title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1739 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Functional and health promoting inherent attributes of Enterococcus hirae F2 as a novel probiotic isolated from the digestive tract of the freshwater fish Catla catla link: https://peerj.com/articles/3085 last-modified: 2017-03-15 description: BackgroundProbiotic microorganisms are gaining global importance because of their use in the preparation of a nutraceutical or in the treatment of infections. As per the health industry demand, there is an urgent need for exploring new indigenous probiotic strains with its specific origin due to variation in gut microflora, different food habits and specific host-microbial interactions. The main objective of the present study was to isolate and identify a novel probiotic Enterococcus strain from the gut of Catla catla fish and evaluate its potentiality as a potent probiotic.MethodsThe whole study was designed with the isolation of novel lactic acid bacterial strain from the gut of Catla catla fish with their biochemical and molecular identifications. The potentiality of the isolated strain as a potent probiotic was carried out according to the parameters described in FAD/WHO guidelines for the evaluation of probiotics in food.ResultsThe isolated strain was confirmed as Enterococcus hirae F2 on the basis of various biochemical and 16s rRNA gene sequencing methods. Enterococcus hirae F2 was able to survive under highly acidic and bile salt concentration with the ability for the production of lipase and Bsh enzyme. It was also able to survive under simulated gastrointestinal conditions with the inhibition ability of various pathogens. The antioxidant potentiality with the cell surface hydrophobicity and cell aggregation ability confirms its potentiality as a potent probiotic. All the results detail the potency of Enterococcus hirae F2 as a novel probiotic for a safer use.DiscussionThe isolation of Enterococcus hirae with probiotic potential from the gut of fish is a new approach and done for the first time. However, the whole study concluded that the isolated strain might be used as a novel probiotic in the food industry for the production of new probiotic products which imparts health benefits to the host. creator: Mohd Adnan creator: Mitesh Patel creator: Sibte Hadi uri: https://doi.org/10.7717/peerj.3085 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Adnan et al. title: Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis link: https://peerj.com/articles/3078 last-modified: 2017-03-15 description: BackgroundRheumatoid arthritis (RA) is a chronic auto-inflammatory disorder of joints. The present study aimed to identify the key genes in RA for better understanding the underlying mechanisms of RA.MethodsThe integrated analysis of expression profiling was conducted to identify differentially expressed genes (DEGs) in RA. Moreover, functional annotation, protein–protein interaction (PPI) network and transcription factor (TF) regulatory network construction were applied for exploring the potential biological roles of DEGs in RA. In addition, the expression level of identified candidate DEGs was preliminarily detected in peripheral blood cells of RA patients in the GSE17755 dataset. Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to validate the expression levels of identified DEGs in RA.ResultsA total of 378 DEGs, including 202 up- and 176 down-regulated genes, were identified in synovial tissues of RA patients compared with healthy controls. DEGs were significantly enriched in axon guidance, RNA transport and MAPK signaling pathway. RBFOX2, LCK and SERBP1 were the hub proteins in the PPI network. In the TF-target gene network, RBFOX2, POU6F1, WIPF1 and PFKFB3 had the high connectivity with TFs. The expression status of 11 candidate DEGs was detected in GSE17755, the expression levels of MAT2A and NSA2 were significantly down-regulated and CD47 had the up-regulated tendency in peripheral blood cells of patients with RA compared with healthy individuals. qRT-PCR results of MAT2A, NSA2, CD47 were compatible with our bioinformatics analyses.DiscussionOur study might provide valuable information for exploring the pathogenesis mechanism of RA and identifying the potential biomarkers for RA diagnosis. creator: Ruihu Hao creator: Haiwei Du creator: Lin Guo creator: Fengde Tian creator: Ning An creator: Tiejun Yang creator: Changcheng Wang creator: Bo Wang creator: Zihao Zhou uri: https://doi.org/10.7717/peerj.3078 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hao et al. title: Three-dimensional visualisation of the internal anatomy of the sparrowhawk (Accipiter nisus) forelimb using contrast-enhanced micro-computed tomography link: https://peerj.com/articles/3039 last-modified: 2017-03-15 description: BackgroundGross dissection is a widespread method for studying animal anatomy, despite being highly destructive and time-consuming. X-ray computed