title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1728 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: gb4gv: a genome browser for geminivirus link: https://peerj.com/articles/3165 last-modified: 2017-04-12 description: BackgroundGeminiviruses (family Geminiviridae) are prevalent plant viruses that imperil agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded genome propensity, resulting in worldwide circulation of diverse and viable genomes. Genomics is a prominent approach taken by researchers in elucidating the infectious mechanism of the virus. Currently, the NCBI Viral Genome website is a popular repository of viral genomes that conveniently provides researchers a centralized data source of genomic information. However, unlike the genome of living organisms, viral genomes most often maintain peculiar characteristics that fit into no single genome architecture. By imposing a unified annotation scheme on the myriad of viral genomes may downplay their hallmark features. For example, the viron of begomoviruses prevailing in America encapsulates two similar-sized circular DNA components and both are required for systemic infection of plants. However, the bipartite components are kept separately in NCBI as individual genomes with no explicit association in linking them. Thus, our goal is to build a comprehensive Geminivirus genomics database, namely gb4gv, that not only preserves genomic characteristics of the virus, but also supplements biologically relevant annotations that help to interrogate this virus, for example, the targeted host, putative iterons, siRNA targets, etc.MethodsWe have employed manual and automatic methods to curate 508 genomes from four major genera of Geminiviridae, and 161 associated satellites obtained from NCBI RefSeq and PubMed databases.ResultsThese data are available for free access without registration from our website. Besides genomic content, our website provides visualization capability inherited from UCSC Genome Browser.DiscussionWith the genomic information readily accessible, we hope that our database will inspire researchers in gaining a better understanding of the incredible degree of diversity of these viruses, and of the complex relationships within and between the different genera in the Geminiviridae.Availability and ImplementationThe database can be found at: http://gb4gv.lafayette.edu. creator: Eric S. Ho creator: Catherine M. Newsom-Stewart creator: Lysa Diarra creator: Caroline S. McCauley uri: https://doi.org/10.7717/peerj.3165 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ho et al. title: Trypanosoma cruzi reservoir—triatomine vector co-occurrence networks reveal meta-community effects by synanthropic mammals on geographic dispersal link: https://peerj.com/articles/3152 last-modified: 2017-04-12 description: Contemporary patterns of land use and global climate change are modifying regional pools of parasite host species. The impact of host community changes on human disease risk, however, is difficult to assess due to a lack of information about zoonotic parasite host assemblages. We have used a recently developed method to infer parasite-host interactions for Chagas Disease (CD) from vector-host co-occurrence networks. Vector-host networks were constructed to analyze topological characteristics of the network and ecological traits of species’ nodes, which could provide information regarding parasite regional dispersal in Mexico. Twenty-eight triatomine species (vectors) and 396 mammal species (potential hosts) were included using a data-mining approach to develop models to infer most-likely interactions. The final network contained 1,576 links which were analyzed to calculate centrality, connectivity, and modularity. The model predicted links of independently registered Trypanosoma cruzi hosts, which correlated with the degree of parasite-vector co-occurrence. Wiring patterns differed according to node location, while edge density was greater in Neotropical as compared to Nearctic regions. Vectors with greatest public health importance (i.e., Triatoma dimidiata, T. barberi, T. pallidipennis, T. longipennis, etc), did not have stronger links with particular host species, although they had a greater frequency of significant links. In contrast, hosts classified as important based on network properties were synanthropic mammals. The latter were the most common parasite hosts and are likely bridge species between these communities, thereby integrating meta-community scenarios beneficial for long-range parasite dispersal. This was particularly true for rodents, >50% of species are synanthropic and more than 20% have been identified as T. cruzi hosts. In addition to