title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1085 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Monitoring rhinoceroses in Namibia’s private custodianship properties link: https://peerj.com/articles/9670 last-modified: 2020-08-14 description: Routinely censusing rhinoceros’ populations is central to their conservation and protection from illegal killing. In Namibia, both white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros occur on private land, in the latter case under a custodianship program of the Namibian Ministry of Environment and Tourism (MET). Black rhinoceros custodian landowners are responsible for the protection of the rhinoceroses on their land and are required to report regularly to the MET. Monitoring imposes a financial burden on custodians yet many of the techniques used involve expensive monitoring techniques that include the need for aerial support and/or animal instrumentation. During May and June 2018, WildTrack undertook a pilot study to census black and white rhinoceros on three private custodianship properties in Namibia. We tested three footprint identification methods for obtaining estimates of rhinoceros populations in an effort to provide less costly alternative monitoring options to rhinoceros custodians. The first was a full monitoring protocol with two components: (a) tracking each individual animal and matching them to their footprints, (b) identifying those individuals from the heel lines on the prints. The second method used simple visual heel line identification ex-situ, and the third method used just an objective footprint identification technique. These methods offer different options of fieldwork labour and cost and were designed to offer monitoring options to custodians that provided information about rhinoceros movement and location, with minimal disturbance to the rhinoceros, and best matched their human and economic resources. In this study, we describe the three methods and report the results of the pilot study to compare and evaluate their utility for rhinoceros monitoring. The first method successfully matched each trail photographed to a known rhinoceros at each site. When the other two methods disagreed with the first, they did so by failing to match single trails to a known rhinoceros, thereby creating fictitious identities consisting of a single trail. This failure occurred twice in one application, but otherwise at most once. We expect this failure can be eliminated through more stringent criteria for collecting photographs of footprints. We also briefly compare the use of footprint monitoring with other commonly used monitoring techniques. On this basis, landowners hosting rhinoceros can evaluate which method best suits their needs and resources. creator: Zoe C. Jewell creator: Sky Alibhai creator: Peter R. Law creator: Kenneth Uiseb creator: Stephen Lee uri: https://doi.org/10.7717/peerj.9670 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jewell et al. title: Identifying disease-associated signaling pathways through a novel effector gene analysis link: https://peerj.com/articles/9695 last-modified: 2020-08-14 description: BackgroundSignaling pathway analysis methods are commonly used to explain biological behaviors of disease cells. Effector genes typically decide functional attributes (associated with biological behaviors of disease cells) by abnormal signals they received. The signals that the effector genes receive can be quite different in normal vs. disease conditions. However, most of current signaling pathway analysis methods do not take these signal variations into consideration.MethodsIn this study, we developed a novel signaling pathway analysis method called signaling pathway functional attributes analysis (SPFA) method. This method analyzes the signal variations that effector genes received between two conditions (normal and disease) in different signaling pathways.ResultsWe compared the SPFA method to seven other methods across 33 Gene Expression Omnibus datasets using three measurements: the median rank of target pathways, the median p-value of target pathways, and the percentages of significant pathways. The results confirmed that SPFA was the top-ranking method in terms of median rank of target pathways and the fourth best method in terms of median p-value of target pathways. SPFA’s percentage of significant pathways was modest, indicating a good false positive rate and false negative rate. Overall, SPFA was comparable to the other methods. Our results also suggested that the signal variations calculated by SPFA could help identify abnormal functional