title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&month=2013-07
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Genome-wide analysis of 3′-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes
link: https://peerj.com/articles/118
last-modified: 2013-07-30
description: In eukaryotic cells, a group of messenger ribonucleic acids (mRNAs) encoding functionally interrelated proteins together with the trans-acting factors that coordinately modulate their expression is termed a post-transcriptional regulon, due to their partial analogy to a prokaryotic polycistron. This mRNA clustering is organized by sequence-specific RNA-binding proteins (RBPs) that bind cis-regulatory elements in the noncoding regions of genes, and mediates the synchronized control of their fate. These recognition motifs are often characterized by conserved sequences and/or RNA structures, and it is likely that various classes of cis-elements remain undiscovered. Current evidence suggests that RNA regulons govern gene expression in trypanosomes, unicellular parasites which mainly use post-transcriptional mechanisms to control protein synthesis. In this study, we used motif discovery tools to test whether groups of functionally related trypanosomatid genes contain a common cis-regulatory element. We obtained conserved structured RNA motifs statistically enriched in the noncoding region of 38 out of 53 groups of metabolically related transcripts in comparison with a random control. These motifs have a hairpin loop structure, a preferred sense orientation and are located in close proximity to the open reading frames. We found that 15 out of these 38 groups represent unique motifs in which most 3′-UTR signature elements were group-specific. Two extensively studied Trypanosoma cruzi RBPs, TcUBP1 and TcRBP3 were found associated with a few candidate RNA regulons. Interestingly, 13 motifs showed a strong correlation with clusters of developmentally co-expressed genes and six RNA elements were enriched in gene clusters affected after hyperosmotic stress. Here we report a systematic genome-wide in silico screen to search for novel RNA-binding sites in transcripts, and describe an organized network of several coordinately regulated cohorts of mRNAs in T. cruzi. Moreover, we found that structured RNA elements are also conserved in other human pathogens. These results support a model of regulation of gene expression by multiple post-transcriptional regulons in trypanosomes.
creator: Javier G. De Gaudenzi
creator: Santiago J. Carmona
creator: Fernán Agüero
creator: Alberto C. Frasch
uri: https://doi.org/10.7717/peerj.118
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 De Gaudenzi et al.

title: Effect of non-crop vegetation types on conservation biological control of pests in olive groves
link: https://peerj.com/articles/116
last-modified: 2013-07-25
description: Conservation biological control (CBC) is an environmentally sound potential alternative to the use of chemical insecticides. It involves modifications of the environment to promote natural enemy activity on pests. Despite many CBC studies increasing abundance of natural enemies, there are far fewer demonstrations of reduced pest density and very little work has been conducted in olive crops. In this study we investigated the effects of four forms of non-crop vegetation on the abundance of two important pests: the olive psyllid (Euphyllura olivina) and the olive moth (Prays oleae). Areas of herbaceous vegetation and areas of woody vegetation near olive crops, and smaller patches of woody vegetation within olive groves, decreased pest abundance in the crop. Inter-row ground covers that are known to increase the abundance of some predators and parasitoids had no effect on the pests, possibly as a result of lack of synchrony between pests and natural enemies, lack of specificity or intra-guild predation. This study identifies examples of the right types of diversity for use in conservation biological control in olive production systems.
creator: Daniel Paredes
creator: Luis Cayuela
creator: Geoff M. Gurr
creator: Mercedes Campos
uri: https://doi.org/10.7717/peerj.116
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Paredes et al.

title: Comparative transcriptomics in three Methylophilaceae species uncover different strategies for environmental adaptation
link: https://peerj.com/articles/115
last-modified: 2013-07-25
description: We carried out whole transcriptome analysis of three species of Methylophilaceae, Methylotenera mobilis, Methylotenera versatilis and Methylovorus glucosotrophus, in order to determine which metabolic pathways are actively transcribed in cultures grown in laboratory on C1 substrates and how metabolism changes under semi-in situ conditions. Comparative analyses of the transcriptomes were used to probe the metabolic strategies utilized by each of the organisms in the environment. Our analysis of transcript abundance data focused on changes in expression of methylotrophy metabolic modules, as well as on identifying any functional modules with pronounced response to in situ conditions compared to a limited set of laboratory conditions, highlighting their potential role in environmental adaptation. We demonstrate that transcriptional responses to environmental conditions involved both methylotrophy and non-methylotrophy metabolic modules as well as modules responsible for functions not directly connected to central metabolism. Our results further highlight the importance of XoxF enzymes that were previously demonstrated to be highly expressed in situ and proposed to be involved in metabolism of methanol by Methylophilaceae. At the same time, it appears that different species employ different homologous Xox systems as major metabolic modules. This study also reinforces prior observations of the apparent importance of the methylcitric acid cycle in the Methylotenera species and its role in environmental adaptation. High transcription from the respective gene clusters and pronounced response to in situ conditions, along with the reverse expression pattern for the ribulose monophosphate pathway that is the major pathway for carbon assimilation in laboratory conditions suggest that a switch in central metabolism of Methylotenera takes place in response to in situ conditions. The nature of the metabolite(s) processed via this pathway still remains unknown. Of the functions not related to central metabolism, flagellum and fimbria synthesis functions appeared to be of significance for environmental adaptation, based on their high abundance and differential expression. Our data demonstrate that, besides shared strategies, the organisms employed in this study also utilize strategies unique to each species, suggesting that the genomic divergence plays a role in environmental adaptation.
creator: Alexey Vorobev
creator: David A.C. Beck
creator: Marina G. Kalyuzhnaya
creator: Mary E. Lidstrom
creator: Ludmila Chistoserdova
uri: https://doi.org/10.7717/peerj.115
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Vorobev et al.

