Investigations of Free Turbulent Mixing

A discussion of the integral relations for the flow of the boundary-layer type is presented. It is shown that the characteristic laws of spread of jets, wakes, and so forth, can be obtained directly for the laminar case and, with the help of dimensional reasoning, for the turbulent case as well. Measurements of the mean velocity, the intensity and scale of the turbulent fluctuations, and of the turbulent shear in a two-dimensional mixing zone are presented. The results of these measurements are compared with the mixing-length theories. It is shown that both mixing length and exchange coefficient vary across the mixing zone. The theories based on the assumption of constant mixing length or exchange coefficient are thus in error. A discussion of the energy balance of the fluctuating motion is given and the triple point correlation is estimated

Identification of juvenile hormone-active alkylphenols in the lobster Homarus americanus and in marine sediments

Author Posting. © Marine Biological Laboratory, 2004. This article is posted here by permission of Marine Biological Laboratory for personal use, not for redistribution. The definitive version was published in Biological Bulletin 206 (2004): 13-24.We have identified, by gas chromatography/mass spectrometry, four alkylphenols that are present in the hemolymph and tissues of the American lobster Homarus americanus and in marine sediments. These alkylphenols are used industrially in antioxidant formulations for plastic and rubber polymer manufacturing, and are similar in structure to a known endocrine disruptor, bisphenol A. The compound 2-t-butyl-4-(dimethylbenzyl)phenol was present at concentrations of 0.02 to 1.15 µg/ml in hemolymph and 8.95 to 21.58 µg/g in sediments. A second compound, 2,4-bis-(dimethylbenzyl)phenol, was present at concentrations between 0.07 and 19.78 µg/ml in hemolymph and 138.94 to 224.89 µg/g in sediment, while a third compound, 2,6-bis-(t-butyl)-4-(dimethylbenzyl)phenol, was found at concentrations between 0.01 and 13.00 µg/ml in hemolymph, 2.55 and 6.11 µg/g in hepatopancreas, and 47.85 and 74.66 µg/g in sediment. A fourth compound, 2,4-bis-(dimethylbenzyl)-6-t-butylphenol, was found at concentrations of 0.20 to 70.71 µg/ml in hemolymph, 23.56 to 26.89 µg/g in hepatopancreas, and 90.68 to 125.58 µg/g in sediment. These compounds, along with bisphenol A, 4-dimethylbenzylphenol, and nonylphenol, display high juvenile hormone activity in bioassays. Alkylphenols at high concentrations are toxic to crustaceans and may contribute significantly to lobster mortality; at lower concentrations, they are likely to have endocrine-disrupting effects.We gratefully acknowledge the Sea Grant College Program, NOAA, and the Connecticut Department of Environmental Protection for providing financial support for this research

The effect of alkylphenols on lobster shell hardening

Author Posting. © National Shellfisheries Association, 2012. This article is posted here by permission of National Shellfisheries Association for personal use, not for redistribution. The definitive version was published in Journal of Shellfish Research 31 (2012): 555-562, doi:10.2983/035.031.0215.Alkylphenols, anthropogenic estrogenic endocrine disruptors in vertebrates, have been found in lobsters (Homarus americanus) in New England sites. We hypothesize that alkylphenols interfere in the shell hardening during molting. We used an in vitro cuticle bioassay to investigate the effects of 2 alkylphenolic compounds—2,4-bis-(dimethylbenzyl) phenol (compound 3) and bisphenol A (BPA; 4,4′-dihydroxy-2,2-diphenylpropane (also referred to as 4,4′-(propan-2-ylidene) diphenol)) on tyrosine incorporation during the hardening of new cuticle following lobster molting. During sclerotization, both alkylphenols and cold tyrosine competed with C14-tyrosine incorporation in a concentration-dependent manner. This process was also phenoloxidase dependent, as treatment with phenylthiourea (PTU; a phenoloxidase inhibitor) significantly decreased C14-tyrosine incorporation. We also found that incorporation of C14-2,4-bis-(dimethylbenzyl) phenol during the shell hardening process was inhibited by cold alkylphenol, cold tyrosine, or PTU, and competition was concentration dependent. Furthermore, incorporation of tyrosine and derivatives into new cuticle decreased with time after molting from 27% incorporation 1 day after a molt to 6% by 4 days after a molt. In nonmolting cuticles, there was no incorporation of alkylphenol or tyrosine derivatives. When lobsters were injected with 2,4-bis-(dimethylbenzyl) phenol during the premolt stage, it took the shells 12 ± 1 days to harden sufficiently to resist deflection by 5 lb pressure exerted by a pressure gauge, compared with 7 ± 1 days for control shells. Thus, shell hardening is delayed significantly by the presence of 2,4-bis-(dimethylbenzyl) phenol. The effects of this compound on shell hardening may result in lobsters' susceptibility to microbial invasion and, therefore, may contribute to the onset of shell disease.This research was supported by the National Marine Fisheries Service as the New England Lobster Research Initiative: Lobster Shell Disease under NOAA grant NA06NMF4720100 to the University of Rhode Island Fisheries Center

