Phylogeny of Greya (Lepidoptera: Prodoxidae), based on nucleotide sequence variation in mitochondrial cytochrome oxidase I and II: congruence with morphological data

The phylogeny of Greya Busck (Lepidoptera: Prodoxidae) was inferred from nucleotide sequence variation across a 765-bp region in the cytochrome oxidase I and II genes of the mitochondrial genome. Most parsimonious relationships of 25 haplotypes from 16 Greya species and two outgroup genera (Tetragma and Prodoxus) showed substantial congruence with the species relationships indicated by morphological variation. Differences between mitochondrial and morphological trees were found primarily in the positions of two species, G. variabilis and G. pectinifera, and in the branching order of the three major species groups in the genus. Conflicts between the data sets were examined by comparing levels of homoplasy in characters supporting alternative hypotheses. The phylogeny of Greya species suggests that host-plant association at the family level and larval feeding mode are conservative characters. Transition/transversion ratios estimated by reconstruction of nucleotide substitutions on the phylogeny had a range of 2.0-9.3, when different subsets of the phylogeny were used. The decline of this ratio with the increase in maximum sequence divergence among taxa indicates that transitions are masked by transversions along deeper internodes or long branches of the phylogeny. Among transitions, substitutions of A-->G and T-->C outnumbered their reciprocal substitutions by 2-6 times, presumably because of the approximately 4:1 (77%) A+T-bias in nucleotide base composition. Of all transversions, 73%-80% were A<-->T substitutions, 85% of which occurred at third positions of codons; these estimates did not decrease with an increase in maximum sequence divergence of taxa included in the analysis. The high frequency of A<-->T substitutions is either a reflection or an explanation of the 92% A+T bias at third codon positions.      

Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.     

Caspase-mediated cleavage of the exosome subunit PM/Scl-75 during apoptosis

Recent studies have implicated the dying cell as a potential reservoir of modified autoantigens that might initiate and drive systemic autoimmunity in susceptible hosts. A number of subunits of the exosome, a complex of 3'→5' exoribonucleases that functions in a variety of cellular processes, are recognized by the so-called anti-PM/Scl autoantibodies, found predominantly in patients suffering from an overlap syndrome of myositis and scleroderma. Here we show that one of these subunits, PM/Scl-75, is cleaved during apoptosis. PM/Scl-75 cleavage is inhibited by several different caspase inhibitors. The analysis of PM/Scl-75 cleavage by recombinant caspase proteins shows that PM/Scl-75 is efficiently cleaved by caspase-1, to a smaller extent by caspase-8, and relatively inefficiently by caspase-3 and caspase-7. Cleavage of the PM/Scl-75 protein occurs in the C-terminal part of the protein at Asp369 (IILD³⁶⁹↓G), and at least a fraction of the resulting N-terminal fragments of PM/Scl-75 remains associated with the exosome. Finally, the implications of PM/Scl-75 cleavage for exosome function and the generation of anti-PM/Scl-75 autoantibodies are discussed.     

Evaluation of water entry into the coelom and different levels of aseptic technique during surgical implantation of electronic tags in freshwater fish

We reviewed the literature in an attempt to determine the importance of aseptic technique when implanting electronic tags in fish. Given that there was negligible information on this topic we embarked on a study where bluegill (Lepomis macrochirus) were used as a model to investigate the effects of different aseptic surgical techniques for the intracoelomic implantation of electronic tags in fish. First we tested the effects of water entry into the incision using five treatments: lake, distilled and saline water introduced into the incision, water-free controls, and non-surgery controls. For fish in the water treatments, 1 mL of the sample was introduced into their coelom prior to incision closure. Fish were held for 10 days to monitor survival and at the end of the study, the survivors were blood sampled and euthanized to evaluate condition and health using the health assessment index. In a second experiment, four aseptic treatments were used: non-sterile, field-based, high-grade sterility, and non-surgery controls and fish were monitored as in the first experiment. For both experiments, no differences in physiological status, health or mortality were noted among treatment groups. However, in the aseptic techniques experiment, surgical times were approximately twice as long for fish in the sterile treatment as compared to other groups and the costs of surgical supplies was greater than that of the less-sterile treatments. Although we failed to document any benefit of keeping water out of the incision or using aseptic technique for bluegill, in other situations and for other species, such approaches may be important. As such, we encourage fish surgeons practicing intracoelomic implants to attempt to prevent water entry into the coelom. We also encourage, at least some level of infection control (e.g., non-sterile gloves, clean tags and surgical tools) consistent with good veterinary practices to maintain the welfare status of tagged fish and ensure that the data from tagged fish representative of untagged conspecifics. However, the most prudent and ethical approach would be to work with veterinarians to incorporate formal sterilization procedures, equipment (e.g., sterile gloves) and aseptic technique into field surgical techniques.     

