Holding of juvenile salmonids for surgical implantation of electronic tags: a review and recommendations

Many telemetry-based studies require that fish be sampled from the wild and then held both prior to and after the implantation of an electronic tag. However, the effects of such holding (or the lack thereof) have yet to be studied intensively. Pre-surgical holding often occurs to facilitate logistical needs of research projects and as an attempt to minimize negative physiological effects due to capture and handling stress. Further, post-surgical holding time and conditions greatly influence the physiological state of fish prior to being returned to the wild. This paper reviews pertinent studies pertaining to the effects of surgical holding on the behavior, physiology, and survival of fishes, with particular emphasis on juvenile salmonids. The effects of individual aspects of surgical holding such as handling, water quality, light conditions, holding density, metabolic scope, and duration of holding are reviewed. Recommendations regarding certain aspects of surgical holding are offered with a goal of reducing bias related to the surgical process.     

Random Transposon-Mediated Mutagenesis of the Essential Large Tegument Protein pUL36 of Pseudorabies Virus

Homologs of the pseudorabies virus (PrV) essential large tegument protein pUL36 are conserved throughout the Herpesviridae. pUL36 functions during transport of the nucleocapsid to and docking at the nuclear pore as well as during virion formation after nuclear egress in the cytoplasm. Deletion analyses revealed several nonessential regions within the 3,084-amino-acid PrV pUL36 (S. Böttcher, B. G. Klupp, H. Granzow, W. Fuchs, K. Michael, and T. C. Mettenleiter, J. Virol. 80:9910-9915, 2006; S. Böttcher, H. Granzow, C. Maresch, B. Möhl, B. G. Klupp, and T. C. Mettenleiter, J. Virol. 81:13403-13411, 2007), while the C-terminal 62 amino acids are essential for virus replication (K. Coller, J. Lee, A. Ueda, and G. Smith, J. Virol. 81:11790-11797, 2007). To identify additional functional domains, we performed random mutagenesis of PrV pUL36 by transposon-mediated insertion of a 15-bp linker. By this approach, 26 pUL36 insertion mutants were selected and tested in transient transfection assays for their ability to complement one-step growth and/or viral spread of a PrV UL36 null mutant. Ten insertion mutants in the N-terminal half and 10 in the C terminus complemented both, whereas six insertion mutants clustering in the center of the protein did not complement in either assay. Interestingly, several insertions within conserved parts yielded positive complementation, including those located within the essential C-terminal 62 amino acids. For 15 mutants that mediated productive replication, stable virus recombinants were isolated and further characterized by plaque assay, in vitro growth analysis, and electron microscopy. Except for three mutant viruses, most insertion mutants replicated like wild-type PrV. Two insertion mutants, at amino acids (aa) 597 and 689, were impaired in one-step growth and viral spread and exhibited a defect in virion maturation in the cytoplasm. In contrast, one functional insertion (aa 1800) in a region which otherwise yielded only nonfunctional insertion mutants was impaired in viral spread but not in one-step growth without a distinctive ultrastructural phenotype. In summary, these studies extend and refine previous analyses of PrV pUL36 and demonstrate the different sensitivities of different regions of the protein to functional loss by insertion.The herpesvirus particle is composed of four structural elements. The DNA genome-containing core is enclosed in an icosahedral capsid, which, in turn, is embedded in a proteinaceous layer termed the tegument and enveloped by a cell-derived membrane containing viral glycoproteins (35). The tegument of the Alphaherpesvirinae contains more than 15 different viral and several cellular proteins and can be structurally and functionally separated into at least two layers: a capsid-proximal “inner” part and an envelope-associated “outer” part (reviewed in references 34 and 35). The largest tegument proteins in all herpesviruses analyzed so far are homologs of herpes simplex virus type 1 (HSV-1) pUL36, which are essential for viral replication. pUL36, its interaction partner, pUL37, and the pUS3 kinase are part of the inner tegument and remain associated with nucleocapsids during their transport along microtubules to the nuclear pore (2, 3, 19, 31). In contrast, other tegument proteins like pUL46, pUL47, and pUL49 rapidly diffuse in the cytoplasm after fusion of the virion envelope with the plasma membrane. Proteolytic cleavage of HSV-1 pUL36 after docking of the nucleocapsid to the nuclear pore appears to be required for release of viral DNA into the nucleus (22). Besides these roles early in