A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model
Development of high-throughput technologies, such as Next-generation sequencing, allows thousands of experiments to be performed simultaneously while reducing resource requirement. Consequently, a massive amount of experiment data is now rapidly generated. Nevertheless, the data are not readily usable or meaningful until they are further analysed and interpreted. Due to the size of the data, a high performance computer (HPC) is required for the analysis and interpretation. However, the HPC is expensive and difficult to access. Other means were developed to allow researchers to acquire the power of HPC without a need to purchase and maintain one such as cloud computing services and grid computing system. In this study, we implemented grid computing in a computer training center environment using Berkeley Open Infrastructure for Network Computing (BOINC) as a job distributor and data manager combining all desktop computers to virtualize the HPC. Fifty desktop computers were used for setting up a grid system during the off-hours. In order to test the performance of the grid system, we adapted the Basic Local Alignment Search Tools (BLAST) to the BOINC system. Sequencing results from Illumina platform were aligned to the human genome database by BLAST on the grid system. The result and processing time were compared to those from a single desktop computer and HPC. The estimated durations of BLAST analysis for 4 million sequence reads on a desktop PC, HPC and the grid system were 568, 24 and 5 days, respectively. Thus, the grid implementation of BLAST by BOINC is an efficient alternative to the HPC for sequence alignment. The grid implementation by BOINC also helped tap unused computing resources during the off-hours and could be easily modified for other available bioinformatics software.
Pinthong et al. (2016) A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model. PeerJ 4:e2248 https://doi.org/10.7717/peerj.2248
The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China
Many studies predict that climate change will cause species movement and turnover, but few have considered the effect of climate change on range fragmentation for current species and/or populations. We used MaxEnt to predict suitable habitat, fragmentation and turnover for 134 amphibian species in China under 40 future climate change scenarios spanning four pathways (RCP2.6, RCP4.5, RCP6 and RCP8.5) and two time periods (the 2050s and 2070s). Our results show that climate change may cause a major shift in spatial patterns of amphibian diversity. Amphibians in China would lose 20% of their original ranges on average; the distribution outside current ranges would increase by 15%. Suitable habitats for over 90% of species will be located in the north of their current range, for over 95% of species in higher altitudes (from currently 137–4,124 m to 286–4,396 m in the 2050s or 314–4,448 m in the 2070s), and for over 75% of species in the west of their current range. Also, our results predict two different general responses to the climate change: some species contract their ranges while moving westwards, southwards and to higher altitudes, while others expand their ranges. Finally, our analyses indicate that range dynamics and fragmentation are related, which means that the effects of climate change on Chinese amphibians might be two-folded.
Duan et al. (2016) The potential effects of climate change on amphibian distribution, range fragmentation and turnover in China. PeerJ 4:e2185 https://doi.org/10.7717/peerj.2185
What are the probable predictors of urinary incontinence during pregnancy?
Objectives. The frequency, predisposing factors and impact of urinary incontinence (UI) on quality of life (QoL) during pregnancy were investigated. Materials and Method. A preliminary cross-sectional survey was studied among pregnant women between January and July of 2014. A total of 132 pregnant women were recruited using a questionnaire form for sociodemographic features, the Turkish version of the International Consultation on Incontinence-Short Form (ICIQ-SF), for the characteristics of UI and Wagner’s Quality of Life scale to assess impact on QoL. p < 0.05 was set significant. Results.Urinary incontinence was present in 56 out of 132 pregnant women (42.4%, UI-present group): mean age, 26.7 ± 5.4y(p = 0.780); median height, 160 cm (min–max: 153–176, p = 0.037); median BMI, 28.7 kg/m2(min–max: 22.4–50.0, p = 0.881); urine leakage occurred per week once (n = 18, 32.1%), twice or thrice (n = 8, 14.3%); per day few times (n = 14, 25%), once (n = 5, 8.9%) and always (n = 8, 14.3%) with mainly a small amount of urine leakage (n = 33, 58.9%) or a moderate (n = 4, 7.1%). There were statistically significant relationships between QoL scores and frequency of UI (p = 0.002) or amount of leakage (p = 0.002). Impact on QoL scores ranged from mild (n = 33, 58.9%), moderate (n = 4, 7.1%) to severe (n = 4, 7.1%) levels in daily life. UI impacted the daily life activities of women by making them less likely to undertake activities outside their homes (23.2%), by affecting their working performance and friendships (8.9%), their daily home activities (7.1%), their general health status (12.5%), their sexual relations (12.5%), by making them more nervous or anxious (10.7%) and by the need to wear pads or protectors (25%). ANOVA, Tukey, and Tamhane tests as the minimal important difference model yielded significant relevance between statistical analyses and clinical outcomes by using standard deviations (p = 0.001, 0.001 and 0.005 respectively). The following features favored the occurence of UI: Age (OR = 0.845, 95% CI [0.268–2.669]), being a housewife (OR = 1.800, 95% CI [0.850–3.810]), anemia (OR = 0.939, 95% CI [0.464–1.901]), parity (OR = 0.519, 95% CI [0.325–0.829]), miscarriage (OR = 1.219, 95% CI [0.588–2.825]) and living in rural areas (OR = 1.800, 95% CI [0.887–3.653]). Height (p = 0, 037), educational status (0.016), miscarriage (0.002), parity (0.006) and place of living (0.020) were significant factors. Conclusions.Many pregnant women are suffering from UI, which warrants a significant public health consideration in the region. Age, height, being a housewife or graduation level higher than primary school, living in rural, parity, miscarriage, and anemia were the factors in favor of the onset of UI. The authors plan a health promotion program in the region according to the results in order to provide information to health caregivers, especially family physicians, and to educate women about the predictors of UI and pelvic floor exercises for primary prevention and secondary relief of UI during and after pregnancy and provide some hygienic supplies to the poor in this aspect.
