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Mycobacterium tuberculosis (Mtb) is still one of the primary pathogens of humans causing tuberculosis (TB) disease. Mtb embraces nine well-defined phylogenetic lineages with biological and geographical disparities. The lineage L4 is the most globally widespread of all lineages and was introduced to America with European colonization. Taking advantage of many genome projects available in public repositories, we undertake an evolutionary and comparative genomic analysis of 522 L4 Latin American Mtb genomes. Initially, we performed careful quality control of public read datasets and applied several thresholds to filter out low-quality data. Using a genome de novo assembly strategy and phylogenomic methods, we spotted novel south American clades that have not been revealed yet. Additionally, we describe genomic deletion profiles of these strains from an evolutionary perspective and report Mycobacterium tuberculosis L4 sublineages signature-like gene deletions, some of the novel. One is a specific deletion of 6.5 kbp that is only present in sublineage 4.1.2.1. This deletion affects a complex group of 10 genes with putative products annotated, among others, as a lipoprotein, transmembrane protein, and toxin/antitoxin system proteins. The second novel deletion spans for 4.9 kbp and specific of a particular clade of the 4.8 sublineage and affects 7 genes. The last novel deletion affects 4 genes, extends for 4.8 kbp., and is specific to some strains within the 4.1.2.1 sublineage that are present in Colombia, Peru and Brasil.

Recent studies have shown how intestinal parasites can modulate gut microbiota. This observation is not surprising since the human intestinal lumen, like any other niche, is a battlefield of microbial competition, and Eukaryotes can affect bacterial populations. Intestinal pathogenic protist has been associated with reshaping the microbial community structure; however, the interactions between the colonic bacterial communities and parasites like Blastocystis spp., Entamoeba coli, and Endolimax nana have been poorly studied. In this work, we studied the distal intestinal bacterial microbiota of 49 children attending 7 public daycare centers in Medellin, Colombia, and compared the bacterial microbiota structure in the presence or absence of the protists Blastocystis spp., E. coli, and E. nana. Parasite colonization was associated with an increase in bacterial richness. Moreover, Blastocystis spp. presented a positive relationship with Prevotella, since this bacterium was selectively enriched in children carrying it. Remarkably, the E. coli colonized children showed a microbial profile that was closer to uninfected controls, although some bacterial taxa displayed to be enriched. This is the case for Akkermansia, which showed to be favored in E. coli colonized individuals, while notably reduced in the Blastocystis spp. parasitized group.

Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), leading to pulmonary and extrapulmonary TB, whereby Mtb is disseminated to many other organs and tissues. Dissemination occurs early during the disease, and bacteria can be found first in the lymph nodes adjacent to the lungs and then later in the extrapulmonary organs, including the spleen. The early global gene expression response of human tissue macrophages and intracellular clinical isolates of Mtb has been poorly studied. Using dual RNA-seq, we have explored the mRNA profiles of two closely related clinical strains of the Latin American and Mediterranean (LAM) family of Mtb in infected human splenic macrophages (hSMs). This work shows that these pathogens mediate a distinct host response despite their genetic similarity. Using a genome-scale host–pathogen metabolic reconstruction to analyze the data further, we highlight that the infecting Mtb strain also determines the metabolic response of both the host and pathogen. Thus, macrophage ontogeny and the genetic-derived program of Mtb direct the host–pathogen interaction.

Tuberculosis (TB) is caused by

Microorganisms are capable of colonizing extreme environments like deep biosphere and oil reservoirs. The prokaryotes diversity in exploited oil reservoirs is composed of indigenous microbial communities and artificially introduced microbes. In the present work, high throughput sequencing techniques were applied to analyze the microbial community from the injected and produced water in a neotropical hyper-thermophile oil reservoir located in the Orinoquia region of Colombia, South America. Tepidiphilus is the dominant bacteria found in both injection and produced waters. The produced water has a higher microbial richness and exhibits a Tepidiphilus microdiversity. The reservoir injected water is recycled and treated with the biocides glutaraldehyde and tetrakis-hydroxymethyl-phosphonium sulfate (THPS) to reduce microbial load. This process reduces microbial richness and selects a single Tepidiphilus genome (T. sp. UDEAICP_D1) as the dominant isolate. Thermus and Hydrogenobacter were subdominants in both water systems. Phylogenomic analysis of the injection water dominant Tepidiphilus positioned it as an independent branch outside T. succinatimandens and T. thermophilus lineage. Comparative analysis of the Tepidiphilus genomes revealed several genes that might be related to the biocide-resistant phenotype and the tolerance to the stress conditions imposed inside the oil well, like RND efflux pumps and type II toxin-antitoxin systems. Comparing the abundance of Tepidiphilus protein-coding genes in both water systems shows that the biocide selected Tepidiphilus sp. UDEAICP_D1 genome has enriched genes annotated as ABC-2 type transporter, ABC transporter, Methionine biosynthesis protein MetW, Glycosyltransferases, and two-component system NarL.

Spiders (Araneae) are the most abundant terrestrial predators and megadiverse on earth. In recent years, the mitochondrial genome of a great diversity of species has been sequenced, mainly for ecological and commercial purposes. These studies have uncovered the existence of a variety of mitochondrial genome rearrangements. However, there is poor genetic information in several taxonomic families of spiders. We have sequenced the complete genome of Phoneutria depilata (Ctenidae) and, based on this, extract the mitogenomes of other ctenid species from published transcriptomes to perform a comparative study among spider species to determine the relationship between the level of mitochondrial rearrangements and its possible relationship with molecular variability in spiders. Complete mitochondrial genomes of eighteen spiders (including eight Ctenidae species) were obtained by two different methodologies (sequencing and transcriptome extraction). Fifty-eight spider mitochondrial genomes were downloaded from the NCBI database for gene order analysis. After verifying the annotation of each mitochondrial gene, a phylogenetic and a gene order analysis from 76 spider mitochondrial genomes were carried out. Our results show a high rate of annotation error in the published spider mitochondrial genomes, which could lead to errors in phylogenetic inference. Moreover, to provide new mitochondrial genomes in spiders by two different methodologies to obtain them, our analysis identifies six different mitochondrial architectures among all spiders. Translocation or tandem duplication random loss (TDRL) events in tRNA genes were identified to explain the evolution of the spider mitochondrial genome. In addition, our findings provide new insights into spider mitochondrial evolution.

