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Search Results: 1 - 10 of 119720 matches for " Nina T. Mikkelsen "
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Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity
Achim Meyer, Christiane Todt, Nina T Mikkelsen, Bernhard Lieb
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-70
Abstract: We report here the first authentic 18S genes of three Solenogastres species (Mollusca), each possessing a unique sequence composition with regions conspicuously rich in guanine and cytosine. For these GC-rich regions we calculated strong secondary structures. The observed high intra-molecular forces hamper standard amplification and appear to increase formation of chimerical sequences caused by contaminating foreign DNAs from potential prey organisms. In our analyses, contamination was avoided by using RNA as a template. Indication for contamination of previously published Solenogastres sequences is presented. Detailed phylogenetic analyses were conducted using RNA specific models that account for compensatory substitutions in stem regions.The extreme morphological diversity of mollusks is mirrored in the molecular 18S data and shows elevated substitution rates mainly in three higher taxa: true limpets (Patellogastropoda), Cephalopoda and Solenogastres. Our phylogenetic tree based on 123 species, including representatives of all mollusk classes, shows limited resolution at the class level but illustrates the pitfalls of artificial groupings formed due to shared biased sequence composition.The small subunit (SSU) 18S rRNA gene is one of the most frequently used genes in phylogenetic studies (see below) and an important marker for random target PCR in environmental biodiversity screening [1]. In general, rRNA gene sequences are easy to access due to highly conserved flanking regions allowing for the use of universal primers [2]. Their repetitive arrangement within the genome provides excessive amounts of template DNA for PCR, even in smallest organisms. The 18S gene is part of the ribosomal functional core and is exposed to similar selective forces in all living beings [3]. Thus, when the first large-scale phylogenetic studies based on 18S sequences were published - first and foremost Field et al.'s [4] phylogeny of the animal kingdom - the gene was celebrated as the
Falcidens sagittiferus Salvini-Plawen, 1968: additional data on
Dimitry L. Ivanov,Nina T. Mikkelsen,Christoffer Schander
Fauna Norvegica , 2010, DOI: 10.5324/fn.v29i0.610
Abstract: Ivanov DL, Mikkelsen NT, Schander C. 2009. Falcidens sagittiferus Salvini-Plawen, 1968: additional data on morphology and distribution (Mollusca, Aplacophora, Caudofoveata). Fauna Norvegica vol 29: 3-9. Falcidens sagittiferus Salvini-Plawen, 1968 is a species of caudofoveate (Chaetodermomorpha) not uncommon in southern Scandinavia. Previous descriptions have however been based mainly on fixed material, and illustrations of sclerites and radula have been incomplete. We here present data from an investigation based on over 70 specimens from Norway (including the type material). Radula, sclerites and living specimens are illustrated.
Lipothymia and Syncope—Aetiology and Outcome in a Prehospital Setting: A Retrospective Study
Stine T. Zwisler,S?ren Mikkelsen
ISRN Emergency Medicine , 2012, DOI: 10.5402/2012/705325
Improved Efficiency and Robustness in qPCR and Multiplex End-Point PCR by Twisted Intercalating Nucleic Acid Modified Primers
Uffe Vest Schneider, Nikolaj Dam Mikkelsen, Anja Lindqvist, Limei Meng Okkels, Nina J?hnk, Gorm Lisby
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038451
Abstract: We introduce quantitative polymerase chain reaction (qPCR) primers and multiplex end-point PCR primers modified by the addition of a single ortho-Twisted Intercalating Nucleic Acid (o-TINA) molecule at the 5′-end. In qPCR, the 5′-o-TINA modified primers allow for a qPCR efficiency of 100% at significantly stressed reaction conditions, increasing the robustness of qPCR assays compared to unmodified primers. In samples spiked with genomic DNA, 5′-o-TINA modified primers improve the robustness by increased sensitivity and specificity compared to unmodified DNA primers. In unspiked samples, replacement of unmodified DNA primers with 5′-o-TINA modified primers permits an increased qPCR stringency. Compared to unmodified DNA primers, this allows for a qPCR efficiency of 100% at lowered primer concentrations and at increased annealing temperatures with unaltered cross-reactivity for primers with single nucleobase mismatches. In a previously published octaplex end-point PCR targeting diarrheagenic Escherichia coli, application of 5′-o-TINA modified primers allows for a further reduction (>45% or approximately one hour) in overall PCR program length, while sustaining the amplification and analytical sensitivity for all targets in crude bacterial lysates. For all crude bacterial lysates, 5′-o-TINA modified primers permit a substantial increase in PCR stringency in terms of lower primer concentrations and higher annealing temperatures for all eight targets. Additionally, crude bacterial lysates spiked with human genomic DNA show lesser formation of non-target amplicons implying increased robustness. Thus, 5′-o-TINA modified primers are advantageous in PCR assays, where one or more primer pairs are required to perform at stressed reaction conditions.
