Unexpected diversity of chlorite dismutases: a catalytically efficient dimeric enzyme from Nitrobacter winogradskyi

Chlorite dismutase (Cld) is a unique heme enzyme catalyzing the conversion of ClO(2)(-) to Cl(-) and O(2). Cld is usually found in perchlorate- or chlorate-reducing bacteria but was also recently identified in a nitrite-oxidizing bacterium of the genus Nitrospira. Here we characterized a novel Cld-like protein from the chemolithoautotrophic nitrite oxidizer Nitrobacter winogradskyi which is significantly smaller than all previously known chlorite dismutases. Its three-dimensional (3D) crystal structure revealed a dimer of two identical subunits, which sharply contrasts with the penta- or hexameric structures of other chlorite dismutases. Despite a truncated N-terminal domain in each subunit, this novel enzyme turned out to be a highly efficient chlorite dismutase (K(m) = 90 μM; k(cat) = 190 s(-1); k(cat)/K(m) = 2.1 × 10(6) M(-1) s(-1)), demonstrating a greater structural and phylogenetic diversity of these enzymes than was previously known. Based on comparative analyses of Cld sequences and 3D structures, signature amino acid residues that can be employed to assess whether uncharacterized Cld-like proteins may have a high chlorite-dismutating activity were identified. Interestingly, proteins that contain all these signatures and are phylogenetically closely related to the novel-type Cld of N. winogradskyi exist in a large number of other microbes, including other nitrite oxidizers.     

Intragene higher order repeats in neuroblastoma breakpoint family genes distinguish humans from chimpanzees

Much attention has been devoted to identifying genomic patterns underlying the evolution of the human brain and its emergent advanced cognitive capabilities, which lie at the heart of differences distinguishing humans from chimpanzees, our closest living relatives. Here, we identify two particular intragene repeat structures of noncoding human DNA, spanning as much as a hundred kilobases, that are present in human genome but are absent from the chimpanzee genome and other nonhuman primates. Using our novel computational method Global Repeat Map, we examine tandem repeat structure in human and chimpanzee chromosome 1. In human chromosome 1, we find three higher order repeats (HORs), two of them novel, not reported previously, whereas in chimpanzee chromosome 1, we find only one HOR, a 2mer alphoid HOR instead of human alphoid 11mer HOR. In human chromosome 1, we identify an HOR based on 39-bp primary repeat unit, with secondary, tertiary, and quartic repeat units, fully embedded in human hornerin gene, related to regenerating and psoriatric skin. Such an HOR is not found in chimpanzee chromosome 1. We find a remarkable human 3mer HOR organization based on the ~1.6-kb primary repeat unit, fully embedded within the neuroblastoma breakpoint family genes, which is related to the function of the human brain. Such HORs are not present in chimpanzees. In general, we find that human-chimpanzee differences are much larger for tandem repeats, in particularly for HORs, than for gene sequences. This may be of great significance in light of recent studies that are beginning to reveal the large-scale regulatory architecture of the human genome, in particular the role of noncoding sequences. We hypothesize about the possible importance of human accelerated HOR patterns as components in the gene expression multilayered regulatory network.     

The novel pyrimidine and purine derivatives of l-ascorbic acid: synthesis, one- and two-dimensional 1H and 13C NMR study, cytostatic and antiviral evaluation

The syntheses of the novel C-5 substituted pyrimidine derivatives of l-ascorbic acid containing free hydroxy groups at C-2' (6-10) or C-2' and C-3' (11-15) positions of the lactone ring are described. Debenzylation of the 6-chloro- and 6-(N-pyrrolyl)purine derivatives of 2,3-O,O-dibenzyl-l-ascorbic acid (16 and 17) gave the new compounds containing hydroxy groups at C-2' (18) and C-2' and C-3' (19 and 20). Z- and E-configuration of the C4'C5' double bond and position of the lactone ring of the compounds 6-9 were deduced from their one- and two-dimensional (1)H and (13)C NMR spectra and connectivities in NOESY and HMBC spectra. Compounds 15 and 18 showed the best inhibitory activities of all evaluated compounds in the series. The compound 15 containing 5-(trifluoromethyl)uracil showed marked inhibitory activity against all human malignant cell lines (IC(50): 5.6-12.8 microM) except on human T-lymphocytes. Besides, this compound influenced the cell cycle by increasing the cell population in G2/M phase and induced apoptosis in SW 620 and MiaPaCa-2 cells. The compound 18 containing 6-chloropurine ring expressed the most pronounced inhibitory activities against HeLa (IC(50): 6.8 microM) and MiaPaCa-2 cells (IC(50): 6.5 microM). The compound 20 with 6-(N-pyrrolyl)purine moiety showed the best differential inhibitory effect against MCF-7 cells (IC(50): 35.9 microM).     