Metabolic signature of breast cancer cell line MCF-7: profiling of modified nucleosides via LC-IT MS coupling

<p>Abstract</p> <p>Background</p> <p>Cancer, like other diseases accompanied by strong metabolic disorders, shows characteristic effects on cell turnover rate, activity of modifying enzymes and DNA/RNA modifications, resulting also in elevated amounts of excreted modified nucleosides. For a better understanding of the impaired RNA metabolism in breast cancer cells, we screened these metabolites in the cell culture supernatants of the breast cancer cell line MCF-7 and compared it to the human mammary epithelial cells MCF-10A. The nucleosides were isolated and analyzed via 2D-chromatographic techniques: In the first dimension by cis-diol specific boronate affinity extraction and subsequently by reversed phase chromatography coupled to an ion trap mass spectrometer.</p> <p>Results</p> <p>Besides the determination of ribonucleosides, additional compounds with cis-diol structure, deriving from cross-linked biochemical pathways, like purine-, histidine- and polyamine metabolism were detected. In total, 36 metabolites were identified by comparison of fragmentation patterns and retention time. Relation to the internal standard isoguanosine yielded normalized area ratios for each identified compound and enabled a semi-quantitative metabolic signature of both analyzed cell lines.</p> <p>13 of the identified 26 modified ribonucleosides were elevated in the cell culture supernatants of MCF-7 cells, with 5-methyluridine, <it>N</it>²,<it>N</it>²,7-trimethylguanosine, <it>N</it>⁶-methyl-<it>N</it>⁶-threonylcarbamoyladenosine and 3-(3-aminocarboxypropyl)-uridine showing the most significant differences. 1-ribosylimidazole-4-acetic acid, a histamine metabolite, was solely found in the supernatants of MCF-10A cells, whereas 1-ribosyl-4-carboxamido-5-aminoimidazole and S-adenosylmethionine occurred only in supernatants of MCF-7 cells.</p> <p>Conclusion</p> <p>The obtained results are discussed against the background of pathological changes in cell metabolism, resulting in new perspectives for modified nucleosides and related metabolites as possible biomedical markers for breast carcinoma <it>in vivo</it>.</p

Endocrine-disrupting alkylphenols are widespread in the blood of lobsters from southern New England and adjacent offshore areas

Author Posting. © National Shellfisheries Association , 2012. This article is posted here by permission of National Shellfisheries Association for personal use, not for redistribution. The definitive version was published in Journal of Shellfish Research 31 (2012): 563-571, doi:10.2983/035.031.0216.Endocrine-disrupting pollutants in rivers and oceans represent a poorly understood but potentially serious threat to the integrity of aquatic and coastal ecosystems. We surveyed the hemolymph of lobsters from across southern New England and adjacent offshore areas for 3 endocrine-disrupting alkylphenols. We found all 3 compounds in hemolymph from every year and almost every region sampled. Prevalence of contamination varied significantly between regions, ranging from 45% of lobsters from southern Massachusetts to 17% of lobsters from central Long Island Sound. Mean contamination levels varied significantly as a function of region, year sampled, and collection trip, and were highest overall in lobsters from western Long Island Sound and lowest in lobsters from central Long Island Sound. Surprisingly, lobsters from offshore areas were not less contaminated than lobsters from inshore areas. Contamination levels also did not vary as a function of lobster size or shell disease signs. Contaminated lobsters held in the laboratory did not retain alkylphenols, suggesting that hemolymph contamination levels represent recent, rather than long-term, exposure. Our data set is the first, to our knowledge, to survey endocrine-disrupting contaminants in a population across such a broad temporal and spatial scale. We show that alkylphenol contamination is a persistent, widespread, but environmentally heterogeneous problem in lobster populations in southern New England and adjacent offshore areas. Our work raises serious questions about the prevalence and accumulation of these endocrine-disrupting pollutants in an important fishery species.This work was supported by the National Marine Fisheries Service as the New England Lobster Research Initiative: Lobster Shell Disease under NOAA grant NA06NMF4720100 to the University of Rhode Island Fisheries Center