Demircan et al. (2016) What are the probable predictors of urinary incontinence during pregnancy?. PeerJ 4:e2283 https://doi.org/10.7717/peerj.2283
Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles
The Chelonid herpesvirus 5 (ChHV5) has been consistently associated with fibropapillomatosis (FP), a transmissible neoplastic disease of marine turtles. Whether ChHV5 plays a causal role remains debated, partly because while FP tumours have been clearly documented to contain high concentrations of ChHV5 DNA, recent PCR-based studies have demonstrated that large proportions of asymptomatic marine turtles are also carriers of ChHV5. We used a real-time PCR assay to quantify the levels of ChHV5 Glycoprotein B (gB) DNA in both tumour and non-tumour skin tissues, from clinically affected and healthy turtles drawn from distant ocean basins across four species. In agreement with previous studies, higher ratios of viral to host DNA were consistently observed in tumour versus non-tumour tissues in turtles with FP. Unexpectedly however, the levels of ChHV5 gB DNA in clinically healthy turtles were significantly higher than in non-tumour tissues from FP positive turtles. Thus, a large proportion of clinically healthy sea turtle populations worldwide across species carry ChHV5 gB DNA presumably through persistent latent infections. ChHV5 appears to be ubiquitous regardless of the animals’ clinical conditions. Hence, these results support the theory that ChHV5 is a near ubiquitous virus with latency characteristics requiring co-factors, possibly environmental or immune related, to induce FP.
Alfaro-Núñez et al. (2016) Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles. PeerJ 4:e2274 https://doi.org/10.7717/peerj.2274
Medium-sized exotic prey create novel food webs: the case of predators and scavengers consuming lagomorphs
Food web interactions are key to community structure. The introduction of species can be seen as an uncontrolled experiment of the addition of species. Introduced species lead to multiple changes, frequently threatening the native biodiversity. However, little is known about their direct effect on the upper level of the food web. In this study we review empirical data on the predator–prey relationship between the introduced lagomorphs and their consumers, and use meta-analytical tools to quantify the strength of their interactions. We expect that exotic lagomorphs will destabilize food webs, affect ecological processes and compromise the conservation of the invaded regions. We found 156 studies on the diet of 43 species of predators that consume lagomorphs as exotic preys in South America and Oceania. We found an average exotic lagomorphs-predator link of 20% which indicates a strong interaction, given that the average for the strongest links with native prey (when lagomorphs are not included in the predator diet) is about 24%. Additionally, this last link decreases to 17% when lagomorphs are present. When lagomorphs arrive in a new environment they may become the most important resource for predators, producing an unstable equilibrium in the novel food web. Any disruption of this interaction could have catastrophic consequences for the native diversity by directly impacting predators or indirectly impacting native preys by apparent competition. Eradication or any change in their abundances should be carefully considered in conservation actions since those will have great impacts on predator populations and ultimately in the whole communities.
Barbar et al. (2016) Medium-sized exotic prey create novel food webs: the case of predators and scavengers consuming lagomorphs. PeerJ 4:e2273 https://doi.org/10.7717/peerj.2273
Competition-function tradeoffs in ectomycorrhizal fungi
Background. The extent to which ectomycorrhizal fungi mediate primary production, carbon storage, and nutrient remineralization in terrestrial ecosystems depends upon fungal community composition. However, the factors that govern community composition at the root system scale are not well understood. Here, we explore a potential tradeoff between ectomycorrhizal fungal competitive ability and enzymatic function. Methods. We grew Pinus muricata (Bishop Pine) seedlings in association with ectomycorrhizal fungi from three different genera in a fully factorial experimental design. We measured seedling growth responses, ectomycorrhizal abundance, and the root tip activity of five different extracellular enzymes involved in the mobilization of carbon and phosphorus. Results. We found an inverse relationship between competitiveness, quantified based on relative colonization levels, and enzymatic activity. Specifically, Thelephora terrestris, the dominant fungus, had the lowest enzyme activity levels, while Suillus pungens, the least dominant fungus, had the highest. Discussion. Our results identify a tradeoff between competition and function in ectomycorrhizal fungi, perhaps mediated by the competing energetic demands associated with competitive interactions and enzymatic production. These data suggest that mechanisms such as active partner maintenance by host trees may be important to maintaining “high-quality” ectomycorrhizal fungal partners in natural systems.
