Histological techniques for marine bivalve mollusks and crustaceans, 2nd edition

Investigators at the Cooperative Oxford Laboratory (COL) diagnose and study crustaceans, mollusks, finfish, and a variety of other marine and estuarine invertebrates to assess animal health. This edition updates the Histological Techniques for Marine Bivalve Mollusks manual by Howard and Smith (1983) with additional chapters on molluscan and crustacean techniques. The new edition is intended to serve as a guide for histological processing of shellfish, principally bivalve mollusks and crustaceans. Basically, the techniques included are applicable for histopathological preparation of all marine animals, recognizing however that initial necropsy is unique to each species. Photographs and illustrations are provided for instruction on necropsy of different species to simplify the processing of tissues. Several of the procedures described are adaptations developed by the COL staff. They represent techniques based on principles established for the histopathologic study of mammalian and other vertebrate tissues, but modified for marine and aquatic invertebrates. Although the manual attempts to provide adequate information on techniques, it is also intended to serve as a useful reference source to those interested in the pathology of marine animals. General references and recommended reading listed in the back of the manual will provide histological information on species not addressed in the text.

Nutrient loading and eutrophication of coastal waters of the South Asian Seas: a scoping study

This study looked at nutrient pollution and how it is affecting coastal and marine ecosystems in Bangladesh, India, Maldives, Pakistan and Sri Lanka. Causes it addressed included: agricultural practices; aquaculture; domestic sewage; industrial actions; and the burning of fossil fuels.

Preparation and characterization of a novel macrocyclic ligand—dinitro-tetraazacyclotetradeca-tetraene—and application as a highly selective extractant for copper(II)

A novel tetraaza macrocyclic Schiff base ligand, 6,13-dinitro-5,7,12,14-tetramethyl-1,4,8,11-tetraazacyclotetradeca-1,5,7,-12-tetraene, was prepared and its copper(II) and nickel(II) complexes were characterized. This ligand was found to be an excellent extractant for copper(II).

Synthesis, crystal structure, spectroscopy and electroluminescence of zinc(II) complexes containing bidentate 2-(2-pyridyl)quinoline derivative ligands

Three bidentate ligands, 4-phenyl-2-(2-pyridyl)-quinoline (ppq), 6-(carbazol-9-yl)-4-phenyl-2-(2-pyridyl)-quinoline (cpq) and 6-diphenylamino-4-phenyl-2-(2-pyridyl)-quinoline (dpq) and their zinc(II) complexes, have been designed and synthesized. The crystal structure of [Zn(ppq)(2)Cl]PF6 shows that the central zinc atom is coordinated with one chloride and four nitrogen atoms from two ligands. The introduction of an electron-donating substituent such as carbazole or an aromatic amine group at the 6-position of the quinoline moiety can generate colored tunable Zn complexes, and the photoluminescence (PL) wavelength was modulated from 418 nm for [Zn(ppq)(2)Cl]PF6 to 591 nm for [Zn(cpq)(2)Cl]PF6 and 638 nm for [Zn(dpq)(2)Cl]PF6 in CH2Cl2 solution. The electroluminescence spectrum of [Zn(dpq)(2)Cl]PF6 exhibits pure red light emission with the Commission Internationale de L'Eclairage (CIE) coordinates (0.63, 0.36) and a maximum at 648 nm.

Electrochemical and in situ spectroelectrochemical behavior of 2,3,7,8,12,13,17,18-octakis(hexyl-thio) tetraazaporphyrin (H(2)OHTTAP) and (Zn(II)OHTTAP)

The characterization of free base porphyrin 2,3,7,8,12,13,17,18-octakis(hexyl-thio) tetraazaporphyrin (H(2)OHTTAP) and its zinc(II) complexes [Zn(II)OHTTAP] containing eight thioether groups at the beta -pyrrole positions of the macrocycle was reported. Results obtained by cyclic voltammetry and differential pulse voltammetry indicated a five-electron reduction in five steps for each complex. They were oxidized in two single-electron-transfer steps to yield pi -cation radicals and dications and reduced in three single-electron-transfer steps to yield pi -anion radicals, dianions and trianions, respectively. The redox property of H(2)OHTTAP was unusual as compared to porphyrins (PPs) and phthalocyanines (Pcs). Each process was monitored by in situ thin-layer spectroelectrochemistry, which indicated that only the Ligand was electroactive. The existence of the eight hexylthio groups was responsible for the intrastack interactions and enhanced intracolumnar and intercolumnar electron motions, resulting in improved conductivity. Copyright (C) 2001 John Wiley & Sons, Ltd.

