Biology subjects

Ortega, J. M.

Publications and source records attributed to Ortega, J. M..

6 recordsLinked to original sources

bioRxiv2026

Inositol Pyrophosphates Mediate Chloroplast Lipid Remodeling and Nuclear Gene Repression during High-Light Acclimation in Chlamydomonas reinhardtii

Microalgae are photosynthetic organisms capable of autotrophic growth. Their applicability in multiple industrial fields has been largely studied, thanks to their ability to fixate CO2 into high added value organic products like fatty acids and carotenoids. However, our understanding of the cellular signaling networks that control carbon flux and acclimation to environmental stress remains incomplete. In this study, we used the Chlamydomonas reinhardtii mutant strain vip1-1, which carries a loss-of-function mutation in the hexakisphosphate kinase re-sponsible for the synthesis of inositol pyrophosphates InsP7 and InsP8 (PP-InsPs), to investi-gate the role of these molecules during high-light acclimation. Our results indicate that PP-InsPs participate in the regulation of carbon storage in the form of starch and their deficiency increases TAGs levels in the algal cells. They also impact chloroplast-specific lipid remodeling by modifying membrane composition and fluidity through fatty acid desaturations and glycer-olipid composition. In addition, our findings suggest that PP-InsPs are involved in chloroplast-nucleus communication, where they coordinate transcriptional repression of photosynthesis associated nuclear genes (PhANGs), fatty acid desaturases and lipid synthases, contributing to cellular acclimation to high light. We also found that PP-InsPs modulating effect extended to protein synthesis and accumulation of Calvin-Benson-Bassham cycle intermediates. Therefore, we propose that PP-InsPs function as integratory molecules that balance carbon allocation between storage and structural pools, in response to environmental cues such as high light. These data uncover a novel function of PP-InsPs in high light acclimation and po-tentially in chloroplast-nucleus communication, providing new insights that may help engineering more resilient and efficient strains.

plant biology↗

bioRxiv2026

AlphaUnfold: Probing Potential Unfolding and Structural Fragility in AlphaFold3 Models via Short-Time High-Pressure MD

We developed AlphaUnfold, an automated pipeline that couples AF3 predictions with short-time (5 ns) high-pressure Molecular Dynamics (MD) using NAMD3. By subjecting models to baric stress, AlphaUnfold acts as a dynamic "stress-test" to identify structural fragility and potential unfolding. Testing a diverse set of proteins revealed a significant inverse correlation between average pLDDT and Root Mean Square Deviation (RMSD) after MD, indicating that lower confidence translates to rapid structural drift. Furthermore, domains with low local pLDDT consistently exhibited high Root Mean Square Fluctuation (RMSF), a behavior also observed in 200 ns simulations under standard pressure, pinpointing specific metastable areas. AlphaUnfold thus provides a viable, computationally efficient framework for assessing the biophysical robustness of AI-generated models, offering an "experimental-like" validation that ensures more reliable downstream applications in structural biology. MotivationAlphaFold3 (AF3) provides high-accuracy protein models characterized by the Predicted Local Distance Difference Test (pLDDT). However, these static predictions may harbor "not well-forged" regions lacking thermodynamic resilience. There is a critical need for rapid computational protocols to validate structural integrity beyond static confidence scores. AvailabilityGitHub: https://github.com/pegados/pipeline_AlphaUnfold Supplementary informationSupplementary data are available at http://biodados.icb.ufmg.br/alphaunfold Contacte-mail fabio, silva-jrp.miguel@ufmg.br