Characterization of a D2-like dopamine receptor (AmDOP3) in honey bee, Apis mellifera

Dopamine is an important neurotransmitter in vertebrate and invertebrate nervous systems and is widely distributed in the brain of the honey bee, Apis mellifera. We report here the functional characterization and cellular localization of the putative dopamine receptor gene, Amdop3, a cDNA clone isolated and identified in previous studies as AmBAR3 (Apis mellifera Biogenic Amine Receptor 3). The Amdop3 cDNA encodes a 694 amino acid protein, AmDOP3. Comparison of AmDOP3 to Drosophila melanogaster sequences indicates that it is orthologous to the D2-like dopamine receptor, DD2R. Using AmDOP3 receptors expressed in HEK293 cells we show that of the endogenous biogenic amines, dopamine is the most potent AmDOP3 agonist, and that activation of AmDOP3 receptors results in down regulation of intracellular levels of cAMP, a property characteristic of D2-like dopamine receptors. In situ hybridization reveals that Amdop3 is widely expressed in the brain but shows a pattern of expression that differs from that of either Amdop1 or Amdop2, both of which encode D1-like dopamine receptors. Nonetheless, overlaps in the distribution of cells expressing Amdop1, Amdop2 and Amdop3 mRNAs suggest the likelihood of D1:D2 receptor interactions in some cells, including subpopulations of mushroom body neurons.     

Novel Tn antigen-containing neoglycopeptides: synthesis and evaluation as anti tumor vaccines

The fully unprotected alpha-C-glycosyl analogue of N-acetylgalactosamine 9 was conjugated by a non-natural oxime bond to the segment peptides (328--340)OVA and (327--339)OVA, affording neoglycopeptides 1--2 and 3, having one or two sugar units, respectively. The three neoglycopeptides were tested in vitro in an antigen presentation assay as antitumor vaccines. Neoglycopeptides 1--3 could be presented to and recognized by the T cell receptor; neoglycopeptide 3, bearing two B-epitopes, was presented to the TCR with higher efficiency, compared to neoglycopeptide 2, having only one B-epitope.     

Application of tree rings [dendrochemistry] for detecting historical trends in air Hg concentrations across multiple scales

Tree rings are a useful long term monitor of climate change indicators and certain atmospheric constituents. Since we have no long-term historical record of air mercury (Hg) concentrations, and previous research demonstrates atmospheric uptake of Hg into vegetative biomass, we hypothesized that tree rings would be a useful archive for monitoring changes in local, regional, and global air Hg concentrations. We developed and tested a method for measurement of Hg in tree rings, and then investigated our hypothesis using species within the genus Pinus. Mercury concentrations declined along a coast-to-interior (California-to-Nevada, USA) gradient with highest mean concentrations (5.7 ng/g) at the coast, and lowest (<1.2 ng/g) at inland locations. Tree ring Hg concentrations recorded the impact of local sources and indicate increasing global concentrations over time. The data also indicate that concentrations are higher in areas impacted by marine air, and this suggests that the atmospheric chemistry is influencing assimilation. Future research should address species- and age-specific variation in the sensitivity of tree-ring samples as proxy data for atmospheric Hg concentrations. Tree rings show great potential as passive recorders of atmospheric Hg for long time periods (centuries to millennia) at time steps of ≤5 years.     

Impact of Progerbalin LG® on the apple fruit physical attributes

During two consecutive years (2010 and 2011) we evaluated the impact of Progerbalin LG^® (mixture of gibberellins (GA₄₊₇) and N ⁶-benzyladenine) on fruit weight, fruit dimensions, elongation, geometric mean diameter or fruit size, aspect ratio, surface area and fruit volume of five apple cultivars belonging to ‘Red Delicious’ group (‘Hapke’ grafted on M.9 and M.26, ‘Hi Red’, ‘Starking’ and ‘Top Red’ on M.9, and ‘Red Chief Camspur’ on MM.106 rootstock). Trees were sprayed twice with 30, 50 or 100 ml L^?1 i.e. between 80 % of open flowers and the following petal fall (first treatment), and 10 days after first application (second treatment); control trees were not sprayed. Results showed that the lowest dose increased fruit weight in all cultivars, except ‘Top Red’ and ‘Red Chief Camspur’; this dose promoted fruit dimensions, fruit size and elongation in ‘Hapke’ on both rootstocks, and also fruit dimensions, surface area and fruit volume in ‘Hi Red’. Regarding ‘Starking’, different doses of Progerbalin LG^® did not affect other properties evaluated, but season played an important role in these cases. In contrast, the highest dose of this hormone improved all physical attributes in ‘Top Red’ and ‘Red Chief Camspur’, except elongation and/or aspect ratio. In some cases, good values were found in control treatment.     

Desiccation tolerance of the resurrection plant Ramonda serbica is associated with dehydration-dependent changes in levels of proteolytic activities

The unique response of desiccation-tolerant, or resurrection plants, to extreme drought is accompanied by major changes in the protein pool, raising the possibility of the involvement of proteases. We detected and characterized proteases present in their active state in leaf extracts of desiccated Ramonda serbica Pan?., a resurrection plant from the Balkan Peninsula. Plants desiccated under laboratory conditions and maintained in anhydrobiosis for 4 and 14 months revived upon rehydration. Protease activities were determined spectrophotometrically in solution and by zymography on gels. Several endo- and aminopeptidases were detected and characterized by their pH profiles. Their enzyme class was determined using specific inhibitors. Those with higher activities were a serine endopeptidase active against Bz-Arg-pNA with a pH optimum around 9, and aminopeptidases optimally active at pHs from 7 to 9 against Leu-pNA, Met-pNA, Phe-pNA, Pro-pNA and Ala-pNA. The levels of their activities in leaf extracts from desiccated plants were significantly higher than those from rehydrated plants and from regularly watered plants, implying their involvement in the recovery of vegetative tissues from desiccation.