Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information.

When inferring the evolution of a gene/gene family, it is advisable to use all available coding sequences (CDS) from as many species genomes as possible in order to infer and date all gene duplications and losses. Nowadays, this means using hundreds or even thousands of CDSs, which makes the inferred phylogenetic trees difficult to visualize and interpret. Therefore, it is useful to have an automated way of collapsing large phylogenetic trees according to a taxonomic term decided by the user (family, class, or order, for instance), in order to highlight the minimal set of sequences that should be used to recapitulate the full history of the gene/gene family being studied at that taxonomic level, that can be refined using additional software. Here we present the Phylogenetic Tree Collapser (PTC) program (https://github.com/pegi3s/phylogenetic-tree-collapser), a flexible tool for automated tree collapsing using taxonomic information, that can be easily used by researchers without a background in informatics, since it only requires the installation of Docker, Podman or Singularity. The utility of PTC is demonstrated by addressing the evolution of the ascorbic acid synthesis pathway in insects. A Docker image is available at Docker Hub (https://hub.docker.com/r/pegi3s/phylogenetic-tree-collapser) with PTC installed and ready-to-run.

Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites.

The vast amount of genome sequence data that is available, and that is predicted to drastically increase in the near future, can only be efficiently dealt with by building automated pipelines. Indeed, the Earth Biogenome Project will produce high-quality reference genome sequences for all 1.8 million named living eukaryote species, providing unprecedented insight into the evolution of genes and gene families, and thus on biological issues. Here, new modules for gene annotation, further BLAST search algorithms, further multiple sequence alignment methods, the adding of reference sequences, further tree rooting methods, the estimation of rates of synonymous and nonsynonymous substitutions, and the identification of positively selected amino acid sites, have been added to auto-phylo (version 2), a recently developed software to address biological problems using phylogenetic inferences. Additionally, we present auto-phylo-pipeliner, a graphical user interface application that further facilitates the creation and running of auto-phylo pipelines. Inferences on S-RNase specificity, are critical for both cross-based breeding and for the establishment of pollination requirements. Therefore, as a test case, we develop an auto-phylo pipeline to identify amino acid sites under positive selection, that are, in principle, those determining S-RNase specificity, starting from both non-annotated Prunus genomes and sequences available in public databases.

Development and Validation of an Anthropometric Equation to Predict Fat Mass Percentage in Professional and Semi-Professional Male Futsal Players.

This study aimed to (i) characterise the body composition of professional and semi-professional male futsal players, (ii) assess the validity of commonly used equations to estimate FM%, (iii) develop and cross-validate a futsal-specific FM% prediction equation. In a cross-sectional design, 78 adult male futsal players were assessed for body mass, stature, skinfolds, and girths as per the International Society for the Advancement of Kinanthropometry protocol and completed a dual-energy X-ray absorptiometry (DXA) scan for reference body composition data. Using paired-sample t-tests, the FM% from the DXA and nine published equations were compared. New sport-specific models were developed by stepwise multiple regression. Existing equations were cross-validated using the least squares regression, concordance correlation coefficient, and the Bland−Altman analyses. New equations were further cross-validated using the PRESS approach. None of the existing equations accurately predicted the DXA-derived FM% (p < 0.001; R2 ≤ 0.76, SEE ≥ 1.59; CCC ≤ 0.83; bias = −8.2% to −1.3%, limited agreement, and varying trends). The novel Bettery® equation: −0.620 + (0.159 ∗ Σ4SKF [triceps, abdominal, iliac crest, and front thigh (mm)]) + (0.120 ∗ waist girth (cm)), demonstrated a high accuracy (R2 = 0.85, SEE = 1.32%), a moderate strength of agreement (CCC = 0.92), no bias (0.2%), good agreement (±2.5%), and no trend (r = −0.157; p = 0.170) against the DXA. The Bettery® equation is the first to allow for a valid and sport-specific assessment of FM% in male futsal players.

Advances in Novel Animal Vitamin C Biosynthesis Pathways and the Role of Prokaryote-Based Inferences to Understand Their Origin.

