The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered.

UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.

The Flexible Genome of Acidophilic Prokaryotes.

Over the last couple of decades there has been considerable progress in the identification and understanding of the mobile genetic elements that are exchanged between microbes in extremely acidic environments, and of the genes piggybacking on them. Numerous plasmid families, unique viruses of bizarre morphologies and lyfe cycles, as well as plasmid-virus chimeras, have been isolated from acidophiles and characterized to varying degrees. Growing evidence provided by omic-studies have shown that the mobile elements repertoire is not restricted to plasmids and viruses, but that a plethora of integrative elements ranging from miniature inverted repeat transposable elements to large integrative conjugative elements populate the genomes of acidophilic bacteria and archaea. This article reviews the diversity of elements that have been found to constitute the flexible genome of acidophiles. Special emphasis is put on the knowledge generated for Sulfolobus (archaea) and species of the bacterial genera Acidithiobacillus and Leptospirillum. Also, recent knowledge on the strategies used by acidophiles to contain deletereous exchanges while allowing innovation, and the emerging details of the molecular biology of these systems, are discussed. Major lacunae in our understanding of the mobilome of acidophilic prokaryotes and topics for further investigations are identified.

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis.

The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman's reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive vaginal health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 31 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, Gardnerella, and 3 pathogens involved in STI, with high sensitivity, specificity, and reproducibility. For each of these taxa, reference ranges were determined in a group of 50 self-reported healthy women. The HPV sequencing portion of the test was evaluated against the digene High-Risk HPV HC2 DNA test. For hrHPV genotyping, agreement was 95.3% with a kappa of 0.804 (601 samples); after removal of samples in which the digene hrHPV probe showed cross-reactivity with lrHPV types, the sensitivity and specificity of the hrHPV genotyping assay were 94.5% and 96.6%, respectively, with a kappa of 0.841. For lrHPV genotyping, agreement was 93.9% with a kappa of 0.788 (148 samples), while sensitivity and specificity were 100% and 92.9%, respectively. This novel assay could be used to complement conventional cervical cancer screening, because its self-sampling format can expand access among women who would otherwise not participate, and because of its additional information about the composition of the vaginal microbiome and the presence of pathogens.

Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome.

[This corrects the article DOI: 10.1371/journal.pone.0176555.].

Aspectos Técnicos de la Pieloplastía Robótica / Technical Aspects of Robotic Pyeloplasty

La cirugía robótica tiene muchos puntos comunes con la cirugía abierta con aumento visual (lupas), determinado por: la visión tridimensional aumentada, la articulación de los instrumentos que permite disecar y pasar puntos en diferentes planos y la precisión con ausencia de temblor en la cirugía.Suman en la pieloplastía robótica: la mínima invasión, el mayor aumento de la imagen, el carácter ambidextro de ella, y la menor tracción de los tejidos, al permitir una cirugía in situ de la unión pieloureteral. El video se inicia con una exposición teórica sobre los puntos importantes referidos a: preservar la irrigación de los tejidos,excision rutinaria de un trozo de uréter proximal para mejorar la distensibilidad y diámetro del uréter y la conveniencia de usar puntos separados en la boca anastomótica para garantizar un buen lumen. Luego se muestra una pieloplastía robótica, enfatizando los puntos señalados durante la cirugía.AU

Robotic surgery has many common points if compared to open surgery with visual magnification (loupes), determined by: increased three-dimensional vision, instruments articulation that enable dissection and passing through points in different planes and precision without tremor in surgery. Additionally, in robotic pyeloplasty, the following must be considered: minimal invasion, greater image magnification, its ambidextrous character and less tissue traction, allowing in situ pyeloureteral junction surgery. The video begins with a theoretical presentation about the important points related: preserving tissue irrigation, routine excision of a section of proximal ureter to improve the distensibility and diameter thereof and the convenience of using separate points in the anastomotic mouth to ensure good lumen. After that, a robotic pyeloplasty is shown, emphasizing the points indicated during the surgery. AU

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome.

