Análisis genético de cinco polimorfismos de nucleótido simple de caseínas lácteas obtenidos con chips genómicos en ganado Holstein de Antioquia, Colombia / Genetic analysis of five single nucleotide polymorphisms of dairy caseins obtained with genomic chips in Holstein cattle from Antioquia, Colombia

RESUMEN Los polimorfismos genéticos asociados con las caseínas de la leche son de gran importancia, ya que pueden ser usados como marcadores genéticos para mejorar el rendimiento productivo en los hatos lecheros. El objetivo de este estudio fue evaluar la diversidad y estructura genética de 5 SNP de caseínas de la leche, obtenidos con chips genómicos en vacas y toros de raza Holstein en Antioquia (Colombia). Fueron muestreados 113 animales de raza Holstein en 3 regiones del departamento de Antioquia (norte, centro y oriente) y un cuarto grupo de sementales comerciales. Los animales fueron genotipificados con chips genómicos de alta densidad (Illumina BovineHD e Illumina SNP50 v2), a partir de los cuales se identificaron 5 SNP (ARS-BFGL-NGS-8140, BTA-77380-no-rs, BTA-32346-no-rs, BTB-00821654 y ARS-BFGL-NGS-15809). Para cada SNP se realizó un análisis genético mediante un análisis de varianza molecular (amova) usando el software GenAIEx 6.501. Los SNP con mayor heterocigosidad total (HT) fueron ARS-BFGL-NGS-8140 y BTA-32346-no-rs, con resultados cercanos al 45%; sin embargo, la Ht para ARS-BFGL-NGS-15809, BTA-77380-no-rs y BTB-00821654 estuvo por debajo del 15%. El SNP con mayor diversidad genética fue BTA-32346-no-rs (Ho-He = 0,06; p < 0,05). En esta investigación se evaluó una subpoblación de toros comerciales extranjeros, en la cual se obtuvieron frecuencias alélicas y genotípicas similares a las obtenidas para las subpoblaciones locales, sugiriendo que los alelos de los toros muy posiblemente están fijados en dichas subpoblaciones, por lo que la estructura y diversidad genética tienden a ser bajas en la muestra de estudio.

ABSTRACT Genetic polymorphisms associated with milk caseins have a great importance since they can be used as genetic markers to improve productive performance in dairy herds. The main goal of the present study was to evaluate the diversity and genetic structure of 5 SNPs of milk caseins, obtained with genomic chip in Holstein cows and bulls from Antioquia (Colombia). 113 Holstein animals were sampled in 3 regions of Antioquia (north, center, and east), and a fourth group of commercial sires. Animals were geno-typed with high-density SNP chips (Illumina BovineHD and Illumina SNP50 v2), from which 5 SNPs were identified (ARS-BFGL-NGS-8140, BTA-77380-no-rs, BTA-32346-no-rs, BTB-00821654 and ARS-BFGL-NGS-15809). For each SNP, a genetic analysis was performed by means of an analysis of molecular variance (AMOVA) using the GenAIEx 6.501 software. The SNPs with the highest total heterozygosity (Ht) were ARS-BFGL-NGS-8140 and BTA-32346-no-rs, with results close to 45%; however, the HT for ARS-BFGL-NGS-15809, BTA-77380-no-rs, and BTB-00821654 were below 15%. The SNP with the highest genetic diversity was BTA-32346-no-rs (Ho-He = 0,06; p < 0,05). In this research a subpopulation of foreign commercial bulls was evaluated, in which similar allelic and genotypic frequencies to those for local subpopulations were obtained, suggesting that the alleles of the bulls are very possibly fixed in these subpopulations, so that the structure and genetic diversity tend to be low in the study sample.

Polimorfismos genéticos de nucleotídeo único relacionados a sintomas depressivos em pacientes oncológicos: uma scoping review / Single nucleotide genetic polymorphisms related to depressive symptoms in cancer patients: a scoping review

Trata-se de uma revisão de escopo que objetivou relatar as evidências científicas reportadas na literatura referentes a polimorfismos genéticos de nucleotídeo único (SNPs) e a sua relação com o desenvolvimento de sintomas depressivos em pessoas com câncer. A pergunta de pesquisa que norteou esta revisão foi: "Quais polimorfismos genéticos de nucleotídeo único estão relacionados ao desenvolvimento de sintomas depressivos em pacientes oncológicos?". Para a sua condução foi utilizado o referencial teórico proposto por Arksey & O'Malley (2005), acrescido de ampliações de Levac, Colquhoun & O'Brien (2010) e Colquhoun, Levac & O'Brien (2014). Realizou-se buscas sistematizadas nas seguintes bases de dados: PubMed, Embase, PsychInfo, Web of Science e Scopus. Encontrou-se 1946 referências únicas e, após rigorosa seleção, 10 artigos atenderam aos três critérios de inclusão propostos: (1) estudos clínicos conduzidos com pacientes oncológicos; (2) apresentar relação entre SNPs e o desenvolvimento de sintomas depressivos; (3) publicados em português, inglês ou espanhol. Dos 10 artigos incluídos na amostra final, 70% tratava-se de estudos longitudinais, a maioria produzidos nos Estados Unidos (40%), com publicação predominante entre os anos 2012-2014 (60%). A população predominantemente estudada foram mulheres acometidas por câncer de mama (60%) e os sintomas depressivos foram, em sua maioria, avaliados por intermédio de instrumentos validados cientificamente (80%). Os SNPs relacionados aos sintomas depressivos foram encontrados, sobretudo, em genes da via inflamatória (6/11, 54,5%), e o polimorfismo mais estudado foi o rs6265 do gene BDNF, da via de transdução de sinais (4/11, 36,3%). Os principais achados dessa revisão, demonstram que portadores do genótipo Met-BDNF tendem a apresentar maior risco de desenvolvimento e agravamento dos sintomas depressivos. Além disso, os SNPs de genes da via da inflamação, especialmente aqueles relacionados à produção de citocinas pró-inflamatórias, podem desempenhar um importante papel preditivo de sintomas depressivos, na referida população. Portanto, pode-se concluir que as evidências disponíveis na literatura apontam que o polimorfismo do gene BDNF Val66Met (rs6265) e SNPs do sistema imunológico, em especial da via inflamatória, despontam como potenciais marcadores biológicos, no contexto do desenvolvimento de sintomas depressivos em pacientes oncológicos

