Identification and analysis of a Scophthalmus maximus ferritin that is regulated at transcription level by oxidative stress and bacterial infection

Ferritins are conserved Iron storage proteins that exist in most living organisms and play an essential role in Iron homeostasis. In this study, we reported the identification and analysis a ferritin M subunit, SmFerM, from turbot Scophthalmus maximus. The full length cDNA of SmFerM contains a 5'-untranslated region (UTR) of 232 bp, an open reading frame (ORF) of 531 bp, and a 3'-UTR of 196 bp The ORF encodes a putative protein of 176 amino acids, which shares extensive sequence identities with the M terrains of several fish species. In silico analysis identified in SmFerM both the ferroxidase center of mammalian H ferritins and the iron nucleation site of mammalian L ferritins. Quantitative real time reverse transcriptase-PCR analysis indicated that SmFerM expression was highest in muscle and lowest in heart and responded positively to experimental challenges with bacterial pathogens and poly(I center dot C) Exposure of cultured turbot hepatocytes to treatment of stress inducers (iron, copper, and H2O2) significantly upregulated the expression of SmFerM in a dose dependent manner. Iron chelating analysis showed that recombinant SmFerM purified from Escherichia coli exhibited apparent iron binding activity. These results suggest that SmFerM is a functional M ferritin and is likely to play a role in iron sequestration and protection against oxidative stress and microbial infection (C) 2010 Elsevier Inc All rights reserved

Diversity and Distribution of Sediment NirS-Encoding Bacterial Assemblages in Response to Environmental Gradients in the Eutrophied Jiaozhou Bay, China

A gene-clone-library-based molecular approach was used to study the nirS-encoding bacteria-environment relationship in the sediments of the eutrophic Jiaozhou Bay. Diverse nirS sequences were recovered and most of them were related to the marine cluster I group, ubiquitous in estuarine, coastal, and marine environments. Some NirS sequences were unique to the Jiaozhou Bay, such as the marine subcluster VIIg sequences. Most of the Jiaozhou Bay NirS sequences had their closest matches originally detected in estuarine and marine sediments, especially from the Chesapeake Bay, indicating similarity of the denitrifying bacterial communities in similar coastal environments in spite of geographical distance. Multivariate statistical analyses indicated that the spatial distribution of the nirS-encoding bacterial assemblages is highly correlated with environmental factors, such as sediment silt content, NH4+ concentration, and OrgC/OrgN. The nirS-encoding bacterial assemblages in the most hypernutrified stations could be easily distinguished from that of the least eutrophic station. For the first time, the sedimentological condition was found to influence the structure and distribution of the sediment denitrifying bacterial community.

Two different proteases produced by a deep-sea psychrotrophic bacterial strain, Pseudoaltermonas sp SM9913

A psychrotrophic bacterial strain, Pseudoaltermonas sp. SM9913, was isolated from deep-sea sediment collected at 1,855 m depth. Two proteases produced by Pseudoaltermonas sp. SM9913 were purified, MPC-01 and MCP-02. MCP-01 is a serine protease with a molecular weight of 60.7 kDa. It is cold-adapted with an optimum temperature of 30-35degreesC. Its K-m and E-a for the hydrolysis of casein were 0.18% and 39.1 kJ mol(-1), respectively. It had low thermostability, and its activity was reduced by 73% after incubation at 40degreesC for 10 min. MCP-02 is a mesophilic metalloprotease with a molecular weight of 36 kDa. Its optimum temperature for the hydrolysis of casein was 50-55degreesC. The K-m and E-a of MCP-02 for the hydrolysis of casein were 0.36% and 59.3 kJ mol(-1), respectively. MCP-02 had high thermostability, and its activity was reduced by only 30.5% after incubation at 60degreesC for 10 min. At low temperatures, Pseudoaltermonas sp. SM9913 mainly produced the psychrophilic protease MCP-01.