Changes in the relative abundances of many intestinal microorganisms, both those that naturally occur in the human gut microbiome and those that are considered pathogens, have been associated with a range of diseases. To more accurately diagnose health conditions, medical practitioners could benefit from a molecular, culture-independent assay for the quantification of these microorganisms in the context of a healthy reference range. Here we present the targeted sequencing of the microbial 16S rRNA gene of clinically relevant gut microorganisms as a method to provide a gut screening test that could assist in the clinical diagnosis of certain health conditions. We evaluated the possibility of detecting 46 clinical prokaryotic targets in the human gut, 28 of which could be identified with high precision and sensitivity by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. These targets included 20 commensal, 3 beneficial (probiotic), and 5 pathogenic intestinal microbial taxa. Using stool microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay quantifies 28 targets in the context of a healthy reference range and correctly reflected 38/38 verification samples of real and synthetic stool material containing known gut pathogens. Thus, we have established a method to determine microbiome composition with a focus on clinically relevant taxa, which has the potential to contribute to patient diagnosis, treatment, and monitoring. More broadly, our method can facilitate epidemiological studies of the microbiome as it relates to overall human health and disease.

Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile.

Leptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod-shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.

Towards the bridging of molecular genetics data across Xenopus species.

BACKGROUND: The clawed African frog Xenopus laevis has been one of the main vertebrate models for studies in developmental biology. However, for genetic studies, Xenopus tropicalis has been the experimental model of choice because it shorter life cycle and due to a more tractable genome that does not result from genome duplication as in the case of X. laevis. Today, although still organized in a large number of scaffolds, nearly 85% of X. tropicalis and 89% of X. laevis genomes have been sequenced. There is expectation for a comparative physical map that can be used as a Rosetta Stone between X. laevis genetic studies and X. tropicalis genomic research. RESULTS: In this work, we have mapped using coarse-grained alignment the 18 chromosomes of X. laevis, release 9.1, on the 10 reference scaffolds representing the haploid genome of X. tropicalis, release 9.0. After validating the mapping with theoretical data, and estimating reference averages of genome sequence identity, 37 to 44% between the two species, we have carried out a synteny analysis for 2,112 orthologous genes. We found that 99.6% of genes are in the same organization. CONCLUSIONS: Taken together, our results make possible to establish the correspondence between 62 and 65.5% of both genomes, percentage of identity, synteny and automatic annotation of transcripts of both species, providing a new and more comprehensive tool for comparative analysis of these two species, by allowing to bridge molecular genetics data among them.

Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum".

BACKGROUND: Members of the genus "Ferrovum" are ubiquitously distributed in acid mine drainage (AMD) waters which are characterised by their high metal and sulfate loads. So far isolation and microbiological characterisation have only been successful for the designated type strain "Ferrovum myxofaciens" P3G. Thus, knowledge about physiological characteristics and the phylogeny of the genus "Ferrovum" is extremely scarce. OBJECTIVE: In order to access the wider genetic pool of the genus "Ferrovum" we sequenced the genome of a "Ferrovum"-containing mixed culture and successfully assembled the almost complete genome sequence of the novel "Ferrovum" strain JA12. PHYLOGENY AND LIFESTYLE: The genome-based phylogenetic analysis indicates that strain JA12 and the type strain represent two distinct "Ferrovum" species. "Ferrovum" strain JA12 is characterised by an unusually small genome in comparison to the type strain and other iron oxidising bacteria. The prediction of nutrient assimilation pathways suggests that "Ferrovum" strain JA12 maintains a chemolithoautotrophic lifestyle utilising carbon dioxide and bicarbonate, ammonium and urea, sulfate, phosphate and ferrous iron as carbon, nitrogen, sulfur, phosphorous and energy sources, respectively. UNIQUE METABOLIC FEATURES: The potential utilisation of urea by "Ferrovum" strain JA12 is moreover remarkable since it may furthermore represent a strategy among extreme acidophiles to cope with the acidic environment. Unlike other acidophilic chemolithoautotrophs "Ferrovum" strain JA12 exhibits a complete tricarboxylic acid cycle, a metabolic feature shared with the closer related neutrophilic iron oxidisers among the Betaproteobacteria including Sideroxydans lithotrophicus and Thiobacillus denitrificans. Furthermore, the absence of characteristic redox proteins involved in iron oxidation in the well-studied acidophiles Acidithiobacillus ferrooxidans (rusticyanin) and Acidithiobacillus ferrivorans (iron oxidase) indicates the existence of a modified pathway in "Ferrovum" strain JA12. Therefore, the results of the present study extend our understanding of the genus "Ferrovum" and provide a comprehensive framework for future comparative genome and metagenome studies.

