A multidisciplinary approach to digital mapping of dinosaurian tracksites in the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia
The abundant dinosaurian tracksites of the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia, form an important part of the West Kimberley National Heritage Place. Previous attempts to document these tracksites using traditional mapping techniques (e.g., surface overlays, transects and gridlines combined with conventional photography) have been hindered by the non-trivial challenges associated with working in this area, including, but not limited to: (1) the remoteness of many of the tracksites; (2) the occurrence of the majority of the tracksites in the intertidal zone; (3) the size and complexity of many of the tracksites, with some extending over several square kilometres. Using the historically significant and well-known dinosaurian tracksites at Minyirr (Gantheaume Point), we show how these issues can be overcome through the use of an integrated array of remote sensing tools. A combination of high-resolution aerial photography with both manned and unmanned aircraft, airborne and handheld high-resolution lidar imaging and handheld photography enabled the collection of large amounts of digital data from which 3D models of the tracksites at varying resolutions were constructed. The acquired data encompasses a very broad scale, from the sub-millimetre level that details individual tracks, to the multiple-kilometre level, which encompasses discontinuous tracksite exposures and large swathes of coastline. The former are useful for detailed ichnological work, while the latter are being employed to better understand the stratigraphic and temporal relationship between tracksites in a broader geological and palaeoecological context. These approaches and the data they can generate now provide a means through which digital conservation and temporal monitoring of the Dampier Peninsula’s dinosaurian tracksites can occur. As plans for the on-going management of the tracks in this area progress, analysis of the 3D data and 3D visualization will also likely provide an important means through which the broader public can experience these spectacular National Heritage listed landscapes.
Romilio et al. (2017) A multidisciplinary approach to digital mapping of dinosaurian tracksites in the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia. PeerJ 5:e3013 https://doi.org/10.7717/peerj.3013
The Non-Recurrent Laryngeal Nerve: a meta-analysis and clinical considerations
Background The Non-Recurrent Laryngeal Nerve (NRLN) is a rare embryologically-derived variant of the Recurrent Laryngeal Nerve (RLN). The presence of an NRLN significantly increases the risk of iatrogenic injury and operative complications. Our aim was to provide a comprehensive meta-analysis of the overall prevalence of the NRLN, its origin, and its association with an aberrant subclavian artery. Methods Through March 2016, a database search was performed of PubMed, CNKI, ScienceDirect, EMBASE, BIOSIS, SciELO, and Web of Science. The references in the included articles were also extensively searched. At least two reviewers judged eligibility and assessed and extracted articles. MetaXL was used for analysis, with all pooled prevalence rates calculated using a random effects model. Heterogeneity among the included studies was assessed using the Chi2 test and the I2 statistic. Results Fifty-three studies (33,571 right RLNs) reported data on the prevalence of a right NRLN. The pooled prevalence estimate was 0.7% (95% CI [0.6–0.9]). The NRLN was found to originate from the vagus nerve at or above the laryngotracheal junction in 58.3% and below it in 41.7%. A right NRLN was associated with an aberrant subclavian artery in 86.7% of cases. Conclusion The NRLN is a rare yet very clinically relevant structure for surgeons and is associated with increased risk of iatrogenic injury, most often leading to temporary or permanent vocal cord paralysis. A thorough understanding of the prevalence, origin, and associated pathologies is vital for preventing injuries and complications.
