The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance
Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible existence of alternative forms of pAsa4, a large plasmid found in A. salmonicida subsp. salmonicida and bearing multiple antibiotic resistance genes. The present study reveals the existence of two newly detected pAsa4 variants, pAsa4b and pAsa4c. We present the extensive characterization of the genomic architecture, the mobile genetic elements and the antimicrobial resistance genes of these plasmids in addition to the reference pAsa4 from the strain A449. The analysis showed differences between the three architectures with consequences on the content of resistance genes. The genomic plasticity of the three pAsa4 variants could be partially explained by the action of mobile genetic elements like insertion sequences. Eight additional isolates from Canada and Europe that bore similar antibiotic resistance patterns as pAsa4-bearing strains were genotyped and specific pAsa4 variants could be attributed to phenotypic profiles. pAsa4 and pAsa4c were found in Europe, while pAsa4b was found in Canada. In accordance with their content in conjugative transfer genes, only pAsa4b and pAsa4c can be transferred by conjugation in Escherichia coli. The plasticity of pAsa4 variants related to the acquisition of antibiotic resistance indicates that these plasmids may pose a threat in terms of the dissemination of antimicrobial-resistant A. salmonicida subsp. salmonicida bacteria.
Tanaka et al. (2016) The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance. PeerJ 4:e2595 https://doi.org/10.7717/peerj.2595
Who’s your mama? Riverine hybridisation of threatened freshwater Trout Cod and Murray Cod
Rates of hybridization and introgression are increasing dramatically worldwide because of translocations, restocking of organisms and habitat modifications; thus, determining whether hybridization is occuring after reintroducing extirpated congeneric species is commensurately important for conservation. Restocking programs are sometimes criticized because of the genetic consequences of hatchery-bred fish breeding with wild populations. These concerns are important to conservation restocking programs, including those from the Australian freshwater fish family, Percichthyidae. Two of the better known Australian Percichthyidae are the Murray Cod, Maccullochella peelii and Trout Cod, Maccullochella macquariensis which were formerly widespread over the Murray Darling Basin. In much of the Murrumbidgee River, Trout Cod and Murray Cod were sympatric until the late 1970s when Trout Cod were extirpated. Here we use genetic single nucleotide polymorphism (SNP) data together with mitochondrial sequences to examine hybridization and introgression between Murray Cod and Trout Cod in the upper Murrumbidgee River and consider implications for restocking programs. We have confirmed restocked riverine Trout Cod reproducing, but only as inter-specific matings, in the wild. We detected hybrid Trout Cod–Murray Cod in the Upper Murrumbidgee, recording the first hybrid larvae in the wild. Although hybrid larvae, juveniles and adults have been recorded in hatcheries and impoundments, and hybrid adults have been recorded in rivers previously, this is the first time fertile F1 have been recorded in a wild riverine population. The F1 backcrosses with Murray cod have also been found to be fertile. All backcrosses noted were with pure Murray Cod. Such introgression has not been recorded previously in these two species, and the imbalance in hybridization direction may have important implications for restocking programs.
Couch et al. (2016) Who’s your mama? Riverine hybridisation of threatened freshwater Trout Cod and Murray Cod. PeerJ 4:e2593 https://doi.org/10.7717/peerj.2593
Comparative internal anatomy of Staurozoa (Cnidaria), with functional and evolutionary inferences
Comparative efforts to understand the body plan evolution of stalked jellyfishes are scarce. Most characters, and particularly internal anatomy, have neither been explored for the class Staurozoa, nor broadly applied in its taxonomy and classification. Recently, a molecular phylogenetic hypothesis was derived for Staurozoa, allowing for the first broad histological comparative study of staurozoan taxa. This study uses comparative histology to describe the body plans of nine staurozoan species, inferring functional and evolutionary aspects of internal morphology based on the current phylogeny of Staurozoa. We document rarely-studied structures, such as ostia between radial pockets, intertentacular lobules, gametoducts, pad-like adhesive structures, and white spots of nematocysts (the last four newly proposed putative synapomorphies for Staurozoa). Two different regions of nematogenesis are documented. This work falsifies the view that the peduncle region of stauromedusae only retains polypoid characters; metamorphosis from stauropolyp to stauromedusa occurs both at the apical region (calyx) and basal region (peduncle). Intertentacular lobules, observed previously in only a small number of species, are shown to be widespread. Similarly, gametoducts were documented in all analyzed genera, both in males and females, thereby elucidating gamete release. Finally, ostia connecting adjacent gastric radial pockets appear to be universal for Staurozoa. Detailed histological studies of medusozoan polyps and medusae are necessary to further understand the relationships between staurozoan features and those of other medusozoan cnidarians.