predicting potential host species using the co-occurrence networks, they reveal regions with greater expected parasite mobility. The Neotropical region, which includes the Mexican south and southeast, and the Transvolcanic belt, had greatest potential active T. cruzi dispersal, as well as greatest edge density. This information could be directly applied for stratification of transmission risk and to design and analyze human-infected vector contact intervention efficacy. creator: Carlos N. Ibarra-Cerdeña creator: Leopoldo Valiente-Banuet creator: Víctor Sánchez-Cordero creator: Christopher R. Stephens creator: Janine M. Ramsey uri: https://doi.org/10.7717/peerj.3152 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ibarra-Cerdeña et al. title: Physiological effects of five different marine natural organic matters (NOMs) and three different metals (Cu, Pb, Zn) on early life stages of the blue mussel (Mytilus galloprovincialis) link: https://peerj.com/articles/3141 last-modified: 2017-04-12 description: Metals are present in aquatic environments as a result of natural and anthropogenic inputs, and may induce toxicity to organisms. One of the main factors that influence this toxicity in fresh water is natural organic matter (NOM) but all NOMs are not the same in this regard. In sea water, possible protection by marine NOMs is not well understood. Thus, our study isolated marine NOMs by solid-phase extraction from five different sites and characterized them by excitation-emission fluorescence analysis—one inshore (terrigenous origin), two offshore (autochthonous origin), and two intermediate in composition (indicative of a mixed origin). The physiological effects of these five NOMS alone (at 8 mg/L), of three metals alone (copper, lead and zinc at 6 µg Cu/L, 20 µg Pb/L, and 25 µg Zn/L respectively), and of each metal in combination with each NOM, were evaluated in 48-h exposures of mussel larvae. Endpoints were whole body Ca2++Mg2+-ATPase activity, carbonic anhydrase activity and lipid peroxidation. By themselves, NOMs increased lipid peroxidation, Ca2++Mg2+-ATPase, and/or carbonic anhydrase activities (significant in seven of 15 NOM-endpoint combinations), whereas metals by themselves did not affect the first two endpoints, but Cu and Pb increased carbonic anhydrase activities. In combination, the effects of NOMs predominated, with the metal exerting no additional effect in 33 out of 45 combinations. While NOM effects varied amongst different isolates, there was no clear pattern with respect to optical or chemical properties. When NOMs were treated as a single source by data averaging, NOM had no effect on Ca2++Mg2+-ATPase activity but markedly stimulated carbonic anhydrase activity and lipid peroxidation, and there were no additional effects of any metal. Our results indicate that marine NOMs may have direct effects on this model marine organism, as well as protective effects against metal toxicity, and the quality of marine NOMs may be an important factor in these actions. creator: Lygia Sega Nogueira creator: Adalto Bianchini creator: Scott Smith creator: Marianna Basso Jorge creator: Rachael L. Diamond creator: Chris M. Wood uri: https://doi.org/10.7717/peerj.3141 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Nogueira et al. title: Performance of interferon-γ release assay in the diagnosis of tuberculous lymphadenitis: a meta-analysis link: https://peerj.com/articles/3136 last-modified: 2017-04-12 description: BackgroundThe diagnostic values of interferon-gamma release assays (IGRA) in tuberculosis (TB) vary a lot with different site of infections, with especially higher sensitivities in chronic forms of TB such as tuberculosis of the lymph node. We conducted a meta-analysis to comprehensively evaluate the overall accuracy of diagnostic IGRA for tuberculous lymphadenitis.MethodsPubmed, Web of Science, EMBASE, Wanfang and CNKI databases up to February 17, 2017 were searched to identify published studies. The study quality was evaluated using the QUADAS-2 checklist. The pooled estimates of diagnostic parameters were generated using a bivariate random-effects model and summary receiver operating characteristic (SROC) curves were used to summarize global performance.ResultsA total of ten qualified studies, performed in Korea or China, including 1,084 patients, were enrolled in this meta-analysis. The pooled estimates of diagnostic accuracy were as follows: sensitivity, 0.89 (95% CI [0.85–0.92]); specificity, 0.81 (95% CI [0.77–0.83]); positive likelihood ratio (PLR), 4.25 (95% CI [2.79–6.47]); negative likelihood ratio (NLR), 0.16 (95% CI [0.12–0.22]); and area under the curve (AUC) was 0.93. According to subgroup analyses, studies