title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1281
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Antimicrobial photodynamic therapy on Staphylococcus aureus and Escherichia coli using malachite green encapsulated mesoporous silica nanoparticles: an in vitro study
link: https://peerj.com/articles/7454
last-modified: 2019-09-12
description: BackgroundRise in the number of healthcare associated or hospital acquired infections is a major problem affecting the global healthcare sector. We evaluated superior antibacterial and antibiofilm photodynamic therapy (aPDT) using malachite green encapsulated mesoporous silica nanoparticles (MG-MSN) against Staphylococcus aureus and Escherichia coli, which are known to be major causative agents of nosocomial infections.MethodsMalachite green (MG) was encapsulated on mesoporous silica nanoparticles (MSN). Fourier-transform infrared spectroscopy, Transmission electron microscopy, and spectroscopic analysis were performed to characterize the MG-MSN. The antimicrobial efficacies of MSN, MG, and MG-MSN were investigated and the results were recorded.ResultsMG-MSN was effective against both the tested bacteria. S. aureus was more phototoxic to MG-MSN compared to E. coli. The antibiofilm efficacy of MG-MSN on E. coli and S. aureus was also studied. Biofilm inhibition was 65.68 ± 2.62% in E. coli and 79.66 ± 3.82% in S. aureus. Cell viability assay, exopolysaccharides quantification, and confocal laser scanning microscopy studies also revealed the enhanced antibiofilm activity of MG-MSN when used as a potential photosensitizer for aPDT. This study can be extended to eradicate these strains from localized superficial infections and medical appliances, preventing nosocomial infections.
creator: Parasuraman Paramanantham
creator: Busi Siddhardha
creator: Sruthil Lal SB
creator: Alok Sharan
creator: Abdullah A. Alyousef
creator: Mohammed Saeed Al Dosary
creator: Mohammed Arshad
creator: Asad Syed
uri: https://doi.org/10.7717/peerj.7454
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Paramanantham et al.

title: Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known
link: https://peerj.com/articles/7500
last-modified: 2019-09-12
description: Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.
creator: Mikhail I. Schelkunov
creator: Maxim S. Nuraliev
creator: Maria D. Logacheva
uri: https://doi.org/10.7717/peerj.7500
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Schelkunov et al.

title: Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses
link: https://peerj.com/articles/7510
last-modified: 2019-09-12
description: Growth-regulating factor (GRF), a small plant-specific transcription factor (TF) family, is extensively involved in the regulation of growth and developmental processes. However, the GRF family has not been comprehensively studied in moso bamboo (Phyllostachys edulis), a typical non-timber forest member. Here, 18 GRF genes were identified and characterized from the moso bamboo genome, and they clustered into three subfamilies (A, B and C). PeGRF genes were analyzed to determine their gene structures, conserved motifs and promoter. The non-synonymous/synonymous substitution ratios of paralogous and orthologous were less than 1, indicating that the GRF family mainly experienced purifying selection during evolution. According to the analysis of tissue-specific expression patterns, the participation of moso bamboo GRFs might be required during the formation and development of these five tissues. Moreover, PeGRF proteins might be involved in the regulation of plant development in biological processes. The qRT-PCR analysis demonstrated that PeGRF genes played essential roles in combating hormonal stresses and they might be involved in hormone regulation. PeGRF11, a nuclear localized protein as assessed by a subcellular localization assay, could interact with PeGIF3 in yeast and in planta according to yeast two-hybridization and bimolecular fluorescence complementation assays (BiFC) assays. But PeGRF11, as a TF, had no transcriptional activity in yeast. These results provide useful information for future functional research on the GRF genes in moso bamboo.
creator: Yanan Shi
creator: Huanlong Liu
creator: Yameng Gao
creator: Yujiao Wang
creator: Min Wu
creator: Yan Xiang
uri: https://doi.org/10.7717/peerj.7510
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Shi et al.