tomography (CT) has been shown to be a non-destructive alternative for studying anatomical structures. However, in the past it has been limited to only being able to visualise mineralised tissues. In recent years, morphologists have started to use traditional X-ray contrast agents to allow the visualisation of soft tissue elements in the CT context. The aim of this project is to assess the ability of contrast-enhanced micro-CT (μCT) to construct a three-dimensional (3D) model of the musculoskeletal system of the bird wing and to quantify muscle geometry and any systematic changes due to shrinkage. We expect that this reconstruction can be used as an anatomical guide to the sparrowhawk wing musculature and form the basis of further biomechanical analysis of flight.MethodsA 3% iodine-buffered formalin solution with a 25-day staining period was used to visualise the wing myology of the sparrowhawk (Accipiter nisus). μCT scans of the wing were taken over the staining period until full penetration of the forelimb musculature by iodine was reached. A 3D model was reconstructed by manually segmenting out the individual elements of the avian wing using 3D visualisation software.ResultsDifferent patterns of contrast were observed over the duration of the staining treatment with the best results occurring after 25 days of staining. Staining made it possible to visualise and identify different elements of the soft tissue of the wing. Finally, a 3D reconstruction of the musculoskeletal system of the sparrowhawk wing is presented and numerical data of muscle geometry is compared to values obtained by dissection.DiscussionContrast-enhanced μCT allows the visualisation and identification of the wing myology of birds, including the smaller muscles in the hand, and provides a non-destructive way for quantifying muscle volume with an accuracy of 96.2%. By combining contrast-enhanced μCT with 3D visualisation techniques, it is possible to study the individual muscles of the forelimb in their original position and 3D design, which can be the basis of further biomechanical analysis. Because the stain can be washed out post analysis, this technique provides a means of obtaining quantitative muscle data from museum specimens non-destructively. creator: Fernanda Bribiesca-Contreras creator: William I. Sellers uri: https://doi.org/10.7717/peerj.3039 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Bribiesca-Contreras and Sellers title: Sympathy for the devil: a conservation strategy for devil and manta rays link: https://peerj.com/articles/3027 last-modified: 2017-03-14 description: BackgroundInternational trade for luxury products, medicines, and tonics poses a threat to both terrestrial and marine wildlife. The demand for and consumption of gill plates (known as Peng Yu Sai, “Fish Gill of Mobulid Ray”) from devil and manta rays (subfamily Mobulinae, collectively referred to as mobulids) poses a significant threat to these marine fishes because of their extremely low productivity. The demand for these gill plates has driven an international trade supplied by largely unmonitored and unregulated catches from target and incidental fisheries around the world. Scientific research, conservation campaigns, and legal protections for devil rays have lagged behind those for manta rays despite similar threats across all mobulids.MethodsTo investigate the difference in attention given to devil rays and manta rays, we examined trends in the scientific literature and updated species distribution maps for all mobulids. Using available information on target and incidental fisheries, and gathering information on fishing and trade regulations (at international, national, and territorial levels), we examined how threats and protective measures overlap with species distribution. We then used a species conservation planning approach to develop the Global Devil and Manta Ray Conservation Strategy, specifying a vision, goals, objectives, and actions to advance the knowledge and protection of both devil and manta rays.Results and DiscussionOur literature review revealed that there had been nearly 2.5-times more “manta”-titled publications, than “mobula” or “devil ray”-titled publications over the past 4.5 years (January 2012–June 2016). The majority of these recent publications were reports on occurrence of mobulid species. These publications contributed to updated Area of Occupancy and Extent of Occurrence maps which showed expanded distributions for most mobulid species and overlap between the two genera. While several international protections have recently expanded to include all mobulids, there remains a greater number of national, state, and territory-level protections for manta rays compared to devil rays. We hypothesize that there are fewer scientific publications and regulatory protections for devil rays due primarily to perceptions of charisma that favour manta rays. We suggest that the well-established species conservation framework used