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.

Phylogenetic analysis of Pneumocystis from pig lungs obtained from slaughterhouses in southern and midwestern regions of Brazil / Análise filogenética de Pneumocystis obtidos de pulmões de suínos provenientes de abatedouros da região sul e centro oeste do Brasil

The Pneumocystis genus is comprised of pathogens dwelling in the lungs of terrestrial, aerial, and aquatic mammals. Occasionally they induce severe pneumonitis, particularly in hosts with severe impairment of the immune system and progressively may fill pulmonary alveolar cavities causing respiratory failure. Molecular genetic studies revealed that Pneumocystis gene sequences present a marked divergence with the host species concerned. In the present study, the genetic diversity of Pneumocystis obtained from lungs of swines was examined by analyzing mitochondrial large subunit (mtLSU) and small subunit (mtSSU) rRNA sequences. The samples were obtained from two slaughterhouses located in two Brazilian states. Phylogenetic analysis demonstrated that genetic groupings within Pneumocystis organisms were in accordance with those of the corresponding hosts and that two clusters were formed. In conclusion, these data show that there are genetically distinct porcine Pneumocystis genotypes with at least two separate clusters in Brazil.

O gênero Pneumocystis compreende patógenos que residem em pulmões de animais terrestres, aéreos e aquáticos. Pode ocasionar uma grave pneumonia, particularmente em hospedeiros com o sistema imunológico seriamente comprometido, o que ocorre por meio de uma progressiva disseminação nas cavidades alveolares, causando insuficiência respiratória. Estudos genéticos, baseados em métodos moleculares, revelaram que as sequências dos genes de Pneumocystis apresentam marcante divergência de acordo com a espécie de hospedeiro. Neste estudo, a diversidade genética das amostras obtidas a partir de pulmões de suínos, provenientes de dois abatedouros localizados em dois estados brasileiros, foi examinada por análise das sequencias dos nucleotídeos dos produtos de PCR dos genes mtLSU e mtSSU do rRNA do Pneumocystis. O resultado confirma a tendência registrada em pesquisas com amostras de outros animais e permite concluir que existem, pelo menos, dois grupos filogenéticos distintos de Pneumocystis de suínos no Brasil.

Signals in the promoter regions of several cancerous genes.

The eukaryotic core promoter regions are complex and fuzzy, usually lacking any conserved regions. However, they contain signals in the form of short stretches of nucleic acid sequences, for transcription start sites (TSS) that are recognized by the transcription factors (TFs). The core promoter region thus plays an important role in biological pathways (gene network and activation). It has been reported that these signals are composed of nucleotide hexamers in the promoter sequence (smaller sequences are likely to have too little information to be useful and longer sequences are too complex to be recognized by proteins) reasonably close to the TSS. The signals (nucleotide hexamers) have been identified by a similarity search on the eukaryotic promoter database (EPD, Homo sapiens). The signals have been classified, depending on their base composition. They have been have clustered using an algorithm, such that there are two and three nucleotide differences between the classes and a single nucleotide difference within a class. We have reclassified the hexamers taking the highest frequent hexamers present in the EPD (Homo sapiens) as the class representatives. Also we have tried to find whether the same composition is reflected on the miRNAs but found that they probably have other functions unrelated to promoter recognition. In this report melanoma carcinoma pathway has been chosen as the reference pathway and the promoters of the driver genes has been searched for the presence of the major classes. A few of these were found and are reported here. Several non-cancerous genes have also been studied as reference and comparison.

Arranjos supramoleculares de oligodeoxinucleotídeos e fragmentos de bicamada catiônica: preparação, caracterização e atividade imunoadjuvante / Supramolecular assemblies of oligodeoxynucleotides and cationic bilayer fragments: preparation, characterization and immunoadjuvant activity