attributes and parts of pathways. The SPFA R code and functions can be accessed at https://github.com/ZhenshenBao/SPFA. creator: Zhenshen Bao creator: Bing Zhang creator: Li Li creator: Qinyu Ge creator: Wanjun Gu creator: Yunfei Bai uri: https://doi.org/10.7717/peerj.9695 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bao et al. title: Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions link: https://peerj.com/articles/9697 last-modified: 2020-08-14 description: The kiwifruit bacterial canker (Pseudomonas syringae pv. actinidiae; Psa) causes severe damage to kiwifruit production worldwide. Psa biovar 6 (Psa6), which was isolated in Japan in 2015, produces two types of phytotoxins: coronatine and phaseolotoxin. To elucidate the unique virulence of Psa6, we performed transcriptomic analysis of phytotoxin synthesis genes and type III effector genes in in vitro cultivation using various media. The genes related to phytotoxin synthesis and effectors of Psa6 were strictly regulated in the coronatine-inducing mediums (HS and HSC); 14 of 23 effector genes and a hrpL sigma factor gene were induced at 3 h after transferring to the media (early-inducible genes), and phytotoxin synthesis genes such as argD of phaseolotoxin and cfl of coronatine were induced at 6 and 12 h after transferring to the media (late-inducible genes). In contrast, induction of these genes was not observed in the hrp-inducing medium. Next, to examine whether the changes in gene expression in different media is specific to Psa6, we investigated gene expression in other related bacteria. For Psa biovar 1 (Psa1), biovar 3 (Psa3), and P. s. pv. glycinea (Psg), no clear trends were observed in expression behavior across various culture media and incubation times. Therefore, Psa6 seems to exert its virulence efficiently by using two phytotoxins and effectors according to environmental changes. This is not seen in other biovars and pathovars, so it is thought that Psa6 has acquired its own balance of virulence. creator: Karin Hirose creator: Yasuhiro Ishiga creator: Takashi Fujikawa uri: https://doi.org/10.7717/peerj.9697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Hirose et al. title: Methylene blue inhibits nucleation and elongation of SOD1 amyloid fibrils link: https://peerj.com/articles/9719 last-modified: 2020-08-14 description: Protein aggregation into highly-structured amyloid fibrils is linked to several neurodegenerative diseases. Such fibril formation by superoxide dismutase I (SOD1) is considered to be related to amyotrophic lateral sclerosis, a late-onset and fatal disorder. Despite much effort and the discovery of numerous anti-amyloid compounds, no effective cure or treatment is currently available. Methylene blue (MB), a phenothiazine dye, has been shown to modulate the aggregation of multiple amyloidogenic proteins. In this work we show its ability to inhibit both the spontaneous amyloid aggregation of SOD1 as well as elongation of preformed fibrils. creator: Greta Musteikyte creator: Mantas Ziaunys creator: Vytautas Smirnovas uri: https://doi.org/10.7717/peerj.9719 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Musteikyte et al. title: Correlation between fruit weight and nutritional metabolism during development in CPPU-treated Actinidia chinensis ‘Hongyang’ link: https://peerj.com/articles/9724 last-modified: 2020-08-14 description: Forchlorfenuron, N-(2-chloro-4-pyridyl)-N-phenylurea (CPPU), is often used to promote fruit growth and improve production. The role of CPPU in kiwifruit growth has been established. However, the correlation between fruit weight and nutritional metabolism during development after CPPU treatments remains largely undetermined. Here, we surveyed the variations in weight and nutrient components of the ‘Hongyang’ kiwifruit (Actinidia chinensis) when CPPU was sprayed on fruit 25 days after anthesis. The CPPU application did not significantly influence the dry matter, soluble solids, starch, vitamin C or protein concentrations. However, the fresh weight, length and maximum diameter were significantly increased compared with the control. Moreover, in fruit of the same developmental stage, the fructose, glucose and soluble sugar levels increased after the CPPU treatment, compared with the control. On the contrary, citric, quinic and titratable acid concentrations decreased. However, a correlation analysis between fresh weight and the nutritional contents revealed that CPPU did not affect the concentrations of the most abundant organic acids (quinic and citric) and sugars (glucose, fructose and sucrose), compared with control fruit of the same