title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1401 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Improvement of hydrogen production from Chlorella sp. biomass by acid-thermal pretreatment link: https://peerj.com/articles/6637 last-modified: 2019-03-21 description: BackgroundOwing to the high growth rate, high protein and carbohydrate contents, and an ability to grow autotrophically, microalgal biomass is regarded as a promising feedstock for fermentative hydrogen production. However, the rigid cell wall of microalgae impedes efficient hydrolysis of the biomass, resulting in low availability of assimilable nutrients and, consequently, low hydrogen production. Therefore, pretreatment of the biomass is necessary in order to achieve higher hydrogen yield (HY). In the present study, acid-thermal pretreatment of Chlorella sp. biomass was investigated. Conditions for the pretreatment, as well as those for hydrogen production from the pretreated biomass, were optimized. Acid pretreatment was also conducted for comparison.ResultsUnder optimum conditions (0.75% (v/v) H2SO4, 160 °C, 30 min, and 40 g-biomass/L), acid-thermal pretreatment yielded 151.8 mg-reducing-sugar/g-biomass. This was around 15 times that obtained from the acid pretreatment under optimum conditions (4% (v/v) H2SO4, 150 min, and 40 g-biomass/L). Fermentation of the acid-thermal pretreated biomass gave 1,079 mL-H2/L, with a HY of 54.0 mL-H2/g-volatile-solids (VS), while only 394 mL/L and 26.3 mL-H2/g-VS were obtained from the acid-pretreated biomass.ConclusionsAcid-thermal pretreatment was effective in solubilizing the biomass of Chlorella sp. Heat exerted synergistic effect with acid to release nutrients from the biomass. Satisfactory HY obtained with the acid-thermal pretreated biomass demonstrates that this pretreatment method was effective, and that it should be implemented to achieve high HY. creator: Tran T. Giang creator: Siriporn Lunprom creator: Qiang Liao creator: Alissara Reungsang creator: Apilak Salakkam uri: https://doi.org/10.7717/peerj.6637 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Giang et al. title: The chemical composition of a new “mica sandwich” foraminiferal species from the East Coast of Korea: Capsammina crassa sp. nov. link: https://peerj.com/articles/6642 last-modified: 2019-03-21 description: We describe a new agglutinated monothalamous foraminiferal species, Capsammina crassa sp. nov., based on integrated observations of the test morphology and the chemical characteristics of materials composing the test. The new species was found at a depth of <60 m on the East coast of Korea. The test morphology is typical of the genus Capsammina, comprising two or more mica plates with a ring of finely agglutinated mineral grains sandwiched between them and surrounding the cell body. There is no distinct test aperture. Elemental analyses of the agglutinated grains revealed 15 different types of mineral grains of which quartz is the most abundant. The surface areas of grains exposed on fractured surfaces ranged from 1.6 to 7,700 μm2 and the large plate-like grains forming the upper and lower surfaces measured about 420–2,350 μm in maximum width. The new species is morphologically similar to C. patelliformis, however, the differences in size, distribution area and depth support that these two species are distinct. This discovery is the first record of the genus Capsammina from the North Pacific. Therefore, it extends the biodiversity and geographical distribution of the genus Capsammina, which has been reported only from the bathyal NE Atlantic. Our finding also suggests the possibility of additional discovery of monothalamous foraminifera from around Korea. creator: Somin Lee creator: Eric Armynot du Châtelet creator: Andrew J. Gooday creator: François Guillot creator: Philippe Recourt creator: Fabrizio Frontalini creator: Wonchoel Lee uri: https://doi.org/10.7717/peerj.6642 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lee et al. title: Dose-dependent and strain-dependent anti-obesity effects of Lactobacillus sakei in a diet induced obese murine model link: https://peerj.com/articles/6651 last-modified: 2019-03-21 description: BackgroundOverweight and abdominal obesity, in addition to medical conditions such as high blood pressure, high blood sugar and triglyceride levels, are typical risk factors associated with metabolic syndrome. Yet, considering the complexity of factors and underlying mechanisms leading to these inflammatory conditions, a deeper understanding of this area is still lacking. Some probiotics have a reputation of a relatively-long history of safe use, and an increasing number of studies are confirming benefits including anti-obesity effects when administered in adequate amounts. Recent reports demonstrate that probiotic functions may widely differ with reference to either intra-species or inter-species related data. Such differences do not necessarily reflect or explain strain-specific functions of a probiotic, and thus require further assessment at the intra-species level. Various anti-obesity clinical trials with probiotics have shown discrepant