infection, pUL36 also functions during later stages of replication in virion maturation. After assembly in the nucleus, nucleocapsids are translocated to the cytoplasm by budding at the inner nuclear membrane and fusion with the outer nuclear membrane (34). Although functional nuclear localization motifs have been described for pseudorabies virus (PrV) and HSV-1 pUL36 (1, 37), in PrV-infected cells, pUL36 was never detected in the nucleus but was added to nascent virions early after nuclear egress (18, 27, 31, 37). It has been suggested that pUL36 interacts either directly (9, 32, 42, 44) or indirectly via capsid-associated pUL25 (10) with the capsid shell starting the tegumentation process in the cytosol.In PrV, pUL36 is the only tegument protein which has been shown to be truly essential. It consists of 3,084 amino acids (aa), resulting in a molecular mass of more than 300 kDa (27). Deletion of pUL36 in HSV-1 and PrV abolished viral replication. Ultrastructurally, similar phenotypes with nonenveloped nucleocapsids present in the cytoplasm and the lack of extracellular particles indicated a defect in virion maturation in the cytoplasm (13, 16). Several functional domains have been identified in pUL36. The interaction domain of pUL36 with pUL37 (5, 16, 20, 27, 36, 42) could be located in the N-terminal part of PrV and HSV-1 pUL36 (16, 36) (Fig. ​(Fig.1).1). Deletion of the pUL37 binding site in PrV pUL36 (PrV-UL36BSF) resulted in a similar phenotype to deletion of pUL37 with an impairment of secondary envelopment in the cytoplasm (16, 26). Unlike in PrV, pUL37 is essential for replication in HSV-1 (14, 30).Open in a separate windowFIG. 1.Schematic overview of PrV pUL36 and corresponding insertion mutants. (A) Diagram of the PrV genome with the unique long (U_L) and unique short (U_S) regions as well as repeat regions (internal repeat, IR; terminal repeat, TR). The positions of BamHI restriction sites are indicated, and restriction fragments are numbered according to their size. (B) Schematic diagram of the UL36 open reading frame with conserved regions. Pfam analysis (4; http://www.sanger.ac.uk/Software/Pfam/) delineated two highly conserved PfamA domains within pUL36 homologs of herpesviruses of all three herpesvirus subfamilies [box I, Herpes_teg_N PrV (p)UL36, aa 11 to 178] and of alphaherpesviruses [box II, Herpes_UL36 PrV (p)UL36, aa 1000 to 1251] as well as PfamB domains (hatched rectangles) (6) (C) Known essential and nonessential regions in PrV pUL36. Nonessential regions are shown in gray, with the positions of the amino acids deleted in the corresponding constructs (6, 8). Deletions tested by Lee et al. (28) are shown below, marked by arrows. The essential C terminus is shown in black. Besides the N-terminal deletion Δ6-225, none of the truncated proteins was functional. (D) Predicted or identified motifs in pUL36: USP (Cys26), active-site cysteine of the deubiquitinating activity (24); pUL37 interaction domain (16, 27); NLS, nuclear localization signal (37); leucine zipper (27); and late domain motifs PPKY and PSAP (6). (E) Locations of linker insertions in pUL36 are indicated by arrows and the position of the amino acid immediately preceding the insertion. Insertions shown by arrows pointing upwards yielded functional proteins, while arrows pointing downwards indicate nonfunctional mutants. Insertions resulting in proteins which were impaired but not fully deficient in complementation are underlined. For orientation, the BamHI site separating BamHI fragments 1 and 2 is indicated.A second functional domain in the N terminus of pUL36 comprises a ubiquitin-specific cysteine protease (USP) activity which could be identified in all three herpesvirus subfamilies (24, 40, 41). Interestingly, the USP activity is not essential for virus replication in cell culture (7, 21, 25, 43). However, it is relevant for oncogenicity of Marek′s disease virus (MDV) (21) and for virion maturation and neuroinvasion of PrV (7, 8, 29).Several other regions in PrV pUL36 were deleted without abolishing virus replication (6, 8, 28). While deletion of nearly 1/3 of the protein in the C-terminal part (aa 2087 to 2981) had only a slight effect, deletion of a region containing two leucine zipper motifs impaired virus replication and spread more strongly (8). The highly conserved C-terminal 62 amino acids, except for the extreme C-terminal 6 amino acids, are essential for virus replication (6, 28). Due to the size of the protein, a more detailed mutagenesis analysis has, however, not yet been undertaken.Therefore, the aim of our study was to construct random insertion mutants of PrV pUL36 using transposon-mediated insertion mutagenesis resulting in a 5-amino-acid linker insertion. Mutant proteins were analyzed functionally in transient transfection assays for complementation, and stable recombinants were isolated and further characterized.     

