Analysis of lncRNAs in Lupinus mutabilis (Tarwi) and Their Potential Role in Drought Response.

Lupinus mutabilis is a legume with high agronomic potential and available transcriptomic data for which lncRNAs have not been studied. Therefore, our objective was to identify, characterize, and validate the drought-responsive lncRNAs in L. mutabilis. To achieve this, we used a multilevel approach based on lncRNA prediction, annotation, subcellular location, thermodynamic characterization, structural conservation, and validation. Thus, 590 lncRNAs were identified by at least two algorithms of lncRNA identification. Annotation with the PLncDB database showed 571 lncRNAs unique to tarwi and 19 lncRNAs with homology in 28 botanical families including Solanaceae (19), Fabaceae (17), Brassicaceae (17), Rutaceae (17), Rosaceae (16), and Malvaceae (16), among others. In total, 12 lncRNAs had homology in more than 40 species. A total of 67% of lncRNAs were located in the cytoplasm and 33% in exosomes. Thermodynamic characterization of S03 showed a stable secondary structure with -105.67 kcal/mol. This structure included three regions, with a multibranch loop containing a hairpin with a SECIS-like element. Evaluation of the structural conservation by CROSSalign revealed partial similarities between L. mutabilis (S03) and S. lycopersicum (Solyc04r022210.1). RT-PCR validation demonstrated that S03 was upregulated in a drought-tolerant accession of L. mutabilis. Finally, these results highlighted the importance of lncRNAs in tarwi improvement under drought conditions.

Classification of Amazonian fast-growing tree species and wood chemical determination by FTIR and multivariate analysis (PLS-DA, PLS).

Fast-growing trees like Capirona, Bolaina, and Pashaco have the potential to reduce forest degradation because of their ecological features, the economic importance in the Amazon Forest, and an industry based on wood-polymer composites. Therefore, a practical method to discriminate specie (to avoid illegal logging) and determine chemical composition (tree breeding programs) is needed. This study aimed to validate a model for the classification of wood species and a universal model for the rapid determination of cellulose, hemicellulose, and lignin using FTIR spectroscopy coupled with chemometrics. Our results showed that PLS-DA models for the classification of wood species (0.84 ≤ R2 ≤ 0.91, 0.12 ≤ RMSEP ≤ 0.20, accuracy, specificity, and sensibility between 95.2 and 100%) were satisfied with the full spectra and the differentiation among these species based on IR peaks related to cellulose, lignin, and hemicellulose. Besides, the full spectra helped build a three-species universal PLS model to quantify the principal wood chemical components. Lignin (RPD = 2.27, [Formula: see text] = 0.84) and hemicellulose (RPD = 2.46, [Formula: see text] = 0.83) models showed a good prediction, while cellulose model (RPD = 3.43, [Formula: see text] = 0.91) classified as efficient. This study showed that FTIR-ATR, together with chemometrics, is a reliable method to discriminate wood species and to determine the wood chemical composition in juvenile trees of Pashaco, Capirona, and Bolaina.

Integrated metabolite analysis and health-relevant in vitro functionality of white, red, and orange maize (Zea mays L.) from the Peruvian Andean race Cabanita at different maturity stages.

The high maize (Zea mays L.) diversity in Peru has been recognized worldwide, but the investigation focused on its integral health-relevant and bioactive characterization is limited. Therefore, this research aimed at studying the variability of the primary and the secondary (free and dietary fiber-bound phenolic, and carotenoid compounds) metabolites of three maize types (white, red, and orange) from the Peruvian Andean race Cabanita at different maturity stages (milk-S1, dough-S2, and mature-S3) using targeted and untargeted methods. In addition, their antioxidant potential, and α-amylase and α-glucosidase inhibitory activities relevant for hyperglycemia management were investigated using in vitro models. Results revealed a high effect of the maize type and the maturity stage. All maize types had hydroxybenzoic and hydroxycinnamic acids in their free phenolic fractions, whereas major bound phenolic compounds were ferulic acid, ferulic acid derivatives, and p-coumaric acid. Flavonoids such as luteolin derivatives and anthocyanins were specific in the orange and red maize, respectively. The orange and red groups showed higher phenolic ranges (free + bound) (223.9-274.4 mg/100 g DW, 193.4- 229.8 mg/100 g DW for the orange and red maize, respectively) than the white maize (162.2-225.0 mg/100 g DW). Xanthophylls (lutein, zeaxanthin, neoxanthin, and a lutein isomer) were detected in all maize types. However, the orange maize showed the highest total carotenoid contents (3.19-5.87 µg/g DW). Most phenolic and carotenoid compounds decreased with kernel maturity in all cases. In relation to the primary metabolites, all maize types had similar fatty acid contents (linoleic acid > oleic acid > palmitic acid > α-linolenic acid > stearic acid) which increased with kernel development. Simple sugars, alcohols, amino acids, free fatty acids, organic acids, amines, and phytosterols declined along with grain maturity and were overall more abundant in white maize at S1. The in vitro functionality was similar among Cabanita maize types, but it decreased with the grain development, and showed a high correlation with the hydrophilic free phenolic fraction. Current results suggest that the nutraceutical characteristics of orange and white Cabanita maize are better at S1 and S2 stages while the red maize would be more beneficial at S3.

