A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton
We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the “analyse skeletons” plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan’s measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions.
Nunez-Iglesias et al. (2018) A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton. PeerJ 6:e4312 https://doi.org/10.7717/peerj.4312
Metagenomic analysis of orange colored protrusions from the muscle of Queen Conch Lobatus gigas (Linnaeus, 1758)
The endangered marine gastropod, Lobatus gigas, is an important fishery resource in the Caribbean region. Microbiological and parasitological research of this species have been poorly addressed despite its role in ecological fitness, conservation status and prevention of potential pathogenic infections. This study identified taxonomic groups associated with orange colored protrusions in the muscle of queen conchs using histological analysis, 454 pyrosequencing, and a combination of PCR amplification and automated Sanger sequencing. The molecular approaches indicate that the etiological agent of the muscle protrusions is a parasite belonging to the subclass Digenea. Additionally, the scope of the molecular technique allowed the detection of bacterial and fungi clades in the assignment analysis. This is the first evidence of a digenean infection in the muscle of this valuable Caribbean resource.
Cuartas et al. (2018) Metagenomic analysis of orange colored protrusions from the muscle of Queen Conch Lobatus gigas (Linnaeus, 1758). PeerJ 6:e4307 https://doi.org/10.7717/peerj.4307
Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico
The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides. These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures.
Domínguez-Contreras et al. (2018) Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico. PeerJ 6:e4295 https://doi.org/10.7717/peerj.4295
Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie
Extremes in climate, such as heat waves and drought, are expected to become more frequent and intense with forecasted climate change. Plant species will almost certainly differ in their responses to these stressors. We experimentally imposed a heat wave and drought in the tallgrass prairie ecosystem near Manhattan, Kansas, USA to assess transcriptional responses of two ecologically important C4 grass species, Andropogon gerardii and Sorghastrum nutans. Based on previous research, we expected that S. nutans would regulate more genes, particularly those related to stress response, under high heat and drought. Across all treatments, S. nutans showed greater expression of negative regulatory and catabolism genes while A. gerardii upregulated cellular and protein metabolism. As predicted, S. nutans showed greater sensitivity to water stress, particularly with downregulation of non-coding RNAs and upregulation of water stress and catabolism genes. A. gerardii was less sensitive to drought, although A. gerardii tended to respond with upregulation in response to drought versus S. nutans which downregulated more genes under drier conditions. Surprisingly, A. gerardii only showed minimal gene expression response to increased temperature, while S. nutans showed no response. Gene functional annotation suggested that these two species may respond to stress via different mechanisms. Specifically, A. gerardii tends to maintain molecular function while S. nutans prioritizes avoidance. Sorghastrum nutans may strategize abscisic acid response and catabolism to respond rapidly to stress. These results have important implications for success of these two important grass species under a more variable and extreme climate forecast for the future.
Hoffman et al. (2018) Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie. PeerJ 6:e4394 https://doi.org/10.7717/peerj.4394
Benthic grazing in a eutrophic river: cascading effects of zoobenthivorous fish mask direct effects of herbivorous fish
Benthic grazing strongly controls periphyton biomass. The question therefore arises whether benthic grazing could be used as a tool to reduce excessive growth of periphyton in nutrient-enriched rivers. Although benthic invertebrate grazers reduce the growth of periphyton, this is highly context dependent. Here we assessed whether the only obligate herbivorous fish in European rivers, the common nase (Chondrostoma nasus L.), is able to reduce periphyton biomass in a eutrophic river. We conducted three consecutive in situ experiments at low, intermediate and high densities of nase in the river using standard tiles on the river bottom naturally covered with periphyton that were accessible to fish and tiles that excluded fish foraging with electric exclosures. The biomass of benthic invertebrate grazers was very low relative to nase. We hypothesised that nase would reduce periphyton biomass on accessible tiles and therefore expected higher periphyton biomass on the exclosure tiles, at least at intermediate and high densities of nase in the river. Contrary to our expectation, the impact of fish grazing was low even at high fish density, as judged by the significantly lower chlorophyll a concentration on exclosure tiles even though the ash-free dry mass on accessible and exclosure tiles did not differ. The lower chlorophyll a concentrations on exclosure tiles might be explained by a higher biomass of invertebrate grazers on the exclosure tiles, which would indicate that the effect of invertebrate grazers was stronger than that of herbivorous fish grazers. The high biomass of invertebrate grazers on exclosure tiles likely arose from the exclusion of zoobenthivorous fish, which occur in the river at high densities. The results of our small-scale experiments suggested that cascading top-down effects of zoobenthivorous fish have a higher impact on periphyton biomass than direct effects of herbivorous nase.
