Pressures in archaeal protein coding genes: a comparative study

Our studies on the bases of codons from 11 completely sequenced archaeal genomes show that, as we move from GC-rich to AT-rich protein-coding gene-containing species, the differences between G and C and between A and T, the purine load (AG content), and also the overall persistence (i.e. the tendency of a base to be followed by the same base) within codons, all increase almost simultaneously, although the extent of increase is different over the three positions within codons. These findings suggest that the deviations from the second parity rule (through the increasing differences between complementary base contents) and the increasing purine load hinder the chance of formation of the intra-strand Watson-Crick base-paired secondary structures in mRNAs (synonymous with the protein-coding genes we dealt with), thereby increasing the translational efficiency. We hypothesize that the ATrich protein-coding gene-containing archaeal species might have better translational efficiency than their GC-rich counterparts.     

Inactivation and reactivation of phosphoprotein phosphatase

Summary The catalytic subunit of phosphoprotein phosphatase (Mr = 35 000) is inactivated by phosphate compounds such as trimetaphosphate, PPi, and ATP. The inactivation of phosphoprotein phosphatase by these phosphate compounds is time- and concentration-dependent, is not reversed by dilution or gel filtration and is protected by Pi. A dissociation constant for the enzyme-trimetaphosphate complex and a rate constant for the reaction were calculated to be 4.6 × 10^–4 M and 0.29 min ¹, respectively. The inactivation of phosphatase by PPi and ATP shows more complex kinetics than that by trimetaphosphate. The addition of EDTA to PPi and ATP exhibits more potent inactivation, even though EDTA alone does not inactivate phosphatase. This phosphoprotein phosphatase is not labeled by [-³²P]ATP. The inactivation of phosphatase by PPi or ATP can only be reversed by Mn²⁺ or Co²⁺, among all other metals or cationic compounds tried. The reactivation also requires sulfhydryl compounds. The effectiveness of sulfhydryl compounds follows the order: dithioerythritol > mercaptoethanol > cysteine. Glutathione was without effect. Metal analysis of the catalytic subunit did not reveal any significant amounts of Ca, Cd, Co, Cu, Fe, Mg, Mn, Ni, Sn, or Zn. Phosphoprotein phosphatase activity from zinc-deficient rat livers also eliminated the possibility of this phosphatase being a zinc metalloenzyme. Inactivation does not seem to be due to a loss of a critical metal ion. Other mechanisms for inactivation are presented.Abbreviations used EDTA Ethylenediamine tetraacetic acid - PPi Inorganic pyrophosphate - DTE Dithioerythritol. To whom requests for reprints should be addressed.     

Cnidae in the sea anemone Sagartiogeton viduatus (Muller, 1776) (Cnidaria,Anthozoa); A comparison to cnidae in the sea anemone Metridium senile (Linnaeus, 1761) (Cnidaria,Anthozoa)

The cnidom of the sea anemone Sagartiogeton viduatus (Muller, 1776) is described from interference‐contrast light micrographs (LMs) and scanning electron micrographs (SEMs). Special attention is given to nematocyst maturation, including the differentiation of the shaft into proximal and main regions as helical folding of the shaft wall proceeds. Comparisons are made with Metridium senile (Linnaeus, 1761), whose cnidom, with a few exceptions, is closely similar to that of S. viduatus. The two anemones possess b‐ and p‐mastigophores, p‐amastigophores, isorhizas and spirocysts. Although the majority of cnidae in S. viduatus is smaller than corresponding ones in M. senile, they are grouped into the same size classes as those of M. senile, namely small, medium and large. The main differences from M. senile cnidae are the followings: (1) Large acontia p‐amastigophores are the largest nematocysts in S. viduatus. (2) They are noticeably larger than the large acontia b‐mastigophores, and (3) they are separated from the p‐amastigophores of M. senile by the sinusoid pattern of their U‐shaped capsular matrix. (4) The large acontia b‐mastigophores are microbasic and not mesobasic as in M. Senile, and (5) they do not produce darts. (6) Another difference from M. senile is the absence of catch‐tentacle isorhizas.     

