value of a specie from the same genus, but this can cause the estimate of %Ndfa to be inaccurate. In this work, we compared two methodologies for determining the B value of Crotalaria juncea, C. spectabilis, C. ochroleuca and Cajanus cajan, using soil as the substrate. One method involvedgrowing plants in soil and averaging the lowest {delta}15N values of plant shoots (B-minimum), while the other consisted in adding sucrose to soil to immobilize the mineral nitrogen (N-immobilized), and then averaging the shoot {delta}15N values of all plants. Results showed that B values of C. cajan and C. ochroleuca obtained using the N-immobilized method were up to 1{per thousand} lower than those reported in the literature for these species. Therefore, we propose that, at least in these species, B values determined with the N-immobilized method should be used to estimate the%Ndfa.

plant biology↗

bioRxiv2018

Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques

The need to reduce per sample cost of RNA-seq profiling for scalable data generation has led to the emergence of highly multiplexed RNA-seq. These technologies utilize barcoding of cDNA sequences in order to combine samples into single sequencing lane to be separated during data processing. In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher. We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq and microarray, as well as another low-cost highly multiplexed technique known as 3 digital gene expression (3DGE). Data was generated for a set of exposure experiments on immortalized human lung epithelial (AALE) cells in a two-by-two study design, in which samples received both genetic and chemical perturbations of known oncogenes/tumor suppressors and lung carcinogens. SFL demonstrated improved performance over 3DGE in terms of coverage, power to detect differential gene expression, and biological recapitulation of patterns of differential gene expression from in vivo lung cancer mutation signatures.

bioinformatics↗

bioRxiv2018

Molecular Subtyping reveals Immune Alterations associated with Progression of Bronchial Premalignant Lesions

Bronchial premalignant lesions (PMLs) are precursors of lung squamous cell carcinoma, but have variable outcome, and we lack tools to identify and treat PMLs at highest risk for progression to invasive cancer. Profiling endobronchial biopsies of PMLs obtained from high-risk smokers by RNA-Seq identified four PML subtypes with differences in epithelial and immune processes. One molecular subtype (Proliferative) is enriched with dysplastic lesions and exhibits up-regulation of metabolic and cell cycle pathways and down-regulation of ciliary processes. RNA-Seq profiles from normal-appearing uninvolved large airway brushings could identify subjects with Proliferative lesions with high specificity. Expression of interferon signaling and antigen processing/presentation pathways are decreased in progressive/persistent Proliferative lesions and immunofluorescence indicates a depletion of innate and adaptive immune cells in these lesions. Molecular biomarkers measured in PMLs or the uninvolved airway can enhance histopathological grading and suggests that immunoprevention strategies may be effective in intercepting the progression of PMLs to lung cancer.

cancer biology↗