Cryptosporidium is a leading cause of waterborne outbreaks globally, and Cryptosporidium hominis and C. parvum are the principal cause of human cryptosporidiosis on the planet. Thanks to the advances in Next-Generation Sequencing (NGS) sequencing and bioinformatic software development, more than 100 genomes have been generated in the last decade using a metagenomic-like strategy. This procedure involves the parasite oocyst enrichment from stool samples of infected individuals, NGS sequencing, metagenomic assembly, parasite genome computational filtering, and comparative genomic analysis. Following this approach, genomes of infected individuals of all continents have been generated, although with striking different quality results. In this study, we performed a thorough comparison, in terms of assembly quality and purity, of 100+ de novo assembled genomes of C. hominis. Remarkably, after quality genome filtering, a comprehensive phylogenomic analysis allowed us to discover that C. hominis encompasses two lineages with continental segregation. These lineages were named based on the observed continental distribution bias as C. hominis Euro-American (EA) and the C. hominis Afro-Asian (AA) lineages.

Spiders are the most abundant land predators and megadiverse on earth. In recent years, the mitochondrial genome has been sequenced, mainly for ecological and commercial purposes, reporting some level of rearrangements in this genome. However, there is poor genetic information in several taxonomic families of spiders. The aim of this study was to obtain the sequence of the complete genome of Phoneutria boliviensis and, based on this, extract the mitogenomes of other species of the family Ctenidae from published transcriptomes to perform a comparative study among spider species to determine the relationship between the level of mitochondrial rearrangement and its possible relationship with molecular variability in spiders. Complete mitochondrial genomes of eighteen spiders (including nine Ctenidae species) were obtained by two different methodologies (sequencing and transcriptome extraction). Fifty-eight spider mitochondrial genomes were downloaded from the NCBI database for gene order analysis. After verifying the annotation of each mitochondrial gene, a phylogeny and gene order, analysis from 76 spider mitochondrial genomes was obtained. Our results show a high rate of annotation error in the mitochondrial genomes of spiders published in databases, which could lead to false phylogenetic relationships. Moreover, to provide new mitochondrial genomes in spiders by two different methodologies to obtain them, our analysis identifies six different mitochondrial architectures among all spiders. Translocation or tandem duplication random loss (TDRL) events in tRNA genes were identified to explain the evolution of the spider mitochondrial genome. In addition, our findings provide new insights into spider mitochondrial evolution.

Cryptosporidium parasites are ubiquitous and can infect a broad range of vertebrates and are considered the most frequent protozoa associated with waterborne parasitic outbreaks. The intestine is the target of three of the species most frequently found in humans: C. hominis, C. parvum, and. C. meleagridis. Despite the recent advance in genome sequencing projects for this apicomplexan, a broad genomic comparison including the three species most prevalent in humans have not been published so far. In this work, we downloaded raw NGS data, assembled it under normalized conditions, and compared 23 publicly available genomes of C. hominis, C. parvum, and C. meleagridis. Although few genomes showed highly fragmented assemblies, most of them had less than 500 scaffolds and mean coverage that ranged between 35X and 511X. Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed. Furthermore, deleterious nucleotide substitutions common to all three species were more common in genes associated with DNA repair, recombination, and chromosome-associated proteins. Indel events were observed in the 23 studied isolates that spanned up to 500 bases. The highest number of deletions was observed in C. meleagridis, followed by C. hominis, with more than 60 species-specific deletions found in some isolates of these two species. Although several genes with indel events have been partially annotated, most of them remain to encode uncharacterized proteins.

Abundance and diversity of microbial communities in biosolids are variable and poorly studied in the tropics, and it is known that rainfall is one of the events that could affect the phylogenetic and functional microbial structure. In the present study, using NGS technics, we studied the microbial diversity as well as the methanogenesis pathway in one of the largest WWTP in Colombia. Besides, we sampled and analyzed biosolids from rainy season and dry season. Phylogenetic classification showed a predominance of bacteria in both samples and difference in the dominant groups depending on the rainfall season. Whereas Pseudomonas was the dominant bacteria in the dry season, Coprothermobacter was in the rainy season. Archaea abundance was higher in the rainy season (11.5%) doubling dry season proportion. The bioreactor biogas production and total solids content showed similar results between rainy and dry season at the sampling dates. The most abundant Archaea related with methanogenesis was Methanosaeta, which is a methanogenic microorganism that exclusively uses acetate to produce methane. Moreover, annotation of the methanogenic pathway in the metagenome showed abundance in genes encoding Acetyl-CoA synthetases (ACSS), an enzyme that catalyzes acetate activation. Our results suggest that the microbial diversity was stable among the two time points tested, rainy season and dry season; and, although there were changes in the microbial abundance of dominant bacterial species, anaerobic digester performance is not affected.

The public-key operation in multivariate encryption and signature schemes evaluates \begin{document}$ m $\end{document} quadratic polynomials in \begin{document}$ n $\end{document} variables. In this paper we analyze how fast this simple operation can be made. We optimize it for different finite fields on modern architectures. We provide an objective and inherent efficiency measure of our implementations, by comparing their performance with the peak performance of the CPU. In order to provide a fair comparison for different parameter sets, we also analyze the expected security based on the algebraic attack taking into consideration the hybrid approach. We compare the attack's efficiency for different finite fields and establish trends. We detail the role that the field equations play in the attack. We then provide a broad picture of efficiency of MQ-public-key operation against security.