Glacial controls on redox-sensitive trace element cycling in Arctic fjord sediments (Spitsbergen, Svalbard)

Glacial meltwater is an important source of bioessential trace elements to high latitude oceans. Upon delivery to coastal waters, glacially sourced particulate trace elements are processed during early diagenesis in sediments and may be sequestered or recycled back to the water column depending on local biogeochemical conditions. In the glaciated fjords of Svalbard, large amounts of reactive Fe and Mn (oxyhydr)oxides are delivered to the sediment by glacial discharge, resulting in pronounced Fe and Mn cycling concurrent with microbial sulfate reduction. In order to investigate the diagenetic cycling of selected trace elements (As, Co, Cu, Mo, Ni, and U) in this system, we collected sediment cores from two Svalbard fjords, Van Keulenfjorden and Van Mijenfjorden, in a transect along the head-to-mouth fjord axis and analyzed aqueous and solid phase geochemistry with respect to trace elements, sulfur, and carbon along with sulfate reduction rates. We found that Co and Ni associate with Fe and Mn (oxyhydr)oxides and enter the pore water upon reductive metal oxide dissolution. Copper is enriched in the solid phase where sulfate reduction rates are high, likely due to reactions with H2S and the formation of sulfide minerals. Uranium accumulates in the solid phase likely following reduction by both Fe- and sulfate-reducing bacteria, while Mo adsorbs to Fe and Mn (oxyhydr)oxides in the surface sediment and is removed from the pore water at depth where sulfidization makes it particle-reactive. Arsenic is tightly coupled to Fe redox cycling and its partitioning between solid and dissolved phases is influenced by competition with FeS for adsorption sites on crystalline Fe oxides. Differences in trace element cycling between the two fjords suggest delivery of varying amount and composition of tidewater glacier (Van Keulenfjorden) and meltwater stream (Van Mijenfjorden) material, likely related to oxidative processes occurring in meltwater streams. This processing produces a partially weathered, more reactive sediment that is subject to stronger redox cycling of Fe, Mn, S, and associated trace elements upon delivery to Van Mijenfjorden. With climate warming, the patterns of trace element cycling observed in Van Mijenfjorden may also become more prevalent in other Svalbard fjords as tidewater glaciers retreat into meltwater stream valleys

The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals

The repertoire of small noncoding RNAs (sncRNAs), particularly miRNAs, in animals is considered to be evolutionarily conserved. Studies on sncRNAs are often largely based on homology-based information, relying on genomic sequence similarity and excluding actual expression data. To obtain information on sncRNA expression (including miRNAs, snoRNAs, YRNAs and tRNAs), we performed low-input-volume next-generation sequencing of 500 pg of RNA from 21 animals at two German zoological gardens. Notably, none of the species under investigation were previously annotated in any miRNA reference database. Sequencing was performed on blood cells as they are amongst the most accessible, stable and abundant sources of the different sncRNA classes. We evaluated and compared the composition and nature of sncRNAs across the different species by computational approaches. While the distribution of sncRNAs in the different RNA classes varied significantly, general evolutionary patterns were maintained. In particular, miRNA sequences and expression were found to be even more conserved than previously assumed. To make the results available for other researchers, all data, including expression profiles at the species and family levels, and different tools for viewing, filtering and searching the data are freely available in the online resource ASRA (Animal sncRNA Atlas) at https://www.ccb.uni-saarland.de/asra/

Large-scale validation of miRNAs by disease association, evolutionary conservation and pathway activity.

The validation of microRNAs (miRNAs) identified by next generation sequencing involves amplification-free and hybridization-based detection of transcripts as criteria for confirming valid miRNAs. Since respective validation is frequently not performed, miRNA repositories likely still contain a substantial fraction of false positive candidates while true miRNAs are not stored in the repositories yet. Especially if downstream analyses are performed with these candidates (e.g. target or pathway prediction), the results may be misleading. In the present study, we evaluated 558 mature miRNAs from miRBase and 1,709 miRNA candidates from next generation sequencing experiments by amplification-free hybridization and investigated their distributions in patients with various disease conditions. Notably, the most significant miRNAs in diseases are often not contained in the miRBase. However, these candidates are evolutionary highly conserved. From the expression patterns, target gene and pathway analyses and evolutionary conservation analyses, we were able to shed light on the complexity of miRNAs in humans. Our data also highlight that a more thorough validation of miRNAs identified by next generation sequencing is required. The results are available in miRCarta ( https://mircarta.cs.uni-saarland.de )

Sample return of interstellar matter (SARIM)

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