results and require additional consolidated studies in order to clarify the correct dose of application for reliable and constant efficacy over a long period.MethodsThree different strains of Lactobacillus sakei were administered in a high-fat diet induced obese murine model using three different doses, 1 × 1010, 1 × 109 and 1 × 108 CFUs, respectively, per day. Changes in body and organ weight were monitored, and serum chemistry analysis was performed for monitoring obesity associated biomarkers.ResultsOnly one strain of L. sakei (CJLS03) induced a dose-dependent anti-obesity effect, while no correlation with either dose or body or adipose tissue weight loss could be detected for the other two L. sakei strains (L338 and L446). The body weight reduction primarily correlated with adipose tissue and obesity-associated serum biomarkers such as triglycerides and aspartate transaminase.DiscussionThis study shows intraspecies diversity of L. sakei and suggests that anti-obesity effects of probiotics may vary in a strain- and dose-specific manner. creator: Yosep Ji creator: Young Mee Chung creator: Soyoung Park creator: Dahye Jeong creator: Bongjoon Kim creator: Wilhelm Heinrich Holzapfel uri: https://doi.org/10.7717/peerj.6651 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ji et al. title: Maintenance of dominant populations in heavily grazed grassland: Inference from a Stipa breviflora seed germination experiment link: https://peerj.com/articles/6654 last-modified: 2019-03-21 description: An understanding of population adaptation and maintenance mechanisms under interference from large herbivores is lacking and is a major focus of ecological research. In the Eurasian steppe, which has been subjected to continuous interference from domesticated ungulates throughout history and shows increased grazing, it is particularly urgent to analyze the ecological adaptation strategies of widely distributed Stipa plants. In this study, Stipa breviflora in a group of desert steppes in the Mongolian Plateau was selected to study the potential mechanism underlying the maintenance of dominant populations under the continuous interference of heavy grazing from the new perspective of seed germination rate. Laboratory experimental results showed that the values of the phenotypic traits of S. breviflora seeds were lower under a heavy grazing treatment than under a non-grazing treatment, but the seed germination rate did not decrease. The awns of non-grazed seeds significantly affected the seed germination rate, while those of heavily grazed seeds did not. Field observations showed that grazing does not significantly affect the population density of S. breviflora at different growth stages except in extremely wet and dry years. Our study suggests that under heavy grazing, S. breviflora uses an “opportunistic” ecological strategy to ensure population maintenance by increasing the seed germination rate and reducing dispersal via changes in associated seed phenotypic traits. creator: Wenting Liu creator: Zhijun Wei creator: Xiaoxia Yang uri: https://doi.org/10.7717/peerj.6654 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: Minimum inhibitory concentration of nano-silver bactericides for beneficial microbes and its effect on Ralstonia solanacearum and seed germination of Japanese Cucumber (Cucumis sativus) link: https://peerj.com/articles/6418 last-modified: 2019-03-20 description: BackgroundPlant growth-promoting rhizobacteria (PGPR) are highly promising biofertilizers that contribute to eco-friendly sustainable agriculture. There have been many reports on the anti-microbial properties of nanoparticles (NPs). Toxic effects of NPs under laboratory conditions have also reported; however, there is a lack of information about their uptake and mobility in organisms under environmental conditions. There is an urgent need to determine the highest concentration of NPs which is not detrimental for growth and proliferation of PGPR.MethodsTransmission electron microscopy (TEM) and scanning electron microscopy (SEM) were used to measure the size and shape of NPs. Minimum inhibitory concentrations (MIC) of nano-silver on selected beneficial microbes and Ralstonia solanacearum were measured using the microdilution broth method. The percentage of seed germination was measured under in vitro conditions.ResultsNPs were spherical with a size of 16 ± 6 nm. Nano-silver at 12–40 mg l−1 inhibited the growth of bacteria. Seed application at 40 mg l−1 protected seeds from R. solanacearum and improved the rate of seed germination. creator: Poopak Sotoodehnia creator: Norida Mazlan creator: Halimi Mohd Saud creator: Wahid A. Samsuri creator: Sheikh Hasna Habib creator: Amin Soltangheisi uri: https://doi.org/10.7717/peerj.6418 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sotoodehnia et al. title: Identification of an eight-gene signature for survival prediction for patients with hepatocellular carcinoma based on integrated bioinformatics analysis link: https://peerj.com/articles/6548 last-modified: 2019-03-20 description: BackgroundHepatocellular carcinoma (HCC) remains one of the leading causes of cancer-related