Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns
Assessment of negative affective states is a key component of animal welfare research. In laying hens, excessive fearfulness results in reduced production and increased sensitivity to stress. Fearfulness can be defined as a response to a known threat, but anxiety is a response to an unknown threat and may have similar negative consequences. The open field test and tonic immobility test are commonly applied to measure fearfulness in laying hens. An attention bias test that measured individual hen’s responses to playback of a conspecific alarm call in the presence of food was recently pharmacologically validated using an anxiogenic drug but was confounded by the hen’s typical motionless response in a novel environment. The current study used 56-week old free-range layers to further assess the validity of an attention bias test to differentiate ranging treatment groups in comparison with the open field and tonic immobility tests. The selected hens varied in their range use patterns as tracked by radio-frequency identification technology. ‘Indoor’ hens did not access the range and ‘outdoor’ hens ranged daily; previous research has confirmed higher fearfulness in hens that remain indoors. The tonic immobility test did not differentiate ranging groups (P = 0.34), but indoor birds were slower to first step (P = 0.03) and stepped less (P = 0.02) in the open field test. The attention bias test occurred in an isolated wooden box using a conspecific alarm call playback (a threat) and mixed grain (a positive stimulus). The behavioural response of latency to resume eating following playback of the alarm call was measured to differentiate the anxiety states of the indoor and outdoor ranging birds. Before the attention bias test could occur, birds had to be habituated to the test box across three separate 5-minute sessions to increase the willingness to feed within the novel test environment. All birds ate faster across time (P < 0.001) but the indoor birds were slower to eat than the outdoor birds (P < 0.001). In this study, the latency to resume eating following an alarm call was determined to be a poor measure for highly anxious birds as they failed to eat at all. Forty-six percent of indoor hens were excluded for not eating across the 5-minute test. Of the birds that did eat, only 7% of indoor hens ate following playback of the alarm call, compared with 36% of outdoor hens. This repetition of an attention bias test for laying hens highlights the challenges in assessing hens with extreme fearful/anxious responses and that information may be missed when non-performing hens are excluded from behavioural tests. We suggest that latency to eat in a novel arena without any alarm call playback is an informative measure of anxious state that can be applied to all hens but consideration must be made of potential differences in food motivation.
Campbell et al. (2019) Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns. PeerJ 7:e8122 https://doi.org/10.7717/peerj.8122
Introducing a new tool to navigate, understand and use International Codes of Nomenclature
Background In order to designate the various concepts of taxa in biology, evolution and paleontology, scientists have developed various rules on how to create unique names for taxa. Different Codes of Nomenclature have been developed for animals, plants, fungi, bacteria etc., with standard sets of Rules that govern the formation, publication and application of the nomina of extant and extinct species. These Codes are the result of decades of discussions, workshops, publications and revisions. The structure and complexity of these Codes have been criticized many times by zoologists. This project aims, using the International Code of Zoological Nomenclature as a case study, to show that the structure of these Codes is better reflected and understood as networks. Methods The majority of the text of the Code has been divided into hundreds of Nodes of different types, connected to each other with different types of Edges to form a network. The various mathematical descriptors of the entire system, as well as for the elements of the network, have been conceptually framed to help describing and understanding the Code as a network. Results The network of the Code comprises 1,379 Nodes, which are connected with 11,276 Edges. The structure of the Code can be accurately described as a network, a mathematical structure that is better suited than any kind of linear text publication to reflect its structure. Discussion Thinking of the Code as a network allows a better, in-depth understanding of the Code itself, as the user can navigate in a more efficient way, as well as to depict and analyze all the implied connections between the various parts of the Code that are not visible immediately. The network of the Code is an open access tool that could also help teaching, using and disseminating the Code. More importantly, this network is a powerful tool that allows identifying a priori the parts of the Code that could be potentially affected by upcoming amendment and revisions. This kind of analysis is not limited to nomenclature, as it could be applied to other fields that use complex textbooks with long editing history, such as Law, Medicine and Linguistics.
