title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1454 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Chondrogenic differentiation of adipose-derived mesenchymal stem cells induced by L-ascorbic acid and platelet rich plasma on silk fibroin scaffold link: https://peerj.com/articles/5809 last-modified: 2018-11-19 description: Articular cartilage is an avascular tissue with limited regenerative property. Therefore, a defect or trauma in articular cartilage due to disease or accident can lead to progressive tissue deterioration. Cartilage tissue engineering, by replacing defective cartilage tissue, is a method for repairing such a problem. In this research, three main aspects—cell, biomaterial scaffold, and bioactive factors—that support tissue engineering study were optimized. Adipose-derived mesenchymal stem cells (ADSC) that become cartilage were grown in an optimized growth medium supplemented with either platelet rich plasma (PRP) or L-ascorbic acid (LAA). As the characterization result, the ADSC used in this experiment could be classified as Mesenchymal Stem Cell (MSC) based on multipotency analysis and cell surface marker analysis. The biomaterial scaffold was fabricated from the Bombyx morii cocoon using silk fibroin by salt leaching method and was engineered to form different sizes of pores to provide optimized support for cell adhesion and growth. Biocompatibility and cytotoxicity evaluation was done using MTT assay to optimize silk fibroin concentration and pore size. Characterized ADSC were grown on the optimized scaffold. LAA and PRP were chosen as bioactive factors to induce ADSC differentiation to become chondrocytes. The concentration optimization of LAA and PRP was analyzed by cell proliferation using MTT assay and chondrogenic differentiation by measuring glycosaminoglycan (GAG) using Alcian Blue at 605 nm wavelength. The optimum silk fibroin concentration, pore size, LAA concentration, and PRP concentration were used to grow and differentiate characterized ADSC for 7, 14, and 21 days. The cell morphology on the scaffold was analyzed using a scanning electron microscope (SEM). The result showed that the ADSC could adhere on plastic, express specific cell surface markers (CD73, CD90, and CD105), and could be differentiated into three types of mature cells. The silk fibroin scaffold made from 12% w/v concentration formed a 500 µm pore diameter (SEM analysis), and was shown by MTT assay to be biocompatible and to facilitate cell growth. The optimum concentrations of the bioactive factors LAA and PRP were 50 µg/mL and 10%, respectively. GAG analysis with Alcian Blue staining suggested that PRP induction medium and LAA induction medium on 12% w/v scaffold could effectively promote not only cell adhesion and cell proliferation but also chondrogenic differentiation of ADSC within 21 days of culture. Therefore, this study provides a new approach to articular tissue engineering with a combination of ADSC as cell source, LAA and PRP as bioactive factors, and silk fibroin as a biocompatible and biodegradable scaffold. creator: Anggraini Barlian creator: Hermawan Judawisastra creator: Nayla M. Alfarafisa creator: Untung A. Wibowo creator: Imam Rosadi uri: https://doi.org/10.7717/peerj.5809 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Barlian et al. title: Recommended nitrogen fertilization enhances soil carbon sequestration in China’s monsoonal temperate zone link: https://peerj.com/articles/5983 last-modified: 2018-11-16 description: China consumes more than one-third of the world’s nitrogen (N) fertilizer, and an increasing amount of N fertilizer has been applied over the past decades. Although N fertilization can increase the carbon sequestration potentials of cropland in China, the quantitative effects of different N fertilizer application levels on soil carbon changes have not been evaluated. Therefore, a 12-year cultivation experiment was conducted under three N fertilizer application levels (no N fertilizer input, the recommended N fertilizer input after soil testing, and the estimated additional fertilizer input) to estimate the effect of N addition on soil carbon changes in the root layer (0–80 cm) and non-root layer (80–200 cm) using a within-study meta-analysis method. The results showed significant declines in the soil inorganic carbon (SIC) in the root layers and significant growth in the SIC in the non-root layers under N fertilizer input. The soil organic carbon (SOC) in the root layers and the non-root layer significantly decreased under all the treatments. In addition, the recommended N fertilizer application level significantly increased the SOC and soil total carbon stocks compared with the future N fertilizer application level and no N input, while the future N fertilization significantly decreased the SIC and soil total carbon compared with no N input. The results suggest that N fertilization can rearrange the soil carbon distribution over the entire soil profile, and the recommended N fertilization rather than excess N input can increase the soil carbon stock, which suggests that the national soil testing program in China can improve the soil carbon sequestration potential. creator: Shaofei Jin uri: https://doi.org/10.7717/peerj.5983 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jin title: Influencing factors and health risk assessment of microcystins in the Yongjiang river (China) by Monte Carlo simulation link: https://peerj.com/articles/5955 last-modified: 2018-11-16 description: