Body Forms in Sharks (Chondrichthyes: Elasmobranchii), and Their Functional, Ecological, and Evolutionary Implications

Sharks are among the oldest vertebrate lineages in which their success has been attributed to their diversity in body shape and locomotor design. In this study, I investigated the diversity of body forms in extant sharks using landmark-based geometric morphometric analyses on lateral view illustrations of nearly all the known (ca. 470) extant sharks in a published guidebook. I ran three different analyses: the ‘full body,\u27 ‘precaudal body,’ and ‘caudal fin\u27 analyses. My study suggests that there are two basic body forms in sharks. The two major body forms are characterized as a ‘shallow-bodied’ form (Group A) and ‘deep-bodied’ form (Group B). This pattern is also present in the precaudal body analysis, but the caudal fin analysis indicates that all sharks essentially have one basic caudal fin design. My geometric morphometric analyses have significant functional, ecological and evolutionary implications. First, I found that swimming modes in sharks are highly correlated with body forms. For example, Group A sharks are predominantly anguilliform swimmers, whereas Group B sharks are represented by carangiform and thunniform swimmers. Second, the majority of Group A sharks are found to be benthic whereas pelagic forms are relatively common among Group B sharks. Third, based on the known fossil record as well as previously published molecular-based phylogenetic trees, each of the two superorders of sharks, Squalomorphii and Galeomorphii, must have gone through complex evolutionary history where each superorder contains both Group A sharks and Group B sharks, possibly involving parallel evolution from one group to the other or at least one episode of evolutionary reversal. Lastly, the most ancestral shark, the clade that unites Squalomorphii and Galeomorphii, was possibly a benthic form with a Group A body form. My study demonstrates that a use of an identification guidebook can be a powerful method for the field of comparative anatomy

Seven benzimidazole pesticides combined at sub-threshold levels induce micronuclei in vitro

This article is made available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http:// creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Benzimidazoles act by disrupting microtubule polymerisation and are capable of inducing the formation of micronuclei. Considering the similarities in their mechanisms of action (inhibition of microtubule assembly by binding to the colchicine-binding site on tubulin monomers), combination effects according to the principles of concentration addition might occur. If so, it is to be expected that several benzimidazoles contribute to micronucleus formation even when each single one is present at or below threshold levels. This would have profound implications for risk assessment, but the idea has never been tested rigorously. To fill this gap, we analysed micronucleus frequencies for seven benzimidazoles, including the fungicide benomyl, its metabolite carbendazim, the anthelmintics albendazole, albendazole oxide, flubendazole, mebendazole and oxibendazole. Thiabendazole was also tested but was inactive. We used the cytochalasin-blocked micronucleus assay with CHO-K1 cells according to OECD guidelines, and employed an automated micronucleus scoring system based on image analysis to establish quantitative concentration–response relationships for the seven active benzimidazoles. Based on this information, we predicted additive combination effects for a mixture of the seven benzimidazoles by using the concepts of concentration addition and independent action. The observed effects of the mixture agreed very well with those predicted by concentration addition. Independent action underestimated the observed combined effects by a large margin. With a mixture that combined all benzimidazoles at their estimated threshold concentrations for micronucleus induction, micronucleus frequencies of ~15.5% were observed, correctly anticipated by concentration addition. On the basis of independent action, this mixture was expected to produce no effects. Our data provide convincing evidence that concentration addition is applicable to combinations of benzimidazoles that form micronuclei by disrupting microtubule polymerisation. They present a rationale for grouping these chemicals together for the purpose of cumulative risk assessment.United Kingdom Food Standards Agenc

Mapping and spatio-temporal analysis of flooded and inundated areas in the Lower Balonne floodplain, Queensland, Australia

[Abstract]: Water storage infrastructure developments and other land use changes may impact the extent of water flows and inundation in the floodplain. This may bring negative environmental effects and conflicts between competing users of water. In a case study of the Lower Balonne floodplain in Queensland, Australia, this project was conducted to quantify the changes on the spatial extent and patterns of flooded and inundated areas in a large, ephemeral floodplain river system. The study employed digital image processing techniques to produce inundation maps from the 1994 and 2004 flood events captured by Landsat 5 imagery. Using a landscape patterns analysis program (Patch Analyst) linked with a geographic information system (GIS), selected landscape metrics pertaining to patch size, shape, and connectivity were calculated and analysed. The results show not only the significant reduction (44,658 ha corresponding to 43% decrease) in the extent of the flooded and inundated areas, but also the changes on the spatial configuration of these patches. They became more fragmented and isolated, particularly in the lower region of the floodplain. This study concluded that the use of landscape metrics could be valuable for floodplain monitoring

