Structure–activity relationships in 1,4-benzodioxan-related compounds. 10. Novel α1-adrenoreceptor antagonists related to openphendioxan: Synthesis,biological evaluation,and α1d computational study

A series of novel openphendioxan analogues were synthesized and tested at α₁-adrenoreceptor (AR) subtypes by binding and functional assays. The α_1d-AR binding profile was also examined by means of 2D, 3D-QSAR together with docking studies. Multiple regression analysis suggested the relevance of adequate number of heteroatoms in the whole molecule and of passive membrane diffusion to enhance α_1d-AR affinity. Docking simulations against a computational structural model of the biological target further proved this evidence and furnished support for chemiometric analysis, where polar, electrostatic, hydrophobic and shape effects of the ortho substituents in the phenoxy terminal, most likely governing ligand binding, helped the depiction of pharmacophore hypothesis for the examined ligands data set.     

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote

The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.     

Structural proteome of human colostral fat globule membrane proteins

Milk fat globule membrane (MFGM) contains proteins derived from the apical membrane of secreting epithelial cells of the mammary gland. Between 2-4% of total human milk protein content is associated with the fat globule fraction, as MFGM proteins. While MFGM proteins have very low classical nutritional value, they play important roles in various cell processes and defence mechanisms for the newborn. To date, fewer than 30 human MFGM proteins have been identified and characterized, either by immunological methods or by Edman sequencing and mass spectrometry. This study aimed to update the structural proteome of human colostral MFGM proteins and to create an annotated two-dimensional electrophoresis (2-DE) MFGM protein database available on-line. More than one hundred 2-DE spots derived from human colostral MFGM proteins were investigated by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and proteins were identified by three different software packages available on the web (PeptIdent, MS-Fit and ProFound); uncertain identifications were solved by nanoelectrospray ionization-ion trap mass spectrometry using SEQUEST software.     

α-Amylase Expression under Anoxia in Rice Seedlings: An Update

Rice grains can germinate under anoxia, while most other cereals fail to behave similarly. The ability of rice grains to degrade starch, thanks to the successful production of -amylase even in the absence of oxygen is likely one of the factors allowing rice to germinate anaerobically. In this paper we review the most recent results concerning the physiology and molecular biology related to the expression of -amylase genes under anoxia. The current view is that expression of sugar-starvation induces isoforms of -amylase playing a major role during germination under anoxia, while gibberellin induces -amylase predominating under aerobic conditions.     

Helicobacter pylori antigen-specific T-cell responses at gastric level in chronic gastritis,peptic ulcer,gastric cancer and low-grade mucosa-associated lymphoid tissue (MALT) lymphoma

Host T-cell response to Helicobacter pylori is important for the clinical outcome of the infection. A Th1-polarized response, preferentially against CagA, is associated with peptic ulcer, whereas mixed Th1 and Th0 responses are present in non-ulcer gastritis. A deregulated H. pylori-driven Th0 cell-dependent B-cell activation is found in low-grade B-cell lymphoma of mucosa-associated lymphoid tissue.     

Immunological analysis of aconitase in pumpkin cotyledons: the absence of aconitase in glyoxysomes

Aconitase (EC 4.2.1.3) was purified by column chromatography and SDS-PAGE. Specific antibodies for aconitase were prepared after affinity purification of the antiserum with purified aconitase. The antibodies reacted with purified pumpkin aconitase, and with the 98 kDa protein band after electrophoretic fractionation of extracts of pumpkin cotyledons. Immunoblot analysis revealed a protein with similar molecular mass in extracts of several plants. The intensity of the 98 kDa band increased as pumpkin cotyledons developed in darkness, and decreased thereafter upon illumination. Aconitase activity showed a similar pattern. Anion exchange chromatography of a homogenate of pumpkin cotyledons, followed by western blotting, displayed the presence of immunoreactive protein bands only in fractions showing aconitase activity. The results indicate that the antibodies were specific for aconitase. When we investigated the presence of immunoreactive bands after sucrose gradient fractionation, aconitase was detected in the supernatant fractions and in mitochondria, while a very low amount was found in glyoxysomes. These data provide additional proof that aconitase is not localized in glyoxysomes.