22q11.2 distal deletion: a recurrent genomic disorder distinct from DiGeorge syndrome and velocardiofacial syndrome

Microdeletions within chromosome 22q11.2 cause a variable phenotype, including DiGeorge syndrome (DGS) and velocardiofacial syndrome (VCFS). About 97% of patients with DGS/VCFS have either a common recurrent ~3 Mb deletion or a smaller, less common, ~1.5 Mb nested deletion. Both deletions apparently occur as a result of homologous recombination between nonallelic flanking low-copy repeat (LCR) sequences located in 22q11.2. Interestingly, although eight different LCRs are located in proximal 22q, only a few cases of atypical deletions utilizing alternative LCRs have been described. Using array-based comparative genomic hybridization (CGH) analysis, we have detected six unrelated cases of deletions that are within 22q11.2 and are located distal to the ~3 Mb common deletion region. Further analyses revealed that the rearrangements had clustered breakpoints and either a ~1.4 Mb or ~2.1 Mb recurrent deletion flanked proximally by LCR22-4 and distally by either LCR22-5 or LCR22-6, respectively. Parental fluorescence in situ hybridization (FISH) analyses revealed that none of the available parents (11 out of 12 were available) had the deletion, indicating de novo events. All patients presented with characteristic facial dysmorphic features. A history of prematurity, prenatal and postnatal growth delay, developmental delay, and mild skeletal abnormalities was prevalent among the patients. Two patients were found to have a cardiovascular malformation, one had truncus arteriosus, and another had a bicuspid aortic valve. A single patient had a cleft palate. We conclude that distal deletions of chromosome 22q11.2 between LCR22-4 and LCR22-6, although they share some characteristic features with DGS/VCFS, represent a novel genomic disorder distinct genomically and clinically from the well-known DGS/VCF deletion syndromes.     

Effects of urban stream burial on nitrogen uptake and ecosystem metabolism: implications for watershed nitrogen and carbon fluxes

Urbanization has resulted in the extensive burial and channelization of headwater streams, yet little is known about the impacts of stream burial on ecosystem functions critical for reducing downstream nitrogen (N) and carbon (C) exports. In order to characterize the biogeochemical effects of stream burial on N and C, we measured NO₃ ^? uptake (using ¹⁵N-NO₃ ^? isotope tracer releases) and gross primary productivity (GPP) and ecosystem respiration (ER) (using whole stream metabolism measurements). Experiments were carried out during four seasons, in three paired buried and open stream reaches, within the Baltimore Ecosystem Study Long-term Ecological Research site. Stream burial increased NO₃ ^? uptake lengths by a factor of 7.5 (p < 0.01) and decreased NO₃ ^? uptake velocity and areal NO₃ ^? uptake rate by factors of 8.2 (p < 0.05) and 9.6 (p < 0.001), respectively. Stream burial decreased GPP by a factor of 11.0 (p < 0.01) and decreased ER by a factor of 5.0 (p < 0.05). From fluorescence Excitation Emissions Matrices analysis, buried streams were found to have significantly altered C quality, showing less labile dissolved organic matter. Furthermore, buried streams had significantly lower transient storage (TS) and water temperatures. Differences in NO₃ ^? uptake, GPP, and ER in buried streams, were primarily explained by decreased TS, light availability, and C quality, respectively. At the watershed scale, we estimate that stream burial decreases NO₃ ^? uptake by 39 % and C production by 194 %. Overall, our results suggest that stream burial significantly impacts NO₃ ^? uptake, stream metabolism, and the quality of organic C exported from watersheds. Given the large impacts of stream burial on stream ecosystem processes, daylighting or de-channelization of streams, through hydrologic floodplain reconnection, may have the potential to alter ecosystem functions in urban watersheds, when used appropriately.     

Precancerous and non-cancer disease endpoints of chronic arsenic exposure: the level of chromosomal damage and XRCC3 T241M polymorphism

Genetic variants are expected to play an important role in arsenic susceptibility. Our previous study revealed deficient DNA repair capacity to be a susceptibility factor for arsenicism. T241M polymorphism in XRCC3 (a homologous recombination repair pathway gene) is widely studied for its association with several cancers. We have investigated the association of XRCC3 T241M polymorphism with arsenic-induced precancerous and non-cancer disease outcomes. The present study evaluated the association of T241M polymorphism with arsenic-induced skin lesions, peripheral neuropathy (neurodegenerative changes), conjunctivitis and other ocular diseases. A case-control study was conducted in West Bengal, India, involving 206 cases with arsenic-induced skin lesions and 215 controls without arsenic-induced skin lesions having similar arsenic exposure. XRCC3 T241M polymorphism was determined using conventional PCR-sequencing method. Chromosomal aberration assay, arsenic-induced neuropathy and ocular diseases were also evaluated. The data revealed that presence of at least one Met allele (Met/Met or Thr/Met) was protective towards development of arsenic-induced skin lesions [OR=0.45, 95% CI: 0.30-0.67], peripheral neuropathy [OR=0.49; 95%CI: 0.30-0.82] and conjunctivitis [OR=0.60; 95%CI: 0.40-0.92]. A significant correlation was also observed between protective genotype and decreased frequency of chromosomal aberrations. Thus the results indicate the protective role of Met allele against the arsenic-induced skin lesions, chromosomal instability, peripheral neuropathy and conjunctivitis.     