Neural network retrieval of ocean surface parameters from SSM/I data

A new algorithm based on the multiparameter neural network is proposed to retrieve wind speed (WS), sea surface temperature (SST), sea surface air temperature, and relative humidity ( RH) simultaneously over the global oceans from Special Sensor Microwave Imager (SSM/I) observations. The retrieved geophysical parameters are used to estimate the surface latent heat flux and sensible heat flux using a bulk method over the global oceans. The neural network is trained and validated with the matchups of SSM/I overpasses and National Data Buoy Center buoys under both clear and cloudy weather conditions. In addition, the data acquired by the 85.5-GHz channels of SSM/I are used as the input variables of the neural network to improve its performance. The root-mean-square (rms) errors between the estimated WS, SST, sea surface air temperature, and RH from SSM/I observations and the buoy measurements are 1.48 m s(-1), 1.54 degrees C, 1.47 degrees C, and 7.85, respectively. The rms errors between the estimated latent and sensible heat fluxes from SSM/I observations and the Xisha Island ( in the South China Sea) measurements are 3.21 and 30.54 W m(-2), whereas those between the SSM/ I estimates and the buoy data are 4.9 and 37.85 W m(-2), respectively. Both of these errors ( those for WS, SST, and sea surface air temperature, in particular) are smaller than those by previous retrieval algorithms of SSM/ I observations over the global oceans. Unlike previous methods, the present algorithm is capable of producing near-real-time estimates of surface latent and sensible heat fluxes for the global oceans from SSM/I data.

Wave parameters retrieved from QuikSCAT data

A new algorithm is proposed to estimate significant wave height from QuikSCAT scatterometer data. The results show that the relationship between wave parameters and the radar backscattering cross section is similar to that between wind and the radar backscattering cross section. Therefore, the relationship between significant wave height and the radar backscattering cross section is established with a neural network algorithm. If the average wave period is less than or equal to 7 s, the root mean square errors of the significant wave height retrieved from QuikSCAT data are 0.58 m for HH polarization (HH-pol) and 0.60 m for VV polarization (VV-pol). If the average wave period is greater than 7 s, the root mean square errors of the significant wave height retrieved from QuikSCAT data are 0.83 m (HH-pol) and 1.10 m (VV-pol), respectively.

The responsive expression of heat shock protein 22 gene in zhikong scallop Chlamys farreri against a bacterial challenge

HSP22 is a member of a small HSP subfamily contributing to the growth, transformation and apoptosis of the cell as well as acting as a molecular chaperone. In the present study, CfHSP22 cDNA was cloned from Chlamys farreri by the rapid amplification of cDNA ends technique. The full-length cDNA of CfHSP22 was of 1279 bp, consisting of a 5'-terminal untranslated region (5'UTR) of 122 bp, a 3'UTR of 581 bp with a canonical polyadenylation signal sequence AATAAA and a poly( A) tail, and an open reading frame of 576 bp encoding a polypeptide with a molecular mass of 22.21 kDa and a predicted isoelectric point of 9.69. There was an alpha-crystallin domain, a hallmark of the sHSP subfamily, in the C-terminus, and the deduced amino acid sequence of CfHSP22 showed high similarity to previously identified HSP22s. CfHSP22 was constitutively expressed in the haemocyte, muscle, kidney, gonad, gill, heart and hepatopancreas, and the expression level in the hepatopancreas was higher than that in the other tissues. CfHSP22 transcription was up-regulated and reached a maximal level at 12 h after the bacterial challenge, and then declined progressively to the original level at 48 h. These results suggested that CfHSP22 perhaps play a critical role in response to the bacterial challenge in haemocytes of scallop C. farreri.