The heterogeneity of the clinical outcome of Mycobacterium tuberculosis (Mtb) infection may be due in part to different strategies used by circulating strains to cause disease. This heterogeneity is one of the main limitations to eradicate tuberculosis disease. In this study, we have compared the transcriptional response of two closely related Colombian clinical isolates (UT127 and UT205) of the LAM family under two axenic media conditions. These clinical isolates are phenotypically different at the level of cell death, cytokine production, growth kinetics upon in vitro infection of human tissue macrophages, and membrane vesicle secretion upon culture in synthetic medium. Using RNA-seq, we have identified different pathways that account for two different strategies to cope with the stressful condition of a carbon-poor media such as Sauton's. We showed that the clinical isolate UT205 focus mainly in the activation of virulence systems such as the ESX-1, synthesis of diacyl-trehalose, polyacyl-trehalose, and sulfolipids, while UT127 concentrates its efforts mainly in the survival mode by the activation of the DNA replication, cell division, and lipid biosynthesis. This is an example of two Mtb isolates that belong to the same family and lineage, and even though they have a very similar genome, its transcriptional regulation showed important differences. This results in summary highlight the necessity to reach a better understanding of the heterogeneity in the behavior of these circulating Mtb strains which may help us to design better treatments and vaccines and to identify new targets for drugs.

Anaerobic digestion is a microbe-driven process widely applied to treat activated sludge from municipal wastewater treatment plants. It is one of the most efficient solutions for sludge reduction along with biogas production. However, the knowledge of the microbial consortium involved in this process is still unknown in full-scale anaerobic digesters from Latin America. This study aimed to elucidate the dynamics of the microbial community of a full-scale anaerobic digester for a year using 16S rDNA amplicon sequencing with the Illumina Miseq platform. The results showed fluctuations in the frequencies of dominant phyla with a decrease of Proteobacteria and Bacteroidetes after a temporary suspension of anaerobic digester. The core community was affiliated with bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Chloroflexi. The core community was represented by 154 OTUs that accounted for 74% of all the processed reads. The Anaerolineaceae family, within Chloroflexi phylum, was the most frequently observed taxonomic group in all samples analyzed. Despite the microbial fluctuations, the biogas production was stable over the studied year (average 66% methane production), which might indicate a functional redundancy in the microbial consortium.

CARD9 deficiency is an inborn error of immunity that predisposes otherwise healthy humans to mucocutaneous and invasive fungal infections, mostly caused by Candida, but also by dermatophytes, Aspergillus, and other fungi. Phaeohyphomycosis are an emerging group of fungal infections caused by dematiaceous fungi (phaeohyphomycetes) and are being increasingly identified in patients with CARD9 deficiency. The Corynespora genus belongs to phaeohyphomycetes and only one adult patient with CARD9 deficiency has been reported to suffer from invasive disease caused by C. cassiicola. We identified a Colombian child with an early-onset, deep, and destructive mucocutaneous infection due to C. cassiicola and we searched for mutations in CARD9. We reviewed the medical records and immunological findings in the patient. Microbiologic tests and biopsies were performed. Whole-exome sequencing (WES) was made and Sanger sequencing was used to confirm the CARD9 mutations in the patient and her family. Finally, CARD9 protein expression was evaluated in peripheral blood mononuclear cells (PBMC) by western blotting. The patient was affected by a large, indurated, foul-smelling, and verrucous ulcerated lesion on the left side of the face with extensive necrosis and crusting, due to a C. cassiicola infectious disease. WES led to the identification of compound heterozygous mutations in the patient consisting of the previously reported p.Q289* nonsense (c.865C > T, exon 6) mutation, and a novel deletion (c.23_29del; p.Asp8Alafs10*) leading to a frameshift and a premature stop codon in exon 2. CARD9 protein expression was absent in peripheral blood mononuclear cells from the patient. We describe here compound heterozygous loss-of-expression mutations in CARD9 leading to severe deep and destructive mucocutaneous phaeohyphomycosis due to C. cassiicola in a Colombian child.

The heterogeneity of the clinical outcome of Mycobacterium tuberculosis (Mtb) infection may be due in part to different strategies used by circulating strains to cause disease. This heterogeneity is one of the main limitations to eradicate tuberculosis disease. In this study, we have compared the transcriptional response of two closely related Colombian clinical isolates (UT127 and UT205) of the LAM family under two axenic media conditions. These clinical isolates are phenotypically different at the level of cell death, cytokine production, growth kinetics upon in vitro infection of human tissue macrophages, and membrane vesicle secretion upon culture in synthetic medium. Using RNA-seq, we have identified different pathways that account for two different strategies to cope with the stressful condition of a carbon-poor media such as Sauton’s. We showed that the clinical isolate UT205 focus mainly in the activation of virulence systems such as the ESX-1, synthesis of diacyl-trehalose, polyacyl-trehalose, and sulfolipids, while UT127 concentrates its efforts mainly in the survival mode by the activation of the DNA replication, cell division, and lipid biosynthesis. This is an example of two Mtb isolates that belong to the same family and lineage, and even though they have a very similar genome, its transcriptional regulation showed important differences. This results in summary highlight the necessity to reach a better understanding of the heterogeneity in the behavior of these circulating Mtb strains which may help us to design better treatments and vaccines and to identify new targets for drugs.

Background A prime objective in metagenomics is to classify DNA sequence fragments into taxonomic units. It usually requires several stages: read’s quality control, de novo assembly, contig annotation, gene prediction, etc. These stages need very efficient programs because of the number of reads from the projects. Furthermore, the complexity of metagenomes requires efficient and automatic tools that orchestrate the different stages. Method DATMA is a pipeline for fast metagenomic analysis that orchestrates the following: sequencing quality control, 16S rRNA-identification, reads binning, de novo assembly and evaluation, gene prediction, and taxonomic annotation. Its distributed computing model can use multiple computing resources to reduce the analysis time. Results We used a controlled experiment to show DATMA functionality. Two pre-annotated metagenomes to compare its accuracy and speed against other metagenomic frameworks. Then, with DATMA we recovered a draft genome of a novel Anaerolineaceae from a biosolid metagenome. Conclusions DATMA is a bioinformatics tool that automatically analyzes complex metagenomes. It is faster than similar tools and, in some cases, it can extract genomes that the other tools do not. DATMA is freely available at https://github.com/andvides/DATMA.