title: Perineuronal satellite neuroglia in the telencephalon of New Caledonian crows and other Passeriformes: evidence of satellite glial cells in the central nervous system of healthy birds?
link: https://peerj.com/articles/110
last-modified: 2013-07-25
description: Glia have been implicated in a variety of functions in the central nervous system, including the control of the neuronal extracellular space, synaptic plasticity and transmission, development and adult neurogenesis. Perineuronal glia forming groups around neurons are associated with both normal and pathological nervous tissue. Recent studies have linked reduction in the number of perineuronal oligodendrocytes in the prefrontal cortex with human schizophrenia and other psychiatric disorders. Therefore, perineuronal glia may play a decisive role in homeostasis and normal activity of the human nervous system.Here we report on the discovery of novel cell clusters in the telencephala of five healthy Passeriforme, one Psittaciform and one Charadriiforme bird species, which we refer to as Perineuronal Glial Clusters (PGCs). The aim of this study is to describe the structure and distribution of the PGCs in a number of avian species.PGCs were identified with the use of standard histological procedures. Heterochromatin masses visible inside the nuclei of these satellite glia suggest that they may correspond to oligodendrocytes. PGCs were found in the brains of nine New Caledonian crows, two Japanese jungle crows, two Australian magpies, two Indian mynah, three zebra finches (all Passeriformes), one Southern lapwing (Charadriiformes) and one monk parakeet (Psittaciformes). Microscopic survey of the brain tissue suggests that the largest PGCs are located in the hyperpallium densocellulare and mesopallium. No clusters were found in brain sections from one Gruiform (purple swamphen), one Strigiform (barn owl), one Trochiliform (green-backed firecrown), one Falconiform (chimango caracara), one Columbiform (pigeon) and one Galliform (chick).Our observations suggest that PGCs in Aves are brain region- and taxon-specific and that the presence of perineuronal glia in healthy human brains and the similar PGCs in avian gray matter is the result of convergent evolution. The discovery of PGCs in the zebra finch is of great importance because this species has the potential to become a robust animal model in which to study the function of neuron-glia interactions in healthy and diseased adult brains.
creator: Felipe S. Medina
creator: Gavin R. Hunt
creator: Russell D. Gray
creator: J. Martin Wild
creator: M. Fabiana Kubke
uri: https://doi.org/10.7717/peerj.110
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Medina et al.

title: Warming increases the top-down effects and metabolism of a subtidal herbivore
link: https://peerj.com/articles/109
last-modified: 2013-07-25
description: Ecological theory and experiments indicate that warming can increase the relative strength of top-down effects via alterations to metabolic rates in several different systems, thereby resulting in decreased plant biomass at higher temperatures. However, the general influence of increased environmental temperature on top-down effects is not well understood in systems where organisms experience relatively large variation in temperature. Rapid ocean temperature changes are pervasive throughout the Galápagos Islands due to upwelling and downwelling of internal waves, ENSO events and seasonality. We measured the effect of large, but not uncommon, water temperature variation on the metabolism and grazing rate of a common subtidal herbivore and on photosynthesis of their algal prey in the Galápagos Islands in July 2012. We found that green urchin consumption and metabolism were greater at the higher temperature treatment (28°C), resulting in significantly less algal biomass. Our result that warming increased green urchin metabolic rates, even in a highly dynamic system, provides further support for a mechanistic link between environmental temperature and feeding rates. And further, our findings suggest individual response to temperature results in changes in top-down effects. And if this response is maintained over longer-time scales of days to weeks, this could translate to alterations of larger-scale ecological patterns, such as primary producer community composition and structure.
creator: Lindsey A. Carr
creator: John F. Bruno
uri: https://doi.org/10.7717/peerj.109
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Carr and Bruno

title: Improving transcriptome assembly through error correction of high-throughput sequence reads
link: https://peerj.com/articles/113
last-modified: 2013-07-23
description: The study of functional genomics, particularly in non-model organisms, has been dramatically improved over the last few years by the use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure, the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on and, while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated and empiric dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, and should be applied to all datasets. A complete collection of commands which will allow for the production of Reptile corrected reads is available at https://github.com/macmanes/error_correction/tree/master/scripts and as File S1.
creator: Matthew D. MacManes
creator: Michael B. Eisen
uri: https://doi.org/10.7717/peerj.113
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 MacManes and Eisen