Distribution of calcifying and silicifying phytoplankton in relation to environmental and biogeochemical parameters during the late stages of the 2005 North East Atlantic Spring Bloom

The late stage of the North East Atlantic (NEA) spring bloom was investigated during June 2005 along a transect section from 45 to 66 degrees N between 15 and 20 degrees W in order to characterize the contribution of siliceous and calcareous phytoplankton groups and describe their distribution in relation to environmental factors. We measured several biogeochemical parameters such as nutrients, surface trace metals, algal pigments, biogenic silica (BSi), particulate inorganic carbon (PIC) or calcium carbonate, particulate organic carbon, nitrogen and phosphorus (POC, PON and POP, respectively), as well as transparent exopolymer particles (TEP). Results were compared with other studies undertaken in this area since the JGOFS NABE program. Characteristics of the spring bloom generally agreed well with the accepted scenario for the development of the autotrophic community. The NEA seasonal diatom bloom was in the late stages when we sampled the area and diatoms were constrained to the northern part of our transect, over the Icelandic Basin (IB) and Icelandic Shelf (IS). Coccolithophores dominated the phytoplankton community, with a large distribution over the Rockall-Hatton Plateau (RHP) and IB. The Porcupine Abyssal Plain (PAP) region at the southern end of our transect was the region with the lowest biomass, as demonstrated by very low Chla concentrations and a community dominated by picophytoplankton. Early depletion of dissolved silicic acid (DSi) and increased stratification of the surface layer most likely triggered the end of the diatom bloom, leading to coccolithophore dominance. The chronic Si deficiency observed in the NEA could be linked to moderate Fe limitation, which increases the efficiency of the Si pump. TEP closely mirrored the distribution of both biogenic silica at depth and prymnesiophytes in the surface layer suggesting the sedimentation of the diatom bloom in the form of aggregates, but the relative contribution of diatoms and coccolithophores to carbon export in this area still needs to be resolved.

Bacterial roles in the formation of high-molecular-weight dissolved organic matter in estuarine and coastal waters: Evidence from lipids and the compound-specific isotopic ratios

High-molecular-weight dissolved organic matter (HMW-DOM, > 1,000 Daltons) is actively involved in the global biogeochemical cycling of many elements, but its carbon sources and detailed formation pathways are still not well understood. In this study, we measured bulk stable carbon and nitrogen isotopic ratios, lipid composition, and compound-specific carbon isotopic ratios of HMW-DOM samples collected from four U.S. estuaries (Boston Harbor/Massachusetts Bay, Delaware/Chesapeake Bay, San Diego Bay, and San Francisco Bay). Analytical results show (1) a fraction of HMW-DOM (lipid associated) in estuarine and coastal waters is derived from bacteria and phytoplankton; (2) this fraction of HMW-DOM is formed by various release processes of bacterial membrane components and bacterial reworking of phytoplankton-derived material; (3) this fraction of HMW-DOM is generally present in all samples from different coastal systems despite variable organic matter inputs and environmental conditions, suggesting an important bacterial role in HMW-DOM formation.

STARVATION-INDUCED CHANGES OF HEMOCYTE PARAMETERS IN THE ZHIKONG SCALLOP CHLAMYS FARRERI

Substantial nutritional and energetic demands m-e associated with immune activation and the maintenance of an efficient immune system. One-year-old Chlamys farreri (Jones and Preston) scallops were maintained ill lantern nets ill different nutritional conditions (satiation and starvation) for 40 days. After the 40-day treatments, the condition index and the total hemocyte count (THC) decreased significantly in the starved group compared with the satiated and initial control groups. The percentage of phagocytic hemocytes also was significantly reduced with starvation. In contrast. no significant effect of starvation was observed oil reactive oxygen species (ROS) production. The acid phosphatase (ACP) activities in cell-free hemolymph increased significantly in scallops in starved and satiated treatments compared with the initial control. whereas ACP activity in hemocyte lysate was significantly lower ill the starved group. These results indicate that starvation stress compromises immunological activities of scallops.