title: A stepping stone to compositionality in chimpanzee communication
link: https://peerj.com/articles/7623
last-modified: 2019-09-12
description: Compositionality refers to a structural property of human language, according to which the meaning of a complex expression is a function of the meaning of its parts and the way they are combined. Compositionality is a defining characteristic of all human language, spoken and signed. Comparative research into the emergence of human language aims at identifying precursors to such key features of human language in the communication of other primates. While it is known that chimpanzees, our closest relatives, produce a variety of gestures, facial expressions and vocalizations in interactions with their group members, little is known about how these signals combine simultaneously. Therefore, the aim of the current study is to investigate whether there is evidence for compositional structures in the communication of chimpanzees. We investigated two semi-wild groups of chimpanzees, with focus on their manual gestures and their combinations with facial expressions across different social contexts. If there are compositional structures in chimpanzee communication, adding a facial expression to a gesture should convey a different message than the gesture alone, a difference that we expect to be measurable by the recipient’s response. Furthermore, we expect context-dependent usage of these combinations. Based on a form-based coding procedure of the collected video footage, we identified two frequently used manual gestures (stretched arm gesture and bent arm gesture) and two facial expression (bared teeth face and funneled lip face). We analyzed whether the recipients’ response varied depending on the signaler’s usage of a given gesture + face combination and the context in which these were used. Overall, our results suggest that, in positive contexts, such as play or grooming, specific combinations had an impact on the likelihood of the occurrence of particular responses. Specifically, adding a bared teeth face to a gesture either increased the likelihood of affiliative behavior (for stretched arm gesture) or eliminated the bias toward an affiliative response (for bent arm gesture). We show for the first time that the components under study are recombinable, and that different combinations elicit different responses, a property that we refer to as componentiality. Yet our data do not suggest that the components have consistent meanings in each combination—a defining property of compositionality. We propose that the componentiality exhibited in this study represents a necessary stepping stone toward a fully evolved compositional system.
creator: Linda S. Oña
creator: Wendy Sandler
creator: Katja Liebal
uri: https://doi.org/10.7717/peerj.7623
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Oña et al.

title: Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum)
link: https://peerj.com/articles/7664
last-modified: 2019-09-12
description: Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioning in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play a critical role in abiotic stress response pathways of plants. As a species closely related to Arabidopsis thaliana, Eutrema salsugineum has been proposed as a model for studying salt resistance in plants. Here we surveyed 35 full-length AQP genes in E. salsugineum, which could be grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), nine NOD-like intrinsic proteins (NIPs), and three small basic intrinsic proteins (SIPs) by phylogenetic analysis. EsAQPs were comprised of 237–323 amino acids, with a theoretical molecular weight (MW) of 24.31–31.80 kDa and an isoelectric point (pI) value of 4.73–10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger’s position and specificity-determining position suggested quite differences in substrate specificities of EsAQPs. EsAQPs exhibited global expressions in all organs as shown by gene expression profiles and should be play important roles in response to salt, cold and drought stresses. This study provides comprehensive bioinformation on AQPs in E. salsugineum, which would be helpful for gene function analysis for further studies.
creator: Weiguo Qian
creator: Xiaomin Yang
creator: Jiawen Li
creator: Rui Luo
creator: Xiufeng Yan
creator: Qiuying Pang
uri: https://doi.org/10.7717/peerj.7664
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Qian et al.

title: Variations in ecosystem service value in response to land use/land cover changes in Central Asia from 1995–2035
link: https://peerj.com/articles/7665
last-modified: 2019-09-12
description: Acute farmland expansion and rapid urbanization in Central Asia have accelerated land use/land cover changes, which have substantial effects on ecosystem services. However, the spatiotemporal variations in ecosystem service values (ESVs) in Central Asia are not well understood. Here, based on land use products with 300-m resolution for the years 1995, 2005 and 2015 and transfer methodology, we predicted land use and land cover (LULC) for 2025 and 2035 using CA-Markov, assessed changes in ESVs in response to LULC dynamics, and explored the elasticity of the response of ESV to LULC changes. We found significant expansions of cropland (+22.10%) and urban areas (+322.40%) and shrinking of water bodies (−38.43%) and bare land (−9.42%) during 1995–2035. The combined value of ecosystem services of water bodies, cropland, and grassland accounted for over 90% of the total ESVs. Our study showed that cropland ecosystem services value increased by 93.45 billion US$ from 1995 to 2035, which was mainly caused by the expansion of cropland area. However, the area of water bodies decreased sharply during 1995–2035, causing a loss of 64.38 billion US$. Biodiversity, food production and water regulation were major ecosystem service functions, accounting for 80.52% of the total ESVs. Our results demonstrated that effective land-use policies should be made to control farmland expansion and protect water bodies, grassland and forestland for more sustainable ecosystem services.
creator: Jiangyue Li
creator: Hongxing Chen
creator: Chi Zhang
creator: Tao Pan
uri: https://doi.org/10.7717/peerj.7665
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Li et al.

