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Tagging
Kinds of Tagging Terms modified by Tagging Selected AbstractsDOES RADIO TAGGING AFFECT THE SURVIVAL OR REPRODUCTION OF SMALL CETACEANS?MARINE MAMMAL SCIENCE, Issue 1 2006A TEST Abstract A long-term study of botos (inia geoffrensis) in the Brazilian Amazon permitted the comparison of survival and reproduction between 51 adults fitted with radio transmitters and an equal number that were captured and handled in the same way but released without a transmitter. For both sexes combined, 47 radio tagged botos (92.2%) survived at least three years after release compared with 42 (82.4%) without radios, equating to annual survival of 97.3% and 93.6% respectively. The difference was not statistically significant. Eight of 15 closely monitored radio tagged females were lactating at capture, and all their calves weaned successfully. Two that were pregnant at capture subsequently gave birth. The mean number of calves per year born to these 15 females after first release was 0.172 (SD = 0.107) and to 17 non-tagged was 0.174 (SD = 0.095), again a non-significant difference. These results indicate that the anchoring of packages to the dorsal fin of dolphins can be accomplished with no measurable impact on their subsequent survival or reproductive output. However, botos may be unusually robust to handling, and this study should not be used to justify using similar techniques on other species without customary caution, diligence, and expert guidance. [source] Postflood movements and population connectivity in gambusia (Gambusia holbrooki)ECOLOGY OF FRESHWATER FISH, Issue 4 2006P. Chapman Abstract , A population of the exotic pest fish Gambusia holbrooki inhabiting a drainage channel was sampled regularly to record responses to flooding and subsequent population reestablishment. The flood reduced numbers in the channel to near-zero levels. After remaining very low for 2 months, densities increased steadily through juvenile recruitment and the concentration of fish in drying pools. Tagging revealed that in general, movements between pools separated by only a few metres were relatively limited. There was evidence for habitat segregation and population subdivision, as fish from different pools varied markedly in terms of mean population density, movement behaviour, sex and size composition and juvenile recruitment. The most favoured pool was relatively deep, well lit and had the greatest habitat diversity. Gambusia control measures are likely to be most effective if timed to coincide with floods (which reduce local population densities) and/or droughts (which concentrate fish and allow targeting of source populations). [source] Tagging (Arene)ruthenium(II) Anticancer Complexes with Fluorescent LabelsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 18 2007Fabio Zobi Abstract Fluorescent (arene)ruthenium(II) complexes have been prepared by tagging a small fluorogenic reporter onto the chelating ligand of complexes of the type [(,6 -arene)RuCl(Z)]+ (Z = chelating ligand). Complexes [(,6 - p -cym)RuCl(NNO)](Cl) (2), [(,6 - p -cym)RuCl(L3)](Cl) (3) and [(,6 - p -cym)RuCl(L4)](Cl) (4) {p -cym = p- cymene, NNO = 2-[(2-aminoethyl)amino]ethanol, L3 = 2-[(2-aminoethyl)amino]ethyl-2-(methylamino)benzoate and L4 = N -{2-[(2-aminoethyl)amino]ethyl}-2-(methylamino)benzamide} were obtained in good yield from the reaction of the Ru dimer [(,6 - p -cym)RuCl2]2 (1) and the corresponding ligand. The compounds have been fully characterized and their X-ray crystal structures are reported. Compounds 3 and 4 show a photoluminescence response centered at 435 nm with partial fluorescence quenching of the fluorogenic reporters L3 and L4 upon coordination to the metal center. Species 2,4 show good solubility both in water and organic solvents. In water, 2,4 readily hydrolyze to form the aqua complexes. These are stable at acidic pH forming 10,15,% of the corresponding hydroxido complexes in buffered solution (25 mM HEPES) as the pH is raised to a physiological value (pH = 7.44). Under these conditions, 4 (but not 2 or 3) undergoes a fast pH-dependent reversible intramolecular rearrangement. Experimental data and semiempirical calculations indicate that the major species arising from this transformation is a complex with a tridentate chelating ligand following deprotonation at the nitrogen atom of the amide group. Esterase-catalyzed hydrolysis of 3 liberates isatoic acid (MIAH) and generates 2 indicating that the complex is a substrate for the enzyme. Complexes similar to 3 may have potential for esterase-activated Ru-based prodrug delivery systems.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007) [source] Combining Fluorous and Triazole Moieties for the Tagging of Chiral Azabis(oxazoline) LigandsADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 11-12 2009Ramesh Rasappan Abstract New fluorous-tagged azabis(oxazoline) ligands were prepared using the copper-catalyzed azide-alkyne cycloaddition as ligation method. The resulting ligands were tested in copper-catalyzed asymmetric benzoylations (up to 99% ee), nitroaldol (up to 90% ee), and Michael reactions (up to 82% ee). The combination of unpolar fluorinated alkyl chains and polar triazole moieties imposes properties that are beneficial for the catalysts with respect to recyclability and selectivity. The scope and limitation of this strategy in comparison to analogous catalysts immobilized on methoxypolyethylene glycol (MeOPEG) or polystyrene is discussed. Moreover, this