Kidney transplant in pediatric patients with severe bladder pathology.

The aim of the current study was to compare results in pediatric renal transplantation of patients with and without SBP. Between 2001 and 2013, a total of 168 kidney transplants were performed at our center. A retrospective analysis was performed and recipients were divided into two groups: NB and SBP. Incidence of surgical complications after procedure, and graft and patient survival were evaluated. A total of 155 recipients (92%) with complete data were analyzed, and 13 recipients that had had previous bladder surgeries were excluded (11 with VUR surgery and two with previous kidney transplants), of the 155 recipients: 123 (79%) patients had NB, and 32 (21%) patients had SBP, with a median follow-up of 60 (1-137) and 52 (1-144) months, respectively. Among post-transplant complications, UTI (68.8% vs. 23%, p < 0.0001) and symptomatic VUR to the graft (40.6% vs. 7.3%, p < 0.0001) were significantly higher in the SBP group. There was no significant difference in overall graft and patient survival between groups. Renal transplantation is safe in pediatric recipients with SBP; however, urologic complications such as UTI and VUR were significantly higher in this group. Graft and patient survival was similar in SBP and NB groups.

Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream.

An acid mine drainage (pH 2.5-2.7) stream biofilm situated 250 m below ground in the low-temperature (6-10°C) Kristineberg mine, northern Sweden, contained a microbial community equipped for growth at low temperature and acidic pH. Metagenomic sequencing of the biofilm and planktonic fractions identified the most abundant microorganism to be similar to the psychrotolerant acidophile, Acidithiobacillus ferrivorans. In addition, metagenome contigs were most similar to other Acidithiobacillus species, an Acidobacteria-like species, and a Gallionellaceae-like species. Analyses of the metagenomes indicated functional characteristics previously characterized as related to growth at low temperature including cold-shock proteins, several pathways for the production of compatible solutes and an anti-freeze protein. In addition, genes were predicted to encode functions related to pH homeostasis and metal resistance related to growth in the acidic metal-containing mine water. Metagenome analyses identified microorganisms capable of nitrogen fixation and exhibiting a primarily autotrophic lifestyle driven by the oxidation of the ferrous iron and inorganic sulfur compounds contained in the sulfidic mine waters. The study identified a low diversity of abundant microorganisms adapted to a low-temperature acidic environment as well as identifying some of the strategies the microorganisms employ to grow in this extreme environment.

Draft Genome Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM 14647.

The genomic features of the Leptospirillum ferriphilum type strain DSM 14647 are described here. An analysis of the predicted genes enriches our knowledge of the molecular basis of iron oxidation, improves our understanding of its role in industrial bioleaching, and suggests how it is adapted to live at extremely low pH.

Draft Genome Sequence of the Iron-Oxidizing, Acidophilic, and Halotolerant "Thiobacillus prosperus" Type Strain DSM 5130.

"Thiobacillus prosperus" is a halotolerant mesophilic acidophile that gains energy through iron and sulfur oxidation. Its physiology is poorly understood. Here, we describe the principal genomic features of the type strain of T. prosperus, DSM 5130. This is the first public genome sequence of an acidophilic halotolerant bacterium.

Draft Genome Sequence of the Nominated Type Strain of "Ferrovum myxofaciens," an Acidophilic, Iron-Oxidizing Betaproteobacterium.

