Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding
DNA metabarcoding, the PCR-based profiling of natural communities, is becoming the method of choice for biodiversity monitoring because it circumvents some of the limitations inherent to traditional ecological surveys. However, potential sources of bias that can affect the reproducibility of this method remain to be quantified. The interpretation of differences in patterns of sequence abundance and the ecological relevance of rare sequences remain particularly uncertain. Here we used one artificial mock community to explore the significance of abundance patterns and disentangle the effects of two potential biases on data reproducibility: indexed PCR primers and random sampling during Illumina MiSeq sequencing. We amplified a short fragment of the mitochondrial Cytochrome c Oxidase Subunit I (COI) for a single mock sample containing equimolar amounts of total genomic DNA from 34 marine invertebrates belonging to six phyla. We used seven indexed broad-range primers and sequenced the resulting library on two consecutive Illumina MiSeq runs. The total number of Operational Taxonomic Units (OTUs) was ∼4 times higher than expected based on the composition of the mock sample. Moreover, the total number of reads for the 34 components of the mock sample differed by up to three orders of magnitude. However, 79 out of 86 of the unexpected OTUs were represented by <10 sequences that did not appear consistently across replicates. Our data suggest that random sampling of rare OTUs (e.g., small associated fauna such as parasites) accounted for most of variation in OTU presence–absence, whereas biases associated with indexed PCRs accounted for a larger amount of variation in relative abundance patterns. These results suggest that random sampling during sequencing leads to the low reproducibility of rare OTUs. We suggest that the strategy for handling rare OTUs should depend on the objectives of the study. Systematic removal of rare OTUs may avoid inflating diversity based on common β descriptors but will exclude positive records of taxa that are functionally important. Our results further reinforce the need for technical replicates (parallel PCR and sequencing from the same sample) in metabarcoding experimental designs. Data reproducibility should be determined empirically as it will depend upon the sequencing depth, the type of sample, the sequence analysis pipeline, and the number of replicates. Moreover, estimating relative biomasses or abundances based on read counts remains elusive at the OTU level.
Leray et al. (2017) Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding. PeerJ 5:e3006 https://doi.org/10.7717/peerj.3006
A cross sectional survey on health-related quality of life of elementary school students using the Korean version of the EQ-5D-Y
Background and Objective The Korean version of the EQ-5D-Y was launched in 2015 by the EuroQol group. Currently, there is no HRQOL data obtained by using the EQ-5D-Y in Korea. This study aimed to measure health-related quality of life of Korean elementary school students using the EQ-5D-Y. Methods Elementary school students were recruited from 11 primary schools in Gyungbuk, South Korea. The EQ-5D-Y was self-administered in the sample population. Demographic characteristics were collected from the subjects’ parents or guardians. The percentage of respondents reporting problems and VAS scores were calculated. Feasibility of the EQ-5D-Y was assessed by analysing the proportion of missing responses. The percentage of reported problems on the dimensions and VAS score between groups were compared by demographic factors. Results A total of 2,494 questionnaires were collected. There were 24 (0.96%) missing responses on the EQ-5D-Y and 187 (7.5%) missing VAS score responses. The proportion of reported problems ranged from 2.3% on the mobility dimension to 9.8% on the “having pain or discomfort” dimension. There was no significant difference in the proportion of problems by age group in male participants. However, in females, the older group reported significantly more problems on the “having pain or discomfort” and “feeling worried, sad, or unhappy” dimensions compared to the younger group. Students living with parents with the lowest educational level reported significantly more problems on the “looking after myself” and “doing usual activities” dimensions than did those living with parents with higher levels of education. Discussion This study showed the distribution of health-related quality of life and explored the feasibility of the EQ-5D-Y for measuring health-related quality of life in Korean elementary school students. Further studies are required to examine other psychometric properties of the Korean EQ-5D-Y.