Henry et al. (2017) The Non-Recurrent Laryngeal Nerve: a meta-analysis and clinical considerations. PeerJ 5:e3012 https://doi.org/10.7717/peerj.3012
Testing of microsatellite multiplexes for individual identification of Cape Parrots (Poicephalus robustus): paternity testing and monitoring trade
Background Illegal trade in rare wildlife species is a major threat to many parrot species around the world. Wildlife forensics plays an important role in the preservation of endangered or threatened wildlife species. Identification of illegally harvested or traded animals through DNA techniques is one of the many methods used during forensic investigations. Natural populations of the South African endemic Cape Parrot (Poicephalus robustus) are negatively affected by the removal of eggs and chicks for the pet trade. Methods In this study, 16 microsatellite markers specifically designed for the South African endemic Cape Parrot (P. robustus) are assessed for their utility in forensic casework. Using these 16 loci, the genetic diversity of a subset of the captive Cape Parrot population was also assessed and compared to three wild Cape Parrot populations. Results It was determined that the full 16 locus panel has sufficient discriminatory power to be used in parentage analyses and can be used to determine if a bird has been bred in captivity and so can be legally traded or if it has been illegally removed from the wild. In cases where birds have been removed from the wild, this study suggests that a reduced 12 locus microsatellite panel has sufficient power to assign confiscated birds to geographic population of origin. Discussion The level of genetic diversity observed within the captive Cape Parrot population was similar to that observed in the wild populations, which suggests that the captive population is not suffering from decreased levels of genetic diversity. The captive Cape Parrots did however have double the number of private alleles compared to that observed in the most genetically diverse wild population. This is probably due to the presence of rare alleles present in the founder population, which has not been lost due to genetic drift, as many of the individuals tested in this study are F1–F3 wild descendants. The results from this study provide a suit of markers that can be used to aid conservation and law enforcement authorities to better control legal and illegal trade of this South African endemic.
Coetzer et al. (2017) Testing of microsatellite multiplexes for individual identification of Cape Parrots (Poicephalus robustus): paternity testing and monitoring trade. PeerJ 5:e2900 https://doi.org/10.7717/peerj.2900
Developmental and loco-like effects of a swainsonine-induced inhibition of α-mannosidase in the honey bee, Apis mellifera
Background Deficiencies in lysosomal a-mannosidase (LAM) activity in animals, caused either by mutations or by consuming toxic alkaloids, lead to severe phenotypic and behavioural consequences. Yet, epialleles adversely affecting LAM expression exist in the honey bee population suggesting that they might be beneficial in certain contexts and cannot be eliminated by natural selection. Methods We have used a combination of enzymology, molecular biology and metabolomics to characterise the catalytic properties of honey bee LAM (AmLAM) and then used an indolizidine alkaloid swainsonine to inhibit its activity in vitro and in vivo. Results We show that AmLAM is inhibited in vitro by swainsonine albeit at slightly higher concentrations than in other animals. Dietary exposure of growing larvae to swainsonine leads to pronounced metabolic changes affecting not only saccharides, but also amino acids, polyols and polyamines. Interestingly, the abundance of two fatty acids implicated in epigenetic regulation is significantly reduced in treated individuals. Additionally, swainsonie causes loco-like symptoms, increased mortality and a subtle decrease in the rate of larval growth resulting in a subsequent developmental delay in pupal metamorphosis. Discussion We consider our findings in the context of cellular LAM function, larval development, environmental toxicity and colony-level impacts. The observed developmental heterochrony in swainsonine-treated larvae with lower LAM activity offer a plausible explanation for the existence of epialleles with impaired LAM expression. Individuals carrying such epialleles provide an additional level of epigenetic diversity that could be beneficial for the functioning of a colony whereby more flexibility in timing of adult emergence might be useful for task allocation.
Wedd et al. (2017) Developmental and loco-like effects of a swainsonine-induced inhibition of α-mannosidase in the honey bee, Apis mellifera. PeerJ 5:e3109 https://doi.org/10.7717/peerj.3109
Plant growth-promoting endophytic bacteria versus pathogenic infections: an example of Bacillus amyloliquefaciens RWL-1 and Fusarium oxysporum f. sp. lycopersici in tomato
Fungal pathogenic attacks are one of the major threats to the growth and productivity of crop plants. Currently, instead of synthetic fungicides, the use of plant growth-promoting bacterial endophytes has been considered intriguingly eco-friendly in nature. Here, we aimed to investigate the in vitro and in vivo antagonistic approach by using seed-borne endophytic Bacillus amyloliquefaciens RWL-1 against pathogenic Fusarium oxysporum f. sp. lycopersici. The results revealed significant suppression of pathogenic fungal growth by Bacillus amyloliquefaciens in vitro. Further to this, we inoculated tomato plants with RWL-1 and F. oxysporum f. sp. lycopersici in the root zone. The results showed that the growth attributes and biomass were significantly enhanced by endophytic-inoculation during disease incidence as compared to F. oxysporum f. sp. lycopersici infected plants. Under pathogenic infection, the RWL-1-applied plants showed increased amino acid metabolism of cell wall related (e.g., aspartic acid, glutamic acid, serine (Ser), and proline (Pro)) as compared to diseased plants. In case of endogenous phytohormones, significantly lower amount of jasmonic acid (JA) and higher amount of salicylic acid (SA) contents was recorded in RWL-1-treated diseased plants. The phytohormones regulation in disease incidences might be correlated with the ability of RWL-1 to produce organic acids (e.g., succinic acid, acetic acid, propionic acid, and citric acid) during the inoculation and infection of tomato plants. The current findings suggest that RWL-1 inoculation promoted and rescued plant growth by modulating defense hormones and regulating amino acids. This suggests that bacterial endophytes could be used for possible control of F. oxysporum f. sp. lycopersici in an eco-friendly way.
