title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1525 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Potent antibacterial, antioxidant and toxic activities of extracts from Passiflora suberosa L. leaves link: https://peerj.com/articles/4804 last-modified: 2018-05-30 description: Passiflora suberosa L. belonging to the family Passifloraceae is an important medicinal plant used in traditional medicinal system in Sri Lanka to treat diabetes, hypertension and skin diseases. We extracted P. suberosa leaves under reflux conditions using different solvents (hexane, chloroform, methanol and water), then subjected to phytochemical screening. Alkaloids, flavonoids and saponins and saponins and anthraquinones were present in hexane and chloroform extracts. Alkaloids, unsaturated sterols, triterpenes, saponins, flavonoids and tannins were observed in both methanol and aqueous extracts. Proanthocyanidins were observed only in the aqueous extract. Hence, aqueous and methanol extracts with most classes of phytochemicals present were subjected to antimicrobial, antioxidant, antihaemolytic activities and Brine shrimp lethality studies. Antibacterial activity and minimum inhibition concentrations were evaluated using three Gram-positive (Bacillus subtilis, Staphylococcus aureus and Enterococcus faecium) and three Gram-negative bacteria (Pseudumonas aeruginosa, Salmonella typhimuriam and Escherichia coli). The results indicated that only the methanol extract of P. suberosa exhibited antibacterial activities against all the strains of Gram-negative and Gram-positive bacterial with stronger activity against Gram-negative bacteria. DPHH (2,2-diphenyl-1-picrylhydrazy) scavenging assay was adopted to evaluate antioxidant properties while antihaemolytic and toxic activities were studied respectively using cow blood and Brine shrimp lethality assay. The IC50 values of the aqueous extract in both antioxidant and antihaemolytic assays were significantly lower than the standard ascorbic acid. Similar results were observed in the Brine shrimp lethality assay. In conclusion both aqueous and methanol extracts of P. suberosa leaves showed the presence of majority of phytochemicals including proanthocyanidins. Antibacterial activity was obtained only for methanol extract with better activity against Gram-negative bacteria. The aqueous extract showed better antioxidant, antihaemolytic and toxic activities than the methanol extract and their respective standards. Further investigations on the chemical composition and possible isolation of active ingredients is warranted. creator: Kumudu R.V. Bandara creator: Chayanika Padumadasa creator: Dinithi C. Peiris uri: https://doi.org/10.7717/peerj.4804 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bandara et al. title: Comparisons of weed community, soil health and economic performance between wheat-maize and garlic-soybean rotation systems under different weed managements link: https://peerj.com/articles/4799 last-modified: 2018-05-30 description: This study compared the impacts of different weed managements on weed community, soil health and economic performance between the wheat–maize (WM) and garlic–soybean (GS) rotations. A total of four treatments (H0T, tillage without herbicide; H0T0, without both herbicide and tillage; HT, both herbicide and tillage; HT0, herbicide without tillage) were designed for both rotations. A total of 16 weed species were recorded in the WM rotation, with life forms of 62% for annuals, 12% for annual + perennial and 20% for perennials. While in the GS rotation, there were 17 weed species, with 71% being annuals. When crop rotation changed from WM to GS, the topsoil layer seed bank (0–5 cm) decreased by 137%. GS rotation always had higher earthworm densities than that of WM under the same condition. Organic weed control (H0T, H0T0) from both WM and GS added more soil organic matters than the chemical methods (HT and HT0). Economically, up to 69% higher net profit had been achieved in the GS than WM for their organic products. This study provides an ecological basis to guide organic farming practices, especially for weed management in the future. creator: Mahmud A. Muminov creator: Liyue Guo creator: Yanjie Song creator: Xian Gu creator: Yu Cen creator: Jie Meng creator: Gaoming Jiang uri: https://doi.org/10.7717/peerj.4799 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Muminov et al. title: Variations in early life history traits of Japanese anchovy Engraulis japonicus in the Yangtze River Estuary link: https://peerj.com/articles/4789 last-modified: 2018-05-30 description: Resources of Japanese anchovy (Engraulis japonicus Temminck & Schlegel, 1846) are undergoing dramatic recessions in China as the consequence of intensifying anthropogenic activities. Elucidating the influences of local-scale environmental factors on early life history traits is of great importance to design strategies conserving and restoring the declining anchovy resources. In this research, we studied hatching date and early growth of anchovy in the Yangtze River Estuary (YRE) using information obtained from otolith microstructure. Onset of hatching season and growth rates of anchovy was compared to populations in Japan and Taiwan. In YRE, the hatching date of anchovy ranged from February 26th to April 6th and mean growth rate ranged from 0.27 to 0.77 mm/d. Anchovies hatching later had higher growth rates than individuals