title: Stability of referential signalling across time and locations: testing alarm calls of Australian magpies (Gymnorhina tibicen) in urban and rural Australia and in Fiji
link: https://peerj.com/articles/112
last-modified: 2013-07-23
description: In many avian species, vocal repertoire expands and changes throughout life as new syllables are added and sounds adapted to neighbours and circumstances. Referential signals, on the other hand, demand stability and lack of variation so that their meaning can be understood by conspecifics at all times. It is not known how stable such signals may be when the context is changed entirely but the point of reference remains unchanged. We investigated these questions in a rare case of forced translocation of an avian species, the Australian magpie (Gymnorhina tibicen), from Australia to the remote Fijian island of Taveuni decades ago. By using playbacks of vocalisations to 45 magpie groups in Australia, we first established that magpies use functionally referential signals in their alarm call repertoire signalling aerial danger (measured as looking up in response to a specific alarm call even though the speakers were on the ground). With these results in hand, we then used the same playbacks to magpie groups on the island of Taveuni. Our results showed that the meaning of one specific call (eagle alarm call) is stable and maintained even in populations that have been isolated from Australian conspecifics over many (at least 10) generations. To our knowledge, this is the first time such a stability of a referential signal has been shown in the natural habitat.
creator: Gisela Kaplan
creator: Lesley J. Rogers
uri: https://doi.org/10.7717/peerj.112
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Kaplan et al.

title: A computational method for the systematic screening of reaction barriers in enzymes: searching for Bacillus circulans xylanase mutants with greater activity towards a synthetic substrate
link: https://peerj.com/articles/111
last-modified: 2013-07-23
description: We present a semi-empirical (PM6-based) computational method for systematically estimating the effect of all possible single mutants, within a certain radius of the active site, on the barrier height of an enzymatic reaction. The intent of this method is not a quantitative prediction of the barrier heights, but rather to identify promising mutants for further computational or experimental study. The method is applied to identify promising single and double mutants of Bacillus circulans xylanase (BCX) with increased hydrolytic activity for the artificial substrate ortho-nitrophenyl β-xylobioside (ONPX2). The estimated reaction barrier for wild-type (WT) BCX is 18.5 kcal/mol, which is in good agreement with the experimental activation free energy value of 17.0 kcal/mol extracted from the observed kcat using transition state theory (Joshi et al., 2001). The PM6 reaction profiles for eight single point mutations are recomputed using FMO-MP2/PCM/6-31G(d) single points. PM6 predicts an increase in barrier height for all eight mutants while FMO predicts an increase for six of the eight mutants. Both methods predict that the largest change in barrier occurs for N35F, where PM6 and FMO predict a 9.0 and 15.8 kcal/mol increase, respectively. We thus conclude that PM6 is sufficiently accurate to identify promising mutants for further study. We prepared a set of all theoretically possible (342) single mutants in which every amino acid of the active site (except for the catalytically active residues E78 and E172) was mutated to every other amino acid. Based on results from the single mutants we construct a set of 111 double mutants consisting of all possible pairs of single mutants with the lowest barrier for a particular position and compute their reaction profile. None of the mutants have, to our knowledge, been prepared experimentally and therefore present experimentally testable predictions.
creator: Martin R. Hediger
creator: Casper Steinmann
creator: Luca De Vico
creator: Jan H. Jensen
uri: https://doi.org/10.7717/peerj.111
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Hediger et al.

title: GNAQ and BRAF mutations show differential activation of the mTOR pathway in human transformed cells
link: https://peerj.com/articles/104
last-modified: 2013-07-23
description: Somatic mutations in GNAQ gene were described as being the main oncogenic activation in uveal melanomas, whereas mutations in BRAF gene have been described as a key genetic alteration that contributes to skin melanoma development. We have previously reported differential activation of the MAPK and AKT/mTOR signalling pathways in uveal and skin melanomas harbouring, respectively, GNAQ and BRAF mutations. The aim of this work was to compare the functional effect of GNAQ and BRAF mutations in mTOR and MAPK pathway activation, cell proliferation and apoptosis. In this work, we performed transient transfection of HEK293 cells with BRAFWT, BRAFV 600E, GNAQWT, GNAQQ209P and GNAQQ209L vectors. We treated melanoma cell lines displaying different BRAF and GNAQ mutational status with the mTOR inhibitor RAD001 and with the MEK1/2 inhibitor U0126 and evaluated the effects in the growth of the cell lines and in mTOR and MAPK pathway effectors expression. At variance with the significant increase in the level of pmTOR Ser2448 and pS6 Ser235/236 proteins observed in cells transfected with BRAF vectors, no significant alteration in mTOR pathway effectors was observed in cells transfected with the three GNAQ expressing vectors. Also, GNAQ overexpression enhances Stat3 activation, which might mediate GNAQ oncogenic effects. None of the vectors led to significant differences in proliferation or apoptosis in the transfected cell lines. Cell lines harbouring a BRAF mutation were more sensitive to RAD001 treatment. U0126 leads to the reduction of MAPK and mTOR pathways activation in all cell lines tested. Our results indicate that GNAQ and BRAF activation drive distinct intracellular signalling pathways that may be useful for therapeutic decisions in human melanomas.
creator: Helena Pópulo
creator: Sandra Tavares
creator: Alexandra Faustino
creator: Joana B. Nunes
creator: José Manuel Lopes
creator: Paula Soares
uri: https://doi.org/10.7717/peerj.104
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Pópulo et al.