here offers an objective solution to close this gap. To advance the goals of the conservation strategy we highlight opportunities for parity in protection and suggest solutions to help reduce target and bycatch fisheries. creator: Julia M. Lawson creator: Sonja V. Fordham creator: Mary P. O’Malley creator: Lindsay N.K. Davidson creator: Rachel H.L. Walls creator: Michelle R. Heupel creator: Guy Stevens creator: Daniel Fernando creator: Ania Budziak creator: Colin A. Simpfendorfer creator: Isabel Ender creator: Malcolm P. Francis creator: Giuseppe Notarbartolo di Sciara creator: Nicholas K. Dulvy uri: https://doi.org/10.7717/peerj.3027 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lawson et al. title: Vector competence of Anopheles and Culex mosquitoes for Zika virus link: https://peerj.com/articles/3096 last-modified: 2017-03-14 description: Zika virus is a newly emergent mosquito-borne flavivirus that has caused recent large outbreaks in the new world, leading to dramatic increases in serious disease pathology including Guillain-Barre syndrome, newborn microcephaly, and infant brain damage. Although Aedes mosquitoes are thought to be the primary mosquito species driving infection, the virus has been isolated from dozens of mosquito species, including Culex and Anopheles species, and we lack a thorough understanding of which mosquito species to target for vector control. We exposed Anopheles gambiae, Anopheles stephensi, and Culex quinquefasciatus mosquitoes to blood meals supplemented with two Zika virus strains. Mosquito bodies, legs, and saliva were collected five, seven, and 14 days post blood meal and tested for infectious virus by plaque assay. Regardless of titer, virus strain, or timepoint, Anopheles gambiae, Anopheles stephensi, and Culex quinquefasciatus mosquitoes were refractory to Zika virus infection. We conclude that Anopheles gambiae, Anopheles stephensi, and Culex quinquefasciatus mosquitoes likely do not contribute significantly to Zika virus transmission to humans. However, future studies should continue to explore the potential for other novel potential vectors to transmit the virus. creator: Brittany L. Dodson creator: Jason L. Rasgon uri: https://doi.org/10.7717/peerj.3096 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dodson and Rasgon title: Interacting effects of early dietary conditions and reproductive effort on the oxidative costs of reproduction link: https://peerj.com/articles/3094 last-modified: 2017-03-14 description: The hypothesis that oxidative damage accumulation can mediate the trade-off between reproduction and lifespan has recently been questioned. However, in captive conditions, studies reporting no evidence in support of this hypothesis have usually provided easy access to food which may have mitigated the cost of reproduction. Here, I test the hypothesis that greater investment in reproduction should lead to oxidative damage accumulation and telomere loss in domestic zebra finches Taeniopygia guttata. Moreover, since the change or fluctuation in diet composition between early and late postnatal period can impair the ability to produce antioxidant defences in zebra finches, I also tested if early nutritional conditions (constant vs fluctuating early diet) influenced the magnitude of any subsequent costs of reproduction (e.g., oxidative damage and/or telomere shortening). In comparison to pairs with reduced broods, the birds that had to feed enlarged broods showed a higher level of oxidative DNA damage (8-OHdG), but brood size had no effect on telomeres. Fluctuating early diet composition reduced the capacity to maintain the activity of endogenous antioxidants (GPx), particularly when reproductive costs were increased (enlarged brood). The decline in GPx in birds feeding enlarged broods was accompanied by a change in bill colouration. This suggests that birds with lower endogenous antioxidant defences might have strategically increased the mobilization of antioxidants previously stored in other tissues (i.e., bill and liver) and thus, preventing an excessive accumulation of damage during reproduction. creator: Jose Carlos Noguera uri: https://doi.org/10.7717/peerj.3094 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Noguera title: MaxEnt’s parameter configuration and small samples: are we paying attention to recommendations? A systematic review link: https://peerj.com/articles/3093 last-modified: 2017-03-14 description: Environmental niche modeling (ENM) is commonly used to develop probabilistic maps of species distribution. Among available ENM techniques, MaxEnt has become one of the most popular tools for modeling species distribution, with hundreds of peer-reviewed articles published each year. MaxEnt’s popularity is mainly due to the use of a graphical interface and automatic parameter configuration capabilities. However, recent studies have shown that using the default automatic configuration may not be always appropriate because it can produce