Background Hot spring bacteria have unique biological adaptations to survive the extreme conditions of these environments; these bacteria produce thermostable enzymes that can be used in biotechnological and industrial applications. However, sequencing these bacteria is complex, since it is not possible to culture them. As an alternative, genome shotgun sequencing of whole microbial communities can be used. The problem is that the classification of sequences within a metagenomic dataset is very challenging particularly when they include unknown microorganisms since they lack genomic reference. We failed to recover a bacterium genome from a hot spring metagenome using the available software tools, so we develop a new tool that allowed us to recover most of this genome. Results We present a proteobacteria draft genome reconstructed from a Colombian’s Andes hot spring metagenome. The genome seems to be from a new lineage within the family Rhodanobacteraceae of the class Gammaproteobacteria, closely related to the genus Dokdonella. We were able to generate this genome thanks to CLAME. CLAME, from Spanish “CLAsificador MEtagenomico”, is a tool to group reads in bins. We show that most reads from each bin belong to a single chromosome. CLAME is very effective recovering most of the reads belonging to the predominant species within a metagenome. Conclusions We developed a tool that can be used to extract genomes (or parts of them) from a complex metagenome. Electronic supplementary material The online version of this article (10.1186/s12864-018-5191-y) contains supplementary material, which is available to authorized users.

Biallelic loss-of-function (LOF) mutations of the NCF4 gene, encoding the p40phox subunit of the phagocyte NADPH oxidase, have been described in only 1 patient. We report on 24 p40phox-deficient patients from 12 additional families in 8 countries. These patients display 8 different in-frame or out-of-frame mutations of NCF4 that are homozygous in 11 of the families and compound heterozygous in another. When overexpressed in NB4 neutrophil-like cells and EBV-transformed B cells in vitro, the mutant alleles were found to be LOF, with the exception of the p.R58C and c.120_134del alleles, which were hypomorphic. Particle-induced NADPH oxidase activity was severely impaired in the patients' neutrophils, whereas PMA-induced dihydrorhodamine-1,2,3 (DHR) oxidation, which is widely used as a diagnostic test for chronic granulomatous disease (CGD), was normal or mildly impaired in the patients. Moreover, the NADPH oxidase activity of EBV-transformed B cells was also severely impaired, whereas that of mononuclear phagocytes was normal. Finally, the killing of Candida albicans and Aspergillus fumigatus hyphae by neutrophils was conserved in these patients, unlike in patients with CGD. The patients suffer from hyperinflammation and peripheral infections, but they do not have any of the invasive bacterial or fungal infections seen in CGD. Inherited p40phox deficiency underlies a distinctive condition, resembling a mild, atypical form of CGD. ispartof: JOURNAL OF CLINICAL INVESTIGATION vol:128 issue:9 pages:3957-3975 ispartof: location:United States status: published

RESUMEN: Objetivo Caracterizar la microbiota bacteriana presente en los biosólidos generados en una de las plantas de tratamiento de aguas residuales más grande de Colombia. Materiales y Métodos Se utilizó la plataforma de secuenciamiento 454 de la compañía Roche para secuenciar las regiones variables V1-V3 y V6-V9 del marcador molecular 16S rRNA y caracterizar la microbiota. Adicionalmente, se aplicaron estrategias filogenéticas para la identificación de especies bacterianas de importancia. Resultados Nuestros análisis muestran que los Phyla más abundantes son Chloroflexi, Proteobacteria, Bacteroidetes, Actinobacteria y Firmicutes. Los géneros clasificados más abundantes fueron Pseudomonas, Dysgonomonas y Proteiniphilum. Sin embargo, el grupo dominante según la región variable V1-V3 es una Anaerolineaceaeque no se ajusta a las especies descritas para esta familia. Conclusiones En las muestras de biosólido analizadas predominan bacterias ambientales que participan en los procesos de estabilización de la materia orgánica durante los tratamientos biológicos de tipo secundario y la digestión anaerobia. Se detectaron secuencias de especies dentro de la familia Anaerolineaceae, los análisis filogenéticos muestran que probablemente se trata de especies no descritas. En el momento del estudio, se encontró que en el sistema de digestión anaerobia se genera biosolido con una baja carga de bacterias potencialmente patógenas. ABSTRACT: Objective To describe bacterial microbiota in the biosolids generated in one of the lar-gest wastewater treatment plants of Colombia.Materials and Methods Using NGS technology, 16S rRNA Gene Amplicon libraries were amplified and sequenced. The Roche 454 FLX Titanium platform was used, while the V1-V3 and V6-V9 hypervariable regions were amplified and analyzed inde-pendently. Amplicon processing and bacterial classification were performed using the AmpliconNoise pipeline and the RDP Classifier tool.Results The analysis showed that the most dominant Phyla in the biosolids were Chlo-roflexi, Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. The most domi-nant genera were Pseudomonas, Dysgonomonas and Proteiniphilum; however, the dominant group according in the V1-V3 variable region was Anaerolineaceae, which does not conform to the species described for this family. Pathogenic bacteria such as Salmonella and E. coli/Shigella were not detected in the studied biosolid sample. Conclusions In the biosolids samples analyzed, environmental bacteria involved in organic matter stabilization processes during secondary biological treatments and anaerobic digestion were predominant. One of the dominant species in this sludge is a novel species of the Anaerolineaceae group. At the time of the study, it was found that the anaerobic digester system was able to maintain pathogenic bacteria at very low concentrations. 0007506

