A quantitative approach to determine the taxonomic identity and ontogeny of the pycnodontiform fish Pycnodus (Neopterygii, Actinopterygii) from the Eocene of Bolca Lagerstätte, Italy
Background The pycnodontiform fish Pycnodus is one of the representatives of the highly diverse actinopterygian fish fauna from the early Eocene Bolca Lagerstätte, representing one of the youngest and thus last occurrences of this extinct neopterygian clade. This genus has historically been used as a wastebasket taxon in regards to poorly known pycnodontiform fossils. Authors have argued over the specific status of the Bolca Lagerstätte Pycnodus in terms of how many species are contained within the genus with some arguing for multiple species and others suggesting lumping all Bolca specimens together into one species. Methods Here, we use a quantitative approach performing biometric and geometric morphometric analyses on 52 specimens of Pycnodus in order to determine if the morphological variability within the sample might be related to inter- or intraspecific variation. Results The analyses revealed that the variations of body shape, morphometric and meristic characters cannot be used to distinguish different morphotypes. On the contrary, our results show a remarkable link between shape and size, related to ontogeny. Discussion Differences in body shape of small (juvenile) and large (adult) individuals is probably related to different microhabitats occupation on the Bolca reef with juveniles sheltering within crevices on the reef and adults being more powerful swimmers that swim above the coral. Taxonomically, we suggest that the Bolca Pycnodus should be referred to strictly as Pycnodus apodus as this was the name given to the holotype. Additionally, an overview of species assigned to Pycnodus is given.
Cawley et al. (2018) A quantitative approach to determine the taxonomic identity and ontogeny of the pycnodontiform fish Pycnodus (Neopterygii, Actinopterygii) from the Eocene of Bolca Lagerstätte, Italy. PeerJ 6:e4809 https://doi.org/10.7717/peerj.4809
Helicobacter pylori genetic diversification in the Mongolian gerbil model
Helicobacter pylori requires genetic agility to infect new hosts and establish long-term colonization of changing gastric environments. In this study, we analyzed H. pylori genetic adaptation in the Mongolian gerbil model. This model is of particular interest because H. pylori-infected gerbils develop a high level of gastric inflammation and often develop gastric adenocarcinoma or gastric ulceration. We analyzed the whole genome sequences of H. pylori strains cultured from experimentally infected gerbils, in comparison to the genome sequence of the input strain. The mean annualized single nucleotide polymorphism (SNP) rate per site was 1.5e−5, which is similar to the rates detected previously in H. pylori-infected humans. Many of the mutations occurred within or upstream of genes associated with iron-related functions (fur, tonB1, fecA2, fecA3, and frpB3) or encoding outer membrane proteins (alpA, oipA, fecA2, fecA3, frpB3 and cagY). Most of the SNPs within coding regions (86%) were non-synonymous mutations. Several deletion or insertion mutations led to disruption of open reading frames, suggesting that the corresponding gene products are not required or are deleterious during chronic H. pylori colonization of the gerbil stomach. Five variants (three SNPs and two deletions) were detected in isolates from multiple animals, which suggests that these mutations conferred a selective advantage. One of the mutations (FurR88H) detected in isolates from multiple animals was previously shown to confer increased resistance to oxidative stress, and we now show that this SNP also confers a survival advantage when H. pylori is co-cultured with neutrophils. Collectively, these analyses allow the identification of mutations that are positively selected during H. pylori colonization of the gerbil model.
Beckett et al. (2018) Helicobacter pylori genetic diversification in the Mongolian gerbil model. PeerJ 6:e4803 https://doi.org/10.7717/peerj.4803
Association of epilepsy and asthma: a population-based retrospective cohort study
Background Epidemiologic data supporting the epilepsy–asthma association are insufficient. Therefore, we examined this association in this study. Methods By using claims data from the National Health Insurance Research Database (Taiwan), we executed a retrospective cohort analysis. Analysis 1 entailed comparing 150,827 patients diagnosed as having incident asthma during 1996–2013 with disease-free controls who were selected randomly during the same period, frequency matched in terms of age and sex. Similarly, analysis 2 entailed comparing 25,274 patients newly diagnosed as having epilepsy with sex- and age-matched controls who were selected randomly. At the end of 2013, we evaluated in analysis 1 the epilepsy incidence and risk and evaluated in analysis 2 the asthma incidence and risk. We applied Kaplan–Meier analysis to derive plots of the proportion of asthma-free seizures. Results In analysis 1, the asthma group exhibited a higher epilepsy incidence than did the control group (3.05 versus 2.26 per 1,000 person-years; adjusted hazard ratio: 1.39, 95% CI [1.33–1.45]). We also noted a greater risk of subsequent epilepsy in women and girls. In analysis 2, we determined that the asthma incidence between the control and epilepsy groups did not differ significantly; however, some age subgroups including children and individuals in their 30s had an increased risk. A negative association was found in adolescents. The Kaplan–Meier analysis revealed epilepsy to be positively associated with subsequent onset of asthma within seven years of epilepsy diagnosis. Discussion Asthma may be associated with high epilepsy risk, and epilepsy may be associated with high asthma risk among children and individuals in their 30s. Nevertheless, people with epilepsy in other age subgroups should be aware of the possibility of developing asthma within seven years of epilepsy diagnosis.