Shahzad et al. (2017) Plant growth-promoting endophytic bacteria versus pathogenic infections: an example of Bacillus amyloliquefaciens RWL-1 and Fusarium oxysporum f. sp. lycopersici in tomato. PeerJ 5:e3107 https://doi.org/10.7717/peerj.3107
Evaluation of procedures for typing of group B Streptococcus: a retrospective study
Background This study evaluates two procedures for typing of Streptococcus agalactiae (group B streptococci; GBS) isolates, using retrospective typing data from the period 2010 to 2014 with a commercial latex agglutination test (latex test) and the Lancefield precipitation test (LP test). Furthermore, the genotype distribution of phenotypically non-typable (NT) GBS isolates is presented. We also raise the awareness, that the difference in typing results obtained by phenotypical methods and genotype based methods may have implications on vaccine surveillance in case a GBS vaccine is introduced. Methods A total of 616 clinical GBS isolates from 2010 to 2014 were tested with both a latex test and the LP test. Among these, 66 isolates were genotyped by PCR, including 41 isolates that were phenotypically NT. Results The latex test provided a serotype for 83.8% of the isolates (95% CI [80.7–86.6]) compared to 87.5% (95% CI [84.6–90.0]) obtained by the LP method. The two assays provided identical capsular identification for all sero-typeable isolates (excluding NT isolates). The PCR assay provided a genotype designation to the 41 isolates defined as phenotypically NT isolates. Discussion We found that the latex test showed a slightly lower identification percentage than the LP test. Our recommendation is to use the latex agglutination as the routine primary assay for GBS surveillance, and then use the more labour intensive precipitation test on the NT isolates to increase the serotyping rate. A genotype could be assigned to all the phenotypically NT isolates, however, as a consequence genotyping will overestimate the coverage from possible future capsular polysaccharide based GBS vaccines.
Slotved et al. (2017) Evaluation of procedures for typing of group B Streptococcus: a retrospective study. PeerJ 5:e3105 https://doi.org/10.7717/peerj.3105
Climate-change-induced range shifts of three allergenic ragweeds (Ambrosia L.) in Europe and their potential impact on human health
Invasive allergenic plant species may have severe health-related impacts. In this study we aim to predict the effects of climate change on the distribution of three allergenic ragweed species (Ambrosia spp.) in Europe and discuss the potential associated health impact. We built species distribution models based on presence-only data for three ragweed species, using MAXENT software. Future climatic habitat suitability was modeled under two IPCC climate change scenarios (RCP 6.0 and RCP 8.5). We quantify the extent of the increase in ‘high allergy risk’ (HAR) areas, i.e., parts of Europe with climatic conditions corresponding to the highest quartile (25%) of present day habitat suitability for each of the three species. We estimate that by year 2100, the distribution range of all three ragweed species increases towards Northern and Eastern Europe under all climate scenarios. HAR areas will expand in Europe by 27–100%, depending on species and climate scenario. Novel HAR areas will occur mostly in Denmark, France, Germany, Russia and the Baltic countries, and overlap with densely populated cities such as Paris and St. Petersburg. We conclude that areas in Europe affected by severe ragweed associated allergy problems are likely to increase substantially by year 2100, affecting millions of people. To avoid this, management strategies must be developed that restrict ragweed dispersal and establishment of new populations. Precautionary efforts should limit the spread of ragweed seeds and reduce existing populations. Only by applying cross-countries management plans can managers mitigate future health risks and economical consequences of a ragweed expansion in Europe.