weight. Therefore, CPPU applications enhance ‘Hongyang’ kiwifruit weight/size. However, there were no significant differences in the nutritional qualities of treated and untreated fruit having the same weights. creator: Guo-liang Qiu creator: Qi-guo Zhuang creator: Yu-fei Li creator: Si-yu Li creator: Cun Chen creator: Zheng-hao Li creator: Yu-yang Zhao creator: Yi Yang creator: Zhi-bin Liu uri: https://doi.org/10.7717/peerj.9724 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Qiu et al. title: Confidence in the dynamic spread of epidemics under biased sampling conditions link: https://peerj.com/articles/9758 last-modified: 2020-08-14 description: The interpretation of sampling data plays a crucial role in policy response to the spread of a disease during an epidemic, such as the COVID-19 epidemic of 2020. However, this is a non-trivial endeavor due to the complexity of real world conditions and limits to the availability of diagnostic tests, which necessitate a bias in testing favoring symptomatic individuals. A thorough understanding of sampling confidence and bias is necessary in order make accurate conclusions. In this manuscript, we provide a stochastic model of sampling for assessing confidence in disease metrics such as trend detection, peak detection and disease spread estimation. Our model simulates testing for a disease in an epidemic with known dynamics, allowing us to use Monte-Carlo sampling to assess metric confidence. This model can provide realistic simulated data which can be used in the design and calibration of data analysis and prediction methods. As an example, we use this method to show that trends in the disease may be identified using under 10,000 biased samples each day, and an estimate of disease spread can be made with additional 1,000–2,000 unbiased samples each day. We also demonstrate that the model can be used to assess more advanced metrics by finding the precision and recall of a strategy for finding peaks in the dynamics. creator: James Brunner creator: Nicholas Chia uri: https://doi.org/10.7717/peerj.9758 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Brunner and Chia title: Resumption of donor-origin spermatogenesis in senescent goldfish Carassius auratus (Linnaeus, 1758) following spermatogonial cell therapy link: https://peerj.com/articles/9116 last-modified: 2020-08-13 description: Stem cell research has come into prominence because of its applications in assisted reproductive technology and the treatment of deadly diseases. In teleost fishes, spermatogonial stem cells have been effectively used to produce surrogate gametes and progeny through germ cell transplantation technique. The present study is the first report of an innovative application of stem cell therapy in fish species for revitalising the reproductive competence of senescent individuals. Senescent male goldfish, Carassius auratus, approximately 10 years of age were procured from a fish-breeding farm and were reared locally in the lab for an additional two years. The senescence of the individuals was then evaluated and confirmed using histological analysis, gonadal index assessment, and germ-cell specific vasa gene expression. Analyses revealed absence of spermatogonial cells and other germ cells in the testes of the senescent fish (n = 5). Spermatogonial cells from sexually immature C. auratus male donor were isolated using discontinuous percoll gradients, labelled with the fluorescent dye PKH-26, and transplanted into the gonads of senescent C. auratus males through urogenital papilla. Six months after the transplant, spermatozoa were collected through applying gentle manual pressure on the abdomen and were observed under a microscope. All C. auratus males with the transplant had produced spermatozoa from the transplanted cells. This was confirmed by the retention of PKH-26 in the spermatozoa and diagnostic SSR locus. Gravid C. auratus females were artificially inseminated with the spermatozoa of those senescent males and natural spawning was allowed. As a result viable progeny were produced. These observation suggests that the reproductive competence of senescent male fishes can be revitalised through spermatogonial stem cell therapy to produce functional gametes. creator: Sullip K. Majhi creator: Mog Chowdhury creator: Santosh Kumar creator: Rajeev K. Singh creator: Vindhya Mohindra creator: Kuldeep K. Lal uri: https://doi.org/10.7717/peerj.9116 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Majhi et al. title: The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research link: https://peerj.com/articles/9467 last-modified: 