Vlachos (2019) Introducing a new tool to navigate, understand and use International Codes of Nomenclature. PeerJ 7:e8127 https://doi.org/10.7717/peerj.8127
Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction
Mycobacterium avium subsp. paratuberculosis (MAP) is a pathogen causing paratuberculosis in cattle and small ruminants. During the long asymptomatic subclinical stage, high numbers of MAP are excreted and can be transmitted to food for human consumption, where they survive many of the standard techniques of food decontamination. Whether MAP is a human pathogen is currently under debate. The aim of this study was a better understanding of the host-pathogen response by analyzing the interaction of peripheral blood lymphocytes (PBL) from cattle with MAP in their exoproteomes/secretomes to gain more information about the pathogenic mechanisms of MAP. Because in other mycobacterial infections, the immune phenotype correlates with susceptibility, we additionally tested the interaction of MAP with recently detected cattle with a different immune capacity referred as immune deviant (ID) cows. In PBL, different biological pathways were enhanced in response to MAP dependent on the immune phenotype of the host. PBL of control cows activated members of cell activation and chemotaxis of leukocytes pathway as well as IL-12 mediated signaling. In contrast, in ID cows CNOT1 was detected as highly abundant protein, pointing to a different immune response, which could be favorable for MAP. Additionally, MAP exoproteomes differed in either GroEL1 or DnaK abundance, depending on the interacting host immune response. These finding point to an interdependent, tightly regulated response of the bovine immune system to MAP and vise versa.
Kleinwort et al. (2019) Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction. PeerJ 7:e8130 https://doi.org/10.7717/peerj.8130
Mapping theme trends and recognizing hot spots in postmenopausal osteoporosis research: a bibliometric analysis
Background This study aimed to draw a series of scientific maps to quantitatively and qualitatively evaluate hot spots and trends in postmenopausal osteoporosis research using bibliometric analysis. Methods Scientific papers published on postmenopausal osteoporosis were extracted from the Web of Science Core Collection and PubMed database. Extracted information was analyzed quantitatively with bibliometric analysis by CiteSpace, the Online Analysis Platform of Literature Metrology and Bibliographic Item Co-Occurrence Matrix Builder (BICOMB). To explore the hot spots in this field, co-word biclustering analysis was conducted by gCLUTO based on the major MeSH terms/MeSH subheading terms-source literatures matrix. Results We identified that a total of 5,247 publications related to postmenopausal osteoporosis were published between 2013 and 2017. The overall trend decreased from 1,071 literatures in 2013 to 1,048 literatures in 2017. Osteoporosis International is the leading journal in the field of postmenopausal osteoporosis research, both in terms of impact factor score (3.819) and H-index value (157). The United States has retained a top position and has exerted a pivotal influence in this field. The University of California, San Francisco was identified as a leading institution for research collaboration, and Professors Reginster and Kanis have made great achievements in this area. Eight research hot spots were identified. Conclusions Our study found that in the past few years, the etiology and drug treatment of postmenopausal osteoporosis have been research hot spots. They provide a basis for the study of the pathogenesis of osteoporosis and guidelines for the drug treatment of osteoporosis.
Zhou et al. (2019) Mapping theme trends and recognizing hot spots in postmenopausal osteoporosis research: a bibliometric analysis. PeerJ 7:e8145 https://doi.org/10.7717/peerj.8145
Molecular characterization of G-protein-coupled receptor (GPCR) and protein kinase A (PKA) cDNA in Perinereis aibuhitensis and expression during benzo(a)pyrene exposure
Background G-protein-coupled receptors (GPCRs) are one of the most important molecules that transfer signals across the plasma membrane, and play central roles in physiological systems. The molecular architecture of GPCRs allows them to bind to diverse chemicals, including environmental contaminants. Methods To investigate the effects of benzo(a)pyrene (B(a)P) on GPCR signaling, GPCR and the protein kinase A (PKA) catalytic subunit of Perinereis aibuhitensis were cloned. The expression patterns of these two genes during B(a)P exposure were determined with real-time fluorescence quantitative PCR. The PKA content in P. aibuhitensis under B(a)P exposure was examined. Results The full-length cDNAs of PaGPCR and the PaPKA catalytic subunit were 1,514 and 2,662 nucleotides, respectively, encoding 338 and 350 amino acids, respectively. Multiple sequence alignments indicated that the deduced amino acid sequence of PaGPCR shared a low level of similarity with the orphan GPCRs of polychaetes and echinoderms, whereas PaPKA shared a high level of identify with the PKA catalytic subunits of other invertebrates. B(a)P exposure time-dependently elevated the expression of PaGPCR and PaPKA. The expression of both PaGPCR and PaPKA was also dose-dependent, except at a dose of 10 μg/L B(a)P. The PKA content in concentration group was elevated on day 4, with time prolonging the PKA content was down-regulated to control level. Discussion These results suggested that GPCR signaling in P. aibuhitensis was involved in the polychaete’s response to environmental contaminants.
