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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.

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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

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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.

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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.

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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.

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"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.

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"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.

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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.

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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.

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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.

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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.

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PURPOSE: Gastric cancer is a curable disease if diagnosed at early stage. However, most cases are diagnosed at advanced stage because of the lack of screening programs. Therefore, the identification of plasma biomarkers for early detection is necessary. EXPERIMENTAL DESIGN: To search for these biomarkers, we evaluated the DNA methylation patterns of 24 genes by Methylation-specific PCR in primary tissues from 32 retrospectively collected gastric cancer cases (testing group). Correlation between methylation and gene expression was evaluated in the MKN-45 cell line after treatment with 5-aza-2'-deoxycytidine. The most frequently hypermethylated genes were next evaluated in primary tissues and plasma samples from 43 prospectively collected gastric cancer cases as well as plasma samples from 31 asymptomatic age- and gender-matched controls (validation group). RESULTS: In the testing group, 11 genes were hypermethylated in at least 50% of cases (APC, SHP1, E-cadherin, ER, Reprimo, SEMA3B, 3OST2, p14, p15, DAPK, and p16). Eight genes (BRCA1, p73, RARbeta, hMLH1, RIZI, RUNX3, MGMT, and TIMP3) were statistically associated with a particular variant of gastric cancer, the signet-ring cell type (P = 0.03). Seven genes (APC, SHP1, E-cadherin, ER, Reprimo, SEMA3B, and 3OST2) were next evaluated in the validation group. We confirm the high frequency of methylation in primary tumors for all seven genes. However, only APC and Reprimo were frequently methylated in pair plasma samples. In asymptomatic controls, only Reprimo was infrequently methylated in comparison with plasma from gastric cancer cases (P < 0.001). CONCLUSION: Our results identified specific methylation profile associated to signet-ring cell-type histology and aberrant hypermethylation of Reprimo as a potential biomarker for early detection of gastric cancer.

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Worldwide gastric carcinoma has marked geographical variations and worse outcome in patients from the West compared to the East. Although these differences has been explained by better diagnostic criteria, improved staging methods and more radical surgery, emerging evidence supports the concept that gene expression differences associated to ethnicity might contribute to this disparate outcome. Here, we collected datasets from 4 normal and 11 gastric carcinoma Serial Gene Expression Analysis (SAGE) libraries from two different ethnicities. All normal SAGE libraries as well as 7 tumor libraries were from the West and 4 tumor libraries were from the East. These datasets we compare by Correspondence Analysis and Support Tree analysis and specific differences in tags expression were identified by Significance Analysis for Microarray. Tags to gene assignments were performed by CGAP-SAGE Genie or TAGmapper. The analysis of global transcriptome shows a clear separation between normal and tumor libraries with 90 tags differentially expressed. A clear separation was also found between the West and the East tumor libraries with 54 tags differentially expressed. Tags to gene assignments identified 15 genes, 5 of them with significant higher expression in the West libraries in comparison to the East libraries. qRT-PCR in cell lines from west and east origin confirmed these differences. Interestingly, two of these genes have been associated to aggressiveness (COL1A1 and KLK10). In conclusion we found that in silico analysis of SAGE libraries from two different ethnicities reveal differences in gene expression profile. These expression differences might contribute to explain the disparate outcome between the West and the East.

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AlterORF is a searchable database that contains information regarding alternate open reading frames (ORFs) for over 1.5 million genes in 481 prokaryotic genomes. The objective of the database is to provide a platform for improving genome annotation and to serve as an aid for the identification of prokaryotic genes that potentially encode proteins in more than one reading frame. The AlterORF Database can be accessed through a web interface at www.alterorf.cl.

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Diffuse type gastric carcinoma is the most aggressive type of gastric cancer. This type of tumor is not preceded by precancerous changes and is associated with early-onset and hereditary syndromes. To test the hypothesis that DNA methylation profile would be useful for molecular classification of the diffuse type gastric carcinoma, DNA methylation patterns of the CpG Island of 17 genes were studied in 104 cases and 47 normal adjacent gastric mucosa by Methylation-specific PCR, Immunohistochemistry and Hierarchical clustering analysis. The most frequent methylated genes were FHIT, E-cadherin, BRCA1 and APC (>50%), followed by p14, p16, p15, p73, MGMT and SEMA3B (20-49%). Hierarchical clustering analysis reveals four groups with different clinical features. The first was characterized by hypermethylation of BRCA1 and younger age (<45 years old), and the second by hypermethylation of p14 and p16 genes, male predominance and Epstein-Barr virus infection. The third group was characterized by hypermethylation of FHIT and antrum located tumors and the fourth was not associated with any clinical variables. In normal adjacent mucosa only the p73 gene was significantly less methylated in comparison to tumor mucosa. DNA methylation identified subgroups of diffuse type gastric cancer. Hypermethylation of BRCA1 associated with young age suggests a role in early-onset gastric carcinoma.

