Short Inverted-Repeat Transposable Elements in Teleost Fish and Implications for a Mechanism of Their Amplification

Angel is the first miniature inverted-repeat transposable element (MITE) isolated from fish. Angel elements are imperfect palindromes with the potential to form stem-loop structures in vitro. Despite sequence divergence of elements of up to 55% within and between species, their inverted repeat structures have been maintained, implying functional importance. We estimate that there are about 10³–10⁴ Angels scattered throughout the zebrafish genome, evidence that this family of transposable elements has been significantly amplified over the course of evolution. Angel elements and Xenopus MITEs carry common sequence motifs at their termini, indicating common origin and/or related mechanisms of transposition. We present a model in which MITEs take advantage of the basic cellular mechanism of DNA replication for their amplification, which is dependent on the characteristic inverted repeat structures of these elements. We propose that MITEs are genomic parasites that transpose via a DNA intermediate, which forms by a folding-back of a single strand of DNA, that borrow all of the necessary factors for their amplification from products encoded in the genomes in which they reside. DNA polymorphisms in different lines of zebrafish were detected by PCR using Angel-specific primers, indicating that such elements, combined with other transposons in vertebrate genomes, will be useful molecular tools for genome mapping and genetic analyses of mutations. Received: 7 April 1998 / Accepted: 7 April 1998     

Integrating disparate datasets to model the functional response of a marine predator: A case study of harbour porpoises in the southern North Sea

1. Quantifying consumption and prey choice for marine predator species is key to understanding their interaction with prey species, fisheries, and the ecosystem as a whole. However, parameterizing a functional response for large predators can be challenging because of the difficulty in obtaining the required data on predator diet and on the availability of multiple prey species.
2. This study modeled a multi‐species functional response (MSFR) to describe the relationship between consumption by harbour porpoises (Phocoena phocoena) and the availability of multiple prey species in the southern North Sea. Bayesian methodology was employed to estimate MSFR parameters and to incorporate uncertainties in diet and prey availability estimates. Prey consumption was estimated from stomach content data from stranded harbour porpoises. Prey availability to harbour porpoises was estimated based on the spatial overlap between prey distributions, estimated from fish survey data, and porpoise foraging range in the days prior to stranding predicted from telemetry data.
3. Results indicated a preference for sandeels in the study area. Prey switching behavior (change in preference dependent on prey abundance) was confirmed by the favored type III functional response model. Variation in the size of the foraging range (estimated area where harbour porpoises could have foraged prior to stranding) did not alter the overall pattern of the results or conclusions.
4. Integrating datasets on prey consumption from strandings, predator foraging distribution using telemetry, and prey availability from fish surveys into the modeling approach provides a methodological framework that may be appropriate for fitting MSFRs for other predators.

     

Enantioselective determination of FCE 28833, a new potential antiischemic agent,in gerbil plasma using column switching HPLC with UV detection

A sensitive and selective high performance liquid chromatographic method using an automated column switching technique for the determination of FCE 28833 enantiomers in gerbil plasma was developed. After solid-liquid extraction using a Supelcosil C₁₈ cartridge FCE 28833 was eluted on a clean-up column (Spherisorb CN) and the enantiomers were separated using an analytical chiral column (Crownpack CR(+)). The mobile phase (15% methanol in HClO₄ 1 mM) was directed through the columns at a flow rate of 1 ml/min and the fraction eluted between 13 and 40 min was transferred from the clean-up column into the analytical column. FCE 28833 enantiomers were monitored at 257 nm. The limit of quantitation of the method was 20 ng/ml plasma for both enantiomers and proved to be linear, precise, and accurate for the assay of both enantiomers in the 20–6,000 ng/ml concentration range. No interference from the blank gerbil plasma sample was observed. The suitability of the method was assessed using plasma samples obtained from male gerbils treated with a single oral dose (400 mg/kg) of FCE 28833. Chirality 9:133–138, 1997. © 1997 Wiley-Liss, Inc.     