Gerke et al. (2018) Benthic grazing in a eutrophic river: cascading effects of zoobenthivorous fish mask direct effects of herbivorous fish. PeerJ 6:e4381 https://doi.org/10.7717/peerj.4381
Catchment land use predicts benthic vegetation in small estuaries
Many estuaries are becoming increasingly eutrophic from human activities within their catchments. Nutrient loads often are used to assess risk of eutrophication to estuaries, but such data are expensive and time consuming to obtain. We compared the percent of fertilized land within a catchment, dissolved inorganic nitrogen loads, catchment to estuary area ratio and flushing time as predictors of the proportion of macroalgae to total vegetation within 14 estuaries in south-eastern Australia. The percent of fertilized land within the catchment was the best predictor of the proportion of macroalgae within the estuaries studied. There was a transition to a dominance of macroalgae once the proportion of fertilized land in the catchment exceeded 24%, highlighting the sensitivity of estuaries to catchment land use.
Cook et al. (2018) Catchment land use predicts benthic vegetation in small estuaries. PeerJ 6:e4378 https://doi.org/10.7717/peerj.4378
Ontogeny of long-range vocalizations in a Neotropical fossorial rodent: the Anillaco Tuco-Tuco (Ctenomys sp.)
Tuco-tucos (Ctenomys spp.) are subterranean rodents that produce territorial, high intensity long-range vocalizations (LRVs) of broadband and low frequency that are essential for long-distance communication between individuals in different tunnel systems. Despite their importance, the development of LRVs remains poorly understood. In adult Anillaco Tuco-Tucos (Ctenomys sp.) the LRV is composed by two types of syllables (series and individual notes) that are repeated a variable number of times. We studied the development of the LRVs in eight juveniles of the Anillaco Tuco-Tuco ranging from 14–28 to 104–118 days after birth. We (1) tested whether the syllables followed any of three alternative developmental modes (retention of juvenile vocalizations, modification of juvenile precursors or de novo appearance in adults), (2) evaluated the development of structural and acoustic features of syllables, and (3) tested the prediction that juveniles should produce a greater proportion of atypical series in precursors of the LRV than adults, due to lack maturation and/or precise coupling of neuromuscular and anatomical structures. The LRV of the Anillaco Tuco-Tuco exhibited a mixed developmental mode: while series developed from juvenile precursors whose acoustic features gradually approached those of adults, individual notes appeared later in the ontogeny and de novo with acoustic features indistinguishable from those of adults. The number of series per vocalization increased through development and varied from one to 25 in juvenile males and from one to six in juvenile females. The structure of the most common series type (triad) did not exhibit ontogenetic changes and was present as such at the onset of the emission of vocalizations. On the contrary, acoustic features of juvenile triad notes changed with age in both sexes (duration 90% increased through development, while bandwidth 90% and peak frequency decreased). Furthermore, juveniles emitted a higher proportion of atypical series than adults (7.4% vs. 0.3%), as expected in the development of any complex behavior that requires practice to be mastered. The maturation of the LRV occurred well before the sexual maturation, presumably due to the protracted time needed to acquire or build a burrow system long before mating is possible. We propose that protracted vocal development is another component in the slow developmental strategy of Ctenomys and subterranean rodents in general.
Amaya et al. (2018) Ontogeny of long-range vocalizations in a Neotropical fossorial rodent: the Anillaco Tuco-Tuco (Ctenomys sp.). PeerJ 6:e4334 https://doi.org/10.7717/peerj.4334
Different intensities of basketball drills affect jump shot accuracy of expert and junior players
Background In basketball a maximum accuracy at every game intensity is required while shooting. The aim of the present study was to investigate the acute effect of three different drill intensity simulation protocols on jump shot accuracy in expert and junior basketball players. Materials & Methods Eleven expert players (age 26 ± 6 yrs, weight 86 ± 11 kg, height 192 ± 8 cm) and ten junior players (age 18 ± 1 yrs, weight 75 ± 12 kg, height 184 ± 9 cm) completed three series of twenty jump shots at three different levels of exertion. Counter Movement Jump (CMJ) height was also measured after each series of jump shots. Exertion’s intensity was induced manipulating the basketball drills. Heart rate was measured for the whole duration of the tests while the rating of perceived exertion (RPE) was collected at the end of each series of shots. Results Heart rate and rating of perceived exertion (RPE) were statistically different in the three conditions for both expert and junior players. CMJ height remained almost unchanged in both groups. Jump shot accuracy decreased with increasing drills intensity both in experts and junior players. Expert players showed higher accuracy than junior players for all the three levels of exertion (83% vs 64%, p < 0.001; 75% vs 57%, p < 0.05; 76% vs 60%, p < 0.01). Moreover, for the most demanding level of exertion, experts showed a higher accuracy in the last ten shots compared to the first ten shots (82% vs 70%, p < 0.05). Discussion Experts coped better with the different exertion’s intensities, thus maintaining a higher level of performance. The introduction of technical short bouts of high-intensity sport-specific exercises into skill sessions should be proposed to improve jump shot accuracy during matches.