study shows that the choice of solvent for a given reaction is crucial to arrive at highly recyclable bis(oxazoline) catalysts. [source] Tagging and tracking juvenile sturgeons in shallow waters of the Caspian Sea (less than 10 m depth) using CWT (Coded Wire Tags) and barbel incisionJOURNAL OF APPLIED ICHTHYOLOGY, Issue 2006B. Fadaee First page of article [source] Molecular Tagging and Mapping of Quantitative Trait Loci for Lint Percentage and Morphological Marker Genes in Upland CottonJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 3 2006Wang-Zhen Guo Abstract Using 219 F2 individuals developed by crossing the genetic standard line TM-1 and the multiple dominant marker line T586 in Gossypium hirsutum L., a genetic linkage map with 19 linkage groups was constructed based on simple sequence repeat (SSR) markers. Compared with our tetraploid backboned molecular genetic map from a(TM-1 × Hai 7124) × TM-1 BC1 population, 17 of the 19 linkage groups were combined and anchored to 12 chromosomes (sub-genomes). Of these groups, four morphological marker genes in T586 had been mapped into the molecular linkage map. Meanwhile, three quantitative trait loci for lint percentage were tagged and mapped separately on the A03 linkage group and chromosome 6. (Managing editor: Li-Hui Zhao) [source] Is There a Place for Virtual Poverty Funds in Pro-Poor Public Spending Reform?DEVELOPMENT POLICY REVIEW, Issue 4 2003Lessons from Uganda's PAF Various developing countries with weak public expenditure management systems are establishing virtual poverty funds (VPFs), drawing on the experience of Uganda's Poverty Action Fund. As a mechanism for tagging and tracking the performance of specific poverty-reducing expenditures in the budget, a VPF can be useful. However, this article argues that such devices should be treated from the outset as transitional, and as part of wider processes of strengthening public expenditure management; otherwise, they can seriously distort public expenditure allocations and management systems, potentially undermining growth. Emphasis needs to be placed on identifying the right balance of expenditures in the entire budget; improving the effectiveness and efficiency of existing allocations; and developing better public-sector policies for promoting pro-poor private sector growth. [source] Epigenetic control of translation regulation: Alterations in histone H3 lysine 9 post-translation modifications are correlated with the expression of the translation initiation factor 2B (Eif2b5) during thermal control establishmentDEVELOPMENTAL NEUROBIOLOGY, Issue 2 2010Tatiana Kisliouk Abstract Thermal control set point is regulated by thermosensitive neurons of the preoptic anterior hypothalamus (PO/AH) and completes its development during postnatal critical sensory period. External stimuli, like increase in environmental temperature, influence the neuronal protein repertoire and, ultimately, cell properties via activation or silencing of gene transcription, both of which are regulated by the "histone code."" Here, we demonstrated an increase in global histone H3 lysine 9 (H3K9) acetylation as well as H3K9 dimethylation in chick PO/AH during heat conditioning at the critical period of sensory development. In contrast to the global profile of H3K9 modifications, acetylation and dimethylation patterns of H3K9 at the promoter of the catalytic subunit of eukaryotic translation initiation factor 2B (Eif2b5) were opposite to each other. During heat conditioning, there was an increase in H3K9 acetylation at the Eif2b5 promoter, simultaneously with decrease in H3K9 dimethylation. These alterations coincided with Eif2b5 mRNA induction. Moreover, exposure to excessive heat during the critical period resulted in long-term effect on both H3K9 tagging at the Eif2b5 promoter and Eif2b5 mRNA expression. These data suggest a role for dynamic H3K9 post-translational modifications in global translation regulation during the thermal control establishment. © 2009 Wiley Periodicals, Inc. Develop Neurobiol, 2010 [source] A probabilistic framework for quantification of aftershock ground-motion hazard in California: Methodology and parametric studyEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 1 2009Gee Liek Yeo Abstract This paper presents a proposed method of aftershock probabilistic seismic hazard analysis (APSHA) similar to conventional ,mainshock' PSHA in that it estimates the likelihoods of ground motion intensity (in terms of peak ground accelerations, spectral accelerations or other ground motion intensity measures) due to aftershocks following a mainshock occurrence. This proposed methodology differs from the conventional mainshock PSHA in that mainshock occurrence rates remain constant for a conventional (homogeneous Poisson) earthquake occurrence model, whereas aftershock occurrence rates decrease with increased elapsed time from the initial occurrence of the mainshock. In addition, the aftershock ground motion hazard at a site depends on the magnitude and location of the causative mainshock, and the location of aftershocks is limited to an aftershock zone, which is also dependent on the location and magnitude of the initial mainshock. APSHA is useful for post-earthquake safety evaluation where there is a need to quantify the rates of occurrence of ground motions caused by aftershocks following the initial rupture. This knowledge will permit, for example, more informed decisions to be made for building tagging and entry of damaged