hatching earlier before the 25th day. Among populations, hatching onsets of anchovy from the higher latitude were later than populations in the lower latitude, and growth rates of anchovy in YRE were much lower than populations in Japan and Taiwan. Variations in hatching onsets and early growth patterns of anchovy thus provide important knowledge on understanding the adaptation of anchovy in YRE and designing management strategies on conserving China’s anchovy resources. creator: Chunlong Liu creator: Weiwei Xian creator: Shude Liu creator: Yifeng Chen uri: https://doi.org/10.7717/peerj.4789 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Liu et al. title: Treatment of collagenase-induced osteoarthritis with a viral vector encoding TSG-6 results in ectopic bone formation link: https://peerj.com/articles/4771 last-modified: 2018-05-30 description: ObjectiveTumor necrosis factor-inducible gene 6 (TSG-6) has anti-inflammatory and chondroprotective effects in mouse models of inflammatory arthritis. Because cartilage damage and inflammation are also observed in osteoarthritis (OA), we determined the effect of viral overexpression of TSG-6 in experimental osteoarthritis.MethodsBone marrow-derived cells were differentiated to multinucleated osteoclasts in the presence of recombinant TSG-6 or after transduction with a lentiviral TSG-6 expression vector. Multi-nucleated osteoclasts were analyzed after tartrate resistant acid phosphatase staining and resorption activity was determined on dentin slices. Collagenase-induced osteoarthritis (CIOA) was induced in C57BL/6 mice after intra-articular injection of an adenoviral TSG-6 or control luciferase expression vector. Inflammation-related protease activity was measured using bioluminescent Prosense probes. After a second adenovirus injection, cartilage damage was assessed in histological sections stained with Safranin-O. Ectopic bone formation was scored in X-ray images of the affected knees.ResultsTSG-6 did not inhibit the formation of multi-nucleated osteoclasts, but caused a significant reduction in the resorption activity on dentin slices. Adenoviral TSG-6 gene therapy in CIOA could not reduce the cartilage damage compared to the luciferase control virus and no significant difference in inflammation-related protease activity was noted between the TSG-6 and control treated group. Instead, X-ray analysis and histological analysis revealed the presence of ectopic bone formation in the TSG-6 treated group.ConclusionGene therapy based on the expression of TSG-6 could not provide cartilage protection in experimental osteoarthritis, but instead resulted in increased ectopic bone formation. creator: Mathijs G.A. Broeren creator: Irene Di Ceglie creator: Miranda B. Bennink creator: Peter L.E.M. van Lent creator: Wim B. van den Berg creator: Marije I. Koenders creator: Esmeralda N. Blaney Davidson creator: Peter M. van der Kraan creator: Fons A.J. van de Loo uri: https://doi.org/10.7717/peerj.4771 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Broeren et al. title: Applying fecal microbiota transplantation (FMT) to treat recurrent Clostridium difficile infections (rCDI) in children link: https://peerj.com/articles/4663 last-modified: 2018-05-30 description: BackgroundFecal Microbiota Transplantation (FMT) is an innovative means of treating recurrent Clostridium difficile infection (rCDI), through restoration of gut floral balance. However, there is a lack of data concerning the efficacy of FMT and its impact on the gut microbiome among pediatric patients. This study analyzes clinical outcomes and microbial community composition among 15 pediatric patients treated for rCDI via FMT.MethodsThis is a prospective, observational, pilot study of 15 children ≤18 years, who presented for rCDI and who met inclusion criteria for FMT at a pediatric hospital and pediatric gastroenterology clinic. Past medical history and demographics were recorded at enrollment and subsequent follow-up. Specimens of the donors’ and the patients’ pre-FMT and post-FMT fecal specimen were collected and used to assess microbiome composition via 16S rRNA gene sequencing.ResultsFMT successfully prevented rCDI episodes for minimum of 3 months post-FMT in all patients, with no major adverse effects. Three patients reported continued GI bleeding; however, all three also had underlying Inflammatory Bowel Disease (IBD). Our analyses confirm a significant difference between pre-and post-FMT gut microbiome profiles (Shannon diversity index), whereas no significant difference was observed between post-FMT and donor microbiome profiles. At the phyla level, post-FMT profiles showed significantly increased levels of Bacteroidetes and significantly decreased levels of Proteobacteria. Subjects with underlying IBD showed no difference in their pre-and post-FMT profiles.ConclusionThe low rate of recurrence or re-infection by C. difficile, coupled with minimal adverse effects post-FMT, suggests that FMT is a viable therapeutic means to treat pediatric rCDI. Post-FMT microbiomes are different from pre-FMT microbiomes, and similar to those of healthy donors, suggesting successful establishment of a healthier microbiome. creator: Shaaz Fareed creator: Neha Sarode creator: Frank J. Stewart creator: Aneeq Malik creator: Elham Laghaie creator: Saadia Khizer creator: Fengxia Yan creator: Zoe Pratte creator: Jeffery Lewis creator: Lilly Cheng Immergluck uri: https://doi.org/10.7717/peerj.4663 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fareed et al. title: Resurrection and typification of Elatine campylosperma (Elatinaceae), a long-forgotten waterwort species link: https://peerj.com/articles/4913 last-modified: 2018-05-29 description: The name Elatine campylosperma Seub. is generally treated as one of the synonyms of E. macropoda Guss. However, recent morphological, phylogenetic and karyological studies indicate that this judgement should be revised. In the present paper we typify the name E. campylosperma, review its taxonomic history and provide a thorough description, with compilation of previously published data and our new measurements from in vitro cultures. Based on our herbarium survey, we outline its Atlantic-Mediterranean distribution area (Spain, France, Italy, Greece, Turkey and Algeria). Habitat preferences are summarized from our field observations, water quality measurements and the label information of the herbarium specimens examined. Intact E. campylosperma seeds were found in faecal samples of the Eurasian Coot (Fulica atra L.) in southern Spain and two of them were germinated, suggesting that E. campylosperma has a capacity for long distance dispersal via endozoochory. creator: Attila Takács creator: Attila Molnár V. creator: Balázs A. Lukács creator: Timea Nagy creator: Ádám Lovas-Kiss creator: Andy J. Green creator: Agnieszka Popiela creator: Lajos Somlyay uri: https://doi.org/10.7717/peerj.4913 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Takács et al. title: Unilateral application of an external pneumatic compression therapy improves skin blood flow and vascular reactivity bilaterally link: https://peerj.com/articles/4878 last-modified: 2018-05-29 description: BackgroundWe sought to determine the effects of unilateral lower-limb external pneumatic compression (EPC) on bilateral lower-limb vascular reactivity and skin blood flow.MethodsThirty-two participants completed this two-aim study. In AIM1 (n = 18, age: 25.5 ± 4.7 years; BMI: 25.6 ± 3.5 kg/m2), bilateral femoral artery blood flow and reactivity (flow mediated dilation [FMD]) measurements were performed via ultrasonography at baseline (PRE) and immediately following 30-min of unilateral EPC treatment (POST). AIM2 (n = 14, age: 25.9 ± 4.5; BMI: 27.2 ± 2.7 kg/m2) involved 30-min unilateral EPC (n = 7) or sham (n = 7) treatment with thermographic bilateral lower-limb mean skin temperature (MST) measurements at baseline, 15-min of treatment (T15) and 0, 30 and 60-min (R0, R30, R60) following treatment.ResultsComparative data herein are presented as mean ± 95% confidence interval. AIM1: No significant effects on total reactive hyperemia blood flow were observed for the treated (i.e., compressed) or untreated (i.e., non-compressed) leg. A significant effect of time, but no time*leg interaction, was observed for relative FMD indicating higher reactivity bilaterally with unilateral EPC treatment (FMD: +0.41 ± 0.09% across both legs; p < 0.05). AIM2: Unilateral EPC treatment was associated with significant increases in whole-leg MST from baseline during (T15: +0.63 ± 0.56 °C in the visible untreated/contralateral leg, p < 0.025) and immediately following treatment (i.e., R0) in both treated (+1.53 ± 0.59 °C) and untreated (+0.60 ± 0.45 °C) legs (p < 0.0125). Across both legs, MST remained elevated with EPC at 30-min post-treatment (+0.60 ± 0.45 °C; p < 0.0167) but not at 60-min post (+0.27 ± 0.46 °C; p = 0.165). Sham treatment was associated with a significant increase in the treated leg immediately post-treatment (+1.12 ± 0.31 °C; p < 0.0167), but not in the untreated leg (−0.27 ± 0.12 °C). MST in neither the treated or untreated leg were increased relative to baseline at R30 or R60 (p > 0.05). Finally, during treatment and at all post-treatment time points (i.e., R0, R30 and R60), independent of treatment group (EPC vs. sham), there was a significant effect of region. The maximum increase in MST was observed at the R0 time point and was significantly (p < 0.05) larger in the thigh region (+1.02 ± 0.31 °C) than the lower-leg (+0.47 ± 0.29 °C) region. However, similar rates of MST decline from R0 in the thigh and lower leg regions were observed at the R30 and R60 time points.DiscussionUnilateral EPC may be an effective intervention for increasing skin blood flow and/or peripheral conduit vascular reactivity in the contralateral limb. While EPC was effective in increasing whole-leg MST bilaterally, there appeared to be a more robust response in the thigh compared to the lower-leg. Thus, proximity along the leg may be an important consideration in prospective treatment strategies. creator: Jeffrey S. Martin creator: Allison M. Martin creator: Petey W. Mumford creator: Lorena P. Salom creator: Angelique N. Moore creator: David D. Pascoe uri: https://doi.org/10.7717/peerj.4878 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Martin et al. title: MIPhy: identify and quantify rapidly evolving members of large gene families link: https://peerj.com/articles/4873 last-modified: 2018-05-29 description: After transitioning to a new environment, species often exhibit rapid phenotypic innovation. One of the fastest mechanisms for this is duplication followed by specialization of existing genes. When this happens to a member of a gene family, it tends to leave a detectable phylogenetic signature of lineage-specific expansions and contractions. These