title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1456 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Blasticidin-S deaminase, a new selection marker for genetic transformation of the diatom Phaeodactylum tricornutum link: https://peerj.com/articles/5884 last-modified: 2018-11-14 description: Most genetic transformation protocols for the model diatom Phaeodactylum tricornutum rely on one of two available antibiotics as selection markers: Zeocin (a formulation of phleomycin D1) or nourseothricin. This limits the number of possible consecutive genetic transformations that can be performed. In order to expand the biotechnological possibilities for P. tricornutum, we searched for additional antibiotics and corresponding resistance genes that might be suitable for use with this diatom. Among the three different antibiotics tested in this study, blasticidin-S and tunicamycin turned out to be lethal to wild-type cells at low concentrations, while voriconazole had no detectable effect on P. tricornutum. Testing the respective resistance genes, we found that the blasticidin-S deaminase gene (bsr) effectively conferred resistance against blasticidin-S to P. tricornutum. Furthermore, we could show that expression of bsr did not lead to cross-resistances against Zeocin or nourseothricin, and that genetically transformed cell lines with resistance against Zeocin or nourseothricin were not resistant against blasticidin-S. In a proof of concept, we also successfully generated double resistant (against blasticidin-S and nourseothricin) P. tricornutum cell lines by co-delivering the bsr vector with a vector conferring nourseothricin resistance to wild-type cells. creator: Jochen M. Buck creator: Carolina Río Bártulos creator: Ansgar Gruber creator: Peter G. Kroth uri: https://doi.org/10.7717/peerj.5884 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Buck et al. title: The most complete enantiornithine from North America and a phylogenetic analysis of the Avisauridae link: https://peerj.com/articles/5910 last-modified: 2018-11-13 description: The most complete known North American enantiornithine was collected in 1992 but never formally described. The so-called “Kaiparowits avisaurid” remains one of the most exceptional Late Cretaceous enantiornithine fossils. We recognize this specimen as a new taxon, Mirarce eatoni (gen. et sp. nov.), and provide a complete anatomical description. We maintain that the specimen is referable to the Avisauridae, a clade previously only known in North America from isolated tarsometatarsi. Information from this specimen helps to clarify evolutionary trends within the Enantiornithes. Its large body size supports previously observed trends toward larger body mass in the Late Cretaceous. However, trends toward increased fusion of compound elements across the clade as a whole are weak compared to the Ornithuromorpha. The new specimen reveals for the first time the presence of remige papillae in the enantiornithines, indicating this feature was evolved in parallel to dromaeosaurids and derived ornithuromorphs. Although morphology of the pygostyle and (to a lesser degree) the coracoid and manus appear to remain fairly static during the 65 million years plus of enantiornithine evolution, by the end of the Mesozoic at least some enantiornithine birds had evolved several features convergent with the Neornithes including a deeply keeled sternum, a narrow furcula with a short hypocleidium, and ulnar quill knobs—all features that indicate refinement of the flight apparatus and increased aerial abilities. We conduct the first cladistic analysis to include all purported avisuarid enantiornithines, recovering an Avisauridae consisting of a dichotomy between North and South American taxa. Based on morphological observations and supported by cladistic analysis, we demonstrate Avisaurus to be paraphyletic and erect a new genus for “A. gloriae,” Gettyia gen. nov. creator: Jessie Atterholt creator: J. Howard Hutchison creator: Jingmai K. O’Connor uri: https://doi.org/10.7717/peerj.5910 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Atterholt et al. title: Microsatellite loci development and population genetics in Neotropical fish Curimata mivartii (Characiformes: Curimatidae) link: https://peerj.com/articles/5959 last-modified: 2018-11-13 description: The Curimatidae family plays an ecological role in the recycling and distribution of nutrients and constitutes a major food source for several commercially important fishes. Curimata mivartii, a member of this family, is considered a short-distance migratory species (≤100 km), categorized by the International Union for Conservation of Nature as a near threatened species, based on its declining population densities and habitat disturbance and fragmentation. Since population