Reversible binding interactions between the tryptophan enantiomers and albumins of different animal species as determined by novel high performance liquid chromatographic methods: an attempt to localize the D- and L-tryptophan binding sites on the human serum albumin polypeptide chain by using protein fragments

The stereoselectivity of the reversible binding interactions between the D- and L-tryptophan enantiomers and serum albumins of different animal species and fragments of human serum albumin (HSA) was investigated by applying three novel high performance liquid chromatographic (HPLC) arrangements. The separations were performed by means of (1) an achiral (diol-bond), (2) a chiral (bovine serum albumin-bond) silica gel sorbent, and (3) a column switching technique which uses both the diol- and HSA-bond HPLC stationary phases. A polarimetric detector and/or an ultraviolet (UV) spectrophotometer were used to monitor the separation process. HPLC arrangement 3 allowed the evaluation of enantioselective binding for D- and L-tryptophan to different albumins and albumin fragments. At present, column switching can be considered the technique of the broadest applicability for investigating the reversible binding interactions between a protein and drug enantiomers. Chirality 9:373–379, 1997. © 1997 Wiley-Liss, Inc.     

Peptide and glycopeptide dendrimers. Part I

Recent progress in peptide and glycopeptide chemistry make the preparation of peptide and glycopeptide dendrimers of acceptable purity, with designed structural and immunochemical properties reliable. New methodologies using unprotected peptide building blocks have been developed to further increase possibilities of their design and improve their preparation and separation. Sophisticated design of peptide and glycopeptide dendrimers has led to their use as antigens and immunogens, for serodiagnosis and other biochemical uses including drug delivery. Dendrimers bearing peptide with predetermined secondary structures are useful tools in protein de novo design. This article covers synthesis and applications of multiple antigen peptides (MAPs), multiple antigen glycopeptides (MAGs), multiple antigen peptides based on sequential oligopeptide carriers (MAP‐SOCs), glycodendrimers and template‐assembled synthetic proteins (TASPs). Part I deals with the development of various structural forms of MAPs as well as their application as antigens, immunogens, and for immunodiagnostic and biochemical purposes. Copyright © 1999 European Peptide Society and John Wiley & Sons, Ltd.     

Assembly of binding loops on aromatic templates as VCAM‐1 mimetics

The design and synthesis of cyclic mimetics of VCAM‐1 protein that reproduce the integrin‐binding domain are presented. The unprotected peptide precursor 37 – 43 , Thr‐Gln‐Ile‐Asp‐Ser‐Pro‐Leu, was grafted onto functional templates of type naphthalene, biphenyl and benzyl through the chemoselective formation of C‐ and N‐terminal oximes resulting in a mixture of four isomeric forms due to syn–anti isomerism of the oxime bonds. Some isomers could be monitored by HPLC and identified by NMR. The molecule containing a naphthalene‐derived template was found to inhibit the VCAM‐1/VLA‐4 interaction more efficiently than previously reported for sulfur‐bridged cyclic peptides containing similar sequences. The finding confirms the importance of incorporating conformational constraints between the terminal ends of the peptide loop 37 – 43 in the design of synthetic inhibitors of the VCAM‐1/integrin interaction. Copyright © 1999 European Peptide Society and John Wiley & Sons, Ltd.     

Switching among natal and auxiliary hosts increases vulnerability of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae) to insecticides

The role of insecticidal application and host plant resistance in managing Spodoptera exigua has been well documented, but the effect of different host plants, on which the pest cycles its population in the field, has seldom been investigated. Therefore, we have studied the vulnerability of S. exigua against commonly used insecticides (cypermethrin, chlorpyrifos, lufenuron, and emamectin benzoate) with different mode of actions when it switches its generations from natal to auxiliary hosts and vice versa. Different field populations being established on different host plants including castor, cauliflower, cotton, okra, and spinach were collected and reared in the laboratory before insecticidal bioassays. The role of larval diet and host plant switching on their response to tolerate applied insecticides was studied using leaf‐dip bioassay methods. Host switching demonstrated a significant role in altering the vulnerability of S. exigua populations to tested insecticides. Spodoptera exigua sourced from castor, when switched host to okra and spinach, exhibited 50% higher mortality when treated with emamectin benzoate. This trend in mortality was consistent upon complete host switch cycle (natal—auxiliary—natal host). However, the highest increase (92%) in vulnerability was recorded when the larvae were shifted to spinach from cotton. In general, chlorpyrifos and lufenuron had highest efficacies in terms of larval mortality. The findings of present studies provide insights to a better understanding the behavior of polyphagous pests and the role of different host plants in altering the susceptibility of these pests against applied insecticides. Ultimately the results warrant that due consideration should be given to cropping patterns and time of host switching by pest population during planning and executing chemical control.     

