Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440

Analysis of the catabolic potential of Pseudomonas putida KT2440 against a wide range of natural aromatic compounds and sequence comparisons with the entire genome of this microorganism predicted the existence of at least four main pathways for the catabolism of central aromatic intermediates, that is, the protocatechuate (pca genes) and catechol (cat genes) branches of the beta-ketoadipate pathway, the homogentisate pathway (hmg/fah/mai genes) and the phenylacetate pathway (pha genes). Two additional gene clusters that might be involved in the catabolism of N-heterocyclic aromatic compounds (nic cluster) and in a central meta-cleavage pathway (pcm genes) were also identified. Furthermore, the genes encoding the peripheral pathways for the catabolism of p-hydroxybenzoate (pob), benzoate (ben), quinate (qui), phenylpropenoid compounds (fcs, ech, vdh, cal, van, acd and acs), phenylalanine and tyrosine (phh, hpd) and n-phenylalkanoic acids (fad) were mapped in the chromosome of P. putida KT2440. Although a repetitive extragenic palindromic (REP) element is usually associated with the gene clusters, a supraoperonic clustering of catabolic genes that channel different aromatic compounds into a common central pathway (catabolic island) was not observed in P. putida KT2440. The global view on the mineralization of aromatic compounds by P. putida KT2440 will facilitate the rational manipulation of this strain for improving biodegradation/biotransformation processes, and reveals this bacterium as a useful model system for studying biochemical, genetic, evolutionary and ecological aspects of the catabolism of aromatic compounds.     

Implication of guanosine 3′,5′-cyclic monophosphate,adenosine 3′,5′-cyclic monophosphate,adenosine 5′-mono-, di- and triphosphate and fructose-2,6-bisphosphate in the regulation of the glycolytic pathway in hypoxic/anoxic mussel,Mytilus galloprovincialis

The change in the content of cyclic GMP, cyclic AMP, ATP, ADP, AMP and fructose-2,6-bisphosphate that occurred in the mantle of the mussel Mytilus galloprovincialis Lmk when specimens of this mollusk were subjected to a hypoxia/anoxia situation were assessed. After the early 24 h in anaerobiosis, a clear decrease was observed in the ATP content, which remained close to that value for the rest of the time. AMP content doubled during the early 24 h in anaerobiosis and, from that time on, it remained close to that value. Fructose-2,6-bisphoshate and cyclic GMP showed a similar behavior. The levels of these compounds rose significantly during the early hours in anaerobiosis, and then fell to values similar to those of aerobiosis, remaining constant for the rest of the time. Neither ADP nor cAMP showed significant variations.     

Two new scorpion toxins that target voltage-gated Ca2+ and Na+ channels

This report describes the isolation, primary structure determination, and functional characterization of two similar toxins from the scorpion Parabuthus granulatus named kurtoxin-like I and II (KLI and KLII, respectively). KLII from P. granulatus is identical to kurtoxin from Parabuthus transvaalicus (a 63 amino-acid long toxin) whereas KLI is a new peptide containing 62 amino acid residues closely packed by four disulfide bridges with a molecular mass of 7244. Functional assays showed that both toxins, KLI and kurtoxin from P. granulatus, potently inhibit native voltage-gated T-type Ca(2+) channel activity in mouse male germ cells. In addition, KLI was shown to significantly affect the gating mechanisms of recombinant Na(+) channels and weakly block alpha(1)3.3Ca(V) channels expressed in Xenopus oocytes. KLI and kurtoxin from P. granulatus represent new probes to study the role of ion channels in germ cells, as well as in cardiac and neural tissue.     

Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes

Lobose amoebae are abundant free-living protists and important pathogenic agents, yet their evolutionary history and position in the universal tree of life are poorly known. Molecular data for lobose amoebae are limited to a few species, and all phylogenetic studies published so far lacked representatives of many of their taxonomic groups. Here we analyze actin and small-subunit ribosomal RNA (SSU rRNA) gene sequences of a broad taxon sampling of naked, lobose amoebae. Our results support the existence of a monophyletic Amoebozoa clade, which comprises all lobose amoebae examined so far, the amitochondriate pelobionts and entamoebids, and the slime molds. Both actin and SSU rRNA phylogenies distinguish two well-defined clades of amoebae, the "Gymnamoebia sensu stricto" and the Archamoebae (pelobionts + entamoebids), and one weakly supported and ill-resolved group comprising some naked, lobose amoebae and the Mycetozoa.     

Pilomatrixoma: a review of 346 cases

Pilomatrixoma, also known as calcifying epithelioma of Malherbe, is a benign skin neoplasm that arises from hair follicle matrix cells. Pilomatrixoma is a common skin neoplasm in the pediatric population that is often misdiagnosed as other skin conditions. This study reviews an 11-year experience at a tertiary children's hospital, examining the cause, clinical and histopathological presentation, management, and treatment outcomes of pilomatrixoma. A review of the pathology database at Children's Hospital Los Angeles revealed 346 pilomatrixomas excised from 336 patients between 1991 and 2001. The hospital charts, pathology records, and plastic surgery clinic charts were reviewed with respect to variables such as sex, age at the time of presentation, clinical and histopathological presentation, preoperative diagnosis, management, recurrence, and treatment outcome. The main presenting symptom was a hard, subcutaneous, slowly growing mass. The preoperative diagnosis was accurate and consistent with the pathological diagnosis of pilomatrixoma in only 100 cases (28.9 percent). This entity should be considered with other benign or malignant conditions in the clinical differential diagnosis of solitary firm skin nodules, especially those on the head, neck, or upper limbs. The diagnosis can generally be made with a clinical examination. Imaging studies are not required unless symptoms or the location of the lesion warrants such diagnostic assessments. The treatment of choice is surgical excision, and the recurrence rate is low.     

Changes in alpha-xylosidase during intact and auxin-induced growth of pine hypocotyls

A complete cDNA from Pinus pinaster Aiton, potentially coding for an alpha-xylosidase able to remove the xylose residue from xyloglucan oligosaccharides, has been cloned. Its sequence was homologous to previously published alpha-xylosidase genes from Arabidopsis and nasturtium. The protein also showed the two signature regions of family 31 of glycosyl hydrolases. The gene expression level was quantified by competitive RT-PCR, under different growth conditions, throughout seedling development, in different regions along the hypocotyls and in auxin-treated hypocotyl segments, and related with growth capacity and alpha-xylosidase activity. A role of alpha-xylosidase in regulating the level of xyloglucan oligosaccharides within the apoplast is proposed. The action of an alpha-xylosidase removing the xylose residue, would make possible the action of a beta-glucosidase deblocking the xyloglucan oligosaccharide degradation and it could serve as a control point for the regulation of the apoplastic levels of xyloglucan oligosaccharides.     

Carbohydrate analysis of floral nectar using medium infrared

An instrumental method based on a chemometric model of the medium region of the infrared (MIR) was developed to analyse total sugar content and the proportions of glucose, fructose and sucrose. In order to construct the model, a set of 127 standard aqueous solutions of different sugars in the concentration range 0-20% (w/v) were prepared and analysed in the interval 4900-700 cm(-1). The MIR was transformed by normalisation, correction of baseline using the second derivative, and suppression of the signals of water and carbon dioxide. The region between 1150 and 950 cm(-1) showed the highest correlation between signal and concentration. The correlation coefficient for total sugar content was 0.956, whilst those for glucose, fructose and sucrose were 0.982, 0.972 and 0.992, respectively. The method was validated using a set of 28 samples of nectar which had been assayed by chromatographic and refractometric methods. The method shows potential utility for the prediction of nectar sugar components.