death worldwide. Despite recent advances in imaging techniques and therapeutic intervention for HCC, the low overall 5-year survival rate of HCC patients remains unsatisfactory. This study aims to find a gene signature to predict clinical outcomes in HCC.MethodsBioinformatics analysis including Cox’s regression analysis, Kaplan-Meier (KM) and receiver operating characteristic curve (ROC) analysis and the random survival forest algorithm were performed to mine the expression profiles of 553 hepatocellular carcinoma (HCC) patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) public database.ResultsWe selected a signature comprising eight protein-coding genes (DCAF13, FAM163A, GPR18, LRP10, PVRIG, S100A9, SGCB, and TNNI3K) in the training dataset (AUC = 0.77 at five years, n = 332). The signature stratified patients into high- and low-risk groups with significantly different survival in the training dataset (median 2.20 vs. 8.93 years, log-rank test P < 0.001) and in the test dataset (median 2.68 vs. 4.24 years, log-rank test P = 0.004, n = 221, GSE14520). Further multivariate Cox regression analysis showed that the signature was an independent prognostic factor for patients with HCC. Compared with TNM stage and another reported three-gene model, the signature displayed improved survival prediction power in entire dataset (AUC signature = 0.66 vs. AUC TNM = 0.64 vs. AUC gene model = 0.60, n = 553). Stratification analysis shows that it can be used as an auxiliary marker for many traditional staging models.ConclusionsWe constructed an eight-gene signature that can be a novel prognostic marker to predict the survival of HCC patients. creator: Guo-jie Qiao creator: Liang Chen creator: Jin-cai Wu creator: Zhou-ri Li uri: https://doi.org/10.7717/peerj.6548 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Qiao et al. title: Effects of handling and short-term captivity: a multi-behaviour approach using red sea urchins, Mesocentrotus franciscanus link: https://peerj.com/articles/6556 last-modified: 2019-03-20 description: Understanding the effects of captivity-induced stress on wild-caught animals after their release back into the wild is critical for the long-term success of relocation and reintroduction programs. To date, most of the research on captivity stress has focused on vertebrates, with far less attention paid to invertebrates. Here, we examine the effect of short-term captivity (i.e., up to four days) on self-righting, aggregation, and predator-escape behaviours in wild-caught red sea urchins, Mesocentrotus franciscanus, after their release back into the wild. Aggregation behaviour, which has been linked to feeding in sea urchins, was not affected by handling or captivity. In contrast, the sea urchins that had been handled and released immediately, as well as those that were handled and held captive, took longer to right themselves and were poorer at fleeing from predators than wild, unhandled sea urchins. These results indicate that handling rather than captivity impaired these behaviours in the short term. The duration of captivity did not influence the sea urchin behaviours examined. Longer-term monitoring is needed to establish what the fitness consequences of these short-term behavioural changes might be. Our study nevertheless highlights the importance of considering a suite of responses when examining the effects of capture and captivity. Our findings, which are based on a locally abundant species, can inform translocation efforts aimed at bolstering populations of ecologically similar but depleted invertebrate species to retain or restore important ecosystem functions. creator: Aneesh P.H. Bose creator: Daniel Zayonc creator: Nikolaos Avrantinis creator: Natasha Ficzycz creator: Jonathan Fischer-Rush creator: Fiona T. Francis creator: Siobhan Gray creator: Faye Manning creator: Haley Robb creator: Coralee Schmidt creator: Christine Spice creator: Aari Umedaly creator: Jeff Warden creator: Isabelle M. Côté uri: https://doi.org/10.7717/peerj.6556 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bose et al. title: High virulence gene diversity in Streptococcus pyogenes isolated in Central Italy link: https://peerj.com/articles/6613 last-modified: 2019-03-20 description: Globally, Streptococcus pyogenes poses a continuous burden on human health, causing both self-limiting and life-threatening diseases. Therefore, studying the profile of virulence genes and their combinations is essential to monitor the epidemiology and pathogenic potential of this important species. Thus, the aim of this study was to analyze related genetic features of clinical strains collected in Italy in 2012 in order to obtain a valid picture of their virulence profile that could be compared to similar studies made in other countries approximately in the same period. We conducted emm typing and fibronectin-collagen-T antigen (FCT) region typing in 122 Streptococcus pyogenes strains. Furthermore, several additional virulence genes were screened by polymerase chain reaction. We found correlations between emm types and FCT region profiles. emm1 strains were mainly associated with FCT2 