Genotipificación de HLA-B en pacientes colombianos afectados por el síndrome Stevens-Johnson y la Necrólisis Epidérmica Tóxica

Las reacciones alérgicas a medicamentos cutáneas severas (RAM) como el Síndrome Stevens Johnson (SJS) y la Necrólisis Epidérmica Tóxica (NET),caracterizadas por exantema, erosión de la piel y las membranas mucosas, flictenas, desprendimiento de la piel secundario a la muerte de queratinocitos y compromiso ocular. Son infrecuentes en la población pero con elevada morbi-mortalidad, se presentan luego de la administración de diferentes fármacos. En Asia se ha asociado el alelo HLA-B*15:02 como marcador genético para SJS. En Colombia no hay datos de la incidencia de estas RAM, ni de la relación con medicamentos específicos o potenciales y tampoco estudios de aproximación genómica de genes de susceptibilidad.

The Fox genes of Branchiostoma floridae

The Fox genes are united by encoding a fork head domain, a deoxyribonucleic acid (DNA)-binding domain of the winged-helix type that marks these genes as encoding transcription factors. Vertebrate Fox genes are classified into 23 subclasses named from FoxA to FoxS. We have surveyed the genome of the amphioxus Branchiostoma floridae, identifying 32 distinct Fox genes representing 21 of these 23 subclasses. The missing subclasses, FoxR and FoxS, are specific to vertebrates, and in addition, B. floridae has one further group, FoxAB, that is not found in vertebrates. Hence, we conclude B. floridae has maintained a high level of Fox gene diversity. Expressed sequence tag and complementary DNA sequence data support the expression of 23 genes. Several linkages between B. floridae Fox genes were noted, including some that have evolved relatively recently via tandem duplication in the amphioxus lineage and others that are more ancient.

Diversification of a large genus in a continental biodiversity hotspot: temporal and spatial origin of Muraltia (Polygalaceae) in the Cape of South Africa

Phylogenetic relationships in the largely South African genus Muraltia (Polygalaceae) are assessed based on DNA sequence data (nuclear ribosomal ITS, plastid atpB-rbcL spacer, trnL intron, and trnL-F spacer) for 73 of the 117 currently recognized species in the genus. The previously recognised subgenus Muraltia is monophyletic, but the South African endemic genus Nylandtia is embedded in Muraltia subgenus Psiloclada. Subgenus Muraltia is found to be sister to subgenus Psiloclada. Estimates show the beginning of diversification of the two subgenera in the early Miocene (Psiloclada, 19.3+/-3.4 Ma; Muraltia, 21.0+/-3.5 Ma) pre-dating the establishment of the Benguela current (intermittent in the middle to late Oligocene and markedly intensifying in the late Miocene), and summer-dry climate in the Cape region. However, the later increase in species numbers is contemporaneous with these climatic phenomena. Results of dispersal-vicariance analyses indicate that major clades in Muraltia diversified from the southwestern and northwestern Cape, where most of the species are found today.

The transcriptome of Populus in elevated CO2

The consequences of increasing atmospheric carbon dioxide for long-term adaptation of forest ecosystems remain uncertain, with virtually no studies undertaken at the genetic level. A global analysis using cDNA microarrays was conducted following 6 yr exposure of Populus × euramericana (clone I-214) to elevated [CO2] in a FACE (free-air CO2 enrichment) experiment.• Gene expression was sensitive to elevated [CO2] but the response depended on the developmental age of the leaves, and < 50 transcripts differed significantly between different CO2 environments. For young leaves most differentially expressed genes were upregulated in elevated [CO2], while in semimature leaves most were downregulated in elevated [CO2].• For transcripts related only to the small subunit of Rubisco, upregulation in LPI 3 and downregulation in LPI 6 leaves in elevated CO2 was confirmed by anova. Similar patterns of gene expression for young leaves were also confirmed independently across year 3 and year 6 microarray data, and using real-time RT–PCR.• This study provides the first clues to the long-term genetic expression changes that may occur during long-term plant response to elevated CO2.