Marcolin et al. (2018) Different intensities of basketball drills affect jump shot accuracy of expert and junior players. PeerJ 6:e4250 https://doi.org/10.7717/peerj.4250
The axial skeleton of Poposaurus langstoni (Pseudosuchia: Poposauroidea) and its implications for accessory intervertebral articulation evolution in pseudosuchian archosaurs
Dinosaurs and their close relatives grew to sizes larger than any other terrestrial animal in the history of life on Earth, and many enormous dinosaurs (e.g., Diplodocus, Spinosaurus, Tyrannosaurus) have accessory intervertebral articulations that have been suggested to support these large body sizes. Some pseudosuchian archosaurs have been reported to have these articulations as well, but few have been characterized in these taxa because of a lower abundance of complete, three-dimensional pseudosuchian vertebral material in relation to dinosaurs. We describe the axial column of the large (∼4–5 m) poposauroid pseudosuchian Poposaurus langstoni from the Upper Triassic of Texas (TMM Locality 31025 of the Otis Chalk localities; Dockum Group, Howard County, TX, USA). P. langstoni was originally named from pelvic girdle elements and vertebrae; here we describe newly discovered and prepared presacral vertebrae and a presacral rib from the original excavation of the holotype in the 1940s. The well-preserved vertebrae have well-defined vertebral laminae and clear hyposphene–hypantrum intervertebral articulations, character states mentioned in pseudosuchians but rarely described. The new material demonstrates variation present in the hyposphene–hypantrum articulation through the vertebral column. We compared these morphologies to other pseudosuchians with and without the hyposphene–hypantrum articulation. Based on these careful comparisons, we provide an explicit definition for the hyposphene–hypantrum articulation applicable across Archosauria. Within Pseudosuchia, we find the hyposphene–hypantrum appeared independently in the clade at least twice, but we also see the loss of these structures in clades that had them ancestrally. Furthermore, we found the presence of large body sizes (femoral lengths >∼300 mm) and the presence of the hyposphene–hypantrum is correlated in most non-crocodylomorph pseudosuchian archosaurs with a few exceptions. This result suggests that the presence of the hyposphene–hypantrum is controlled by the increases and decreases in body size and not strictly inheritance.
Stefanic et al. (2018) The axial skeleton of Poposaurus langstoni (Pseudosuchia: Poposauroidea) and its implications for accessory intervertebral articulation evolution in pseudosuchian archosaurs. PeerJ 6:e4235 https://doi.org/10.7717/peerj.4235
Factors associated with elevated blood pressure or hypertension in Afro-Caribbean youth: a cross-sectional study
Background Although several studies have identified risk factors for high blood pressure (BP), data from Afro-Caribbean populations are limited. Additionally, less is known about how putative risk factors operate in young adults and how social factors influence the risk of high BP. In this study, we estimated the relative risk for elevated BP or hypertension (EBP/HTN), defined as BP ≥ 120/80 mmHg, among young adults with putative cardiovascular disease (CVD) risk factors in Jamaica and evaluated whether relative risks differed by sex. Methods Data from 898 young adults, 18–20 years old, were analysed. BP was measured with a mercury sphygmomanometer after participants had been seated for 5 min. Anthropometric measurements were obtained, and glucose, lipids and insulin measured from a fasting venous blood sample. Data on socioeconomic status (SES) were obtained via questionnaire. CVD risk factor status was defined using standard cut-points or the upper quintile of the distribution where the numbers meeting standard cut-points were small. Relative risks were estimated using odds ratios (OR) from logistic regression models. Results Prevalence of EBP/HTN was 30% among males and 13% among females (p < 0.001 for sex difference). There was evidence for sex interaction in the relationship between EBP/HTN and some of risk factors (obesity and household possessions), therefore we report sex-specific analyses. In multivariable logistic regression models, factors independently associated with EBP/HTN among men were obesity (OR 8.48, 95% CI [2.64–27.2], p < 0.001), and high glucose (OR 2.01, CI [1.20–3.37], p = 0.008), while high HOMA-IR did not achieve statistical significance (OR 2.08, CI [0.94–4.58], p = 0.069). In similar models for women, high triglycerides (OR 1.98, CI [1.03–3.81], p = 0.040) and high HOMA-IR (OR 2.07, CI [1.03–4.12], p = 0.039) were positively associated with EBP/HTN. Lower SES was also associated with higher odds for EBP/HTN (OR 4.63, CI [1.31–16.4], p = 0.017, for moderate vs. high household possessions; OR 2.61, CI [0.70–9.77], p = 0.154 for low vs. high household possessions). Alcohol consumption was associated with lower odds of EBP/HTN among females only; OR 0.41 (CI [0.18–0.90], p = 0.026) for drinking <1 time per week vs. never drinkers, and OR 0.28 (CI [0.11–0.76], p = 0.012) for drinking ≥3 times per week vs. never drinkers. Physical activity was inversely associated with EBP/HTN in both males and females. Conclusion Factors associated with EBP/HTN among Jamaican young adults include obesity, high glucose, high triglycerides and high HOMA-IR, with some significant differences by sex. Among women lower SES was positively associated with EBP/HTN, while moderate alcohol consumption was associated lower odds of EBP/HTN.
Ferguson et al. (2018) Factors associated with elevated blood pressure or hypertension in Afro-Caribbean youth: a cross-sectional study. PeerJ 6:e4385 https://doi.org/10.7717/peerj.4385