To describe bacterial microbiota in the biosolids generated in one of the largest wastewater treatment plants of Colombia.Using NGS technology, 16S rRNA Gene Amplicon libraries were amplified and sequenced. The Roche 454 FLX Titanium platform was used, while the V1-V3 and V6-V9 hypervariable regions were amplified and analyzed independently. Amplicon processing and bacterial classification were performed using the AmpliconNoise pipeline and the RDP Classifier tool.The analysis showed that the most dominant Phyla in the biosolids were Chlo-roflexi, Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. The most dominant genera were Pseudomonas, Dysgonomonas and Proteiniphilum; however, the dominant group according in the V1-V3 variable region was Anaerolineaceae, which does not conform to the species described for this family. Pathogenic bacteria such as Salmonella and E. coli/Shigella were not detected in the studied biosolid sample.In the biosolids samples analyzed, environmental bacteria involved in organic matter stabilization processes during secondary biological treatments and anaerobic digestion were predominant. One of the dominant species in this sludge is a novel species of the Anaerolineaceae group. At the time of the study, it was found that the anaerobic digester system was able to maintain pathogenic bacteria at very low concentrations.Caracterizar la microbiota bacteriana presente en los biosólidos generados en una de las plantas de tratamiento de aguas residuales más grande de Colombia.Se utilizó la plataforma de secuenciamiento 454 de la compañía Roche para secuenciar las regiones variables V1-V3 y V6-V9 del marcador molecular 16S rRNA y caracterizar la microbiota. Adicionalmente, se aplicaron estrategias filogenéticas para la identificación de especies bacterianas de importancia.Nuestros análisis muestran que los Phyla más abundantes son Chloro-flexi, Proteobacteria, Bacteroidetes, Actinobacteria y Firmicutes. Los géneros clasificados más abundantes fueron Pseudomonas, Dysgonomonas y Proteiniphilum. Sin embargo, el grupo dominante según la región variable V1-V3 es una Anaerolineaceae que no se ajusta a las especies descritas para esta familia.En las muestras de biosólido analizadas predominan bacterias ambientales que participan en los procesos de estabilización de la materia orgánica durante los tratamientos biológicos de tipo secundario y la digestión anaerobia. Se detectaron secuencias de especies dentro de la familia Anaerolineaceae, los análisis filogenéticos muestran que probablemente se trata de especies no descritas. En el momento del estudio, se encontró que en el sistema de digestión anaerobia se genera biosolido con una baja carga de bacterias potencialmente patógenas.

Background: The transcription factor STAT1 plays a critical role in the immune response against mycobacterial, viral and fungal infections. Different mutations in STAT1 result in diverse clinical phenotypes: AR complete/partial biallelic mutations are associated with mycobacterial and viral infections while AD loss-of-function (LOF) mutations with mycobacterial disease only; in addition, AD gain-of-function (GOF) mutations are associated with autoimmunity and fungal infections. We now report novel mutations in STAT1 in six individuals from a large cohort of Colombians affected with mycobacterial, fungal and bacterial infectious diseases. Methods: We performed whole exome sequencing (WES) in four sporadic cases (P1, P2, P3 and P4) and the proband of one family case (P5). We confirmed mutations via Sanger sequencing in patients and family members. To assess the functional impact, we evaluated the STAT1 phosphorylation after stimulation with IFN-gamma in patients’ PBMC by flow cytometry and using the in vitro dual-glo luciferase assay. Results: Infections in the patients included chronic mucocutaneous candidiasis and pulmonary histoplasmosis in P1, chronic mucocutaneous candidiasis and pulmonary tuberculosis in P2, and chronic mucocutaneous candidiasis in P3, P4, P5 and P6. We found three novel (Q20R, E235G and L354R) and one previously reported (C324Y), heterozygous missense mutations in STAT1 in four sporadic cases (P1, P3, P2 and P4, respectively) and the previously reported P329L mutation in P5 and her father (P6). The novel mutations are predicted to be deleterious by SIFT and polyphen2. Patients’ PBMCs and the GAS reporter assay showed higher phosphorylation of STAT1 in response to IFN-gamma stimulation demonstrating that all mutant alleles were GOF. Conclusions: GOF-STAT1 mutations in our patients lead to a spectrum of chronic mucocutaneous candidiasis, histoplasmosis and tuberculosis, therefore STAT1 investigation should be addressed in patients with these types of infectious diseases. In addition, WES has become an important tool in the identification of genetic defects in patients with PID.

Background: The genetic etiology of several primary immunodeficiency diseases (PID) remains elusive. Next generation technologies represent a cost-effective and rapid first-line genetic approach for the evaluation of diseases underlying mendelian traits involved in PID which are characterized by a difficult and late diagnosis. Methods: In the PID group in Medellin (Colombia), up-today we have performed whole exome sequencing in 93 patients and relatives with severe phenotypes expecting for a gene causing disease underlying a PID. Results: From 93 WES analysis, gene causing disease have been identified in (n = 15/93) as follows: recurrent infections (n = 4/5, CYBB), BCGitis (n = 1/1, AR IL-12RB1), disseminated infection by Mycobacterium sp. (n = 1/7, AR IL-12RB1), BCGosis, salmonellosis, Mycobacterium tuberculosis and Klebsiella (n = 1, (PR)-IFNGR1), disseminated infection such as candidiasis (n = 5/5, AD- STAT1-GOF), histoplasmosis (n = 1/6, AR NCF4), invasive Corynespora cassiicola infection (n = 1/1, AR CARD9), recurrent infections and glomerulonephritis (n = 1/1, AR C3). Also, we have found several good candidate genes in a cohort of selective IgA deficiency (n = 2/23, PIK3CD, NFKB2), juvenile paracoccidioidomycosis (n = 3/3, IL17RA, IL18R1, PIK3CA) and finally, a cohort with impaired response against pneumococcal vaccines (n = 1/4, NFKBIA). We are performing further analysis in these candidate genes and exome reanalysis in the rest of patients. Conclusions: We analyzed 93 WES in patients and relatives with several PID phenotypes, we found gene causing defect (n = 15/93) from different cohort of PID patients. WES is emerging as a valuable tool to reach in a timely manner, a PID diagnosis with considerable potential to draw genotype-phenotype correlation.

Background: Chronic granulomatous disease (CGD) is a primary immunodeficiency characterized by susceptibility to early-onset life-threatening bacterial and fungal infections as well as dysregulated chronic inflammation. CGD results from mutations in one of the components of the phagocyte NADPH oxidase, a multimeric complex that consists of two membrane-bound components (gp91phox and p22phox) and 3 cytoplasmic subunits (p40phox, p47phox y p67phox) that function to induce reactive O2 species (ROS) in phagocytic cells to induce microbial killing. To date, only a single patient with granulomatous colitis and compound heterozygous mutations in NCF4 encoding p40phox has been reported as a genetic subgroup of CGD. Method: We performed whole exome-sequencing in a patient with early-onset systemic histoplasmosis. Functional testing to Investigate phagocyte NADPH oxidase included dihydrorhodamine oxidation assay as well as amplex red and luminol. Protein expression was assessed by FACS and immunoblotting. Results: We found a missense homozygous variation in NCF4 within the phox homology (PX) domain, predicted to be damaging by polyphen and SIFT2 with a CADD score of 35. RT-PCR and immunoblotting demonstrated decreased p40phox protein expression protein both in neutrophils and EBV-transformed B cells from the patient, but not from controls. In addition, intracellular (IC) ROS production was significantly impaired after physiological stimulation with fMLP, Histoplasma capsulatum and Candida albicans on neutrophils and EBV-B, but not with phorbol 12-myristate 13-acetate (PMA). Conclusions: We report a novel homozygous mutation in NCF4 selectively impairing IC ROS production in a Colombian child. Remarkably, systemic histoplasmosis has not been previously reported in association with classical CGD, therefore our results expand the spectrum of genetic and infectious diseases underlying CGD in humans.