Chiang et al. (2018) Association of epilepsy and asthma: a population-based retrospective cohort study. PeerJ 6:e4792 https://doi.org/10.7717/peerj.4792
Diagnostic accuracy of Onen’s Alternative Grading System combined with Doppler evaluation of ureteral jets as an alternative in the diagnosis of obstructive hydronephrosis in children
Introduction Ureteropelvic junction obstruction (UPJO) is a common congenital anomaly leading to varying degrees of hydronephrosis (HN), ranging from no apparent effect on the renal function to atrophy. Evaluation of these children is based on Diuretic Renal Scintigraphy (DRS) and Ultrasonography (US). Recent studies have suggested that new parameters of conventional and color Doppler ultrasonography (CDUS) may be useful in discriminating which kidneys are obstructed. The present study aims to assess the diagnostic accuracy of such parameters in the diagnosis of obstruction in children with UPJO. Methods We evaluated 44 patients (33 boys) with a mean age of 6.53 ± 4.39 years diagnosed with unilateral high-grade hydronephrosis (SFU grades 3 and 4). All underwent DRS and index tests (conventional US and CDUS to evaluate ureteral jets frequency) within a maximum interval of two weeks. Hydronephrotic units were reclassified according to the alternative grading system (AGS) proposed by Onen et al. Obstruction in the DRS was defined as a differential renal function <40% on the affected side and/or features indicating poor drainage function like T1/2 >20 minutes after the administration of furosemide, and a plateau or ascending pattern of the excretion curve. Results Nineteen hydronephrotic units (43.1%) were obstructed. Some degree of cortical atrophy—grades 3 (segmental) or 4 (diffuse)—was present in those obstructed units. AGS grades had 100% sensitivity, 76% of specificity and 86.4% of accuracy. The absence of ureteral jets had a sensitivity of 73.68%, a specificity of 100% with an accuracy of 88.6%. When we analyzed the two aspects together and considered obstructed the renal units classified as AGS grade 3 or 4 with no jets, sensitivity increased to 78.9%, accuracy to 92%, remaining with a maximum specificity of 100%. These features combined would allow us to avoid performing DRS in 61% of our patients, leaving more invasive tests to inconclusive cases. Conclusions Although DRS remains the mainstay to distinguishing obstructive from non-obstructive kidneys, grade of hydronephrosis and frequency of ureteral jets, independently or in combination may be a reliable alternative in the mostly cases.This alternative approach has high accuracy, it is less invasive, easily reproducible and may play a role in the diagnosis of obstruction in pediatric population.