and FCT6, while emm89 and emm12 strains were associated with FCT4. FCT5 was mainly represented in emm4, emm6, and emm75 strains. Significantly, we defined subtypes for each FCT type based on the differences in single and double loci compared to the reference scheme used for the classification of the FCT region. In addition, new FCT-region variants with differences in multiple loci were also recorded. Cluster analysis based on virulence gene profiling showed a non-random distribution within each emm type. This study added new data to existing studies conducted worldwide and revealed new variability scores in circulating Streptococcus pyogenes strains and new assortments in well-established virulence gene signatures. creator: Daniela Bencardino creator: Maria Chiara Di Luca creator: Dezemona Petrelli creator: Manuela Prenna creator: Luca Agostino Vitali uri: https://doi.org/10.7717/peerj.6613 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bencardino et al. title: Evolution of host plant use and diversification in a species complex of parasitic weevils (Coleoptera: Curculionidae) link: https://peerj.com/articles/6625 last-modified: 2019-03-20 description: Weevils (Coleoptera: Curculionoidea) represent one of the most diverse groups of organisms on Earth; interactions with their host plants have been recognized to play a central role in their remarkable diversity, yet the exact mechanisms and factors still remain poorly understood. Using phylogenetic comparative analyses, here we investigate the evolution of host use and its possible role in diversification processes of Rhinusa and Gymnetron, two closely related groups of weevils that feed and develop inside plant tissues of hosts within the families Scrophulariaceae and Plantaginaceae. We found strong evidence for phylogenetic conservatism of host use at the plant family level, most likely due to substantial differences in the chemical composition of hosts, reducing the probability of shifts between host families. In contrast, the use of different plant organs represents a more labile ecological trait and ecological niche expansion that allows a finer partitioning of resources. Rhinusa and Gymnetron weevils initially specialized on plants within Scrophulariaceae and then shifted to the closely related Plantaginaceae; likewise, a gall inducing behavior evolved from non-galler weevils, possibly in response to resource competition, as galls facilitate larval development by providing enhanced nutrition and a favorable microhabitat. Results from trait-dependent diversification analyses suggest that both use of hosts within Plantaginaceae and parasitism on fruits and seed capsules are associated with enhanced diversification of Rhinusa and Gymnetron via low extinction rates. Our study provides quantitative evidence and insights on the ecological factors that can promote diversification in phytophagous insects that feed and develop inside plant tissues. creator: Gerardo Hernández-Vera creator: Ivo Toševski creator: Roberto Caldara creator: Brent C. Emerson uri: https://doi.org/10.7717/peerj.6625 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hernández-Vera et al. title: Transcriptome sequencing of olfactory-related genes in olfactory transduction of large yellow croaker (Larimichthy crocea) in response to bile salts link: https://peerj.com/articles/6627 last-modified: 2019-03-20 description: Fish produce and release bile salts as chemical signalling substances that act as sensitive olfactory stimuli. To investigate how bile salts affect olfactory signal transduction in large yellow croaker (Larimichthy crocea), deep sequencing of olfactory epithelium was conducted to analyse olfactory-related genes in olfactory transduction. Sodium cholates (SAS) have typical bile salt chemical structures, hence we used four different concentrations of SAS to stimulate L. crocea, and the fish displayed a significant behavioural preference for 0.30% SAS. We then sequenced olfactory epithelium tissues, and identified 9938 unigenes that were significantly differentially expressed between SAS-stimulated and control groups, including 9055 up-regulated and 883 down-regulated unigenes. Subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses found eight categories linked to the olfactory transduction pathway that was highly enriched with some differentially expressed genes (DEGs), including the olfactory receptor (OR), Adenylate cyclase type 3 (ADCY3) and Calmodulin (CALM). Genes in these categories were analysed by RT-qPCR, which revealed aspects of the pathway transformation between odor detection, and recovery and adaptation. The results provide new insight into the effects of bile salt stimulation in olfactory molecular mechanisms in fishes, and expands our knowledge of olfactory transduction, and signal generation and decline. creator: Jiabao Hu creator: Yajun Wang creator: Qijun Le creator: Na Yu creator: Xiaohuan Cao creator: Siwen Kuang creator: Man Zhang creator: Weiwei Gu creator: Yibo Sun creator: Yang Yang creator: Xiaojun Yan uri: https://doi.org/10.7717/peerj.6627 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hu et al.