Antecedentes: La enfermedad granulomatosa crónica es una inmunodeficiencia primaria producida por mutaciones en los genes que codifican para alguna de las cinco proteínas que conforman el sistema NADPH oxidasa, el cual se encarga de destruir los microorganismos fagocitados mediante la producción de especies reactivas de oxígeno. El diagnóstico bioquímico se realiza mediante la prueba de dihidrorodamina 123 y el diagnóstico definitivo mediante técnicas moleculares como la secuenciación completa del exoma. Objetivo: Describir las características clínicas y realizar el diagnóstico molecular mediante la secuenciación completa del exoma de cuatro pacientes colombianos con enfermedad granulomatosa crónica. Métodos: Se revisaron las historias clínicas de los pacientes; se analizó la explosión respiratoria a través de la prueba de dihidrorodamina 123; se realizó secuenciación completa del exoma y las variantes encontradas se confirmaron por secuenciación de Sanger. Resultados: Los cuatro pacientes son de sexo masculino, con padres no consanguíneos, que presentaron manifestaciones clínicas desde temprana edad. El paciente 1 tuvo abscesos, lesiones osteolíticas e infecciones recurrentes. El paciente 2 presentó infección del tracto urinario (ITU) complicada, neumonía necrotizante multilobar e infecciones gastrointestinales a repetición. Los pacientes 3 y 4 son gemelos; el paciente 3 presentó neumonías e ITU recurrentes, absceso cervical y linfadenitis, mientras que el paciente 4 presentó síndrome febril sin foco, colitis granulomatosa, adenomegalias mesentéricas y retroperitoneales. Todos los pacientes obtuvieron resultados anormales en la dihidrorodamina 123 y mediante secuenciación completa del exoma y Sanger se hallaron las siguientes mutaciones en el gen CYBB ubicado en el cromosoma X que codifica para la proteína gp91phox: el paciente 1 presentó una mutación sin sentido en el exón 8 (c.G809A:p.W270X), el paciente 2 una mutación no sinónima en el exón 9 (c.T935A:p.M312K), los pacientes 3 y 4, cuatro una mutación sin sentido en el exón 6 (c.T563G:p.L188X). Conclusiones: La técnica de secuenciación completa del exoma es de gran utilidad en el diagnóstico de la enfermedad granulomatosa crónica pues permite determinar mutaciones en los genes del sistema NADPH oxidasa y brindar la adecuada consejería genética al paciente y su familia. Los pacientes con enfermedad granulomatosa crónica presentaron una mutación ligada al cromosoma X en el gen CYBB, dos de ellas corresponden a mutaciones sin sentido y una es no sinónima.

Biological sequence comparison is one of the most important tasks in Bioinformatics. Owing to the fast growth of databases that contain biological information, sequence comparison represents an important challenge for high-performance computing, especially when very long sequences are compared, i.e. the complete genome of several organisms. The Smith–Waterman (SW) algorithm is an exact method based on dynamic programming to quantify local similarity between sequences. The inherent large parallelism of the algorithm makes it ideal for architectures supporting multiple dimensions of parallelism (TLP, DLP and ILP). Concurrently, there is a paradigm shift towards chip multiprocessors in computer architecture, which offer a huge amount of potential performance that can only be exploited efficiently if applications are effectively mapped and parallelized. In this work, we analyze how large-scale biology sequence comparison takes advantage of the current and future multicore architectures. Our starting point is the performance analysis of the current multicore IBM Cell B.E. processor; we analyze two different SW implementations on the Cell B.E. Then, using simulation tools, we study the performance scalability when a many-core architecture is used for performing long DNA sequence comparison. We investigate the efficient memory organization that delivers the maximum bandwidth with the minimum cost. Our results show that a heterogeneous architecture can be an efficient alternative to execute challenging bioinformatic workloads. Copyright © 2011 John Wiley & Sons, Ltd.

Cell Superscalar's (CellSs) main goal is to provide a simple, flexible and easy programming approach for the Cell Broadband Engine (Cell/B.E.) that automatically exploits the inherent concurrency of the applications at a task level. The CellSs environment is based on a source-to-source compiler that translates annotated C or Fortran code and a runtime library tailored for the Cell/B.E. that takes care of the concurrent execution of the application. The first efforts for task scheduling in CellSs derived from very simple heuristics. This paper presents new scheduling techniques that have been developed for CellSs for the purpose of improving an application's performance. Additionally, the design of a new scheduling algorithm is detailed and the algorithm evaluated. The CellSs scheduler takes an extension of the memory hierarchy for Cell/B.E. into account, with a cache memory shared between the SPEs. All new scheduling practices have been evaluated showing better behavior of our system.

Neurocysticercosis (NC) is a serious public health problem mainly in developing countries. NC caused by the cysticercus stage from cestode Taenia solium is considered by the WHO and ITFDE as a potentially eradicable disease. Definitive diagnosis of NC is challenging because of the unspecific clinical manifestations such as the non-definitive evidence presented by neuroimaging (in most cases) and the lack of definitive serological test. Taenia crassiceps (ORF strain) is a cestode closely related to T. solium and it has frequently been used as a source of antigens for immunodiagnostics. A murine model to study host immune response to infection has also been established by using T. crassiceps. Despite the extensive use of T. crassiceps for research, molecular information for this cestode is scarce in public databases. With the aim of providing more extensive information on T. crassiceps biology, an RNA-seq experiment and subsequent bioinformatic transcriptome processing of this cestode parasite mRNA in its cysticercus stage were carried out. A total of 227,082 read/ESTs were sequenced using the 454-GS FLX Titanium technology and assembled into 10,787 contigs. This transcriptome dataset represents new and valuable molecular information of the cestode T. crassiceps (ORF). This information will substantially improve public information and will help to achieve a better understanding of the biology of T. crassiceps and to identify target proteins for serodiagnosis and vaccination.