The Yongjiang river is a large, shallow, hyper-trophic, freshwater river in Guangxi, China. To investigate the presence of microcystin-RR, microcystin-LR, and microcystin-YR (MC-RR, MC-LR, and MC-YR) in the Yongjiang river and describe their correlation with environmental factors, as well as, assess health risk using Monte Carlo simulation, 90 water samples were collected at three sample points from March to December 2017. Results showed that during the monitoring period, total concentrations of MC-RR (TMC-RR), MC-YR (TMC-YR), and MC-LR (TMC-LR) varied from 0.0224 to 0.3783 μg/L, 0.0329 to 0.1433 μg/L, and 0.0341 to 0.2663 μg/L, respectively. Total phosphorus (TP) content appeared to be related to TMC-LR and the total concentrations of microcystins (TMCs), while pH and total nitrogen (TN)/TP ratio appeared to be related to TMC-RR and TMC-YR, respectively. Using the professional health risk assessment software @Risk7.5, the risks of dietary intake of microcystins (MCs), including the carcinogenic risk and non-carcinogenic risk, were evaluated. It was found that the carcinogenic risk of MC-RR from drinking water was higher than MC-LR and MC-YR, and the presence of MCs would lead to high potential health risks, especially in children. The carcinogenic risk of MC-RR to children was >1 × 10−4, the maximum allowance level recommended by the US Environmental Protection Agency; as for adults, it was >5 × 10−5, the maximum allowance level recommended by the International Commission on Radiological Protection. The non-carcinogenic hazard index (HI) of MC-RR, MC-YR, and MC-LR increased successively, indicating that MC-LR was more hazardous to human health than MC-YR and MC-RR, but its HI was <1. This suggests that MCs pose less risk to health. However, it is necessary to strengthen the protection and monitoring of drinking water source for effective control of water pollution and safeguarding of human health. creator: Chan-Chan Xiao creator: Mao-Jian Chen creator: Fan-Biao Mei creator: Xiang Fang creator: Tian-Ren Huang creator: Ji-Lin Li creator: Wei Deng creator: Yuan-Dong Li uri: https://doi.org/10.7717/peerj.5955 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Xiao et al. title: An emerging viral pathogen truncates population age structure in a European amphibian and may reduce population viability link: https://peerj.com/articles/5949 last-modified: 2018-11-16 description: Infectious diseases can alter the demography of their host populations, reducing their viability even in the absence of mass mortality. Amphibians are the most threatened group of vertebrates globally, and emerging infectious diseases play a large role in their continued population declines. Viruses belonging to the genus Ranavirus are responsible for one of the deadliest and most widespread of these diseases. To date, no work has used individual level data to investigate how ranaviruses affect population demographic structure. We used skeletochronology and morphology to evaluate the impact of ranaviruses on the age structure of populations of the European common frog (Rana temporaria) in the UK. We compared ecologically similar populations that differed most notably in their historical presence or absence of ranavirosis (the acute syndrome caused by ranavirus infection). Our results suggest that ranavirosis may truncate the age structure of R. temporaria populations. One potential explanation for such a shift might be increased adult mortality and subsequent shifts in the life history of younger age classes that increase reproductive output earlier in life. Additionally, we constructed population projection models which indicated that such increased adult mortality could heighten the vulnerability of frog populations to stochastic environmental challenges. creator: Lewis J. Campbell creator: Trenton W.J. Garner creator: Giulia Tessa creator: Benjamin C. Scheele creator: Amber G.F. Griffiths creator: Lena Wilfert creator: Xavier A. Harrison uri: https://doi.org/10.7717/peerj.5949 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Campbell et al. title: Soil moisture dynamics under two rainfall frequency treatments drive early spring CO2 gas exchange of lichen-dominated biocrusts in central Spain link: https://peerj.com/articles/5904 last-modified: 2018-11-16 description: BackgroundBiocrusts, communities dominated by mosses, lichens, cyanobacteria, and other microorganisms, largely affect the carbon cycle of drylands. As poikilohydric organisms, their activity time is often limited to short hydration events. The photosynthetic and respiratory response of biocrusts to hydration events is not only determined by the overall amount of available water, but also by the frequency and size of individual rainfall pulses.MethodsWe experimentally assessed the carbon exchange of a biocrust community dominated by the lichen Diploschistes diacapsis in central Spain. We compared the effect of two simulated precipitation patterns providing the same overall amount of water, but with different pulse sizes and frequency (high frequency: five mm/day vs. low frequency: 15 mm/3 days), on net/gross photosynthesis and dark respiration.ResultsRadiation and soil temperature, together with the watering treatment, affected the rates of net and gross photosynthesis, as well as dark respiration. On average, the low frequency treatment showed a 46% ± 3% (mean ± 1 SE) lower rate of net photosynthesis, a 13% ± 7% lower rate of dark respiration, and a 24% ± 8% lower rate of gross photosynthesis. However, on