title: Influence of coral and algal exudates on microbially mediated reef metabolism
link: https://peerj.com/articles/108
last-modified: 2013-07-16
description: Benthic primary producers in tropical reef ecosystems can alter biogeochemical cycling and microbial processes in the surrounding seawater. In order to quantify these influences, we measured rates of photosynthesis, respiration, and dissolved organic carbon (DOC) exudate release by the dominant benthic primary producers (calcifying and non-calcifying macroalgae, turf-algae and corals) on reefs of Mo‘orea French Polynesia. Subsequently, we examined planktonic and benthic microbial community response to these dissolved exudates by measuring bacterial growth rates and oxygen and DOC fluxes in dark and daylight incubation experiments. All benthic primary producers exuded significant quantities of DOC (roughly 10% of their daily fixed carbon) into the surrounding water over a diurnal cycle. The microbial community responses were dependent upon the source of the exudates and whether the inoculum of microbes included planktonic or planktonic plus benthic communities. The planktonic and benthic microbial communities in the unamended control treatments exhibited opposing influences on DO concentration where respiration dominated in treatments comprised solely of plankton and autotrophy dominated in treatments with benthic plus plankon microbial communities. Coral exudates (and associated inorganic nutrients) caused a shift towards a net autotrophic microbial metabolism by increasing the net production of oxygen by the benthic and decreasing the net consumption of oxygen by the planktonic microbial community. In contrast, the addition of algal exudates decreased the net primary production by the benthic communities and increased the net consumption of oxygen by the planktonic microbial community thereby resulting in a shift towards net heterotrophic community metabolism. When scaled up to the reef habitat, exudate-induced effects on microbial respiration did not outweigh the high oxygen production rates of benthic algae, such that reef areas dominated with benthic primary producers were always estimated to be net autotrophic. However, estimates of microbial consumption of DOC at the reef scale surpassed the DOC exudation rates suggesting net consumption of DOC at the reef-scale. In situ mesocosm experiments using custom-made benthic chambers placed over different types of benthic communities exhibited identical trends to those found in incubation experiments. Here we provide the first comprehensive dataset examining direct primary producer-induced, and indirect microbially mediated alterations of elemental cycling in both benthic and planktonic reef environments over diurnal cycles. Our results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs.
creator: Andreas F. Haas
creator: Craig E. Nelson
creator: Forest Rohwer
creator: Linda Wegley-Kelly
creator: Steven D. Quistad
creator: Craig A. Carlson
creator: James J. Leichter
creator: Mark Hatay
creator: Jennifer E. Smith
uri: https://doi.org/10.7717/peerj.108
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Haas et al.

title: Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates
link: https://peerj.com/articles/107
last-modified: 2013-07-16
description: Algae-derived dissolved organic matter has been hypothesized to induce mortality of reef building corals. One proposed killing mechanism is a zone of hypoxia created by rapidly growing microbes. To investigate this hypothesis, biological oxygen demand (BOD) optodes were used to quantify the change in oxygen concentrations of microbial communities following exposure to exudates generated by turf algae and crustose coralline algae (CCA). BOD optodes were embedded with microbial communities cultured from Montastraea annularis and Mussismilia hispida, and respiration was measured during exposure to turf and CCA exudates. The oxygen concentrations along the optodes were visualized with a low-cost Submersible Oxygen Optode Recorder (SOOpR) system. With this system we observed that exposure to exudates derived from turf algae stimulated higher oxygen drawdown by the coral-associated bacteria than CCA exudates or seawater controls. Furthermore, in both turf and CCA exudate treatments, all microbial communities (coral-, algae-associated and pelagic) contributed significantly to the observed oxygen drawdown. This suggests that the driving factor for elevated oxygen consumption rates is the source of exudates rather than the initially introduced microbial community. Our results demonstrate that exudates from turf algae may contribute to hypoxia-induced coral stress in two different coral genera as a result of increased biological oxygen demand of the local microbial community. Additionally, the SOOpR system developed here can be applied to measure the BOD of any culturable microbe or microbial community.
creator: AK Gregg
creator: M Hatay
creator: AF Haas
creator: NL Robinett
creator: K Barott
creator: MJA Vermeij
creator: KL Marhaver
creator: P Meirelles
creator: F Thompson
creator: F Rohwer
uri: https://doi.org/10.7717/peerj.107
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Gregg et al.