The design of a source-controlled turbo coding scheme for the transmission of strongly nonuniform binary memoryless sources over additive white Gaussian noise (AWGN) channels is considered. The use of nonbinary signaling allows performance improvements over previous existing schemes that use binary modulation. The basic idea is to allocate more energy to the transmitted symbols associated with the information bits that occur less likely and to exploit the source nonuniformity in the decoding process. If the source and channel parameters are unknown, they can be estimated jointly with the encoding/decoding process. No performance degradation is observed in this case.

Simulation is a key tool for computer architecture research. In particular, cycle-accurate simulators are extremely important for microarchitecture exploration and detailed design decisions, but they are slow and, so, not suitable for simulating large-scale architectures, nor are they meant for this. Moreover, microarchitecture design decisions are irrelevant, or even misleading, for early processor design stages and high-level explorations. This allows one to raise the abstraction level of the simulated architecture, and also the application abstraction level, as it does not necessarily have to be represented as an instruction stream. In this paper we introduce a definition of different application abstraction levels, and how these are employed in TaskSim, a multi-core architecture simulator, to provide several architecture modeling abstractions, and simulate large-scale architectures with hundreds of cores. We compare the simulation speed of these abstraction levels to the ones in existing simulation tools, and also evaluate their utility and accuracy. Our simulations show that a very high-level abstraction, which may be even faster than native execution, is useful for scalability studies on parallel applications; and that just simulating explicit memory transfers, we achieve accurate simulations for architectures using non-coherent scratchpad memories, with just a 25x slowdown compared to native execution. Furthermore, we revisit trace memory simulation techniques, that are more abstract than instruction-by-instruction simulations and provide an 18x simulation speedup.

In throughput-aware CMPs like GPUs and DSPs, software-managed streaming memory systems are an effective way to tolerate high latencies. E.g., the Cell/B.E. incorporates local memories, and data transfers to/from those memories are overlapped with computation using DMAs. In such designs, the latency of the memory system has little impact on performance; instead, memory bandwidth becomes critical. With the increase in the number of cores, conventional DRAMs no longer suffice to satisfy the bandwidth demand. Hence, recent throughput-aware CMPs adopted caches to filter off-chip traffic. However, such caches are optimized for latency, not bandwidth. This work presents a re-design of the memory system in throughput-aware CMPs. Instead of a traditional latency-aware cache, we propose to spread the address space using fine-grained interleaving all over a shared non-coherent last-level cache (LLC). In this way, on-chip storage is optimally used, with no need to keep coherency. On the memory side, we also propose the use of interleaving across DRAMs but with a much finer granularity than usual page-size approaches. Our proposal is highly optimized for bandwidth, not latency, by avoiding data replication in the LLC and by using fine-grained address space interleaving in both the LLC and the memory. For a CMP with 128 cores and 64-MB LLC, performance is improved by 21% due to the LLC optimizations and an extra 42% due to the off-chip memory optimizations, for a total 1.7 times performance improvement.

Sequence alignment is one of the fundamental tasks in bioinformatics. Due to the exponential growth of biological data and the computational complexity of the algorithms used, high performance computing systems are required. Although multicore architectures have the potential of exploiting the task-level parallelism found in these workloads, efficiently harnessing systems with hundreds of cores requires deep understanding of the applications and the architecture. When incorporating large numbers of cores, performance scalability will likely saturate shared hardware resources like buses and memories. In this paper we evaluate the performance impact of various configurations of an accelerator-based multicore architecture with the aim of revealing and quantifying the bottlenecks. Then, we compare against a multicore using general-purpose processors and discuss the performance gap. Our target application is ClustalW, one of the most popular programs for Multiple Sequence Alignment. Different input data sets are characterized and we show how they influence performance. Simulation results show that due to the high computation-to-communication ratio and the transfer of data in large chunks, memory latency is well tolerated. However, bandwidth is critical to achieving maximum performance. Using a 32KB cache configuration with 4 banks can capture most of the memory traffic and therefore avoid expensive off-chip transactions. On the other hand, using a hardware queue for the tasks synchronization allows us to handle a large number of cores. Finally, we show that using a simple load balancing strategy, we can increase performance of general-purpose cores by 28%.

We present Task Superscalar, an abstraction of instruction-level out-of-order pipeline that operates at the tasklevel. Like ILP pipelines, which uncover parallelism in a sequential instruction stream, task superscalar uncovers tasklevel parallelism among tasks generated by a sequential thread. Utilizing intuitive programmer annotations of task inputs and outputs, the task superscalar pipeline dynamically detects intertask data dependencies, identifies task-level parallelism, and executes tasks out-of-order. Furthermore, we propose a design for a distributed task superscalar pipeline frontend, that can be embedded into any manycore fabric, and manages cores as functional units. We show that our proposed mechanism is capable of driving hundreds of cores simultaneously with non-speculative tasks, which allows our pipeline to sustain work windows consisting of tens of thousands of tasks. We further show that our pipeline can maintain a decode rate faster than 60ns per task and dynamically uncover data dependencies among as many as ~50,000 in-flight tasks, using 7MB of on-chip eDRAM storage. This configuration achieves speedups of 95–255x (average 183x) over sequential execution for nine scientific benchmarks, running on a simulated CMP with 256 cores. Task superscalar thus enables programmers to exploit manycore systems effectively, while simultaneously simplifying their programming model.

Biological sequence comparison is one of the most important tasks in Bioinformatics. Due to the growth of biological databases, sequence comparison is becoming an important challenge for high performance computing, especially when very long sequences are compared. The Smith-Waterman (SW) algorithm is an exact method based on dynamic programming to quantify local similarity between sequences. The inherent large parallelism of the algorithm makes it ideal for architectures supporting multiple dimensions of parallelism (TLP, DLP and ILP). In this work, we show how long sequences comparison takes advantage of current and future multicore architectures. We analyze two different SW implementations on the CellBE and use simulation tools to study the performance scalability in a multicore architecture. We study the memory organization that delivers the maximum bandwidth with the minimum cost. Our results show that a heterogeneous architecture is an valid alternative to execute challenging bioinformatic workloads.