buildings for rescue, repair or normal occupancy. Copyright © 2008 John Wiley & Sons, Ltd. [source] Tagging effects on three non-native fish species in England (Lepomis gibbosus, Pseudorasbora parva, Sander lucioperca) and of native Salmo truttaECOLOGY OF FRESHWATER FISH, Issue 2 2009S. Stak Abstract,,, To address the dearth of information on tagging effects and long-term survivorship of tagged fish in native and introduced species, laboratory and field investigations were undertaken on three non-native fish species (pumpkinseed Lepomis gibbosus; topmouth gudgeon Pseudorasbora parva; pikeperch Sander lucioperca) tagged with coded-wire (CW), passive integrated transponder (PIT), radio (RT) telemetry and/or acoustic tags (AT), with survivorship of native brown trout (Salmo trutta) examined in the field. Laboratory results revealed high survivorship following tag attachment/insertion and resumption of feeding within 24,48 h of tagging (all mortalities could be attributed to an unrelated outbreak of fungal infection), with retention rates being high in both pumpkinseed and pikeperch but low in topmouth gudgeon (excluded from field studies). In the field, short-term post-operation survival was high in pikeperch, pumpkinseed and brown trout. In pumpkinseed and trout, 100% of RT fish survived a 24,30 day tracking study, with 60% and 80%, respectively, recaptured alive at least 3 months post-tagging. Of PIT tagged pumpkinseed, 44% were recaptured (after 6,18 months), with small-sized, CW-tagged fish (0.38 g weight) captured up to 1 year after tagging. In pikeperch, all AT fish except one (the smallest specimen) survived their full expected tracking period (i.e. tag life) , the single lost specimen survived at least half of its expected tracking period (i.e. 6 month battery life). Overall, the tagging methods used were highly effective in pumpkinseed and pikeperch, showing good retention and survival, but PIT tagging of topmouth gudgeon was plagued by low survivorship and tag rejection. [source] Movement patterns of endangered Roanoke logperch (Percina rex)ECOLOGY OF FRESHWATER FISH, Issue 3 2008J. H. Roberts Abstract,,, Using mark,recapture methods, we studied movements of endangered Roanoke logperch (Percina rex Jordan & Evermann), a benthic darter, at 12 riffle,run sites over a 9-year-long period in the Roanoke River, Virginia, USA. Our primary objective was to characterise movements among transects within sites, but we opportunistically recorded two between-site movements as well. Our recapture rate was low (22 of 485 marked fish), but most recaptured fish exhibited movements between tagging and recapture, relocating either to another transect within a site (12 fish) or to another site altogether (two fish). Within sites, Roanoke logperch exhibited fidelity over time to the areas in which they were initially marked. These restricted areas were lengthier than transects (>15 m) but shorter than entire riffle,runs (<150 m). The two between-site movements were extensive (3.2 and 2.5 km), observed over a long mark,recapture interval (2 and 5 years, respectively), and may have represented migratory or dispersal movements. Their detection required an unusually extensive study design. Both small- and large-scale movements fulfil important ecological functions for Roanoke logperch, and greater study of such movements in this and other darter species is needed to inform conservation choices. [source] Length-dependent DNA separations using multiple end-attached peptide nucleic acid amphiphiles in micellar electrokinetic chromatographyELECTROPHORESIS, Issue 13 2008Jeffrey M. Savard Abstract End-labeled free-solution electrophoresis (ELFSE) is an alternative approach to gel-based methods for size-based electrophoretic separation of DNA. In ELFSE, an electrically neutral "drag-tag" is appended to DNA to add significant hydrodynamic drag, thereby breaking its constant charge-to-friction ratio. Current drag-tag architecture relies on covalent attachment of polymers to each DNA molecule. We have recently proposed the use of micellar drag-tags in conjunction with sequence-specific hybridization of peptide nucleic acid amphiphiles (PNAAs). This work investigates the effect of multiple PNAA attachment on DNA resolution using MEKC. Simultaneous PNAA hybridization allows for the separation of long DNA targets, up to 1012,bases, using micellar drag-tags. Each PNAA handle independently interacts with the micellar phase, reducing the overall mobility of this complex relative to individual PNAA binding. The sequence- and size-based dependence of this separation technique is maintained with multiple PNAA binding over a range of DNA sizes. Results are accurately described by ELFSE theory, yielding , = 54 for single-micelle tagging and , = 142 for dual-micelle tagging. This method is the first example of a non-covalent drag-tag used to separate DNA of 1000,bases based on both size and sequence. [source] Model of cryptogenic infantile spasms after prenatal corticosteroid primingEPILEPSIA, Issue 2010Libor Velí Summary Infantile spasms (IS) is a devastating epilepsy syndrome of childhood. IS occurs in 3,12-month-old infants and is characterized by spasms, interictal electroencephalography (EEG) hypsarrhythmia, and profound mental retardation. Hormonal therapy [adrenocorticotropic hormone (ACTH), corticosteroids] is frequently used, but its efficacy is tainted by severe side effects. For research of novel therapies, a validated animal model of IS is required. We propose the