title: Dietary fermented products using koji mold and sweet potato-shochu distillery by-product promotes hepatic and serum cholesterol levels and modulates gut microbiota in mice fed a high-cholesterol diet
link: https://peerj.com/articles/7671
last-modified: 2019-09-12
description: It has been reported that fermented products (FPs) prepared from sweet potato-shochu distillery by-product suppressed weight gain and decreased serum cholesterol levels in mice under normal dietary conditions. Furthermore, from the information gained from the above data regarding health benefits of the FPs, the aim of this study was evaluating the effects of dietary FPs on lipid accumulation and gut microbiota in mice with or without cholesterol-load in the diet. C57BL/6N mice were fed normal (CO) diet, CO with 10% FPs (CO + FPs) diet, cholesterol loaded (HC) diet, or HC with 10% FPs (HC + FPs) diet for 8 weeks. The mice were then euthanized, and blood samples, tissue samples, and feces were collected. The adipose tissue weight and liver triglyceride levels in the HC + FPs diet groups were significantly reduced compared to that in the HC diet groups. However, FPs significantly increased the serum non-high-density lipoprotein cholesterol (HDL-C) levels, the ratio of non-HDL-C to HDL-C and hepatic total cholesterol levels in mice fed cholesterol-loaded diet compared with that of the HC diet group. Since dietary FPs significantly decreased the protein expression levels of cholesterol 7 alpha-hydroxylase 1 in the HC + FPs diet groups, the cholesterol accumulation in FPs group may be explained by insufficient catabolism from cholesterol to bile acid. In addition, the dietary FPs tended to increase Clostridium cluster IV and XIVa, which are butyrate-producing bacteria. Related to the result, n-butyrate was significantly increased in the CO + FPs and the HC + FPs diet groups compared to their respective control groups. These findings suggested that dietary FPs modulated the lipid pool and gut microbiota.
creator: Toshiki Kosakai
creator: Hirotaka Kato
creator: Cho Sho
creator: Kuniaki Kawano
creator: Ken-ichi Iwai
creator: Yoshikazu Takase
creator: Kenjiro Ogawa
creator: Kazuo Nishiyama
creator: Masao Yamasaki
uri: https://doi.org/10.7717/peerj.7671
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2019 Kosakai et al.

title: Arbuscular mycorrhizal fungi alter the food utilization, growth, development and reproduction of armyworm (Mythimna separata) fed on Bacillus thuringiensis maize
link: https://peerj.com/articles/7679
last-modified: 2019-09-12
description: BackgroundThe cultivation of Bt maize (maize genetically modified with Bacillus thuringiensis) continues to expand globally. Arbuscular mycorrhizal fungi (AMF), an important kind of microorganism closely related to soil fertility and plant nutrition, may influence the ecological risk of target lepidopteran pests in Bt crops.MethodsIn this study, transgenic Bt maize (Line IE09S034 with Cry1Ie vs. its parental line of non-Bt maize cv. Xianyu335) was inoculated with a species of AMF, Glomus caledonium (GC). Its effects on the food utilization, reproduction and development of armyworm, Mythimna separata, were studied in a potted experiment from 2017 to 2018.ResultsGC inoculation increased the AMF colonization of both modified and non-modified maize, and also increased the grain weight per plant and 1,000-grain weight of modified and non-modified maize. However, the cultivation of Bt maize did not significantly affect the AMF colonization. The feeding of M. separata with Bt maize resulted in a notable decrease in RCR (relative consumption rate), RGR (relative growth rate), AD (approximate digestibility), ECD (efficiency of conversion of digested food) and ECI (efficiency of conversion of ingested food) parameters in comparison to those observed in larvae fed with non-Bt maize in 2017 and 2018, regardless of GC inoculation. Furthermore, remarkable prolongation of larval life span and decreases in the rate of pupation, weight of pupa, rate of eclosion, fecundity and adult longevity of M. separata were observed in the Bt treatment regardless of GC inoculation during the two-year experiment. Also, when M. separata was fed with Bt maize, a significant prolongation of larval life and significant decreases in the pupal weight, fecundity and adult longevity of M. separata were observed when inoculated with GC. However, it was just the opposite for larvae fed with non-Bt maize that was inoculated with GC. The increased percentage of larval life-span, the decreased percentages of the food utilization, and the other indexes of reproduction, growth, and development of M. separata fed on Bt maize relative to non-Bt maize were all visibly lower when under GC inoculation in contrast to the CK.DiscussionIt is presumed that Bt maize has a marked adverse impact on M. separata development, reproduction and feeding, especially when in combination with the GC inoculation. Additionally, GC inoculation favors the effectiveness of Bt maize against M. separata larvae by reducing their food utilization ability, which negatively affects the development and reproduction of the armyworm. Thus, Bt maize inoculated with AMF (here, GC) can reduce the severe threats arising of armyworms, and hence the AMF inoculation may play an important ecological functions in the field of Bt maize ecosystem, with potentially high control efficiency for the target lepidopteran pests.
creator: Long Wang
creator: Sabin Saurav Pokharel
creator: Fajun Chen
uri: https://doi.org/10.7717/peerj.7679
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Wang et al.