Magnetic and contrast properties of labeled platelets for magnetomotive optical coherence tomography

This article introduces a new functional imaging paradigm that uses optical coherence tomography (OCT) to detect rehydrated, lyophilized platelets (RL platelets) that are in the preclinical trial stage and contain superparamagnetic iron oxides (SPIOs) approved by the U.S. Food and Drug Administration. Platelets are highly functional blood cells that detect and adhere to sites of vascular endothelial damage by forming primary hemostatic plugs. By applying magnetic gradient forces, induced nanoscale displacements (magnetomotion) of the SPIO-RL platelets are detected as optical phase shifts in OCT. In this article, we characterize the iron content and magnetic properties of SPIO-RL platelets, construct a model to predict their magnetomotion in a tissue medium, and demonstrate OCT imaging in tissue phantoms and ex vivo pig arteries. Tissue phantoms containing SPIO-RL platelets exhibited >3 dB contrast/noise ratio at ≥1.5 × 10⁹ platelets/cm³. OCT imaging was performed on ex vivo porcine arteries after infusion of SPIO-RL platelets, and specific contrast was obtained on an artery that was surface-damaged (P < 10⁻⁶). This may enable new technologies for in vivo monitoring of the adherence of SPIO-RL platelets to sites of bleeding and vascular damage, which is broadly applicable for assessing trauma and cardiovascular diseases.     

Distribution of deoxynivalenol inFusarium-infected forage maize

A time course study was carried out to assess the appearance and distribution of DON in different organs of forage maize cultivated in the field. DON was produced after the flowering period and increased until harvest to high amounts in the rudimentary ears and leaf sheaths/leaf blades deriving from nodes located below the ear node, whereas nodes and internodes were either not or only slightly contaminated with DON. Genrally, DON was not detected in the ears, including husks, during the whole cultivation time.Fusarium biomass determined in the infected organs confirmed these findings. It seems that the contribution of DON containing rudimentary ears, leaf sheaths and leaf blades to the total DON contamination of forage maize is so far widely underestimated. Therefore advanced evaluation procedures are recommended to get a better understanding of the infection and contamination process and to prove genotypic differences in the resistance of forage maize genotypes againstFusarium infection.     

Cholinergic interneurons mediate fast VGluT3-dependent glutamatergic transmission in the striatum

The neurotransmitter glutamate is released by excitatory projection neurons throughout the brain. However, non-glutamatergic cells, including cholinergic and monoaminergic neurons, express markers that suggest that they are also capable of vesicular glutamate release. Striatal cholinergic interneurons (CINs) express the Type-3 vesicular glutamate transporter (VGluT3), although whether they form functional glutamatergic synapses is unclear. To examine this possibility, we utilized mice expressing Cre-recombinase under control of the endogenous choline acetyltransferase locus and conditionally expressed light-activated Channelrhodopsin2 in CINs. Optical stimulation evoked action potentials in CINs and produced postsynaptic responses in medium spiny neurons that were blocked by glutamate receptor antagonists. CIN-mediated glutamatergic responses exhibited a large contribution of NMDA-type glutamate receptors, distinguishing them from corticostriatal inputs. CIN-mediated glutamatergic responses were insensitive to antagonists of acetylcholine receptors and were not seen in mice lacking VGluT3. Our results indicate that CINs are capable of mediating fast glutamatergic transmission, suggesting a new role for these cells in regulating striatal activity.     

Roles of Thermophiles and Fungi in Bitumen Degradation in Mostly Cold Oil Sands Outcrops

Oil sands are surface exposed in river valley outcrops in northeastern Alberta, where flat slabs (tablets) of weathered, bitumen-saturated sandstone can be retrieved from outcrop cliffs or from riverbeds. Although the average yearly surface temperature of this region is low (0.7°C), we found that the temperatures of the exposed surfaces of outcrop cliffs reached 55 to 60°C on sunny summer days, with daily maxima being 27 to 31°C. Analysis of the cooccurrence of taxa derived from pyrosequencing of 16S/18S rRNA genes indicated that an aerobic microbial network of fungi and hydrocarbon-, methane-, or acetate-oxidizing heterotrophic bacteria was present in all cliff tablets. Metagenomic analyses indicated an elevated presence of fungal cytochrome P450 monooxygenases in these samples. This network was distinct from the heterotrophic community found in riverbeds, which included fewer fungi. A subset of cliff tablets had a network of anaerobic and/or thermophilic taxa, including methanogens, Firmicutes, and Thermotogae, in the center. Long-term aerobic incubation of outcrop samples at 55°C gave a thermophilic microbial community. Analysis of residual bitumen with a Fourier transform ion cyclotron resonance mass spectrometer indicated that aerobic degradation proceeded at 55°C but not at 4°C. Little anaerobic degradation was observed. These results indicate that bitumen degradation on outcrop surfaces is a largely aerobic process with a minor anaerobic contribution and is catalyzed by a consortium of bacteria and fungi. Bitumen degradation is stimulated by periodic high temperatures on outcrop cliffs, which cause significant decreases in bitumen viscosity.     

