title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1917 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Intergenic incompatibilities reduce fitness in hybrids of extremely closely related bacteriophages link: https://peerj.com/articles/1320 last-modified: 2015-10-22 description: Horizontal gene transfer and recombination occur across many groups of viruses and play key roles in important viral processes such as host-range expansion and immune-system avoidance. To have any predictive power regarding the ability of viruses to readily recombine, we must determine the extent to which epistasis restricts the success of recombinants, particularly as it relates to the genetic divergence between parental strains. In any hybridization event, the evolutionary success or failure of hybrids is largely determined by the pervasiveness of epistasis in the parental genomes. Recombination has previously been shown to incur steep fitness costs in highly divergent viruses as a result of disrupted epistatic interactions. We used a pair of bacteriophages of the family Microviridae to demonstrate that epistasis may evidence itself in the form of fitness costs even in the case of the exchange of alleles at a locus with amino acid divergence as low as 1%. We explored a possible biophysical source of epistasis in the interaction of viral coat and scaffolding proteins and examined a recovery mutation that likely repairs interactions disrupted by recombination. creator: Andrew M. Sackman creator: Danielle Reed creator: Darin R. Rokyta uri: https://doi.org/10.7717/peerj.1320 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Sackman et al. title: ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins link: https://peerj.com/articles/1344 last-modified: 2015-10-20 description: We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively. creator: Anders S. Larsen creator: Lars A. Bratholm creator: Anders S. Christensen creator: Maher Channir creator: Jan H. Jensen uri: https://doi.org/10.7717/peerj.1344 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Larsen et al. title: What do giant titanosaur dinosaurs and modern Australasian megapodes have in common? link: https://peerj.com/articles/1341 last-modified: 2015-10-20 description: Titanosauria is a globally distributed clade of sometimes extremely large Mesozoic herbivorous sauropod dinosaurs. On the basis of current evidence these giant dinosaurs seem to have reproduced in specific and localized nesting sites. However, no investigations have been performed to understand the possible ecological and geological biases that acted for the selection of these nesting sites worldwide. In this study, observations were performed on the best-known Cretaceous nesting sites around the world. Our observations strongly suggest their eggs were incubated with environmental sources of heat, in burial conditions. Taking into account the clutch composition and geometry, the nature and properties of the sediments, the eggshells’ structures and conductance, it would appear that titanosaurs adopted nesting behaviors comparable to the modern Australasian megapodes, using burrow-nesting in diverse media and mound-building strategies. creator: E. Martín Hechenleitner creator: Gerald Grellet-Tinner creator: Lucas E. Fiorelli uri: https://doi.org/10.7717/peerj.1341 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Hechenleitner et al. title: Epidemiological evidence on extra-medical use of prescription pain relievers: transitions from newly incident use to dependence among 12–21 year olds in the United States using meta-analysis, 2002–13 link: https://peerj.com/articles/1340 last-modified: 2015-10-20 description: Background. When 12-to-21-year-olds start using prescription pain relievers extra-medically, some of them transition into opioid dependence within 12 months after such use. Our main aim for this epidemiological research on 12-to-21-year-olds in the United States (US) is to estimate the risk of becoming a newly incident case of opioid dependence within 12 months after onset of using prescription pain relievers extra-medically (EMPPR).Methods. Meta-analyses from multiple independent replication samples now are possible, based upon nationally representative survey samples of US adolescents age 12–21 years. All 12-to-21-year-olds were sampled and recruited for the US National Surveys on Drug Use and Health, with standardized assessments of EMPPR use and opioid dependence (NSDUH, 2002–2013).Results. Peak risk for a transition from start of EMPPR use to opioid dependence within 12 months is seen at mid-adolescence among 14-to-15-year-olds (6.3%, 8.7% per year), somewhat earlier than peak risk for starting EMPPR use (seen for 16-to-19-year-olds at 4.1%, 5.9% per year). Applied to 12-to-21-year-olds in the US between 2002–2013, an estimated 8 million started using PPR extra-medically. Each year, roughly 42,000 to 58,000 transitioned into opioid dependence within 12 months after onset of such use.Discussion. These epidemiological estimates for the US in recent years teach us to expect one transition into adolescent-onset opioid dependence within 12 months for every 11–16 newly incident EMPPR users, yielding perhaps 120 newly incident opioid dependent cases in need of practitioner attention or treatment services, each day of each year. This evidence can be used to motivate more effective public health prevention, outreach, and early intervention programs as might prevent or delay occurrence of EMPPR use and opioid dependence. creator: Maria A. Parker creator: James C. Anthony uri: https://doi.org/10.7717/peerj.1340 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Parker and Anthony title: Two continents and two names for a Neotropical colletid bee species (Hymenoptera: Colletidae: Neopasiphaeinae): Hoplocolletes ventralis (Friese, 1924) link: https://peerj.com/articles/1338 last-modified: 2015-10-20 description: Neopasiphaeine bees (Apoidea: Colletidae) are known for their Amphinotic distribution in the Australian and Neotropical regions. Affinities between colletid taxa in Australia and South America have been speculated for decades, and have been confirmed by recent phylogenetic hypotheses that indicate a biogeographic scenario compatible with a trans-Antarctic biotic connection during the Paleogene. No neopasiphaeine species occurs on both sides of the Pacific Ocean, but the Neotropical species Hoplocolletes ventralis (Friese, 1924) was described as an Australian taxon due to an error in the specimen labels. This mistake was recognized by CD Michener 50 years ago. We herein report that the same labeling problem also happened with Dasycolletes chalceusFriese, 1924, which remained as a tentatively placed species in the Australian genus Leioproctus until now. Moreover, Dasycolletes chalceus is interpreted as a synonym of Hoplocolletes ventralis. We also provide a revised diagnosis for Hoplocolletes, describe the male of H. ventralis in detail for the first time, including a comparative study of its genitalia and associated sterna. creator: Eduardo A.B. Almeida creator: Fábio B. Quinteiro uri: https://doi.org/10.7717/peerj.1338 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Almeida and Quinteiro title: miRMOD: a tool for identification and analysis of 5′ and 3′ miRNA modifications in Next Generation Sequencing small RNA data link: https://peerj.com/articles/1332 last-modified: 2015-10-20 description: In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA stability and ability to bind mRNA targets, hence affecting target gene repression. Next Generation Sequencing (NGS) of the small RNA (sRNA) provides an efficient and reliable method to explore miRNA modifications. The need for dedicated software, especially for users with little knowledge of computers, to determine and analyze miRNA modifications in sRNA NGS data, motivated us to develop miRMOD. miRMOD is a user-friendly, Microsoft Windows and Graphical User Interface (GUI) based tool for identification and analysis of 5′ and 3′ miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data. In addition to identification of miRNA modifications, the tool also predicts and compares the targets of query and modified miRNAs. In order to compare binding affinities for the same target, miRMOD utilizes minimum free energies of the miRNA:target and modified-miRNA:target interactions. Comparisons of the binding energies may guide experimental exploration of miRNA post-transcriptional modifications. The tool is available as a stand-alone package to overcome large data transfer problems commonly faced in web-based high-throughput (HT) sequencing data analysis tools. miRMOD package is freely available at http://bioinfo.icgeb.res.in/miRMOD. creator: Abhinav Kaushik creator: Shradha Saraf creator: Sunil K. Mukherjee creator: Dinesh Gupta uri: https://doi.org/10.7717/peerj.1332 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kaushik et al. title: Replacement of native by non-native animal communities assisted by human introduction and management on Isla Victoria, Nahuel Huapi National Park link: https://peerj.com/articles/1328 last-modified: 2015-10-20 description: One of the possible consequences of biological invasions is the decrease of native species abundances or their replacement by non-native species. In Andean Patagonia, southern Argentina and Chile, many non-native animals have been introduced and are currently spreading. On Isla Victoria, Nahuel Huapi National Park, many non-native vertebrates were introduced ca. 1937. Records indicate that several native vertebrates were present before these species were introduced. We hypothesize that seven decades after the introduction of non-native species and without appropriate management to maintain native diversity, non-native vertebrates have displaced native species (given the known invasiveness and impacts of some of the introduced species). We conducted direct censuses in linear transects 500 m long (n = 10) in parallel with camera-trapping (1,253 camera-days) surveys in two regions of the island with different levels of disturbance: high (n = 4) and low (n = 6) to study the community of terrestrial mammals and birds and the relative abundances of native and non-native species. Results show that currently non-native species are dominant across all environments; 60.4% of census records and 99.7% of camera trapping records are of non-native animals. We detected no native large mammals; the assemblage of large vertebrates consisted of five non-native mammals and one non-native bird. Native species detected were one small mammal and one small bird. Species with the highest trapping rate were red and fallow deer, wild boar, silver pheasant (all four species are non-native) and chucao (a native bird). These results suggest that native species are being displaced by non-natives and are currently in very low numbers. creator: Valeria L. Martin-Albarracin creator: Martin A. Nuñez creator: Guillermo C. Amico uri: https://doi.org/10.7717/peerj.1328 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Martin-Albarracin et al. title: A reappraisal of the morphology and systematic position of the theropod dinosaur Sigilmassasaurus from the “middle” Cretaceous of Morocco link: https://peerj.com/articles/1323 last-modified: 2015-10-20 description: Sigilmassasaurus brevicollis is an enigmatic theropod dinosaur from the early Late Cretaceous (Cenomanian) of Morocco, originally based on a few isolated cervical vertebrae. Ever since its original description, both its taxonomic validity and systematic affinities were contentious. Originally considered to represent its own family, Sigilmassasauridae, the genus has variously been suggested to represent a carcharodontosaurid, an ornithischian, and, more recently, a spinosaurid. Here we describe new remains referrable to this taxon and re-evaluate its taxonomic status and