This is a scoping review that aimed to report the scientific evidence reported in the literature regarding single nucleotide genetic polymorphisms (SNPs) and their relation with the development of depressive symptoms in people with cancer. The research question that guided this review was: "Which single nucleotide genetic polymorphisms are related to the development of depressive symptoms in cancer patients?". The theoretical reference proposed by Arksey & O'Malley (2005) was used to conduct it, plus extensions by Levac, Colquhoun & O'Brien (2010) and Colquhoun, Levac & O'Brien (2014). Systematic searches were carried out in the following databases: PubMed, Embase, PsychInfo, Web of Science, and Scopus. 1946 unique references were found and, after rigorous selection, 10 articles met the three proposed inclusion criteria: (1) clinical studies conducted with cancer patients; (2) presenting a relation between SNPs and the development of depressive symptoms; (3) published in Portuguese, English or Spanish. Of the 10 articles included in the final sample, 70% were longitudinal studies, most of them produced in the United States (40%), with a predominant publication between the years 2012-2014 (60%). The predominantly studied population were women affected by breast cancer (60%) and the depressive symptoms were mostly evaluated using scientifically validated instruments (80%). SNPs related to depressive symptoms were found, mainly, in genes of the inflammatory pathway (6/11, 54.5%), and the most studied polymorphism was the rs6265 of the BDNF gene, of the signal transduction pathway (4/11, 36.3%). The main findings of this review demonstrate that patients with the Met-BDNF genotype tend to have a higher risk of developing and worsening depressive symptoms. In addition, the SNPs of genes in the inflammation pathway, especially those related to the production of pro-inflammatory cytokines, can play an important predictive role of depressive symptoms in this population. Therefore, it can be concluded that the evidence available in the literature indicates that the polymorphism of the BDNF gene Val66Met (rs6265) and SNPs of the immune system, especially of the inflammatory pathway, emerge as potential biological markers, in the context of the development of depressive symptoms in oncological patients

Genetic Influence in Disc Degeneration - Systematic Review of Literature / A influência genética na degeneração discal - Revisão sistemática da literatura

Abstract Disc degeneration is a condition that compromises the intervertebral disc functions, which can lead to several important pathological processes, such as disc herniation and canal stenosis. Although its etiology is still unknown, more and more studies have demonstrated the preponderant role of genetic factors to the detriment of environmental factors. Aiming to review the current knowledge about the genes associated with intervertebral disc degeneration, we have performed a narrative review based on the medical literature in the English language from the last 10 years regarding this subject. We have concluded that several genes have been associated with disc degeneration in humans, including the genes for collagen I α-1 (COL1A1), collagen IX (COL9A2 and COL9A3), collagen XI (COL11A2), interleukin 6 (IL-6), aggrecan (AGC1), vitamin D receptor (VDR), and matrix metalloproteinase 3 (MMP-3), in addition to microRNAs. Therefore, the present review emphasizes the latest advancements in the association of genes with specific phenotypes of degenerated discs, single-nucleotide polymorphisms, heritage and genetic-environmental interactions in relation to disc degeneration to help future reviews regarding the genetic mechanisms underlying these processes.

Resumo A degeneração discal é uma condição que compromete as funções do disco intervertebral, podendo levar a vários processos patológicos importantes, como hérnias discais e estenoses de canal. Apesar de sua etiologia ainda ser desconhecida, cada vez mais estudos têm demonstrado o papel preponderante de fatores genéticos em detrimento de fatores ambientais. Com o objetivo de revisar o conhecimento atual sobre os genes associados à degeneração do disco intervertebral, foi realizada uma revisão narrativa da literatura inglesa nos últimos 10 anos sobre o tema. Concluímos que há uma série de genes que foram associados à degeneração discal em seres humanos, incluindo genes codificando colágeno I α-1 (COL1A1), colágeno IX (COL9A2 e COL9A3), colágeno XI (COL11A2), interleucina 6 (IL-6), agrecano (AGC1), receptor de vitamina D (VDR), metaloproteinase de matriz 3 (MMP-3), além de microRNAs. Dessa forma, a presente revisão enfatiza os últimos avanços na associação de genes com fenótipos de discos degenerados específicos, polimorfismos de nucleotídeos únicos, hereditariedade e interações genético-ambientais em relação à degeneração discal, com o intuito de permitir ao clínico entender esse mecanismo de degeneração e estar preparado para as novas terapêuticas que estão por vir baseadas na genética.

Recomendaciones en el tratamiento actual de la infección crónica por el virus de la hepatitis B / Current recommendations for the treatment of chronic hepatitis B infection

La infección crónica por el virus de la hepatitis B (VHB) se considera un problema de salud pública mundial. Se estima que al menos dos mil millones de personas han estado expuestas al VHB, y a pesar de una vacuna efectiva, 300 millones de personas están infectadas crónicamente a nivel mundial. Aunque el virus no es directamente citopático, la infección puede desencadenar cirrosis hepática y aun, carcinoma hepatocelular (CHC). El ADN circular cerrado covalentemente (ADNccc) en el núcleo de los hepatocitos y la incapacidad del sistema inmunitario para eliminar la infección crónica por el virus son los mecanismos más importantes de la infección por VHB. Las diferentes entidades, como la Asociación Europea para el Estudio del Hígado (EASL) y la Asociación Americana para el Estudio de las Enfermedades Hepáticas (AASLD), ponen a disposición las pautas para el manejo de esta enfermedad. A pesar de los avances en el tratamiento de la infección crónica por el VHB, en particular con el desarrollo de los análogos de los nucleótidos/ nucleósidos, quedan aún muchos interrogantes. Las investigaciones continúan para el desarrollo de nuevas opciones de tratamiento enfocadas principalmente en evitar que la suspensión de la terapia conlleve a un incremento de la carga viral, con el consecuente aumento del riesgo de progresión de la enfermedad hepática, y un eventual CHC.

