A precision overview of genomic resistance screening in Ecuadorian isolates of Mycobacterium tuberculosis using web-based bioinformatics tools.

Introduction: Tuberculosis (TB) is among the deadliest diseases worldwide, and its impact is mainly due to the continuous emergence of resistant isolates during treatment due to the laborious process of resistance diagnosis, nonadherence to treatment and circulation of previously resistant isolates of Mycobacterium tuberculosis. In this study, we evaluated the performance and functionalities of web-based tools, including Mykrobe, TB-profiler, PhyResSE, KvarQ, and SAM-TB, for detecting resistance in 88 Ecuadorian isolates of Mycobacterium tuberculosis drug susceptibility tested previously. Statistical analysis was used to determine the correlation between genomic and phenotypic analysis.

Deep serological profiling of the Trypanosoma cruzi TSSA antigen reveals different epitopes and modes of recognition by Chagas disease patients.

Background: Trypanosoma cruzi, the agent of Chagas disease, displays a highly structured population, with multiple strains that can be grouped into 6-7 evolutionary lineages showing variable eco-epidemiological traits and likely also distinct disease-associated features. Previous works have shown that antibody responses to 'isoforms' of the polymorphic parasite antigen TSSA enable robust and sensitive identification of the infecting strain with near lineage-level resolution. To optimize the serotyping performance of this molecule, we herein used a combination of immunosignaturing approaches based on peptide microarrays and serum samples from Chagas disease patients to establish a deep linear B-cell epitope profiling of TSSA.

Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador.

Background: Tuberculosis is a serious infectious disease affecting millions of people. In spite of efforts to reduce the disease, increasing antibiotic resistance has contributed to persist in the top 10 causes of death worldwide. In fact, the increased cases of multi (MDR) and extreme drug resistance (XDR) worldwide remains the main challenge for tuberculosis control.

The Elusive Mitochondrial Genomes of Apicomplexa: Where Are We Now?

Mitochondria are vital organelles of eukaryotic cells, participating in key metabolic pathways such as cellular respiration, thermogenesis, maintenance of cellular redox potential, calcium homeostasis, cell signaling, and cell death. The phylum Apicomplexa is entirely composed of obligate intracellular parasites, causing a plethora of severe diseases in humans, wild and domestic animals. These pathogens include the causative agents of malaria, cryptosporidiosis, neosporosis, East Coast fever and toxoplasmosis, among others.

Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex.

We sequenced maxicircles from T. cruzi strains representative of the species evolutionary diversity by using long-read sequencing, which allowed us to uncollapse their repetitive regions, finding that their real lengths range from 35 to 50 kb. T.

Nanopore Long Read DNA Sequencing of Protozoan Parasites: Hybrid Genome Assembly of Trypanosoma cruzi.

Due to highly repetitive genome sequences, short-read-based Trypanosoma cruzi genomes are extremely fragmented. Contiguous trypanosomatid genomes assemblies have resulted in the advent of third-generation sequencing technologies. Long reads span several to hundreds of kbps allowing to correct assemblies of repeated and low complexity DNA regions.

Reevaluation of the and genomes reveals misassembly, karyotype differences, and chromosomal rearrangements.

primarily infects cattle, causing abortions, with an estimated impact of a billion dollars on the worldwide economy annually. However, the study of its biology has been unheeded by the established paradigm that it is virtually identical to its close relative, the widely studied human pathogen By revisiting the genome sequence, assembly, and annotation using third-generation sequencing technologies, here we show that the genome was originally incorrectly assembled under the presumption of synteny with We show that major chromosomal rearrangements have occurred between these species. Importantly, we show that chromosomes originally named Chr VIIb and VIII are indeed fused, reducing the karyotype of both and to 13 chromosomes.

Isolation and molecular characterization of four novel Neospora caninum strains.

Neospora caninum causes neosporosis, a leading cause of bovine abortion worldwide. Uruguay is a developing economy in South America that produces milk to feed seven times its population annually. Naturally, dairy production is paramount to the country's economy, and bovine reproductive failure impacts it profoundly.

Transcriptome Studies in Trypanosoma cruzi Using RNA-seq.

RNA-seq is a powerful method to study in detail transcriptome changes in defined conditions, providing enormous amount of information on RNA stability and gene regulation. In this chapter, we describe a directional and a nondirectional library preparation protocol for RNA-seq in Trypanosoma cruzi, as well as a pipeline for bioinformatic analysis, which includes read trimming, alignment to a reference genome, and differential expression.

Genomic and Transcriptomic Basis of Hanseniaspora vineae's Impact on Flavor Diversity and Wine Quality.

is the main genus of the apiculate yeast group that represents approximately 70% of the grape-associated microflora. is emerging as a promising species for quality wine production compared to other non- species. Wines produced by with consistently exhibit more intense fruity flavors and complexity than wines produced by alone.

Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut.

The quest to discover the variety of ecological niches inhabited by Saccharomyces cerevisiae has led to research in areas as diverse as wineries, oak trees and insect guts. The discovery of fungal communities in the human gastrointestinal tract suggested the host's gut as a potential reservoir for yeast adaptation. Here, we report the existence of yeast populations associated with the human gut (HG) that differ from those isolated from other human body sites.

Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi.

Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degrees of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T.

Genomic and Phenotypic Variation in Morphogenetic Networks of Two Isolates Subtends Their Different Pathogenic Potential.

The transition from commensalism to pathogenicity of reflects both the host inability to mount specific immune responses and the microorganism's dimorphic switch efficiency. In this study, we used whole genome sequencing and microarray analysis to investigate the genomic determinants of the phenotypic changes observed in two clinical isolates (YL1 and YQ2). experiments employing epithelial, microglial, and peripheral blood mononuclear cells were thus used to evaluate isolates interaction with first line host defenses, measuring adhesion, susceptibility to phagocytosis, and induction of secretory responses.

Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates.

Background: Bovine tuberculosis (bTB) poses serious risks to animal welfare and economy, as well as to public health as a zoonosis. Its etiological agent, Mycobacterium bovis, belongs to the Mycobacterium tuberculosis complex (MTBC), a group of genetically monomorphic organisms featured by a remarkably high overall nucleotide identity (99.9%).

Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax.

Background: The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P.

Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in .

American trypanosomiasis is a chronic and endemic disease which affects millions of people. , its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation.

Social wasps are a Saccharomyces mating nest.

The reproductive ecology of Saccharomyces cerevisiae is still largely unknown. Recent evidence of interspecific hybridization, high levels of strain heterozygosity, and prion transmission suggest that outbreeding occurs frequently in yeasts. Nevertheless, the place where yeasts mate and recombine in the wild has not been identified.

riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics.

Non-targeted metagenomics offers the unprecedented possibility of simultaneously investigate the microbial profile and the genetic capabilities of a sample by a direct analysis of its entire DNA content. The assessment of the microbial taxonomic composition is frequently obtained by mapping reads to genomic databases that, although growing, are still limited and biased. Here we present riboFrame, a novel procedure for microbial profiling based on the identification and classification of 16S rDNA sequences in non-targeted metagenomics datasets.

Whole-Genome Sequences of Mycobacterium bovis Strain MbURU-001, Isolated from Fresh Bovine Infected Samples.

Bovine tuberculosis in cattle has a high incidence in Uruguay, where it is considered a disease of national importance. We present the genome sequence of Mycobacterium bovis strain MbURU-001, isolated from pectoral lymph nodes of a bovine host from a cattle farm.

Evolutionary volatile Cysteines and protein disorder in the fast evolving tunicate Oikopleura dioica.

Cysteine (Cys) is regarded as the most conservative amino acid in nature, something that does not occur in the tunicate Oikopleura dioica, where this amino acid is one of the fastest evolving. In this work we analyze some of the causes of this intriguing absence of conservation. Considering the well-known stabilizing role of Cys, it was first investigated whether the lack of conservation was accompanied by an increase in intrinsic protein disorder.

Hsp12p and PAU genes are involved in ecological interactions between natural yeast strains.

The coexistence of different yeasts in a single vineyard raises the question on how they communicate and why slow growers are not competed out. Genetically modified laboratory strains of Saccharomyces cerevisiae are extensively used to investigate ecological interactions, but little is known about the genes regulating cooperation and competition in ecologically relevant settings. Here, we present evidences of Hsp12p-dependent altruistic and contact-dependent competitive interactions between two natural yeast isolates.

Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis.

A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi).

Whole-Genome Sequencing of an Isoniazid-Resistant Clinical Isolate of Mycobacterium tuberculosis Strain MtURU-002 from Uruguay.

The incidence of tuberculosis in Uruguay has been effectively reduced to <30 per 100,000 population, although an increase in nonrisk populations in the last few years is evident. Here, we present the genome sequence of Mycobacterium tuberculosis strain MtURU-002 isolated from a patient showing bilateral pulmonary tuberculosis that was resistant to isoniazid.

Evolutionary genomics of fast evolving tunicates.

Tunicates have been extensively studied because of their crucial phylogenetic location (the closest living relatives of vertebrates) and particular developmental plan. Recent genome efforts have disclosed that tunicates are also remarkable in their genome organization and molecular evolutionary patterns. Here, we review these latter aspects, comparing the similarities and specificities of two model species of the group: Oikopleura dioica and Ciona intestinalis.