model of spastic seizures triggered by N -methyl- d -aspartate (NMDA) in infant rats prenatally exposed to betamethasone. The spasms have remarkable similarity to human IS, including motor flexion spasms, ictal EEG electrodecrement, and responsiveness to ACTH. Interestingly, the spasms do not involve the hippocampus. Autoradiographic metabolic mapping as well as tagging of the areas of neuronal excitation with c-fos indicates a strong involvement of hypothalamic structures such as the arcuate nucleus, which has significant bilateral connections with other hypothalamic nuclei as well as with the brainstem. [source] Elements of a neurobiological theory of hippocampal function: the role of synaptic plasticity, synaptic tagging and schemasEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 11 2006R. G. M. MorrisArticle first published online: 8 JUN 200 Abstract The 2004 EJN Lecture was an attempt to lay out further aspects of a developing neurobiological theory of hippocampal function [Morris, R.G.M., Moser, E.I., Riedel, G., Martin, S.J., Sandin, J., Day, M. & O'Carroll, C. (2003) Phil. Trans. R. Soc. Lond. B Biol. Sci., 358, 773,786.] These are that (i) activity-dependent synaptic plasticity plays a key role in the automatic encoding and initial storage of attended experience; (ii) the persistence of hippocampal synaptic potentiation over time can be influenced by other independent neural events happening closely in time, an idea with behavioural implications for memory; and (iii) that systems-level consolidation of memory traces within neocortex is guided both by hippocampal traces that have been subject to cellular consolidation and by the presence of organized schema in neocortex into which relevant newly encoded information might be stored. Hippocampal memory is associative and, to study it more effectively than with previous paradigms, a new learning task is described which is unusual in requiring the incidental encoding of flavour,place paired associates, with the readout of successful storage being successful recall of a place given the flavour with which it was paired. NMDA receptor-dependent synaptic plasticity is shown to be critical for the encoding and intermediate storage of memory traces in this task, while AMPA receptor-mediated fast synaptic transmission is necessary for memory retrieval. Typically, these rapidly encoded traces decay quite rapidly over time. Synaptic potentiation also decays rapidly, but can be rendered more persistent by a process of cellular consolidation in which synaptic tagging and capture play a key part in determining whether or not it will be persistent. Synaptic tags set at the time of an event, even many trivial events, can capture the products of the synthesis of plasticity proteins set in train by events before, during or even after an event to be remembered. Tag,protein interactions stabilize synaptic potentiation and, by implication, memory. The behavioural implications of tagging are explored. Finally, using a different protocol for flavour,place paired associate learning, it is shown that rats can develop a spatial schema which represents the relative locations of several different flavours of food hidden at places within a familiar space. This schema is learned gradually but, once acquired, enables new paired associates to be encoded and stored in one trial. Their incorporation into the schema prevents rapid forgetting and suggests that schema play a key and hitherto unappreciated role in systems-level memory consolidation. The elements of what may eventually mature into a more formal neurobiological theory of hippocampal memory are laid out as specific propositions with detailed conceptual discussion and reference to recent data. [source] Metaplasticity of the late-phase of long-term potentiation: a critical role for protein kinase A in synaptic taggingEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 7 2006Jennie Z. Young Abstract The late-phase of long-term potentiation (L-LTP) in hippocampal area CA1 requires gene expression and de novo protein synthesis but it is expressed in an input-specific manner. The ,synaptic tag' theory proposes that gene products can only be captured and utilized at synapses that have been ,tagged' by previous activity. The mechanisms underlying synaptic tagging, and its activity dependence, are largely undefined. Previously, we reported that low-frequency stimulation (LFS) decreases the stability of L-LTP in a cell-wide manner by impairing synaptic tagging. We show here that a phosphatase inhibitor, okadaic acid, blocked homosynaptic and heterosynaptic inhibition of L-LTP by prior LFS. In addition, prior LFS homosynaptically and heterosynaptically impaired chemically induced synaptic facilitation elicited by forskolin/3-isobutyl-1-methylxanthine, suggesting that there is a cell-wide dampening of cAMP/protein kinase A (PKA) signaling concurrent with phosphatase activation. We propose that prior LFS impairs expression of L-LTP by inhibiting synaptic tagging through its actions on the cAMP/PKA pathway. In support of this notion, we show that hippocampal slices from transgenic mice that have genetically reduced hippocampal PKA activity display impaired synaptic capture of L-LTP. An inhibitor of PKA, KT-5720, also blocked synaptic capture of L-LTP. Moreover, pharmacological activation of the cAMP/PKA pathway can produce a synaptic tag to capture L-LTP expression, resulting in persistent synaptic facilitation. Collectively, our results show that PKA is critical