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
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