2020-08-13 description: Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database. creator: Benjamin Bolduc creator: Suzanne B. Hodgkins creator: Ruth K. Varner creator: Patrick M. Crill creator: Carmody K. McCalley creator: Jeffrey P. Chanton creator: Gene W. Tyson creator: William J. Riley creator: Michael Palace creator: Melissa B. Duhaime creator: Moira A. Hough creator: Scott R. Saleska creator: Matthew B. Sullivan creator: Virginia I. Rich uri: https://doi.org/10.7717/peerj.9467 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bolduc et al. title: Effects of Sr2 + on the preparation of Escherchia coli DH5α competent cells and plasmid transformation link: https://peerj.com/articles/9480 last-modified: 2020-08-13 description: Bacterial gene transformation used with Escherichia coli as a desired microorganism is one of the important techniques in genetic engineering. In this study, the preparation of E. coli DH5α competent cells treated with SrCl2 and transformation by heat-shock with pUC19 plasmid was optimized by Response Surface Methodology (RSM). Other five E. coli strains including BL21 (DE3), HB-101, JM109, TOP10 and TG1, three different sizes plasmids (pUC19, pET32a, pPIC9k) were used to verify the protocol, respectively. The transformation mechanism was explored by scanning electron microscope combined with energy dispersive spectrometer (SEM-EDS), atomic absorption spectroscopy (AAS) and Fourier-transform infrared spectroscopy (FT-IR). An equation of regression model was obtained, and the ideal parameters were Sr2 + ions of 90 mM, heat-shock time of 90 s and 9 ng of plasmid. Under this conditions, the transformation efficiency could almost reach to 106 CFU/µg DNA. A small change of the cell surface structure has been observed between E. coli DH5α strain and competent cells by abovementioned spectrum technologies, which implied that a strict regulation mechanism involved in the formation of competent cells and transformation of plasmids. An equation of regression model for the competent cells preparation and plasmid transformation could be applied in gene cloning technology creator: Yonggang Wang creator: Xinjian Wang creator: Linmiao Yu creator: Yuan Tian creator: Shaowei Li creator: Feifan Leng creator: Jianzhong Ma creator: Jixiang Chen uri: https://doi.org/10.7717/peerj.9480 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Steroid hormones and chondrichthyan reproduction: physiological functions, scientific research, and implications for conservation link: https://peerj.com/articles/9686 last-modified: 2020-08-13 description: The study of the reproductive aspects of chondrichthyans through the analysis of steroid hormones has been carried out for more than five decades in several species around the world. This scientific knowledge constitutes the basis of the reproductive endocrinology of chondrichthyans, which has provided information regarding their sexual maturation, gametogenesis, mating seasons, gestation periods, and parturition. The present review summarises the existing literature on steroid hormones in chondrichthyan reproduction and identifies future research directions addressing critical knowledge gaps in the reproductive physiology of this taxon. A total of 59 peer reviewed scientific papers from 1963 to 2020 were reviewed and the following parameters analysed: species, steroid hormones, biological matrix, field sampling (year, location), and methodology (assays, sample size, precision, and recoveries). We provided a summary of the methods, biological matrices, and the functions of up to 19 hormones on the biology of 34 species of chondrichthyans that have been analysed to date. The majority of the studies used radioimmunoassay as the main methodology (76.3%; n = 45/49); while the most frequent biological matrix used was plasma (69.5%; n = 41/49). A Kernel’s heat map was generated to present the scientific effort according to geographic location and evidenced a lack of research in high biodiversity areas for chondrichthyans worldwide. The implications of the study of steroid hormones for the conservation of chondrichthyans are discussed, as only 2.9% of the species of this group have been analysed and most of the scientific effort (93.2%; n = 55/59 papers) has focused on the analysis of less than six hormones. creator: Edgar Eduardo Becerril-García creator: Marcial Arellano-Martínez creator: Daniela Bernot-Simon creator: Edgar Mauricio Hoyos-Padilla creator: Felipe Galván-Magaña creator: Céline Godard-Codding uri: https://doi.org/10.7717/peerj.9686 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Becerril-García et al.