for synaptic tagging and for input-specific L-LTP. PKA-mediated signaling can be constrained by prior episodes of synaptic activity to regulate subsequent L-LTP expression and perhaps control the integration of multiple synaptic events over time. [source] Endophytic root colonization of gramineous plants by Herbaspirillum frisingenseFEMS MICROBIOLOGY ECOLOGY, Issue 1 2008Michael Rothballer Abstract Herbaspirillum frisingense is a diazotrophic betaproteobacterium isolated from C4-energy plants, for example Miscanthus sinensis. To demonstrate endophytic colonization unequivocally, immunological labeling techniques using monospecific polyclonal antibodies against two H. frisingense strains and green fluorescent protein (GFP)-fluorescence tagging were applied. The polyclonal antibodies enabled specific in situ identification and very detailed localization of H. frisingense isolates Mb11 and GSF30T within roots of Miscanthus×giganteus seedlings. Three days after inoculation, cells were found inside root cortex cells and after 7 days they were colonizing the vascular tissue in the central cylinder. GFP-tagged H. frisingense strains could be detected and localized in uncut root material by confocal laser scanning microscopy and were found as endophytes in cortex cells, intercellular spaces and the central cylinder of barley roots. Concerning the production of potential plant effector molecules, H. frisingense strain GSF30T tested positive for the production of indole-3-acetic acid, while Mb11 was shown to produce N -acylhomoserine lactones, and both strains were able to utilize 1-aminocyclopropane-1-carboxylate (ACC), providing an indication of the activity of an ACC-deaminase. These results clearly present H. frisingense as a true plant endophyte and, although initial greenhouse experiments did not lead to clear plant growth stimulation, demonstrate the potential of this species for beneficial effects on the growth of crop plants. [source] Evaluating the physiological and physical consequences of capture on post-release survivorship in large pelagic fishesFISHERIES MANAGEMENT & ECOLOGY, Issue 2 2007G. B. SKOMAL Abstract, Sharks, tunas and billfishes are fished extensively throughout the world. Domestic and international management measures (quotas, minimum sizes, bag limits) mandate release of a large, yet poorly quantified, number of these fishes annually. Post-release survivorship is difficult to evaluate, because standard methods are not applicable to large oceanic fishes. This paper presents information on the current approaches to characterising capture stress and survivorship in sharks, tunas and marlins. To assess mortality associated with capture stress, researchers must examine the cumulative impacts of physical trauma and physiological stress. Physical trauma, manifested as external and internal tissue and organ damage, is caused by fishing gear and handling. Gross examination and histopathological sampling have been used to assess physical trauma and to infer post-release survivorship. Exhaustive anaerobic muscular activity and time out of water cause physiological stress, which has been quantified in these fishes through the analyses of blood chemistry. Conventional, acoustic and archival tagging have been used to assess post-release survivorship in these species. Future studies relating capture stress and post-release survivorship could yield information that helps fishermen increase survivorship when practicing catch and release. [source] Long-term retention of coded wire tags in juvenile Arctic charr Salvelinus alpinusFISHERIES MANAGEMENT & ECOLOGY, Issue 3 2006I. KOLARI Abstract, A hatchery experiment was organised to find out if the high loss rate of coded wire tags, noticed in connection with an Arctic charr Salvelinus alpinus (L.) restocking programme, was size-dependent and also to test head moulds for future taggings. Six moulds made by Northwest Marine Technology Inc. and five moulds made at the Finnish Game and Fisheries Research Institute were used. A total of 100 charr were tagged with standard-length coded wire tags using each mould. One-summer old charr at tagging were held for 534 days and two-summer old charr for 320 days. The tag loss rate varied between 0% and 54% and was negatively related to the size of the charr at tagging. The high loss rate was connected with the poor alignment of some moulds, such that a large proportion of the tags were located in the nasal cavity instead of the nasal cartilage. Testing of the moulds and careful grading of the fish for tagging is emphasised, especially if Arctic charr smaller than 20 g in weight are to be tagged. [source] Plasticity in vertical behaviour of migrating juvenile southern bluefin tuna (Thunnus maccoyii) in relation to oceanography of the south Indian OceanFISHERIES OCEANOGRAPHY, Issue 4 2009SOPHIE BESTLEY Abstract Electronic tagging provides unprecedented information on the habitat use and behaviour of highly migratory marine predators, but few analyses have developed quantitative links between animal behaviour and their oceanographic context. In this paper we use archival tag data from juvenile southern bluefin tuna (Thunnus maccoyii, SBT) to (i) develop a novel approach characterising the oceanographic habitats used throughout an annual migration cycle on the basis of water column structure (i.e., temperature-at-depth data from tags), and (ii) model how the vertical behaviour of SBT altered in relation to habitat type and other factors. Using this approach, we