Miranda et al. (2016) Comparative internal anatomy of Staurozoa (Cnidaria), with functional and evolutionary inferences. PeerJ 4:e2594 https://doi.org/10.7717/peerj.2594
Pacing during an ultramarathon running event in hilly terrain
Purpose The dynamics of speed selection as a function of distance, or pacing, are used in recreational, competitive, and scientific research situations as an indirect measure of the psycho-physiological status of an individual. The purpose of this study was to determine pacing on level, uphill and downhill sections of participants in a long (>80 km) ultramarathon performed on trails in hilly terrain. Methods Fifteen ultramarathon runners competed in a 173 km event (five finished at 103 km) carrying a Global-Positioning System (GPS) device. Using the GPS data, we determined the speed, relative to average total speed, in level (LEV), uphill (UH) and downhill (DH) gradient categories as a function of total distance, as well as the correlation between overall performance and speed variability, speed loss, and total time stopped. Results There were no significant differences in normality, variances or means in the relative speed in 173-km and 103-km participants. Relative speed decreased in LEV, UH and DH. The main component of speed loss occurred between 5% and 50% of the event distance in LEV, and between 5% and 95% in UH and DH. There were no significant correlations between overall performance and speed loss, the variability of speed, or total time stopped. Conclusions Positive pacing was observed at all gradients, with the main component of speed loss occurring earlier (mixed pacing) in LEV compared to UH and DH. A speed reserve (increased speed in the last section) was observed in LEV and UH. The decrease in speed and variability of speed were more important in LEV and DH than in UH. The absence of a significant correlation between overall performance and descriptors of pacing is novel and indicates that pacing in ultramarathons in trails and hilly terrain differs to other types of running events.
Kerhervé et al. (2016) Pacing during an ultramarathon running event in hilly terrain. PeerJ 4:e2591 https://doi.org/10.7717/peerj.2591
The influence of socioeconomic factors on the densities of high-value cross-border species, the African elephant
Unprecedented poaching levels triggered by demand for ivory in Far East Asia are threatening the persistence of African elephant Loxodonta africana. Southern African countries make an important contribution to elephant conservation and could soon become the last stronghold of elephant conservation in Africa. While the ecological factors affecting elephant distribution and densities have extensively been accounted for, there is a need to understand which socioeconomic factors affect elephant numbers in order to prevent conflict over limited space and resources with humans. We used elephant count data from aerial surveys for seven years in a generalized linear model, which accounted for temporal correlation, to investigate the effect of six socioeconomic and ecological variables on the number of elephant at the country level in the Greater Mapungubwe Transfrontier Conservation Area (GMTFCA). Important factors in predicting elephant numbers were the proportion of total land surface under cultivation, human population density and the number of tourists visiting the country. Specifically, elephant numbers were higher where the proportion of total land surface under cultivation was the lowest; where population density was the lowest and where tourist numbers had increased over the years. Our results confirm that human disturbance is affecting elephant numbers, but highlight that the benefits provided by ecotourism could help enhance elephant conservation. While future studies should include larger areas and more detailed data at the site level, we stress that the development of coordinated legislation and policies to improve land-use planning are needed to reduce the impact of increasing human populations and agriculture on elephant.
