title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1389 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Understanding the NaCl-dependent behavior of hydrogen production of a marine bacterium, Vibrio tritonius link: https://peerj.com/articles/6769 last-modified: 2019-04-17 description: Biohydrogen is one of the most suitable clean energy sources for sustaining a fossil fuel independent society. The use of both land and ocean bioresources as feedstocks show great potential in maximizing biohydrogen production, but sodium ion is one of the main obstacles in efficient bacterial biohydrogen production. Vibrio tritonius strain AM2 can perform efficient hydrogen production with a molar yield of 1.7 mol H2/mol mannitol, which corresponds to 85% theoretical molar yield of H2 production, under saline conditions. With a view to maximizing the hydrogen production using marine biomass, it is important to accumulate knowledge on the effects of salts on the hydrogen production kinetics. Here, we show the kinetics in batch hydrogen production of V. tritonius strain AM2 to investigate the response to various NaCl concentrations. The modified Han–Levenspiel model reveals that salt inhibition in hydrogen production using V. tritonius starts precisely at the point where 10.2 g/L of NaCl is added, and is critically inhibited at 46 g/L. NaCl concentration greatly affects the substrate consumption which in turn affects both growth and hydrogen production. The NaCl-dependent behavior of fermentative hydrogen production of V. tritonius compared to that of Escherichia coli JCM 1649 reveals the marine-adapted fermentative hydrogen production system in V. tritonius. V. tritonius AM2 is capable of producing hydrogen from seaweed carbohydrate under a wide range of NaCl concentrations (5 to 46 g/L). The optimal salt concentration producing the highest levels of hydrogen, optimal substrate consumption and highest molar hydrogen yield is at 10 g/L NaCl (1.0% (w/v)). creator: Nurhidayu Al-saari creator: Eri Amada creator: Yuta Matsumura creator: Mami Tanaka creator: Sayaka Mino creator: Tomoo Sawabe uri: https://doi.org/10.7717/peerj.6769 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Al-saari et al. title: Patient-reported fatigue in patients with rheumatoid arthritis who commence biologic therapy: a longitudinal study link: https://peerj.com/articles/6771 last-modified: 2019-04-17 description: Aims and objectivesTo examine changes in patient-reported fatigue, over a twelve month period, in rheumatoid arthritis patients who commence biologic treatment, and to identify possible predictors for such changes.BackgroundFatigue is a burdensome symptom for patients with rheumatoid arthritis. Despite biologics being effective in reducing disease activity, patients still report fatigue.DesignA longitudinal observational study.MethodsA total of 48 patients were enrolled in the study. Fatigue was measured by the Fatigue Severity Scale. Independent samples T-tests were used to test gender differences, and paired samples T-tests were used to measure differences between repeated measures. Bivariate and multiple regression analyses were used to examine potential predictors for changes in fatigue, such as age, sex, Disease Activity Score 28, pain and physical and emotional well-being.ResultsForty-seven patients completed the study. From baseline to 12-month follow-up, fatigue decreased significantly in both women and men. Analyses of predictors were performed step-wise, and the final model included sex and physical well-being. The results from this final step showed that female sex was the only significant predictor for changes in fatigue.ConclusionPatients commencing biologic therapy reported a significant reduction in fatigue. Female sex was a significant predictor of changes in fatigue.Relevance to clinical practiceDespite improvements in pharmacological treatment, patients with rheumatoid arthritis still report fatigue. This is a multifaceted health problem encompassing personal and emotional factors in addition to the clinical factors directly connected to the disease. creator: Hege Selheim Rinke creator: Clara Beate Gram Gjesdal creator: Heidi Markussen creator: Jörg Assmus creator: Gerd Karin Natvig uri: https://doi.org/10.7717/peerj.6771 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Rinke et al. title: Molecular characterization and phylogenetic analysis of a Squash leaf curl virus isolate from Baja California Sur, Mexico link: https://peerj.com/articles/6774 last-modified: 2019-04-17 description: BackgroundThe begomovirus, squash leaf curl virus (SLCuV) is one of the causal agents of squash leaf curl (SLC) disease, which is among the most destructive diseases of cucurbit crops in tropical, subtropical, and semiarid regions worldwide. This disease was originally reported in the American continent with subsequent spread to the Mediterranean basin. Up to now, SLCuV has only been detected by PCR in Mexico. This study provides the first complete sequence of a Mexican SLCuV isolate from Baja California Sur (BCS). In addition, the genome of the virus was characterized, establishing its phylogenetic relationship with other SLCuV isolates.MethodsThe full genome (DNA-A and DNA-B) was amplified by rolling circle amplification, cloned and