Classification of α-Helical Membrane Proteins Using Predicted Helix Architectures

Despite significant methodological advances in protein structure determination high-resolution structures of membrane proteins are still rare, leaving sequence-based predictions as the only option for exploring the structural variability of membrane proteins at large scale. Here, a new structural classification approach for α-helical membrane proteins is introduced based on the similarity of predicted helix interaction patterns. Its application to proteins with known 3D structure showed that it is able to reliably detect structurally similar proteins even in the absence of any sequence similarity, reproducing the SCOP and CATH classifications with a sensitivity of 65% at a specificity of 90%. We applied the new approach to enhance our comprehensive structural classification of α-helical membrane proteins (CAMPS), which is primarily based on sequence and topology similarity, in order to find protein clusters that describe the same fold in the absence of sequence similarity. The total of 151 helix architectures were delineated for proteins with more than four transmembrane segments. Interestingly, we observed that proteins with 8 and more transmembrane helices correspond to fewer different architectures than proteins with up to 7 helices, suggesting that in large membrane proteins the evolutionary tendency to re-use already available folds is more pronounced.     

Size and Structure of Replicating Mitochondrial DNA in Cultured Tobacco Cells

The BY-2 tobacco cell line was used to study the size and structure of replicating mitochondrial DNA (mtDNA). Approximately 70 to 90% of the newly synthesized mtDNA did not migrate during pulsed-field gel electrophoresis. Moving pictures of the fluorescently labeled molecules showed that most of the immobile well-bound DNA was in structures larger than the size of the BY-2 mitochondrial genome of ~270 kb. Most of the structures appeared as complex forms with multiple DNA fibers. The sizes of the circular molecules that were also observed ranged continuously from ~20 to 560 kb without prominent size classes. Pulse-chase and mung bean nuclease experiments showed that the well-bound DNA contained single-stranded regions and was converted to linear molecules of between 50 and 150 kb. MtDNA replication in plants may be initiated by recombination events that create branched structures of multigenomic concatemers that are then processed to 50- to 150-kb subgenomic fragments.     

Mapping of linear epitopes recognized by monoclonal antibodies with gene-fragment phage display libraries

Epitope mapping with mono- or polyclonal antibodies has so far been done either by dissecting the antigens into overlapping polypeptides in the form of recombinantly expressed fusion proteins, or by synthesizing overlapping short peptides, or by a combination of both methods. Here, we report an alternative method which involves the generation of random gene fragments of approximately 50–200 by in length and cloning these into the 5 terminus of the protein III gene of fd phages. Selection for phages that bind a given monoclonal antibody and sequencing the DNA inserts of immunopositive phages yields derived amino acid sequences containing the desired epitope. A monoclonal antibody (mAb 215) directed against the largest subunit of Drosophila RNA polymerase II (RPB215) was used to map the corresponding epitope in a fUSE5 phage display library made of random DNA fragments from plasmid DNA containing the entire gene. After a single round of panning with this phage library, bacterial colonies were obtained which produced fd phages displaying the mAb 215 epitope. Sequencing of single-stranded phage DNA from a number of positive colonies (recognized by the antibody on colony immunoblots) resulted in overlapping sequences all containing the 15mer epitope determined by mapping with synthetic peptides. Similarly, we have localized the epitopes recognized by a mouse monoclonal antibody directed against the human p53 protein, and by a mouse monoclonal antibody directed against the human cytokeratin 19 protein. Identification of positive colonies after the panning procedure depends on the detection system used (colony immunoblot or ELISA) and there appear to be some restrictions to the use of linker-encoded amino acids for optimal presentation of epitopes. A comparison with epitope mapping by synthetic peptides shows that the phage display method allows one to map linear epitopes down to a size only slightly larger than the true epitope. In general, our phage display method is faster, easier, and cheaper than the construction of overlapping fusion proteins or the use of synthetic peptides, especially in cases where the antigen is a large polypeptide such as the 215 kDa subunit of eukaryotic RNA polymerase II.