non-optimal models; particularly when dealing with a small number of species presence points. Thus, the recommendation is to evaluate the best potential combination of parameters (feature classes and regularization multiplier) to select the most appropriate model. In this work we reviewed 244 articles published between 2013 and 2015 to assess whether researchers are following recommendations to avoid using the default parameter configuration when dealing with small sample sizes, or if they are using MaxEnt as a “black box tool.” Our results show that in only 16% of analyzed articles authors evaluated best feature classes, in 6.9% evaluated best regularization multipliers, and in a meager 3.7% evaluated simultaneously both parameters before producing the definitive distribution model. We analyzed 20 articles to quantify the potential differences in resulting outputs when using software default parameters instead of the alternative best model. Results from our analysis reveal important differences between the use of default parameters and the best model approach, especially in the total area identified as suitable for the assessed species and the specific areas that are identified as suitable by both modelling approaches. These results are worrying, because publications are potentially reporting over-complex or over-simplistic models that can undermine the applicability of their results. Of particular importance are studies used to inform policy making. Therefore, researchers, practitioners, reviewers and editors need to be very judicious when dealing with MaxEnt, particularly when the modelling process is based on small sample sizes. creator: Narkis S. Morales creator: Ignacio C. Fernández creator: Victoria Baca-González uri: https://doi.org/10.7717/peerj.3093 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Morales et al. title: Contrasting determinants for the introduction and establishment success of exotic birds in Taiwan using decision trees models link: https://peerj.com/articles/3092 last-modified: 2017-03-14 description: BackgroundBiological invasions have become a major threat to biodiversity, and identifying determinants underlying success at different stages of the invasion process is essential for both prevention management and testing ecological theories. To investigate variables associated with different stages of the invasion process in a local region such as Taiwan, potential problems using traditional parametric analyses include too many variables of different data types (nominal, ordinal, and interval) and a relatively small data set with too many missing values.MethodsWe therefore used five decision tree models instead and compared their performance. Our dataset contains 283 exotic bird species which were transported to Taiwan; of these 283 species, 95 species escaped to the field successfully (introduction success); of these 95 introduced species, 36 species reproduced in the field of Taiwan successfully (establishment success). For each species, we collected 22 variables associated with human selectivity and species traits which may determine success during the introduction stage and establishment stage. For each decision tree model, we performed three variable treatments: (I) including all 22 variables, (II) excluding nominal variables, and (III) excluding nominal variables and replacing ordinal values with binary ones. Five performance measures were used to compare models, namely, area under the receiver operating characteristic curve (AUROC), specificity, precision, recall, and accuracy.ResultsThe gradient boosting models performed best overall among the five decision tree models for both introduction and establishment success and across variable treatments. The most important variables for predicting introduction success were the bird family, the number of invaded countries, and variables associated with environmental adaptation, whereas the most important variables for predicting establishment success were the number of invaded countries and variables associated with reproduction.DiscussionOur final optimal models achieved relatively high performance values, and we discuss differences in performance with regard to sample size and variable treatments. Our results showed that, for both the establishment model and introduction model, the number of invaded countries was the most important or second most important determinant, respectively. Therefore, we suggest that future success for introduction and establishment of exotic birds may be gauged by simply looking at previous success in invading other countries. Finally, we found that species traits related to reproduction were more important in establishment models than in introduction models; importantly, these determinants were not averaged but either minimum or maximum values of species traits. Therefore, we suggest that in addition to averaged values, reproductive potential represented by minimum and maximum values of species