Vitamin C (VC) is an essential nutrient required for the optimal function and development of many organisms. VC has been studied for many decades, and still today, the characterization of its functions is a dynamic scientific field, mainly because of its commercial and therapeutic applications. In this review, we discuss, in a comparative way, the increasing evidence for alternative VC synthesis pathways in insects and nematodes, and the potential of myo-inositol as a possible substrate for this metabolic process in metazoans. Methodological approaches that may be useful for the future characterization of the VC synthesis pathways of Caenorhabditis elegans and Drosophila melanogaster are here discussed. We also summarize the current distribution of the eukaryote aldonolactone oxidoreductases gene lineages, while highlighting the added value of studies on prokaryote species that are likely able to synthesize VC for both the characterization of novel VC synthesis pathways and inferences on the complex evolutionary history of such pathways. Such work may help improve the industrial production of VC.

The evolution of vitamin C biosynthesis and transport in animals.

BACKGROUND: Vitamin C (VC) is an indispensable antioxidant and co-factor for optimal function and development of eukaryotic cells. In animals, VC can be synthesized by the organism, acquired through the diet, or both. In the single VC synthesis pathway described in animals, the penultimate step is catalysed by Regucalcin, and the last step by L-gulonolactone oxidase (GULO). The GULO gene has been implicated in VC synthesis only, while Regucalcin has been shown to have multiple functions in mammals. RESULTS: Both GULO and Regucalcin can be found in non-bilaterian, protostome and deuterostome species. Regucalcin, as here shown, is involved in multiple functions such as VC synthesis, calcium homeostasis, and the oxidative stress response in both Deuterostomes and Protostomes, and in insects in receptor-mediated uptake of hexamerin storage proteins from haemolymph. In Insecta and Nematoda, however, there is no GULO gene, and in the latter no Regucalcin gene, but species from these lineages are still able to synthesize VC, implying at least one novel synthesis pathway. In vertebrates, SVCT1, a gene that belongs to a family with up to five members, as here shown, is the only gene involved in the uptake of VC in the gut. This specificity is likely the result of a subfunctionalization event that happened at the base of the Craniata subphylum. SVCT-like genes present in non-Vertebrate animals are likely involved in both VC and nucleobase transport. It is also shown that in lineages where GULO has been lost, SVCT1 is now an essential gene, while in lineages where SVCT1 gene has been lost, GULO is now an essential gene. CONCLUSIONS: The simultaneous study, for the first time, of GULO, Regucalcin and SVCTs evolution provides a clear picture of VC synthesis/acquisition and reveals very different selective pressures in different animal taxonomic groups.

SEDA: A Desktop Tool Suite for FASTA Files Processing.

SEDA (SEquence DAtaset builder) is a multiplatform desktop application for the manipulation of FASTA files containing DNA or protein sequences. The convenient graphical user interface gives access to a collection of simple (filtering, sorting, or file reformatting, among others) and advanced (BLAST searching, protein domain annotation, gene annotation, and sequence alignment) utilities not present in similar applications, which eases the work of life science researchers working with DNA and/or protein sequences, especially those who have no programming skills. This paper presents general guidelines on how to build efficient data handling protocols using SEDA, as well as practical examples on how to prepare high-quality datasets for single gene phylogenetic studies, the characterization of protein families, or phylogenomic studies. The user-friendliness of SEDA also relies on two important features: (i) the availability of easy-to-install distributable versions and installers of SEDA, including a Docker image for Linux, and (ii) the facility with which users can manage large datasets. SEDA is open-source, with GNU General Public License v3.0 license, and publicly available at GitHub (https://github.com/sing-group/seda). SEDA installers and documentation are available at https://www.sing-group.org/seda/.

Multiple independent L-gulonolactone oxidase (GULO) gene losses and vitamin C synthesis reacquisition events in non-Deuterostomian animal species.