title: Visualization of oxygen distribution patterns caused by coral and algae
link: https://peerj.com/articles/106
last-modified: 2013-07-16
description: Planar optodes were used to visualize oxygen distribution patterns associated with a coral reef associated green algae (Chaetomorpha sp.) and a hermatypic coral (Favia sp.) separately, as standalone organisms, and placed in close proximity mimicking coral-algal interactions. Oxygen patterns were assessed in light and dark conditions and under varying flow regimes. The images show discrete high oxygen concentration regions above the organisms during lighted periods and low oxygen in the dark. Size and orientation of these areas were dependent on flow regime. For corals and algae in close proximity the 2D optodes show areas of extremely low oxygen concentration at the interaction interfaces under both dark (18.4 ± 7.7 µmol O2 L- 1) and daylight (97.9 ± 27.5 µmol O2 L- 1) conditions. These images present the first two-dimensional visualization of oxygen gradients generated by benthic reef algae and corals under varying flow conditions and provide a 2D depiction of previously observed hypoxic zones at coral algae interfaces. This approach allows for visualization of locally confined, distinctive alterations of oxygen concentrations facilitated by benthic organisms and provides compelling evidence for hypoxic conditions at coral-algae interaction zones.
creator: Andreas F. Haas
creator: Allison K. Gregg
creator: Jennifer E. Smith
creator: Maria L. Abieri
creator: Mark Hatay
creator: Forest Rohwer
uri: https://doi.org/10.7717/peerj.106
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Haas et al.

title: Theoretical modelling of wakes from retractable flapping wings in forward flight
link: https://peerj.com/articles/105
last-modified: 2013-07-16
description: A free-wake method is used to simulate the wake from retractable, jointed wings. The method serves to complement existing experimental studies that visualise flying animal wakes. Simulated wakes are shown to be numerically convergent for a case study of the Rock Pigeon in minimum power cruising flight. The free-wake model is robust in simulating wakes for a range of wing geometries and dynamics without requiring changes to the numerical method. The method is found to be useful for providing low order predictions of wake geometries. However, it is not well suited to reconstructing 3d flowfields as solutions are sensitive to the numerical mesh node locations.
creator: Ben Parslew
creator: William J. Crowther
uri: https://doi.org/10.7717/peerj.105
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Parslew and Crowther

title: Real-time bioacoustics monitoring and automated species identification
link: https://peerj.com/articles/103
last-modified: 2013-07-16
description: Traditionally, animal species diversity and abundance is assessed using a variety of methods that are generally costly, limited in space and time, and most importantly, they rarely include a permanent record. Given the urgency of climate change and the loss of habitat, it is vital that we use new technologies to improve and expand global biodiversity monitoring to thousands of sites around the world. In this article, we describe the acoustical component of the Automated Remote Biodiversity Monitoring Network (ARBIMON), a novel combination of hardware and software for automating data acquisition, data management, and species identification based on audio recordings. The major components of the cyberinfrastructure include: a solar powered remote monitoring station that sends 1-min recordings every 10 min to a base station, which relays the recordings in real-time to the project server, where the recordings are processed and uploaded to the project website (arbimon.net). Along with a module for viewing, listening, and annotating recordings, the website includes a species identification interface to help users create machine learning algorithms to automate species identification. To demonstrate the system we present data on the vocal activity patterns of birds, frogs, insects, and mammals from Puerto Rico and Costa Rica.
creator: T. Mitchell Aide
creator: Carlos Corrada-Bravo
creator: Marconi Campos-Cerqueira
creator: Carlos Milan
creator: Giovany Vega
creator: Rafael Alvarez
uri: https://doi.org/10.7717/peerj.103
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Aide et al.

title: A holistic approach to development of diets for Ballan wrasse (Labrus berggylta) – a new species in aquaculture
link: https://peerj.com/articles/99
last-modified: 2013-07-16
description: Wild wrasses are used for delousing of farmed salmon but increasing demands have prompted the salmon industry to develop cultures of Ballan wrasse. One of the bottlenecks has been nutrition and feed intake in the juvenile phase, while broodstock nutrition is considered critical for production of viable offspring. The present study was aimed at developing functioning ongrowing and broodstock diets for Ballan wrasse. In juveniles the best lengthwise growth was identified at 65% dietary protein, 12% lipid and 16% carbohydrate. To investigate if the requirements for the other nutrients were covered by the diets developed for the species, the nutrient composition in juveniles (whole body) and broodstock (female gonad) were analyzed and compared to the composition in wild fish. We found that the levels of the lipid soluble Vitamins A, K and D were lower in cultured than in wild fish, however, the requirements for these nutrients in Ballan wrasse are not known. Other candidate nutrients for more in-depth investigation are the bone minerals, zinc, taurine and fatty acids.
creator: Kristin Hamre
creator: Andreas Nordgreen
creator: Espen Grøtan
creator: Olav Breck
uri: https://doi.org/10.7717/peerj.99
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Hamre et al.