Rasmussen et al. (2017) Climate-change-induced range shifts of three allergenic ragweeds (Ambrosia L.) in Europe and their potential impact on human health. PeerJ 5:e3104 https://doi.org/10.7717/peerj.3104
Testing the habituation assumption underlying models of parasitoid foraging behavior
Background Habituation, a form of non-associative learning, has several well-defined characteristics that apply to a wide range of physiological and behavioral responses in many organisms. In classic patch time allocation models, habituation is considered to be a major mechanistic component of parasitoid behavioral strategies. However, parasitoid behavioral responses to host cues have not previously been tested for the known, specific characteristics of habituation. Methods In the laboratory, we tested whether the foraging behavior of the egg parasitoid Trissolcus basalis shows specific characteristics of habituation in response to consecutive encounters with patches of host (Nezara viridula) chemical contact cues (footprints), in particular: (i) a training interval-dependent decline in response intensity, and (ii) a training interval-dependent recovery of the response. Results As would be expected of a habituated response, wasps trained at higher frequencies decreased their behavioral response to host footprints more quickly and to a greater degree than those trained at low frequencies, and subsequently showed a more rapid, although partial, recovery of their behavioral response to host footprints. This putative habituation learning could not be blocked by cold anesthesia, ingestion of an ATPase inhibitor, or ingestion of a protein synthesis inhibitor. Discussion Our study provides support for the assumption that diminishing responses of parasitoids to chemical indicators of host presence constitutes habituation as opposed to sensory fatigue, and provides a preliminary basis for exploring the underlying mechanisms.
Abram et al. (2017) Testing the habituation assumption underlying models of parasitoid foraging behavior. PeerJ 5:e3097 https://doi.org/10.7717/peerj.3097
Effect of method of deduplication on estimation of differential gene expression using RNA-seq
Background RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. Results To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI). We also analyzed the influence of sequencing layout (single read or paired end) and read length. We found that deduplication without MI greatly affects estimated expression values; this effect is the most pronounced for highly expressed genes. Conclusion The use of unique molecular identifiers greatly improves accuracy of RNA-seq analysis, especially for highly expressed genes. We developed a set of scripts that enable handling of MI and their incorporation into RNA-seq analysis pipelines. Deduplication without MI affects results of differential gene expression analysis, producing a high proportion of false negative results. The absence of duplicate read removal is biased towards false positives. In those cases where using MI is not possible, we recommend using paired-end sequencing layout.
Klepikova et al. (2017) Effect of method of deduplication on estimation of differential gene expression using RNA-seq. PeerJ 5:e3091 https://doi.org/10.7717/peerj.3091
High unexpected genetic diversity of a narrow endemic terrestrial mollusc
The Iberian Peninsula has an extensive record of species displaying strong genetic structure as a result of their survival in isolated pockets throughout the Pleistocene ice ages. We used mitochondrial and nuclear sequence data to analyze phylogeographic patterns in endemic land snails from a valley of central Portugal (Vale da Couda), putatively assigned to Candidula coudensis, that show an exceptionally narrow distributional range. The genetic survey presented here shows the existence of five main mitochondrial lineages in Vale da Couda that do not cluster together suggesting independent evolutionary histories. Our results also indicate a departure from the expectation that species with restricted distributions have low genetic variability. The putative past and contemporary models of geographic distribution of Vale da Couda lineages are compatible with a scenario of species co-existence in more southern locations during the last glacial maximum (LGM) followed by a post-LGM northern dispersal tracking the species optimal thermal, humidity and soil physical conditions.
Madeira et al. (2017) High unexpected genetic diversity of a narrow endemic terrestrial mollusc. PeerJ 5:e3069 https://doi.org/10.7717/peerj.3069