Ozymandias: a biodiversity knowledge graph
Enormous quantities of biodiversity data are being made available online, but much of this data remains isolated in silos. One approach to breaking these silos is to map local, often database-specific identifiers to shared global identifiers. This mapping can then be used to construct a knowledge graph, where entities such as taxa, publications, people, places, specimens, sequences, and institutions are all part of a single, shared knowledge space. Motivated by the 2018 GBIF Ebbe Nielsen Challenge I explore the feasibility of constructing a “biodiversity knowledge graph” for the Australian fauna. The data cleaning and reconciliation steps involved in constructing the knowledge graph are described in detail. Examples are given of its application to understanding changes in patterns of taxonomic publication over time. A web interface to the knowledge graph (called “Ozymandias”) is available at https://ozymandias-demo.herokuapp.com.
Page (2019) Ozymandias: a biodiversity knowledge graph. PeerJ 7:e6739 https://doi.org/10.7717/peerj.6739
Genotypic variation in disease susceptibility among cultured stocks of elkhorn and staghorn corals
Disease mortality has been a primary driver of population declines and the threatened status of the foundational Caribbean corals, Acropora palmata and A. cervicornis. There remain few tools to effectively manage coral disease. Substantial investment is flowing into in situ culture and population enhancement efforts, while disease takes a variable but sometimes high toll in restored populations. If genetic resistance to disease can be identified in these corals, it may be leveraged to improve resistance in restored populations and possibly lead to effective diagnostic tests and disease treatments. Using a standardized field protocol based on replicated direct-graft challenge assays, we quantified this important trait in cultured stocks from three field nurseries in the Florida Keys. Field tests of 12 genotypes of A. palmata and 31 genotypes of A. cervicornis revealed significant genotypic variation in disease susceptibility of both species measured both as risk of transmission (percent of exposed fragments that displayed tissue loss) and as the rate of tissue loss (cm2 d–1) in fragments with elicited lesions. These assay results provide a measure of relative disease resistance that can be incorporated, along with consideration of other important traits such as growth and reproductive success, into restoration strategies to yield more resilient populations.
Miller et al. (2019) Genotypic variation in disease susceptibility among cultured stocks of elkhorn and staghorn corals. PeerJ 7:e6751 https://doi.org/10.7717/peerj.6751
Efficacy and potential of phage therapy against multidrug resistant Shigella spp.
Shigella-infected bacillary dysentery or commonly known as Shigellosis is a leading cause of morbidity and mortality worldwide. The gradual emergence of multidrug resistant Shigella spp. has triggered the search for alternatives to conventional antibiotics. Phage therapy could be one such suitable alternative, given its proven long term safety profile as well as the rapid expansion of phage therapy research. To be successful, phage therapy will need an adequate regulatory framework, effective strategies, the proper selection of appropriate phages, early solutions to overcome phage therapy limitations, the implementation of safety protocols, and finally improved public awareness. To achieve all these criteria and successfully apply phage therapy against multidrug resistant shigellosis, a comprehensive study is required. In fact, a variety of phage-based approaches and products including single phages, phage cocktails, mutated phages, genetically engineered phages, and combinations of phages with antibiotics have already been carried out to test the applications of phage therapy against multidrug resistant Shigella. This review provides a broad survey of phage treatments from past to present, focusing on the history, applications, limitations and effective solutions related to, as well as the prospects for, the use of phage therapy against multidrug resistant Shigella spp. and other multidrug resistant bacterial pathogens.
Tang et al. (2019) Efficacy and potential of phage therapy against multidrug resistant Shigella spp.. PeerJ 7:e6225 https://doi.org/10.7717/peerj.6225
Enhancement of carbon monoxide concentration in atmosphere due to large scale forest fire of Uttarakhand
The richly forested Indian state of Uttarakhand experienced widespread forest fires in April to May 2016. The current study examines dispersion of carbon monoxide (CO) from the source regions of forest fire to distant places, using the Lagrangian particle dispersion model, FLEXPART. Atmospheric Infrared Sounder (AIRS) observations revealed that CO columnar concentrations had increased by almost 28 percentage during 24 April to 02 May 2016 with respect to the previous non-burning period of April 2016 at Uttarakhand. It is also seen that there is considerable enhancement of 45 percentage in average columnar concentration of CO during the burning period, compared to that in the previous 5 years as observed by AIRS. In the present study, concentrations of CO at different pressure levels and columnar CO over Uttarakhand during the forest fire event have been simulated using FLEXPART. The area averaged profile of model derived CO has been compared with the profile from AIRS onboard Aqua. Comparison between model derived columnar CO and satellite observations shows good agreement with coefficient of correlation (r) approximately 0.91 over the burnt areas. Further analysis using FLEXPART reveals that the transport of pollutants is towards north-eastern and eastern regions from the locations of forest fire events. Model derived vertical distribution of CO over Tibet, which is situated at the north-east of Uttarakhand, shows significant increase of CO concentration at higher altitudes around 3 km from the mean sea level during the fire event. FLEXPART results show that the emissions from the Uttarakhand fires were transported to Tibet during the study period.