2006 IASME/WSEAS International Conference on Energy, Environment, Ecosystems and Sustainable Development (EEESD'06)

[Abstract]: A case study of the Lower Balonne floodplain in Queensland, Australia, was conducted to quantify the changes on the spatial extent and patterns of flooded and inundated areas in a large, ephemeral floodplain. The study employed digital image processing techniques to produce inundation maps from the 1994 and 2004 flood events captured by Landsat 5 imagery. Using a geographic information system (GIS) based landscape patterns analysis program (Patch Analyst), selected landscape metrics pertaining to patch size, shape, and connectivity were calculated and analysed. The results show not only the significant reduction (44,658 ha corresponding to 43% decrease) in the extent of the flooded and inundated areas, but also the changes on the configuration of these patches. They became more fragmented and isolated, particularly in the lower region of the floodplain. The use of region-based analysis, rather than focusing solely on total area, has provided more information that subsequently linked these changes with water storage developments. This study concluded that the use of landscape metrics, along with conventional mapping of inundation extent, can support the monitoring of floodplain areas

Impedance bridge balancing using perturbation theory

This paper describes a technique for separating the two signal voltages which are necessary for balancing an ac impedance bridge from its detector output voltage. The technique is unique in that the necessary information is derived from modulations on the generator voltage. These modulations are formed by perturbing the variable arms at a fixed frequency but phased 90° apart. The two signals are then separated by phase detectors referenced to the modulation frequency and the proper phase. The perturbation increases and decreases the arm by a small amount; comparable to the action of a human operator increasing and decreasing the variable arm slightly to see which direction appears to lead to a null. Although no attempt was made to automate a bridge, this paper discusses the theoretical considerations for deriving the proper control signals for automating a bridge as well as experimental results obtained from a working model of such a system

Erratum to: ‘Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni’

<b>Background</b>\ud \ud <i>Oenococcus oeni</i> is a lactic acid bacterium that is specialised for growth in the ecological niche of wine, where it is noted for its ability to perform the secondary, malolactic fermentation that is often required for many types of wine. Expanding the understanding of strain-dependent genetic variations in its small and streamlined genome is important for realising its full potential in industrial fermentation processes.\ud \ud <b>Results</b>\ud \ud Whole genome comparison was performed on 191 strains of <i>O. oeni</i>; from this rich source of genomic information consensus pan-genome assemblies of the invariant (core) and variable (flexible) regions of this organism were established. Genetic variation in amino acid biosynthesis and sugar transport and utilisation was found to be common between strains. Furthermore, we characterised previously-unreported intra-specific genetic variations in the natural competence of this microbe.\ud \ud <b>Conclusion</b>\ud \ud By assembling a consensus pan-genome from a large number of strains, this study provides a tool for researchers to readily compare protein-coding genes across strains and infer functional relationships between genes in conserved syntenic regions. This establishes a foundation for further genetic, and thus phenotypic, research of this industrially-important species

HLA‑A alleles including HLA‑A29 affect the composition of the gut microbiome: A potential clue to the pathogenesis of birdshot retinochoroidopathy

Birdshot retinochoroidopathy occurs exclusively in individuals who are HLA-A29 positive. The mechanism to account for this association is unknown. The gut microbiome has been causally implicated in many immune-mediated diseases. We hypothesized that HLA-A29 would affect the composition of the gut microbiome, leading to a dysbiosis and immune-mediated eye disease. Fecal and intestinal biopsy samples were obtained from 107 healthy individuals from Portland, Oregon environs, 10 of whom were HLA-A29 positive, undergoing routine colonoscopy. Bacterial profiling was achieved via 16S rRNA metabarcoding. Publicly available whole meta-genome sequencing data from the Human Microbiome Project (HMP), consisting of 298 healthy controls mostly of US origin, were also interrogated. PERMANOVA and sparse partial least squares discriminant analysis (sPLSDA) demonstrated that subjects who were HLA-A29 positive differed in bacterial species composition (beta diversity) compared to HLA-A29 negative subjects in both the Portland (p = 0.019) and HMP cohorts (p = 0.0002). The Portland and HMP cohorts evidenced different subsets of bacterial species associated with HLA-A29 status, likely due to differences in the metagenomic techniques employed. The functional composition of the HMP cohort did not differ overall (p = 0.14) between HLA-A29 positive and negative subjects, although some distinct pathways such as heparan sulfate biosynthesis showed differences. As we and others have shown for various HLA alleles, the HLA allotype impacts the composition of the microbiome. We hypothesize that HLA-A29 may predispose chorioretinitis via an altered gut microbiome.</p