"Ferrovum myxofaciens" is an iron-oxidizing betaproteobacterium with widespread distribution in acidic low-temperature environments, such as acid mine drainage streams. Here, we describe the genomic features of this novel acidophile and investigate the relevant metabolic pathways that enable its survival in these environments.

Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms.

All metals are toxic at high concentrations and consequently their intracellular concentrations must be regulated. Extremely acidophilic microorganisms have an optimum growth of pH <3 and proliferate in natural and anthropogenic low pH environments. Some acidophiles are involved in the catalysis of sulfide mineral dissolution, resulting in high concentrations of metals in solution. Acidophiles are often described as highly metal resistant via mechanisms such as multiple and/or more efficient active resistance systems than are present in neutrophiles. However, this is not the case for all acidophiles and we contend that their growth in high metal concentrations is partially due to an intrinsic tolerance as a consequence of the environment in which they live. In this perspective, we highlight metal tolerance via complexation of free metals by sulfate ions and passive tolerance to metal influx via an internal positive cytoplasmic transmembrane potential. These tolerance mechanisms have been largely ignored in past studies of acidophile growth in the presence of metals and should be taken into account.

Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus.

Acidithiobacillus thiooxidans is a mesophilic, extremely acidophilic, chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation of sulfur and inorganic sulfur compounds. Here we present the draft genome sequence of A. thiooxidans ATCC 19377, which has allowed the identification of genes for survival and colonization of extremely acidic environments.

Expresión diferencial de genes asociados a carcinoma de próstata / Differential expression of genes associated with prostate carcinoma

Objetivo: La introducción del Antígeno Prostático Específico (APE) como herramienta de uso masivo en la detección precoz de cáncer prostático (CaP), parece ser al menos parcialmente responsable de la disminución en la mortalidad observada en el último tiempo. Sin embargo, el APE tiene una baja especificidad como marcador de cáncer, especialmente en el rango de 4 a 10 ng/ml donde existe una alta sobreposición con otras patologías de mayor prevalencia como por ejemplo, Hiperplasia Prostática Benigna (HPB). Es por esto, que existe una búsqueda constante de nuevos marcadores. Nuestro objetivo fue caracterizar el perfil de expresión génica del CaP utilizando microarray. Material y métodos: Doce casos de CaP con PSA <10 ng/ml y 4 casos con PSA >10 ng/ml fueron seleccionados prospectivamente para análisis de microarray para 96 genes característicos de tejido prostático. Los análisis se efectuaron por el método de Hierarchical Clustering y se realizó Transcripción Reversa y Reacción de Polimerasa en Cadena para confirmar la información obtenida mediante microarray. Además, se evaluó la presencia en sangre periférica de los genes sobre-expresados en tejido y que pudieran ser marcadores sistémicos de CaP. Resultados: Se definieron 13 genes basándose en su alta expresión, los cuales se agruparon en NCOA4/NDRG1, LDHA/LIM/GSTP1 y KLK2/KLK4 y estos con CALR y CSTB. Los genes SPARCL1, KLK3(PSA), ARSDR1 y ACPP se ordenaron en ramas independientes. El gen ACPP (fosfatasa ácida prostática) fue el más independientemente sobreexpresado. Realizamos RT-PCR para ACPP en 15 tumores primarios y sangre periférica observando señal positiva en 10 (71 por ciento) de 14 casos analizados. Conclusiones: Nuestros resultados indican que el gen ACPP se encuentra sobreexpresado a nivel molecular en tumor primario y sangre periférica, convirtiéndolo en un potencial marcador de CaP con niveles de PSA <10 ng/ml.