Diversity of the Peruvian Andean maize (Zea mays L.) race Cabanita: Polyphenols, carotenoids, in vitro antioxidant capacity, and physical characteristics.

The high diversity of the Peruvian Andean maize (Zea mays L.) represents a biological and genetic heritage relevant for food security, but few studies are targeted toward its characterization and consequent valorization and preservation. The objective of this study was to evaluate the potential of the Peruvian Andean maize race Cabanita with respect to its bioactive profiles (free and bound phenolic and carotenoid composition), physical characteristics, and in vitro antioxidant properties. Maize landraces with variable kernel pigmentation were collected from two provinces (Caylloma and Castilla) within the Arequipa region (among ten Andean sites) and the phytochemical profile was evaluated by Ultra High-Performance Liquid Chromatography with diode array detector (UHPLC-DAD). All maize samples were important sources of phenolic compounds mainly soluble p-coumaric and ferulic acid derivatives whereas anthocyanins were only detected in maize with partially red pigmented kernels. Major phenolic compounds in the bound phenolic fractions were ferulic acid and its derivatives along with p-coumaric acid. Carotenoid compounds including xanthophylls such as lutein, lutein isomers, and zeaxanthin were only detected in orange and white-yellow pigmented maize and are reported for the first time in Peruvian landraces. The multivariate analysis using Principal Components Analysis (PCA) revealed low variability of all data which may indicate a level of similarity among maize samples based on evaluated variables. However, maize grown in Caylloma province showed more homogeneous physical characteristics and higher yield, whereas higher phenolic contents and antioxidant capacity were observed in maize from Castilla. Samples CAY (yellow-pigmented kernel, Castilla) and COM (orange-pigmented kernel, Caylloma) had the highest total phenolic (246.7 mg/100 g dried weight basis, DW) and carotenoid (1.95 µg/g DW) contents among all samples. The variable Andean environmental conditions along with differences in farming practices may play a role and should be confirmed with further studies. Current results provide the metabolomic basis for future research using integrated omics platforms targeted toward the complete characterization of the ethnic-relevant maize race Cabanita.

The micronutrient content in underutilized crops: the Lupinus mutabilis sweet case.

Adequate intake of micronutrients is necessary to reduce widespread health issues linked to low intake of iron (Fe), zinc (Zn), boron (B), copper (Cu), and manganese (Mn). Because more than two billion people suffer from micronutrient deficiency globally, to address this problem, highly-nutritious ancestral Peruvian crops like tarwi can be an important component of food security. Thus, our work explores the tarwi micronutrient variability to select biofortified genotypes without affecting seed size and weight. Tarwi is a biofortified food because of its seeds' Fe, Zn, and B content. Furthermore, Boron showed a positive correlation between seed size and weight. At the same time, copper showed a negative correlation. Finally, six accessions (P14, P16, P21, T05, T08, and T25) that are biofortified for Fe, Zn, and B with excellent seed size and weight and with adequate levels of Cu and Mn; adding value to Peruvian biodiversity at a low cost is a starting point for a breeding program to prevent micronutrient disorders.

Evaluation of in vitro susceptibility to sparteine in four strains of Mycobacterium tuberculosis. / Evaluación de la susceptibilidad in vitro a esparteína, en cuatro cepas de Mycobacterium tuberculosis.