A interação entre fragmentos de bicamada (BF) de brometo de dioctadecildimetilamônio (DODAB) e um mononucleotídeo-modelo (deoxiadenosina monofosfato, dAMP) ou um oligodeoxinucleotídeo-modelo (5'- AAAAAAAAAA-3', poli(dA)) ou um oligodeoxinucleotídeo terapêutico (5'- TTGACGTTCG -3', CpG) foi investigada por turbidimetria, espalhamento de luz dinâmico, espectroscopia de dicroísmo circular e de fluorescência e calorimetria diferencial de varredura (DSC). Respostas imunológicas foram caracterizadas com ensaio de hipersensibilidade tardia por inchamento de coxim patelar de camundongo, dosagem de anticorpos IgG1 e IgG2a e de citocinas secretadas por células de linfonodo em cultura. Poli(dA), em contraste com dAMP, induziu fusão máxima de DODAB BF a partir da neutralização de cargas, quando houve obtenção de um tamanho máximo e um potencial-zeta igual a zero para os arranjos. Para [poli(dA)] maiores do que aquela correspondente à neutralização de cargas, houve recuperação da estabilidade coloidal com reversão do potencial-zeta e com obtenção de tamanhos que foram aproximadamente o dobro daqueles determinados inicialmente para DODAB BF. A proporção molar de neutralização poli(dA): DODAB foi 1:10 para DODAB BF e 1:20 para vesículas grandes (LV) de DODAB, de acordo com as estruturas de bicamada aberta e fechada dessas duas dispersões de bicamada de DODAB. A fusão de DODAB BF induzida por poli(dA) foi extensiva aumentando o grau de empacotamento das bicamadas formadas conforme inferido a partir dos termogramas de DSC. Em condições de equivalencia de cargas, nucleotídeo não causou fusão de DODAB BF, mostrando a importância do caráter de polieletrólito do poli(dA) para induzir fusão. O sal divalente Na2HPO4 causou fusão e aumentou o empacotamento da bicamada graças à blindagem eficiente de cargas. Reestabilização coloidal como aquela induzida por poli(dA) não ocorreu em presença de Na2HPO4, NaCl ou nucleotídeo. Para complexos DODAB BF/CpG em presença de ovalbumina (OVA)...

The interaction between bilayer fragments (BF) of dioctadecyldimethylammonium bromide (DODAB) and a model nucleotide (deoxyadenosine monophosphate, dAMP) or a model oligodeoxynucleotide (5'- AAAAAAAAAA-3', poly(dA)) or a therapeutic oligodeoxynucleotide (5'- TTGACGTTCG -3', CpG) was investigated by means of turbidimetry, dynamic light scattering, circular dichroism and fluorescence spectroscopies and differential scanning calorimetry. Immune responses were characterized using footpad swelling delayed type hipersensitivity assay and antibody and cytokine measurements. In contrast to dAMP, poly(dA) induced maximal DODAB BF fusion from charge neutralization, where assemblies presented maximal size and zero zeta-potential. Above charge neutralization colloid stability was recovered with negative zeta-potentials and sizes that were about the double of those initially determined for DODAB BF. The poly(dA):DODAB molar ratio for neutralization was 1:10 for DODAB BF and 1:20 for DODAB LV, in agreement with the open and closed bilayer structures of these two DODAB bilayer dispersions. The poly(dA)-induced DODAB BF fusion was extensive and increased the packing of the formed bilayers, as inferred from DSC thermograms. In conditions of charge equivalence, nucleotide did not cause DODAB BF fusion, highlighting the importance of poly(dA)'s polyelectrolyte character to induce fusion. Divalent Na2HPO4 salt caused fusion and increased bilayer packing due to efficient BF charge shielding. Colloid restabilization as induced by poly(dA) was not observed in presence of Na2HPO4, NaCl and nucleotide. For DODAB BF/CpG complexes in presence of the ovalbumin (OVA) model antigen, the charge neutralization of DODAB BF/OVA by CpG reduced colloid stability, while charge overcompensation led to restabilization due to electrostatic repulsion, as observed for DODAB BF/poly(dA) interaction. Differences in size and neutralization proportions by CpG indicate that BF are able to load more OVA…

Indirect inhibition by antibiotics of nucleotide and deoxynucleotide biosynthesis in Plasmodium falciparum.

The effects of the antibiotics, doxycycline, azithromycin, ciprofloxacin and chloramphenicol, upon levels of nucleoside-5'-triphosphates (NTPs) and 2'-deoxynucleoside-5'-triphosphates (dNTPs) have been compared in the malarial parasite, Plasmodium falciparum, and in human CCRF-CEM leukemia cells. All 4 antibiotics had more severe effects upon levels of NTPs and dNTPs in P. falciparum compared with leukemia cells providing an explanation for their selective toxicity against malaria and their utility as antimalarial drugs. In bacteria, the first 3 drugs inhibit protein synthesis while ciprofloxacin inhibits topoisomerase II. The observed depletions of NTPs and dNTPs would be a secondary effect of the drug but may result in death of the parasite.