title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1779 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone link: https://peerj.com/articles/2687 last-modified: 2016-11-08 description: Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10–20 cm and 30–40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics. creator: Cristina N. Butterfield creator: Zhou Li creator: Peter F. Andeer creator: Susan Spaulding creator: Brian C. Thomas creator: Andrea Singh creator: Robert L. Hettich creator: Kenwyn B. Suttle creator: Alexander J. Probst creator: Susannah G. Tringe creator: Trent Northen creator: Chongle Pan creator: Jillian F. Banfield uri: https://doi.org/10.7717/peerj.2687 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Butterfield et al. title: Cranial bone histology of Metoposaurus krasiejowensis (Amphibia, Temnospondyli) from the Late Triassic of Poland link: https://peerj.com/articles/2685 last-modified: 2016-11-08 description: In this study, 21 skull bones of Metoposaurus krasiejowensis from the Late Triassic of Poland were investigated histologically. Dermal bones show a diploë structure, with an ornamented external surface. The ridges consist of mostly well vascularized parallel-fibered bone; the valleys are built of an avascular layer of lamellar bone. The thick middle region consists of cancellous bone, with varying porosity. The thin and less vascularized internal cortex consists of parallel-fibered bone. The numerous Sharpey’s fibers and ISF are present in all bones. The cyclicity of growth is manifested as an alternation of thick, avascular annuli and high vascularized zones as well as a sequence of resting lines. The detailed histological framework of dermal bones varies even within a single bone; this seems to be related to the local biomechanical loading of the particular part of the skull. The dynamic processes observed during the ornamentation creation indicate that the positions of the ridges and grooves change during growth and could be a specific adaptation to changing biomechanical conditions and stress distribution during bone development. In the supratemporal, the cementing lines show that the remodeling process could be involved in the creations of sculpture. The common occurrence of ISF suggests that metaplastic ossification plays an important role during cranial development. Endochondral bones preserved the numerous remains of calcified cartilage. This indicates that ossification follows a pattern known for stereospondyl intercentra, with relatively slow ossification of the trabecular part and late development of the periosteal cortex. The large accumulation of Sharpey’s fibers in the occipital condyles indicates the presence of strong muscles and ligaments connecting the skull to the vertebral column. creator: Kamil Gruntmejer creator: Dorota Konietzko-Meier creator: Adam Bodzioch uri: https://doi.org/10.7717/peerj.2685 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gruntmejer et al. title: Comparisons of forecasting for hepatitis in Guangxi Province, China by using three neural networks models link: https://peerj.com/articles/2684 last-modified: 2016-11-08 description: This study compares and evaluates the prediction of hepatitis in Guangxi Province, China by using back propagation neural networks based genetic algorithm (BPNN-GA), generalized regression neural networks (GRNN), and wavelet neural networks (WNN). In order to compare the results of forecasting, the data obtained from 2004 to 2013 and 2014 were used as modeling and forecasting samples, respectively. The results show that when the small data set of hepatitis has seasonal fluctuation, the prediction result by BPNN-GA will be better than the two other methods. The WNN method is suitable for predicting the large data set of hepatitis that has seasonal fluctuation and the same for the GRNN method when the data increases steadily. creator: Ruijing Gan creator: Ni Chen creator: Daizheng Huang uri: https://doi.org/10.7717/peerj.2684 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Gan et al. title: RGFA: powerful and convenient handling of assembly graphs link: https://peerj.com/articles/2681 last-modified: 2016-11-08 description: The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed using a script based on RGFA. Furthermore, we show how the API provided by RGFA can be employed to design complex graph editing algorithms. As an example, we developed a detection algorithm for CRISPRs in a de Bruijn graph. Finally, RGFA can be used for comparing assembly graphs, e.g., to document the changes in a graph after applying a GUI editor. A program, GFAdiff is provided, which compares the information in two graphs, and generate a report or a Ruby script documenting the transformation steps between the graphs. creator: Giorgio Gonnella creator: Stefan Kurtz uri: https://doi.org/10.7717/peerj.2681 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Gonnella and Kurtz title: Community assembly and functional leaf traits mediate precipitation use efficiency of alpine grasslands along environmental gradients on the Tibetan Plateau link: https://peerj.com/articles/2680 last-modified: 2016-11-08 description: The alpine grasslands on the Tibetan Plateau are sensitive and vulnerable to climate change. However, it is still unknown how precipitation use efficiency (PUE), the ratio of aboveground net primary productivity (ANPP) to precipitation, is related to community assembly of plant species, functional groups or traits for the Tibetan alpine grasslands along actual environmental gradients. We