Isolation and characterization of the oxygen-evolving photosystem II complex from the economical red alga Bangia fusco-purpurea

The highly pure and active photosystem II (PSII) complex was isolated from Bangia fusco-purpurea (Dillw) Lyngb., an important economic red alga in China, through two steps of sucrose density gradient ultracentrifugation and characterized by the room absorption and fluorescence emission spectra, DCIP (2,6-dichloroindophenol) reduction, and oxygen evolution rates. The PSII complex from B. fusco-purpurea had the characteristic absorption peaks of chlorophyll (Chl) a (436 and 676 nm) and typical fluorescence emission peak at 685 nm (Ex = 436 nm). Moreover, the acquired PSII complex displayed high oxygen evolution (139 mu mol O-2/(mg Chl h) in the presence of 2.5 mM 2,6-dimethybenzoqinone as an artificial acceptor and was active in photoreduction of DCIP (2,6-dichloroindophenol) by DPC (1,5-diphenylcarbazide) at 163 U/(mg Chl a h). SDS-PAGE also suggested that the purified PSII complex contained four intrinsic proteins (D1, D2, CP43, and CP47) and four extrinsic proteins (33-kD protein, 20-kD protein, cyt c-550, and 14-kD protein).

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.

Sources and preservation of organic matter in Plum Island salt marsh sediments (MA, USA): long-chain n-alkanes and stable carbon isotope compositions

Elemental (TOC, TN, C/N) and stable carbon isotopic (delta(13)C) compositions and n-alkane (nC(16-38)) concentrations were measured for Spartina alterniflora, a C-4 marsh grass, Typha latifolia, a C-3 marsh grass, and three sediment cores collected from middle and upper estuarine sites from the Plum Island salt marshes. Our results indicated that the organic matter preserved in the sediments was highly affected by the marsh plants that dominated the sampling sites. delta(13)C values of organic matter preserved in the upper fresh water site sediment were more negative (-23.0+/-0.3) as affected by the C-3 plants than the values of organic matter preserved in the sediments of middle (-18.9+/-0.8) and mud flat sites (-19.4+/-0.1) as influenced mainly by the C4 marsh plants. The distribution of n-alkanes measured in all sediments showed similar patterns as those determined in the marsh grasses S. alterniflora and T. latifolia, and nC(21) to nC(33) long-chain n-alkanes were the major compounds determined in all sediment samples. The strong odd-to-even carbon numbered n-alkane predominance was found in all three sediments and nC(29) was the most abundant homologue in all samples measured. Both delta(13)C compositions of organic matter and n-alkane distributions in these sediments indicate that the marsh plants could contribute significant amount of organic matter preserved in Plum Island salt marsh sediments. This suggests that salt marshes play an important role in the cycling of nutrients and organic carbon in the estuary and adjacent coastal waters. (C) 2003 Elsevier Ltd. All rights reserved.

Historical changes in nutrient structure and its influences on phytoplantkon composition in Jiaozhou Bay

Due to the influence of human activities, nutrient concentrations, nutrient ratios and phytoplankton composition have notably changed in Jiaozhou Bay, China since the 1960s. From the 1960s to the 1990s, nutrient concentrations have increased 1.4 times for PO4-P, 4.3 times for NO3-N, 4.1 times for NH4-N and 3.9 times for DIN. The atomic ratio of DIN:PO4-P increased very rapidly from 15.9 +/- 6.3 for the 1960s, to 37.8 +/- 22.9 for the 1990s. SiO3-Si concentration has remained at a very low level from the 1980s to the 1990s. The high ratio of DIN: PO4-P and low ratios of SiO3-Si:PO4-P (7.6 +/- 8.9) and SiO3-Si:DIN (0.19 +/- 0.15) showed the nutrient structure of Jiaozhou Bay has changed from more balanced to unbalanced during the last 40 years. The possibility that DIN and/or PO4-P as limiting factors of Jiaozhou Bay phytoplankton has been lessened or eliminated and that of SiO3-Si limiting has been increased. The changes in nutrient structure may have led to the decrease of large diatoms and a shift of phytoplankton species composition. It is likely that there is a trend from large diatoms to smaller cells in Jiaozhou Bay. (C) 2001 Academic Press.

