title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1932 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Influence of a hyperlipidic diet on the composition of the non-membrane lipid pool of red blood cells of male and female rats link: https://peerj.com/articles/1083 last-modified: 2015-07-14 description: Background and objectives. Red blood cells (RBC) are continuously exposed to oxidative agents, affecting their membrane lipid function. However, the amount of lipid in RBCs is higher than the lipids of the cell membrane, and includes triacylglycerols, which are no membrane components. We assumed that the extra lipids originated from lipoproteins attached to the cell surface, and we intended to analyse whether the size and composition of this lipid pool were affected by sex or diet.Experimental design. Adult male and female Wistar rats were fed control or cafeteria diets. Packed blood cells and plasma lipids were extracted and analysed for fatty acids by methylation and GC-MS, taking care of not extracting membrane lipids.Results. The absence of ω3-PUFA in RBC extracts (but not in plasma) suggest that the lipids extracted were essentially those in the postulated lipid surface pool and not those in cell membrane. In cells’ extracts, there was a marked depletion of PUFA (and, in general, of insaturation). Fatty acid patterns were similar for all groups studied, with limited effects of sex and no effects of diet in RBC (but not in plasma) fatty acids. Presence of trans fatty acids was small but higher in RBC lipids, and could not be justified by dietary sources.Conclusions. The presence of a small layer of lipid on the RBC surface may limit oxidative damage to the cell outer structures, and help explain its role in the transport of lipophilic compounds. However, there may be other, so far uncovered, additional functions for this lipid pool. creator: Xavier Remesar creator: Arantxa Antelo creator: Clàudia Llivina creator: Emma Albà creator: Lourdes Berdié creator: Silvia Agnelli creator: Sofía Arriarán creator: José Antonio Fernández-López creator: Marià Alemany uri: https://doi.org/10.7717/peerj.1083 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Remesar et al. title: Urinary microRNA can be concentrated, dried on membranes and stored at room temperature in vacuum bags link: https://peerj.com/articles/1082 last-modified: 2015-07-14 description: Urine accumulates traces of changes that occur in the body and can potentially serve as a better biomarker source. Urinary microRNA is a promising class of non-invasive disease biomarkers. However, long-term frozen human urine samples are not a good source for the extraction of urinary microRNA. In this paper, we demonstrate that urinary microRNA can be concentrated, dried on membranes and stored in vacuum bags at room temperature for several months. The amount of total RNA on the membranes after storage at room temperature for three months was unchanged. The levels of miR-16 and miR-21 exhibited no significant differences (P = 0.564, 0.386). This simple and economical method makes the large-scale storage of clinical samples of urinary microRNA or other nucleic acids possible. creator: Fanshuang Zhang creator: Xiaoyu Cheng creator: Yuan Yuan creator: Jianqiang Wu creator: Youhe Gao uri: https://doi.org/10.7717/peerj.1082 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Zhang et al. title: Using signals associated with safety in avoidance learning: computational model of sex differences link: https://peerj.com/articles/1081 last-modified: 2015-07-14 description: Avoidance behavior involves learning responses that prevent upcoming aversive events; these responses typically extinguish when the aversive events stop materializing. Stimuli that signal safety from aversive events can paradoxically inhibit extinction of avoidance behavior. In animals, males and females process safety signals differently. These differences help explain why women are more likely to be diagnosed with an anxiety disorder and exhibit differences in symptom presentation and course compared to men. In the current study, we extend an existing model of strain differences in avoidance behavior to simulate sex differences in rats. The model successfully replicates data showing that the omission of a signal associated with a period of safety can facilitate extinction in females, but not males, and makes novel predictions that this effect should depend on the duration of the period, the duration of the signal itself, and its occurrence within that period. Non-reinforced responses during the safe period were also found to be important in the expression of these patterns. The model also allowed us to explore underlying mechanisms for the observed sex effects, such as whether safety signals serve as occasion setters for aversive events, to determine why removing them can facilitate extinction of avoidance. The simulation results argue against this account, and instead suggest the signal may serve as a conditioned reinforcer of avoidance behavior. creator: Milen L. Radell creator: Kevin D. Beck creator: Kevin C.H. Pang creator: Catherine E. Myers uri: https://doi.org/10.7717/peerj.1081 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Allele specific expression in worker reproduction genes in the bumblebee Bombus terrestris link: https://peerj.com/articles/1079 last-modified: 2015-07-14 description: Methylation has previously been associated with allele specific expression in ants. Recently, we found methylation is important in worker reproduction in the bumblebee Bombus terrestris. Here we searched for allele specific expression in twelve genes associated with worker reproduction in bees. We found allele specific expression in Ecdysone 20 monooxygenase and IMP-L2-like. Although we were unable to confirm a genetic or epigenetic cause for this allele specific expression, the expression patterns of the two genes match those predicted for imprinted