BACKGROUND: L-ascorbate (Vitamin C) is an important antioxidant and co-factor in eukaryotic cells, and in mammals it is indispensable for brain development and cognitive function. Vertebrates usually become L-ascorbate auxothrophs when the last enzyme of the synthetic pathway, an L-gulonolactone oxidase (GULO), is lost. Since Protostomes were until recently thought not to have a GULO gene, they were considered to be auxothrophs for Vitamin C. RESULTS: By performing phylogenetic analyses with tens of non-Bilateria and Protostomian genomes, it is shown, that a GULO gene is present in the non-Bilateria Placozoa, Myxozoa (here reported for the first time) and Anthozoa groups, and in Protostomians, in the Araneae family, the Gastropoda class, the Acari subclass (here reported for the first time), and the Priapulida, Annelida (here reported for the first time) and Brachiopoda phyla lineages. GULO is an old gene that predates the separation of Animals and Fungi, although it could be much older. We also show that within Protostomes, GULO has been lost multiple times in large taxonomic groups, namely the Pancrustacea, Nematoda, Platyhelminthes and Bivalvia groups, a pattern similar to that reported for Vertebrate species. Nevertheless, we show that Drosophila melanogaster seems to be capable of synthesizing L-ascorbate, likely through an alternative pathway, as recently reported for Caenorhabditis elegans. CONCLUSIONS: Non-Bilaterian and Protostomians seem to be able to synthesize Vitamin C either through the conventional animal pathway or an alternative pathway, but in this animal group, not being able to synthesize L-ascorbate seems to be the exception rather than the rule.

Bioinformatics Protocols for Quickly Obtaining Large-Scale Data Sets for Phylogenetic Inferences.

Useful insight into the evolution of genes and gene families can be provided by the analysis of all available genome datasets rather than just a few, which are usually those of model species. Handling and transforming such datasets into the desired format for downstream analyses is, however, often a difficult and time-consuming task for researchers without a background in informatics. Therefore, we present two simple and fast protocols for data preparation, using an easy-to-install, open-source, cross-platform software application with user-friendly, rich graphical user interface (SEDA; http://www.sing-group.org/seda/index.html ). The first protocol is a substantial improvement over one recently published (López-Fernández et al. Practical applications of computational biology and bioinformatics, 12th International conference. Springer, Cham, pp 88-96 (2019)[1]), which was used to study the evolution of GULO, a gene that encodes the enzyme responsible for the last step of vitamin C synthesis. In this paper, we show how the sequence data file used for the phylogenetic analyses can now be obtained much faster by changing the way coding sequence isoforms are removed, using the newly implemented SEDA operation "Remove isoforms". This protocol can be used to easily show that putative functional GULO genes are present in several Prostotomian groups such as Molluscs, Priapulida and Arachnida. Such findings could have been easily missed if only a few Protostomian model species had been used. The second protocol allowed us to identify positively selected amino acid sites in a set of 19 primate HLA immunity genes. Interestingly, the proteins encoded by MHC class II genes can show just as many positively selected amino acid sites as those encoded by classical MHC class I genes. Although a significant percentage of codons, which can be as high as 14.8%, are evolving under positive selection, the main mode of evolution of HLA immunity genes is purifying selection. Using a large number of primate species, the probability of missing the identification of positively selected amino acid sites is lower. Both projects were performed in less than one week, and most of the time was spent running the analyses rather than preparing the files. Such protocols can be easily adapted to answer many other questions using a phylogenetic approach.

Herpesvirus saimiri-transformed CD8+ T cells as a tool to study Chediak-Higashi syndrome cytolytic lymphocytes.

Cytolytic CD8+ T lymphocytes are the main cell type involved in the fatal lymphoproliferative-accelerated phase of the Chediak-Higashi syndrome (CHS). To generate a cellular tool to study the defects of this T cell subset in vitro, we have used Herpesvirus saimiri, a lymphotropic virus that transforms human T lymphocytes into extended growth and in addition, endows them with natural killer (NK) features. Transformed CHS CD8+ T cells were generated and characterized in comparison with healthy controls. The results showed that transformed CHS T cells maintained the defects described in primary CHS lymphocytes, such as giant secretory lysosomes and impaired NK and T cell receptor/CD3-induced, perforin-mediated cytolytic activity [which, however, could be restored after extended culture in the presence of interleukin-2 (IL-2)]. Upon activation with phorbol ester plus calcium ionophore or upon extended culture with IL-2, transformed CHS T cells showed normal, perforin-independent plasma membrane CD178/CD95L/FasL-mediated cytolytic activity but negligible secretion of microvesicle-bound CD95L. Transformed (and primary) CHS T cells were otherwise normal for cytolysis-independent activation functions, such as proliferation, surface expression of several activation markers including major histocompatibility complex class II, and cytokine or surface activation-marker induction. Therefore, the CHS protein [CHS1/LYST (for lysosomal traffic regulator)] can be dispensable for certain NK and T cell cytolytic activities of activated CHS CD8+ T lymphocytes, but it seems to be required for microvesicle secretion of CD95L. We conclude that transformed CHS T cells may be useful as a tool to study in vitro the relative role of CHS1/LYST in NK and T lymphocyte cytolysis and antigen presentation.