systematic affinities. Based on the new remains, a re-evaluation of the original materials, and comparisons with other spinosaurids, the holotype of Sigilmassasaurus brevicollis is identified as an anterior dorsal, rather than a cervical vertebra, and differences between elements referred to this taxon can be explained by different positions of the elements in question within the vertebral column. Many characters used previously to diagnose the genus and species are found to be more widespread among basal tetanurans, and specifically spinosaurids. However, the taxon shows several autapomorphies that support its validity, including the presence of a strongly rugose, ventrally offset triangular platform that is confluent with a ventral keel anteriorly in the mid-cervical vertebral centra and a strongly reduced lateral neural arch lamination, with no or an incomplete distinction between anterior and posterior centrodiapophyseal laminae in the posterior cervical and anterior dorsal vertebrae. We argue furthermore that Spinosaurus maroccanus, also described on the basis of isolated cervical vertebrae from the same stratigraphic unit and in the same paper as Sigilmassasaurus brevicollis, is a subjective synonym of the latter. Both a detailed comparison of this taxon with other theropods and a formal phylogenetic analysis support spinosaurid affintities for Sigilmassasaurus. However, we reject the recently proposed synonymy of both Spinosaurus maroccanus and Sigilmassasurus brevicollis with Spinosaurus aegyptiacus from the Cenomanian of Egypt, as there are clear differences between the vertebrae of these taxa, and they do not share any derived character that is not found in other spinosaurids. Together with a comparison with other spinosaurid vertebral material from the Kem Kem, this suggests that more than one taxon of spinosaurid was present in the Kem Kem assemblage of Morocco, so the referral of non-overlapping material from this unit to a single taxon should be regarded with caution. creator: Serjoscha W. Evers creator: Oliver W.M. Rauhut creator: Angela C. Milner creator: Bradley McFeeters creator: Ronan Allain uri: https://doi.org/10.7717/peerj.1323 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Evers et al. title: Allocation trade-off under climate warming in experimental amphibian populations link: https://peerj.com/articles/1326 last-modified: 2015-10-20 description: Climate change could either directly or indirectly cause population declines via altered temperature, rainfall regimes, food availability or phenological responses. However few studies have focused on allocation trade-offs between growth and reproduction under marginal resources, such as food scarce that may be caused by climate warming. Such critical changes may have an unpredicted impact on amphibian life-history parameters and even population dynamics. Here, we report an allocation strategy of adult anuran individuals involving a reproductive stage under experimental warming. Using outdoor mesocosm experiments we simulated a warming scenario likely to occur at the end of this century. We examined the effects of temperature (ambient vs. pre-/post-hibernation warming) and food availability (normal vs. low) on reproduction and growth parameters of pond frogs (Pelophylax nigromaculatus). We found that temperature was the major factor influencing reproductive time of female pond frogs, which showed a significant advancing under post-hibernation warming treatment. While feeding rate was the major factor influencing reproductive status of females, clutch size, and variation of body size for females, showed significant positive correlations between feeding rate and reproductive status, clutch size, or variation of body size. Our results suggested that reproduction and body size of amphibians might be modulated by climate warming or food availability variation. We believe this study provides some new evidence on allocation strategies suggesting that amphibians could adjust their reproductive output to cope with climate warming. creator: Xu Gao creator: Changnan Jin creator: Arley Camargo creator: Yiming Li uri: https://doi.org/10.7717/peerj.1326 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gao et al. title: Growing coral larger and faster: micro-colony-fusion as a strategy for accelerating coral cover link: https://peerj.com/articles/1313 last-modified: 2015-10-20 description: Fusion is an important life history strategy for clonal organisms to increase access to shared resources, to compete for space, and to recover from disturbance. For reef building corals, fragmentation and colony fusion are key components of resilience to disturbance. Observations of small fragments spreading tissue and fusing over artificial substrates prompted experiments aimed at further characterizing Atlantic and Pacific corals under various conditions. Small (∼1–3 cm2) fragments from the same colony spaced regularly over ceramic tiles resulted in spreading at rapid rates (e.g., tens of square centimeters per month) followed by isogenic fusion. Using this strategy, we demonstrate growth, in terms of area encrusted and covered by living tissue, of Orbicella faveolata, Pseudodiploria clivosa, and Porites lobata as high as 63, 48, and 23 cm2 per month respectively. We found a relationship between starting and ending size of fragments, with larger fragments growing at a faster rate. Porites lobata showed significant tank effects on rates of tissue spreading indicating sensitivity to biotic and abiotic factors. The tendency of small coral fragments to encrust and fuse over a variety of surfaces can be exploited for a variety of applications such as coral cultivation, assays for coral growth, and reef restoration. creator: Zac H. Forsman creator: Christopher A. Page creator: Robert J. Toonen creator: David Vaughan uri: https://doi.org/10.7717/peerj.1313 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Forsman et al.