Selective and specific detection of sulfate-reducing bacteria using potentiometric stripping analysis

A fast, sensitive and reliable potentiometric stripping analysis (PSA) is described for the selective detection of the marine pathogenic sulfate-reducing bacterium (SRB). Desulforibrio caledoiensis. The chemical and electrochemical parameters that exert influence on the deposition and stripping of lead ion, such as deposition potential, deposition time and pH value were carefully studied. The concentration of SRB was determined in acetate buffer solution (pH 5.2) under the optimized condition (deposition potential of -1.3 V. deposition time of 250 s, ionic strength of 0.2 mol L-1 and oxidant mercury (II) concentration of 40 mg L-1). A linear relationship between the stripping response and the logarithm of the bacterial concentration was observed in the range of 2.3 x 10 to 2.3 x 10(7) cfu mL(-1). In addition, the potentiometric stripping technique gave a distinct response to the SRB, but had no obvious response to Escherichia coli. The measurement system has a potential for further applications and provides a facile and sample method for detection of pathogenic bacteria. (C) 2010 Elsevier B.V. All rights reserved.

Short-term effect of targeted placements of sheep excrement on grassland in inner mongolia on soil and plant parameters

Grazing animal excrement plays an important role in nutrient cycling and redistribution in grazing ecosystems, due to grazing in large areas and return in small areas. To elucidate the changes to the soil and pasture caused by sheep urine, fresh dung, and compost patches, a short- term field experiment using artificially placed pats was set up in the autumn of 2003 in the Inner Mongolian steppe. Urine application significantly increased soil pH during the first 32 days in soil layers at depths of both 0 - 5 cm and 5 - 15 cm. Rapid hydrolysis of urea gave large amounts of urine- nitrogen ( N) as ammonium ( NH4+) in soil extracts and was followed by apparent nitrification from day 2. Higher inorganic N content in the urine- treated soil was found throughout the experiment compared with the control. No significant effects of sheep excrement on soil microbial carbon ( C) and soil microbial N was found, but microbial activities significantly increased compared with the control after application of sheep excrement. Forty- six percent of dung- N and 27% of compost- N were transferred into vegetation after the experiment. The results from this study suggest that large amounts of nutrients have been lost from the returned excrement patches in the degraded grassland of Inner Mongolia, especially from sheep urine- N.

