Top 10 Principles for Designing Healthy Coastal Ecosystems Like the Salish Sea

Like other coastal zones around the world, the inland sea ecosystem of Washington (USA) and British Columbia (Canada), an area known as the Salish Sea, is changing under pressure from a growing human population, conversion of native forest and shoreline habitat to urban development, toxic contamination of sediments and species, and overharvest of resources. While billions of dollars have been spent trying to restore other coastal ecosystems around the world, there still is no successful model for restoring estuarine or marine ecosystems like the Salish Sea. Despite the lack of a guiding model, major ecological principles do exist that should be applied as people work to design the Salish Sea and other large marine ecosystems for the future. We suggest that the following 10 ecological principles serve as a foundation for educating the public and for designing a healthy Salish Sea and other coastal ecosystems for future generations: (1) Think ecosystem: political boundaries are arbitrary; (2) Account for ecosystem connectivity; (3) Understand the food web; (4) Avoid fragmentation; (5) Respect ecosystem integrity; (6) Support nature’s resilience; (7) Value nature: it’s money in your pocket; (8) Watch wildlife health; (9) Plan for extremes; and (10) Share the knowledge.     

Data on the adult marine and migratory phases in the life cycle of the southern hemisphere lamprey,Geotria australis Gray

Synopsis Large numbers of the Southern Hemisphere lamprey, Geotria australis, have been found in the regurgitated food of albatrosses breeding on South Georgia. This finding suggests that this lamprey is found in large groups at sea, presumably associated with its host, and can travel very large distances from its natal streams. The length and morphology of the individuals from South Georgia, which almost certainly represent a South American stock, were compared with those of representatives of the immediately pre- and post-marine trophic stages of G. australis caught in Western Australia. No significant differences could be detected either in the number of trunk myomeres or in the number and arrangement of the teeth. The mean length of the animals (± 95% confidence limits) from South Georgia was 45.9 ± 0.90 cm compared with 10.0 ± 0.23 cm and 62.5 ± 0.85 cm in G. australis collected from Western Australia just before they had entered and returned from the sea respectively.     

Estrogenic regulation of uterine cyclic amp metabolism

Ovariectomized and ovariectomized, estrogen-treated (48 h) rats were injected intravenously with increasing doses of epinephrine. Uteri were frozen in situ 30 s later. Estrogen pre-treatment significantly increased the sensitivity of both cyclic AMP and phosphorylase to epinephrine. The cyclic AMP response to intravenous injection of the pure β-agonist, isoproterenol, was enhanced by estrogen pre-treatment (48 h) and the cyclic AMP response of isolated uteri treated with epinephrine in vitro was also enhanced by in vivo estrogen pre-treatment (48 h). Other groups of ovariectomized rats were treated with estrogen and cyclic AMP levels were estimated at various times after estrogen treatment. 6 h after intraperitoneal injection and 48 h after subcutaneous injection, estrogen caused 20 and 30% increases in cyclic AMP. Estrogen had no effect on cyclic AMP 30 s after intravenous injection or 15 min after intraperitoneal injection. The was also no change in uterine catecholamine sensitivity 30 s after intravenous estrogen injection.The uterine site(s) at which estrogen acts to alter uterine cyclic AMP metabolism could be uterine β-adrenergic receptors, adenyl cyclase, and/or phosphodiesterase.     

Isocratic separation of estrogen conjugates on DEAE-sephadex.

Mixtures of estrogen conjugates containing estrone-3-glucosiduronate, 17β-estradiol-3-glucosiduronate, 17β-estradiol-17-glucosiduronate, estrone-3-sulfate and 17β-estradiol-3-sulfate have been separated on DEAE-Sephadex resin by isocratic elution using NaCI concentrations ranging from 0.05M to 0.4M. The results indicate that an NaCI gradient is not necessary for the Chromatographic separation of these estrogen conjugates. An NaCl concentration of 0.05M was adequate to separate the various monoglucosiduronates and sulfates. Isocratic elution of the columns with or without a possible stepup in the salt concentration was shown to give a higher resolution of estrogen conjugates in a more convenient volume than a gradient elution. For ideal chromatography of estrogen conjugates on a DEAE-Sephadex column, isocratic elution with 0.05 or 0. IM NaCl is preferred for the separation of monoglucosiduronates and 0.2 or 0.25M NaCl for the separation of sulfate conjugates. Contrary to current expectations, the molarity at which a particular conjugate elutes in a gradient mode does not bear a consistent relationship to the structure of the conjugate. However, the holdback volume in the isocratic mode may be used for identification purposes. When holdback volume was plotted against molarity, separate curves were obtained for each of the above mentioned conjugates. Tests of fit were carried out using a number of models. The best fit was obtained using the simple model $\text{y}\text{=}\text{a}\text{+}\text{b}\text{1}\text{x}$ where the independent variable, x, is the molarity; the dependent variable, y, is the volume and a and b are the intercept and slope respectively. Each curve fitted the model, but the values for a and b were significantly different. Using this model, a simple and predictable relationship between molarity and holdback volume can be demonstrated for each of the estrogen conjugates. The advantages of the isocratic mode of elution over gradient elution are discussed.     

