Biology subjects

Gutierrez, N.

Publications and source records attributed to Gutierrez, N..

4 recordsLinked to original sources

bioRxiv2023

Soils-on-a-chip reveal unforeseen motility parameters of confined Bradyrhizobium diazoefficiens

Soil bacteria of the order of the Rhizobiales associate symbiotically with legume plants. Particulary, Bradyrhizobium diazoefficiens is a nitrogen-fixing symbiont of soybean, that helps to improve grain quality among other benefits. This bacterium possess two flagellar systems, which enable it to swim in water-saturated pores. However, the motility of B. diazoefficiens, which may be crucial for its competitiveness in root nodulation, has not been well understood. To address this knowledge gap, we designed and fabricated microfluidic soil-on-a-chip (SOC) devices that offer sustainable agriculture an original tool for directly visualizing bacterial behavior in confined-environments. Using these microdevices, we measured the population velocities and changes of direction along their paths for two strains of B. diazoefficiens, namely the wild-type and a mutant with only one flagellar system. Our detailed statistical analysis revealed that both strains exhibited reduced speeds and increased changes of direction of 180{degrees}, in channels of decreasing microscopic cross sectional area, down to a few microns. Interestingly, while the wild-type strain displayed faster swimming speeds in unconfined spaces, this advantage was negated in the SOCs that mimicked porous soils. Moreover, we employed the measured motility parameters to model and simulate B. diazoefficiens motion in SOC devices for extended periods and larger scales, enabling further predictions of diffusion in real soils. Thanks to miniaturization, microfabrication, and multidisciplinary knowledge, this study represents a significant breakthrough in soil bacteria field and methods, useful both for farmers and environment. Furthermore, the potential applications of this work extend to multiple beneficial bacteria widely used as biofertilizers.

ecology↗

bioRxiv2022

Genetic analysis of global faba bean germplasm maps agronomic traits and identifies strong selection signatures for geographical origin

Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for further cultivation. However, little is known about the genetics underlying trait diversity. In this study, we use 21,345 high-quality SNP markers to genetically characterise 2,678 faba bean genotypes. We perform genome-wide association studies of key agronomic traits using a Seven-parent-MAGIC population and detect 238 significant marker-trait associations linked to 12 traits of agronomic importance, with 65 of these being stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identify 3 subpopulations differentiated by geographical origin and 33 genomic regions subject to strong diversifying selection between subpopulations. We find that SNP markers associated with the differentiation of northern and southern accessions were able to explain a significant proportion of agronomic trait variance in the Seven-parent-MAGIC population, suggesting that some of these traits have played an important role in breeding. Altogether, our findings point to genomic regions associated with important agronomic traits and selection in faba bean, which can be used for breeding purposes. Key MessageWe identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection.

genetics↗

bioRxiv2022

Identification of leukemia-associated immunophenotypes by database-guided flow cytometry provides a highly sensitive and reproduciblestrategy for the study of measurable residual disease in acutemyeloblastic leukemia

BackgroundMultiparametric Flow Cytometry (MFC) is an essential tool to study the involved cell lineages, the aberrant differentiation/maturation patterns and the expression of aberrant antigens in acute myeloid leukemia (AML). The characterization of leukemia-associated immunophenotypes (LAIPs) at the moment of diagnosis is critical to establish reproducible strategies for the study of measurable residual disease using MFC (MFC-MRD). MethodsIn this study, we identified and characterized LAIPs by comparing the leukemic populations of 145 AML patients, using the EuroFlow AML/ MDS MFC panel, with 6 databases of normal myeloid progenitors (MPCs). Principal component analysis was used to identify and characterize the LAIPs, which were then used to generate individual profiles for MFC-MRD monitoring. Furthermore, we investigated the relationship between the expression patterns of LAIPs and the different subtypes of AML. The MFC-MRD study was performed by identifying residual AML populations that matched with the LAIPs at diagnosis. To further validate this approach, the presence of MRD was also assessed by qPCR (qPCR-MRD). Finally, we studied the association between MFC-MRD and progression-free survival (PFS). ResultsThe strategy used in this study allowed us to describe more than 300 different LAIPs and facilitated the association of specific phenotypes with certain subtypes of AML. The MFC-MRD monitoring based on LAIPs with good/strong specificity was applicable to virtually all patients and showed a good correlation with qPCR-MRD and PFS. ConclusionsThe described methodology provides an objective method to identify and characterize LAIPs. Furthermore, it provides a theoretical basis to develop highly sensitive MFC-MRD strategies.

cancer biology↗

bioRxiv2018

Transcription factor activity and nucleosome organisation in mitosis

Mitotic bookmarking transcription factors (BFs) maintain the capacity to bind to their targets during mitosis, despite major rearrangements of the chromatin. While they were thought to propagate gene regulatory information through mitosis by statically occupying their DNA targets, it has recently become clear that BFs are highly dynamic in mitotic cells. This represents both a technical and a conceptual challenge to study and understand the function of BFs: first, formaldehyde has been suggested to be unable to efficiently capture these transient interactions, leading to profound contradictions in the literature; second, if BFs are not permanently bound to their targets during mitosis, it becomes unclear how they convey regulatory information to daughter cells. Here, comparing formaldehyde to alternative fixatives we clarify the nature of the chromosomal association of previously proposed BFs in embryonic stem cells: while Esrrb can be considered as a canonical BF that binds at selected regulatory regions in mitosis, Sox2 and Oct4 establish DNA sequence independent interactions with the mitotic chromosomes, either throughout the chromosomal arms (Sox2) or at pericentromeric regions (Oct4). Moreover, we show that ordered nucleosomal arrays are retained during mitosis at Esrrb book-marked sites, whereas regions losing transcription factor binding display a profound loss of order. By maintaining nucleosome positioning during mitosis, Esrrb might ensure the rapid post-mitotic re-establishment of functional regulatory complexes at selected enhancers and promoters. Our results provide a mechanistic framework that reconciles dynamic mitotic binding with the transmission of gene regulatory information across cell division.

genomics↗