title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1777 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: Herbarium-based studies on taxonomy, biogeography and ecology of Psilochilus (Orchidaceae) link: https://peerj.com/articles/2600 last-modified: 2016-11-08 description: BackgroundPsilochilus is a poorly studied orchid genus distributed from southern Mexico to south-eastern Brazil. A taxonomic revision of this Neotropical endemic based on morphological data is presented.Material and MethodsOver 170 dried herbarium specimens and flowers preserved in liquid of Psilochilus were analyzed. Morphological variation among examined taxa was described based on multivariate analysis. To evaluate the similarity between niches occupied by various Psilochilus species ecological niche modeling (ENM) was applied. Species richness and the distribution patterns of Psilochilus representatives were analyzed based on squares of 5° latitude and longitude while similarities among floras between biogeographical units were measured using the Bray-Curtis index for presence/absence data.Results and DiscussionA new species of the P. physurifolius-complex is described based on Central American material. Psilochilus crenatifolius is reduced to the rank of variety as P. macrophyllus var. crenatifolius. A key to 18 accepted Psilochilus species is provided. The illustrations of perianth segments of all recognized taxa are presented. The climatic niches preferred by the particular Psilochilus representatives are well separated based on ecological niche modeling analysis. Their distribution is limited mainly by the isothermality and temperature seasonality. The highest Psilochilus species richness is observed in the North Andean, Panamanian, Brazilian Planalto and Central American biogeographical provinces. A high level of endemism is observed in all those regions as well as Yungas biogeographical province. Most Psilochilus species occur in areas above 800 m of elevation. The populations were most often reported from the tropical rain forest and tropical moist deciduous forest. creator: Marta Kolanowska creator: Aleksandra M. Naczk creator: Radomir Jaskuła uri: https://doi.org/10.7717/peerj.2600 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Kolanowska et al. title: Supply-side barriers to maternal health care utilization at health sub-centers in India link: https://peerj.com/articles/2675 last-modified: 2016-11-03 description: IntroductionThere exist several barriers to maternal health service utilization in developing countries. Most of the previous studies conducted in India have focused on demand-side barriers, while only a few have touched upon supply-side barriers. None of the previous studies in India have investigated the factors that affect maternal health care utilization at health sub-centers (HSCs) in India, despite the fact that these institutions, which are the geographically closest available public health care facilities in rural areas, play a significant role in providing affordable maternal health care. Therefore, this study aims to examine the supply-side determinants of maternal service utilization at HSCs in rural India.Data and MethodsThis study uses health facility data from the nationally representative District-Level Household Survey, which was administered in 2007–2008 to examine the effect of supply-side variables on the utilization of maternal health care services across HSCs in rural India. Since the dependent variables (the number of antenatal registrations, in-facility deliveries, and postnatal care services) are count variables and exhibit considerable variability, the data were analyzed using negative binomial regression instead of Poisson regression.ResultsThe results show that those HSCs run by a contractual auxiliary nurse midwife (ANM) are likely to offer a lower volume of services when compared to those run by a permanent ANM. The availability of obstetric drugs, weighing scales, and blood pressure equipment is associated with the increased utilization of antenatal and postnatal services. The unavailability of a labor/examination table and bed screen is associated with a reduction in the number of deliveries and postnatal services. The utilization of services is expected to increase if essential facilities, such as water, telephones, toilets, and electricity, are available at the HSCs. Monitoring of ANM’s work by Village Health and Sanitation Committee (VHSC) and providing in-service training to ANM appear to have positive impacts on service utilization. The distance of ANM’s actual residence from the sub-center village where she works is negatively associated with the utilization of delivery and postnatal services. These findings are robust to the inclusion of several demand-side factors.ConclusionTo improve maternal health care utilization at HSCs, the government shouldensure the availability of basic infrastructure, drugs, and equipment at all locations. Monitoring of the ANMs’ work by VHSCs could play an important role in improving health care utilization at the HSCs; therefore, it is important to establish VHSCs in each sub-center village. The relatively low utilization of maternity services in those HSCs that are run solely by contractual ANMs requires further investigation. creator: Aditya Singh uri: https://doi.org/10.7717/peerj.2675 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Singh title: Hydrogen peroxide induced loss of heterozygosity correlates with replicative lifespan and mitotic asymmetry in Saccharomyces cerevisiae link: https://peerj.com/articles/2671 last-modified: 2016-11-03 description: Cellular aging in Saccharomyces cerevisiae can lead to genomic instability and impaired mitotic asymmetry. To investigate the role of oxidative stress in cellular aging, we examined the effect of exogenous hydrogen peroxide on genomic instability and mitotic asymmetry in a collection of yeast strains with diverse backgrounds. We treated yeast cells with hydrogen peroxide and monitored the changes of viability and the frequencies of loss of heterozygosity (LOH) in response to hydrogen peroxide doses. The mid-transition points of viability and LOH were quantified using sigmoid mathematical functions. We found that the increase of hydrogen peroxide dependent genomic instability often occurs before a drop in viability. We previously observed that elevation of genomic instability generally lags behind the drop in viability during chronological aging. Hence, onset of genomic instability induced by exogenous hydrogen peroxide treatment is opposite to that induced by endogenous oxidative stress during chronological aging, with regards to the midpoint of viability. This contrast argues that the effect of endogenous oxidative stress on genome integrity is well suppressed up to the dying-off phase during chronological aging. We found that the leadoff of exogenous hydrogen peroxide induced genomic instability to viability significantly correlated with replicative lifespan (RLS), indicating that yeast cells’ ability to counter oxidative stress contributes to their replicative longevity. Surprisingly, this leadoff is positively correlated with an inverse measure of endogenous mitotic asymmetry, indicating a trade-off between mitotic asymmetry and cell’s ability to fend off hydrogen peroxide induced oxidative stress. Overall, our results demonstrate strong associations of oxidative stress to genomic instability and mitotic asymmetry at the population level of budding yeast. creator: Emine Güven creator: Lindsay A. Parnell creator: Erin D. Jackson creator: Meighan C. Parker creator: Nilin Gupta creator: Jenny Rodrigues creator: Hong Qin uri: https://doi.org/10.7717/peerj.2671 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Guven et al.