sequenced and the open reading frames (ORF) were annotated. Virus identification was performed according to the International Committee on Taxonomy of Viruses (ICTV) criteria for begomovirus species demarcation. To infer evolutionary relationship with other SLCuV isolates, phylogenetic and recombination analyses were performed.ResultsThe SLCuV-[MX-BCS-La Paz-16] genome (DNA-A and DNA-B) had 99% identity with SLCuV reference genomes. The phylogenetic analysis showed that SLCuV-[MX-BCS-La Paz-16] is closely related to SLCuV isolates from the Middle East (Egypt, Israel, Palestine and Lebanon). No evidence of interspecific recombination was determined and iterons were 100% identical in all isolates in the SLCuV clade.ConclusionsSLCuV-[MX-BCS-La Paz-16] showed low genetic variability in its genome, which could be due to a local adaptation process (isolate environment), suggesting that SLCuV isolates from the Middle East could have derived from the southwestern United States of America (USA) and northwestern Mexico. creator: Diana Medina-Hernández creator: M. Goretty Caamal-Chan creator: Mayela Vargas-Salinas creator: Abraham Loera-Muro creator: Aarón Barraza creator: Ramón Jaime Holguín-Peña uri: https://doi.org/10.7717/peerj.6774 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Medina-Hernández et al. title: Assessment on latitudinal tree species richness using environmental factors in the southeastern United States link: https://peerj.com/articles/6781 last-modified: 2019-04-17 description: The southeastern region of the United States exhibits an unusual trend of decreasing tree species richness (TSR) from higher to lower latitudes over the Florida peninsula. This trend contradicts the widely marked latitudinal diversity gradient where species richness is highest in tropical zones and decreases towards extratropical regions. This study aims to assess the environmental factors that prompt this atypical inverse latitudinal gradient seen in TSR using the USDA Forest Service’s Forest Inventory and Analysis (FIA) database. Fifteen variables under four categories of forested area, groundwater, soil properties, and climate groups were examined to model TSR in the region. Generalized linear models (GLMs) with Poisson distributions first assessed individual variables to test explanatory power then the LASSO regularization method was utilized to extract two subsets of the most influential variables to predict TSR. Forest area and four climate variables (mean annual temperature, precipitation seasonality, mean temperature of coldest quarter, and mean precipitation of driest quarter) were the top five variables during the initial GLM assessment implying their potential individual influence in regulating TSR. Two subsets of LASSO models contained seven and three predictor variables, respectively. Frist subset includes seven predictors, presented in highest to low standardized coefficient, mean temperature of coldest quarter, forested area, precipitation seasonality, mean precipitation of driest quarter, water table depth, spodosol, and available water storage. The other subset further excluded four lowest influential variables from the first set, leaving the top three variables from the first subset. The first subset of the LASSO model predicted TSR with 63.4% explained deviance while the second subset reproduced 60.2% of deviance explained. With only three variables used, the second model outperformed the first model evaluated by the AIC value. We conclude that forest patch area, mean temperature of coldest quarter, and precipitation seasonality are the highly influential variables of TSR among environmental factors in the southeastern region of U.S., but evolutionary or historic cause should be further incorporated to fully understand tree species diversity pattern in this region. creator: Youngsang Kwon creator: Taesoo Lee creator: Alison Lang creator: Dorian Burnette uri: https://doi.org/10.7717/peerj.6781 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kwon et al. title: The synergistic effect of concatenation in phylogenomics: the case in Pantoea link: https://peerj.com/articles/6698 last-modified: 2019-04-16 description: With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes. creator: Marike Palmer creator: Stephanus N. Venter creator: Alistair R. McTaggart creator: Martin P.A. Coetzee creator: Stephanie Van Wyk creator: Juanita R. Avontuur creator: Chrizelle W. Beukes creator: Gerda Fourie creator: Quentin C. Santana creator: Magriet A. Van Der Nest creator: Jochen Blom creator: Emma T. Steenkamp uri: https://doi.org/10.7717/peerj.6698 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Palmer et al. title: Cloning and characterization of a tyrosine decarboxylase involved in the biosynthesis of galanthamine in Lycoris aurea link: https://peerj.com/articles/6729 last-modified: 2019-04-16 description: BackgroundGalanthamine, one kind of Amaryllidaceae alkaloid extracted from the Lycoris species, is used in the treatment of Alzheimer’s disease. In regards to medical and economic importance, the biosynthesis and regulatory mechanism of the secondary metabolites in Lycoris remain uninvestigated.MethodsBLAST was used to identify the sequence of tyrosine decarboxylase in the transcriptome of Lycoris aurea (L’Hér) Herb. The enzyme activity of this TYDC was determined by using heterologous expressed protein in the Escherichia coli cells. The related productive contents of tyramine were detected using High Performance Liquid Chromatography (HPLC). According to the available micro RNA sequencing profiles and degradome database of L. aurea, microRNA396 were isolated, which targets to LaTYDC1 and RNA Ligase-Mediated-Rapid Amplification of cDNA Ends (RLM-RACE) were used to confirm the cleavage. The expression levels of miR396 and LaTYDC1 were measured using a quantitative real-time polymerase chain reaction (qRT-PCR).ResultsLaTYDC1 was mainly expressed in root, bulb, leaf and flower fitting the models for galanthamine accumulation. This decarboxylase efficiently catalyzes tyrosine to tyramine conversion. Under methyl jasmonate (MeJA) treatment, the expression of LaTYDC1 and the content of tyramine sharply increase. The use of RLM-RACE confirms that miR396 promotes the degradation of LaTYDC1 mRNA. Under MeJA treatment, the expression of miR396 was suppressed while the expression level of LaTYDC1 sharply increased. Following the increase of the miR396 transcriptional level, LaTYDC1 was significantly repressed.ConclusionLaTYDC1 participates in the biosynthesis of galanthamine, and is regulated by miR396. This finding also provides genetic strategy for improving the yield of galanthamine in the future. creator: Rong Wang creator: Xiaokang Han creator: Sheng Xu creator: Bing Xia creator: Yumei Jiang creator: Yong Xue creator: Ren Wang uri: https://doi.org/10.7717/peerj.6729 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Simulating the effects of climate change across the geographical distribution of two medicinal plants in the genus Nardostachys link: https://peerj.com/articles/6730 last-modified: 2019-04-16 description: BackgroundThe medicinal plants of Radix et Rhizoma Nardostachyos include Nardostachys jatamansi and N. chinensis. Traditionally, the two plants have been used to treat many diseases. Because of their special aroma, they are also commonly used in the food and cosmetics industry. Recently, N. jatamansi and N. chinensis have been overexploited due to their economic importance, resulting in a sharp decline in their wild resources. Predicting potential distributions of the genus Nardostachys under different climate scenarios and understanding its preferred habitat are of great significance for their conservation, artificial cultivation, and assessment of their value.MethodsThe Maxent model was used to predict the potential geographical distributions of the genus Nardostachys under current and future climatic conditions based on two representative concentration pathways (RCP2.6 and RCP8.5) for the 2050s and 2070s. These data were used to study the effects of climate variables.ResultsThe results show that the potential distribution of the two species will increase, thus more suitable habitats will be present in China. The suitable habitat for N. chinensis presents a relatively stable growth compared to N. jatamansi. In addition, precipitation plays a crucial role in modeling the effects of climate change on the genus Nardostachys. This study provides theoretical guidance for the cultivation of N. chinensis. creator: Junjun Li creator: Jie Wu creator: Kezhong Peng creator: Gang Fan creator: Haiqing Yu creator: Wenguo Wang creator: Yang He uri: https://doi.org/10.7717/peerj.6730 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Characterization of the iPSC-derived conditioned medium that promotes the growth of bovine corneal endothelial cells link: https://peerj.com/articles/6734 last-modified: 2019-04-16 description: Corneal endothelial cells (CECs) maintain corneal transparency and visual acuity. However, the limited proliferative capability of these cells in vitro has prompted researchers to find efficient culturing techniques for them. The aim of our study was to evaluate the use of conditioned medium (CM) obtained from induced pluripotent stem cells (iPSCs) as a source for the effective proliferation of bovine CECs (B-CECs). In our study, the proliferative ability of B-CECs was moderately enhanced when the cells were grown in 25% iPSC conditioned medium (iPSC-CM). Additionally, hexagonal cell morphology was maintained until passage 4, as opposed to the irregular and enlarged shape observed in control corneal endothelial medium (CEM). B-CECs in both the 25% iPSC-CM and CEM groups expressed and Na+-K+-ATPase. The gene expression levels of NIFK, Na+-K+-ATPase, Col4A and Col8A and the percentage of cells entering S and G2 phases were higher in the iPSC-CM group. The number of apoptotic cells also decreased in the iPSC-CM group. In comparison to the control cultures, iPSC-CM facilitated cell migration, and these cells showed better barrier functions after several passages. The mechanism of cell proliferation mediated by iPSC-CM was also investigated, and phosphorylation of Akt was observed in B-CECs after exposure to iPSC-CM and showed sustained phosphorylation induced for up to 180 min in iPSC-CM. Our findings indicate that iPSC-CM may employ PI3-kinase signaling in regulating cell cycle progression, which can lead to enhanced cellular proliferation. Effective component analysis of the CM showed that in the iPSC-CM