bioinformatics↗

bioRxiv2020

TaxOnTree: a tool that generates trees annotated with taxonomic information

Phylogenetic analysis is a widely used approach for analyzing and illustrating gene/protein/species evolution and is being benefited by the increasing number of species with their DNA/genome sequenced. Generating a phylogenetic tree with sequences from hundreds of species can be considered a routine task. However, tree visualization has been challenged to organize and bring by accessible means relevant information, e.g. taxonomy, about the sampled genes/proteins. Here we present TaxOnTree, a computational tool that incorporates and allows a quick accession of the taxonomic information of samples in a phylogenetic tree. TaxOnTree takes as input a single phylogenetic tree in Newick format containing gene/protein identifiers from NCBI or Uniprot databases in their leaves but TaxOnTree also allows users to have as input a protein identifier, a single protein in FASTA, a list of protein accessions, or a(n) (un)aligned multi-FASTA file. Non-tree inputs are submitted to a phylogenetic reconstruction pipeline implemented into TaxOnTree. The tree provided by the user or generated by the pipeline is converted to Nexus format and then automatically annotated with the taxonomic information of each sample comprising the tree. The taxonomic information is retrieved by web requests from NCBI or Uniprot servers or from a local MySQL database and annotated as tags in the tree nodes. The final tree archive is in Nexus format and should be opened with FigTree software which allows visual inspection, by branch coloring or tip/node labeling, of the taxonomic information incorporated in the tree. TaxOnTree provides prompt inspection of the taxonomic distribution of orthologs and paralogs. It can be used for manual curation of taxonomic/phylogenetic scenarios and coupled to any tool that links homologous sequences to a seed sequence. TaxOnTree provides computational support to help users to inspect phylogenetic trees with a taxonomic view, even without being taxonomy experts. TaxOnTree is available at http://bioinfo.icb.ufmg.br/taxontree.

bioinformatics↗

bioRxiv2020

Taxallnomy: Closing gaps in the NCBI Taxonomy

NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Despite the extensive use and application of this data source, taking advantage of its taxonomic tree could be challenging because (1) some taxonomic ranks are missing in some lineages and (2) some nodes in the tree do not have a taxonomic rank assigned (referred to as "no rank"). To address this issue, we developed an algorithm that takes the tree structure from NCBI Taxonomy and generates a hierarchically complete taxonomic tree. The procedures performed by the algorithm consist of attempting to assign a taxonomic rank to "no rank" nodes and of creating/deleting nodes throughout the tree. The algorithm also creates a name for the new nodes by borrowing the names from its ranked child or, if there is no child, from its ranked parent node. The new hierarchical structure was named taxallnomy and it contains 33 hierarchical levels corresponding to the 33 taxonomic ranks currently used in the NCBI Taxonomy database. From taxallnomy, users can obtain the complete taxonomic lineage with 33 nodes of all taxa available in the NCBI Taxonomy database. Taxallnomy is applicable to several bioinformatics analyses that depend on NCBI Taxonomy data. In this work, we demonstrate its applicability by embedding taxonomic information of a specified rank into a phylogenetic tree; and by making metagenomics profiles. Taxallnomy algorithm was written in PERL and all its resources are available at bioinfo.icb.ufmg.br/taxallnomy. Database URL: http://bioinfo.icb.ufmg.br/taxallnomy

bioinformatics↗

bioRxiv2020

Assessing the sex-related genomic composition difference using a K-mer-based approach: a case of study in Arapaima gigas (Pirarucu).

Arapaima gigas is one of the largest freshwater bony fish in the world, in which adults could weigh 200 kilograms and measure 3 meters in length. Due to its large size and its low-fat meat, Arapaima gigas has quickly become a species of special interest in fish-farming. One challenge faced during their production is the lack of an efficient sexing methodology, since their sexual maturation occurs late (around the third to the fifth year) and the genetic mechanisms linked to their sex determination system are not known yet. For a more sustainable management, it is of paramount importance to seek an effective and non-invasive method to differentiate sexually juvenile individuals of Arapaima gigas. For this, the establishment of genetic markers associated with sexual differentiation would be an advantageous tool. In this study, we proposed a k-mer based approach to identify genome features with sex-determining properties. For this purpose, we used genomic data from four adult representatives of Arapaima gigas, two males and two females, and counted the k-mers comprising them. As result, we found k-mers from repetitive regions with high difference and disproportion in the count among individuals of the opposite sex. These differences in the k-mer-based genomic composition indicate the existence of genetic factors involved in the sexing of individuals in Arapaima gigas.

genomics↗

bioRxiv2019

A potential genomic recombination site upstream of the rfb locus in Leptospira interrogans is associated with serogroup Serjoe and serovar Hardjo classification

