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
From eggs to bites: do ovitrap data provide reliable estimates of Aedes albopictus biting females?
Background Aedes albopictus is an aggressive invasive mosquito species that represents a serious health concern not only in tropical areas, but also in temperate regions due to its role as vector of arboviruses. Estimates of mosquito biting rates are essential to account for vector-human contact in models aimed to predict the risk of arbovirus autochthonous transmission and outbreaks, as well as nuisance thresholds useful for correct planning of mosquito control interventions. Methods targeting daytime and outdoor biting Ae. albopictus females (e.g., Human Landing Collection, HLC) are expensive and difficult to implement in large scale schemes. Instead, egg-collections by ovitraps are the most widely used routine approach for large-scale monitoring of the species. The aim of this work was to assess whether ovitrap data can be exploited to estimate numbers of adult biting Ae. albopictus females and whether the resulting relationship could be used to build risk models helpful for decision-makers in charge of planning of mosquito-control activities in infested areas. Method Ovitrap collections and HLCs were carried out in hot-spots of Ae. albopictus abundance in Rome (Italy) along a whole reproductive season. The relationship between the two sets of data was assessed by generalized least square analysis, taking into account meteorological parameters. Result The mean number of mosquito females/person collected by HLC in 15′ (i.e., females/HLC) and the mean number of eggs/day were 18.9 ± 0.7 and 39.0 ± 2.0, respectively. The regression models found a significant positive relationship between the two sets of data and estimated an increase of one biting female/person every five additional eggs found in ovitraps. Both observed and fitted values indicated presence of adults in the absence of eggs in ovitraps. Notably, wide confidence intervals of estimates of biting females based on eggs were observed. The patterns of exotic arbovirus outbreak probability obtained by introducing these estimates in risk models were similar to those based on females/HLC (R0 > 1 in 86% and 40% of sampling dates for Chikungunya and Zika, respectively; R0 < 1 along the entire season for Dengue). Moreover, the model predicted that in this case-study scenario an R0 > 1 for Chikungunya is also to be expected when few/no eggs/day are collected by ovitraps. Discussion This work provides the first evidence of the possibility to predict mean number of adult biting Ae. albopictus females based on mean number of eggs and to compute the threshold of eggs/ovitrap associated to epidemiological risk of arbovirus transmission in the study area. Overall, however, the large confidence intervals in the model predictions represent a caveat regarding the reliability of monitoring schemes based exclusively on ovitrap collections to estimate numbers of biting females and plan control interventions.
Manica et al. (2017) From eggs to bites: do ovitrap data provide reliable estimates of Aedes albopictus biting females?. PeerJ 5:e2998 https://doi.org/10.7717/peerj.2998
Urban forests sustain diverse carrion beetle assemblages in the New York City metropolitan area
Urbanization is an increasingly pervasive form of land transformation that reduces biodiversity of many taxonomic groups. Beetles exhibit a broad range of responses to urbanization, likely due to the high functional diversity in this order. Carrion beetles (Order: Coleoptera, Family: Silphidae) provide an important ecosystem service by promoting decomposition of small-bodied carcasses, and have previously been found to decline due to forest fragmentation caused by urbanization. However, New York City (NYC) and many other cities have fairly large continuous forest patches that support dense populations of small mammals, and thus may harbor relatively robust carrion beetle communities in city parks. In this study, we investigated carrion beetle community composition, abundance and diversity in forest patches along an urban-to-rural gradient spanning the urban core (Central Park, NYC) to outlying rural areas. We conducted an additional study comparing the current carrion beetle community at a single suburban site in Westchester County, NY that was intensively surveyed in the early 1970’s. We collected a total of 2,170 carrion beetles from eight species at 13 sites along this gradient. We report little to no effect of urbanization on carrion beetle diversity, although two species were not detected in any urban parks. Nicrophorus tomentosus was the most abundant species at all sites and seemed to dominate the urban communities, potentially due to its generalist habits and shallower burying depth compared to the other beetles surveyed. Variation between species body size, habitat specialization, and % forest area surrounding the surveyed sites also did not influence carrion beetle communities. Lastly, we found few significant differences in relative abundance of 10 different carrion beetle species between 1974 and 2015 at a single site in Westchester County, NY, although two of the rare species in the early 1970’s were not detected in 2015. These results indicate that NYC’s forested parks have the potential to sustain carrion beetle communities and the ecosystem services they provide.