Chronic hepatitis B virus (HBV) infection is considered a global public health problem. It is estimated that at least two billion people have been exposed to HBV, and despite an effective vaccine, 300 million people are chronically infected worldwide. Although the virus is not directly cytopathic, the infection can trigger liver cirrhosis and even hepatocellular carcinoma (HCC). Covalently closed circular DNA (cccDNA) in the nucleus of hepatocytes and the inability of the immune system to eliminate chronic virus infection are the most important mechanisms of chronic HBV infection. Different entities, such as the European Association for the Study of the Liver (EASL) and the American Association for the Study of Liver Diseases (AASLD), provide guidelines for the management of this disease. Despite advances in the treatment of chronic HBV infection, including the development of nucleotide and nucleoside analogs, many questions remain. Research continues for the development of new treatment options focused mainly on avoiding a relapse on viral load after therapy discontinuation, with an increased risk of liver disease progression, and an eventual CHC.

Gene sequence analysis of toxins from the spider Phoneutria nigriventer revealed an intronless feature

Phoneutria nigriventer spider venom contains several cysteine-rich peptide toxins that act on different ion channels. Despite extensive studies on its venom and description of cDNA sequences of several of its toxin precursors, the gene structure of these toxins remains unknown. Methods: Genomic regions encoding the precursors of three previously characterized P. nigriventer toxins - PnTx1, PnTx2-5 and PnTx4(5-5) - were amplified by PCR using specific primers. PCR fragments were cloned and sequenced. Obtained sequences were compared with their corresponding cDNA sequences. Results: The size of PCR fragments obtained and sequences corresponding to genomic regions encoding for the toxin precursors matched their cDNA sequences. Conclusions: Despite a few nucleotide substitutions in the genomic regions encoding for the toxin precursors when compared with cDNA sequences, the results of the present work indicate that P. nigriventer toxins do not contain introns in their genes sequences.(AU)

In vitro-induction of metronidazole-resistant Giardia duodenalis is not associated with nucleotide alterations in the genes involved in pro-drug activation

Giardiasis is an infectious disease caused by Giardia duodenalis. The pro-drug metronidazole (MTZ) is the first-line treatment for giardiasis. Parasite's proteins as pyruvate:ferredoxin oxidoreductase (PFOR), ferredoxin (Fd), nitroreductase-1 (NR-1) and thioredoxin reductase (TrxR) participate in MTZ activation. Here, we showed Giardia trophozoites long-term exposed to MTZ presented higher IC50 than controls, showing the drug influenced the parasite survival. That reduction in MTZ's susceptibility does not seem to be related to mutations in the genes pfor, fd, nr-1 or trxr. It points that different mechanism as alterations in other metabolic pathways can account for Giardia resistance to MTZ therapy.

Expression Analysis of Pyrenophora teres f. maculata-Responsive Loci in Hordeum vulgare

Abstract Pyrenophora teres f. maculata is the causal agent of barley spot form net blotch (SFNB), a major stubble-borne disease in many barley-growing areas worldwide. In plants, the Nucleotide-Binding Site-Leucine-Rich Repeat (NBS-LRR) gene family functions in immunity against a variety of pathogens and pests. From a pre-established set of NBS-type resistance gene candidates, we have selected three candidate genes, HvNBS10, HvNBS72 and HvNBS85, to analyze their possible involvement in P. teres f. maculata resistance. The studied genes were mapped on chromosomes 5H and 7H. Expression profiles using qRT-PCR, 48 hours after infection by P. teres. f. maculata, revealed that the transcription of all genes acted in the same direction (down-regulation) in both resistant and susceptible cultivars, although they showed a variation in transcript dosage. This result suggests that coordinated transcriptional responses of multiple barley NBS genes would be required to an efficient response against P. teres f. maculata. Moreover, the phylogenetic analysis revealed that the studied barley candidate R genes were characterized by a high homology with the barley Nbs2-Rdg2a gene conferring resistance to the fungus Pyrenophora graminea, suggesting a common origin of P. graminea and P. teres resistance genes in barley, following pathogens evolution. The genes characterized in the present study hold potential in elucidating the molecular pathways and developing novel markers associated with SFNB resistance in barley.

Aplicación farmacogenómica de los genes CYP2C19, CYP2C9 y VKORC1 implicados en el metabolismo de los fármacos clopidogrel y warfarina / Pharmacogenomic application of the CYP2C19, CYP2C9 and VKORC1 genes implicated in the metabolism of clopidogrel and warfarin

Resumen El estudio de las variaciones de las secuencias de ADN y ARN en relación con la respuesta a diferentes fármacos, se ha convertido en un área de estudio particularmente prometedora para la aplicación en genómica clínica y estudios de genomas personalizados. Medicamentos de uso diario en el tratamiento de enfermedades cardiovasculares han demostrado variaciones en la respuesta en función de las variantes genéticas de los individuos. Dos fármacos han concentrado el interés mundial: la warfarina, un anticoagulante oral, y el clopidogrel, un antiagregante plaquetario, los cuales actúan alterando diferentes vías que conforman la cascada de la coagulación, ya sea limitando directamente la producción de trombina o bloqueando otros activadores de la ruta. Los cambios genéticos que se han asociado a la reducción de la actividad enzimática de estos fármacos ocurren en los genes, CYP2C19 para clopidogrel y CYP2C9 y VKORC1 para warfarina. Las variaciones genéticas identificadas para estos genes se relacionan con perfiles genotípicos que determinan la dosis requerida para el paciente. Es allí donde ciencias como la farmacogenómica tienen como fin brindar una ayuda diagnóstica más objetiva al optimizar tiempo y recursos, así como disminuir el riesgo del paciente a sufrir complicaciones que comprometan su vida.

