A stepping stone to compositionality in chimpanzee communication
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.
Oña et al. (2019) A stepping stone to compositionality in chimpanzee communication. PeerJ 7:e7623 https://doi.org/10.7717/peerj.7623
Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum)
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.
Qian et al. (2019) Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum). PeerJ 7:e7664 https://doi.org/10.7717/peerj.7664
Variations in ecosystem service value in response to land use/land cover changes in Central Asia from 1995–2035
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.
Spatial and Geographic Information Science
Li et al. (2019) Variations in ecosystem service value in response to land use/land cover changes in Central Asia from 1995–2035. PeerJ 7:e7665 https://doi.org/10.7717/peerj.7665
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
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.
Kosakai et al. (2019) 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. PeerJ 7:e7671 https://doi.org/10.7717/peerj.7671
Arbuscular mycorrhizal fungi alter the food utilization, growth, development and reproduction of armyworm (Mythimna separata) fed on Bacillus thuringiensis maize
Background The 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. Methods In 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. Results GC 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. Discussion It 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.
Wang et al. (2019) Arbuscular mycorrhizal fungi alter the food utilization, growth, development and reproduction of armyworm (Mythimna separata) fed on Bacillus thuringiensis maize. PeerJ 7:e7679 https://doi.org/10.7717/peerj.7679
Mental practice in isolation improves cervical joint position sense in patients with chronic neck pain: a randomized single-blind placebo trial
Objective The 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). Methods A 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. Results The 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). Conclusions Although 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.
Cuenca-Martínez et al. (2019) Mental practice in isolation improves cervical joint position sense in patients with chronic neck pain: a randomized single-blind placebo trial. PeerJ 7:e7681 https://doi.org/10.7717/peerj.7681
Simultaneous molecular docking of different ligands to His6-tagged organophosphorus hydrolase as an effective tool for assessing their effect on the enzyme
Background Enzymatic 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. Methods In 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. Results Interactions 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. Conclusions It 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.
Aslanli et al. (2019) Simultaneous molecular docking of different ligands to His6-tagged organophosphorus hydrolase as an effective tool for assessing their effect on the enzyme. PeerJ 7:e7684 https://doi.org/10.7717/peerj.7684
Effect of biomimetic material on stress distribution in mandibular molars restored with inlays: a three-dimensional finite element analysis
Background Although biomimetic material has become increasingly popular in dental cosmetology nowadays, it remains unclear how it would affect the restored teeth during chewing. It is necessary to study the influence of biomimetic material on stress distribution in the restored teeth. Methods Eight three-dimensional finite element (FE) models were constructed and divided into two groups. Group 1 included the FE model of intact molar, and the FE models of inlay-restored molars fabricated from IPS e.max CAD, Lava Ultimate and biomimetic materials individually. Enamel was considered a homogeneous material. Group 2 included the FE models of intact molar and molars restored with inlays using IPS e.max CAD, Lava Ultimate and biomimetic materials individually, considering enamel as an inhomogeneous material. Results In Group 1, compared with that in the intact molar, the maximum tensile stress (MTS) in the occlusal grooves decreased in the inlay-restored molars fabricated from IPS e.max CAD and was concentrated on the cavity floor at the buccal side in the inner dentin around inlay. When Lava Ultimate was selected, MTS decreased in the occlusal grooves and on the cavity floor but increased in the lateral walls. In the restored molar using biomimetic material, the MTS on the cavity floor was distributed more evenly than that in the molar using IPS e.max CAD, and no obvious changes were noted in the lateral walls. The same changes were observed in Group 2. No differences in the stress distribution pattern were noted among the FE models in Groups 1 and 2. Conclusions Molars restored with inlays fabricated from biomimetic material exhibit a more uniform stress distribution in the dentin around restoration. The consideration of enamel as a homogeneous tissue is acceptable for analyzing the maximum principal stress distribution in the inlay-restored molar.
Zhu et al. (2019) Effect of biomimetic material on stress distribution in mandibular molars restored with inlays: a three-dimensional finite element analysis. PeerJ 7:e7694 https://doi.org/10.7717/peerj.7694
Relationship between ROS production, MnSOD activation and periods of fasting and re-feeding in freshwater shrimp Neocaridina davidi (Crustacea, Malacostraca)
The middle region of the digestive system, the midgut of freshwater shrimp Neocaridina davidi is composed of a tube-shaped intestine and the hepatopancreas formed by numerous caeca. Two types of cells have been distinguished in the intestine, the digestive cells (D-cells) and regenerative cells (R-cells). The hepatopancreatic tubules have three distinct zones distinguished along the length of each tubule—the distal zone with R-cells, the medial zone with differentiating cells, and the proximal zone with F-cells (fibrillar cells) and B-cells (storage cells). Fasting causes activation of cell death, a reduction in the amount of reserve material, and changes in the mitochondrial membrane potential. However, here we present how the concentration of ROS changes according to different periods of fasting and whether re-feeding causes their decrease. In addition, the activation/deactivation of mitochondrial superoxide dismutase (MnSOD) was analyzed. The freshwater shrimps Neocaridina davidi (Crustacea, Malacostraca, Decapoda) were divided into experimental groups: animals starved for 14 days, animals re-fed for 4, 7, and 14 days. The material was examined using the confocal microscope and the flow cytometry. Our studies have shown that long-term starvation increases the concentration of free radicals and MnSOD concentration in the intestine and hepatopancreas, while return to feeding causes their decrease in both organs examined. Therefore, we concluded that a distinct relationship between MnSOD concentration, ROS activation, cell death activation and changes in the mitochondrial membrane potential occurred.
Włodarczyk et al. (2019) Relationship between ROS production, MnSOD activation and periods of fasting and re-feeding in freshwater shrimp Neocaridina davidi (Crustacea, Malacostraca). PeerJ 7:e7399 https://doi.org/10.7717/peerj.7399
Plant host and drought shape the root associated fungal microbiota in rice
Background and Aim Water is an increasingly scarce resource while some crops, such as paddy rice, require large amounts of water to maintain grain production. A better understanding of rice drought adaptation and tolerance mechanisms could help to reduce this problem. There is evidence of a possible role of root-associated fungi in drought adaptation. Here, we analyzed the endospheric fungal microbiota composition in rice and its relation to plant genotype and drought. Methods Fifteen rice genotypes (Oryza sativa ssp. indica) were grown in the field, under well-watered conditions or exposed to a drought period during flowering. The effect of genotype and treatment on the root fungal microbiota composition was analyzed by 18S ribosomal DNA high throughput sequencing. Grain yield was determined after plant maturation. Results There was a host genotype effect on the fungal community composition. Drought altered the composition of the root-associated fungal community and increased fungal biodiversity. The majority of OTUs identified belonged to the Pezizomycotina subphylum and 37 of these significantly correlated with a higher plant yield under drought, one of them being assigned to Arthrinium phaeospermum. Conclusion This study shows that both plant genotype and drought affect the root-associated fungal community in rice and that some fungi correlate with improved drought tolerance. This work opens new opportunities for basic research on the understanding of how the host affects microbiota recruitment as well as the possible use of specific fungi to improve drought tolerance in rice.
Andreo-Jimenez et al. (2019) Plant host and drought shape the root associated fungal microbiota in rice. PeerJ 7:e7463 https://doi.org/10.7717/peerj.7463