title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1743 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Bax-inhibitor-1 knockdown phenotypes are suppressed by Buffy and exacerbate degeneration in a Drosophila model of Parkinson disease link: https://peerj.com/articles/2974 last-modified: 2017-02-21 description: BackgroundBax inhibitor-1 (BI-1) is an evolutionarily conserved cytoprotective transmembrane protein that acts as a suppressor of Bax-induced apoptosis by regulation of endoplasmic reticulum stress-induced cell death. We knocked down BI-1 in the sensitive dopa decarboxylase (Ddc) expressing neurons of Drosophila melanogaster to investigate its neuroprotective functions. We additionally sought to rescue the BI-1-induced phenotypes by co-expression with the pro-survival Buffy and determined the effect of BI-1 knockdown on the neurodegenerative α-synuclein-induced Parkinson disease (PD) model.MethodsWe used organismal assays to assess longevity of the flies to determine the effect of the altered expression of BI-1 in the Ddc-Gal4-expressing neurons by employing two RNAi transgenic fly lines. We measured the locomotor ability of these RNAi lines by computing the climbing indices of the climbing ability and compared them to a control line that expresses the lacZ transgene. Finally, we performed biometric analysis of the developing eye, where we counted the number of ommatidia and calculated the area of ommatidial disruption.ResultsThe knockdown of BI-1 in these neurons was achieved under the direction of the Ddc-Gal4 transgene and resulted in shortened lifespan and precocious loss of locomotor ability. The co-expression of Buffy, the Drosophila anti-apoptotic Bcl-2 homologue, with BI-1-RNAi resulted in suppression of the reduced lifespan and impaired climbing ability. Expression of human α-synuclein in Drosophila dopaminergic neurons results in neuronal degeneration, accompanied by the age-dependent loss in climbing ability. We exploited this neurotoxic system to investigate possible BI-1 neuroprotective function. The co-expression of α-synuclein with BI-1-RNAi results in a slight decrease in lifespan coupled with an impairment in climbing ability. In supportive experiments, we employed the neuron-rich Drosophila compound eye to investigate subtle phenotypes that result from altered gene expression. The knockdown of BI-1 in the Drosophila developing eye under the direction of the GMR-Gal4 transgene results in reduced ommatidia number and increased disruption of the ommatidial array. Similarly, the co-expression of BI-1-RNAi with Buffy results in the suppression of the eye phenotypes. The expression of α-synuclein along with the knockdown of BI-1 resulted in reduction of ommatidia number and more disruption of the ommatidial array.ConclusionKnockdown of BI-1 in the dopaminergic neurons of Drosophila results in a shortened lifespan and premature loss in climbing ability, phenotypes that appear to be strongly associated with models of PD in Drosophila, and which are suppressed upon overexpression of Buffy and worsened by co-expression with α-synuclein. This suggests that BI-1 is neuroprotective and its knockdown can be counteracted by the overexpression of the pro-survival Bcl-2 homologue. creator: P. Githure M’Angale creator: Brian E. Staveley uri: https://doi.org/10.7717/peerj.2974 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 M’Angale & Staveley title: Intersexual differences of heat shock response between two amphipods (Eulimnogammarus verrucosus and Eulimnogammarus cyaneus) in Lake Baikal link: https://peerj.com/articles/2864 last-modified: 2017-02-21 description: Acute temperature fluctuations are common in surface waters, and aquatic organisms may manifest physiological responses to punctuated temperature spikes long before behavioral responses. Ectotherms, especially cryophilic stenotherms such as those endemic to Lake Baikal (Siberia), may demonstrate specialized physiological responses to acute temperature increases because their proteomes have evolved to function most efficiently at lower temperatures (e.g., <10 °C). Therefore, our study questioned the nature and degree of variation in physiological response to acute thermal stress in two congenerous, endemic Baikal amphipod species, Eulimnogammarus verrucosus and Eulimnogammarus cyaneus. We hypothesized that because interspecific and intersexual thermosensitivity varies significantly among ectotherms, there would be divergent intersexual and interspecific strategies to withstand acute thermal stress, manifested in different protein compositions and concentrations. We exposed individuals to the species’ respective LT50 for one hour followed by a three-hour recovery period. We then performed 1D-PAGE, Western blotting, 2D-PAGE, and Mass Spectrometry techniques and assessed relative intersexual and interspecific changes in proteomic