traits should be considered in invasion studies. creator: Shih-Hsiung Liang creator: Bruno Andreas Walther creator: Bao-Sen Shieh uri: https://doi.org/10.7717/peerj.3092 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Liang et al. title: From big data to diagnosis and prognosis: gene expression signatures in liver hepatocellular carcinoma link: https://peerj.com/articles/3089 last-modified: 2017-03-14 description: BackgroundLiver hepatocellular carcinoma accounts for the overwhelming majority of primary liver cancers and its belated diagnosis and poor prognosis call for novel biomarkers to be discovered, which, in the era of big data, innovative bioinformatics and computational techniques can prove to be highly helpful in.MethodsBig data aggregated from The Cancer Genome Atlas and Natural Language Processing were integrated to generate differentially expressed genes. Relevant signaling pathways of differentially expressed genes went through Gene Ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes and Panther pathway enrichment analysis and protein-protein interaction network. The pathway ranked high in the enrichment analysis was further investigated, and selected genes with top priority were evaluated and assessed in terms of their diagnostic and prognostic values.ResultsA list of 389 genes was generated by overlapping genes from The Cancer Genome Atlas and Natural Language Processing. Three pathways demonstrated top priorities, and the one with specific associations with cancers, ‘pathways in cancer,’ was analyzed with its four highlighted genes, namely, BIRC5, E2F1, CCNE1, and CDKN2A, which were validated using Oncomine. The detection pool composed of the four genes presented satisfactory diagnostic power with an outstanding integrated AUC of 0.990 (95% CI [0.982–0.998], P < 0.001, sensitivity: 96.0%, specificity: 96.5%). BIRC5 (P = 0.021) and CCNE1 (P = 0.027) were associated with poor prognosis, while CDKN2A (P = 0.066) and E2F1 (P = 0.088) demonstrated no statistically significant differences.DiscussionThe study illustrates liver hepatocellular carcinoma gene signatures, related pathways and networks from the perspective of big data, featuring the cancer-specific pathway with priority, ‘pathways in cancer.’ The detection pool of the four highlighted genes, namely BIRC5, E2F1, CCNE1 and CDKN2A, should be further investigated given its high evidence level of diagnosis, whereas the prognostic powers of BIRC5 and CCNE1 are equally attractive and worthy of attention. creator: Hong Yang creator: Xin Zhang creator: Xiao-yong Cai creator: Dong-yue Wen creator: Zhi-hua Ye creator: Liang Liang creator: Lu Zhang creator: Han-lin Wang creator: Gang Chen creator: Zhen-bo Feng uri: https://doi.org/10.7717/peerj.3089 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yang et al. title: Computer modelling reveals new conformers of the ATP binding loop of Na+/K+-ATPase involved in the transphosphorylation process of the sodium pump link: https://peerj.com/articles/3087 last-modified: 2017-03-14 description: Hydrolysis of ATP by Na+/K+-ATPase, a P-Type ATPase, catalyzing active Na+ and K+ transport through cellular membranes leads transiently to a phosphorylation of its catalytical α-subunit. Surprisingly, three-dimensional molecular structure analysis of P-type ATPases reveals that binding of ATP to the N-domain connected by a hinge to the P-domain is much too far away from the Asp369 to allow the transfer of ATP’s terminal phosphate to its aspartyl-phosphorylation site. In order to get information for how the transfer of the γ-phosphate group of ATP to the Asp369 is achieved, analogous molecular modeling of the M4–M5 loop of ATPase was performed using the crystal data of Na+/K+-ATPase of different species. Analogous molecular modeling of the cytoplasmic loop between Thr338 and Ile760 of the α2-subunit of Na+/K+-ATPase and the analysis of distances between the ATP binding site and phosphorylation site revealed the existence of two ATP binding sites in the open conformation; the first one close to Phe475 in the N-domain, the other one close to Asp369 in the P-domain. However, binding of Mg2+•ATP to any of these sites in the “open conformation” may not lead to phosphorylation of Asp369. Additional conformations of the cytoplasmic loop were found wobbling between “open conformation” <==> “semi-open conformation <==> “closed conformation” in the absence of 2Mg2+•ATP. The cytoplasmic loop’s conformational change to the “semi-open conformation”—characterized by a hydrogen bond between Arg543 and Asp611—triggers by binding of 2Mg2+•ATP to a single ATP site and conversion to the “closed conformation” the phosphorylation of Asp369 in the P-domain, and hence the start of Na+/K+-activated ATP hydrolysis. creator: Gracian Tejral creator: Bruno Sopko creator: Alois Necas creator: Wilhelm Schoner creator: Evzen Amler uri: https://doi.org/10.7717/peerj.3087 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Tejral et al.