Kim et al. (2017) A cross sectional survey on health-related quality of life of elementary school students using the Korean version of the EQ-5D-Y. PeerJ 5:e3115 https://doi.org/10.7717/peerj.3115
Grape seed proanthocyanidin extract protects lymphocytes against histone-induced apoptosis
Apoptosis of lymphocytes is associated with immunosuppression and poor prognosis in sepsis. Our previous report showed that histones, nuclear proteins released from damaged or dying cells in sepsis, can mediate lymphocyte apoptosis via mitochondria damage. Grape seed proanthocyanidin extract (GSPE), a natural substance with protective properties against oxidative stress, plays a vital role in cell and mitochondria protection. We thus hypothesized that GSPE may play a protective role in histone-induced lymphocyte apoptosis through its anti-oxidative properties. In this study, we investigated the protective efficacy of GSPE on lymphocyte apoptosis induced by extracellular histones, a main contributor of death in sepsis. Human blood lymphocytes were treated with 50 μg/ml histones, 2 μg/ml GSPE, or a combination of both. A total of 100 μM N-acetylcysteine (NAC), a reactive oxygen species (ROS) inhibitor, was used as a positive control for GSPE. Apoptosis, intracellular ROS levels, mitochondrial membrane potential, Bcl-2 expression, and caspase-3 cleavage were measured. Our data clearly indicate that GSPE significantly inhibited lymphocyte apoptosis, generation of ROS, the loss of mitochondrial membrane potential, the decrease in Bcl-2 expression, and caspase-3 activation induced by extracellular histones. In conclusion, we show that GSPE has a protective effect on lymphocyte apoptosis induced by extracellular histones. This study suggests GSPE as a potential therapeutic agent that could help reduce lymphocyte apoptosis, and thus the state of immunosuppression was observed in septic patients.
Chang et al. (2017) Grape seed proanthocyanidin extract protects lymphocytes against histone-induced apoptosis. PeerJ 5:e3108 https://doi.org/10.7717/peerj.3108
Exploring differential health effects of work stress: a latent class cluster approach
Background While evidence highlights the detrimental health consequences of adverse working conditions, effect sizes vary by the stressor examined. In this study, we aimed to explore the differential effects various constellations of job demands have on prevalent symptom clusters. Methods We analysed self-reported data from a nationwide Austrian survey (N = 16,466), based on a cross-sectional design. By means of latent class analysis, a set of items was used to assess the burden from several job demands as well as the frequency of occurrence of mental and physical symptoms in order to identify stress profiles and symptom clusters, respectively. Results Analysis revealed four subgroups that each demonstrated a typological response pattern regarding job demands and health symptoms, respectively. The revealed stress profiles were found to be strongly related to the symptom clusters, while the effects differed considerably depending on the types of demands experienced. Conclusion The current study presents an alternative method of examining the stress-health link by using a combined person- and variable-centred approach. The findings suggest a hierarchy in stress exposure with the most pronounced health consequences found for a synchronous burden from physical, psychosocial and organizational demands.
Mayerl et al. (2017) Exploring differential health effects of work stress: a latent class cluster approach. PeerJ 5:e3106 https://doi.org/10.7717/peerj.3106
Evolution of the patellar sesamoid bone in mammals
The patella is a sesamoid bone located in the major extensor tendon of the knee joint, in the hindlimb of many tetrapods. Although numerous aspects of knee morphology are ancient and conserved among most tetrapods, the evolutionary occurrence of an ossified patella is highly variable. Among extant (crown clade) groups it is found in most birds, most lizards, the monotreme mammals and almost all placental mammals, but it is absent in most marsupial mammals as well as many reptiles. Here, we integrate data from the literature and first-hand studies of fossil and recent skeletal remains to reconstruct the evolution of the mammalian patella. We infer that bony patellae most likely evolved between four and six times in crown group Mammalia: in monotremes, in the extinct multituberculates, in one or more stem-mammal genera outside of therian or eutherian mammals and up to three times in therian mammals. Furthermore, an ossified patella was lost several times in mammals, not including those with absent hindlimbs: once or more in marsupials (with some re-acquisition) and at least once in bats. Our inferences about patellar evolution in mammals are reciprocally informed by the existence of several human genetic conditions in which the patella is either absent or severely reduced. Clearly, development of the patella is under close genomic control, although its responsiveness to its mechanical environment is also important (and perhaps variable among taxa). Where a bony patella is present it plays an important role in hindlimb function, especially in resisting gravity by providing an enhanced lever system for the knee joint. Yet the evolutionary origins, persistence and modifications of a patella in diverse groups with widely varying habits and habitats—from digging to running to aquatic, small or large body sizes, bipeds or quadrupeds—remain complex and perplexing, impeding a conclusive synthesis of form, function, development and genetics across mammalian evolution. This meta-analysis takes an initial step toward such a synthesis by collating available data and elucidating areas of promising future inquiry.