The role of prophage-like elements in the diversity of Salmonella enterica serovars

The Salmonella enterica serovar Typhi CT18 (S. Typhi) chromosome harbours seven distinct prophage-like elements, some of which may encode functional bacteriophages. In silico analyses were used to investigate these regions in S. Typhi CT18, and ultimately compare these integrated bacteriophages against 40 other Salmonella isolates using DNA microarray technology. S. Typhi CT18 contains prophages that show similarity to the lambda, Mu, P2 and P4 bacteriophage families. When compared to other S. Typhi isolates, these elements were generally conserved, supporting a clonal origin of this serovar. However, distinct variation was detected within a broad range of Salmonella serovars; many of the prophage regions are predicted to be specific to S. Typhi. Some of the P2 family prophage analysed have the potential to carry non-essential "cargo" genes within the hyper-variable tail region, an observation that suggests that these bacteriophage may confer a level of specialisation on their host. Lysogenic bacteriophages therefore play a crucial role in the generation of genetic diversity within S. enterica. (C) 2004 Elsevier Ltd. All rights reserved.

Species concepts in Cercospora: spotting the weeds among the roses

The genus Cercospora contains numerous important plant pathogenic fungi from a diverse range of hosts. Most species of Cercospora are known only from their morphological characters in vivo. Although the genus contains more than 5 000 names, very few cultures and associated DNA sequence data are available. In this study, 360 Cercospora isolates, obtained from 161 host species, 49 host families and 39 countries, were used to compile a molecular phylogeny. Partial sequences were derived from the internal transcribed spacer regions and intervening 5.8S nrRNA, actin, calmodulin, histone H3 and translation elongation factor 1-alpha genes. The resulting phylogenetic clades were evaluated for application of existing species names and five novel species are introduced. Eleven species are epi-, lecto- or neotypified in this study. Although existing species names were available for several clades, it was not always possible to apply North American or European names to African or Asian strains and vice versa. Some species were found to be limited to a specific host genus, whereas others were isolated from a wide host range. No single locus was found to be the ideal DNA barcode gene for the genus, and species identification needs to be based on a combination of gene loci and morphological characters. Additional primers were developed to supplement those previously published for amplification of the loci used in this study. TAXONOMIC NOVELTIES: New species - Cercospora coniogrammes Crous & R.G. Shivas, Cercospora delaireae C. Nakash., Crous, U. Braun & H.D. Shin, Cercospora euphorbiae-sieboldianae C. Nakash., Crous, U. Braun & H.D. Shin, Cercospora pileicola C. Nakash., Crous, U. Braun & H.D. Shin, Cercospora vignigena C. Nakash., Crous, U. Braun & H.D. Shin. Typifications: epitypifications - Cercospora alchemillicola U. Braun & C.F. Hill, Cercospora althaeina Sacc., Cercospora armoraciae Sacc., Cercospora corchori Sawada, Cercospora mercurialis Pass., Cercospora olivascens Sacc., Cercospora violae Sacc.; neotypifications - Cercospora fagopyri N. Nakata & S. Takim., Cercospora sojina Hara.