Sparteine is an alkaloid with bacteriostatic activity on the genus Mycobacterium. The aim of this study was to evaluate the antimicrobial activity of sparteine on the growth of 4 ATCC strains of Mycobacterium tuberculosis (susceptible, resistant to isoniazid, resistant to rifampicin and multidrug-resistant) in vitro. Validation of bactericidal activity of sparteine sulfate was carried out through an adaptation of the Microscopic-Observation Drug-Susceptibility (MODS) method according to the guidelines of the Peruvian National Health Institute. The results demonstrate that at concentrations of 25; 50 and 100 Mm of sparteine sulfate, there is no development of colony-forming units in any of the 4 evaluated strains. Our results demonstrate the potential in vitro antimicrobial effect of sparteine on multidrug-resistant tuberculosis.

La esparteína es un alcaloide con actividad bacteriostática sobre el género Mycobacterium. El objetivo de este trabajo fue evaluar la acción antimicrobiana de la esparteína en el crecimiento de cuatro cepas ATCC de Mycobacterium tuberculosis (susceptible, resistente a isoniazida, resistente a rifampicina y multidrogorresistente) in vitro. La evaluación de la actividad bactericida del sulfato de esparteína se realizó a través de una adaptación del método de ensayo de cultivo y susceptibilidad a medicamentos antituberculosos mediante observación microscópica (MODS, por sus siglas en inglés), según el protocolo descrito en el manual técnico elaborado por el Instituto Nacional de Salud. Los resultados demuestran que a concentraciones de 25; 50 y 100 mM de sulfato de esparteína, no se desarrollan unidades formadoras de colonia en las cuatro cepas evaluadas de Mycobacterium tuberculosis. Los resultados demuestran el potencial efecto antimicrobiano in vitro de la esparteína en la tuberculosis multidrogorresistente.

Evaluación de la susceptibilidad in vitro a esparteína, en cuatro cepas de Mycobacterium tuberculosis / Evaluation of in vitro susceptibility to sparteine in four strains of Mycobacterium tuberculosis

RESUMEN La esparteína es un alcaloide con actividad bacteriostática sobre el género Mycobacterium. El objetivo de este trabajo fue evaluar la acción antimicrobiana de la esparteína en el crecimiento de cuatro cepas ATCC de Mycobacterium tuberculosis (susceptible, resistente a isoniazida, resistente a rifampicina y multidrogorresistente) in vitro. La evaluación de la actividad bactericida del sulfato de esparteína se realizó a través de una adaptación del método de ensayo de cultivo y susceptibilidad a medicamentos antituberculosos mediante observación microscópica (MODS, por sus siglas en inglés), según el protocolo descrito en el manual técnico elaborado por el Instituto Nacional de Salud. Los resultados demuestran que a concentraciones de 25; 50 y 100 mM de sulfato de esparteína, no se desarrollan unidades formadoras de colonia en las cuatro cepas evaluadas de Mycobacterium tuberculosis. Los resultados demuestran el potencial efecto antimicrobiano in vitro de la esparteína en la tuberculosis multidrogorresistente.

ABSTRACT Sparteine is an alkaloid with bacteriostatic activity on the genus Mycobacterium. The aim of this study was to evaluate the antimicrobial activity of sparteine on the growth of 4 ATCC strains of Mycobacterium tuberculosis (susceptible, resistant to isoniazid, resistant to rifampicin and multidrug-resistant) in vitro. Validation of bactericidal activity of sparteine sulfate was carried out through an adaptation of the Microscopic-Observation Drug-Susceptibility (MODS) method according to the guidelines of the Peruvian National Health Institute. The results demonstrate that at concentrations of 25; 50 and 100 Mm of sparteine sulfate, there is no development of colony-forming units in any of the 4 evaluated strains. Our results demonstrate the potential in vitro antimicrobial effect of sparteine on multidrug-resistant tuberculosis.

An Insight of RuBisCO Evolution through a Multilevel Approach.