Objective: The introduction of prostate specific antigen (PSA) as a screening tool for early detection of prostate cancer (CaP), seems to take a role in being responsible for the decreasing of mortality observed in the last time. Nevertheless, the APE has a low specificity like cancer marker, especially in the rank from 4 to 10 ng/ml where a high superposition with other pathologies of greater prevalence like Benign Prostate Hiperplasia (HPB) exists. This is why there is a constant research for new markers. Our objective was to characterize the gene expression profile of prostate using microarray. Material and Methods: Twelve cases of CaP with PSA <10 ng/ml and 4 cases with PSA >10 ng/ml were prospectively selected for microarray analysis for 96 genes characteristic of prostate tissue. The analysis was performed by the method of Hierarchical Clustering and performed reverse transcription polymerase chain reaction to confirm the information obtained by microarray. We assessed the presence in peripheral blood of over-expressed genes in tissue that could become in systemic markers of PC. Results: We identified 13 genes based on their high expression, which were grouped into NCOA4/NDRG1, LDHA/LIM/GSTP1 and KLK2/KLK4 and those with CALR and CSTB. Genes SPARCL1, KLK3 (PSA) and ACPP ARSDR1 were ordered in separate branches. The ACPP gene (prostatic acid phosphatase) was overexpressed more independently. We RT-PCR for ACPP in 15 primary tumors and peripheral blood positive signal observed in 10 (71per cent) of 14 cases analyzed. Conclusions: Our results indicate that the ACPP gene is overexpressed in a molecular level in primary tumor and peripheral blood, making it a potential marker for prostate cancer with PSA levels <10 ng/ml.

Lipoblastoma with unique localization requiring tracheal and esophageal resection.

Lipoblastoma and lipoblastomatosis are rare tumors of infancy. They originate from embryonic fat and localize in soft tissues. We present the case of a lipoblastoma of the neck with localization in tracheal and esophageal walls that required an extended laryngotracheal and esophageal resection. To our knowledge, this is the first report of such localization of this tumor.

Analysis of the intronic single nucleotide polymorphism rs#466452 of the nephrin gene in patients with diabetic nephropathy.

We present the analysis of an intronic polymorphism of the nephrin gene and its relationship to the development of diabetic nephropathy in a study of diabetes type 1 and type 2 patients. The frequency of the single nucleotide polymorphism rs#466452 in the nephrin gene was determined in 231 patients and control subjects. The C/T status of the polymorphism was assessed using restriction enzyme digestions and the nephrin transcript from a kidney biopsy was examined. Association between the polymorphism and clinical parameters was evaluated using multivariate correspondence analysis. A bioinformatics analysis of the single nucleotide polymorphism rs#466452 suggested the appearance of a splicing enhancer sequence in intron 24 of the nephrin gene and a modification of proteins that bind to this sequence. However, no change in the splicing of a nephrin transcript from a renal biopsy was found. No association was found between the polymorphism and diabetes or degree of renal damage in diabetes type 1 or 2 patients. The single nucleotide polymorphism rs#466452 of the nephrin gene seems to be neutral in relation to diabetes and the development of diabetic nephropathy, and does not affect the splicing of a nephrin transcript, in spite of a splicing enhancer site.

Analysis of the intronic single nucleotide polymorphism rs#466452 of the nephrin gene in patients with diabetic nephropathy

We present the analysis of an intronic polymorphism of the nephrin gene and its relationship to the development of diabetic nephropathy in a study of diabetes type 1 and type 2 patients. The frequency of the single nucleotide polymorphism rs#466452 in the nephrin gene was determined in 231 patients and control subjects. The C/T status of the polymorphism was assessed using restriction enzyme digestions and the nephrin transcript from a kidney biopsy was examined. Association between the polymorphism and clinical parameters was evaluated using multivaríate correspondence analysis. A bioinformatics analysis of the single nucleotide polymorphism rs#466452 suggested the appearance of a splicing enhancer sequence in intron 24 of the nephrin gene and a modification of proteins that bind to this sequence. However, no change in the splicing of a nephrin transcript from a renal biopsy was found. No association was found between the polymorphism and diabetes or degree of renal damage in diabetes type 1 or 2 patients. The single nucleotide polymorphism rs#466452 of the nephrin gene seems to be neutral in relation to diabetes and the development of diabetic nephropathy, and does not affect the splicing of a nephrin transcript, in spite of a splicing enhancer site.