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation

Wine is a complex beverage, comprising hundreds of metabolites produced through the action of yeasts and bacteria in fermenting grape must. To ensure a robust and reliable fermentation, most commercial wines are produced via inoculation with commercial strains of the major wine yeast, Saccharomyces cerevisiae. However, there is a growing trend towards the use of uninoculated or "wild" fermentations, in which the yeasts and bacteria that are naturally associated with the vineyard and winery, perform the fermentation. In doing so, the varied metabolic contributions of the numerous non-Saccharomyces species in this microbial community are thought to impart complexity and desirable taste and aroma attributes to wild ferments in comparison to their inoculated counterparts. In order the map the microflora of spontaneous fermentation, metagenomic techniques were used to characterize and monitor the progression of fungal species in several wild fermentations. Both amplicon-based ITS phylotyping (meta-barcoding) and shotgun metagenomics were used to assess community structure. While providing a sensitive and highly accurate means of characterizing the wine microbiome, the shotgun metagenomic data also uncovered a significant over-abundance bias in the ITS phylotyping abundance estimations for the common non-Saccharomyces wine yeast genus Metschnikowia

The biogeography of the mucosa-associated microbiome in health and disease

IntroductionLittle is known about the biogeography of the mucosa associated microbiome (MAM) in patients with inflammatory bowel disease (IBD) versus controls in different segments of the gastrointestinal tract, as well as the links between the MAM, gastrointestinal symptoms, and use of proton pump inhibitors (PPI).MethodsWe recruited 59 controls (without structural abnormalities and gastrointestinal symptoms), 44 patients with ulcerative colitis (UC) and 31 with Crohn’s disease (CD). Biopsies from various segments of the upper and lower gastrointestinal tract were collected. Microbial composition was assessed via 16S rRNA gene amplicon analysis and the bacterial load of the mucosal biopsies were assessed via qPCR. The MAM was examined in the context of disease status, PPI usage, the severity of gastrointestinal symptoms, and the symptom response to a standardised nutrient challenge (SNC).ResultsMicrobial communities of the MAM in the upper and lower gastrointestinal tract differed. IBD patients were characterised by relative and absolute depletion of numerous genera known to produce butyrate and/or propionate, with the largest differentiation being the depletion of Faecalibacterium in the lower gastrointestinal tract of CD patients. Notably, PPI users exhibited an enrichment of Faecalibacterium in the lower gastrointestinal tract. The severity of gastrointestinal symptoms, as well as the symptom response to the SNC, were significantly associated with MAM composition in the gastrointestinal tract.ConclusionThe absolute and relative composition of the MAM is variable across different segments of the gastrointestinal tract. These quantitative changes indicates that MAM can be targeted in specific segments of the GI tract to improve patient outcomes

Epstein–Barr Virus DNase (BGLF5) induces genomic instability in human epithelial cells

Epstein–Barr Virus (EBV) DNase (BGLF5) is an alkaline nuclease and has been suggested to be important in the viral life cycle. However, its effect on host cells remains unknown. Serological and histopathological studies implied that EBV DNase seems to be correlated with carcinogenesis. Therefore, we investigate the effect of EBV DNase on epithelial cells. Here, we report that expression of EBV DNase induces increased formation of micronucleus, an indicator of genomic instability, in human epithelial cells. We also demonstrate, using γH2AX formation and comet assay, that EBV DNase induces DNA damage. Furthermore, using host cell reactivation assay, we find that EBV DNase expression repressed damaged DNA repair in various epithelial cells. Western blot and quantitative PCR analyses reveal that expression of repair-related genes is reduced significantly in cells expressing EBV DNase. Host shut-off mutants eliminate shut-off expression of repair genes and repress damaged DNA repair, suggesting that shut-off function of BGLF5 contributes to repression of DNA repair. In addition, EBV DNase caused chromosomal aberrations and increased the microsatellite instability (MSI) and frequency of genetic mutation in human epithelial cells. Together, we propose that EBV DNase induces genomic instability in epithelial cells, which may be through induction of DNA damage and also repression of DNA repair, subsequently increases MSI and genetic mutations, and may contribute consequently to the carcinogenesis of human epithelial cells