Thakur et al. (2019) Enhancement of carbon monoxide concentration in atmosphere due to large scale forest fire of Uttarakhand. PeerJ 7:e6507 https://doi.org/10.7717/peerj.6507
Evaluation of potential molecular interaction between quorum sensing receptor, LuxP and grouper fatty acids: in-silico screening and simulation
Pathologically relevant behaviors of Vibrio, such as the expression of virulence factors, biofilm production, and swarming motility, have been shown to be controlled by quorum sensing. The autoinducer-2 quorum sensing receptor protein LuxP is one of the target proteins for drug development to suppress the virulence of Vibrio. Here, we reported the potential molecular interaction of fatty acids identified in vibriosis-resistant grouper with LuxP. Fatty acid, 4-oxodocosahexaenoic acid (4R8) showed significant binding affinity toward LuxP (−6.0 kcal/mol) based on molecular docking analysis. The dynamic behavior of the protein–ligand complex was illustrated by molecular dynamic simulations. The fluctuation of the protein backbone, the stability of ligand binding, and hydrogen bond interactions were assessed, suggesting 4R8 possesses potential interaction with LuxP, which was supported by the low binding free energy (−29.144 kJ/mol) calculated using the molecular mechanics Poisson–Boltzmann surface area.
Low et al. (2019) Evaluation of potential molecular interaction between quorum sensing receptor, LuxP and grouper fatty acids: in-silico screening and simulation. PeerJ 7:e6568 https://doi.org/10.7717/peerj.6568
Cafeteria diet increased adiposity in comparison to high fat diet in young male rats
Background Dietary intervention studies in animal models of obesity are crucial to elucidate the mechanistic effects of specific nutrients and diets. Although several models of diet induced obesity have been examined in rodents to assess obesity, there are few studies that have researched influence of different high fat and/or westernized diets. The aim of this study was to compare a high fat diet and a cafeteria diet on obesity related biochemical and physiological parameters in young male rats. Methods Five week old Wistar male rats were fed a control chow diet (C), butter-based high fat diet (HF) or cafeteria diet (CAF) for twelve weeks. In HF, 40% of energy came from fat and this ratio was 46% in CAF. CAF composed of highly energetic and palatable human foods along with chow diet. At the end of the feeding protocol all animals were culled using CO2 asphyxia and cervical dislocation after an overnight fasting. Results Total energy and fat intake of CAF was significantly higher than C and HF. CAF was more effective in inducing obesity, as demonstrated by increased weight gain, Lee index, fat depot weights and total body fat in comparison to C and HF. Despite increased adiposity in CAF, plasma glucose, insulin and HOMA-IR levels were similar between the groups. Plasma leptin and cholesterol levels were markedly higher in CAF than C and HF. Discussion We have demonstrated that there are differential effects of high fat diet and cafeteria diet upon obesity and obesity-related parameters, with CAF leading to a more pronounced adiposity in comparison to high fat diet in young male rats. Future studies should consider the varied outcomes of different diet induced obesity models and development of a standardized approach in similar research practices.
Buyukdere et al. (2019) Cafeteria diet increased adiposity in comparison to high fat diet in young male rats. PeerJ 7:e6656 https://doi.org/10.7717/peerj.6656
Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica
Background Lysyl oxidases (LOX) have been extensively studied in mammals, whereas properties and functions of recently found homologues in prokaryotic genomes remain enigmatic. Methods LOX open reading frame was cloned from Haloterrigena turkmenica in an E. coli expression vector. Recombinant Haloterrigena turkmenica lysyl oxidase (HTU-LOX) proteins were purified using metal affinity chromatography under denaturing conditions followed by refolding. Amine oxidase activity has been measured fluorometrically as hydrogen peroxide release coupled with the oxidation of 10-acetyl-3,7-dihydroxyphenoxazine in the presence of horseradish peroxidase. Rabbit polyclonal antibodies were obtained and used in western blotting. Results Cultured H. turkmenica has no detectable amine oxidase activity. HTU-LOX may be expressed in E. coli with a high protein yield. The full-length protein gives no catalytic activity. For this reason, we hypothesized that the hydrophobic N-terminal region may interfere with proper folding and its removal may be beneficial. Indeed, truncated His-tagged HTU-LOX lacking the N-terminal hydrophobic signal peptide purified under denaturing conditions can be successfully refolded into an active enzyme, and a larger N-terminal truncation further increases the amine oxidase activity. Refolding is optimal in the presence of Cu2+ at pH 6.2 and is not sensitive to salt. HTU-LOX is sensitive to LOX inhibitor 3-aminopropionitrile. HTU-LOX deaminates usual substrates of mammalian LOX such as lysine-containing polypeptides and polymers. The major difference between HTU-LOX and mammalian LOX is a relaxed substrate specificity of the former. HTU-LOX readily oxidizes various primary amines including such compounds as taurine and glycine, benzylamine being a poor substrate. Of note, HTU-LOX is also active towards several aminoglycoside antibiotics and polymyxin. Western blotting indicates that epitopes for the anti-HTU-LOX polyclonal antibodies coincide with a high molecular weight protein in H. turkmenica cells. Conclusion H. turkmenica contains a lysyl oxidase gene that was heterologously expressed yielding an active recombinant enzyme with important biochemical features conserved between all known LOXes, for example, the sensitivity to 3-aminopropionitrile. However, the native function in the host appears to be cryptic. Significance This is the first report on some properties of a lysyl oxidase from Archaea and an interesting example of evolution of enzymatic properties after hypothetical horizontal transfers between distant taxa.