the days when samples of both treatments were watered, no differences between their carbon fluxes were observed. The carbon flux response of D. diacapsis was modulated by the environmental conditions and was particularly dependent on the antecedent soil moisture.DiscussionIn line with other studies, we found a synergetic effect of individual pulse size, frequency, environmental conditions, and antecedent moisture on the carbon exchange fluxes of biocrusts. However, most studies on this subject were conducted in summer and they obtained results different from ours, so we conclude that there is a need for long-term experiments of manipulated precipitation impacts on the carbon exchange of biocrusts. This will enable a more complete assessment of the impacts of climate change-induced alterations in precipitation patterns on biocrust communities. creator: Selina Baldauf creator: Mónica Ladrón de Guevara creator: Fernando T. Maestre creator: Britta Tietjen uri: https://doi.org/10.7717/peerj.5904 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Baldauf et al. title: A new microvertebrate assemblage from the Mussentuchit Member, Cedar Mountain Formation: insights into the paleobiodiversity and paleobiogeography of early Late Cretaceous ecosystems in western North America link: https://peerj.com/articles/5883 last-modified: 2018-11-16 description: The vertebrate fauna of the Late Cretaceous Mussentuchit Member of the Cedar Mountain Formation has been studied for nearly three decades, yet the fossil-rich unit continues to produce new information about life in western North America approximately 97 million years ago. Here we report on the composition of the Cliffs of Insanity (COI) microvertebrate locality, a newly sampled site containing perhaps one of the densest concentrations of microvertebrate fossils yet discovered in the Mussentuchit Member. The COI locality preserves osteichthyan, lissamphibian, testudinatan, mesoeucrocodylian, dinosaurian, metatherian, and trace fossil remains and is among the most taxonomically rich microvertebrate localities in the Mussentuchit Member. To better refine taxonomic identifications of isolated theropod dinosaur teeth, we used quantitative analyses of taxonomically comprehensive databases of theropod tooth measurements, adding new data on theropod tooth morphodiversity in this poorly understood interval. We further provide the first descriptions of tyrannosauroid premaxillary teeth and document the earliest North American record of adocid remains, extending the appearance of this ancestrally Asian clade by 5 million years in western North America and supporting studies of pre-Cenomaninan Laurasian faunal exchange across Beringia. The overabundance of mesoeucrocodylian remains at the COI locality produces a comparatively low measure of relative biodiversity when compared to other microvertebrate sites in the Mussentuchit Member using both raw and subsampling methods. Much more microvertebrate research is necessary to understand the roles of changing ecology and taphonomy that may be linked to transgression of the Western Interior Seaway or microhabitat variation. creator: Haviv M. Avrahami creator: Terry A. Gates creator: Andrew B. Heckert creator: Peter J. Makovicky creator: Lindsay E. Zanno uri: https://doi.org/10.7717/peerj.5883 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Avrahami et al. title: Enhancement of a protocol purifying T1 lipase through molecular approach link: https://peerj.com/articles/5833 last-modified: 2018-11-16 description: T1 Lipase is a thermostable secretary protein of Geobacillus zalihae strain previously expressed in a prokaryotic system and purified using three-step purification: affinity 1, affinity 2, and ion exchange chromatography (IEX). This approach is time consuming and offers low purity and recovery yield. In order to enhance the purification strategy of T1 lipase, affinity 2 was removed so that after affinity 1, the cleaved Glutathione S-transferase (GST) and matured T1 lipase could be directly separated through IEX. Therefore, a rational design of GST isoelectric point (pI) was implemented by prediction using ExPASy software in order to enhance the differences of pI values between GST and matured T1 lipase. Site-directed mutagenesis at two locations flanking the downstream region of GST sequences (H215R and G213R) was successfully performed. Double point mutations changed the charge on GST from 6.10 to 6.53. The purified lipase from the new construct GST tag mutant-T1 was successfully purified using two steps of purification with 6,849 U/mg of lipase specific activity, 33% yield, and a 44-fold increase in purification. Hence, the increment of the pI values in the GST tag fusion T1 lipase resulted in a successful direct separation through IEX and lead to successful purification. creator: Che Haznie Ayu Che Hussian creator: Raja Noor Zaliha Raja Abd. Rahman creator: Adam Leow Thean Chor creator: Abu Bakar Salleh creator: Mohd Shukuri Mohamad Ali uri: https://doi.org/10.7717/peerj.5833 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Che Hussian et al. title: beadplexr: reproducible and automated analysis of multiplex bead assays link: https://peerj.com/articles/5794 last-modified: 2018-11-16 description: Multiplex bead assays are an extension of the commonly used sandwich ELISA. The advantage over ELISA is that they make simultaneous evaluation of several analytes possible. Several commercial assay systems, where the beads are acquired on a standard