Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

Background: Serine/threonine kinases (STKs) have been found in an increasing number of prokaryotes, showing important roles in signal transduction that supplement the well known role of two-component system. Cyanobacteria are photoautotrophic prokaryotes able to grow in a wide range of ecological environments, and their signal transduction systems are important in adaptation to the environment. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of this kinase family. In this study, we extracted information regarding Ser/Thr kinases from 21 species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. Results: 286 putative STK homologues were identified. STKs are absent in four Prochlorococcus strains and one marine Synechococcus strain and abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic STKs were conserved well in these proteins, and six more cyanobacteria- or bacteria-specific conserved residues were found. These STK proteins were classified into three major families according to their domain structures. Fourteen types and a total of 131 additional domains were identified, some of which are reported to participate in the recognition of signals or substrates. Cyanobacterial STKs show rather complicated phylogenetic relationships that correspond poorly with phylogenies based on 16S rRNA and those based on additional domains. Conclusion: The number of STK genes in different cyanobacteria is the result of the genome size, ecophysiology, and physiological properties of the organism. Similar conserved motifs and amino acids indicate that cyanobacterial STKs make use of a similar catalytic mechanism as eukaryotic STKs. Gene gain-and-loss is significant during STK evolution, along with domain shuffling and insertion. This study has established an overall framework of sequence-structure-function interactions for the STK gene family, which may facilitate further studies of the role of STKs in various organisms.

Preliminary study on a potential antibacterial peptide derived from histone H2A in hemocytes of scallop Chlamys farreri

Histone H2A is reported to participate in host defense response through producing novel antimicrobial peptides (AMPs) from its N-terminus in vertebrates and invertebrates, while the AMPs derived from H2A have not to our knowledge been reported in mollusca. In the present study, gene cloning, mRNA expression of H2A from scallop Chlamys farreri, and the recombinant expression of its N-terminus were conducted to investigate whether a similar mechanism exists in mollusca. The full-length DNA of H2A was identified by the techniques of homology cloning and genomic DNA walking, The full-length DNA of the scallop H2A was 696 bp long, including a 5'-terminal untranslated region (UTR) of 90 bp, a 3'-terminal UTR of 228 bp with a stem-loop structure and a canonical polyadenylation signal sequence AATAAA, and an open reading frame of 375 bp encoding a polypeptide of 125 amino acids. The mRNA expression of H2A in the hemocytes of scallop challenged by microbe was measured by semi-quantitative RT-PCR. The expression of H2A was not upregulated after stimulation, suggesting that H2A did not participate in immunity response directly. The DNA fragment of 117 bp encoding 39 amino acids corresponding to the N-terminus of scallop H2A, which was homologous to buforin I in vertebrates, was cloned into Pichia pastoris GS115. The transformants (His(+) Mut(+)) containing multi-copy gene insertion were selected with increasing concentration of antibiotic G418. The peptide of 39 amino acids was expressed by induction of 0.5% methanol. The recombinant product exerted antibacterial activity against both Gram-positive (G(+)) and Gram-negative (G(-)) bacteria. The antibacterial activity toward G(+) bacteria was 2.5 times more than that against G(-) bacteria. The results elucidated that N-terminus of H2A was a potential AMP and provided a promising candidate for a new antibiotic screening. However, whether H2A is really involved in scallop immune response mechanisms needs to be further investigated. (C) 2006 Elsevier Ltd. All rights reserved.

Characteristics and Formation Mechanism of Polygonal Faults in Qiongdongnan Basin, Northern South China Sea

Based on high-resolution 3D seismic data, we document the polygonal faults within the Miocene Meishan (sic) Formation and Huangliu (sic) Formation of the Qiongdongnan (sic) basin, northern South China Sea. Within the seismic section and time coherent slice, densely distributed extensional faults with small throw and polygonal shape were identified in map view. The orientation of the polygonal faults is almost isotropic, indicating a non-tectonic origin. The deformation is clearly layer-bounded, with horizontal extension of 11.2% to 16%, and 13.2% on average. The distribution of polygonal faults shows a negative correlation with that of gas chimneys. The development of polygonal faults may be triggered by over-pressure pore fluid which is restricted in the fine-grained sediments of bathyal facies when the sediments is compacted by the burden above. The polygonal faults developed to balance the volumetric contraction and restricted extension. The product of hydrocarbon in the Meishan Formation may have contributed to the development of the polygonal faults. In the study area, it was thought that the petroleum system of the Neogene post-rift sequence is disadvantageous because of poor migration pathway. However, the discovery of polygonal faults in the Miocene strata, which may play an important role on the fluid migration, may change this view. A new model of the petroleum system for the study area is proposed.