The neurogenic potential of astrocytes is regulated by inflammatory signals

Although the adult brain contains neural stem cells (NSCs) that generate new neurons throughout life, these astrocyte-like populations are restricted to two discrete niches. Despite their terminally differentiated phenotype, adult parenchymal astrocytes can re-acquire NSC-like characteristics following injury, and as such, these 'reactive' astrocytes offer an alternative source of cells for central nervous system (CNS) repair following injury or disease. At present, the mechanisms that regulate the potential of different types of astrocytes are poorly understood. We used in vitro and ex vivo astrocytes to identify candidate pathways important for regulation of astrocyte potential. Using in vitro neural progenitor cell (NPC)-derived astrocytes, we found that exposure of more lineage-restricted astrocytes to either tumor necrosis factor alpha (TNF-α) (via nuclear factor-κB (NFκB)) or the bone morphogenetic protein (BMP) inhibitor, noggin, led to re-acquisition of NPC properties accompanied by transcriptomic and epigenetic changes consistent with a more neurogenic, NPC-like state. Comparative analyses of microarray data from in vitro-derived and ex vivo postnatal parenchymal astrocytes identified several common pathways and upstream regulators associated with inflammation (including transforming growth factor (TGF)-β1 and peroxisome proliferator-activated receptor gamma (PPARγ)) and cell cycle control (including TP53) as candidate regulators of astrocyte phenotype and potential. We propose that inflammatory signalling may control the normal, progressive restriction in potential of differentiating astrocytes as well as under reactive conditions and represent future targets for therapies to harness the latent neurogenic capacity of parenchymal astrocytes.

Cardiac protein kinases: the cardiomyocyte kinome and differential kinase expression in human failing hearts

Aims. Protein kinases are potential therapeutic targets for heart failure, but most studies of cardiac protein kinases derive from other systems, an approach that fails to account for specific kinases expressed in the heart and the contractile cardiomyocytes. We aimed to define the cardiomyocyte kinome (i.e. the protein kinases expressed in cardiomyocytes) and identify kinases with altered expression in human failing hearts. Methods and Results. Expression profiling (Affymetrix microarrays) detected >400 protein kinase mRNAs in rat neonatal ventricular myocytes (NVMs) and/or adult ventricular myocytes (AVMs), 32 and 93 of which were significantly upregulated or downregulated (>2-fold), respectively, in AVMs. Data for AGC family members were validated by qPCR. Proteomics analysis identified >180 cardiomyocyte protein kinases, with high relative expression of mitogen-activated protein kinase cascades and other known cardiomyocyte kinases (e.g. CAMKs, cAMP-dependent protein kinase). Other kinases are poorly-investigated (e.g. Slk, Stk24, Oxsr1). Expression of Akt1/2/3, BRaf, ERK1/2, Map2k1, Map3k8, Map4k4, MST1/3, p38-MAPK, PKCδ, Pkn2, Ripk1/2, Tnni3k and Zak was confirmed by immunoblotting. Relative to total protein, Map3k8 and Tnni3k were upregulated in AVMs vs NVMs. Microarray data for human hearts demonstrated variation in kinome expression that may influence responses to kinase inhibitor therapies. Furthermore, some kinases were upregulated (e.g. NRK, JAK2, STK38L) or downregulated (e.g. MAP2K1, IRAK1, STK40) in human failing hearts. Conclusions. This characterization of the spectrum of kinases expressed in cardiomyocytes and the heart (cardiomyocyte and cardiac kinomes) identified novel kinases, some of which are differentially expressed in failing human hearts and could serve as potential therapeutic targets.

Identifying the generic limits of the Cheilanthoid genus Doryopteris

Morphology-based delimitation of genera in the Cheilanthoid ferns has proved to be problematic and understanding of the phylogeny and relationships amongst Cheilanthoid ferns based on morphological characters has posed even further difficulties, owing perhaps in large part to adaptation by many taxa to xeric habitats, as well as convergent evolution. It is only now with the application of DNA sequence data that relationships of species and genera are becoming clear. Here, we present results of cpDNA sequence data from species that have been traditionally placed in the genus Doryopteris and, based on both these results, and morphological and distribution data, this study helps clarify the concept of the genus Doryopteris its position within the Cheilanthoid ferns and the status of Lytoneuron. As a result, three genera are redefined: Doryopteris, Lytoneuron and Ormopteris.