Samuels et al. (2017) Evolution of the patellar sesamoid bone in mammals. PeerJ 5:e3103 https://doi.org/10.7717/peerj.3103
Insect herbivores increase mortality and reduce tree seedling growth of some species in temperate forest canopy gaps
Insect herbivores help maintain forest diversity through selective predation on seedlings of vulnerable tree species. Although the role of natural enemies has been well-studied in tropical systems, relatively few studies have experimentally manipulated insect abundance in temperate forests and tracked impacts over multiple years. We conducted a three-year experiment (2012–2014) deterring insect herbivores from seedlings in new treefall gaps in deciduous hardwood forests in Maryland. During this study, we tracked recruitment of all tree seedlings, as well as survivorship and growth of 889 individual seedlings from five tree species: Acer rubrum, Fagus grandifolia, Fraxinus spp., Liriodendron tulipifera, and Liquidambar styraciflua. Insect herbivores had little effect on recruitment of any tree species, although there was a weak indication that recruitment of A. rubrum was higher in the presence of herbivores. Insect herbivores reduced survivorship of L. tulipifera, but had no significant effects on A. rubrum, Fraxinus spp., F. grandifolia, or L. styraciflua. Additionally, insects reduced growth rates of early pioneer species A. rubrum, L. tulipifera, and L. styraciflua, but had little effect on more shade-tolerant species F. grandifolia and Fraxinus spp. Overall, by negatively impacting growth and survivorship of early pioneer species, forest insects may play an important but relatively cryptic role in forest gap dynamics, with potentially interesting impacts on the overall maintenance of diversity.
Lemoine et al. (2017) Insect herbivores increase mortality and reduce tree seedling growth of some species in temperate forest canopy gaps. PeerJ 5:e3102 https://doi.org/10.7717/peerj.3102
Comparison of consumption behavior and appetite sensations among patients with type 2 diabetes mellitus after bariatric surgery
Background The promising postsurgical weight loss and remission of type 2 diabetes (T2D) from bariatric surgery can be attributed to modified eating physiology after surgical procedures. We sought to investigate the changes in the parameters of consumption behaviors and appetite sensations induced by a mixed meal tolerance test, and to correlate these alterations with age, body mass index, C-peptide levels, and duration of T2D 1 year after bariatric surgery. Methods A total of 16 obese patients with T2D who underwent mini-gastric bypass (GB) and 16 patients who underwent sleeve gastrectomy (SG) were enrolled in this study and evaluated using a mixed meal tolerance test one year after surgery. A visual analogue scale was used for scoring appetite sensation at different time points. The area under the curve (AUC) and the incremental or decremental AUC (ΔAUC) were compared between the two groups. Results One year after surgery, a decreasing trend in the consumption time was observed in the GB group compared to the SG group, while the duration of T2D before surgery was negatively correlated with the post-operative consumed time in those after GB. Patients who underwent GB had significantly higher fasting scores for fullness and desire to eat, higher AUC0′–180′ of scores for desire to eat, as well as more effective post-meal suppression of hunger and desire to eat compared with those undergoing SG one year after surgery. Post-operative C-peptide levels were negatively correlated with ΔAUC0′–180′ for hunger and ΔAUC0′–180′ for desire to eat in the GB group, while negatively correlated with ΔAUC0′–180′ for fullness in the SG group. Discussion Patients with T2D after either GB or SG exhibit distinct nutrient-induced consumption behaviors and appetite sensations post-operatively, which may account for the differential effects on weight loss and glycemic control after different surgery.
Yeh et al. (2017) Comparison of consumption behavior and appetite sensations among patients with type 2 diabetes mellitus after bariatric surgery. PeerJ 5:e3090 https://doi.org/10.7717/peerj.3090
Isolation and characterization of human articular chondrocytes from surgical waste after total knee arthroplasty (TKA)
Background Cartilage tissue engineering is a fast-evolving field of biomedical engineering, in which the chondrocytes represent the most commonly used cell type. Since research in tissue engineering always consumes a lot of cells, simple and cheap isolation methods could form a powerful basis to boost such studies and enable their faster progress to the clinics. Isolated chondrocytes can be used for autologous chondrocyte implantation in cartilage repair, and are the base for valuable models to investigate cartilage phenotype preservation, as well as enable studies of molecular features, nature and scales of cellular responses to alterations in the cartilage tissue. Methods Isolation and consequent cultivation of primary human adult articular chondrocytes from the surgical waste obtained during total knee arthroplasty (TKA) was performed. To evaluate the chondrogenic potential of the isolated cells, gene expression of collagen type 2 (COL2), collagen 1 (COL1) and aggrecan (ACAN) was evaluated. Immunocytochemical staining of all mentioned proteins was performed to evaluate chondrocyte specific production. Results Cartilage specific gene expression of COL2 and ACAN has been shown that the proposed protocol leads to isolation of cells with a high chondrogenic potential, possibly even specific phenotype preservation up to the second passage. COL1 expression has confirmed the tendency of the isolated cells dedifferentiation into a fibroblast-like phenotype already in the second passage, which confirms previous findings that higher passages should be used with care in cartilage tissue engineering. To evaluate the effectiveness of our approach, immunocytochemical staining of the evaluated chondrocyte specific products was performed as well. Discussion In this study, we developed a protocol for isolation and consequent cultivation of primary human adult articular chondrocytes with the desired phenotype from the surgical waste obtained during TKA. TKA is a common and very frequently performed orthopaedic surgery during which both femoral condyles are removed. The latter present the ideal source for a simple and relatively cheap isolation of chondrocytes as was confirmed in our study.