group, the expression of activin-A was significantly increased. If activin-A is added as a supplement, it could help to maintain the morphology of the cells, similar to that of CM. Hence, we conclude that activin-A is one of the effective components of CM in promoting cell proliferation and maintaining cell morphology. creator: Qing Liu creator: Yonglong Guo creator: Shiwei Liu creator: Peiyuan Wang creator: Yunxia Xue creator: Zekai Cui creator: Jiansu Chen uri: https://doi.org/10.7717/peerj.6734 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: Identification and expression analysis of the GDSL esterase/lipase family genes, and the characterization of SaGLIP8 in Sedum alfredii Hance under cadmium stress link: https://peerj.com/articles/6741 last-modified: 2019-04-16 description: BackgroundThe herb Sedum alfredii (S. alfredii) Hance is a hyperaccumulator of heavy metals (cadmium (Cd), zinc (Zn) and lead (Pb)); therefore, it could be a candidate plant for efficient phytoremediation. The GDSL esterase/lipase protein (GELP) family plays important roles in plant defense and growth. Although the GELP family members in a variety of plants have been cloned and analyzed, there are limited studies on the family’s responses to heavy metal-stress conditions.MethodsMultiple sequence alignments and phylogenetic analyses were performed according to the criteria described. A WGCNA was used to construct co-expression regulatory networks. The roots of S. alfredii seedlings were treated with 100 µM CdCl2 for qRT-PCR to analyze expression levels in different tissues. SaGLIP8 was transformed into the Cd sensitive mutant strain yeast Δycf1 to investigate its role in resistance and accumulation to Cd.ResultsWe analyzed GELP family members from genomic data of S. alfredii. A phylogenetic tree divided the 80 identified family members into three clades. The promoters of the 80 genes contained certain elements related to abiotic stress, such as TC-rich repeats (defense and stress responsiveness), heat shock elements (heat stress) and MYB-binding sites (drought-inducibility). In addition, 66 members had tissue-specific expression patterns and significant responses to Cd stress. In total, 13 hub genes were obtained, based on an existing S. alfredii transcriptome database, that control 459 edge genes, which were classified into five classes of functions in a co-expression subnetwork: cell wall and defense function, lipid and esterase, stress and tolerance, transport and transcription factor activity. Among the hub genes, Sa13F.102 (SaGLIP8), with a high expression level in all tissues, could increase Cd tolerance and accumulation in yeast when overexpressed.ConclusionBased on genomic data of S. alfredii, we conducted phylogenetic analyses, as well as conserved domain, motif and expression profiling of the GELP family under Cd-stress conditions. SaGLIP8 could increase Cd tolerance and accumulation in yeast. These results indicated the roles of GELPs in plant responses to heavy metal exposure and provides a theoretical basis for further studies of the SaGELP family’s functions. creator: He Li creator: Xiaojiao Han creator: Wenmin Qiu creator: Dong Xu creator: Ying Wang creator: Miao Yu creator: Xianqi Hu creator: Renying Zhuo uri: https://doi.org/10.7717/peerj.6741 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Risk of acute exacerbation between acetaminophen and ibuprofen in children with asthma link: https://peerj.com/articles/6760 last-modified: 2019-04-16 description: BackgroundAntipyretics are widely prescribed in pediatric practice. Some reports have mentioned that acetaminophen and non-steroid anti-inflammatory drugs may negatively affect asthma control by causing asthma exacerbation (AE). However, many confounding factors can also influence the risks. We assessed the impact of using acetaminophen or ibuprofen on AE in asthmatic children, especially those with strong risk factors.MethodsWe used the 2010 Taiwan National Health Insurance Research Database and identified 983 children with persistent asthma aged 1–5 years old; among them, 591 used acetaminophen alone and 392 used ibuprofen alone in 2010. Then, we analyzed the risk of AE over 52 weeks in the patients with and without severe AE in the previous year.ResultsThe ibuprofen group had a higher risk of an emergency room (ER) visit or hospitalization for AE (odds ratio (OR) = 2.10, 95% confidence interval (CI) [1.17–3.76], P = 0.01). Among asthmatic children who had severe AE in the previous year, the risk of AE was higher in the ibuprofen group than in the acetaminophen group (OR = 3.28, 95% CI [1.30–8.29], P = 0.01), where as among those who did not, the risks of AE were similar between the acetaminophen and ibuprofen groups (OR = 1.52, 95% CI [0.71–3.25], P = 0.28).ConclusionsAmong young asthmatic children, use of ibuprofen was associated with a higher risk of AE than acetaminophen, if they had severe AE with ER visit or hospitalization in the previous year. Pediatricians should use antipyretics among children with asthma after a full evaluation of the risk. creator: Lin-Shien Fu creator: Che-Chen Lin creator: Chia-Yi Wei creator: Ching-Heng Lin creator: Yung-Chieh Huang uri: https://doi.org/10.7717/peerj.6760 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Fu et al.