title: Affect-focused psychodynamic psychotherapy for depression and anxiety through the Internet: a randomized controlled trial
link: https://peerj.com/articles/102
last-modified: 2013-07-09
description: Background. Psychodynamic psychotherapy is a psychological treatment approach that has a growing empirical base. Research has indicated an association between therapist-facilitated affective experience and outcome in psychodynamic therapy. Affect-phobia therapy (APT), as outlined by McCullough et al., is a psychodynamic treatment that emphasizes a strong focus on expression and experience of affect. This model has neither been evaluated for depression nor anxiety disorders in a randomized controlled trial. While Internet-delivered psychodynamic treatments for depression and generalized anxiety disorder exist, they have not been based on APT. The aim of this randomized controlled trial was to investigate the efficacy of an Internet-based, psychodynamic, guided self-help treatment based on APT for depression and anxiety disorders.Methods. One hundred participants with diagnoses of mood and anxiety disorders participated in a randomized (1:1 ratio) controlled trial of an active group versus a control condition. The treatment group received a 10-week, psychodynamic, guided self-help treatment based on APT that was delivered through the Internet. The treatment consisted of eight text-based treatment modules and included therapist contact (9.5 min per client and week, on average) in a secure online environment. Participants in the control group also received online therapist support and clinical monitoring of symptoms, but received no treatment modules. Outcome measures were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). Process measures were also included. All measures were administered weekly during the treatment period and at a 7-month follow-up.Results. Mixed models analyses using the full intention-to-treat sample revealed significant interaction effects of group and time on all outcome measures, when comparing treatment to the control group. A large between-group effect size of Cohen’s d = 0.77 (95% CI: 0.37–1.18) was found on the PHQ-9 and a moderately large between-group effect size d = 0.48 (95% CI: 0.08–0.87) was found on the GAD-7. The number of patients who recovered (had no diagnoses of depression and anxiety, and had less than 10 on both the PHQ-9 and the GAD-7) were at post-treatment 52% in the treatment group and 24% in the control group. This difference was significant, χ2(N = 100, df = 1) = 8.3, p < .01. From post-treatment to follow-up, treatment gains were maintained on the PHQ-9, and significant improvements were seen on the GAD-7.Conclusion. This study provides initial support for the efficacy of Internet-delivered psychodynamic therapy based on the affect-phobia model in the treatment of depression and anxiety disorders. The results support the conclusion that psychodynamic treatment approaches may be transferred to the guided self-help format and delivered via the Internet.
creator: Robert Johansson
creator: Martin Björklund
creator: Christoffer Hornborg
creator: Stina Karlsson
creator: Hugo Hesser
creator: Brjánn Ljótsson
creator: Andréas Rousseau
creator: Ronald J. Frederick
creator: Gerhard Andersson
uri: https://doi.org/10.7717/peerj.102
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Johansson et al.

title: Looking at microbial metabolism by high-resolution 2H-NMR spectroscopy
link: https://peerj.com/articles/101
last-modified: 2013-07-09
description: We analyzed the applicability of high-resolution 2H-HMR spectroscopy for the analysis of microbe metabolism in samples of mitochondrion isolated from rat liver and from aqueous extracts of homogenates of rat liver and other organs and tissues in the presence of high D2O contents. Such analysis is possible due to the fast microbe adaptation to life in the heavy water. It is also shown that some enzymatic processes typical for the intact cells are preserved in the homogenized tissue preparations. The microbial and cellular metabolic processes can be differentiated via the strategic use of cell poisons and antibiotics.
creator: Victor P. Kutyshenko
creator: Petr M. Beskaravayny
creator: Maxim V. Molchanov
creator: Svetlana I. Paskevich
creator: Dmitry A. Prokhorov
creator: Vladimir N. Uversky
uri: https://doi.org/10.7717/peerj.101
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Uversky et al.