Fusco et al. (2017) Urban forests sustain diverse carrion beetle assemblages in the New York City metropolitan area. PeerJ 5:e3088 https://doi.org/10.7717/peerj.3088
Functional and health promoting inherent attributes of Enterococcus hirae F2 as a novel probiotic isolated from the digestive tract of the freshwater fish Catla catla
Background Probiotic microorganisms are gaining global importance because of their use in the preparation of a nutraceutical or in the treatment of infections. As per the health industry demand, there is an urgent need for exploring new indigenous probiotic strains with its specific origin due to variation in gut microflora, different food habits and specific host-microbial interactions. The main objective of the present study was to isolate and identify a novel probiotic Enterococcus strain from the gut of Catla catla fish and evaluate its potentiality as a potent probiotic. Methods The whole study was designed with the isolation of novel lactic acid bacterial strain from the gut of Catla catla fish with their biochemical and molecular identifications. The potentiality of the isolated strain as a potent probiotic was carried out according to the parameters described in FAD/WHO guidelines for the evaluation of probiotics in food. Results The isolated strain was confirmed as Enterococcus hirae F2 on the basis of various biochemical and 16s rRNA gene sequencing methods. Enterococcus hirae F2 was able to survive under highly acidic and bile salt concentration with the ability for the production of lipase and Bsh enzyme. It was also able to survive under simulated gastrointestinal conditions with the inhibition ability of various pathogens. The antioxidant potentiality with the cell surface hydrophobicity and cell aggregation ability confirms its potentiality as a potent probiotic. All the results detail the potency of Enterococcus hirae F2 as a novel probiotic for a safer use. Discussion The isolation of Enterococcus hirae with probiotic potential from the gut of fish is a new approach and done for the first time. However, the whole study concluded that the isolated strain might be used as a novel probiotic in the food industry for the production of new probiotic products which imparts health benefits to the host.
Adnan et al. (2017) Functional and health promoting inherent attributes of Enterococcus hirae F2 as a novel probiotic isolated from the digestive tract of the freshwater fish Catla catla. PeerJ 5:e3085 https://doi.org/10.7717/peerj.3085
Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis
Background Rheumatoid arthritis (RA) is a chronic auto-inflammatory disorder of joints. The present study aimed to identify the key genes in RA for better understanding the underlying mechanisms of RA. Methods The integrated analysis of expression profiling was conducted to identify differentially expressed genes (DEGs) in RA. Moreover, functional annotation, protein–protein interaction (PPI) network and transcription factor (TF) regulatory network construction were applied for exploring the potential biological roles of DEGs in RA. In addition, the expression level of identified candidate DEGs was preliminarily detected in peripheral blood cells of RA patients in the GSE17755 dataset. Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to validate the expression levels of identified DEGs in RA. Results A total of 378 DEGs, including 202 up- and 176 down-regulated genes, were identified in synovial tissues of RA patients compared with healthy controls. DEGs were significantly enriched in axon guidance, RNA transport and MAPK signaling pathway. RBFOX2, LCK and SERBP1 were the hub proteins in the PPI network. In the TF-target gene network, RBFOX2, POU6F1, WIPF1 and PFKFB3 had the high connectivity with TFs. The expression status of 11 candidate DEGs was detected in GSE17755, the expression levels of MAT2A and NSA2 were significantly down-regulated and CD47 had the up-regulated tendency in peripheral blood cells of patients with RA compared with healthy individuals. qRT-PCR results of MAT2A, NSA2, CD47 were compatible with our bioinformatics analyses. Discussion Our study might provide valuable information for exploring the pathogenesis mechanism of RA and identifying the potential biomarkers for RA diagnosis.