conducted using QuantiFERON-TB, in Korean population and focusing on cervical lymphadenitis exhibited relative higher specificity while lower sensitivity. No evidence of publication bias was identified.ConclusionsIGRA exhibits high diagnostic accuracy in tuberculous lymphadenitis. The diagnostic value of IGRA differed by different IGRA methods, ethnicity and lymphadenitis location. Our conclusion may be more applicable to population from TB prevalent areas. creator: Qianqian Liu creator: Wenzhang Li creator: Yunfeng Chen creator: Xinmiao Du creator: Chengdi Wang creator: Binmiao Liang creator: Yin Tang creator: Yulin Feng creator: Chuanmin Tao creator: Jian-Qing He uri: https://doi.org/10.7717/peerj.3136 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Liu et al. title: Direct imaging of APP proteolysis in living cells link: https://peerj.com/articles/3086 last-modified: 2017-04-12 description: Alzheimer’s disease is a multifactorial disorder caused by the interaction of genetic, epigenetic and environmental factors. The formation of cytotoxic oligomers consisting of Aβ peptide is widely accepted as being one of the main key events triggering the development of Alzheimer’s disease. Aβ peptide production results from the specific proteolytic processing of the amyloid precursor protein (APP). Deciphering the factors governing the activity of the secretases responsible for the cleavage of APP is still a critical issue. Kits available commercially measure the enzymatic activity of the secretases from cells lysates, in vitro. By contrast, we have developed a prototypal rapid bioassay that provides visible information on the proteolytic processing of APP directly in living cells. APP was fused to a monomeric variant of the green fluorescent protein and a monomeric variant of the red fluorescent protein at the C-terminal and N-terminal (mChAPPmGFP), respectively. Changes in the proteolytic processing rate in transfected human neuroblastoma and rat neuronal cells were imaged with confocal microscopy as changes in the red/green fluorescence intensity ratio. The significant decrease in the mean red/green ratio observed in cells over-expressing the β-secretase BACE1, or the α-secretase ADAM10, fused to a monomeric blue fluorescent protein confirms that the proteolytic site is still accessible. Specific siRNA was used to evaluate the contribution of endogenous BACE1. Interestingly, we found that the degree of proteolytic processing of APP is not completely homogeneous within the same single cell, and that there is a high degree of variability between cells of the same type. We were also able to follow with a fluorescence spectrometer the changes in the red emission intensity of the extracellular medium when BACE1 was overexpressed. This represents a complementary approach to fluorescence microscopy for rapidly detecting changes in the proteolytic processing of APP in real time. In order to allow the discrimination between the α- and the β-secretase activity, we have created a variant of mChAPPmGFP with a mutation that inhibits the α-secretase cleavage without perturbing the β-secretase processing. Moreover, we obtained a quantitatively robust estimate of the changes in the red/green ratio for the above conditions by using a flow cytometer able to simultaneously excite and measure the red and green fluorescence. Our novel approach lay the foundation for a bioassay suitable to study the effect of drugs or particular conditions, to investigate in an unbiased way the the proteolytic processing of APP in single living cells in order, and to elucidate the causes of the variability and the factors driving the processing of APP. creator: Niccoló Parenti creator: Ambra Del Grosso creator: Claudia Antoni creator: Marco Cecchini creator: Renato Corradetti creator: Francesco S. Pavone creator: Martino Calamai uri: https://doi.org/10.7717/peerj.3086 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Parenti et al. title: Calcification and growth rate recovery of the reef-building Pocillopora species in the northeast tropical Pacific following an ENSO disturbance link: https://peerj.com/articles/3191 last-modified: 2017-04-11 description: Pocilloporids are one of the major reef-building corals in the eastern tropical Pacific (ETP) and also the most affected by thermal stress events, mainly those associated with El Niño/Southern Oscillation (ENSO) periods. To date, coral growth parameters have been poorly reported in Pocillopora species in the northeastern region of the tropical Pacific. Monthly and annual growth rates of the three most abundant morphospecies (P. cf. verrucosa, P. cf. capitata, and P. cf. damicornis) were evaluated during two annual periods at a