Selier et al. (2016) The influence of socioeconomic factors on the densities of high-value cross-border species, the African elephant. PeerJ 4:e2581 https://doi.org/10.7717/peerj.2581
A retrospective study detects a novel variant of porcine epidemic diarrhea virus in England in archived material from the year 2000
Outbreaks of porcine epidemic diarrhea (PED) were first recorded in England in the 1970s and continued to be confirmed until 2002. Retrospective analysis of archived material from one of the last confirmed cases in England in the year 2000 demonstrates the previous existence of a very diverse PED virus strain. Following the outbreaks of PED in North America in 2013, there has been renewed interest in phylogenetic analysis of sequences from PEDV strains worldwide. There is a gap in the available sequence data between the mid 1980s and the mid 2000s. This work is an example of how this gap can be at least partially filled by the examination of archived material.
Steinbach et al. (2016) A retrospective study detects a novel variant of porcine epidemic diarrhea virus in England in archived material from the year 2000. PeerJ 4:e2564 https://doi.org/10.7717/peerj.2564
Post-reproductive parthenogenetic pea aphids (Acyrthosiphon pisum) are visually identifiable and disproportionately positioned distally to clonal colonies
The role of kin-selection in the evolution of post-reproductive life is controversial. While anthropological and demographic studies strongly suggest that humans and a few other species experience kin selection for significant post-reproductive survival, these results are necessarily correlational. Understanding could therefore be advanced by the development of a globally available, field and laboratory tractable experimental model of kin-selected post-reproductive survival. In only one invertebrate (Quadrartus yoshinomiyai, a gall-forming aphid endemic to Japan) have individuals too old to reproduce been shown to be both numerous in natural habitats and able to help close relatives survive or reproduce. Pea aphids, (Acyrthosiphon pisum), common, tractable organisms, frequently outlive their reproductive ages in laboratories, live in tight interacting groups that are often clonal, and therefore should be evaluated as potential model organisms for the study of adaptive post-reproductive life. The first major step in this process is to identify an optimal method for assessing if a parthenogenetic adult is post-reproductive. We evaluated three methods, relying respectively on isolation in clip cages, visual examination for embryonic eyespots, and dissection. In every case each method identified the same individuals as reproductive versus post-reproductive. While the clip-cage method requires a multi-day wait to produce data, and dissection is inevitably fatal, the eyespot method is quick (under one minute per individual) easy, and non-invasive. This method makes it possible to accurately assess the post-reproductive status of a large number of parthenogenetic pea aphids. We demonstrate the usefulness of the eyespot method in showing that while reproductively valuable adults tend to place themselves near the centers of clonal colonies, less valuable post-reproductive adults are more often at or beyond the edges of colonies. These encouraging early results provide both impetuous and aid for further investigations into the post-reproductive lives of pea aphids.
Saberski et al. (2016) Post-reproductive parthenogenetic pea aphids (Acyrthosiphon pisum) are visually identifiable and disproportionately positioned distally to clonal colonies. PeerJ 4:e2631 https://doi.org/10.7717/peerj.2631
Early evolution of polyisoprenol biosynthesis and the origin of cell walls
After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted. By contrast, cenancestral cell walls have attracted less attention, probably owing to the large diversity of cell walls that exist in the three domains of life. Many prokaryotic cell walls, however, are synthesized using glycosylation pathways with similar polyisoprenol lipid carriers and topology (i.e., orientation across the cell membranes). Here, we provide the first systematic phylogenomic report on the polyisoprenol biosynthesis pathways in the three domains of life. This study shows that, whereas the last steps of the polyisoprenol biosynthesis are unique to the respective domain of life of which they are characteristic, the enzymes required for basic unsaturated polyisoprenol synthesis can be traced back to the respective last common ancestor of each of the three domains of life. As a result, regardless of the topology of the tree of life that may be considered, the most parsimonious hypothesis is that these enzymes were inherited in modern lineages from the cenancestor. This observation supports the presence of an enzymatic mechanism to synthesize unsaturated polyisoprenols in the cenancestor and, since these molecules are notorious lipid carriers in glycosylation pathways involved in the synthesis of a wide diversity of prokaryotic cell walls, it provides the first indirect evidence of the existence of a hypothetical unknown cell wall synthesis mechanism in the cenancestor.