Moeller et al. (2016) Competition-function tradeoffs in ectomycorrhizal fungi. PeerJ 4:e2270 https://doi.org/10.7717/peerj.2270
Community shelter use in response to two benthic decapod predators in the Long Island Sound
To investigate community shelter effects of two invasive decapod species, Hemigrapsus sanguineus and Carcinus maenas, in the Long Island Sound (LIS), we deployed artificial shelters in the intertidal and immediate subtidal zones. These consisted of five groups during the summer: a control, a resident H. sanguineus male or female group, and a resident C. maenas male or female group. We quantified utilization of the shelters at 24 h by counting crabs and fish present. We found significant avoidance of H. sanguineus in the field by benthic hermit crabs (Pagurus spp.) and significant avoidance of C. maenas by the seaboard goby (Gobiosoma ginsburgi). The grubby (Myoxocephalus aenaeus) avoided neither treatment, probably since it tends to be a predator of invertebrates. H. sanguineus avoided C. maenas treatments, whereas C. maenas did not avoid any treatment. Seasonal deployments in the subtidal indicated cohabitation of a number of benthic species in the LIS, with peak shelter use corresponding with increased predation and likely reproductive activity in spring and summer for green crabs (C. maenas), hermit crabs (Pagurus spp.), seaboard gobies (G. ginsburgi), and grubbies (Myoxocephalus aenaeus).
Hudson et al. (2016) Community shelter use in response to two benthic decapod predators in the Long Island Sound. PeerJ 4:e2265 https://doi.org/10.7717/peerj.2265
Dropping behaviour of pea aphid nymphs increases their development time and reduces their reproductive capacity as adults
Background. Many aphid species, including the pea aphid Acyrthosiphon pisum, exhibit a behaviour where they drop or fall from their host plant, a commonly used strategy to avoid predation, parasitism or physical disturbance. We hypothesised that there was a physiological non-consumptive cost due to such dropping behaviour because aphids would expend energy re-establishing themselves on a host plant and also lose feeding time. Methods. We evaluated this non-consumptive cost by determining the development time and reproductive potential of pea aphids that whilst developing as nymphs had regularly dropped to the ground following dislodgment from their host plant. Using a microcosm approach, in a replicated and balanced laboratory experiment, we caused aphid dropping behaviour by tapping the plants on which they were feeding. Results. The results demonstrated that disturbance by dropping behaviour increased nymphal development time and reduced their subsequent reproductive capacity as adults. Discussion. We conclude that dropping behaviour had a strong negative effect on the development of nymphs and their subsequent reproductive capacity. This implies that the physiological cost of such a behaviour choice is substantial, and that such avoidance strategies require a trade-off which reduces the capacity of a population to increase.
Agabiti et al. (2016) Dropping behaviour of pea aphid nymphs increases their development time and reduces their reproductive capacity as adults. PeerJ 4:e2236 https://doi.org/10.7717/peerj.2236
Development and characterization of novel microsatellite markers by Next Generation Sequencing for the blue and red shrimp Aristeus antennatus
The blue and red shrimp, Aristeus antennatus, is a commercially important crustacean, in the Mediterranean Sea, which has been listed as a priority species for fishery management. Hypervariable microsatellite markers could be a useful tool to identify genetic stocks among geographically close fishing grounds. Potential microsatellite markers (97) identified from next-generation sequencing of an individual shrimp using a 454 GS Junior Pyrosequencer were tested on a preliminary panel of 15 individuals representing the four worldwide genetic stocks of the species from which 35 polymorphic loci were identified and used to characterize an additional 20 individuals from the Western Mediterranean Sea. In the Western Mediterranean sample, 32 out of 35 were polymorphic loci and the number of alleles per locus ranged from 2 to 14 and expected heterozygosity ranged from 0.050 to 0.968. No linkage disequilibrium was detected, indicating the independence of the loci. These novel microsatellites provide additional tools to address questions relating to genetic diversity, parentage studies and connectivity patterns of A. antennatus populations and help develop effective strategies to ensure long-term sustainability of this resource.
Heras et al. (2016) Development and characterization of novel microsatellite markers by Next Generation Sequencing for the blue and red shrimp Aristeus antennatus. PeerJ 4:e2200 https://doi.org/10.7717/peerj.2200
Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase
The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent RNA polymerase (RdRp) gene, we found that a tandem duplication occurred after the divergence of potato and its wild relatives among other Solanum plants. The duplicated sequence crosses the intron-exon boundary of the first intron and the second exon. A new intron was detected at this duplicated region, and it includes a small previously exonic segment of the upstream copy of the duplicated sequence and the intronic segment of the downstream copy of the duplicated sequence. The donor site of this new intron was directly obtained from the small previously exonic segment. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3′ splicing site, two putative exonic splicing enhancers, and the GC contents differed between the intron and exon. In the widely cited model of intron gain by tandem genomic duplication, the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals.
Ma et al. (2016) Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PeerJ 4:e2272 https://doi.org/10.7717/peerj.2272