Elevated CO(2) increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane

Because of the economical relevance of sugarcane and its high potential as a source of biofuel, it is important to understand how this crop will respond to the foreseen increase in atmospheric [CO(2)]. The effects of increased [CO(2)] on photosynthesis, development and carbohydrate metabolism were studied in sugarcane (Saccharum ssp.). Plants were grown at ambient (similar to 370 ppm) and elevated (similar to 720 ppm) [CO(2)] during 50 weeks in open-top chambers. The plants grown under elevated CO(2) showed, at the end of such period, an increase of about 30% in photosynthesis and 17% in height, and accumulated 40% more biomass in comparison with the plants grown at ambient [CO(2)]. These plants also had lower stomatal conductance and transpiration rates (-37 and -32%, respectively), and higher water-use efficiency (c.a. 62%). cDNA microarray analyses revealed a differential expression of 35 genes on the leaves (14 repressed and 22 induced) by elevated CO(2). The latter are mainly related to photosynthesis and development. Industrial productivity analysis showed an increase of about 29% in sucrose content. These data suggest that sugarcane crops increase productivity in higher [CO(2)], and that this might be related, as previously observed for maize and sorghum, to transient drought stress.

Molecular phylogeny of tribe Rhipsalideae (Cactaceae) and taxonomic implications for Schlumbergera and Hatiora

Tribe Rhipsalideae is composed of unusual epiphytic or lithophytic cacti that inhabit humid tropical and subtropical forests. Members of this tribe present a reduced vegetative body, a specialized adventitious root system, usually spineless areoles and flowers and fruits reduced in size. Despite the debate surrounding the classification of Rhipsalideae, no studies have ever attempted to reconstruct phylogenetic relationships among its members or to test the monophyly of its genera using DNA sequence data; all classifications formerly proposed for this tribe have only employed morphological data. In this study, we reconstruct the phylogeny of Rhipsalideae using plastid (trnQ-rps16, rpl32-trnL, psbA-trnH) and nuclear (ITS) markers to evaluate the classifications previously proposed for the group. We also examine morphological features traditionally used to delimit genera within Rhipsalideae in light of the resulting phylogenetic trees. In total new sequences for 35 species of Rhipsalideae were produced (out of 55: 63%). The molecular phylogeny obtained comprises four main clades supporting the recognition of genera Lepismium, Rhipsalis, Hatiora and Schlumbergera. The evidence gathered indicate that a broader genus Schlumbergera, including Hatiora subg. Rhipsalidopsis, should be recognized. Consistent morphological characters rather than homoplastic features are used in order to establish a more coherent and practical classification for the group. Nomenclatural changes and a key for the identification of the genera currently included in Rhipsalideae are provided. (C) 2011 Elsevier Inc. All rights reserved.

Gracilariopsis mclachlanii sp nov and Gracilariopsis persica sp nov of the Gracilariaceae (Gracilariales, Rhodophyceae) from the Indian Ocean

Two new species of Gracilariopsis from the Indian Ocean are proposed-Gracilariopsis (Gp.) mclachlanii Buriyo, Bellorin et M. C. Oliveira sp. nov. from Tanzania and Gracilariopsis persica Bellorin, Sohrabipour et E. C. Oliveira sp. nov. from Iran-based on morphology and DNA sequence data (rbcL gene and SSU rDNA). Both species fit the typical features of Gracilariopsis: axes cylindrical throughout, freely and loosely ramified up to four orders, with an abrupt transition in cell size from medulla to cortex, cystocarps lacking tubular nutritive cells and superficial spermatangia. Nucleotide sequence comparisons of rbcL and SSU rDNA placed both species into the Gracilariopsis clade as distinct species from all the accepted species for this genus, forming a deeply divergent lineage together with some species from the Pacific. The new species are very difficult to distinguish on morphological grounds from other species of Gracilariopsis, stressing the importance of homologous molecular marker comparisons for the species recognition in this character-poor genus.