Naranda et al. (2017) Isolation and characterization of human articular chondrocytes from surgical waste after total knee arthroplasty (TKA). PeerJ 5:e3079 https://doi.org/10.7717/peerj.3079
Can video playback provide social information for foraging blue tits?
Video playback is becoming a common method for manipulating social stimuli in experiments. Parid tits are one of the most commonly studied groups of wild birds. However, it is not yet clear if tits respond to video playback or how their behavioural responses should be measured. Behaviours may also differ depending on what they observe demonstrators encountering. Here we present blue tits (Cyanistes caeruleus) videos of demonstrators discovering palatable or aversive prey (injected with bitter-tasting Bitrex) from coloured feeding cups. First we quantify variation in demonstrators’ responses to the prey items: aversive prey provoked high rates of beak wiping and head shaking. We then show that focal blue tits respond differently to the presence of a demonstrator on a video screen, depending on whether demonstrators discover palatable or aversive prey. Focal birds faced the video screen more during aversive prey presentations, and made more head turns. Regardless of prey type, focal birds also hopped more frequently during the presence of a demonstrator (compared to a control video of a different coloured feeding cup in an empty cage). Finally, we tested if demonstrators’ behaviour affected focal birds’ food preferences by giving individuals a choice to forage from the same cup as a demonstrator, or from the cup in the control video. We found that only half of the individuals made their choice in accordance to social information in the videos, i.e., their foraging choices were not different from random. Individuals that chose in accordance with a demonstrator, however, made their choice faster than individuals that chose an alternative cup. Together, our results suggest that video playback can provide social cues to blue tits, but individuals vary greatly in how they use this information in their foraging decisions.
Hämäläinen et al. (2017) Can video playback provide social information for foraging blue tits?. PeerJ 5:e3062 https://doi.org/10.7717/peerj.3062
Temporal patterns and geographic heterogeneity of Zika virus (ZIKV) outbreaks in French Polynesia and Central America
Background Zika virus (ZIKV) transmission has been reported in 67 countries/territories in the Oceania region and the Americas since 2015, prompting the World Health Organization (WHO) to declare ZIKV as a Public Health Emergency of International Concern in February 2016, due to its strong association with medical complications such as microcephaly and Guillain–Barré Syndrome (GBS). However, a substantial gap in knowledge still exists regarding differing temporal pattern and potential of transmission of ZIKV in different regions of the world. Methods We use a phenomenological model to ascertain the temporal patterns and transmission potential of ZIKV in various countries/territories, by fitting the model to Zika case data from Yap Island and French Polynesia in the Oceania region and 11 countries/territories with confirmed case data, namely, Colombia, Ecuador, French Guiana, Guadeloupe, Guatemala, Mexico, Nicaragua, Panama, Puerto Rico, Saint Martin, and Suriname, to pinpoint the waves of infections in each country/territory and to estimate the respective basic reproduction number R0. Results Six of these time series datasets resulted in statistically significant model fit of at least one wave of reported cases, namely that of French Polynesia, Colombia, Puerto Rico, Guatemala, Suriname and Saint Martin. However, only Colombia and Guatemala exhibited two waves of cases while the others had only one wave. Temporal patterns of the second wave in Colombia and the single wave in Suriname are very similar, with the respective turning points separated by merely a week. Moreover, the mean estimates of R0 for Colombia, Guatemala and Suriname, all land-based populations, range between 1.05 and 1.75, while the corresponding mean estimates for R0 of island populations in French Polynesia, Puerto Rico and Saint Martin are significantly lower with a range of 5.70–6.89. We also fit the Richards model to Zika case data from six main archipelagos in French Polynesia, suggesting the outbreak in all six island populations occurred during the same time, albeit with different peak time, with mean R0 range of 3.09–5.05. Discussion Using the same modeling methodology, in this study we found a significant difference between transmissibility (as quantified by R0) in island populations as opposed to land-based countries/territories, possibly suggesting an important role of geographic heterogeneity in the spread of vector-borne diseases and its future course, which requires further monitoring. Our result has potential implications for planning respective intervention and control policies targeted for island and land-based populations.
Hsieh (2017) Temporal patterns and geographic heterogeneity of Zika virus (ZIKV) outbreaks in French Polynesia and Central America. PeerJ 5:e3015 https://doi.org/10.7717/peerj.3015