genetics and species-specific molecular tools remain unknown for all members of the Curimatidae family, this study developed a set of microsatellite loci and studied the population genetics of C. mivartii in the lower section of the Colombian Magdalena-Cauca basin. The results showed high levels of genetic diversity and evidence of gene flow even between locations separated over 350 km. This information provides a baseline for designing conservation and management programs for C.mivartii and constitutes the first study of population genetics in Curimatidae. creator: Ricardo M. Landínez-García creator: Edna J. Marquez uri: https://doi.org/10.7717/peerj.5959 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Landínez-García and Marquez title: Do fish get wasted? Assessing the influence of effluents on parasitic infection of wild fish link: https://peerj.com/articles/5956 last-modified: 2018-11-13 description: Many ecosystems are influenced simultaneously by multiple stressors. One important environmental stressor is aquatic pollution via wastewater treatment plant (WWTP) effluents. WWTP effluents may contribute to eutrophication or contain anthropogenic contaminants that directly and/or indirectly influence aquatic wildlife. Both eutrophication and exposure to anthropogenic contaminants may affect the dynamics of fish-parasite systems. With this in mind, we studied the impact of WWTP effluents on infection of brown trout by the parasite Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease (PKD). PKD is associated with the long-term decline of wild brown trout (Salmo trutta) populations in Switzerland. We investigated PKD infection of brown trout at two adjacent sites (≈400 m apart) of a Swiss river. The sites are similar in terms of ecology except that one site receives WWTP effluents. We evaluated the hypothesis that fish inhabiting the effluent site will show greater susceptibility to PKD in terms of prevalence and disease outcome. We assessed susceptibility by (i) infection prevalence, (ii) parasite intensity, (iii) host health in terms of pathology, and (iv) estimated apparent survival rate. At different time points during the study, significant differences between sites concerning all measured parameters were found, thus providing evidence of the influence of effluents on parasitic infection of fish in our study system. However, from these findings we cannot determine if the effluent has a direct influence on the fish host via altering its ability to manage the parasite, or indirectly on the parasite or the invertebrate host via increasing bryozoa (the invertebrate host) reproduction. On a final note, the WWTP adhered to all national guidelines and the effluent only resulted in a minor water quality reduction assessed via standardized methods in this study. Thus, we provide evidence that even a subtle decrease in water quality, resulting in small-scale pollution can have consequences for wildlife. creator: Christyn Bailey creator: Aurélie Rubin creator: Nicole Strepparava creator: Helmut Segner creator: Jean-François Rubin creator: Thomas Wahli uri: https://doi.org/10.7717/peerj.5956 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bailey et al. title: Relationship between vertical and horizontal force-velocity-power profiles in various sports and levels of practice link: https://peerj.com/articles/5937 last-modified: 2018-11-13 description: This study aimed (i) to explore the relationship between vertical (jumping) and horizontal (sprinting) force–velocity–power (FVP) mechanical profiles in a large range of sports and levels of practice, and (ii) to provide a large database to serve as a reference of the FVP profile for all sports and levels tested. A total of 553 participants (333 men, 220 women) from 14 sport disciplines and all levels of practice participated in this study. Participants performed squat jumps (SJ) against multiple external loads (vertical) and linear 30–40 m sprints (horizontal). The vertical and horizontal FVP profile (i.e., theoretical maximal values of force (F0), velocity (v0), and power (Pmax)) as well as main performance variables (unloaded SJ height in jumping and 20-m sprint time) were measured. Correlations coefficient between the same mechanical variables obtained from the vertical and horizontal modalities ranged from −0.12 to 0.58 for F0, −0.31 to 0.71 for v0, −0.10 to 0.67 for Pmax, and −0.92 to −0.23 for the performance variables (i.e, SJ height and sprint time). Overall, results showed a decrease in the magnitude of the correlations for higher-level athletes. The low correlations generally observed between jumping and sprinting mechanical outputs suggest that both tasks provide distinctive information regarding the FVP profile of lower-body muscles. Therefore, we recommend the