Lombard (2016) Early evolution of polyisoprenol biosynthesis and the origin of cell walls. PeerJ 4:e2626 https://doi.org/10.7717/peerj.2626
In silico study on anti-Chikungunya virus activity of hesperetin
Background The re-emerging, Aedes spp. transmitted Chikungunya virus (CHIKV) has recently caused large outbreaks in a wide geographical distribution of the world including countries in Europe and America. Though fatalities associated with this self-remitting disease were rarely reported, quality of patients’ lives have been severely diminished by polyarthralgia recurrence. Neither effective antiviral treatment nor vaccines are available for CHIKV. Our previous in vitro screening showed that hesperetin, a bioflavonoid exhibits inhibitory effect on the virus intracellular replication. Here, we present a study using the computational approach to identify possible target proteins for future mechanistic studies of hesperetin. Methods 3D structures of CHIKV nsP2 (3TRK) and nsP3 (3GPG) were retrieved from Protein Data Bank (PDB), whereas nsP1, nsP4 and cellular factor SPK2 were modeled using Iterative Threading Assembly Refinement (I-TASSER) server based on respective amino acids sequence. We performed molecular docking on hesperetin against all four CHIKV non-structural proteins and SPK2. Proteins preparation and subsequent molecular docking were performed using Discovery Studio 2.5 and AutoDock Vina 1.5.6. The Lipinski’s values of the ligand were computed and compared with the available data from PubChem. Two non-structural proteins with crystal structures 3GPG and 3TRK in complexed with hesperetin, demonstrated favorable free energy of binding from the docking study, were further explored using molecular dynamics (MD) simulations. Results We observed that hesperetin interacts with different types of proteins involving hydrogen bonds, pi-pi effects, pi-cation bonding and pi-sigma interactions with varying binding energies. Among all five tested proteins, our compound has the highest binding affinity with 3GPG at −8.5 kcal/mol. The ligand used in this study also matches the Lipinski’s rule of five in addition to exhibiting closely similar properties with that of in PubChem. The docking simulation was performed to obtain a first guess of the binding structure of hesperetin complex and subsequently analysed by MD simulations to assess the reliability of the docking results. Root mean square deviation (RMSD) of the simulated systems from MD simulations indicated that the hesperetin complex remains stable within the simulation timescale. Discussion The ligand’s tendencies of binding to the important proteins for CHIKV replication were consistent with our previous in vitro screening which showed its efficacy in blocking the virus intracellular replication. NsP3 serves as the highest potential target protein for the compound’s inhibitory effect, while it is interesting to highlight the possibility of interrupting CHIKV replication via interaction with host cellular factor. By complying the Lipinski’s rule of five, hesperetin exhibits drug-like properties which projects its potential as a therapeutic option for CHIKV infection.
Oo et al. (2016) In silico study on anti-Chikungunya virus activity of hesperetin. PeerJ 4:e2602 https://doi.org/10.7717/peerj.2602
Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae)
Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum. Methods The Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed. Results The 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispersed repeats are more abundant, but a smaller fraction of the Oedocladium genome is occupied by introns. Six additional group II introns are present, five of which lack ORFs and carry highly similar sequences to that of the ORF-less IIA intron shared with Oedogonium. Secondary structure analysis of the group IIA introns disclosed marked differences in the exon-binding sites; however, each intron showed perfect or nearly perfect base pairing interactions with its target site. Discussion Our results suggest that chloroplast genes rearrange more slowly in the Oedogoniales than in the Chaetophorales and raise questions as to what was the nature of the foreign coding sequences in the IR of the common ancestor of the Oedogoniales. They provide the first evidence for intragenomic proliferation of group IIA introns in the Viridiplantae, revealing that intron spread in the Oedocladium lineage likely occurred by retrohoming after sequence divergence of the exon-binding sites.
Brouard et al. (2016) Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae). PeerJ 4:e2627 https://doi.org/10.7717/peerj.2627