Quantitative relationships in delphinid neocortex
Heidi S. Mortensen,Bente Pakkenberg,Maria Dam,Christian Sonne,Bjarni Mikkelsen,Nina Eriksen
Frontiers in Neuroanatomy , 2014, DOI: 10.3389/fnana.2014.00132
Abstract: Possessing large brains and complex behavioral patterns, cetaceans are believed to be highly intelligent. Their brains, which are the largest in the Animal Kingdom and have enormous gyrification compared with terrestrial mammals, have long been of scientific interest. Few studies, however, report total number of brain cells in cetaceans, and even fewer have used unbiased counting methods. In this study, using stereological methods, we estimated the total number of cells in the neocortex of the long-finned pilot whale (Globicephala melas) brain. For the first time, we show that a species of dolphin has more neocortical neurons than any mammal studied to date including humans. These cell numbers are compared across various mammals with different brain sizes, and the function of possessing many neurons is discussed. We found that the long-finned pilot whale neocortex has approximately 37.2 × 109 neurons, which is almost twice as many as humans, and 127 × 109 glial cells. Thus, the absolute number of neurons in the human neocortex is not correlated with the superior cognitive abilities of humans (at least compared to cetaceans) as has previously been hypothesized. However, as neuron density in long-finned pilot whales is lower than that in humans, their higher cell number appears to be due to their larger brain. Accordingly, our findings make an important contribution to the ongoing debate over quantitative relationships in the mammalian brain.
Review of Survey activities 2011: Methane and possible gas hydrates in the Disko Bugt region, central West Greenland
Mikkelsen, N.,Laier, T.,Nielsen, T.,Kuijpers, A.
Geological Survey of Denmark and Greenland Bulletin , 2012,
UV-induced carbon monoxide emission from sand and living vegetation
D. Bruhn,K. R. Albert,T. N. Mikkelsen,P. Ambus
Biogeosciences Discussions , 2012, DOI: 10.5194/bgd-9-8449-2012
Abstract: The global burden of carbon monoxide, CO, is rather uncertain. In this paper we address the potential of UV-induced CO emission by terrestrial surfaces. Real-time measurements of [CO] were made with a cavity enhanced laser connected in closed loop to either an ecosystem chamber or a leaf scale chamber. Sand and leaves of all examined plant species exhibited emission of CO in response to artificial UV-radiation and the UV-component of natural solar radiation. The UV-induced rate of CO emission exhibited a rather low dependence on temperature, indicating an abiotic process. The emission of CO in response to the UV-component of natural solar radiation was also evident at the ecosystem scale. When scaled to the global level, the UV-induced emission of CO by the major types of terrestrial surfaces, living leaves and soil (here represented by sand), amounts up to 28 Tg yr 1. This source has till now not been accounted for by IPCC, but is equivalent to 14–56% of the 50–200 Tg yr 1 from sources currently accounted for (IPCC 2001). In addition to this are other known sources that ought to be considered. The hitherto unaccounted for terrestrial sources of CO amounts up to 207 Tg yr 1, almost two-thirds of the latest estimated global CO burden of 360 Tg yr 1 (IPCC, 2001).