de Bessa Jr et al. (2018) Diagnostic accuracy of Onen’s Alternative Grading System combined with Doppler evaluation of ureteral jets as an alternative in the diagnosis of obstructive hydronephrosis in children. PeerJ 6:e4791 https://doi.org/10.7717/peerj.4791
Effects of sandfish (Holothuria scabra) removal on shallow-water sediments in Fiji
Sea cucumbers play an important role in the recycling and remineralization of organic matter (OM) in reef sands through feeding, excretion, and bioturbation processes. Growing demand from Asian markets has driven the overexploitation of these animals globally. The implications of sea cucumber fisheries for shallow coastal ecosystems and their management remain poorly understood. To address this knowledge gap, the current study manipulated densities of Holothuria scabra within enclosures on a reef flat in Fiji, between August 2015 and February 2016, to study the effects of sea cucumber removal on sedimentary function as a biocatalytic filter system. Three treatments were investigated: (i) high density (350 g m−2 wet weight; ca. 15 individuals); (ii) natural density (60 g m−2; ca. 3 individuals); and (iii) exclusion (0 g m−2). Quantity of sediment reworked through ingestion by H. scabra, grain size distribution, O2 penetration depth, and sedimentary oxygen consumption (SOC) were quantified within each treatment. Findings revealed that the natural population of H. scabra at the study site can rework ca. 10,590 kg dry sediment 1,000 m−2 year−1; more than twice the turnover rate recorded for H. atra and Stichopus chloronotus. There was a shift towards finer fraction grains in the high treatment. In the exclusion treatment, the O2 penetration depth decreased by 63% following a 6 °C increase in water temperature over the course of two months, while in the high treatment no such change was observed. SOC rates increased ca. two-fold in the exclusion treatment within the first month, and were consistently higher than in the high treatment. These results suggest that the removal of sea cucumbers can reduce the capacity of sediments to buffer OM pulses, impeding the function and productivity of shallow coastal ecosystems.
Lee et al. (2018) Effects of sandfish (Holothuria scabra) removal on shallow-water sediments in Fiji. PeerJ 6:e4773 https://doi.org/10.7717/peerj.4773
Larval exposure to the neonicotinoid imidacloprid impacts adult size in the farmland butterfly Pieris brassicae
Populations of farmland butterflies have been suffering from substantial population declines in recent decades. These declines have been correlated with neonicotinoid usage both in Europe and North America but experimental evidence linking these correlations is lacking. The potential for non-target butterflies to be exposed to trace levels of neonicotinoids is high, due to the widespread contamination of agricultural soils and wild plants in field margins. Here we provide experimental evidence that field realistic, sub-lethal exposure to the neonicotinoid imidacloprid negatively impacts the development of the common farmland butterfly Pieris brassicae. Cabbage plants were watered with either 0, 1, 10, 100 or 200 parts per billion imidacloprid, to represent field margin plants growing in contaminated agricultural soils and these were fed to P. brassicae larvae. The approximate digestibility (AD) of the cabbage as well as behavioural responses by the larvae to simulated predator attacks were measured but neither were affected by neonicotinoid treatment. However, the duration of pupation and the size of the adult butterflies were both significantly reduced in the exposed butterflies compared to the controls, suggesting that adult fitness is compromised through exposure to this neonicotinoid.
Whitehorn et al. (2018) Larval exposure to the neonicotinoid imidacloprid impacts adult size in the farmland butterfly Pieris brassicae. PeerJ 6:e4772 https://doi.org/10.7717/peerj.4772
Effect of elevated temperature on membrane lipid saturation in Antarctic notothenioid fish
Homeoviscous adaptation (HVA) is a key cellular response by which fish protect their membranes against thermal stress. We investigated evolutionary HVA (long time scale) in Antarctic and non-Antarctic fish. Membrane lipid composition was determined for four Perciformes fish: two closely related Antarctic notothenioid species (Trematomus bernacchii and Pagothenia borchgrevinki); a diversified related notothenioid Antarctic icefish (Chionodraco hamatus); and a New Zealand species (Notolabrus celidotus). The membrane lipid compositions were consistent across the three Antarctic species and these were significantly different from that of the New Zealand species. Furthermore, acclimatory HVA (short time periods with seasonal changes) was investigated to determine whether stenothermal Antarctic fish, which evolved in the cold, stable environment of the Southern Ocean, have lost the acclimatory capacity to modulate their membrane saturation states, making them vulnerable to anthropogenic global warming. We compared liver membrane lipid composition in two closely related Antarctic fish species acclimated at 0 °C (control temperature), 4 °C for a period of 14 days in T. bernacchii and 28 days for P. borchgrevinki, and 6 °C for 7 days in both species. Thermal acclimation at 4 °C did not result in changed membrane saturation states in either Antarctic species. Despite this, membrane functions were not compromised, as indicated by declining serum osmolality, implying positive compensation by enhanced hypo-osmoregulation. Increasing the temperature to 6 °C did not change the membrane lipids of P. borchgrevinki. However, in T. bernacchii, thermal acclimation at 6 °C resulted in an increase of membrane saturated fatty acids and a decline in unsaturated fatty acids. This is the first study to show a homeoviscous response to higher temperatures in an Antarctic fish, although for only one of the two species examined.