HICOPS: human interface computer program in space.

BACKGROUND: During long experimental set ups, a protocol book usually guides cosmonauts. This is not very easy to work with in microgravity conditions and is not very efficient. For the cardiovascular physiology experiment CARDIOCOG during the Belgian Soyuz Mission (Odissea, November 2002) we developed a software program that guided the cosmonauts through the experiment. The software was developed in LabVIEW, thoroughly tested by CNES and the Russian space authorities and transported to the ISS as a stand-alone application. An adapted version was used during the Spanish Cervantes Mission in October 2003. RESULTS: This program provided several advantages: (1) error procedures could be easily dealt with in using the program's incorporated error structure; (2) the experimental sequences were easy to follow for the cosmonauts; (3) the experimental duration was exactly the same for all repetitions of the experiment, since the program imposed the timing; (4) after the flight, we were able to reconstruct all sequences of the experiment using a log-file that was automatically created during the different steps of the experiment; and (5) we were able to impose exact breathing frequencies to the cosmonauts using a visual aid. CONCLUSION: Less training was necessary for the cosmonauts to learn the experiment. Reconstruction of the experiment timing was easy. Exact breathing frequencies were obtained at each repetition. The program HICOPS worked to the overall satisfaction of the cosmonauts and they preferred working with HICOPS instead of with paper flow sheets. Data for the cardiovascular experiment during both missions were obtained in a standardised way.

Infiltración leucémica de glándulas mamarias / Leukemias infiltration of glands mammary

Las leucemias agudas son proliferaciones malignas de células hematopoyéticas inmaduras de tipo blástico, cuya acumulación progresiva se acompaña de una disminución en la producción de los elementos mieloides normales. Generalmente no existe un síntoma específico de leucemia y cualquier órgano puede sufrir la infiltración leucémica. En el presente reporte, se describe el caso de una paciente femenina de 20 años de edad, quien cursaba con 14 semanas de gestación. Asistió a control prenatal por presentar aumento de volumen de las glándulas mamarias que adquirieron una consistencia pétrea, lesiones nodulares en cuero cabelludo e hiperplasia gingival. En vista de las condiciones clínicas de la paciente, fue hospitalizada. A su ingreso lucía regulares condiciones generales, fascie abotagada, palidez cutáneo mucosa, adenopatías submaxilares, laterocervicales e omguinales; macromastia bilateral; hallazgo semiológicos de derrame pleural izquierdo y hepatomegalia dolorosa. Los exámenes paraclínicos revelaron: Hb: 4gr/dl, Hto: 14 por ciento leucocitos: 5000/mm3 seg:50 por ciento, linf:25 por ciento, mieloblastos: 5 por ciento, normoblastos: 20 por ciento plaquetas: 81000/mm3. Frotis de sangre periférica: células de tamaño aumentado, algunas con nucleolos y otras sin granulaciones, presencia de normoblastos y trombocitopenia. Aspirado de médula ósea: presencia de células mononucleares, de tamaño aumentado, algunas sin nucleolos, otras con vacuolas en su citoplasma y otras sin granulaciones, depresión severa de las otras series. Previa interrupción de la gestación y realización de legrado uterino se inicio quimioterapia de inducción, observándose mejoría clínica y respuesta al tratamiento médico, a las 24 horas de haberse iniciado el mismo. Se concluye en Leucemia Monocítica Aguda con infiltración a glándulas mamarias, presentación clínica poco frecuente de esta patología. En vista de lo inusual de esta presentación se reporta el caso