油气、微生物与砂岩型铀矿形成关系研究——以东胜铀矿床和钱家店铀矿床为例

Sandstone-type uranium deposits are frequently found close to oil fields or uraniferous sandstones contain bitumen or petroleum. However, few evidence has been presented to indicate the association of uranium mineralization with petroleum oxidation. Thus, Dongsheng uranium deposit in Ordos Basin and Qianjiadian deposit in Kailu Basin are taken for examples to solve the puzzle. Integration data from sedimentary petrology, mineralogy, race elements geochemistry, isotope geochemistry and organic geochemistry, the uranium and petroleum sources, and diagenetic paragenesis of the host sandstone are analyzed, and then the genetic relationship between microbes, petroleum and uranium deposits are discussed. The observation under microscope shows that the host sandstone samples from Middle Jurassic Zhiluo Formation in the Dongsheng deposit contained different kinds of metamorphic rock fragments, which should have been derived form outcrops north to this basin. The LREE/HREE ratios of gneiss and amphibolite sampled from outcrops were close to the highest and the lowest LREE/HREE ratios of the sandstones with well-compared chondrite-normalized REE patterns, respectively. So these results consistently indicated that parent rocks of sandstones were mainly contributed from these two kinds of metamorphic rocks. There was very high Th/U ratio for granite gneiss, which was a mainly potential U resource. Hydrocarbon inclusions and adsorbed hydrocarbons are observed under fluorescence microscope in the host sandstone of Dongsheng uranium deposit, suggesting that the sandstones may have been utilized as oil migration pathways. Based on biomarker parameters, it is indicated that the inclusion oils and adsorbed hydrocarbons were marginally mature to mature, and were derived from humic-sapropel type organic matter under poor reducing freshwater to semi-saline environment. The features are similar to those of organic matter extracted from Triassic sandstone and source rock, but are different from that of cretaceous sandstone. Thus, it can be concluded that the inclusion oils and adsorbed hydrocarbons were mainly derived from Triassic lacustrine facies source rock. Observation results under Scanning Electron Microscopy and Electron Microprobe with Energy Spectrum Analysis show that, in Dongsheng area, the main uranium ore mineral is coffinite. The coffinite is intimately intergrown or coexists with pyrite and calcite, thus, the solution during mineralization stage is inferred to be alkaline. The alkaline environment is not favored for uranium to be pre-concentrated by absorption, and then be reduced abiogenetically. δ34S of pyrite and δ13C of calcite indicate that pyrite was formed by bacterial sulfate reduction (BSR) and part of the carbon of calcite has been dirived from oxidation of petroleum, respectively. Additionally, petroleum is found biodegraded. All the lines of evidence consistently indicate that petroleum was involved in uranium mineralization. Coffinite with microbe-like structures is found in the high U sandstone samples and is composed of nanoparticles, indicating the coffinite is biogenic. The conclusion are also supportted by laboratory experiment studies, which have shown that SRB are capable of utilizing U(VI) as the preferred electron acceptor for respiration and reduce U(VI) to U(IV) directly, coupled the oxidaton of organic matter and sulfate reduction. Based on the research results mentioned above, in the Dongsheng area, coffinite is likely to have formed by mixing of brine containing petroleum derived from Triassic with uranium-bearing meteoric water from outcrops north to Ordos Basin. SRB utilize hydrocarbon as carbon source, and directly reduce U(VI) resulting in precipitation of coffinite. The product of metabolism, H2S and CO2, was precipitated as pyrite and calcite during mineralization stage. Petroleum in fluid inclusions and adsorbed type in host sandstone from Lower Cretaceous Yaojia Formation in Qianjiadian uranium deposit, Kailu Basin, are derived from Jurassic Jiufotang Formation in this basin and the uranium mineral consists mainly of pitchblende. The δ34S and δ13C values of pyrite and calcite during mineralization stage indicate SRB have likely degraded petroleum, which is similar to that of Dongsheng deposit. The alkaline environment as indicated by the diagenetic mineral assemblage calcite, Fe dolomite, pyrite and pitchblende deposit suggests that U ore in the Qiangjiajiadian has a similar origin, i.e., direct reduction by SRB. However, less part of pitchblende is intergrown with kaolinite, suggesting the solution during mineralization stage is acidic. The environment is favorable for U(VI) to be adsorded on quartz or other mineral, and then reduced by H2S produced by SRB. Thus, it can be concluded that U(VI) reduction with petroleum oxidation by SRB and other microbes is an important ore-forming mechanism in petroleum-related sandstone-type uranium deposits. The finding is significant in that it provides a theoretical basis for exploration of both uranium and petroleumr.