can be identified by analyzing the gene family across several species and identifying patterns of gene duplication and loss that do not correlate with the known relationships between those species. This signature, termed phylogenetic instability, has been previously linked to adaptations that change the way an organism samples and responds to its environment; conversely, low phylogenetic instability has been previously linked to proteins with endogenous functions. With the increase in genome-level data, there is a need to identify and quantify phylogenetic instability. Here, we present Minimizing Instability in Phylogenetics (MIPhy), a tool that solves this problem by quantifying the incongruence of a gene’s evolutionary history. The motivation behind MIPhy was to produce a tool to aid in interpreting phylogenetic trees. It can predict which members of a gene family are under adaptive evolution, working only from a gene tree and the relationship between the species under consideration. While it does not conduct any estimation of positive selection—which is the typical indication of adaptive evolution—the results tend to agree. We demonstrate the usefulness of MIPhy by accurately predicting which members of the mammalian cytochrome P450 gene superfamily metabolize xenobiotics and which metabolize endogenous compounds. Our predictions correlate very well with known substrate specificities of the human enzymes. We also analyze the Caenorhabditis collagen gene family and use MIPhy to predict genes that produce an observable phenotype when knocked down in C. elegans, and show that our predictions correlate well with existing knowledge. The software can be downloaded and installed from https://github.com/dave-the-scientist/miphy and is also available as an online web tool at http://www.miphy.wasmuthlab.org. creator: David M. Curran creator: John S. Gilleard creator: James D. Wasmuth uri: https://doi.org/10.7717/peerj.4873 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Curran et al. title: Associations between psychometrically assessed life history strategy and daily behavior: data from the Electronically Activated Recorder (EAR) link: https://peerj.com/articles/4866 last-modified: 2018-05-29 description: Life history theory has generated cogent, well-supported hypotheses about individual differences in human biodemographic traits (e.g., age at sexual maturity) and psychometric traits (e.g., conscientiousness), but little is known about how variation in life history strategy (LHS) is manifest in quotidian human behavior. Here I test predicted associations between the self-report Arizona Life History Battery and frequencies of 12 behaviors observed over 72 h in 91 US college students using the Electronically Activated Recorder (EAR), a method of gathering periodic brief audio recordings as participants go about their daily lives. Bayesian multi-level aggregated binomial regression analysis found no strong associations between ALHB scores and behavior frequencies. One behavior, presence at amusement venues (bars, concerts, sports events) was weakly positively associated with ALHB-assessed slow LHS, contrary to prediction. These results may represent a challenge to the ALHB’s validity. However, it remains possible that situational influences on behavior, which were not measured in the present study, moderate the relationships between psychometrically-assessed LHS and quotidian behavior. creator: Joseph H. Manson uri: https://doi.org/10.7717/peerj.4866 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Manson title: Socio-economic factors and management regimes as drivers of tree cover change in Nepal link: https://peerj.com/articles/4855 last-modified: 2018-05-29 description: Despite the local and global importance of forests, deforestation is driven by various socio-economic and biophysical factors continues in many countries. In Nepal, in response to massive deforestation, the community forestry program has been implemented to reduce deforestation and support livelihoods. After four decades of its inception, the effectiveness of this program on forest cover change remains mostly unknown. This study analyses the spatial and temporal patterns of tree cover change along with a few socio-economic drivers of tree cover change to examine the effectiveness of the community forestry program for conserving forests or in reducing deforestation. We also investigate the socio-economic factors and policy responses as manifested through the community forestry program responsible for the tree cover change at the district level. The total tree cover area in the year 2000 in Nepal was ∼4,746,000 hectares, and our analysis reveals that between 2001 and 2016, Nepal has lost ∼46,000 ha and gained ∼12,200 ha of areas covered by trees with a substantial spatial and temporal variations. After accounting socio-economic drivers of forest cover change, our analysis showed that districts with the larger number of community forests had a minimum loss in tree cover, while districts with the higher proportion of vegetation covered by community forests had a maximum gain in tree cover. This indicates a positive contribution of the community forestry program to reducing deforestation and increasing tree cover. creator: Sujata Shrestha creator: Uttam B. Shrestha creator: Kamal Bawa uri: https://doi.org/10.7717/peerj.4855 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shrestha et al.