Abstract The study of the variations in DNA and RNA sequencing as regards the response to different drugs has become a particularly promising area for their application in clinical genomics and personalised genome studies. Drugs of daily use in the treatment of cardiovascular diseases have shown variations in the response depending on the genetic variations of the individuals. Two drugs have gathered worldwide interest: warfarin, an oral anticoagulant, and clopidogrel, an antiplatelet drug, which act by altering different pathways that constitute the clotting cascade either by directly limiting the production of thrombin, or by blocking other activators of the pathway. The genetic changes that have been associated with the reduction in the enzyme activity of these drugs occur in the genes, CYP2C19 for clopidogrel, and the genes, CYP2C9 and VKORC1 for warfarin. The genetic variations identified for these genes are associated with genotype profiles that determine the dose required by the patient. It is from there, sciences like pharmacogenomics have as their aim to provide a more objective diagnostic aid in order to optimise time and resources, as well as to reduce the risk of the patient suffering complications that may compromise their life.

Uso do LLLT e nucleotídeos no manejo de parestesia do nervo mentual / Management of mentual nerve paresthesia with LLLT and nucleotides

Os fascículos nervosos periféricos estão sujeitos a diferentes tipos de injúrias. Várias terapias são propostas pela literatura, entre elas, a laserterapia e a terapia farmacológica. Estudos têm mostrado a influência da laserterapia no metabolismo celular, de maneira a exercer uma ação positiva em níveis moleculares diminuindo o dano nervoso, aliviando a dor e acelerando os processos de reparação tecidual neural. Paralelamente os ribonucleotídeos pirimidínicos são bastante utilizados no tratamento de distúrbios ortopédicos degenerativos com compressão neuronal. O objetivo deste trabalho é relatar um caso clínico de uma paciente que possuía um pré-molar inferior incluso associado a um dente supra-numerário, cujo risco de lesão nervosa por meio da cirurgia era muito alto. Nas avaliações de imagem pode se notar uma relação de intimo contato do supranumerário com a cortical basal mandibular e com o canal mandibular. Foi elaborado um planejamento ortodôntico-cirúrgico, de forma a utilizar-se a laserterapia e ribonucleotídeos pirimidínicos para tratar a parestesia, classificada como neuropraxia, devido à longa exposição e ao tracionamento do dente. Este caso clínico ilustra opções de tratamento que os cirurgiões dentistas podem utilizar ao se depararem em situações clínicas inusitadas... (AU)

The peripheral nerve fascicles are subjected to different types of injuries. Several therapies are proposed in the literature, among them, laser therapy and pharmacological therapy. Studies have shown the influence of laser therapy on cellular metabolism, in order to exert a positive action at molecular levels, reducing nerve damage, relieving pain and accelerating neural tissue repair processes. In parallel, the use of pyrimidine ribonucleotides are widely used in the treatment of degenerative orthopedic disorders with neuronal compression. The objective of this study is to report a clinical case of a patient with an inferior pre-molar associated with a supra-dental tooth whose risk of Nerve injury through surgery was very high. In the image evaluations one can notice a relation of intimate contact of the supernumerary with the basal bone of the mandible and with the mandibular canal. Orthodontic-surgical planning was done in order to use laser therapy and pyrimidine ribonucleotides to treat paresthesia, classified as neuropraxia, due to long exposure and tooth traction. This clinical case illustrates treatment options that dentists can use when encountering unusual clinical conditions... (AU)

Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses

Direct tests of the random or non-random distribution of nucleotides on genomes have been devised to test the hypothesis of neutral, nearly-neutral or selective evolution. These tests are based on the direct base distribution and are independent of the functional (coding or non-coding) or structural (repeated or unique sequences) properties of the DNA. The first approach described the longitudinal distribution of bases in tandem repeats under the Bose-Einstein statistics. A huge deviation from randomness was found. A second approach was the study of the base distribution within dinucleotides whose bases were separated by 0, 1, 2... K nucleotides. Again an enormous difference from the random distribution was found with significances out of tables and programs. These test values were periodical and included the 16 dinucleotides. For example a high ¨positive¨ (more observed than expected dinucleotides) value, found in dinucleotides whose bases were separated by (3K + 2) sites, was preceded by two smaller ¨negative¨ (less observed than expected dinucleotides) values, whose bases were separated by (3K) or (3K + 1) sites. We examined mtDNAs, prokaryote genomes and some eukaryote chromosomes and found that the significant non-random interactions and periodicities were present up to 1000 or more sites of base separation and in human chromosome 21 until separations of more than 10 millions sites. Each nucleotide has its own significant value of its distance to neutrality; this yields 16 hierarchical significances. A three dimensional table with the number of sites of separation between the bases and the 16 significances (the third dimension is the dinucleotide, individual or taxon involved) gives directly an evolutionary state of the analyzed genome that can be used to obtain phylogenies. An example is provided.

Un método basado en la PCR para la identificación rápida de levaduras acumuladoras de astaxantina (Phaffia spp. ) / PCR-based method for the rapid identification of astaxanthin-accumulating yeasts (Phaffia spp.)