富硫流体的成因与硫酸盐还原作用研究

Origins of H_2S, thiols, thiophenes in natural gases and sulphur-enriched oils are complicated and thus some debates exist on them. The post-doctoral research is based upon oil- and gas-field data. Cases for study include Triassic Jianglingjiang Formation natural gases, Wolonghe Field, Sichuan Basin, Paleozoic oils and bitumen, Central Tarim, gases reserviored nearby Carboniferious - Ordovician unconformity, Hetianhe Field, Tarim Basin and sulphur-enriched oils in Tertiary reserviors in Jinxian Sag, Bohai Bay Basin. We have carried out analyses on the oils and gases for chemistry, δ~(13)C, δ~(34)S, and molecular composition of biomarkers, analyzed authigenetic pyrite forδ~(34)S, formation water for chemistry and δD and δ~(18)O along with petroleum system and burial history analyses, The aims are to assess the origins of the H2S and authigenetic pyrite, to discuss the possibility of reduced sulphur incorporation into hydrocarbons and to determine the mechanisms of hydrocarbon secondary alteration in the above four cases by comparison. The research shows that the reduced sulphur in the four cases is the result of thermochemical and biological sulphate reduction., TSR and BSR, respectively. No evidence indicates an origin of decomposition of organic matter or mantle - derived H2S in the cases. Elevated H_2S contents (up to 32%) in the Triassic Jialingjiang Formation are considered to result from TSR while relatively low H_2S (up to 2000ppm) in the Hetianhe Field resulted from BSR. However, it is not the case for the Central Tarim where relatively low H2S but abundant authigenetic pyrite occurr. Part of the H_2S in the Central Tarim reservoirs has reacted with iron released from clay minerals to precipitate pyrite. Thus, reduced sulphur δ~(34)S and reservoir temperatures rather than the H2S amount are reliable parameters to distinguish between TSR and BSR. TSR in Sichuan Basin Triassic Jialingjiang Formation and Central Tarim Paleozoic reservoirs are showed to take place at more than 125℃. the H2S and authigenetic pyrite have δ~(34)S close to parent anhydrite. In contrast, BSR in the reservoirs near the Carboniferous - Ordovician unconformity in the Hetianhe Field and in the Tertiary in the Jinxian Sag took place at temperatures less than 80℃with sulphide δ~(34)S as light as -24.9‰ and -12.5‰, anhydrite δ~(34)S as heavy as +26‰and +3 5-+40‰, respectively. Chemistry and isotopic composition of the natural gases change as the result of sulphate reduction. It has been observed that relative composition of light hydrocarbon gases is changed along with a rise in H_2S and CO_2. TSR in the Triassic Jialingjiang Formation and BSR in the Hetianhe Field result in a greater degree of preferential depletion of methane than larger molecular hydrocarbon gases. As TSR or BSR proceeds, hydrocarbon gases evolved to heavier carbon isotope as the result of kinetic isotopic fractionation, i.e., selective anaerobic oxidation of ~(12)C. Using the model of residual methane (Whiticar, 1999) to describe the relationship among the proportion of methane oxidation, isotopic shift and fraction factor, about 30% methane is calculated to have been oxidized during BSR in the western part of the Hetianhe Field. From the above, it can be concluded that in the area where H_2S is abundant, empiricalδ~(13)C -Ro relationships do not work. Sulphate reduction results in a rise in sulphur content, gravity and viscosity of an oil as well as changes in δ~(13)C and δ~(34)S. On special conditions, the reduced sulphur from sulphates might be incorporated into oils, i.e., the increasing sulphur is derived from secondarily reduced sulphur. A positive correlative relationship exists between sulphur content and δ~(34)S in the oils in Paleozoic reservoirs in Central Tarim, indicating that enhanced sulphur is ~(34)S-enriched, originated from TSR. The Jinxian oil with the highest sulphur content has the lightest δ~(34)S, suggesting part of the sulphur in the oil is ~(34)S-depleted, originated from BSR. In the Jinxian oil with increasing sulphur content, asphaltenes shows higher content and more negative δ~(13)C, and saturates shows evidence of biodegradetion and a decreasing content and a positive δ~(13)C shift. Thus, asphaltenes have δ~(13)C values closer to saturates. All the above indicate that the reduced sulphur has been incorporated into biodegradated saturates to generate new asphaltenes with relatively light δ~(13)C of saturates. Thiols and thiophenes in natural gases in the Triassic Jialingjiang Formation may result from reaction of H_2S with hydrocarbon. In the Jialingjiang Formation hydrocarbon gases are dominated by methane thus have a high dryness coefficient and thiols are showed to be positively related to H_2S content, suggesting that the thiols may result from H_2S reaction with short chain hydrocarbons. In contrast, high thiophenes occur in wet gases in Jurassic reservoirs with their source rock from sulphur - depleted type I kerogen, indicating that thiophenes may be a product of reaction of H2S with longer chain hydrocarbons.