Malekar et al. (2018) Effect of elevated temperature on membrane lipid saturation in Antarctic notothenioid fish. PeerJ 6:e4765 https://doi.org/10.7717/peerj.4765
Tetrapod tracks in Permo–Triassic eolian beds of southern Brazil (Paraná Basin)
Tetrapod tracks in eolianites are widespread in the fossil record since the late Paleozoic. Among these ichnofaunas, the ichnogenus Chelichnus is the most representative of the Permian tetrapod ichnological record of eolian deposits of Europe, North America and South America, where the Chelichnus Ichnofacies often occurs. In this contribution, we describe five sets of tracks (one of which is preserved in cross-section), representing the first occurrence of Dicynodontipus and Chelichnus in the “Pirambóia Formation” of southern Brazil. This unit represents a humid desert in southwestern Pangea and its lower and upper contacts lead us to consider its age as Lopingian–Induan. The five sets of tracks studied were compared with several ichnotaxa and body fossils with appendicular elements preserved, allowing us to attribute these tracks to dicynodonts and other indeterminate therapsids. Even though the “Pirambóia Formation” track record is sparse and sub-optimally preserved, it is an important key to better understand the occupation of arid environments by tetrapods across the Permo–Triassic boundary.
Francischini et al. (2018) Tetrapod tracks in Permo–Triassic eolian beds of southern Brazil (Paraná Basin). PeerJ 6:e4764 https://doi.org/10.7717/peerj.4764
Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles
The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely related Costa Rican Cephaloleia species comprises only eight bacterial groups, including members of the Acinetobacter, Enterobacteriacea, Pseudomonas, Lactococcus, and Comamonas. The Acinetobacter and Enterobacteriacea together accounted for 35% of the total average 16S rRNA ribotypes recovered from all specimens. Further, microbiome diversity and community structure was significantly linked to beetle diet breadth, between those foraging on less than two plant types (specialists) versus over nine plant types (generalists). Moraxellaceae, Enterobacteriaceae, and Pseudomonadaceae were highly prevalent in specialist species, and also present in eggs, while Rickettsiaceae associated exclusively with generalist beetles. Bacteria isolated from Cephaloleia digestive systems had distinct capabilities and suggested a possible beneficial role in both digestion of plant-based compounds, including xylose, mannitol, and pectin, and possible detoxification, via lipases. Cephaloleia species are currently expanding their diets to include exotic invasive plants, yet it is unknown whether their microbial community plays a role in this transition. In this study, colonization of invasive plants was correlated with a dysbiosis of the microbiome, suggesting a possible relationship between gut bacteria and niche adaptation.
Blankenchip et al. (2018) Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles. PeerJ 6:e4793 https://doi.org/10.7717/peerj.4793
The effect of climate change on the distribution of a tropical zoanthid (Palythoa caribaeorum) and its ecological implications
Palythoa caribaeorum is a zoanthid often dominant in shallow rocky environments along the west coast of the Atlantic Ocean, from the tropics to the subtropics. This species has high environmental tolerance and is a good space competitor in reef environments. Considering current and future scenarios in the global climate regime, this study aimed to model and analyze the distribution of P. caribaeorum, generating maps of potential distribution for the present and the year 2100. The distribution was modeled using maximum entropy (Maxent) based on 327 occurrence sites retrieved from the literature. Calcite concentration, maximum chlorophyll-a concentration, salinity, pH, and temperature range yielded a model with the smallest Akaike information criterion (2649.8), and were used in the present and future distribution model. Data from the HadGEM2-ES climate model were used to generate the projections for the year 2100. The present distribution of P. caribaeorum shows that parts of the Brazilian coast, Caribbean Sea, and Florida are suitable regions for the species, as they are characterized by high salinity and pH and small temperature variation. An expansion of the species’ distribution was forecast northward under mild climate scenarios, while a decrease of suitable areas was forecast in the south. In the climate scenario with the most intense changes, P. caribaeorum would lose one-half of its suitable habitats, including the northernmost and southernmost areas of its distribution. The Caribbean Sea and northeastern Brazil, as well as other places under the influence of coastal upwellings, may serve as potential havens for this species.
Durante et al. (2018) The effect of climate change on the distribution of a tropical zoanthid (Palythoa caribaeorum) and its ecological implications. PeerJ 6:e4777 https://doi.org/10.7717/peerj.4777