Historical seismicity of the Faroe Islands
R. M. W. Musson,T. Mikkelsen,H. Ziska
Annals of Geophysics , 2001, DOI: 10.4401/ag-3554
Abstract: A study is presented of the historical seismicity of the Faroe Islands, an area of low seismicity where no previous search for historical earthquakes was ever made. This presents a novel problem, since most studies of historical seismicity usually have previous catalogues to use as starting points. In this case the only information available at the start of the study related to a short sequence of small events in 1967 and two newspaper reports from the 1920s-1930s of strange phenomena which could be discounted from being earthquake related. The methodology of researching historical seismicity from scratch is described in detail. The results of the study were that no genuine historical earthquakes were found. However, in the first case, the fact that no events were found indicates that the lack of historical events in the Faroes is real and not just a function of no-one ever having looked for them before. In the second case, a positive statement (from 1906, in connection with a spurious earthquake report) was found that no earthquakes were known ever to have occurred in the Faroes. This means that two types of argument can be adduced: that there is no evidence that there were earthquakes (argument from the negative), and that there is evidence that there weren t earthquakes (argument from the positive). Taking into consideration the historical and cultural factors, some limits are drawn up for the probable extent to which one can rule out the occurrence of earthquakes of different intensities for different time periods.
Increasing the Analytical Sensitivity by Oligonucleotides Modified with Para- and Ortho-Twisted Intercalating Nucleic Acids – TINA
Uffe V. Schneider, Imrich Géci, Nina J?hnk, Nikolaj D. Mikkelsen, Erik B. Pedersen, Gorm Lisby
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0020565
Abstract: The sensitivity and specificity of clinical diagnostic assays using DNA hybridization techniques are limited by the dissociation of double-stranded DNA (dsDNA) antiparallel duplex helices. This situation can be improved by addition of DNA stabilizing molecules such as nucleic acid intercalators. Here, we report the synthesis of a novel ortho-Twisted Intercalating Nucleic Acid (TINA) amidite utilizing the phosphoramidite approach, and examine the stabilizing effect of ortho- and para-TINA molecules in antiparallel DNA duplex formation. In a thermal stability assay, ortho- and para-TINA molecules increased the melting point (Tm) of Watson-Crick based antiparallel DNA duplexes. The increase in Tm was greatest when the intercalators were placed at the 5′ and 3′ termini (preferable) or, if placed internally, for each half or whole helix turn. Terminally positioned TINA molecules improved analytical sensitivity in a DNA hybridization capture assay targeting the Escherichia coli rrs gene. The corresponding sequence from the Pseudomonas aeruginosa rrs gene was used as cross-reactivity control. At 150 mM ionic strength, analytical sensitivity was improved 27-fold by addition of ortho-TINA molecules and 7-fold by addition of para-TINA molecules (versus the unmodified DNA oligonucleotide), with a 4-fold increase retained at 1 M ionic strength. Both intercalators sustained the discrimination of mismatches in the dsDNA (indicated by ΔTm), unless placed directly adjacent to the mismatch – in which case they partly concealed ΔTm (most pronounced for para-TINA molecules). We anticipate that the presented rules for placement of TINA molecules will be broadly applicable in hybridization capture assays and target amplification systems.
Biomarkers of Immunotoxicity for Environmental and Public Health Research
Paurene Duramad,Nina T. Holland
International Journal of Environmental Research and Public Health , 2011, DOI: 10.3390/ijerph8051388
Abstract: The immune response plays an important role in the pathophysiology of numerous diseases including asthma, autoimmunity and cancer. Application of biomarkers of immunotoxicity in epidemiology studies and human clinical trials can improve our understanding of the mechanisms that underlie the associations between environmental exposures and development of these immune-mediated diseases. Immunological biomarkers currently used in environmental health studies include detection of key components of innate and adaptive immunity (e.g., complement, immunoglobulin and cell subsets) as well as functional responses and activation of key immune cells. The use of high-throughput assays, including flow cytometry, Luminex, and Multi-spot cytokine detection methods can further provide quantitative analysis of immune effects. Due to the complexity and redundancy of the immune response, an integrated assessment of several components of the immune responses is needed. The rapidly expanding field of immunoinformatics will also aid in the synthesis of the vast amount of data being generated. This review discusses and provides examples of how the identification and development of immunological biomarkers for use in studies of environmental exposures and immune-mediated disorders can be achieved.
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