genes. creator: Harindra E. Amarasinghe creator: Bradley J. Toghill creator: Despina Nathanael creator: Eamonn B. Mallon uri: https://doi.org/10.7717/peerj.1079 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Amarasinghe et al. title: Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox link: https://peerj.com/articles/1078 last-modified: 2015-07-14 description: Aim. In recent years, connectivity studies using neuroimaging data have increased the understanding of the organization of large-scale structural and functional brain networks. However, data analysis is time consuming as rigorous procedures must be assured, from structuring data and pre-processing to modality specific data procedures. Until now, no single toolbox was able to perform such investigations on truly multimodal image data from beginning to end, including the combination of different connectivity analyses. Thus, we have developed the Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox with the goal of diminishing time waste in data processing and to allow an innovative and comprehensive approach to brain connectivity.Materials and Methods. The MIBCA toolbox is a fully automated all-in-one connectivity toolbox that offers pre-processing, connectivity and graph theoretical analyses of multimodal image data such as diffusion-weighted imaging, functional magnetic resonance imaging (fMRI) and positron emission tomography (PET). It was developed in MATLAB environment and pipelines well-known neuroimaging softwares such as Freesurfer, SPM, FSL, and Diffusion Toolkit. It further implements routines for the construction of structural, functional and effective or combined connectivity matrices, as well as, routines for the extraction and calculation of imaging and graph-theory metrics, the latter using also functions from the Brain Connectivity Toolbox. Finally, the toolbox performs group statistical analysis and enables data visualization in the form of matrices, 3D brain graphs and connectograms. In this paper the MIBCA toolbox is presented by illustrating its capabilities using multimodal image data from a group of 35 healthy subjects (19–73 years old) with volumetric T1-weighted, diffusion tensor imaging, and resting state fMRI data, and 10 subjets with 18F-Altanserin PET data also.Results. It was observed both a high inter-hemispheric symmetry and an intra-hemispheric modularity associated with structural data, whilst functional data presented lower inter-hemispheric symmetry and a high inter-hemispheric modularity. Furthermore, when testing for differences between two subgroups (<40 and >40 years old adults) we observed a significant reduction in the volume and thickness, and an increase in the mean diffusivity of most of the subcortical/cortical regions.Conclusion. While bridging the gap between the high numbers of packages and tools widely available for the neuroimaging community in one toolbox, MIBCA also offers different possibilities for combining, analysing and visualising data in novel ways, enabling a better understanding of the human brain. creator: Andre Santos Ribeiro creator: Luis Miguel Lacerda creator: Hugo Alexandre Ferreira uri: https://doi.org/10.7717/peerj.1078 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ribeiro et al. title: Retrodeformation and muscular reconstruction of ornithomimosaurian dinosaur crania link: https://peerj.com/articles/1093 last-modified: 2015-07-09 description: Ornithomimosaur dinosaurs evolved lightweight, edentulous skulls that possessed keratinous rhamphothecae. Understanding the anatomy of these taxa allows for a greater understanding of “ostrich-mimic” dinosaurs and character change during theropod dinosaur evolution. However, taphonomic processes during fossilisation often distort fossil remains. Retrodeformation offers a means by which to recover a hypothesis of the original anatomy of the specimen, and 3D scanning technologies present a way to constrain and document the retrodeformation process. Using computed tomography (CT) scan data, specimen specific retrodeformations were performed on three-dimensionally preserved but taphonomically distorted skulls of the deinocheirid Garudimimus brevipesBarsbold, 1981 and the ornithomimids Struthiomimus altusLambe, 1902 and Ornithomimus edmontonicusSternberg, 1933. This allowed for a reconstruction of the adductor musculature, which was then mapped onto the crania, from which muscle mechanical advantage and bite forces were calculated pre- and post-retrodeformation. The extent of the rhamphotheca was varied in each taxon to represent morphologies found within modern Aves. Well constrained retrodeformation allows for increased confidence in anatomical and functional analysis of fossil specimens and offers an opportunity to more fully understand the soft tissue anatomy of extinct taxa. creator: Andrew R. Cuff creator: Emily J. Rayfield uri: https://doi.org/10.7717/peerj.1093 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Cuff and Rayfield title: Two new species of fossil Leggadina (Rodentia: Muridae) from Northwestern Queensland link: https://peerj.com/articles/1088 last-modified: 2015-07-09 description: Only three species of fossil murine have been described to date in Australia even though they are often found in fossil deposits and can be highly useful in understanding environmental change over time. Until now the genus Leggadina, a group of short-tailed mice that is particularly well adapted to an arid environment, was only known from two extant species: L. forresti and L. lakedownensis. Here two new fossil species of the genus are described from sites in northwestern Queensland. Leggadina gregoriensis sp. nov. comes from the Early Pleistocene Rackham’s Roost Site in the Riversleigh World Heritage Area and Leggadina macrodonta sp. nov. is from the Plio-Pleistocene Site 5C at Floraville Station. The evolution of the genus Leggadina and the lineage’s response to palaeoecological factors is considered. Taphonomy