It has been recently found that the natural distribution, habitat, and genetic diversity of astaxanthin-producing yeasts (i.e. Phaffia rhodozyma, synonym Xanthophyllomyces dendrorhous) is much greater than previously thought. P. rhodozyma is biotechnologically exploited due to its ability to produce the carotenoid pigment astaxanthin and thus, it is used as a natural source of this pigment for aquaculture. P. rhodozyma was also capable of synthesizing the potent UVB sunscreen mycosporine-glutaminol-glucoside (MGG). Therefore, further environmental studies are needed to elucidate its ecological aspects and detect new potential strains for the production of astaxanthin and MGG. However, obtaining new isolates of P. rhodozyma and related species is not always easy due to its low abundance and the presence of other sympatric and pigmented yeasts. In this work we report a successful development of a species-specific primer which has the ability to quickly and accurately detecting isolates representing all known lineages of the genus Phaffia (including novel species of the genus) and excluding closely related taxa. For this purpose, a primer of 20 nucleotides (called PhR) was designed to be used in combination with universal primers ITS3 and NL4 in a multiplex amplification. The proposed method has the sensitivity and specificity required for the precise detection of new isolates, and therefore represents an important tool for the environmental search for novel astaxanthin-producing yeasts.

Recientemente, se ha encontrado que la distribución natural, el hábitat y la diversidad genética de levaduras productoras de astaxantina (p. ej., Phaffia rhodozyma, sinónimo Xanthophyllomyces dendrorhous) son mucho mayores de lo que se pensaba. P. rhodozyma se explota biotecnológicamente debido a su capacidad para producir el pigmento carotenoide astaxantina y, por lo tanto, se utiliza como una fuente natural de este pigmento para la acuicultura. También se encontró que esta levadura es capaz de sintetizar el potente protector solar UVB micosporina-glutaminol-glucósido (MGG). Por lo tanto, más estudios ambientales para dilucidar sus aspectos ecológicos y detectar nuevas cepas potenciales productoras de astaxantina y MGG son necesarios. Sin embargo, la obtención de nuevos aislamientos de P. rhodozyma y especies relacionadas no siempre es fácil debido a su baja abundancia y a la presencia de otras levaduras simpátricas y pigmentadas. En este trabajo se describe el desarrollo exitoso de un cebador especie-específico que tiene la capacidad de detectar rápidamente y con precisión cepas representativas de todos los linajes del género Phaffia previamente reportados (incluyendo nuevas especies del género) y excluir especies estrechamente relacionadas. Para ello, se diseñó un cebador de 20 nucleótidos (denominado PhR) para ser utilizado en combinación con los cebadores universales ITS3 y NL4 en una amplificación multiplex. El método propuesto tiene la sensibilidad y la especificidad requerida para la detección precisa de nuevos aislamientos y, por lo tanto, representa una importante herramienta para la búsqueda ambiental de nuevas levaduras productoras de astaxantina.

Clinical outcomes and mortality in elderly peritoneal dialysis patients

OBJECTIVES: To evaluate the clinical outcomes and identify the predictors of mortality in elderly patients undergoing peritoneal dialysis. METHODS: We conducted a retrospective study including all incident peritoneal dialysis cases in patients ≥65 years of age treated from 2001 to 2014. Demographic and clinical data on the initiation of peritoneal dialysis and the clinical events during the study period were collected. Infectious complications were recorded. Overall and technique survival rates were analyzed. RESULTS: Fifty-eight patients who began peritoneal dialysis during the study period were considered for analysis, and 50 of these patients were included in the final analysis. Peritoneal dialysis exchanges were performed by another person for 65% of the patients, whereas 79.9% of patients preferred to perform the peritoneal dialysis themselves. Peritonitis and catheter exit site/tunnel infection incidences were 20.4±16.3 and 24.6±17.4 patient-months, respectively. During the follow-up period, 40 patients were withdrawn from peritoneal dialysis. Causes of death included peritonitis and/or sepsis (50%) and cardiovascular events (30%). The mean patient survival time was 38.9±4.3 months, and the survival rates were 78.8%, 66.8%, 50.9% and 19.5% at 1, 2, 3 and 4 years after peritoneal dialysis initiation, respectively. Advanced age, the presence of additional diseases, increased episodes of peritonitis, the use of continuous ambulatory peritoneal dialysis, and low albumin levels and daily urine volumes (<100 ml) at the initiation of peritoneal dialysis were predictors of mortality. The mean technique survival duration was 61.7±5.2 months. The technique survival rates were 97.9%, 90.6%, 81.5% and 71% at 1, 2, 3 and 4 years, respectively. None of the factors analyzed were predictors of technique survival. CONCLUSIONS: Mortality was higher in elderly patients. Factors affecting mortality in elderly patients included advanced age, ...

Desempenho e morfologia intestinal de frangos de corte na fase de crescimento, com e sem adição de nucleotídeos na dieta, em diferentes níveis proteicos / Performance and morphology of the intestinal mucosa of broilers during growth, with or without nucleotides, at different protein levels

O experimento foi conduzido com o objetivo de avaliar o desempenho e a morfologia intestinal de frangos de corte na fase de crescimento, com e sem adição de nucleotídeos na dieta, em diferentes níveis proteicos. Foram utilizados 868 pintos de cortes machos de 21 dias de idade, da linhagem Cobb, submetidos a um delineamento inteiramente casualizado. As dietas foram compostas por dois controles, de alta e baixa proteína bruta, com 18,86% e 16,80% respectivamente, com a exigência de 1,062% de lisina digestível. Tendo como base a dieta controle de baixa proteína foram traçados mais cinco tratamentos com adição de 0,5 kg de nucleotídeos/ton de ração, e diferentes níveis de lisina digestível: 1,262%, 1,162%, 1,062%, 0962% e 0,862%, com quatro repetições cada. O consumo alimentar (g) diminuiu linearmente (P≤0,05) no período de 20 a 27, de 20 a 35 e de 20 a 42 dias de idade, em que aumentando os níveis de lisina digestível na dieta, observou-se diminuição no consumo de ração. A conversão alimentar teve efeito quadrático (P≤0,05) para as aves do período de 20 a 27, de 20 a 35 e de 20 a 42 dias de idade, diminuindo à medida que os níveis de lisina digestível aumentaram, atingindo o mínimo com 1,119, 1,187 e 1,132% de lisina digestível, respectivamente. A dieta com 1,062% de lisina digestível não diferiu (P>0.05) da dieta controle com alta proteína, para altura das vilosidades e profundidade de cripta, no duodeno, ilustrando então efeito benéfico do uso de nucleotídeos em dietas com baixa proteína bruta.