Summertime ciliate and copepod nauplii distributions and micro-zooplankton herbivorous activity in the Laizhou Bay, Bohai Sea, China

The abundance and biomass of ciliated protozoa and copepod nauplii were investigated at 21 grid stations and two anchored stations in the Laizhou Bay, Bohai Sea, China in June 1998. Dilution incubations were carried out to investigate micro-zooplankton grazing pressure at the anchored stations during spring tide and neap tide. The dominant species were Tintinnopsis amoyensis, T. chinglanensis, T. pallida and aloricate ciliates. A total of 13 species of tintinnids were found. The total abundance of ciliates and nauplii ranged from 30 to 2390 ind l(-1) at grid stations. Tintinnopsis amoyensis was the only ciliate found at the anchored stations and in concentrations which varied from 0 to 6700 ind l(-1). The spatial distribution of ciliates was patchy. Tintinnopsis amoyensis and T. pallida were distributed in the Weihe River mouth and Xiaoqinghe River mouth respectively. The aloricate ciliates, T. chinglanensis and Codonellopsis ostenfeldi dominated offshore in sequence. The water mixing process may affect the spatial pattern of the dominant ciliate species. The abundance and biomass of copepod nauplii were in the range of 0-140 ind l(-1) and 0-7 mu g C l(-1) respectively, with the peak appearing at grid station 15. The total biomass of ciliates and copepod nauplii was in the range of 1(.)5-25 mu g C l(-1). Water column biomass of ciliates and nauplii varied from 2(.)37 to 52(.)3 mg C m(-2). At the anchored stations, the phytoplankton growth rates ranged from undetectable to 0 21 d(-1) and micro-zooplankton grazing rates from 0 13 to 0(.)57 d(-1). The grazing pressure of micro-zooplankton were 12 to 43% of the chlorophyll standing stock and 84 to 267% of the chlorophyll (C) 2000 Academic Press.

Preliminary study of the dynamic origin of the distribution pattern of bottom sediments on the continental shelves of the Bohai Sea, Yellow Sea and East China Sea

The bottom sediment types in the Bohai Sea, Yellow Sea and East China Sea (BYECS) are diversified, and their distribution pattern is very complicated. However, the bottom sediment types can be simplified to be sandy sediment, clayey sediment and mixed sediment, which comprise the complicated distribution pattern of bottom sediment in the BYECS. The continental shelves of the BYECS are broad, with shallow water depths and tidal currents which are permanent and dominate the marine dynamics in the BYECS. Based on numerical simulation of tidal elevations and currents in the BYECS, the rates of suspended load transport and bed load transport during a single tidal cycle for sediments of eight different grain size ranges are calculated. The results show that any sediment, whose threshold velocity is less than that of tidal current, has the same transport trend. Suspended load transport rare, bed load transport rate, and the ratio of the former to the latter decrease with grain size becoming coarser and coarser. The erosion/accretion patterns of sediments with different grain sizes are determined by the sediment transport rate divergences, and the results show that the patterns are the same for sediments with different grain sizes. Three main bottom sediment types, i.e. sandy sediment mainly composed of fine sand, clayey sediment mainly composed of silty clay, and mixed sediment mainly composed of fine sand, silt, and clay, are obtained by computation. The three bottom sediment types and their distribution pattern are consistent not only with sediment transport field and the sea bed erosion/accretion pattern obtained by simulation, but also with field data of bottom sediment types and divisions. In the BYECS, sand ridges form mainly in the areas with strong rectilinear tidal currents, sand sheets form mainly in the areas dominated by strong rotatory tidal currents, and clayey sediments, i.e. mud patches, form mainly in the areas with weak tidal currents. Hence, not only the sandy sediments but also the clayey sediments in the BYECS are formed under the control of the whole tidal current field of the BYECS. The three main bottom sediment types are not isolated respectively-in fact, they constitute a whole tidal depositional system. Under the condition with no cyclonic cold eddy, the clayey sediments in the BYECS can form in weak tidal current environments. Therefore, a cold eddy is not necessary for the deposition of clayey sediments in the BYECS. (C) 2000 Academic Press.

Transfer and transport of phosphorus and silica in the turbidity maximum zone of the Changjiang estuary

The concentration of suspended particulate matter (SPM), sedimentation flux, and various forms of phosphorus and silica in turbidity maximum zone (TMZ) in the Changjiang (Yangtze) estuary was studied. Based on the budget of P and Si, their mass balances in the TMZ were calculated. Results show that the variation in concentration of dissolved inorganic silicon (DISi) was mainly controlled by seawater dilution, while that of dissolved inorganic phosphor-us (DIP) was considerably affected by the buffering of suspended matter and sediment. Our experiments showed that the sedimentation fluxes of SPM and particulate inorganic phosphorus (PIP), total particulate phosphorus (TPP), particulate inorganic silicon (PISi), and biological silicon (BSi) in the TMZ were 238.4 g m(-2) d(-1) and 28.3, 43.1, 79.0, 63.0 mg m(-2) d(-1), respectively. In addition, a simple method to estimate the ratio of resuspension of sediment in the TMZ was established, with which the rate in surface and bottom waters of the TMZ accounted for 55.7 and 66.1% of the total SPM, respectively, indicating that the sediment resuspension in the TMZ influenced significantly the mass balances of P and Si. Particulate adsorbed P (60.8%) and 35.5% of total particulate P discharged from the river were filtered and then deposited in the TMZ. The input flux of PIP from the river mouth was 55.9% of that of DIP, being important as biologically available P, while that of PISi was only 3.5% of DISi, showing that particulate adsorbed Si was much less important than particulate adsorbed P. (c) 2008 Elsevier Ltd. All rights reserved.