flow cytometer, exist. These assay systems come with their own software tool for analysis and evaluation of the concentration of the analyzed analytes. However, these tools are either tied to particular commercial software or impose other limitations to their licenses, such as the number of events which can be analyzed. In addition, all these solutions are ‘point and click’ which potentially obscures the steps taken in the analysis. Here we present beadplexer, an open-source R-package for the reproducible analysis of multiplex bead assay data. The package makes it possible to automatically identify bead clusters, and provides functionality to easily fit a standard curve and calculate the concentrations of the analyzed analytes. beadplexer is available from CRAN and from https://gitlab.com/ustervbo/beadplexr. creator: Ulrik Stervbo creator: Timm H. Westhoff creator: Nina Babel uri: https://doi.org/10.7717/peerj.5794 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Stervbo et al. title: Serotonin 5-HT1A receptor binding and self-transcendence in healthy control subjects—a replication study using Bayesian hypothesis testing link: https://peerj.com/articles/5790 last-modified: 2018-11-16 description: ObjectiveA putative relationship between markers for the serotonin system and the personality scale self-transcendence (ST) and its subscale spiritual acceptance (SA) has been demonstrated in a previous PET study of 5-HT1A receptor binding in healthy control subjects. The results could however not be replicated in a subsequent PET study at an independent centre. In this study, we performed a replication of our original study in a larger sample using Bayesian hypothesis testing to evaluate relative evidence both for and against this hypothesis.MethodsRegional 5-HT1A receptor binding potential (BPND) was examined in 50 healthy male subjects using PET with the radioligand [11C]WAY100635. 5-HT1Aavailability was calculated using the simplified reference tissue model (SRTM) yielding regional BPND. ST and SA were measured using the Temperament and Character Inventory (TCI) questionnaire. Correlations between ST/SA scores and 5-HT1ABPND in frontal cortex, hippocampus and raphe nuclei were examined by calculation of default correlation Bayes factors (BFs) and replication BFs.ResultsThere were no significant correlations between 5-HT1A receptor binding and ST/SA scores. Rather, five of six replication BFs provided moderate to strong evidence for no association between 5-HT1A availability and ST/SA, while the remaining BF provided only weak evidence.ConclusionWe could not replicate our previous findings of an association between 5-HT1A availability and the personality trait ST/SA. Rather, the Bayesian analysis provided evidence for a lack of correlation. Further research should focus on whether other components of the serotonin system may be related to ST or SA. This study also illustrates how Bayesian hypothesis testing allows for greater flexibility and more informative conclusions than traditional p-values, suggesting that this approach may be advantageous for analysis of molecular imaging data. creator: Gina Griffioen creator: Granville J. Matheson creator: Simon Cervenka creator: Lars Farde creator: Jacqueline Borg uri: https://doi.org/10.7717/peerj.5790 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Griffioen et al. title: Saccades and handedness interact to affect scene memory link: https://peerj.com/articles/5969 last-modified: 2018-11-15 description: Repetitive saccades benefit memory when executed before retrieval, with greatest effects for episodic memory in consistent-handers. Questions remain including how saccades affect scene memory, an important visual component of episodic memory. The present study tested how repetitive saccades affect working and recognition memory for novel scenes. Handedness direction (left–right) and degree (strong/consistent vs. mixed/inconsistent) was measured by raw and absolute laterality quotients respectively from an 8-question handedness inventory completed by 111 adults. Each then performed either 30 s of repetitive horizontal saccades or fixation before or after tasks of scene working memory and scene recognition. Regression with criterion variables of overall percent correct accuracy and d-prime sensitivity showed that when saccades were made before working memory, there was better overall accuracy as a function of increased direction but not degree of handedness. Subjects who made saccades before working memory also performed worse during subsequent recognition memory, while subjects who fixated or made saccades after the working memory task performed better. Saccades made before recognition resulted in recognition accuracy that was better (Cohen’s d = 0.3729), but not significantly different from fixation before recognition. The results demonstrate saccades and handedness interact to affect scene memory with larger effects on encoding than recognition. Saccades before scene encoding in working memory are detrimental to short- and long-term memory, especially for those who are not consistently right-handed, while saccade execution before scene recognition does not appear to benefit recognition accuracy. The findings are discussed with respect to theories of interhemispheric interaction and control of visuospatial attention. creator: Timothy M. Ellmore creator: Bridget Mackin creator: Kenneth Ng uri: https://doi.org/10.7717/peerj.5969 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ellmore et al.