title: Local and latitudinal variation in abundance: the mechanisms shaping the distribution of an ecosystem engineer
link: https://peerj.com/articles/100
last-modified: 2013-07-09
description: Ecological processes that determine the abundance of species within ecological communities vary across space and time. These scale-dependent processes are especially important when they affect key members of a community, such as ecosystem engineers that create shelter and food resources for other species. Yet, few studies have examined the suite of processes that shape the abundance of ecosystem engineers. Here, we evaluated the relative influence of temporal variation, local processes, and latitude on the abundance of an engineering insect—a rosette-galling midge, Rhopalomyia solidaginis (Diptera: Cecidomyiidae). Over a period of 3–5 years, we studied the density and size of galls across a suite of local experiments that manipulated genetic variation, soil nutrient availability, and the removal of other insects from the host plant, Solidago altissima (tall goldenrod). We also surveyed gall density within a single growing season across a 2,300 km latitudinal transect of goldenrod populations in the eastern United States. At the local scale, we found that host-plant genotypic variation was the best predictor of rosette gall density and size within a single year. We found that the removal of other insect herbivores resulted in an increase in gall density and size. The amendment of soil nutrients for four years had no effect on gall density, but galls were smaller in carbon-added plots compared to control and nitrogen additions. Finally, we observed that gall density varied several fold across years. At the biogeographic scale, we observed that the density of rosette gallers peaked at mid-latitudes. Using meta-analytic approaches, we found that the effect size of time, followed by host-plant genetic variation and latitude were the best predictors of gall density. Taken together, our study provides a unique comparison of multiple factors across different spatial and temporal scales that govern engineering insect herbivore density.
creator: Gregory M. Crutsinger
creator: Angélica L. Gonzalez
creator: Kerri M. Crawford
creator: Nathan J. Sanders
uri: https://doi.org/10.7717/peerj.100
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Crutsinger et al.

title: Depression, anxiety and their comorbidity in the Swedish general population: point prevalence and the effect on health-related quality of life
link: https://peerj.com/articles/98
last-modified: 2013-07-09
description: Background. Depression and anxiety disorders are major world-wide problems. There are no or few epidemiological studies investigating the prevalence of depression, generalized anxiety disorder and anxiety disorders in general in the Swedish population.Methods. Data were obtained by means of a postal survey administered to 3001 randomly selected adults. After two reminders response rate was 44.3%. Measures of depression and general anxiety were the 9-item Patient Health Questionnaire Depression Scale (PHQ-9) and the 7-item Generalized Anxiety Disorder Scale (GAD-7). The PHQ-9 identified participants who had experienced clinically significant depression (PHQ-9 ≥ 10), and who had a diagnosis of major depression (defined by using a PHQ-9 scoring algorithm). Clinically significant anxiety was defined as having a GAD-7 score ≥ 8. To specifically measure generalized anxiety disorder, the Generalized Anxiety Disorder Questionnaire-IV (GAD-Q-IV) was used with an established cut-off. Health-related quality of life was measured using the EuroQol (EQ-5D). Experiences of treatments for psychiatric disorders were also assessed.Results. Around 17.2% (95% CI: 15.1–19.4) of the participants were experiencing clinically significant depression (10.8%; 95% CI: 9.1–12.5) and clinically significant anxiety (14.7%; 95% CI: 12.7–16.6). Among participants with either clinically significant depression or anxiety, nearly 50% had comorbid disorders. The point prevalence of major depression was 5.2% (95% CI: 4.0–6.5), and 8.8% (95% CI: 7.3–10.4) had GAD. Among those with either of these disorders, 28.2% had comorbid depression and GAD. There were, generally, significant gender differences, with more women having a disorder compared to men. Among those with depression or anxiety, only between half and two thirds had any treatment experience. Comorbidity was associated with higher symptom severity and lower health-related quality of life.Conclusions. Epidemiological data from the Swedish community collected in this study provide point prevalence rates of depression, anxiety disorders and their comorbidity. These conditions were shown in this study to be undertreated and associated with lower quality of life, that need further efforts regarding preventive and treatment interventions.
creator: Robert Johansson
creator: Per Carlbring
creator: Åsa Heedman
creator: Björn Paxling
creator: Gerhard Andersson
uri: https://doi.org/10.7717/peerj.98
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Johansson et al.

title: Generalized linear mixed models can detect unimodal species-environment relationships
link: https://peerj.com/articles/95
last-modified: 2013-07-09
description: Niche theory predicts that species occurrence and abundance show non-linear, unimodal relationships with respect to environmental gradients. Unimodal models, such as the Gaussian (logistic) model, are however more difficult to fit to data than linear ones, particularly in a multi-species context in ordination, with trait modulated response and when species phylogeny and species traits must be taken into account. Adding squared terms to a linear model is a possibility but gives uninterpretable parameters.This paper explains why and when generalized linear mixed models, even without squared terms, can effectively analyse unimodal data and also presents a graphical tool and statistical test to test for unimodal response while fitting just the generalized linear mixed model. The R-code for this is supplied in Supplemental Information 1.
creator: Tahira Jamil
creator: Cajo J.F. ter Braak
uri: https://doi.org/10.7717/peerj.95
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Jamil and ter Braak