Point Mutations in FimH Adhesin of Crohn's Disease-Associated Adherent-Invasive Escherichia coli Enhance Intestinal Inflammatory Response

Adherent-invasive Escherichia coli (AIEC) are abnormally predominant on Crohn''s disease (CD) ileal mucosa. AIEC reference strain LF82 adheres to ileal enterocytes via the common type 1 pili adhesin FimH and recognizes CEACAM6 receptors abnormally expressed on CD ileal epithelial cells. The fimH genes of 45 AIEC and 47 non-AIEC strains were sequenced. The phylogenetic tree based on fimH DNA sequences indicated that AIEC strains predominantly express FimH with amino acid mutations of a recent evolutionary origin - a typical signature of pathoadaptive changes of bacterial pathogens. Point mutations in FimH, some of a unique AIEC-associated nature, confer AIEC bacteria a significantly higher ability to adhere to CEACAM-expressing T84 intestinal epithelial cells. Moreover, in the LF82 strain, the replacement of fimH _LF82 (expressing FimH with an AIEC-associated mutation) with fimH _K12 (expressing FimH of commensal E. coli K12) decreased the ability of bacteria to persist and to induce severe colitis and gut inflammation in infected CEABAC10 transgenic mice expressing human CEACAM receptors. Our results highlight a mechanism of AIEC virulence evolution that involves selection of amino acid mutations in the common bacterial traits, such as FimH protein, and leads to the development of chronic inflammatory bowel disease (IBD) in a genetically susceptible host. The analysis of fimH SNPs may be a useful method to predict the potential virulence of E. coli isolated from IBD patients for diagnostic or epidemiological studies and to identify new strategies for therapeutic intervention to block the interaction between AIEC and gut mucosa in the early stages of IBD.     

Mechanism of the inhibition of milk xanthine oxidase activity by metal ions: a transient kinetic study

The nature and mechanism of the inhibition of the oxidoreductase activity of milk xanthine oxidase (XO) by Cu(2+), Hg(2+) and Ag(+) ions has been studied by steady state and stopped flow transient kinetic measurements. The results show that the nature of the inhibition is noncompetitive. The inhibition constants for Cu(2+) and Hg(2+) are in the micromolar and that for Ag(+) is in the nanomolar range. This suggests that the metal ions have strong affinity towards XO. pH dependence studies of the inhibition indicate that at least two ionisable groups of XO are involved in the binding of these metal ions. The effect of the interaction of the metal ions on the reductive and oxidative half reactions of XO has been investigated, and it is observed that the kinetic parameters of the reductive half reaction are not affected by these metal ions. However, the interaction of these metal ions with XO significantly affects the kinetic parameters of the oxidative half reaction. It is suggested that this may be the main cause for the inhibition of XO activity by the metal ions.     

Sea cucumbers of the genus Stichopus Brandt, 1835 (Holothuroidea,Stichopodidae) in Straits of Malacca with description of a new species

Five sea cucumber species including one new species of the genus Stichopus are reported from the shallow coral reefs of Straits of Malacca. The new species Stichopus fusiformiossa has unusual fusiform spicules in the tentacles, which are not found in the other species of the genus. Pseudo-tables and large perforated plates are newly recorded for Stichopus hermanni Semper, 1868 and Stichopus vastus Sluiter, 1887, respectively.     

Cloning and sequencing analysis of the repressor gene of temperate mycobacteriophage L1

The wild-type and temperature-sensitive (ts) repressor genes were cloned from the temperate mycobacteriophage L1 and its mutant L1cIts391, respectively. A sequencing analysis revealed that the 131st proline residue of the wild-type repressor was changed to leucine in the ts mutant repressor. The 100% identity that was discovered between the two DNA regions of phages L1 and L5, carrying the same sets of genes including their repressor genes, strengthened the speculation that L1 is a minor variant of phage L5 or vice versa. A comparative analysis of the repressor proteins of different mycobacteriophages suggests that the mycobacteriophage-specific repressor proteins constitute a new family of repressors, which were possibly evolved from a common ancestor. Alignment of the mycobacteriophage-specific repressor proteins showed at least 7 blocks (designated I-VII) that carried 3-8 identical amino acid residues. The amino acid residues of blocks V, VI, and some residues downstream to block VI are crucial for the function of the L1 (or L5) repressor. Blocks I and II possibly form the turn and helix 2 regions of the HTH motif of the repressor. Block IV in the L1 repressor is part of the most charged region encompassing amino acid residues 72-92, which flanks the putative N-terminal basic (residues 1-71) and C-terminal acidic (residues 93-183) domains of L1 repressor.