identified eight habitat types occupied by juvenile SBT between the southern margin of the subtropical gyre and the northern edge of the Subantarctic Front in the south Indian Ocean. Although a high degree of variability was evident both within and between fish, mixed-effect models identified consistent behavioural responses to habitat, lunar phase, migration status and diel period. Our results indicate SBT do not act to maintain preferred depth or temperature ranges, but rather show highly plastic behaviours in response to changes in their environment. This plasticity is discussed in terms of the potential proximate causes (physiological, ecological) and with reference to the challenges posed for habitat-based standardisation of fishery data used in stock assessments. [source] Geolocation of Atlantic cod (Gadus morhua) movements in the Gulf of Maine using tidal informationFISHERIES OCEANOGRAPHY, Issue 4 2007J. P. GRÖGER Abstract Information derived from archival tags (digital storage tags, DSTs) were used to backtrack the migration of 11 tagged Atlantic cod (Gadus morhua) during 2001 in Massachusetts Bay, the Gulf of Maine, and Georges Bank. The DST tags continuously recorded time, temperature and depth. To geolocate fish positions during its time at large, we first extracted the tidal signal from the pressure recordings on the DST tags, and then compared the resulting data to data predicted with a Massachusetts Bay tidal model that provided us with geographical coordinates at a given date and time. Using least-squares criteria within an estimated geographical region of confidence that was constrained by biological and statistical information (e.g. swimming speed, known release and recapture location, and bottom depth) we were able to geolocate the fish. The resultant geolocated migration tracks indicate a large degree of movement of Atlantic cod in the region and an elevated importance of the Great South Channel (GSC) migration corridor between Massachusetts Bay and the western Georges Bank and Nantucket Shoals region. This observation contrasts strongly with inferences of limited movements by Atlantic cod based on conventional tag recapture methods (mean of 1200 km traveled versus 44 km traveled as measured by conventional tagging and geolocation, respectively). This study demonstrates that geolocation methodologies applied to archival tag studies hold great promise of becoming an important new tool for fisheries managers to quantify the movements of fishes. It also points out the need for greater collaboration between fisheries scientists and oceanographers, and particularly for the development of improved tidal models to cover stock regions more accurately and with higher precision. [source] Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chainsGENES TO CELLS, Issue 10 2004Takeshi Tenno Ubiquitination, a modification in which single or multiple ubiquitin molecules are attached to a protein, serves as a signalling function that controls a wide variety of cellular processes. To date, two major forms of polyubiquitin chain have been functionally characterized, in which the isopeptide bond linkages involve Lys48 or Lys63. Lys48-linked polyubiquitin tagging is mostly used to target proteins for degradation by the proteasome, whereas Lys63-linked polyubiquitination has been linked to numerous cellular events that do not rely on degradative signalling via the proteasome. Apparently linkage-specific conformations of polyubiquitin chains are important for these cellular functions, but the structural bases distinguishing Lys48- and Lys63-linked chains remain elusive. Here, we report NMR and small-angle X-ray scattering (SAXS) studies on the intersubunit interfaces and conformations of Lys63- and Lys48-linked di- and tetraubiquitin chains. Our results indicate that, in marked contrast to Lys48-linked chains, Lys63-linked chains are elongated molecules with no stable non-covalent intersubunit interfaces and thus adopt a radically different conformation from that of Lys48-linked chains. [source] SsrA-mediated protein tagging in the presence of miscoding drugs and its physiological role in Escherichia coliGENES TO CELLS, Issue 7 2002Tatsuhiko Abo Background: We have shown recently that read-through of a normal stop codon by a suppressor tRNA in specific genes possessing a Rho-independent terminator leads to SsrA-mediated tagging of extended proteins in Escherichia coli cells. Miscoding antibiotics such as kanamycin and streptomycin reduce translational fidelity by binding to the 30S ribosomal subunit. The aim of the present study was to address how miscoding antibiotics affect the read-through of stop codons and SsrA-mediated protein tagging. Results: Miscoding antibiotics caused translational read-through of stop codons when added to the culture medium at sublethal concentrations. Under the same conditions, the drugs enhanced SsrA-mediated tagging of bulk cellular proteins, as observed in cells carrying an ochre suppressor tRNA. Translational read-through products generated from the crp gene in the presence of the antibiotics was efficiently tagged by the SsrA system, presumably because the ribosome reached the 3, end of the mRNA defined by the terminator hairpin. The SsrA-defective cells were more sensitive to the miscoding antibiotics compared to the wild-type cells. Conclusion: We conclude that the SsrA system contributes to the survival of cells by dealing with translational errors in the presence of low concentrations of miscoding antibiotics. [source] Population differences in the International Multi-Centre ADHD Gene ProjectGENETIC EPIDEMIOLOGY, Issue 2 2008Benjamin M. Neale Abstract The International Multi-Centre ADHD Gene sample consists of 674 families from eight countries (Belgium, England, Germany, Holland, Ireland, Israel, Spain, and Switzerland) ascertained from clinics for combined-type attention definity hyperactivity disorder in an offspring. 