Hydrothermal synthesis and characterization of a zinc-substituted gallium phosphite, [H3N(CH2)2NH3]1/2 · [GaZn(HPO3)3(H2O)2]

An organically templated zinc-substituted gallium phosphite, [H₃N(CH₂)₂NH₃]_1/2 · [GaZn(HPO₃)₃(H₂O)₂] was synthesized under mild hydrothermal conditions in the presence of ethylenediamine (en) as structure-directing agent and characterized by single-crystal X-ray diffraction analysis. It crystallizes in the orthorhombic space group Pbcn with unit cell parameters: a = 18.6146(10) Å, b = 11.0454(6) Å, c = 10.9074(4) Å, V = 2242.62(19) Å³ and Z = 8. This compound has a three-dimensional framework built up from secondary building units (SBU) of Ga(III) (or Zn(II)) and HPO₃ pseudopyramid by sharing vertices. The structure displays a two-dimensional channel system running along the [0 0 1] and [0 1 0] direction with 5-, 8- and 10-membered rings. The diprotonated ethylenediamine template molecules are located in the channels. In this structure, some of the Ga(III) sites are occupied by Zn(II) atoms. The compound was also characterized by IR spectroscopy, inductively coupled plasma (ICP), X-ray photoelectron spectra (XPS), differential thermal and thermogravimetric analyses.     

Predictors of clutch predation of a globally significant avifauna in New Zealand's braided river ecosystems

Predation by introduced mammals is decimating New Zealand's indigenous fauna. Understanding factors that influence this process allows resources for predator control to be applied with maximum effect. This study examines how predation of a secondary prey species (a relatively common but declining native plover, the banded dotterel Charadrius bicinctus ) varied with reductions in abundance of a major prey source (rabbits), kill-trapping of predators, nest density and habitat complexity. Banded dotterels mostly nest in open braided riverbeds alongside a number of endemic threatened species. We measured the fate of 753 dotterel clutches exposed to predation by cats, ferrets and hedgehogs. We found key times and places of high predation risk. Immediately after widespread reduction in rabbit populations by rabbit haemorrhagic disease (RHD), clutch predation rates were almost as high (mean, 50%) as those recorded during past rabbit poisoning programmes (mean, 57%). Both rates were significantly higher than the mean predation rate of 22% without rabbit control, suggesting a shift in predator diet immediately after rabbit population declines. Unlike after rabbit poisoning, clutch predation rate remained high in the years after RHD. Other patterns observed included higher clutch predation rate where nest density was lower, suggesting that predation can potentially cause local extinction. Clutch predation was also higher along riverbed margins where vegetation was dense. There was equivocal evidence for an effect of predator kill-trapping on clutch predation rate. Management strategies that could potentially reduce clutch predation risks include focusing predator mitigation measures during periods of rabbit decline, maintaining them for more than one breeding season if the rabbit declines are widespread (e.g. RHD epidemics), and applying greater effort at sites with relatively low nest density and along riverbed margins where predator use is more frequent.     

Mechanism for the definition of elongation and termination by the class II CCA‐adding enzyme

The CCA‐adding enzyme synthesizes the CCA sequence at the 3′ end of tRNA without a nucleic acid template. The crystal structures of class II Thermotoga maritima CCA‐adding enzyme and its complexes with CTP or ATP were determined. The structure‐based replacement of both the catalytic heads and nucleobase‐interacting neck domains of the phylogenetically closely related Aquifex aeolicus A‐adding enzyme by the corresponding domains of the T. maritima CCA‐adding enzyme allowed the A‐adding enzyme to add CCA in vivo and in vitro. However, the replacement of only the catalytic head domain did not allow the A‐adding enzyme to add CCA, and the enzyme exhibited (A, C)‐adding activity. We identified the region in the neck domain that prevents (A, C)‐adding activity and defines the number of nucleotide incorporations and the specificity for correct CCA addition. We also identified the region in the head domain that defines the terminal A addition after CC addition. The results collectively suggest that, in the class II CCA‐adding enzyme, the head and neck domains collaboratively and dynamically define the number of nucleotide additions and the specificity of nucleotide selection.