Binding of terbium(III) to yeast enolase

Several independent criteria indicate 2 mol of terbium(III) bind to yeast enolase in the absence of substrate-fluorescence titrations of enzyme and metal, effects on thermal stability and published ultrafiltration and inhibition experiments. These measurements also suggest the terbium binding sites are the same as those normally occupied by “conformational” magnesium. Terbium binds much more strongly than magnesium, however, and measurements of the kinetics of the absorbance change in the terbium-enzyme on adding excess EDTA suggest the terbium-enzyme dissociation constant is about $\text{1}\text{500}$ that of the magnesium-enzyme. Measurements of enzyme activity as a function of substrate concentration show that terbium permits no enzymatic activity. However, magnesium competes more effectively with the lanthanide if the substrate analogue 3-aminoenolpyruvate 2-phosphate (AEP) is present.The fluorescence of the lanthanide is not readily observed on exciting the terbium-enzyme at 280 nm, indicating the absence of tyrosines or tryptophans in the coordination sphere of the metal. Excitation of terbium using 488 nm radiation from an argon ion laser shows the fluorescence of the metal is enhanced by binding to the enzyme. EDTA and carbonate have similar effects. This suggests carboxyl groups are involved in binding metal at the conformational sites of yeast enolase. Measurements of lifetimes of enzyme-bound terbium in the presence and absence of D₂O indicated three moles of water remained on each of the bound metals, independently of the buffer used. If enzyme-bound terbium is assumed to be nine-coordinate, the metal must bind to six groups from the enzyme. The presence of substrate does not markedly affect the emission spectrum of the bound terbium or the number of water molecules remaining on the metal, but calorimetric measurements show that substrate binds to the terbium enzyme.     

Geographic and genetic boundaries of brown bear (Ursus arctos) population in the Caucasus

The taxonomic status of brown bears in the Caucasus remains unclear. Several morphs or subspecies have been identified from the morphological (craniological) data, but the status of each of these subspecies has never been verified by molecular genetic methods. We analysed mitochondrial DNA sequences (control region) to reveal phylogenetic relationships and infer divergence time between brown bear subpopulations in the Caucasus. We estimated migration and gene flow from both mitochondrial DNA and microsatellite allele frequencies, and identified possible barriers to gene flow among the subpopulations. Our suggestion is that all Caucasian bears belong to the nominal subspecies of Ursus arctos. Our results revealed two genetically and geographically distinct maternal haplogroups: one from the Lesser Caucasus and the other one from the Greater Caucasus. The genetic divergence between these haplogroups dates as far back as the beginning of human colonization of the Caucasus. Our analysis of the least‐cost distances between the subpopulations suggests humans as a major barrier to gene flow. The low genetic differentiation inferred from microsatellite allele frequencies indicates that gene flow between the two populations in the Caucasus is maintained through the movements of male brown bears. The Likhi Ridge that connects the Greater and Lesser Caucasus mountains is the most likely corridor for this migration.     

Species identification and likely catch time period of whale bones from South Georgia

Skeletal remains of baleen whales killed during the onset of 20th century commercial whaling lie scattered across the shores and abandoned whaling stations of the subantarctic island of South Georgia. Here we report on genetic species identification of whale bones collected from South Georgia using standard historical DNA protocols. We amplified and sequenced short fragments of the mitochondrial DNA (mtDNA) control region from 281 available bone samples. Of these, 231 provided mtDNA sequences of sufficient quality and length (174–194 bp) for species identification: 158 bones were identified as humpback whale (Megaptera novaeangliae), 51 bones were identified as fin whale (Balaenoptera physalus), 18 bones were identified as blue whale (B. musculus), two bones were identified as sei whale (B. borealis), one bone was identified as a southern right whale (Eubalaena australis), and one bone was identified as a southern elephant seal (Mirounga leonina). The prominence of humpback, fin, and blue whale bones in the sample collection corresponds to the catch record of the early years of whaling on the island of South Georgia (pre‐1915), prior to the depletion of these populations.     

Nucleotide sequence analysis of a gene encoding a streptomycin/spectinomycin adenylyltransferase

The nucleotide sequence of 1400 bp from R-plasmid R538-1 containing the streptomycin/spectinomycin adenyltransferase gene (aadA) was determined, and the location of the aadA gene was identified by a combination of insertion and deletion mutants. Its gene product, aminoglycoside 3"-adenylyltransferase (AAD(3")(9), has a Mr of 31,600.     

Optimizing multiplex SNP-based data analysis for genotyping of Mycobacterium tuberculosis isolates

Background

Multiplex ligation-dependent probe amplification (MLPA) is a powerful tool to identify genomic polymorphisms. We have previously developed a single nucleotide polymorphism (SNP) and large sequence polymorphisms (LSP)-based MLPA assay using a read out on a liquid bead array to screen for 47 genetic markers in the Mycobacterium tuberculosis genome. In our assay we obtain information regarding the Mycobacterium tuberculosis lineage and drug resistance simultaneously. Previously we called the presence or absence of a genotypic marker based on a threshold signal level. Here we present a more elaborate data analysis method to standardize and streamline the interpretation of data generated by MLPA. The new data analysis method also identifies intermediate signals in addition to classification of signals as positive and negative. Intermediate calls can be informative with respect to identifying the simultaneous presence of sensitive and resistant alleles or infection with multiple different Mycobacterium tuberculosis strains.

Results

To validate our analysis method 100 DNA isolates of Mycobacterium tuberculosis extracted from cultured patient material collected at the National TB Reference Laboratory of the National Center for Tuberculosis and Lung Diseases in Tbilisi, Republic of Georgia were tested by MLPA. The data generated were interpreted blindly and then compared to results obtained by reference methods. MLPA profiles containing intermediate calls are flagged for expert review whereas the majority of profiles, not containing intermediate calls, were called automatically. No intermediate signals were identified in 74/100 isolates and in the remaining 26 isolates at least one genetic marker produced an intermediate signal.

Conclusion

Based on excellent agreement with the reference methods we conclude that the new data analysis method performed well. The streamlined data processing and standardized data interpretation allows the comparison of the Mycobacterium tuberculosis MLPA results between different experiments. All together this will facilitate the implementation of the MLPA assay in different settings.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-572) contains supplementary material, which is available to authorized users.