of the two fossil deposits is examined and shows marked differences in both faunal composition of the assemblages and preservation. Description of L. gregoriensis and L. macrodonta extends the known temporal range of the Leggadina lineage by over 2 million years. creator: Ada J. Klinkhamer creator: Henk Godthelp uri: https://doi.org/10.7717/peerj.1088 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Klinkhamer and Godthelp title: Rearing the scuttle fly Megaselia scalaris (Diptera: Phoridae) on industrial compounds: implications on size and lifespan link: https://peerj.com/articles/1085 last-modified: 2015-07-09 description: Megaselia scalaris (Loew, 1866) (Diptera, phoridae) is a cosmopolitan fly species used in forensic science, and has been developed as a laboratory model species. They feed on decaying corpses as well as a wide variety of organic matter, and previous studies have even found them feeding on liquid paint or shoe polish, suggesting the possibility that they could breakdown industrial compounds. To test this possibility, we fed M. scalaris on a variety of industrially obtained materials and found that it was unable to complete its life cycle, dying at the larval stage, with the majority of compounds tested. However, when fed on modeling clay, a substrate that contains starch and inedible compounds, it was able to complete its life cycle. On this diet we observed increased larval development time, decreased pupal development time and a shortened adult life span. Additionally, pupae and adult flies were smaller than control flies. Contrary to previous reports, we find no evidence that M. scalaris is able to survive on modern formulations of liquid paint. creator: Anna Alcaine-Colet creator: Karl R. Wotton creator: Eva Jimenez-Guri uri: https://doi.org/10.7717/peerj.1085 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Alcaine-Colet et al. title: The seasonal reproduction number of dengue fever: impacts of climate on transmission link: https://peerj.com/articles/1069 last-modified: 2015-07-09 description: Background. Dengue fever is a mosquito-borne viral disease and a regular epidemic in Thailand. The peak of the dengue epidemic period is around June to August during the rainy season. It is believed that climate is an important factor for dengue transmission.Method. A mathematical model for vector–host infectious disease was used to calculate the impacts of climate to the transmission of dengue virus. In this study, the data of climate and dengue fever cases were derived from Chiang Mai during 2004–2014, Thailand. The value of seasonal reproduction number was calculated to evaluate the potential, severity and persistence of dengue infection.Results. The mosquito population was increasing exponentially from the start of the rainy season in early May and reached its the peak in late June. The simulations suggest that the greatest potential for the dengue transmission occurs when the temperature is 28.9 °C. The seasonal reproduction numbers were larger than one from late March to end of August and reaching the peak in June. The highest incidences occurred in August due to the delay of transmission humans-mosquito-humans. Increasing mean temperature by 1 °C, the number of incidences increases 28.1%. However, a very high or very low temperature reduces the number of infection.Discussion and Conclusion. The results show that the dengue infection depends on the seasonal variation of the climate. The rainfall provides places for the mosquitoes to lay eggs and develop to the adult stage. The temperature plays an important role in the life cycle and behavior of the mosquitoes. A very high or very low temperature reduces the risk of the dengue infection. creator: Sittisede Polwiang uri: https://doi.org/10.7717/peerj.1069 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Polwiang title: Relative availability of natural prey versus livestock predicts landscape suitability for cheetahs Acinonyx jubatus in Botswana link: https://peerj.com/articles/1033 last-modified: 2015-07-09 description: Prey availability and human-carnivore conflict are strong determinants that govern the spatial distribution and abundance of large carnivore species and determine the suitability of areas for their conservation. For wide-ranging large carnivores such as cheetahs (Acinonyx jubatus), additional conservation areas beyond protected area boundaries are crucial to effectively conserve them both inside and outside protected areas. Although cheetahs prefer preying on wild prey, they also cause conflict with people by predating on especially small livestock. We investigated whether the distribution of cheetahs’ preferred prey and small livestock biomass could be used to explore the potential suitability of agricultural areas in Botswana for the long-term persistence of its cheetah population. We found it gave a good point of departure for identifying priority areas for land management, the threat to connectivity between cheetah populations, and areas where the reduction and mitigation of human-cheetah conflict is critical. Our analysis showed the existence of a wide prey base for cheetahs across large parts of Botswana’s agricultural areas, which provide additional large areas with high conservation potential. Twenty percent of wild prey biomass appears to be the critical point to distinguish between high and low probable levels of human-cheetah conflict. We identified focal areas in the agricultural zones where restoring wild prey numbers in concurrence with effective human-cheetah conflict mitigation efforts are the most immediate conservation strategies needed to maintain Botswana’s still large and contiguous cheetah population. creator: Hanlie E.K. Winterbach creator: Christiaan W. Winterbach creator: Lorraine K. Boast creator: Rebecca Klein creator: Michael J. Somers uri: https://doi.org/10.7717/peerj.1033 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Winterbach et al.