Evolutionary history of Ramphastos toucans: Molecular phylogenetics, temporal diversification, and biogeography

The toucan genus Ramphastos (Piciformes: Ramphastidae) has been a model in the formulation of Neotropical paleobiogeographic hypotheses. Weckstein (2005) reported on the phylogenetic history of this genus based on three mitochondrial genes, but some relationships were weakly supported and one of the subspecies of R. vitellinus (citreolaemus) was unsampled. This study expands on Weckstein (2005) by adding more DNA sequence data (including a nuclear marker) and more samples, including R v. citreolaemus. Maximum parsimony, maximum likelihood, and Bayesian methods recovered similar trees, with nodes showing high support. A monophyletic R. vitellinus complex was strongly supported as the sister-group to R. brevis. The results also confirmed that the southeastern and northern populations of R. vitellinus ariel are paraphyletic. X v. citreolaemus is sister to the Amazonian subspecies of the vitellinus complex. Using three protein-coding genes (COI, cytochrome-b and ND2) and interval-calibrated nodes under a Bayesian relaxed-clock framework, we infer that ramphastid genera originated in the middle Miocene to early Pliocene, Ramphastos species originated between late Miocene and early Pleistocene, and intra-specific divergences took place throughout the Pleistocene. Parsimony-based reconstruction of ancestral areas indicated that evolution of the four trans-Andean Ramphastos taxa (R. v. citreolaemus, R. a. swainsonii, R. brevis and R. sulfuratus) was associated with four independent dispersals from the cis-Andean region. The last pulse of Andean uplift may have been important for the evolution of R. sulfuratus, whereas the origin of the other trans-Andean Ramphastos taxa is consistent with vicariance due to drying events in the lowland forests north of the Andes. Estimated rates of molecular evolution were higher than the ""standard"" bird rate of 2% substitutions/site/million years for two of the three genes analyzed (cytochrome-b and ND2). (C) 2009 Elsevier Inc. All rights reserved.

Partitions selection strategy for set of clustering solutions

Clustering is a difficult task: there is no single cluster definition and the data can have more than one underlying structure. Pareto-based multi-objective genetic algorithms (e.g., MOCK Multi-Objective Clustering with automatic K-determination and MOCLE-Multi-Objective Clustering Ensemble) were proposed to tackle these problems. However, the output of such algorithms can often contains a high number of partitions, becoming difficult for an expert to manually analyze all of them. In order to deal with this problem, we present two selection strategies, which are based on the corrected Rand, to choose a subset of solutions. To test them, they are applied to the set of solutions produced by MOCK and MOCLE in the context of several datasets. The study was also extended to select a reduced set of partitions from the initial population of MOCLE. These analysis show that both versions of selection strategy proposed are very effective. They can significantly reduce the number of solutions and, at the same time, keep the quality and the diversity of the partitions in the original set of solutions. (C) 2010 Elsevier B.V. All rights reserved.

The transcriptional response to cadmium, organic hydroperoxide, singlet oxygen and UV-A mediated by the sigma(E)-ChrR system in Caulobacter crescentus

Caulobacter crescentus sigma(E) belongs to the ECF (extracytoplasmic function) subfamily of RNA polymerase sigma factors, whose members regulate gene expression in response to distinct environmental stresses. During physiological growth conditions, data indicate that sigma(E) is maintained in reduced levels due to the action of ChrR, a negative regulator of rpoE gene expression and function. However, once bacterial cells are exposed to cadmium, organic hydroperoxide, singlet oxygen or UV-A irradiation, transcription of rpoE is induced in a sigma(E)-dependent manner. Site-directed mutagenesis indicated that residue C188 in ChrR is critical for the cadmium response while residues H140 and H142 are required for the bacterial response to organic hydroperoxide, singlet oxygen and UV-A. Global transcriptional analysis showed that sigma(E) regulates genes involved in protecting cells against oxidative damages. A combination of transcriptional start site identification and promoter prediction revealed that some of these genes contain a putative sigma(E)-dependent motif in their upstream regions. Furthermore, deletion of rpoE and two sigma(E)-dependent genes (cfaS and hsp20) impairs Caulobacter survival when singlet oxygen is constantly generated in the cells.