assessment of the FVP profile both in jumping and sprinting to gain a deeper insight into the maximal mechanical capacities of lower-body muscles, especially at high and elite levels. creator: Pedro Jiménez-Reyes creator: Pierre Samozino creator: Amador García-Ramos creator: Víctor Cuadrado-Peñafiel creator: Matt Brughelli creator: Jean-Benoît Morin uri: https://doi.org/10.7717/peerj.5937 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Jiménez-Reyes et al. title: A general pattern of the species abundance distribution link: https://peerj.com/articles/5928 last-modified: 2018-11-13 description: Since the 1970s, species abundance distributions (SADs) have been one of the most fundamental issues in ecology and have frequently been investigated and reviewed. However, there was surprisingly little consensus. This study focuses on three essential questions. (1) Is there a general pattern of SAD that no community can violate it? (2) If it exists, what does it look like? (3) Why is it like this? The frequency distributions of 19,833 SADs from eight datasets (including eleven taxonomic groups from terrestrial, aquatic, and marine ecosystems) suggest that a general pattern of SAD might exist. According to two hypotheses (the finiteness of the total energy and the causality from the entropy to the diversity), this study assumes that the general pattern of SAD is approximately consistent with Zipf’s law, which means that Zipf’s law might be more easily to observe when one investigates any SAD. In the future, this conjecture not only needs to be tested (or supported) by more and more datasets, but also depends on how well it is explained from different angles of theories. creator: Qiang Su uri: https://doi.org/10.7717/peerj.5928 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Su title: Family-based whole-exome sequencing identifies novel loss-of-function mutations of FBN1 for Marfan syndrome link: https://peerj.com/articles/5927 last-modified: 2018-11-13 description: BackgroundMarfan syndrome (MFS) is an inherited connective tissue disorder affecting the ocular, skeletal and cardiovascular systems. Previous studies of MFS have demonstrated the association between genetic defects and clinical manifestations. Our purpose was to investigate the role of novel genetic variants in determining MFS clinical phenotypes.MethodsWe sequenced the whole exome of 19 individuals derived from three Han Chinese families. The sequencing data were analyzed by a standard pipeline. Variants were further filtered against the public database and an in-house database. Then, we performed pedigree analysis under different inheritance patterns according to American College of Medical Genetics guidelines. Results were confirmed by Sanger sequencing.ResultsTwo novel loss-of-function indels (c.5027_5028insTGTCCTCC, p.D1677Vfs*8; c.5856delG, p.S1953Lfs*27) and one nonsense variant (c.8034C>A, p.Y2678*) of FBN1 were identified in Family 1, Family 2 and Family 3, respectively. All affected members carried pathogenic mutations, whereas other unaffected family members or control individuals did not. These different kinds of loss of function (LOF) variants of FBN1 were located in the cbEGF region and a conserved domain across species and were not reported previously.ConclusionsOur study extended and strengthened the vital role of FBN1 LOF mutations in the pathogenesis of MFS with an autosomal dominant inheritance pattern. We confirm that genetic testing by next-generation sequencing of blood DNA can be fundamental in helping clinicians conduct mutation-based pre- and postnatal screening, genetic diagnosis and clinical management for MFS. creator: Zhening Pu creator: Haoliang Sun creator: Junjie Du creator: Yue Cheng creator: Keshuai He creator: Buqing Ni creator: Weidong Gu creator: Juncheng Dai creator: Yongfeng Shao uri: https://doi.org/10.7717/peerj.5927 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Pu et al. title: MTBseq: a comprehensive pipeline for whole genome sequence analysis of Mycobacterium tuberculosis complex isolates link: https://peerj.com/articles/5895 last-modified: 2018-11-13 description: Analyzing whole-genome sequencing data of Mycobacterium tuberculosis complex (MTBC) isolates in a standardized workflow enables both comprehensive antibiotic resistance profiling and outbreak surveillance with highest resolution up to the identification of recent transmission chains. Here, we present MTBseq, a bioinformatics pipeline for next-generation genome sequence data analysis of MTBC isolates. Employing a reference mapping based workflow, MTBseq reports detected variant positions annotated with known association to antibiotic resistance and performs a lineage classification based on phylogenetic single nucleotide polymorphisms (SNPs). When comparing multiple