title: Optimising locational access of deprived populations to farmers’ markets at a national scale: one route to improved fruit and vegetable consumption?
link: https://peerj.com/articles/94
last-modified: 2013-07-02
description: Background. Evidence suggests that improved locational access to farmers’ markets increases fruit and vegetable (FV) consumption, particularly for low-income groups. Therefore, we modelled potential alternative distributions of farmers’ markets in one country (New Zealand) to explore the potential impact for deprived populations and an indigenous population (Māori).Methods. Data were collected on current farmers’ markets (n = 48), population distributions, area deprivation, and roads. Geographic analyses were performed to optimize market locations for the most deprived populations.Results. We found that, currently, farmers’ markets provided fairly poor access for the total population: 7% within 12.5 km (15 min driving time); 5% within 5 km; and 3% within 2 km. Modelling the optimal distribution of the 48 markets substantially improved access for the most deprived groups: 9% (vs 2% currently) within 12.5 km; 5% (vs 1%) within 5 km; and 3% (vs 1%) within 2 km. Access for Māori also improved: 22% (vs 7%) within 12.5 km; 12% (vs 4%) within 5 km; and 6% (vs 2%) within 2 km. Smaller pro-equity results arose from optimising the locations of the 18 least pro-equity markets or adding 10 new markets.Conclusion. These results highlight the potential for improving farmers’ market locations to increase accessibility for groups with low FV consumption. Given that such markets are easily established and relocated, local governments could consider these results to inform decisions, including subsidies for using government land and facilities. Such results can also inform central governments planning around voucher schemes for such markets and exempting them from taxes (e.g., VAT/GST).
creator: Amber L. Pearson
creator: Nick Wilson
uri: https://doi.org/10.7717/peerj.94
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Pearson and Wilson

title: Feasibility of using microbeads with holographic barcodes to track DNA specimens in the clinical molecular laboratory
link: https://peerj.com/articles/91
last-modified: 2013-07-02
description: We demonstrate the feasibility of using glass microbeads with a holographic barcode identifier to track DNA specimens in the molecular pathology laboratory. These beads can be added to peripheral blood specimens and are carried through automated DNA extraction protocols that use magnetic glass particles. We found that an adequate number of microbeads are consistently carried over during genomic DNA extraction to allow specimen identification, that the beads do not interfere with the performance of several different molecular assays, and that the beads and genomic DNA remain stable when stored together under regular storage conditions in the molecular pathology laboratory. The beads function as an internal, easily readable specimen barcode. This approach may be useful for identifying DNA specimens and reducing errors associated with molecular laboratory testing.
creator: Jason D. Merker
creator: Naomi O’Grady
creator: Linda Gojenola
creator: Mai Dao
creator: Ross Lenta
creator: Joanne M. Yeakley
creator: Iris Schrijver
uri: https://doi.org/10.7717/peerj.91
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Merker et al.

title: Activity in ventral premotor cortex is modulated by vision of own hand in action
link: https://peerj.com/articles/88
last-modified: 2013-07-02
description: Parietal and premotor cortices of the macaque monkey contain distinct populations of neurons which, in addition to their motor discharge, are also activated by visual stimulation. Among these visuomotor neurons, a population of grasping neurons located in the anterior intraparietal area (AIP) shows discharge modulation when the own hand is visible during object grasping. Given the dense connections between AIP and inferior frontal regions, we aimed at investigating whether two hand-related frontal areas, ventral premotor area F5 and primary motor cortex (area F1), contain neurons with similar properties. Two macaques were involved in a grasping task executed in various light/dark conditions in which the to-be-grasped object was kept visible by a dim retro-illumination. Approximately 62% of F5 and 55% of F1 motor neurons showed light/dark modulations. To better isolate the effect of hand-related visual input, we introduced two further conditions characterized by kinematic features similar to the dark condition. The scene was briefly illuminated (i) during hand preshaping (pre-touch flash, PT-flash) and (ii) at hand-object contact (touch flash, T-flash). Approximately 48% of F5 and 44% of F1 motor neurons showed a flash-related modulation. Considering flash-modulated neurons in the two flash conditions, ∼40% from F5 and ∼52% from F1 showed stronger activity in PT- than T-flash (PT-flash-dominant), whereas ∼60% from F5 and ∼48% from F1 showed stronger activity in T- than PT-flash (T-flash-dominant). Furthermore, F5, but not F1, flash-dominant neurons were characterized by a higher peak and mean discharge in the preferred flash condition as compared to light and dark conditions. Still considering F5, the distribution of the time of peak discharge was similar in light and preferred flash conditions. This study shows that the frontal cortex contains neurons, previously classified as motor neurons, which are sensitive to the observation of meaningful phases of the own grasping action. We conclude by discussing the possible functional role of these populations.
creator: Luciano Fadiga
creator: Luana Caselli
creator: Laila Craighero
creator: Benno Gesierich
creator: Andriy Oliynyk
creator: Banty Tia
creator: Riccardo Viaro
uri: https://doi.org/10.7717/peerj.88
license: http://creativecommons.org/licenses/by/3.0/
rights: © 2013 Fadiga et al.