Multimedia extensions based on Single-Instruction Multiple-Data (SIMD) units are widespread. They are used both in processors and accelerators (e.g., the Cell SPEs), since some time ago. SIMD units have usually big memory alignment constraints in order to meet power requirements and design simplicity. This increases the complexity of the code generated by the compiler, as in the general case, the compiler cannot be sure of the proper alignment of data. For that, the ISA provides either unaligned memory load and store instructions, or a special set of instructions to perform the realignments in software. In this paper, we propose a hardware realignment unit that takes advantage of the DMA transfers needed in accelerators with local memories. While the data is being transferred, it is realigned on the fly by our realignment unit, and stored with the proper alignment in the accelerator memory. The accelerator can then access the data with no special instructions. Finally, the data is realigned properly also when put back to main memory. Our experiments with four applications show that with our approach, the bandwidth of the DMA transfers is not penalized. And the performance of the synthetic benchmarks shows that aligned code is 1.5 to 2 times better with respect using unaligned code.

Memory bandwidth has always been a critical factor for the performance of many data intensive applications. The increasing processor performance, and the advert of single chip multiprocessors have increased the memory bandwidth demands beyond what a single commodity memory device can provide. The immediate solution is to use more than one memory device, and interleave data across them so they can be used in parallel as if they were a single device of higher bandwidth. In this paper we showed that fine-grain memory interleaving on the evaluated many-core architectures with many DRAM channels was critical to achieve high memory bandwidth efficiency. Our results showed that performance can degrade up to 50% due to achievable bandwidths being far from the maximum installed.

We propose the utilization of non-binary trellis codes as constituent codes for turbo codes. This allows to increase the free distance of the resulting turbo code with respect to traditional schemes, and leads to a reduction in the error floor. The price to pay is a slight performance degradation at low values of E/sub b//N/sub 0/. The proposed approach can be applied with other techniques based on interleaver design, therefore producing further reduction in the error floor.

This paper presents an analytical model that explores the Quality of Service of a satellite constellation operating according to the guaranteed handover procedure, GH, exposed in a former paper [1]. Here, the model takes into consideration the rotation of the earth, and therefore can be applied to constellations where the earth rotation effect is not negligible with respect to that of satellite velocity. Hence it applies both to LEO and MEO constellations, and not LEO only, as with former models.

A source-controlled turbo coding scheme for nonuniform binary memoryless sources sent over AWGN channels is designed. The use of nonbinary signaling allows performance improvements over previous schemes. The source and channel parameters can be estimated in the encoding and decoding processes.

The emergence of hardware accelerators, such as graphics processing units (GPUs), has challenged the interaction between processing elements (PEs) and main memory. In architectures like the Cell/B.E. or GPUs, the PEs incorporate local memories which are fed with data transferred from memory using direct memory accesses (DMAs). We expect that chip multiprocessors (CMP) with DMA-managed local memories will become more popular in the near future due to the increasing interest in accelerators. In this work we show that, in that case, the way cache hierarchies are conceived should be revised. Particularly for last-level caches, the norm today is to use latency-aware organizations. For instance, in dynamic nonuniform cache architectures (D-NUCA) data is migrated closer to the requester processor to optimize latency. However, in DMA-based scenarios, the memory system latency becomes irrelevant compared with the time consumed for moving the DMA data, so latency-aware designs are, a priori, inefficient. In this work, we revisit the last-level cache designs in DMA-based CMP architectures with master-worker execution. Two scenarios are evaluated. First, we consider a set of private caches with data replication across them, where coherency of the copies is ensured through a hardware protocol. In this scenario, a PE has a nearby copy of the datum, improving cache access latency. Second, we consider a partitioned cache, where the allocation of a datum to a cache block is determined based on its physical address. In this scenario, there are no copies of data, and access to a datum has a variable latency. In contrast with traditional load/store-based architectures, we found that the partitioned last-level cache scheme outperforms the cache with data replication for DMA-based scenarios.

The SARC architecture is composed of multiple processor types and a set of user-managed direct memory access (DMA) engines that let the runtime scheduler overlap data transfer and computation. The runtime system automatically allocates tasks on the heterogeneous cores and schedules the data transfers through the DMA engines. SARC's programming model supports various highly parallel applications, with matching support from specialized accelerator processors.

We propose a method that allows the use of practical error correcting codes of fixed length to achieve performance close to the Slepian-Wolf boundary without the use of explicit time-sharing arguments

We study the effect of asymmetric energy allocations to the output bits of turbo codes. We show that the error floor improves as more energy is given to the non-systematic bits. The standard (symmetric) energy allocation scheme achieves the best results in the waterfall region. However, the degradation observed in the waterfall region is practically non-existent when asymmetric energy allocation schemes close to the standard one are utilized. This implies that by using an appropriate energy allocation strategy, significant improvement in the error floor can be achieved with no practical degradation in the waterfall region.

Over the past few years, computer architecture research has moved towards execution-driven simulation, due to the inability of traces to capture timing-dependent thread execution interleaving. However, trace-driven simulation has many advantages over execution-driven that are being missed in multithreaded application simulations. We present a methodology to properly simulate multithreaded applications using trace-driven environments. We distinguish the intrinsic application behavior from the computation for managing parallelism. Application traces capture the intrinsic behavior in the sections of code that are independent from the dynamic multithreaded nature, and the points where parallelism-management computation occurs. The simulation framework is composed of a trace-driven simulation engine and a dynamic-behavior component that implements the parallelism-management operations for the application. Then, at simulation time, these operations are reproduced by invoking their implementation in the dynamic-behavior component. The decisions made by these operations are based on the simulated architecture, allowing to dynamically reschedule sections of code taken from the trace to the target simulated components. As the captured sections of code are independent from the parallel state of the application, they can be simulated on the trace-driven engine, while the parallelism-management operations, that require to be re-executed, are carried out by the execution-driven component, thus achieving the best of both trace- and execution-driven worlds. This simulation methodology creates several new research opportunities, including research on scheduling and other parallelism-management techniques for future architectures, and hardware support for programming models.