The experiment was conducted to evaluate the performance and intestinal morphology of growing broilers, with and without addition of nucleotides in the diet at different protein levels. A total of 868 21-day-old male Cobb broiler chicks were used in a completely randomized design. The diets were: control with high crude protein (18.86%) and low crude protein (16.80%), both without nucleotides, meeting the requirement of 1.062% digestible lysine; and five treatments with the addition of 0.5 kg of nucleotides/ton of feed, with different levels of digestible lysine (1.262%, 1.162%, 1.062%, 0962% and 0.862%), all formulated based on the low-protein diet (16.80%), with four replications each. Feed intake (g) decreased linearly (P≤0.05) in the period from 20 to 27, 20 to 35, and 20 to 42 days of age; feed intake decreased by increasing levels of lysine in the diet. Feed-to-gain ratio showed a quadratic effect (P≤0.05) for birds of the period from 20 to 27, 20 to 35 and 20 to 42 days of age, decreasing as levels of digestible lysine increased, with minimum levels reaching 1.119%, 1.187% and 1.132% digestible lysine, respectively. The diet with 1.062% of lysine did not differ (P>0.05) from the negative control for villus height and crypt depth in the duodenum.

The structure of selective dinucleotide interactions and periodicities in D melanogaster mtDNA

BACKGROUND: We found a strong selective 3-sites periodicity of deviations from randomness of the dinucleotide (DN) distribution, where both bases of DN were separated by 1, 2, K sites in prokaryotes and mtDNA. Three main aspects are studied. I) the specific 3 K-sites periodic structure of the 16 DN. II) to discard the possibility that the periodicity was produced by the highly nonrandom interactive association of contiguous bases, by studying the interaction of non-contiguous bases, the first one chosen each I sites and the second chosen J sites downstream. III) the difference between this selective periodicity of association (distance to randomness) of the four bases with the described fixed periodicities of base sequences. RESULTS: I) The 16 pairs presented a consistent periodicity in the strength of association of both bases of the pairs; the most deviated pairs are those where G and C are involved and the least deviated ones are those where A and T are involved. II) we found significant non-random interactions when the first nucleotide is chosen every I sites and the second J sites downstream until I=J=76. III) we showed conclusive differences between these internucleotide association periodicities and sequence periodicities. CONCLUSIONS: This relational selective periodicity is different from sequence periodicities and indicates that any base strongly interacts with the bases of the residual genome; this interaction and periodicity is highly structured and systematic for every pair of bases. This interaction should be destroyed in few generations by recurrent mutation; it is only compatible with the Synthetic Theory of Evolution and agrees with the Wright's adaptive landscape conception and evolution by shifting balanced adaptive peaks.

IgG AVIDITY WESTERN BLOT USING Toxoplasma gondii rGRA-7 CLONED FROM NUCLEOTIDES 39-711 FOR SERODIAGNOSIS OF ACUTE TOXOPLASMOSIS / Avidez do IgG pelo Western Blot usando o r GRA-7 do Toxoplasma gondii clonado de nucleotídeos 39-711 para sorodiagnóstico de toxoplasmose aguda

Toxoplasmosis is an important cause of congenital infection. The present study was performed to evaluate the usefulness of recombinant (r) GRA-7 cloned from nucleotides (n) 39-711 in discriminating between acute and chronic toxoplasmosis. First, commercial IgM, IgG and IgG avidity ELISAs were used to determine the serological profile of the sera. Serum samples were from 20 symptomatic patients with acute infection (low IgG avidity, IgM positive), 10 with chronic infection (high IgG avidity, IgM negative) and 10 with indeterminate IgG avidity (IgM positive) which were tested for IgG avidity status with an in-house developed IgG avidity Western blot using the rGRA-7 recombinant antigen. All 20 sera from cases of probable acute infection showed bands which either faded out completely or reduced significantly in intensity after treatment with 8 M urea, whereas the band intensities of the 10 serum samples from chronic cases remained the same. Of the 10 sera with indeterminate IgG avidity status, after treatment with 8 M urea the band intensities with six sera remained the same, two sera had completely faded bands and another two sera had significantly reduced band intensities. Discrimination between acute and chronic toxoplasmosis was successfully performed by the in-house IgG avidity Western blot.

Toxoplasmose é uma causa importante de infecção congênita. O presente estudo foi feito para avaliar o uso do recombinante (r) GRA-7 clonado de nucleotídeos (n) 30-711 para discriminar entre toxoplasmose aguda e crônica. Inicialmente IgM, IgG e ELISA avidez IgG comerciais foram usados para determinar o perfil sorológico do soro. Amostras de soro de 20 pacientes sintomáticos com infecção aguda (IgG avidez baixa, IgM positivo), 10 com infecção crônica (alta avidez IgG, IgM negativo) e 10 com avidez IgG indeterminada (IgM positivo) que foram testados para o status de avidez IgG com um doméstico Western Blot desenvolvendo avidez IgG usando o rGRA-7 antígeno recombinante. Todos os 20 soros de provável infecção aguda mostraram bandas que ou se apagaram completamente ou tiveram a sua intensidade significantemente reduzida após tratamento com uréia 8 M, enquanto as intensidades das bandas das 10 amostras de soros de casos crônicos permaneceram iguais. Dos 10 soros com status indeterminado de avidez de IgG, após tratamento com uréia 8 M a intensidade das bandas em seis soros permaneceram iguais, dois soros tiveram bandas apagadas completamente e dois outros tiveram significante redução da intensidade das bandas. Discriminação entre toxoplasmose aguda e crônica foi feita com sucesso através do IgG avidez Western blot doméstico.