Leptospirosis is a zoonotic disease caused by pathogenic spirochetes of the genus Leptospira. It has a global distribution and affects domestic animals, including cattle. In livestock production, Leptospira interrogans serogroup Sejroe serovar Hardjo is the major reproductive disease leading to economic losses. The whole-genome sequence of the first Brazilian clinical isolate classified as L. interrogans serogroup Sejroe serovar Hardjo strain Norma enabled the evaluation of its genomic features. Here, we investigated particularities of this isolate, obtained from a leptospirosis outbreak. Bioinformatic analysis using the L. interrogans serovar Hardjo str. Norma was applied as a reference for genomic evaluation and comparative analysis among L. interrogans and L. borgpetersenii serovars. Our data suggest the occurrence of genomic recombination in L. interrogans serovar Hardjo str. Norma encompassing 45 Kb located upstream of the rfb locus. A hallmark of genetic evolution was predicted through an orthologue analysis that identified that sugar enzymes associated with carbohydrate and lipid biosynthesis and metabolism composed this genetic module. Comparative genomics revealed a wide range of relatedness among the bacterial strains of serogroup Sejroe that are classified as L. interrogans and L. borgpetersenii species. Furthermore, identification of an IS3 family suggests a genetic recombination site in L. interrogans serovar Hardjo str. Norma that is distinct among L. interrogans serovars and may contribute to clarify the taxonomic classification of Leptospira spp.\n\nImpact StatementLeptospirosis remains an important neglected disease with worldwide distribution. This zoonotic disease impacts in the livestock production and the bovine infection is currently associated to species L. borgpetersenii and L. interrogans serovar Hardjo. L.interrogans serovar Hardjo infection is recognized as reproductive disease associated with abortion and economic lost. In this context, we studied a unique whole genome sequence of L. interrogans serovar Hardjo subtype Hardjo-prajitno isolated from bovine leptospirosis outbreaks in Brazilian dairy farm, one of the greatest country of milk production in world. We compared L. interrogans and L. borgpetersenii genomes with L. interrogans serogroup Sejroe serovar Hardjo subtype Hardjo-prajitno focusing on rfb locus and sugars biosynthesis. Leptospira spp. taxonomy and serology information are strictly associated with rfb locus and we found high correlation among bacterial strains classified in serogroup Sejroe. Although L. interrogans and L. borgpetersenii classified in serogroup Sejroe possess a greater genetic correlation, we uniquely identified that serovar Hardjo strains often possess identical loci carrying predicted sugar biossinthesis genes and mobile elements. The Sru (Sejroe specific Rfb Upstream locus) locus associated to rfb locus probably contribute to Leptospira spp. genetic information concerning serogroup and serovar degrees of taxonomic and serology in this microbiology field.\n\nData SummaryAll Leptospira spp. genome sequences used in this study were retrieved from National Center for Biotechnology Information (NCBI) (Table 1) with NCBI ID: NZ_CP006723.1, NZ_CP012603.1, NC_004342.2, NZ_CP011934.1, NZ_AKXA02000040.1, NZ_CP013147.1, NZ_CP012029.1, NZ_CP015048.1, NC_008508.1, GCA_000216175.3,GCA_000244115.3, NC005823.1, GCA_000244395.3, GCA_000346975.1.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@843b1eorg.highwire.dtl.DTLVardef@1453917org.highwire.dtl.DTLVardef@1a75127org.highwire.dtl.DTLVardef@1c0e185org.highwire.dtl.DTLVardef@160aa4_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1:C_FLOATNO O_TABLECAPTIONLeptospira spp. strains used in this study.\n\nC_TABLECAPTION C_TBL HighlightsO_LIThe study identified potential molecular features associated with serovar Hardjo subtype Hardjo-prajitno, present in both L. interrogans and L. borgpetersenii, by comparative genomics.\nC_LIO_LIA new potential recombinant site found upstream of the rfb locus contains proteins that correlate with serogroup taxonomy in the Leptospira genus.\nC_LIO_LIThe proteins encoded in the recombinant locus are associated with the synthesis of serological surface determinants such as carbohydrates and lipopolysaccharides.\nC_LI

genomics↗