Huang et al. (2019) Molecular characterization of G-protein-coupled receptor (GPCR) and protein kinase A (PKA) cDNA in Perinereis aibuhitensis and expression during benzo(a)pyrene exposure. PeerJ 7:e8044 https://doi.org/10.7717/peerj.8044
Oral toxicity of arjunolic acid on hematological, biochemical and histopathological investigations in female Sprague Dawley rats
Background Arjunolic acid (AA) is a potent phytochemical with wider pharmacological activities. Despite potential medicinal properties on various in vitro and in vivo studies, there is still a dearth of scientific data related to its safety profile and toxicological parameters. The current study aimed to investigate acute toxicity of AA in normal female Sprague Dawley rats. Methods In this study, AA was administered orally at an individual dose of 300 and 2000 mg/kg body weight to group 1 and 2 respectively, while group 3 served as normal control. All the animals were observed for 2 weeks to determine any behavioral and physical changes. On day 15, blood was collected for hematological and biochemical investigation, later animals from all the three groups were euthanized to harvest and store essential organs for histopathological analysis. Four different staining techniques; hematoxylin and eosin, Masson trichrome, Periodic acid Schiff and Oil O Red were used to investigate any alterations in different tissues through microscopical observation. Results The results of the study showed no morbidity and mortality at two different dosage of AA treatment. Daily food & water intake, body weight, relative organ weight, hematological and biochemical parameters were detected to be normal with no severe alteration seen through microscopical investigation in the structure of harvested tissues. Our findings support the safety profile of AA, which was well tolerated at higher dose. Thus, an in-detail study on the subacute disease model is warranted.
Aamir et al. (2019) Oral toxicity of arjunolic acid on hematological, biochemical and histopathological investigations in female Sprague Dawley rats. PeerJ 7:e8045 https://doi.org/10.7717/peerj.8045
Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks
Purpose To investigate whether multi-view convolutional neural networks can improve a fully automated lymph node detection system for pelvic MR Lymphography (MRL) images of patients with prostate cancer. Methods A fully automated computer-aided detection (CAD) system had been previously developed to detect lymph nodes in MRL studies. The CAD system was extended with three types of 2D multi-view convolutional neural networks (CNN) aiming to reduce false positives (FP). A 2D multi-view CNN is an efficient approximation of a 3D CNN, and three types were evaluated: a 1-view, 3-view, and 9-view 2D CNN. The three deep learning CNN architectures were trained and configured on retrospective data of 240 prostate cancer patients that received MRL images as the standard of care between January 2008 and April 2010. The MRL used ferumoxtran-10 as a contrast agent and comprised at least two imaging sequences: a 3D T1-weighted and a 3D T2*-weighted sequence. A total of 5089 lymph nodes were annotated by two expert readers, reading in consensus. A first experiment compared the performance with and without CNNs and a second experiment compared the individual contribution of the 1-view, 3-view, or 9-view architecture to the performance. The performances were visually compared using free-receiver operating characteristic (FROC) analysis and statistically compared using partial area under the FROC curve analysis. Training and analysis were performed using bootstrapped FROC and 5-fold cross-validation. Results Adding multi-view CNNs significantly (p < 0.01) reduced false positive detections. The 3-view and 9-view CNN outperformed (p < 0.01) the 1-view CNN, reducing FP from 20.6 to 7.8/image at 80% sensitivity. Conclusion Multi-view convolutional neural networks significantly reduce false positives in a lymph node detection system for MRL images, and three orthogonal views are sufficient. At the achieved level of performance, CAD for MRL may help speed up finding lymph nodes and assessing them for potential metastatic involvement.
Debats et al. (2019) Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks. PeerJ 7:e8052 https://doi.org/10.7717/peerj.8052
Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ
Background In the predator–sea urchin–macrophyte trophic cascade, the ecological effect of sea urchins as grazers depends both on their density and the changes in foraging activity, which are influenced by various disturbing factors. However, the complete duration of the alarm reactions of echinoids has not been studied until now. Here, we tested a hypothesis that two cohabiting sea urchins, Mesocentrotus nudus and Strongylocentrotus intermedius, which differ morphologically, might display different behavioral responses to high hydrodynamic activity and predation. Methods We used continuous time-lapse video recording to clarify behavioral patterns of M. nudus and S. intermedius in presence of a large quantity of food (the kelp Saccharina japonica) but under different weather conditions and different types of predation threat: (1) calm weather conditions, (2) stormy weather conditions, (3) predation risk associated with the presence of several sea star species and (4) predation risk associated with an alarm stimulus (crushed conspecifics or heterospecifics). Three separate video recording experiments (134 days in total) were conducted under field conditions. Video recording analysis was performed to determine the number of specimens of each sea urchin species in the cameras’ field of view, size of sea urchins’ groups, movement patterns and the duration of the alarm responses of both sea urchin species. Results We showed that in the presence of kelp, M. nudus and S. intermedius exhibited both similar and different behavioral responses to hydrodynamics and predation threat. Under calm weather, movement patterns of both echinoids were similar but M. nudus exhibited the higher locomotion speed and distance traveled. Furthermore, S. intermedius but not M. nudus tended to group near the food substrate. The stormy weather caused a sharp decrease in movement activity followed by escape response in both echinoids. Six starfish species failed to predate on healthy sea urchins of either species and only a few attacks on ailing S. intermedius specimens were successful. The alarm response of S. intermedius lasted approximately 90 h and 20 h for starfish attacks on ailing conspecifics and for simulated attacks (crushed conspecifics or heterospecifics), respectively and involved several phases: (1) flight response, (2) grouping close to the food, (3) leaving the food and (4) return to the food. Phase three was the more pronounced in a case of starfish attack. M. nudus only responded to crushed conspecifics and exhibited no grouping behavior but displayed fast escape (during 4 h) and prolonged (up to 19 days) avoidance of the food source. This outcome is the longest alarm response reported for sea urchins. Discussion The most interesting finding is that two cohabiting sea urchin species, M. nudus and S. intermedius, display different alarm responses to predation threat. Both alarm responses are interpreted as defensive adaptations against visual predators.