DNA sequence variation of drought-response candidate genes in Austrocedrus chilensis

Background: Austrocedrus chilensis (D. Don) Pic. Ser. et Bizzarri commonly known as Patagonian cypress is a member of the Cupressaceae family, characterized by a high adaptive potential for growing in marginal areas and good timber quality. The species grows over a wide area and under a wide range of rainfall. This study assessed adaptive genetic variation at SNP level in candidate genes involved in response to drought stress. Results: A total of 18 single nucleotide polymorphisms (SNPs) were found among 1,428 bp. Average nucleotide diversity value (π = 0.00312) was similar to those previously reported in other Cupressaceae. The Fst average among genes and populations was 0.163 and the lowest differentiation was observed in continuous and humid populations. A number of neutrality tests were applied to find evidence of positive selection in our candidate gene set, but only AcAQP2 gene in Pedregoso and San Ramón populations revealed significant departures from neutrality with positive values suggesting balancing selection. Conclusions: In this study we report the levels of nucleotide diversity searched in some drought stress candidate genes in Austrocedrus chilensis and the selective factors that may be acting on this species.

SncSequm pipeline para análise de dados de sequenciamento de alta vazão de RNAs não-codificantes pequenos / SncSequm pipeline for data analysis of high-throughput sequencing of small non-coding RNAs

Os RNAs não-codificadores (ncRNAs) são moléculas importantes para a homeostase e para o desenvolvimento de doenças, sendo considerados potenciais biomarcadores de tratamento e diagnóstico. Uma das tecnologias para obtenção de perfis e identificação de ncRNAs diferencialmente expressos é o sequenciamento de alta vazão (HTS). Apesar de esta técnica ter alta resolução e vazão, a quantidade de dados produzida faz que conhecimentos em bioinformática sejam fundamentais para sua análise. Alguns grupos de bioinformática desenvolveram programas pipelines para facilitar a análise de dados de ncRNAs obtidos por HTS. Contudo, estes programas e pipelines ou são limitados pelo tipo de ncRNA avaliado ou pelos tipos de desenhos experimentais permitidos. Por isso, desenvolvemos o SncSeq, um pipeline para análise de qualquer ncRNA pequeno em qualquer organismo capaz de lidar com diversos desenhos experimentais, incluindo séries temporais...

A fim de testar nosso pipeline, obtivemos dados públicos de HTS de miRNAs e comparamos os resultados do SncSeq com os de outros programas e pipelines, bem como com bancos de dados de expressão diferencial de miRNAs. Dentre os programas e pipelines avaliados, somente o SncSeq e o miRNAkey apresentaram resultados similares ao dados publicados originalmente e presentes nos repositórios selecionados. Porém, a abordagem estatística implementada no miRNAkey não é adequada para lidar com experimentos com répli cas ou análise de séries temporais, limitando as possíveis atuações deste pipeline. Por outro lado, o SncSeq foi desenvolvido para permitir a analise de qualquer tipo de ncRNA pequeno em diversos tipos de desenhos experimentais, incluindo experimentos com réplicas biológicas e séries temporais..

Identificação de RNAs longos não-codificadores de proteínas regulados por micro-RNAs / Identification of long non-protein coding RNAs regulated by micro-RNAs

Estudos recentes têm revelado que a maior parte dos transcritos gerados em células humanas é composta por RNAs não-codificadores de proteínas (ncRNAs). Uma parte desses ncRNAs compreende a classe de RNAs curtos, que possuem menos que 200 nucleotídeos. Os micro-RNAs (miRNAs) fazem parte dessa classe e têm sido alvo de grande interesse, pois são preditos como possíveis reguladores de mais de 60% dos RNAs mensageiros (mRNAs) humanos. Outra classe dos ncRNAs é composta por ncRNAs longos (lncRNAs, com mais de 200 nucleotídeos), que são transcritos a partir de regiões intergênicas e intrônicas do genoma humano e possuem várias funções, muitas delas relacionadas ao controle da expressão de mRNAs. Recentemente, os lncRNAs têm sido caracterizados quanto à sua estrutura e função. No entanto, muito pouco se sabe sobre os mecanismos pelos quais os lncRNAs são regulados. Este trabalho teve como objetivo avaliar se lncRNAs são regulados por miRNAs em células humanas. Para tanto, identificamos lncRNAs ligados ao complexo de silenciamento induzido por RNA (RISC) em células da linhagem HeLa, utilizando um método aqui desenvolvido de geração de bibliotecas de cDNA direcionadas para sequenciamento em larga escala na plataforma 454/Roche. Em paralelo, sequenciamos os miRNAs ligados ao RISC nestas mesmas células. Os resultados obtidos mostram que centenas de lncRNAs de diversas classes se ligam ao RISC em células HeLa, juntamente com milhares de mRNAs e várias centenas de miRNAs. Entre os miRNAs, encontramos 37 que são preditos como alvejando os lncRNAs detectados. Estes miRNAs constituem possíveis reguladores dos lncRNAs e, portanto, nosso trabalho estabelece um mapa experimental de interações diretas entre lncRNAs e miRNAs. Dentre os lncRNAs identificados ligados ao RISC neste trabalho, destaca-se o TUG1, lincRNA sabidamente envolvido na regulação de genes relacionados à apoptose e ao ciclo celular. Mostramos por ensaio de super-expressão de miRNAs e qPCR que TUG1 é regulado pelo miRNA-148b, um dos miRNAs por nós detectados que possui um sítio alvo altamente conservado em mamíferos localizado na extremidade 3' de TUG1. Em conjunto, este trabalho contribui para o entendimento da regulação dos níveis de expressão de lncRNAs em células humanas e abre perspectivas para a modulação de miRNAs como estratégia de regulação dos níveis e das funções de lncRNAs