conducted a multi-site field survey at grazing-excluded pastures across meadow, steppe and desert-steppe to measure aboveground biomass (AGB) in August, 2010. We used species richness (SR), the Shannon diversity index, and cover-weighted functional group composition (FGC) of 1-xerophytes, 2-mesophytes, and 3-hygrophytes to describe community assembly at the species level; and chose community-level leaf area index (LAIc), specific leaf area (SLAc), and species-mixed foliar δ13C to quantify community assembly at the functional trait level. Our results showed that PUE decreased with increasing accumulated active temperatures (AccT) when daily temperature average is higher than 5 °C, but increased with increasing climatic moisture index (CMI), which was demined as the ratio of growing season precipitation (GSP) to AccT. We also found that PUE increased with increasing SR, the Shannon diversity index, FGC and LAIc, decreased with increasing foliar δ13C, and had no relation with SLAc at the regional scale. Neither soil total nitrogen (STN) nor organic carbon has no influence on PUE at the regional scale. The community assembly of the Shannon index, LAIc and SLAc together accounted for 46.3% of variance in PUE, whilst CMI accounted for 47.9% of variance in PUE at the regional scale. This implies that community structural properties and plant functional traits can mediate the sensitivity of alpine grassland productivity in response to climate change. Thus, a long-term observation on community structural and functional changes is recommended for better understanding the response of alpine ecosystems to regional climate change on the Tibetan Plateau. creator: Shaowei Li creator: Jianshuang Wu uri: https://doi.org/10.7717/peerj.2680 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Li and Wu title: Cloning, expression and characterization of a cold-adapted endo-1, 4-β-glucanase from Citrobacter farmeri A1, a symbiotic bacterium of Reticulitermes labralis link: https://peerj.com/articles/2679 last-modified: 2016-11-08 description: BackgroundMany biotechnological and industrial applications can benefit from cold-adapted EglCs through increased efficiency of catalytic processes at low temperature. In our previous study, Citrobacter farmeri A1 which was isolated from a wood-inhabiting termite Reticulitermes labralis could secrete a cold-adapted EglC. However, its EglC was difficult to purify for enzymatic properties detection because of its low activity (0.8 U/ml). The objective of the present study was to clone and express the C. farmeri EglC gene in Escherichia coli to improve production level and determine the enzymatic properties of the recombinant enzyme.MethodsThe EglC gene was cloned from C. farmeri A1 by thermal asymmetric interlaced PCR. EglC was transformed into vector pET22b and functionally expressed in E. coli. The recombination protein EglC22b was purified for properties detection.ResultsSDS-PAGE revealed that the molecular mass of the recombinant endoglucanase was approximately 42 kDa. The activity of the E. coli pET22b-EglC crude extract was 9.5 U/ml. Additionally, it was active at pH 6.5–8.0 with an optimum pH of 7.0. The recombinant enzyme had an optimal temperature of 30–40 °C and exhibited >50% relative activity even at 5 °C, whereas it lost approximately 90% of its activity after incubation at 60 °C for 30 min. Its activity was enhanced by Co2+ and Fe3+, but inhibited by Cd2+, Zn2+, Li+, Triton X-100, DMSO, acetonitrile, Tween 80, SDS, and EDTA.ConclusionThese biochemical properties indicate that the recombinant enzyme is a cold-adapted endoglucanase that can be used for various industrial applications. creator: Xi Bai creator: Xianjun Yuan creator: Aiyou Wen creator: Junfeng Li creator: Yunfeng Bai creator: Tao Shao uri: https://doi.org/10.7717/peerj.2679 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bai et al. title: Planning horizon affects prophylactic decision-making and epidemic dynamics link: https://peerj.com/articles/2678 last-modified: 2016-11-08 description: The spread of infectious diseases can be impacted by human behavior, and behavioral decisions often depend implicitly on a planning horizon—the time in the future over which options are weighed. We investigate the effects of planning horizons on epidemic dynamics. We developed an epidemiological agent-based model (along with an ODE analog) to explore the decision-making of self-interested individuals on adopting prophylactic behavior. The decision-making process incorporates prophylaxis efficacy and disease prevalence with the individuals’ payoffs and planning horizon. Our results show that for short and long planning horizons individuals do not consider engaging in prophylactic behavior. In contrast, individuals adopt prophylactic behavior when considering intermediate planning horizons. Such adoption, however, is not always monotonically associated with the prevalence of the disease, depending on the perceived protection efficacy and the disease parameters. Adoption of prophylactic behavior reduces the epidemic peak size while prolonging the epidemic and potentially generates secondary waves of infection. These effects can be made stronger by increasing the behavioral decision frequency or distorting an individual’s perceived risk of infection. creator: Luis G. Nardin creator: Craig R. Miller creator: Benjamin J. Ridenhour creator: Stephen M. Krone creator: Paul Joyce creator: Bert O. Baumgaertner uri: https://doi.org/10.7717/peerj.2678 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Nardin et