Pestov et al. (2019) Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica. PeerJ 7:e6691 https://doi.org/10.7717/peerj.6691
Diet and mitochondrial DNA haplotype of a sperm whale (Physeter macrocephalus) found dead off Jurong Island, Singapore
Despite numerous studies across the large geographic range of the sperm whale (Physeter macrocephalus), little is known about the diet and mitochondrial DNA haplotypes of this strongly female philopatric species in waters off Southeast Asia. A female sperm whale found dead in Singapore waters provided the opportunity to study her diet and mitochondrial DNA haplotype. Here we report on the identification of stomach contents and mitochondrial DNA haplotype of this individual, and we include coastal hydrodynamic modelling to determine the possible geographic origin of the whale. At least 28 species of prey were eaten by this adult female whale, most of which were cephalopods. The mesopelagic squids Taonius pavo, Histioteuthis pacifica, Chiroteuthis imperator,and Ancistrocheirus lesueurii made up over 65% of the whale’s stomach contents. Plastic debris was also found in the whale’s stomach. Based on the diet, genetics, and coastal hydrodynamic modelling that suggest an easterly drift of the whale carcass over several days, the dead sperm whale in Singapore probably originated from a pod in the Southern Indian Ocean. This study provides an increase in the understanding the diet and natural history of the sperm whale in Southeast Asia. The combined analyses of stomach contents, DNA, and hydrodynamic modeling could provide a context to future studies on the sperm whale strandings, and have broader applicability for other marine mammals in the region.
Chua et al. (2019) Diet and mitochondrial DNA haplotype of a sperm whale (Physeter macrocephalus) found dead off Jurong Island, Singapore. PeerJ 7:e6705 https://doi.org/10.7717/peerj.6705
HERVs, immunity, and autoimmunity: understanding the connection
Since their discovery in the 1960s, further investigation into endogenous retroviruses (ERVs) has challenged the conventional view of viral sequences as exclusively parasitic elements. Once presumed to be a group of passive genetic relics, it is becoming increasingly clear that this view of ERVs, while generally accurate, is incorrect in many specific cases. Research has identified ERV genes that appear to be co-opted by their mammalian hosts, but the biological function of ERV elements in humans remains a controversial subject. One area that has attracted some attention in this domain is the role of co-opted ERV elements in mammalian immune systems. The relationship between ERVs and human autoimmune diseases has also been investigated, but has historically been treated as a separate topic. This review will summarize the current evidence concerning the phenotypic significance of ERVs, both in the healthy immune system and in manifestations of autoimmunity. Furthermore, it will evaluate the relationship between these fields of study, and propose previously-unexplored molecular mechanisms through which human endogenous retroviruses might contribute to certain autoimmune pathologies. Investigation into these novel mechanisms could further our understanding of the molecular basis of autoimmune disease, and may one day provide new targets for treatment.
Greenig (2019) HERVs, immunity, and autoimmunity: understanding the connection. PeerJ 7:e6711 https://doi.org/10.7717/peerj.6711
Overexpression of lncRNA H19 changes basic characteristics and affects immune response of bovine mammary epithelial cells
The function of long non-coding RNA H19 (H19) on cell proliferation has been observed in various cell types, and the increased expression of H19 was also found in the lipopolysaccharide (LPS)-induced inflammatory bovine mammary epithelial cells (MAC-T). However, the roles of H19 in the inflammatory response and physiological functions of bovine mammary epithelial cell are not clear. In the present study, we found that overexpression of H19 in MAC-T cells significantly promoted cell proliferation, increased the protein and mRNA level of β-casein, and enhanced the expression of tight junction (TJ)-related proteins while inhibited staphylococcus aureus adhesion to cells. In addition, results demonstrated that overexpression of H19 affected the LPS-induced immune response of MAC-T cells by promoting expressions of inflammatory factors, including TNF-α, IL-6, CXCL2 and CCL5, and activating the NF-κB signal pathway. Our findings indicate that H19 is likely to play an important role in maintaining normal functions and regulating immune response of bovine mammary epithelial cells.
Li et al. (2019) Overexpression of lncRNA H19 changes basic characteristics and affects immune response of bovine mammary epithelial cells. PeerJ 7:e6715 https://doi.org/10.7717/peerj.6715