Trends in the reporting of tagging procedures for fish telemetry studies that have used surgical implantation of transmitters: a call for more complete reporting

The intracoelomic surgical implantation of telemetry transmitters in fish is becoming the “standard” tagging approach for most field telemetry studies. Subsequently, efforts must be made to ensure the welfare of the fish are maintained and that fish do not experience significant mortality or sublethal impairments in health, behavior or physiology as a result of surgical procedures. Therefore, it is essential to adequately report information relating to all aspects of the surgical procedure to enable the reader to make an accurate interpretation of study results. We conducted a quantitative literature review aimed at characterizing trends in data reporting by examining a sample of fish telemetry studies published in peer-reviewed outlets during the last 20 years. We used a repeatability score, based on 16 predetermined criteria, to evaluate the reporting of surgical procedures in telemetry studies. The majority of studies failed to report basic information relating to the surgical procedures used. Repeatability scores were highly variable between studies and ranged from 0–93.8%. No single study provided complete information (mean repeatability score = 50.7%) and repeatability showed no trend over time. Some study information was consistently well reported (e.g. tag size and dimensions, the type of anaesthetic used and the location of incision). In contrast, the type of suture knots, duration or level of anaesthesia and precautions taken to minimize infection were consistently left out of the methods section of most telemetry studies. Our review was confounded by the large proportion of studies that cited other sources for their surgical methods, many of which themselves lacked complete information. We recommend that future electronic tagging studies that involve intracoelomic implantation include the minimum reporting standards presented in this paper. Increasing the detail of reporting will improve the quality of data presented, minimize welfare and ethical concerns and allow transparency for study repeatability.     

Enhanced tolerance to autoimmune uveitis in CD200-deficient mice correlates with a pronounced Th2 switch in response to antigen challenge

A single exposure to inhaled Ag 10 days before immunization leads to long term, Ag-specific tolerance. Respiratory tract myeloid APCs are implicated, but how regulation is invoked, and how tolerance is sustained are unclear. This study examines the in vivo function of the myeloid regulatory molecule CD200 in the process of tolerance induction. Despite earlier onset of experimental autoimmune uveitis in sham-tolerized, CD200-deficient mice, disease incidence and subsequent severity were actually reduced compared with those in wild-type mice. Protection was more effective and long term, lasting at least 28 days. Halting disease progression and tolerance in CD200(-/-) mice correlated with a marked increase in Th2-associated cytokine production by Ag-challenged splenocytes. Reduced overall disease and enhanced tolerance in the CD200-deficient mice in this model system were unexpected and may be related to altered populations of MHC class II(low) APC in the respiratory tract compared with wild-type mice together with associated activation of STAT6 in draining lymph nodes of tolerized mice. These data indicate that in the absence of default inhibitory CD200 receptor signaling, alternative, powerful regulatory mechanisms are invoked. This may represent either permissive dominant Th2 activation or an altered hierarchy of negative signaling by other myeloid cell-expressed regulatory molecules.     

The human exosome: an autoantigenic complex of exoribonucleases in myositis and scleroderma

The anti-PM/Scl autoantibodies are known to characterize a subset of autoimmune patients with myositis, scleroderma (Scl), and the PM/Scl overlap syndrome. The major autoantigens that are recognized by anti-PM/Scl autoantibodies are designated PM/Scl-100 and PM/Scl-75. These autoantigens have been reported to associate into a large complex consisting of 11 to 16 proteins and to play a role in ribosome synthesis. Recently, it was discovered that the PM/Scl complex is the human counterpart of the yeast (Saccharomyces cerevisiae) exosome, which is an RNA-processing complex consisting of 11 3' → 5' exoribonucleases. To date, 10 human exosome components have been identified, although only some of these were studied in more detail. In this review, we discuss some recent advances in the characterization of the PM/Scl complex.