RuBisCO is the most abundant enzyme on earth; it regulates the organic carbon cycle in the biosphere. Studying its structural evolution will help to develop new strategies of genetic improvement in order to increase food production and mitigate CO2 emissions. In the present work, we evaluate how the evolution of sequence and structure among isoforms I, II and III of RuBisCO defines their intrinsic flexibility and residue-residue interactions. To do this, we used a multilevel approach based on phylogenetic inferences, multiple sequence alignment, normal mode analysis, and molecular dynamics. Our results show that the three isoforms exhibit greater fluctuation in the loop between αB and ßC, and also present a positive correlation with loop 6, an important region for enzymatic activity because it regulates RuBisCO conformational states. Likewise, an increase in the flexibility of the loop structure between αB and ßC, as well as Lys330 (form II) and Lys322 (form III) of loop 6, is important to increase photosynthetic efficiency. Thus, the cross-correlation dynamics analysis showed changes in the direction of movement of the secondary structures in the three isoforms. Finally, key amino acid residues related to the flexibility of the RuBisCO structure were indicated, providing important information for its enzymatic engineering.

Determination of hemicellulose, cellulose, holocellulose and lignin content using FTIR in Calycophyllum spruceanum (Benth.) K. Schum. and Guazuma crinita Lam.

Capirona (Calycophyllum spruceanum (Benth.) K. Schum.) and Bolaina (Guazuma crinita Lam.) are fast-growing Amazonian trees with increasing demand in timber industry. Therefore, it is necessary to determine the content of cellulose, hemicellulose, holocellulose and lignin in juvenile trees to accelerate forest breeding programs. The aim of this study was to identify chemical differences between apical and basal stem of Capirona and Bolaina to develop models for estimating the chemical composition using Fourier transform infrared (FTIR) spectra. FTIR-ATR spectra were obtained from 150 samples for each species that were 1.8 year-old. The results showed significant differences between the apical and basal stem for each species in terms of cellulose, hemicellulose, holocellulose and lignin content. This variability was useful to build partial least squares (PLS) models from the FTIR spectra and they were evaluated by root mean squared error of predictions (RMSEP) and ratio of performance to deviation (RPD). Lignin content was efficiently predicted in Capirona (RMSEP = 0.48, RPD > 2) and Bolaina (RMSEP = 0.81, RPD > 2). In Capirona, the predictive power of cellulose, hemicellulose and holocellulose models (0.68 < RMSEP < 2.06, 1.60 < RPD < 1.96) were high enough to predict wood chemical composition. In Bolaina, model for cellulose attained an excellent predictive power (RMSEP = 1.82, RPD = 6.14) while models for hemicellulose and holocellulose attained a good predictive power (RPD > 2.0). This study showed that FTIR-ATR together with PLS is a reliable method to determine the wood chemical composition in juvenile trees of Capirona and Bolaina.

Artículo de congreso / Aplicaciones de citometría de flujo en fitomejoramiento

Abstract Population growth, climate change and global warming are the great challenges facing agriculture in the 21st century. Therefore, it is necessary to increase the efficiency of selection of new varieties in plant breeding programs. In this regard, flow cytometry has proven to be a very powerful tool to speed-up selection processes in plant breeding because of its versatility and capacity to evaluate large populations.

Resumen El crecimiento de la población mundial, el cambio climático y el calentamiento global son los grandes desafíos que enfrenta la agricultura en el siglo XXI para lograr un mundo sin hambre. Para lograr la seguridad alimentaria a través del fitomejoramiento es crucial desarrollar germoplasma en menos tiempo que esté bien adaptado. Por lo tanto, es necesario aumentar la eficiencia en las técnicas de fitomejoramiento. En este sentido, la citometría de flujo ha demostrado ser una herramienta muy poderosa para acelerar el mejoramiento genético de las plantas debido a su versatilidad y capacidad para evaluar grandes poblaciones.

The Arabidopsis STRESS RESPONSE SUPPRESSOR DEAD-box RNA helicases are nucleolar- and chromocenter-localized proteins that undergo stress-mediated relocalization and are involved in epigenetic gene silencing.

DEAD-box RNA helicases are involved in many aspects of RNA metabolism and in diverse biological processes in plants. Arabidopsis thaliana mutants of two DEAD-box RNA helicases, STRESS RESPONSE SUPPRESSOR1 (STRS1) and STRS2 were previously shown to exhibit tolerance to abiotic stresses and up-regulated stress-responsive gene expression. Here, we show that Arabidopsis STRS-overexpressing lines displayed a less tolerant phenotype and reduced expression of stress-induced genes confirming the STRSs as attenuators of Arabidopsis stress responses. GFP-STRS fusion proteins exhibited localization to the nucleolus, nucleoplasm and chromocenters and exhibited relocalization in response to abscisic acid (ABA) treatment and various stresses. This relocalization was reversed when stress treatments were removed. The STRS proteins displayed mis-localization in specific gene-silencing mutants and exhibited RNA-dependent ATPase and RNA-unwinding activities. In particular, STRS2 showed mis-localization in three out of four mutants of the RNA-directed DNA methylation (RdDM) pathway while STRS1 was mis-localized in the hd2c mutant that is defective in histone deacetylase activity. Furthermore, heterochromatic RdDM target loci displayed reduced DNA methylation and increased expression in the strs mutants. Taken together, our findings suggest that the STRS proteins are involved in epigenetic silencing of gene expression to bring about suppression of the Arabidopsis stress response.

Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior.

It is known that environmental factors can affect the biosynthesis of leaf metabolites. Similarly, specific pairwise plant-microbe interactions modulate the plant's metabolome by stimulating production of phytoalexins and other defense-related compounds. However, there is no information about how different soil microbiomes could affect the plant growth and the leaf metabolome. We analyzed experimentally how diverse soil microbiomes applied to the roots of Arabidopsis thaliana were able to modulate plant growth and the leaf metabolome, as assessed by GC-MS analyses. Further, we determined the effects of soil microbiome-driven changes in leaf metabolomics on the feeding behavior of Trichopulsia ni larvae. Soil microbiomes differentially impacted plant growth patterns as well as leaf metabolome composition. Similarly, most microbiome-treated plants showed inhibition to larvae feeding, compared with unamended control plants. Pyrosequencing analysis was conducted to determine the soil microbial composition and diversity of the soils used in this study. Correlation analyses were performed to determine relationships between various factors (soil microbial taxa, leaf chemical components, plant growth patterns and insect feeding behavior) and revealed that leaf amino acid content was positively correlated with both microbiome composition and insect feeding behavior.

Mild salinity stimulates a stress-induced morphogenic response in Arabidopsis thaliana roots.

Plant roots exhibit remarkable developmental plasticity in response to local soil conditions. It is shown here that mild salt stress stimulates a stress-induced morphogenic response (SIMR) in Arabidopsis thaliana roots characteristic of several other abiotic stresses: the proliferation of lateral roots (LRs) with a concomitant reduction in LR and primary root length. The LR proliferation component of the salt SIMR is dramatically enhanced by the transfer of seedlings from a low to a high NO3- medium, thereby compensating for the decreased LR length and maintaining overall LR surface area. Increased LR proliferation is specific to salt stress (osmotic stress alone has no stimulatory effect) and is due to the progression of more LR primordia from the pre-emergence to the emergence stage, in salt-stressed plants. In salt-stressed seedlings, greater numbers of LR primordia exhibit expression of a reporter gene driven by the auxin-sensitive DR5 promoter than in unstressed seedlings. Moreover, in the auxin transporter mutant aux1-7, the LR proliferation component of the salt SIMR is completely abrogated. The results suggest that salt stress promotes auxin accumulation in developing primordia thereby preventing their developmental arrest at the pre-emergence stage. Examination of ABA and ethylene mutants revealed that ABA synthesis and a factor involved in the ethylene signalling network also regulate the LR proliferation component of the salt SIMR.

Functional-genomics-based identification of genes that regulate Arabidopsis responses to multiple abiotic stresses.

Abiotic stresses are a primary cause of crop loss worldwide. The convergence of stress signalling pathways to a common set of transcription factors suggests the existence of upstream regulatory genes that control plant responses to multiple abiotic stresses. To identify such genes, data from published Arabidopsis thaliana abiotic stress microarray analyses were combined with our presented global analysis of early heat stress-responsive gene expression, in a relational database. A set of Multiple Stress (MST) genes was identified by scoring each gene for the number of abiotic stresses affecting expression of that gene. ErmineJ over-representation analysis of the MST gene set identified significantly enriched gene ontology biological processes for multiple abiotic stresses and regulatory genes, particularly transcription factors. A subset of MST genes including only regulatory genes that were designated 'Multiple Stress Regulatory' (MSTR) genes, was identified. To validate this strategy for identifying MSTR genes, mutants of the highest-scoring MSTR gene encoding the circadian clock protein CCA1, were tested for altered sensitivity to stress. A double mutant of CCA1 and its structural and functional homolog, LATE ELONGLATED HYPOCOTYL, exhibited greater sensitivity to salt, osmotic and heat stress than wild-type plants. This work provides a reference data set for further study of MSTR genes.