site on the Pacific coast of Mexico. The first annual period, 2010–2011 was considered a strong ENSO/La Niña period with cool sea surface temperatures, then followed by a non-ENSO period in 2012–2013. The linear extension rate, skeletal density, and calcification rate averaged (±SD) were 2.31 ± 0.11 cm yr−1, 1.65 ± 0.18 g cm−3, 5.03 ± 0.84 g cm−2 yr-1 respectively, during the strong ENSO event. In contrast, the respective non-ENSO values were 3.50 ± 0.64 cm yr−1, 1.70 ± 0.18 g cm−3, and 6.02 ± 1.36 g cm−2 yr−1. This corresponds to 52% and 20% faster linear extension and calcification rates, respectively, during non-ENSO period. The evidence suggests that Pocillopora branching species responded positively with faster growth rates following thermal anomalies, which allow them to maintain coral communities in the region. creator: Jose de Jesús A. Tortolero-Langarica creator: Alma P. Rodríguez-Troncoso creator: Amílcar L. Cupul-Magaña creator: Juan P. Carricart-Ganivet uri: https://doi.org/10.7717/peerj.3191 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Tortolero-Langarica et al. title: Effects of chronic exposure to clothianidin on the earthworm Lumbricus terrestris link: https://peerj.com/articles/3177 last-modified: 2017-04-11 description: Although neonicotinoids are targeted at insects, their predominant use as a seed dressing and their long persistence in soils mean that non-target soil organisms such as earthworms are likely to be chronically exposed to them. Chronic exposure may pose risks that are not evaluated in most toxicity tests. We experimentally tested the effect of field-realistic concentrations of a commonly used neonicotinoid, clothianidin, on mortality, weight gain, and food consumption to assess the impacts of chronic exposure over four months on fitness of L. terrestris individuals. We undertook three separate experiments, each with different exposure routes: treated soil only (experiment A), treated food and soil combined (experiment B) and treated food only (experiment C). Mortality was negatively affected by exposure from treated soil only with greatest mortality observed in the groups exposed to the two highest concentrations (20 ppb and 100 ppb), but no clear effect on mortality was found in the other two experiments. When clothianidin was present in the food, an anti-feedant effect was present in months one and two which subsequently disappeared; if this occurs in the field, it could result in reduced rates of decomposition of treated crop foliage. We found no significant effects of any treatment on worm body mass. We cannot rule out stronger adverse effects if worms come into close proximity to treated seeds, or if other aspects of fitness were examined. Overall, our data suggest that field-realistic exposure to clothianidin has a significant but temporary effect on food consumption and can have weak but significant impacts on mortality of L. terrestris. creator: Kate Basley creator: Dave Goulson uri: https://doi.org/10.7717/peerj.3177 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Basley and Goulson title: Mechanism of endothelial nitric oxide synthase phosphorylation and activation by tentacle extract from the jellyfish Cyanea capillata link: https://peerj.com/articles/3172 last-modified: 2017-04-11 description: Our previous study demonstrated that tentacle extract (TE) from the jellyfish Cyanea capillata (C. capillata) could cause a weak relaxation response mediated by nitric oxide (NO) using isolated aorta rings. However, the intracellular mechanisms of TE-induced vasodilation remain unclear. Thus, this study was conducted to examine the role of TE on Akt/eNOS/NO and Ca2+ signaling pathways in human umbilical vein endothelial cells (HUVECs). Our results showed that TE induced dose- and time-dependent increases of eNOS activity and NO production. And TE also induced Akt and eNOS phosphorylation in HUVECs. However, treatment with specific PI3-kinase inhibitor (Wortmannin) significantly inhibited the increases in NO production and Akt/eNOS phosphorylation. In addition, TE also stimulated an increase in the intracellular Ca2+ concentration ([Ca2+]i), which was significantly attenuated by either IP3 receptor blocker (Heparin) or PKC inhibitor (PKC 412). In contrast, extracellular Ca2+-free, L-type calcium channel blocker (Nifedipine), or PKA inhibitor (H89) had no influence on the [Ca2+]i elevation. Since calcium ions also play a critical role in stimulating eNOS activity, we next explored the role of Ca2+ in TE-induced Akt/eNOS activation. In consistent with the attenuation of [Ca2+]i elevation, we found that Akt/eNOS phosphorylation was also dramatically decreased by Heparin or PKC 412, but not affected