al. title: Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C) link: https://peerj.com/articles/2676 last-modified: 2016-11-08 description: BackgroundChromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of microorganisms living in naturally occuring environments. Metagenomic Hi-C and 3C-seq datasets have begun to emerge, but the feasibility of resolving genomes when closely related organisms (strain-level diversity) are present in the sample has not yet been systematically characterised.MethodsWe developed a computational simulation pipeline for metagenomic 3C and Hi-C sequencing to evaluate the accuracy of genomic reconstructions at, above, and below an operationally defined species boundary. We simulated datasets and measured accuracy over a wide range of parameters. Five clustering algorithms were evaluated (2 hard, 3 soft) using an adaptation of the extended B-cubed validation measure.ResultsWhen all genomes in a sample are below 95% sequence identity, all of the tested clustering algorithms performed well. When sequence data contains genomes above 95% identity (our operational definition of strain-level diversity), a naive soft-clustering extension of the Louvain method achieves the highest performance.DiscussionPreviously, only hard-clustering algorithms have been applied to metagenomic 3C and Hi-C data, yet none of these perform well when strain-level diversity exists in a metagenomic sample. Our simple extension of the Louvain method performed the best in these scenarios, however, accuracy remained well below the levels observed for samples without strain-level diversity. Strain resolution is also highly dependent on the amount of available 3C sequence data, suggesting that depth of sequencing must be carefully considered during experimental design. Finally, there appears to be great scope to improve the accuracy of strain resolution through further algorithm development. creator: Matthew Z. DeMaere creator: Aaron E. Darling uri: https://doi.org/10.7717/peerj.2676 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 DeMaere and Darling title: Yangtze River, an insignificant genetic boundary in tufted deer (Elaphodus cephalophus): the evidence from a first population genetics study link: https://peerj.com/articles/2654 last-modified: 2016-11-08 description: Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities. creator: Zhonglou Sun creator: Tao Pan creator: Hui Wang creator: Mujia Pang creator: Baowei Zhang uri: https://doi.org/10.7717/peerj.2654 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Sun et al. title: Iron overload induced death of osteoblasts in vitro: involvement of the mitochondrial apoptotic pathway link: https://peerj.com/articles/2611 last-modified: 2016-11-08 description: BackgroundIron overload is recognized as a new pathogenfor osteoporosis. Various studies demonstrated that iron overload could induce apoptosis in osteoblasts and osteoporosis in vivo. However, the exact molecular mechanisms involved in the iron overload-mediated induction of apoptosis in osteoblasts has not been explored.PurposeIn this study, we attempted to determine whether the mitochondrial apoptotic pathway is involved in iron-induced osteoblastic cell death and to investigate the beneficial effect of N-acetyl-cysteine (NAC) in iron-induced cytotoxicity.MethodsThe MC3T3-E1 osteoblastic cell line was treated with various concentrations of ferric ion in the absence or presence of NAC, and intracellular iron, cell viability, reactive oxygen species, functionand morphology changes of mitochondria and mitochondrial apoptosis related key indicators were detected by commercial kits. In addition, to further explain potential mechanisms underlying iron overload-related osteoporosis, we also assessed cell viability, apoptosis, and osteogenic differentiation potential in bone marrow-derived mesenchymal stemcells(MSCs) by commercial kits.ResultsFerric ion demonstrated concentration-dependent cytotoxic effects on osteoblasts. After incubation with iron, an elevation of intracelluar labile iron levels and a concomitant over-generation of reactive oxygen species (ROS) were detected by flow cytometry in osteoblasts. Nox4 (NADPH oxidase 4), an important ROS producer, was also evaluated by western blot. Apoptosis, which was evaluated by Annexin V/propidium iodide staining, Hoechst 33258 staining, and the activation of caspase-3, was detected after exposure to iron. Iron contributed to the permeabilizatio of mitochondria, leading to the release of cytochrome C (cyto C), which, in turn, induced mitochondrial apoptosis in osteoblasts via activation of Caspase-3, up-regulation of Bax, and down-regulation of Bcl-2. NAC could reverse iron-mediated mitochondrial dysfunction and blocked the apoptotic events through inhibit the generation of ROS. In addition, iron could significantly promote apoptosis and suppress osteogenic differentiation and mineralization in bone marrow-derived MSCs.ConclusionsThese findings firstly demonstrate that the mitochondrial apoptotic pathway involved in iron-induced osteoblast apoptosis. NAC could relieved the oxidative stress and shielded osteoblasts from apoptosis casused by iron-overload. We also reveal that iron overload in bone marrow-derived MSCs results in increased apoptosis and the impairment of osteogenesis and mineralization. creator: Qing Tian creator: Shilei Wu creator: Zhipeng Dai creator: Jingjing Yang creator: Jin Zheng creator: Qixin Zheng creator: Yong Liu uri: https://doi.org/10.7717/peerj.2611 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Tian et al.