863 SNPs were successfully genotyped across 47 autosomal genes implicated in psychiatric disorders yielding a single nucleotide polymorphism (SNP) density of approximately one SNP per 2.5,kb. A global test of heterogeneity showed 269 SNPs nominally significant (expected 43). Inclusion of the Israeli population accounted for approximately 70% of these nominally significant tests. Hardy-Weinberg equilibrium tests suggest that combining all these populations would induce stratification, but that the Northern European populations (Belgium, England, Germany, Holland, and Ireland) could be appropriate. Tag SNPs were generated using pair-wise and aggressive tagging from Carlson et al. [2004] and de Bakker et al. [2005], respectively, in each population and applied to the other populations. Cross-population performance across Northern Europe was consistent with within population comparisons. Smaller sample size for each population tended to yield more problems for the generation of aggressive tags and the application of pair-wise tags. Any case-control sample employing an Israeli sample with Northern Europeans must consider stratification. A Northern European tag set, however, appears to be appropriate for capturing the variation across populations. Genet. Epidemiol. 2008. © 2007 Wiley-Liss, Inc. [source] A sparse marker extension tree algorithm for selecting the best set of haplotype tagging single nucleotide polymorphismsGENETIC EPIDEMIOLOGY, Issue 4 2005Ke Hao Abstract Single nucleotide polymorphisms (SNPs) play a central role in the identification of susceptibility genes for common diseases. Recent empirical studies on human genome have revealed block-like structures, and each block contains a set of haplotype tagging SNPs (htSNPs) that capture a large fraction of the haplotype diversity. Herein, we present an innovative sparse marker extension tree (SMET) algorithm to select optimal htSNP set(s). SMET reduces the search space considerably (compared to full enumeration strategy), and therefore improves computing efficiency. We tested this algorithm on several datasets at three different genomic scales: (1) gene-wide (NOS3, CRP, IL6 PPARA, and TNF), (2) region-wide (a Whitehead Institute inflammatory bowel disease dataset and a UK Graves' disease dataset), and (3) chromosome-wide (chromosome 22) levels. SMET offers geneticists with greater flexibilities in SNP tagging than lossless methods with adjustable haplotype diversity coverage (,). In simulation studies, we found that (1) an initial sample size of 50 individuals (100 chromosomes) or more is needed for htSNP selection; (2) the SNP tagging strategy is considerably more efficient when the underlying block structure is taken into account; and (3) htSNP sets at 80,90% , are more cost-effective than the lossless sets in term of relative power, relative risk ratio estimation, and genotyping efforts. Our study suggests that the novel SMET algorithm is a valuable tool for association tests. Genet. Epidemiol. 29:336,352, 2005. © 2005 Wiley-Liss, Inc. [source] Breaking the Barriers in Bio ResearchIMAGING & MICROSCOPY (ELECTRONIC), Issue 1 2007STED Superresolution Microscopy More than 130 years ago, Ernst Abbe set up the law that far-field optical microscopes are limited in resolution to approximately half of the wavelength of light. Today, these limits have been broken by two new concepts of microscopy: 4Pi and STED (Stimulated Emission Depletion) microscopy. Both techniques are revolutionizing the biomedical research environment, by providing resolution beyond what is possible with best light microscopes today, while maintaining all advantages of structure-specific fluorescence tagging. The principles have been invented by Stefan Hell of the Max Planck Institute for Biophysical Chemistry in Goettingen, Germany, and are commercialized by Leica Microsystems CMS. While the Leica TCS 4Pi is already available, the Leica TCS STED system will be introduced to the market in 2007. [source] Frequent decreased expression of candidate tumor suppressor gene, DEC1, and its anchorage-independent growth properties and impact on global gene expression in esophageal carcinomaINTERNATIONAL JOURNAL OF CANCER, Issue 3 2008Alfred Chi Chung Leung Abstract Previous studies showed that expression of the novel candidate tumor suppressor gene, DEC1 (Deleted in Esophageal Cancer 1), is reduced in esophageal carcinoma and suppresses cancer cell growth in vitro and tumor growth in vivo in nude mice. This study shows that DEC1 gene expression was downregulated in 100% of 16 esophageal squamous cell carcinoma (ESCC) cell lines and 52 and 45%, respectively, of esophageal tumor specimens from Hong Kong and a high-risk ESCC region of Henan, China. Using epitope tagging, the DEC1 protein was localized to both the cytoplasm and nucleus of the cell. In 3D Matrigel culture, no significant difference in colony numbers formed was observed for DEC1 stable transfectants, as compared to vector-alone transfectant controls. However, significantly smaller colony sizes were observed for the DEC1 transfectants. In in