by Nifedipine or H89. However, the phosphorylation level could also be decreased by the removal of extracellular calcium. Taken together, our findings indicated that TE-induced eNOS phosphorylation and activation were mainly through PI3K/Akt-dependent, PKC/IP3R-sensitive and Ca2+-dependent pathways. creator: Beilei Wang creator: Dan Liu creator: Chao Wang creator: Qianqian Wang creator: Hui Zhang creator: Guoyan Liu creator: Xia Tao creator: Liming Zhang uri: https://doi.org/10.7717/peerj.3172 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: A transdisciplinary approach to the initial validation of a single cell protein as an alternative protein source for use in aquafeeds link: https://peerj.com/articles/3170 last-modified: 2017-04-11 description: The human population is growing and, globally, we must meet the challenge of increased protein needs required to feed this population. Single cell proteins (SCP), when coupled to aquaculture production, offer a means to ensure future protein needs can be met without direct competition with food for people. To demonstrate a given type of SCP has potential as a protein source for use in aquaculture feed, a number of steps need to be validated including demonstrating that the SCP is accepted by the species in question, leads to equivalent survival and growth, does not result in illness or other maladies, is palatable to the consumer, is cost effective to produce and can easily be incorporated into diets using existing technology. Here we examine white shrimp (Litopenaeus vannamei) growth and consumer taste preference, smallmouth grunt (Haemulon chrysargyreum) growth, survival, health and gut microbiota, and Atlantic salmon (Salmo salar) digestibility when fed diets that substitute the bacterium Methylobacterium extorquens at a level of 30% (grunts), 100% (shrimp), or 55% (salmon) of the fishmeal in a compound feed. In each of these tests, animals performed equivalently when fed diets containing M. extorquens as when fed a standard aquaculture diet. This transdisciplinary approach is a first validation of this bacterium as a potential SCP protein substitute in aquafeeds. Given the ease to produce this SCP through an aerobic fermentation process, the broad applicability for use in aquaculture indicates the promise of M. extorquens in leading toward greater food security in the future. creator: Michael Tlusty creator: Andrew Rhyne creator: Joseph T. Szczebak creator: Bradford Bourque creator: Jennifer L. Bowen creator: Gary Burr creator: Christopher J. Marx creator: Lawrence Feinberg uri: https://doi.org/10.7717/peerj.3170 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Are anti-ganglioside antibodies associated with proventricular dilatation disease in birds? link: https://peerj.com/articles/3144 last-modified: 2017-04-11 description: The identification of Parrot bornaviruses (PaBV) in psittacine birds with proventricular dilatation disease (PDD) has not been sufficient to explain the pathogenesis of this fatal disease, since not all infected birds develop clinical signs. Although the most accepted theory indicates that PaBV directly triggers an inflammatory response in this disease, another hypothesis suggests the disease is triggered by autoantibodies targeting neuronal gangliosides, and PDD might therefore resemble Guillain-Barré Syndrome (GBS) in its pathogenesis. Experimental inoculation of pure gangliosides and brain-derived ganglioside extracts were used in two different immunization studies. The first study was performed on 17 healthy chickens (Gallus gallus domesticus): 11 chickens were inoculated with a brain ganglioside extract in Freund’s complete adjuvant (FCA) and six chickens inoculated with phosphate-buffered saline. A second study was performed five healthy quaker parrots (Myiopsitta monachus) that were divided into three groups: Two quaker parrots received purified gangliosides in FCA, two received a crude brain extract in FCA, and one control quaker parrot received FCA alone. One chicken developed difficult in walking. Histologically, only a mild perivascular and perineural lymphocytic infiltrate in the proventriculus. Two quaker parrots (one from each treatment group) had mild lymphoplasmacytic encephalitis and myelitis. However, none of the quaker parrots developed myenteric ganglioneuritis, suggesting that autoantibodies against gangliosides in birds are not associated with a condition resembling PDD. creator: Jeann Leal de Araujo creator: Ian Tizard creator: Jianhua Guo creator: J Jill Heatley creator: Aline Rodrigues Hoffmann creator: Raquel R. Rech uri: https://doi.org/10.7717/peerj.3144 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Leal de Araujo et al.