Hao et al. (2017) Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis. PeerJ 5:e3078 https://doi.org/10.7717/peerj.3078
Three-dimensional visualisation of the internal anatomy of the sparrowhawk (Accipiter nisus) forelimb using contrast-enhanced micro-computed tomography
Background Gross dissection is a widespread method for studying animal anatomy, despite being highly destructive and time-consuming. X-ray computed tomography (CT) has been shown to be a non-destructive alternative for studying anatomical structures. However, in the past it has been limited to only being able to visualise mineralised tissues. In recent years, morphologists have started to use traditional X-ray contrast agents to allow the visualisation of soft tissue elements in the CT context. The aim of this project is to assess the ability of contrast-enhanced micro-CT (μCT) to construct a three-dimensional (3D) model of the musculoskeletal system of the bird wing and to quantify muscle geometry and any systematic changes due to shrinkage. We expect that this reconstruction can be used as an anatomical guide to the sparrowhawk wing musculature and form the basis of further biomechanical analysis of flight. Methods A 3% iodine-buffered formalin solution with a 25-day staining period was used to visualise the wing myology of the sparrowhawk (Accipiter nisus). μCT scans of the wing were taken over the staining period until full penetration of the forelimb musculature by iodine was reached. A 3D model was reconstructed by manually segmenting out the individual elements of the avian wing using 3D visualisation software. Results Different patterns of contrast were observed over the duration of the staining treatment with the best results occurring after 25 days of staining. Staining made it possible to visualise and identify different elements of the soft tissue of the wing. Finally, a 3D reconstruction of the musculoskeletal system of the sparrowhawk wing is presented and numerical data of muscle geometry is compared to values obtained by dissection. Discussion Contrast-enhanced μCT allows the visualisation and identification of the wing myology of birds, including the smaller muscles in the hand, and provides a non-destructive way for quantifying muscle volume with an accuracy of 96.2%. By combining contrast-enhanced μCT with 3D visualisation techniques, it is possible to study the individual muscles of the forelimb in their original position and 3D design, which can be the basis of further biomechanical analysis. Because the stain can be washed out post analysis, this technique provides a means of obtaining quantitative muscle data from museum specimens non-destructively.
Bribiesca-Contreras et al. (2017) Three-dimensional visualisation of the internal anatomy of the sparrowhawk (Accipiter nisus) forelimb using contrast-enhanced micro-computed tomography. PeerJ 5:e3039 https://doi.org/10.7717/peerj.3039
Sympathy for the devil: a conservation strategy for devil and manta rays
Background International trade for luxury products, medicines, and tonics poses a threat to both terrestrial and marine wildlife. The demand for and consumption of gill plates (known as Peng Yu Sai, “Fish Gill of Mobulid Ray”) from devil and manta rays (subfamily Mobulinae, collectively referred to as mobulids) poses a significant threat to these marine fishes because of their extremely low productivity. The demand for these gill plates has driven an international trade supplied by largely unmonitored and unregulated catches from target and incidental fisheries around the world. Scientific research, conservation campaigns, and legal protections for devil rays have lagged behind those for manta rays despite similar threats across all mobulids. Methods To investigate the difference in attention given to devil rays and manta rays, we examined trends in the scientific literature and updated species distribution maps for all mobulids. Using available information on target and incidental fisheries, and gathering information on fishing and trade regulations (at international, national, and territorial levels), we examined how threats and protective measures overlap with species distribution. We then used a species conservation planning approach to develop the Global Devil and Manta Ray Conservation Strategy, specifying a vision, goals, objectives, and actions to advance the knowledge and protection of both devil and manta rays. Results and Discussion Our literature review revealed that there had been nearly 2.5-times more “manta”-titled publications, than “mobula” or “devil ray”-titled publications over the past 4.5 years (January 2012–June 2016). The majority of these recent publications were reports on occurrence of mobulid species. These publications contributed to updated Area of Occupancy and Extent of Occurrence maps which showed expanded distributions for most mobulid species and overlap between the two genera. While several international protections have recently expanded to include all mobulids, there remains a greater number of national, state, and territory-level protections for manta rays compared to devil rays. We hypothesize that there are fewer scientific publications and regulatory protections for devil rays due primarily to perceptions of charisma that favour manta rays. We suggest that the well-established species conservation framework used here offers an objective solution to close this gap. To advance the goals of the conservation strategy we highlight opportunities for parity in protection and suggest solutions to help reduce target and bycatch fisheries.
Lawson et al. (2017) Sympathy for the devil: a conservation strategy for devil and manta rays. PeerJ 5:e3027 https://doi.org/10.7717/peerj.3027