Recent studies have revealed that the largest fraction of the transcripts generated in human cells is composed of non-protein coding RNAs (ncRNAs). A portion of these RNAs encompasses the class of short RNAs, which are less than 200 nucleotides in length. Micro-RNAs (miRNAs) are part of this class and are of great interest, as they are predicted to target over 60% of the human messenger RNAs (mRNAs). Another class of ncRNAs is composed of long ncRNAs (lncRNAs, longer than 200 nucleotides), which are transcribed from intergenic and intronic regions of the human genome and have several functions, many of them related to the control of the mRNA expression. Recently, the structure and function of lncRNAs have been characterized. However, little is known about the mechanisms involved in lncRNA regulation. This work aimed to evaluate whether lncRNAs are regulated by miRNAs in human cells. For this purpose, we identified lncRNAs bound to the RNA-induced silencing complex (RISC) in HeLa cells using a method developed here for the generation of strand-specific cDNA libraries for large scale RNA-sequencing in the 454/Roche plataform. In parallel, we sequenced the miRNAs bound to RISC in these cells. Our results show that hundreds of lncRNAs from diverse classes are bound to RISC in HeLa cells, along with thousands of mRNAs and several hundred miRNAs. Among the miRNAs we identified 37 that are predicted to target the detected lncRNAs. These miRNAs are possible regulators of the lncRNAs, and therefore our work establishes an experimental map of direct interactions between lncRNAs and miRNAs. The lncRNA TUG1, a lincRNA involved in the regulation of genes related to apoptosis and cell cycle, was identified among the lncRNAs bound to RISC. We showed by miRNA over-expression and qPCR that TUG-1 is regulated by the miRNA-148b, which is one of the miRNAs detected in our sequencings and has a binding site highly conserved in mammals located at the TUG1 3` end. Taken together, our results contribute to the understanding of the regulation of the lncRNA expression levels in human cells and open perspectives for the modulation of miRNAs as a strategy to regulate the levels and functions of lncRNAs

RIC-8B, um fator trocador de nucleotídeo guanina (GEF), é essencial para a embriogênese / RIC-8B, a guanine nucleotide exchange factor (GEF), is essential for embryogenesisPalavras-chave em inglês Cilia

RIC-8B é uma proteína que apresenta, in vitro, atividade de fator de troca de nucleotídeos guanina (GEF). No entanto, seu papel in vivo não é conhecido. Dados anteriores do nosso laboratório demonstraram que essa proteína interage especificamente com Gαolf, que é uma proteína G exclusiva do sistema olfatório, presente nos cílios dos neurônios olfatórios, onde ocorre a transdução de sinal ativada pelos odorantes. No camundongo adulto verificou-se, por meio de ensaios de hibridização in situ, que RIC-8B está presente somente em regiões de expressão de Gαolf: no epitélio olfatório maduro e no núcleo estriado do sistema nervoso central. Para avaliar a função fisiológica de RIC-8B in vivo, resolvemos gerar uma linhagem de camundongo knockout para Ric-8B. Verificamos que a linhagem é inviável devido à letalidade dos embriões já em fases precoces do desenvolvimento (por volta de E8,5 e E9,0). A coloração de embriões com X-gal mostra que RIC-8B é especificamente expressa em regiões que darão origem ao sistema nervoso, como na região ventral do tubo neural, e em regiões cefálicas. Interessantemente, mostramos que RIC-8B é expressa na placa do assoalho do tubo neural, de uma maneira muito semelhante ao padrão de expressão de Sonic Hedgehog (SHH), que apresenta um papel fundamental para a organização do sistema nervoso, entre outras funções. Nossos resultados indicam, portanto, que RIC-8B desempenha um papel crucial durante a embriogênese, e que este papel pode estar relacionado com o papel exercido por SHH. Além disso, como a via de sinalização de SHH ocorre em cílios primários nas células alvo, nossos dados levantam a interessante possibilidade de que RIC-8B apresenta funções relacionadas a cílios, tanto no camundongo adulto (neste caso nos cílios dos neurônios olfatórios) como no embrião (neste caso nos cílios primários)

RIC-8B is a protein that, in vitro, acts as a guanine nucleotide exchange factor (GEF). However, its role in vivo remains unknown. Previous data from our laboratory demonstrated that this protein is able to interact specifically with Gαolf, a G protein found only in the olfactory system. This G protein is located in the cilia from olfactory neurons, where odorant signaling occurs. In situ hybridization experiments showed that RIC-8B, in adult mice, is expressed only in regions where Gαolf is expressed, such as the olfactory epithelium and the nucleus striatum in the central nervous system. In order to determine the function of RIC-8B in vivo, we decided to generate a knockout mouse strain for Ric-8B. We found that this strain is not viable due to the lethality of embryos in the early stages of development (around days E8.5 and E9.0). X-gal staining of embryos shows that RIC-8B is specifically expressed in regions that originate the nervous system, such as the ventral neural tube and also cephalic regions. Interestingly, we show that RIC-8B is restrictedly expressed in the floor plate of the neural tube, in a pattern that is very similar to the one shown by Sonic Hedgehog (SHH). The SHH protein plays a fundamental role in the organization of the nervous system, among other functions. Therefore, our results indicate that RIC-8B plays an essential role during the embryogenesis, and that this role can be related to the role played by SHH. Furthermore, because the SHH signaling pathway occurs in primary cilia in the target cells, our data raise the interesting possibility that the role played by RIC-8B is related to ciliary functions, both in adult mice (in this case, in olfactory cilia), and in the embryo (in this case, in primary cilia)