Analysis of characteristics and mechanism of current system on the west coast of Guangdong of China in summer

On the basis of data of drifting bottles' tracks and the current measured in anchored stations, as well as temperature and salinity observed in cruise investigations and coastal stations, ADCP current data and AVHRR surface sea temperature (SST) data on the western coast of Guangdong, synthetic results of analysis showed that the coastal currents in the west of the mouth of the Zhujiang River were mainly westward in summer, which constituted the north branch of cyclonic gyre in the east of the Qiongzhou Straits. Part of its water flowed westward into the Beibu Gulf through the Qiongzhou Straits. The coastal current pattern was not identical with the traditional current system which flowed westward in the Qiongzhou Straits in winter and eastward in summer. The summertime's coastal current was always westward, maybe temporarily turning northeast only when the southwest wind was strong. The important characteristics of coastal current on the western coast of Guangdong, in the Qiongzhou Straits and in the north of the Beibu Gulf were analyzed and their mechanisms also were explained.

Physical mechanism and numerical simulations of surface layer temperature inversion in tropical ocean

The one-dimensional Kraus-Turner mixed layer model improved by Liu is developed to consider the effect of salinity and the equations of temperature and salinity under the mixed layer. On this basis, the processes of growth and death of surface layer temperature inversion is numerically simulated under different environmental parameters. At the same time, the physical mechanism is preliminarily discussed combining the observations at the station of TOGA-COARE 0 degrees N, 156 degrees E. The results indicate that temperature inversion sensitively depends on the mixed layer depth, sea surface wind speed and solar shortwave radiation, etc., and appropriately meteorological and hydrological conditions often lead to the similarly periodical occurrence of this inversion phenomenon.

Ocean wave imaging mechanism by imaging radar

Analytical representations of the high frequency spectra of ocean wave and its variation due to the variation of ocean surface current are derived from the wave-number spectrum balance equation. The ocean surface imaging formulation of real aperture radar (RAR) is given using electromagnetic wave backscattering theory of ocean surface and the modulations of ocean surface winds, currents and their variations to RAR are described. A general representation of the phase modulation induced by the ocean surface motion is derived according to standard synthetic aperture radar (SAR) imaging theory. The detectability of ocean current and sea bottom topography by imaging radar is discussed. The results constitute the theoretical basis for detecting ocean wave fields, ocean surface winds, ocean surface current fields, sea bottom topography, internal wave and so on.

STUDY ON THE FORMATIONAL MECHANISM OF THE NORTHERN YELLOW (HUANGHAI) SEA COLD WATER MASS(I)

A hydrodynamic-thermodynamic equation set was set up to reflect the formational mechanism and evolution of the Northern Yellow (Huanghai) Sea cold water mass (NYSCWM) and its density circulation. Appropriate mathematical physical models were established by using some physical postulations. An approximate analytic solution to expound the distributions of temperature and three-dimensional current velocity, which can be used to expound the formational mechanism of the NYSCWM and its density circulation is obtained by using the theory of boundary layer and perturbational analyses.

STUDY ON THE FORMATIONAL MECHANISM OF THE NORTHERN YELLOW (HUANGHAI) SEA COLD WATER MASS .2. DISCUSSION ON THE SOLUTION OF THE MODEL

The theoretical solution of the model of the Northern Yellow (Huanghai) Sea Cold Water Mass (NYSCWM) reveals that the NYSCWM is mainly formed through the continuous temperature increase of the overwintered water body above the Northern Yellow Sea Depression (NYSD) after spring when heat is continuously conducted from the sea surface to the deeper layer. In the NYSCWM's growing period, (June-July), nonlinear vertical convection and advection effects continuously increase, and are gradually balanced by the heat diffusion effect as the temperature increases from the surface to the bottom, which leads to the formation of an intensive thermocline and lateral front. Meanwhile, the three-dimensional circulation correspondingly occurs. In the NYSCWM's entire growing period, the horizontal circulation is always in the cyclonic motion, while the vertical circulation passes through a transition from a period with the cold centre as downwelling to a period with the cold centre as upwelling.

A preliminary study on the mechanism of harmful algal bloom mitigation by use of sophorolipid treatment

in order to investigate a new method of mitigating the deleterious effect of harmful algal blooms (HABs), the inhibition of the glycolipid biosurfactant sophorolipid on three common harmful algae Alexandrium tamarense, Heterosigma akashiwo and Cochlodinium polykrikoides was studied. The optimum preparation condition for sophorolipid, the inhibition capability of sophorolipid and the interaction mechanism of sophorolipid on the three algal species were investigated. Results showed that sophorolipid prepared by extraction with ethyl acetate exhibited the most prominent inhibition effect and that storage time of one year had little influence on the inhibition effect of sophorolipid. The optimum concentration of 10-20 mg/l sophorolipid inhibited the motility of about 90% of the tested harmful algal cells without recovery. Investigation of the algicidal process revealed that sophorolipid induced ecdysis of A. tamarense, quick lysis of H. akashiwo and swelling of C. polykrikoides in a relatively short time. Investigation of the nucleotides showed that more than 15% of the nucleotides were released from the cytoplasm under the effect of 10-20 mg/l sophorolipid, indicating the irreversible damage on the cellular membrane, which resulted in the disintegration of the harmful algal cells. (C) 2004 Elsevier B.V. All rights reserved.