title: Mental practice in isolation improves cervical joint position sense in patients with chronic neck pain: a randomized single-blind placebo trial
link: https://peerj.com/articles/7681
last-modified: 2019-09-12
description: ObjectiveThe main objective of this trial was to assess whether action observation (AO) training and motor imagery (MI) produced changes in the cervical joint position sense (CJPS) both at the end of the intervention and 10 min postintervention compared with a placebo intervention in patients with nonspecific chronic neck pain (NSCNP).MethodsA single-blind placebo clinical trial was designed. A total of 30 patients with NSCNP were randomly assigned to the AO group, MI group or placebo observation (PO) group. CJPS in flexion, extension and rotation movements in both planes were the main variables.ResultsThe results obtained in the vertical plane showed that the AO group obtained greater improvements than the PO group in the CJPS in terms of cervical extension movement both at the end of the intervention and 10 min postintervention (p = .001, d = 1.81 and p = .004, d = 1.74, respectively), and also in cervical flexion movement, although only at 10 min after the intervention (p = .035, d = 0.72). In addition, the AO group obtained greater improvements than the MI group in the CJPS only at the end of the intervention in cervical extension movement (p = .041, d = 1.17). Regarding the left rotation cervical movement, both the MI and AO groups were superior to the PO group in both planes at the end of the intervention (p < .05, d > 0.80).ConclusionsAlthough both AO and MI could be a useful strategy for CJPS improvement, the AO group showed the strongest results. The therapeutic potential of the application of mental practice in a clinical context in the early stages of rehabilitation of NSCNP should be considered.
creator: Ferran Cuenca-Martínez
creator: Roy La Touche
creator: Jose Vicente León-Hernández
creator: Luis Suso-Martí
uri: https://doi.org/10.7717/peerj.7681
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Cuenca-Martínez et al.

title: Simultaneous molecular docking of different ligands to His6-tagged organophosphorus hydrolase as an effective tool for assessing their effect on the enzyme
link: https://peerj.com/articles/7684
last-modified: 2019-09-12
description: BackgroundEnzymatic hydrolysis of N-acyl homoserine lactones (AHLs), which are signaling molecules responsible for the development of antibiotic resistance in gram-negative bacteria, is a potential solution to overcoming antibiotic resistance problem. It has been established that hexahistidine-tagged organophosphorus hydrolase (His6-OPH) exhibits lactonase activity against a number of AHLs and that the combined application of His6-OPH with β-lactam antibiotics leads to an increase in the efficiency of the action of both the enzyme and antibiotics. The use of computational methods can be an effective way to search for and select from the known antibiotics to find the most rational “partners” for combining with this enzyme and creating effective antibacterial agents with a dual (lactonase and antibacterial) functional activity.MethodsIn this study, by using AutoDock Vina and Gromacs softwares the molecular docking and the molecular dynamics methods were adopted to simulate models of puromycin, ceftiofur, and/or AHLs docked to the surface of a dimer molecule of His6-OPH and to study their binding properties. GABEDIT and GAMESS-US packages were used to generate and simulate electron densities of docked AHLs.ResultsInteractions of N-butyryl-DL-homoserine lactone (C4-HSL), N-(3-oxooctanoyl)-L-homoserine lactone (C8-HSL) and N-(3-oxododecanoyl)-L-homoserine lactone (C12-HSL) with His6-OPH dimer active sites in the presence of puromycin and ceftiofur were simulated and studied. The possible intersection of long-chain AHLs with antibiotic molecules in the active sites of the enzyme was revealed. The binding energies of antibiotics and AHLs with the His6-OPH surface were estimated. Statistically significant differences (p = 0.003) were observed between the values calculated for both C4-HSL and C12-HSL, whereas there were no statistically significant differences between the values of the other groups (p ≥ 0.100). The binding energies of AHLs with His6-OPH were slightly higher as compared with the binding energies of antibiotics with the enzyme. The dynamics of the most probable models obtained from docking were investigated. RMSD and RMSF analysis of His6-OPH-AHL complexes in the absence and presence of antibiotics were performed. The interaction energy values of antibiotics and AHLs with the His6-OPH were assessed. Significant increase of the AHLs steadiness in enzyme-substrate complexes in the presence of antibiotics was revealed. The interaction between His6-OPH and C12-HSL was established as thermodynamically more favored.ConclusionsIt has been established that the studied antibiotics puromycin and ceftiofur steady the enzyme-substrate complexes, but at the same time lead to a decrease in the long-chain AHL-hydrolytic activity of His6-OPH in such a combination as compared to a native enzyme, and, therefore, it should be taken into account when creating a therapeutic composition based on combining antibiotics with His6-OPH.
creator: Aysel Aslanli
creator: Elena Efremenko
uri: https://doi.org/10.7717/peerj.7684
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2019 Aslanli and Efremenko