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Diffuse type gastric carcinoma is the most aggressive type of gastric cancer. This type of tumor is not preceded by precancerous changes and is associated with early-onset and hereditary syndromes. To test the hypothesis that DNA methylation profile would be useful for molecular classification of the diffuse type gastric carcinoma, DNA methylation patterns of the CpG Island of 17 genes were studied in 104 cases and 47 normal adjacent gastric mucosa by Methylation-specific PCR, Immunohistochemistry and Hierarchicalclustering analysis. The most frequent methylated genes were FHIT, E-cadherin, BRCA1 and APC (>50%),followed by p14, p16, p15, p73, MGMT and SEMA3B (20-49%). Hierarchical clustering analysis reveals four groups with different clinical features. The first was characterized by hypermethylation of BRCA1 and younger age (<45 years old), and the second by hypermethylation of p14 and p16 genes, male predominance and Epstein-Barr virus infection. The third group was characterized by hypermethylation of FHIT and antrum located tumors and the fourth was not associated with any clinical variables. In normal adjacent mucosa only the p73 gene was significantly less methylated in comparison to tumor mucosa. DNA methylation identified subgroups of diffuse type gastric cancer. Hypermethylation of BRCA1 associated with young age suggests a role in early-onset gastric carcinoma.

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La obstrucción ureteral post trasplante renal es una complicación tardía del trasplante y la incidencia actual ha disminuido a un 5-10 por ciento en la literatura. Reportamos el caso y describimos la técnica quirúrgica, de una estenosis ureteral post trasplante renal en una niña, resuelta en forma exitosa con una anastomosis de la pelvis renal del injerto al uréter nativo. La estenosis ureteral post trasplante renal en niños es poco frecuente, puede ser manejada en forma exitosa con esta técnica quirúrgica.

Ureteral obstruction is a late complication in renal transplant. The current incidence has lowered to 5- 10 percent in the literature. We report a case of ureteral stenosis post renal transplant in a 12 years old girl. We describe the surgical technique used to correct this complication an anastomosis between the native ureter and the renal pelvis of the graft. Post renal transplant ureteral stenosis is an uncommon complication in children, and can be successfully managed using this surgical procedure.

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El dolor abdominal es uno de los motivos más frecuentes de consulta en los Servicios de Urgencias Pediátricas, siendo lo más importante diferenciar aquel cuadro que requiere tratamiento médico versus aquél que requería una solución quirúrgica. Aproximadamente el 5 por ciento al 15 por ciento de los niños que consultan por dolor abdominal agudo de más de 2 horas de duración serán intervenidos quirúrgicamente. La mayoría de los casos presentan una causa benigna, pero algunas requerirán un rápido diagnóstico y tratamiento para minimizar la morbimortalidad.

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PURPOSE: Excisional ureteroplasty carries the risks of jeopardizing the ureteral vasculature and leakage from the suture. The folding techniques are theoretically less prone to these risks, although they have other disadvantages due to the bulky ureter. According to the literature, these 2 approaches have similar complication rates of 4% to 25%, to include stenosis, reflux and leakage. We introduce a modified ureteroplasty technique with the aim of ensuring effective reduction of the ureteral diameter with minor risks to the vasculature. MATERIALS AND METHODS: A total of 42 consecutive patients underwent ureteroplasty and reimplantation (Cohen 16, Politano-Leadbetter 3, psoas hitch 23) between 1994 and 2004, and were followed for 1 to 9 years. The ureter was opened longitudinally on its less vascularized area. Two parallel longitudinal incisions were made from the luminal side up to the musculature layer, leaving the adventitia untouched. The mucosal aspects lateral to these lines were discarded. The inner layer was closed with a running suture. The adventitial layer was closed with single stitches. RESULTS: No leakage, stenosis or reflux was observed. In 3 ureters persistent dilatation was observed, without obstruction or reflux. CONCLUSIONS: Our modification combines some principles of the 2 classic techniques, with the purpose of decreasing the risks and disadvantages of both. We believe that our approach affords better preservation of the ureteral vasculature because the adventitia is preserved untouched, as well as effective caliber reduction so that the bulking problem is avoided. In addition, the technique is associated with a minor risk of leakage. Our results show that this approach is a valid option for megaureter correction in children.

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Se presentan 10 casos de diagnóstico antenatal urológico y su evolución posterior. La ecografía en nuestras manos fue muy sensible en el diagnóstico de obstrucción no así en el diagnóstico fino de la afección causal. Ello pensamos mejorará con mayor experiencia. Los resultados de la cirugía neonatal por obstrucción pieloureteral (6 riñones) fueron buenos, recuperándose incluso un riñón excluido en la pielografía. No se usó nefrostomía ni tutor en la pieloplastía. También evolucionaron bien los casos que requirieron heminefrectomía superior, y nefrectomía con sección del puente de riñón en herradura. Sólo una vesicostomía temporal requirió de cirugía posterior al fallar por presentar prolapso grave. No se operó y mejoró en forma espontánea, al hacer una colostomía, un caso con hidronefrosis bilateral a comprensión vesical por el recto ciego de una imperforación anal

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