datasets, MTBseq provides a joint list of variants and a FASTA alignment of SNP positions for use in phylogenomic analysis, and identifies groups of related isolates. The pipeline is customizable, expandable and can be used on a desktop computer or laptop without any internet connection, ensuring mobile usage and data security. MTBseq and accompanying documentation is available from https://github.com/ngs-fzb/MTBseq_source. creator: Thomas Andreas Kohl creator: Christian Utpatel creator: Viola Schleusener creator: Maria Rosaria De Filippo creator: Patrick Beckert creator: Daniela Maria Cirillo creator: Stefan Niemann uri: https://doi.org/10.7717/peerj.5895 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kohl et al. title: Optimizing the trainable B-COSFIRE filter for retinal blood vessel segmentation link: https://peerj.com/articles/5855 last-modified: 2018-11-13 description: Segmentation of the retinal blood vessels using filtering techniques is a widely used step in the development of an automated system for diagnostic retinal image analysis. This paper optimized the blood vessel segmentation, by extending the trainable B-COSFIRE filter via identification of more optimal parameters. The filter parameters are introduced using an optimization procedure to three public datasets (STARE, DRIVE, and CHASE-DB1). The suggested approach considers analyzing thresholding parameters selection followed by application of background artifacts removal techniques. The approach results are better than the other state of the art methods used for vessel segmentation. ANOVA analysis technique is also used to identify the most significant parameters that are impacting the performance results (p-value ¡ 0.05). The proposed enhancement has improved the vessel segmentation accuracy in DRIVE, STARE and CHASE-DB1 to 95.47, 95.30 and 95.30, respectively. creator: Sufian A. Badawi creator: Muhammad Moazam Fraz uri: https://doi.org/10.7717/peerj.5855 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Badawi and Fraz title: The relationship between social rank and spatial learning in pheasants, Phasianus colchicus: cause or consequence? link: https://peerj.com/articles/5738 last-modified: 2018-11-13 description: Individual differences in performances on cognitive tasks have been found to differ according to social rank across multiple species. However, it is not clear whether an individual’s cognitive performance is flexible and the result of their current social rank, modulated by social interactions (social state dependent hypothesis), or if it is determined prior to the formation of the social hierarchy and indeed influences an individual’s rank (prior attributes hypothesis). We separated these two hypotheses by measuring learning performance of male pheasants, Phasianus colchicus, on a spatial discrimination task as chicks and again as adults. We inferred adult male social rank from observing agonistic interactions while housed in captive multi-male multi-female groups. Learning performance of adult males was assayed after social rank had been standardised; by housing single males with two or four females. We predicted that if cognitive abilities determine social rank formation we would observe: consistency between chick and adult performances on the cognitive task and chick performance would predict adult social rank. We found that learning performances were consistent from chicks to adults for task accuracy, but not for speed of learning and chick learning performances were not related to adult social rank. Therefore, we could not support the prior attributes hypothesis of cognitive abilities aiding social rank formation. Instead, we found that individual differences in learning performances of adults were predicted by the number of females a male was housed with; males housed with four females had higher levels of learning performance than males housed with two females; and their most recent recording of captive social rank, even though learning performance was assayed while males were in a standardized, non-competitive environment. This does not support the hypothesis that direct social pressures are causing the inter-individual variation in learning performances that we observe. Instead, our results suggest that there may be carry-over effects of aggressive social interactions on learning performance. Consequently, whether early life spatial learning performances influence social rank is unclear but these performances are modulated by the current social environment and a male’s most recent social rank. creator: Ellis J.G. Langley creator: Jayden O. van Horik creator: Mark A. Whiteside creator: Christine E. Beardsworth creator: Joah R. Madden uri: https://doi.org/10.7717/peerj.5738 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Langley et al.