Inhibition Effect of 2,3,5-Triphenyl-2H-tetrazolium Chloride and 2,4,6-Tri(2-pyridyl)-s-triazine on the Corrosion of Mild Steel in 1 mol/L HCl and Mechanism Study (II)

The inhibitory effect of 2,3,5-triphenyl-2H-tetrazolium chloride (TTC) and 2,4,6-tri(2-pyridyl)-s-triazine (TPT) molecules on the corrosion of mild steel in 1 mol/L HCl and microcosmic inhibitory mechanism were investigated by X-ray photoelectron spectroscopy and ellipsometry. XPS results showed that C Is and N Is peaks of TTC, C Is and N Is peaks of TPT and their integral areas were obtained, which suggested the layer of the inhibitors (TTC or TPT) should have effectively protected the mild steel surface from the corrosion; and the depression from the inhibitors for the corrosion of mild steel surface was studied using ellipsometry combined with potentiodynamic polarization and the phasic difference was gained, which displayed the inhibitory coverage of the inhibitors formed.

Electrochemical, quantum chemical and SEM investigation of the inhibiting effect and mechanism of ciprofloxacin, norfloxacin and ofloxacin on the corrosion for mild steel in hydrochloric acid

The inhibiting effect and mechanism of 1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinoline carboxylicacid(ciprofloxacin), 1-ethyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinoline carboxylic acid (norfloxacin) and (-)-(S)-9-fluoro-2,3-dihydro-3-methyl-10-(4-methyl-1-piperazinyl)-7-oxo-7 H-pyrido(1,2,3-de)-1,4-benzoxazine-6 carboxylic acid (ofloxacin) on the corrosion of mild steel in 1 mol/L HCl have been studied using electrochemical method, quantum chemical method and SEM at 303 K. The potentiodynamic results showed that these compounds suppressed both cathodic and anodic processes of mild steel corrosion in 1 mol/L HCl. The impedance spectroscopy showed that R-p values increased, and C-dl values decreased with the rising of the working concentration. Quantum chemical calculation showed that there was a positive correlation between some inhibitors structure properties and the inhibitory efficiency. The inhibitors function through adsorption followed Langmuir isotherm, and chemisorption made more contribution to the adsorption of the inhibitors on the steel surface compared with physical adsorption. SEM analysis suggested that the metal had been protected from aggressive corrosion because of the addition of the inhibitors.

Mechanism for Giycinebetaine to Improve Plant Salt Resistance and Its Research Advances in Genetic Engineering

The paper systematically discusses the mechanism for glycinebetaine to improve plant salt resistance and its research advances in genetic engineering at home and abroad as well as summarizing the research progresses about the key enzymes and their genetic engineering in glycinebetaine biosynthesis. It suggests that on the basis of further understanding the mechanism for glycinebetaine to improve plant salt resistance,the transformation of the genes relating to glycinebetaine biosynthesis should be carried out in major crops so that new plant varieties resistant to salt can be obtained.

Theoretical study on the mechanism for the addition reaction of SiH3 with propylene and acetic acid

To explore the reactivities of alkene (-CH=CH2) and carboxy (-COOH) group with H-Si under UV irradiation, the addition mechanism for the reactions of SiH3 radical with propylene and acetic acid was studied by using the B3LYP/6-311++ G(d,p) method. Based on the surface energy profiles, the dominant reaction pathways can be established; i.e., SiH3 adds to the terminal carbon atom of the alkene (-CH=CH2) to form an anti-Markovnikov addition product, or adds to the oxygen atom of the carboxy group (-COOH) to form silyl acetate (CH3-COOSiH3). Because the barrier in the reaction of the carboxy group (39.9 kJ/ mol) is much larger than that of alkene (11.97 kJ/mol), we conclude that the reaction of bifunctional molecules (e.g., omega-alkenoic acid) with H-Si under irradiation condition is highly selective; i.e., the alkene group (-CH= CH2) reacts with SiH3 substantially faster than the carboxyl group (-COOH), which agrees well with the experimental results. This provides the possibility of preparing carboxy-terminated monolayers on silicon surface from omega-alkenoic acids via direct photochemical reaction.