Seasonal and spatial variation in abundance and egg production of Paracalanus parvus (Copepoda: Calanoida) in/out Jiaozhou Bay, China

The spatial distribution of stage-specific abundance and reproduction of the copepod Paracalanus parvus were studied from October 2005 to September 2006 in the Jiaozhou Bay. This copepod occurred continuously in this bay throughout the year. The species reached the lowest abundance in April and peaked in June. From October to December, distribution center mainly occurred in offshore water and at the mouth of the bay. In winter, early copepodites and adults gradually decreased and till February, most of the population was only comprised of CIV-CV stages. Overwintering copepodites matured in March and males tended to mature before female. From May to September, each stage occurred in the population and gradually reached high abundance. Temperature and chlorophyll a (Chl-a) concentration in the three stations can't clearly explain the seasonal variation in stage-specific abundance, so we surmised the important effect of the Yellow Sea. Egg production rate (EPR) reached its lowest in winter and peaked in June at 60.8 eggs female(-1) day(-1) in nearshore water. In the warming period, EPR in nearshore water was statistically higher and EPR > 10 eggs female(-1) day(-1) lasted longer than that in offshore water, showing the importance of nearshore water for recruitment of R parvus. Our study showed that EPR was positively related to temperature and total chlorophyll a in offshore water and mouth of the bay. In nearshore water, the relationships between EPR and temperature and Chl-a in three size fractions were not the same as those in offshore water, suggesting complicated ecosystem in such a eutrophic area in warming period. (C) 2008 Elsevier Ltd. All rights reserved.

Nutrient structure of seawater and ecological responses in Jiaozhou Bay, China

Nutrient concentrations in seawater, and C, N, P, Si and chlorophyll a content in different-sized particulates were measured in Jiaozhou Bay, and C, N, P, Si composition in different-sized fractions of phytoplankton and their ecological responses to nutrient structure of the seawater were studied. Microphytoplankton and nanophytoplankton were dominant in Jiaozhou Bay. High C (16.50-20.97 unol L-1), N (2.46-2.99 mu mol L-1) and low P (0.06-0.12 mu mol L-1), Si (0.18-0.57 mu mol L-1) content, and high N/P (24.7-64.6) and low SUP (4.4-10.8), Si/N (0.06-0.20) ratios were found in all sized groups of particulates. These values reflected the elemental compositions of different-sized fractions of phytoplankton as being an ecological response to the nutrients in the seawater. The ratios deviated significantly from the Redfield values. The nutrient composition of seawater and particulates and their relationship to chlorophyll a showed that phytoplankton growth was possibly limited by Si. Si limitation appears favorable for controlling the ecological equilibrium of Jiaozhou Bay. Different-sized fractions of phytoplankton had different suitability to nutrient structures of the seawater. Among phytoplankton size groups, nanophytoplankton and microphytoplankton growths were more adaptable in eutrophic Jiaozhou Bay, and more competitive for assimilation of Si. This is consistent with their diatom-dominated composition, controlling the biomass and productivity of phytoplankton in Jiaozhou Bay. (c) 2006 Elsevier Ltd. All rights reserved.

Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler.

BACKGROUND: The rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many of the most pathogenic viruses in humans. There are two bat genome projects currently underway, a circumstance that promises to speed the discovery host factors important in the coevolution of bats with their viruses. These genomes, however, are not yet assembled and one of them will provide only low coverage, making the inference of most genes of immunological interest error-prone. Many more wildlife genome projects are underway and intend to provide only shallow coverage. RESULTS: We have developed a statistical method for the assembly of gene families from partial genomes. The method takes full advantage of the quality scores generated by base-calling software, incorporating them into a complete probabilistic error model, to overcome the limitation inherent in the inference of gene family members from partial sequence information. We validated the method by inferring the human IFNA genes from the genome trace archives, and used it to infer 61 type-I interferon genes, and single type-II interferon genes in the bats Pteropus vampyrus and Myotis lucifugus. We confirmed our inferences by direct cloning and sequencing of IFNA, IFNB, IFND, and IFNK in P. vampyrus, and by demonstrating transcription of some of the inferred genes by known interferon-inducing stimuli. CONCLUSION: The statistical trace assembler described here provides a reliable method for extracting information from the many available and forthcoming partial or shallow genome sequencing projects, thereby facilitating the study of a wider variety of organisms with ecological and biomedical significance to humans than would otherwise be possible.