composition and heat shock protein 70 level. Our results demonstrate that females tend to be more sensitive to an acute thermal stimulus than males, most likely because females allocate significant energy to reproduction and less to heat shock response, evidenced by females’ significantly lower LT50time. Lower level of Hsp70 was found in females of the thermosensitive E. verrucosus compared to males of this species. No intersexual differences were found in Hsp70 level in thermotolerant E. cyaneus. Higher levels of hemocyanin subunits and arginine kinase were found in E. cyaneus females after heat shock and recovery compared to males, which was not found for E. verrucosus, suggesting interspecific mechanisms for E. cyaneus’s higher thermotolerance. These differing responses between species and sexes of Baikal amphipods may reflect more general strategies for maintaining homeostatic conditions during acute thermal stress. As mean surface water temperatures increase worldwide, the net efficiency and efficacy of these strategies could give rise to long term changes in physiology, behavior, and interactions with other species, potentially precipitating population and community level alterations. creator: Daria Bedulina creator: Michael F. Meyer creator: Anton Gurkov creator: Ekaterina Kondratjeva creator: Boris Baduev creator: Roman Gusdorf creator: Maxim A. Timofeyev uri: https://doi.org/10.7717/peerj.2864 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bedulina et al. title: Species coexistence and the superior ability of an invasive species to exploit a facilitation cascade habitat link: https://peerj.com/articles/2848 last-modified: 2017-02-21 description: Facilitation cascades generated by co-occurring foundation species can enhance the abundance and diversity of associated organisms. However, it remains poorly understood how differences among native and invasive species in their ability to exploit these positive interactions contribute to emergent patterns of community structure and biotic acceptance. On intertidal shorelines in New England, we examined the patterns of coexistence between the native mud crabs and the invasive Asian shore crab in and out of a facilitation cascade habitat generated by mid intertidal cordgrass and ribbed mussels. These crab species co-occurred in low intertidal cobbles adjacent to the cordgrass–mussel beds, despite experimental findings that the dominant mud crabs can kill and displace Asian shore crabs and thereby limit their successful recruitment to their shared habitat. A difference between the native and invasive species in their utilization of the facilitation cascade likely contributes to this pattern. Only the Asian shore crabs inhabit the cordgrass–mussel beds, despite experimental evidence that both species can similarly benefit from stress amelioration in the beds. Moreover, only Asian shore crabs settle in the beds, which function as a nursery habitat free of lethal mud crabs, and where their recruitment rates are particularly high (nearly an order of magnitude higher than outside beds). Persistence of invasive adult Asian shore crabs among the dominant native mud crabs in the low cobble zone is likely enhanced by a spillover effect of the facilitation cascade in which recruitment-limited Asian shore crabs settle in the mid intertidal cordgrass–mussel beds and subsidize their vulnerable populations in the adjacent low cobble zone. This would explain why the abundances of Asian shore crabs in cobbles are doubled when adjacent to facilitation cascade habitats. The propensity for this exotic species to utilize habitats created by facilitation cascades, despite the lack of a shared evolutionary history, contributes to species coexistence and the acceptance of invasives into a diverse community. creator: Andrew H. Altieri creator: Andrew D. Irving uri: https://doi.org/10.7717/peerj.2848 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Altieri and Irving title: Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies link: https://peerj.com/articles/2988 last-modified: 2017-02-16 description: BackgroundDe novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved.ResultsWe built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts.ConclusionTranscriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap. creator: Cédric Cabau creator: Frédéric Escudié creator: Anis Djari creator: Yann Guiguen creator: Julien Bobe creator: Christophe Klopp uri: https://doi.org/10.7717/peerj.2988 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cabau et al. title: Variant profiling of evolving prokaryotic populations link: https://peerj.com/articles/2997 last-modified: 2017-02-16 description: Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver, which is accessible at http://galaxy.csb.univie.ac.at. creator: Markus Zojer creator: Lisa N. Schuster creator: Frederik Schulz creator: Alexander Pfundner creator: Matthias Horn creator: Thomas Rattei uri: https://doi.org/10.7717/peerj.2997 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zojer et al. title: Understanding morphological variability in a taxonomic context in Chilean diplomystids (Teleostei: Siluriformes), including the description of a new species link: https://peerj.com/articles/2991 last-modified: 2017-02-16 description: Following study of the external morphology and its unmatched variability throughout ontogeny and a re-examination of selected morphological characters based on many specimens of diplomystids from Central and South Chile, we revised and emended previous specific diagnoses and consider Diplomystes chilensis, D. nahuelbutaensis, D. camposensis, and Olivaichthys viedmensis (Baker River) to be valid species. Another group, previously identified as Diplomystes sp., D. spec., D. aff. chilensis, and D. cf. chilensis inhabiting rivers between Rapel and Itata Basins is given a new specific name (Diplomystes incognitus) and is diagnosed. An identification key to the Chilean species, including the new species, is presented. All specific diagnoses are based on external morphological characters, such as aspects of the skin, neuromast lines, and main lateral line, and position of the anus and urogenital pore, as well as certain osteological characters to facilitate the identification of these species that previously was based on many internal characters. Diplomystids below 150 mm standard length (SL) share a similar external morphology and body proportions that make identification difficult; however, specimens over 150 mm SL can be diagnosed by the position of the urogenital pore and anus, and a combination of external and internal morphological characters. According to current knowledge, diplomystid species have an allopatric distribution with each species apparently endemic to particular basins in continental Chile and one species (O. viedmensis) known only from one river in the Chilean Patagonia, but distributed extensively in southern Argentina. creator: Gloria Arratia creator: Claudio Quezada-Romegialli uri: https://doi.org/10.7717/peerj.2991 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Arratia and Quezada-Romegialli title: High richness of insect herbivory from the early Miocene Hindon Maar crater, Otago, New Zealand link: https://peerj.com/articles/2985 last-modified: 2017-02-16 description: Plants and insects are key components of terrestrial ecosystems and insect herbivory is the most important type of interaction in these ecosystems. This study presents the first analysis of associations between plants and insects for the early Miocene Hindon Maar fossil lagerstätte, Otago, New Zealand. A total of 584 fossil angiosperm leaves representing 24 morphotypes were examined to determine the presence or absence of insect damage types. Of these leaves, 73% show signs of insect damage; they comprise 821 occurrences of damage from 87 damage types representing all eight functional feeding groups. In comparison to other fossil localities, the Hindon leaves display a high abundance of insect damage and a high diversity of damage types. Leaves of Nothofagus(southern beech), the dominant angiosperm in the fossil assemblage, exhibit a similar leaf damage pattern to leaves from the nearby mid to late Miocene Dunedin Volcano Group sites but display a more diverse spectrum and much higher percentage of herbivory damage than a comparable dataset of leaves from Palaeocene and Eocene sites in the Antarctic Peninsula. creator: Anna Lena Möller creator: Uwe Kaulfuss creator: Daphne E. Lee creator: Torsten Wappler uri: https://doi.org/10.7717/peerj.2985 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Möller et al. title: Exoskeletons of Bougainvilliidae and other Hydroidolina (Cnidaria, Hydrozoa): structure and composition link: https://peerj.com/articles/2964 last-modified: 2017-02-16 description: The exoskeleton is an important source of characters for the taxonomy of Hydroidolina. It originates as epidermal secretions and, among other functions, protects the coenosarc of the polypoid stage. However, comparative studies on the exoskeletal tissue origin, development, chemical, and structural characteristics, as well as its evolution and homology, are few and fragmented. This study compares the structure and composition of the exoskeleton and underlying coenosarc in members of “Anthoathecata” and some Leptothecata, but does so mainly in bougainvilliid polyps histological analyses. We also studied the development of the exoskeleton under experimental conditions. We identified three types of glandular epidermal cells related to the origin of the exoskeleton and the secretion of its polysaccharides component. The exoskeleton of the species studied is either bilayered (perisarc and exosarc, especially in bougainvilliids) or corneous (perisarc). The exoskeleton varies in chemical composition, structural rigidity, thickness, extension, and coverage in the different regions of the colony. In bilayered exoskeletons, the exosarc is produced first and appears to be a key step in the formation of the rigid exoskeleton. The exoskeleton contains anchoring structures such as desmocytes and “perisarc extensions.” creator: María A. Mendoza-Becerril creator: José Eduardo A.R. Marian creator: Alvaro Esteves Migotto creator: Antonio Carlos Marques uri: https://doi.org/10.7717/peerj.2964 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Mendoza-Becerril et al. title: Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor link: https://peerj.com/articles/3004 last-modified: 2017-02-15 description: Management of the few regulated ornamental fisheries relies on inadequate information about the life history of the target species. Herein, we investigated the reproductive biology of the most heavily traded marine invertebrate in the western Atlantic; the blue-legged hermit crab Clibanarius tricolor. We report on density, individual-level, and population-level reproductive parameters in 14 populations spanning the Florida Keys. In C. tricolor, abundance, population-level, and individual-level reproductive parameters exhibited substantial small-scale spatial variation in the Florida Keys. For instance, the proportion of brooding females varied between 10–94% across localities. In females, average (±SD) fecundity varied between 184 (±54) and 614 (±301) embryos crab-1 across populations. Fecundity usually increases with female body size in hermit crabs. However, we found no effect of female body size on fecundity in three of the populations. Altogether, our observations suggest that C. tricolor may fit a source-sink metapopulation dynamic in the Florida Keys with low reproductive intensity and absence of a parental body size—fecundity relationship resulting in net reproductive loses at some localities. We argue in favor of additional studies describing population dynamics and other aspects of the natural history of C. tricolor (e.g., development type, larval duration) to reveal ‘source’ populations, capable of exporting larvae to nearby populations. Our observations imply that future studies aimed at assessing standing stocks or describing other aspects of the life history of this hermit crab need to focus on multiple localities simultaneously. This and future studies on the reproductive biology of this species will form the baseline for models aimed at assessing the stock condition and sustainability of this heavily harvested crustacean. creator: J. Antonio Baeza creator: Donald C. Behringer uri: https://doi.org/10.7717/peerj.3004 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Baeza and Behringer title: Risk analysis of colorectal cancer incidence by gene expression analysis link: https://peerj.com/articles/3003 last-modified: 2017-02-15 description: BackgroundColorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular characterization and treatment prediction.ObjectiveMicroarray gene expression data from the online Gene Expression Omnibus (GEO) database were used to to distinguish colorectal cancer from normal colon tissue samples.MethodsWe collected microarray data from the GEO database to establish colorectal cancer microarray gene expression datasets for a combined analysis. Using the Prediction Analysis for Microarrays (PAM) method and the GSEA MSigDB resource, we analyzed the 14,698 genes that were identified through an examination of their expression values between normal and tumor tissues.ResultsTen genes (ABCG2, AQP8, SPIB, CA7, CLDN8, SCNN1B, SLC30A10, CD177, PADI2, and TGFBI) were found to be good indicators of the candidate genes that correlate with CRC. From these selected genes, an average of six significant genes were obtained using the PAM method, with an accuracy rate of 95%. The results demonstrate the potential of utilizing a model with the PAM method for data mining. After a detailed review of the published reports, the results confirmed that the screened candidate genes are good indicators for cancer risk analysis using the PAM method.ConclusionsSix genes were selected with 95% accuracy to effectively classify normal and colorectal cancer tissues. We hope that these results will provide the basis for new research projects in clinical practice that aim to rapidly assess colorectal cancer risk using microarray gene expression analysis. creator: Wei-Chuan Shangkuan creator: Hung-Che Lin creator: Yu-Tien Chang creator: Chen-En Jian creator: Hueng-Chuen Fan creator: Kang-Hua Chen creator: Ya-Fang Liu creator: Huan-Ming Hsu creator: Hsiu-Ling Chou creator: Chung-Tay Yao creator: Chi-Ming Chu creator: Sui-Lung Su creator: Chi-Wen Chang uri: https://doi.org/10.7717/peerj.3003 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shangkuan et al.