Zhadan et al. (2019) Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ. PeerJ 7:e8087 https://doi.org/10.7717/peerj.8087
Munidopsis species (Crustacea: Decapoda: Munidopsidae) from carcass falls in Weijia Guyot, West Pacific, with recognition of a new species based on integrative taxonomy
Several squat lobster specimens of the genus Munidopsis were collected from an artificially placed carcass fall (cow bones) on Weijia Guyot in the western Pacific Ocean. Based on morphological comparisons and molecular analysis, three specimens were confirmed as juveniles of M. albatrossae Pequegnat & Pequegnat, 1973, which represents the first record of this species in the western Pacific. The other specimens collected are newly described as Munidopsis spinifrons sp. nov., which is distinguished from the closely related species in having a spinose rostrum and basal lateral eyespine on the eyestalk. The M. albatrossae from Weijia Guyot exhibited very low genetic distances when compared with a conspecific sample from Monterey Bay, USA, and the closely related species M. aries (A. Milne Edwards, 1880) from the northeastern Atlantic. A phylogenetic tree based on the mtCOI gene shows M. spinifrons sp. nov. as sister to M. vrijenhoeki Jones & Macpherson, 2007 and M. nitida (A. Milne Edwards, 1880), although M. vrijenhoeki presents a complex relationship with other species in the clade. The systematic status of the new species and the closely related species are discussed.
Dong et al. (2019) Munidopsis species (Crustacea: Decapoda: Munidopsidae) from carcass falls in Weijia Guyot, West Pacific, with recognition of a new species based on integrative taxonomy. PeerJ 7:e8089 https://doi.org/10.7717/peerj.8089
Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene
Delta bovine papillomaviruses (δBPVs) causes fibropapillomas or bladder cancer in cattle. E5 is the major oncogene of δBPVs; however, the influence that E5 oncogene has on host microRNA (miRNA) and mRNA expression profiles remains little elucidated. In the present study, small RNA sequencing and RNA sequencing were used to explore alterations in miRNAs and mRNAs in E5 over-expressing Madin-Darby bovine kidney (MDBK) cells compared with controls. In total, 77 miRNAs (including 30 bovine-derived miRNAs) and 223 genes were differentially expressed (DE) following E5 overexpression. The dysregulated genes were mainly involved in metabolic and biosynthetic processes. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, 22 DEGs and nine DE miRNAs were selected for RT-qPCR validation. Of these, downregulation of six miRNAs, bta-miR-34c, bta-miR-122, bta-miR-195, bta-miR-449b, bta-miR-2425-5p, and bta-miR-2428-3p were confirmed; In addition, upregulation of 16 genes, ACSS2, DDIT4, INHBE, INSIG1, PNRC1, PSAT1, PSPH, PYCR1, SC4MOL, SLC34A2, SCD, SPARC, IDI1, PCK2, HMGCS1, and SMIM14 and downregulation of two genes, BATF3 and WFDC2 were confirmed. Specially, bta-miR-34c and bta-miR-449b potentially regulated PYCR1 and DDIT4, which were involved in cancer progression and angiogenesis. Our study presented for the first time the comprehensive miRNA and mRNA alterations in MDBK cells expressing the BPV E5 oncogene, providing new insights into the tumorigenesis induced by BPV E5.
Pang et al. (2019) Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene. PeerJ 7:e8098 https://doi.org/10.7717/peerj.8098