vitro cell migration, invasion and soft agar assays of DEC1 transfectants, only the soft agar assay showed statistically significant differences in colony numbers with the vector-alone controls, indicating that DEC1 may be involved in anchorage-independent cell growth. In addition, the global gene expression affected by DEC1 in tumor-suppressive stable transfectants was investigated using cDNA oligonucleotide microarray hybridization. Three candidate genes, TFPI-2, GDF15 and DUSP6, were identified through this approach; they are downregulated in tumor segregants of DEC1 stable transfectants, ESCC cell lines and esophageal tumors and have a potential role in tumor growth and progression. These studies show that DEC1 is involved in esophageal cancer development and help elucidate its functional role in tumor development. © 2007 Wiley-Liss, Inc. [source] Protein Detecting Arrays Based on Cationic Polythiophene,DNA-Aptamer Complexes,ADVANCED MATERIALS, Issue 20 2006Abérem, M. Béra By combining an appropriate DNA aptamer with a cationic polythiophene optical transducer, human thrombin can be specifically detected on microarrays in the attomole range in less than one hour without any tagging of the target. The system can be modified and utilized as a probe for the detection of various proteins or other biomolecules. This work opens new interesting possibilities for simple and rapid multiparametric analysis in genomics and proteomics. [source] Evaluation of VIE and PIT tagging methods for juvenile cyprinid fishesJOURNAL OF APPLIED ICHTHYOLOGY, Issue 4 2009J. D. Bolland Summary Retention and mortality associated with visible implant elastomer (VIE) and passive integrated transponder (PIT) tagged juvenile chub [Leuciscus cephalus (L.)], dace [Leuciscus leuciscus (L.)] and roach [Rutilus rutilus (L.)] were evaluated. PIT tag retention (96.6,100%) was higher than VIE over the 6-month duration of the experiment. VIE retention was significantly better in the head (96.3,98.8%) than in the fins (78.8,90.9%) the first month after tagging, but the opposite was found after 6 months (head = 21.5,57.5%; fins = 77.2,88.8%). Survival was not significantly different from controls for any treatment, except dace tagged with 23-mm PIT (significantly influenced by mass of fish at tagging) and sham PIT tagged dace, because of initial losses. PIT tags are recommended as the most suitable method for tagging individual juvenile chub, dace and roach based on high retention and survival. VIE implantation in the head (studies < 30 days) and fins (studies > 30 days) could provide a cheap, batch-marking alternative, provided retention rates are monitored. [source] Effect of origin, sex and sea age of Atlantic salmon on their recapture rate after river ascentJOURNAL OF APPLIED ICHTHYOLOGY, Issue 6 2006E. Jokikokko Summary The recapture rate of Atlantic salmon (Salmo salar L.) after river ascent was examined by the trapping and tagging of ascending spawners in the lower reaches of the Simojoki River, which flows into the northern Baltic Sea. In 1997 and 1998, altogether 825 Carlin-tagged salmon were released to continue their upstream migration. Of these, 800 could be sexed and categorized as reared (91%) or wild (9%) salmon. In 1997, most of the ascending salmon were multi-sea-winter (MSW) fish, whereas in 1998 almost all were one-sea-winter (1SW) male grilse due to the late trapping season. About 10% of all tagged fish were recaptured, two-thirds of which were caught in the river before their descent to the sea. There was no difference in the recapture rate between salmon of wild (8.5%) or reared (9.5%) origin, or between females (11.6%) and males (9.3%). Generalized linear models for data from 1997 showed that the recapture rate increased with length and age of females, but that the opposite was true for males. River fishing did not seem to remove proportionally more early ascending salmon than fish that ascended later. [source] Microgeographic population structure of brook charr: a comparison of microsatellite and mark-recapture dataJOURNAL OF FISH BIOLOGY, Issue 3 2003B. K. Adams Polymorphism at five microsatellite genetic markers (genotyped n = 496) and mark-recapture tagging data (tagged n = 9813) were used to define the population structure of brook charr, Salvelinus fontinalis from the Indian Bay watershed, Newfoundland, Canada. Despite the absence of physical barriers to migration among lakes, both genetic and tagging data suggest that brook charr in each lake represent reproductively isolated populations. Exact tests comparing allele frequencies, , (global value = 0·063), Rst (global value = 0·052), individual assignment tests, and Nei's genetic distance provided congruent estimates of population subdivision in agreement with the tagging data (only 2·2% of recaptures were lake-to-lake). The genetic structure of the brook charr populations corresponded with the geographic structure of the drainage basin on a qualitative level, although linear distance over water was not significantly correlated with the tagging data or the genetic distance measures. The agreement between the tagging and the genetic data suggest that microsatellite markers can be useful tools for defining real biological units. The results also suggest that brook charr exhibit microgeographic population structure at the watershed scale, and that this is the scale at which conservation and management of this salmonid might best be implemented. [source] | ||||||||||||||||||||||||||||||||||||||||||||||