Specific and reliable detection of Myosin 1C isoform A by RTqPCR in prostate cancer cells
Background Prostate cancer (PC) diagnostics and treatment often present a challenging task due to cancer subtype heterogeneity and differential disease progression in patient subgroups. Hence, the critical issue is finding a reliable and sensitive diagnostic and prognostic PC marker, especially for cases of biopsies with low percentages of cancer cells. Isoform A of myosin 1C was shown to be expressed in PC cells and responsible for their invasive properties, however, its feasibility for diagnostic purposes remains to be elucidated. Methods To verify the role of myosin 1C isoform A mRNA expression as a putative prostate cancer marker we performed RT qPCR normalized by three reference genes (GAPDH, YWHAZ, HPRT1) on PC3, RWPE-1, LNCaP and 22Rv1 cell lines. Myosin 1C isoform A detection specificity was confirmed by immunofluorescence staining, cancer and non-cancer prostate cell lines were immunophenotyped by flow cytometry. Results Median normalized mRNA expression level of myosin 1C isoform A in PC cells (PC3 and 22Rv1) is two orders of magnitude higher compared to RWPE-1 cells, which functionally correspond to benign prostate cells. Myosin 1C isoform A expression allows PC cell detection even at a dilution ratio of 1:1000 cancer to non-cancer cells. At the protein level, the mean fluorescence intensity of myosin 1C isoform A staining in PC3 nuclei was only twice as high as in RWPE-1, while the immunophenotypes of both cell lines were similar (CD44+/CD90-/CD133-/CD57-/CD24+-). Conclusions We report a distinct difference in myosin 1C isoform A mRNA levels in malignant (PC3) and benign (RWPE-1) prostate cell lines and suggest a combination of three reference genes for accurate data normalization. For the first time we provide an immunophenotype comparison of RWPE-1 and PC3 cells and demonstrate that RT qPCR analysis of MYO 1C A using appropriate reference genes is sufficient for PC detection even in low-abundance cancer specimens.
Saidova et al. (2018) Specific and reliable detection of Myosin 1C isoform A by RTqPCR in prostate cancer cells. PeerJ 6:e5970 https://doi.org/10.7717/peerj.5970
Reassessing public opinion of captive cetacean attractions with a photo elicitation survey
Background Captive cetacean attractions are growing in number globally, their operators citing entertainment, education, and conservation as benefits. Those for and against developing such attractions claim public support. Previous public opinion research, however, shows little consensus, partly due to the introduction of biases in study design that influence participants’ responses. Those involved in, or concerned with, developing and licensing these attractions need to better understand what drives the lack of consensus to take socially-acceptable decisions. Methods We reviewed previous research on public opinion of cetacean captivity, noting possible sources of bias. Survey question wording can be a major source of introduced bias, so we used an open-ended photo elicitation approach. We showed tourists in the Turks Caicos Islands (N = 292) images of a marine mammal park (MMP) killer whale show and a swim-with-the-dolphins (SWTD) attraction and asked for their qualitative comments on the potential development of each. They also indicated how likely they would be to visit each on a Likert scale. Results Respondents were generally against visiting MMP killer whale shows, with 60.9% not likely to visit. SWTD attractions were more popular; 60.3% were likely to visit. For SWTD, USA residents were more likely to visit; older respondents and those staying in all-inclusive resorts were less likely. Those staying in all-inclusive resorts were also less likely to visit MMP killer whale shows. The great majority of qualitative comments centred on either entertainment value or animal welfare concerns. There were very few, if any, comments on the education or conservation value of these attractions. Discussion Our findings contradict several previous studies on public opinion of captive cetaceans that did not use photo elicitation. The support shown for MMP killer whale shows in this survey was well below that claimed by studies conducted on behalf of captive cetacean attraction operators. Opposition to SWTD was also noticeably lower than that found in surveys conducted with wild cetacean tourism participants. This difference can likely be attributed to the different survey populations and settings, but this variation is also very likely attributable to researcher-introduced bias. While photo selection can introduce bias, photo elicitation reduces reliance on pre-scripted questions and responses, and seems to effectively reduce other forms of bias. Allowing open-ended responses, where participants responded to an image, seems to have given a more representative understanding of what is at the forefront of the public’s mind than closed questioning. These conclusions, among others made in this study, suggest that development decisions for captive cetacean attractions are being made on imprecise data. Going forward, data collected via responder-led, open-ended, bias-minimising approaches should at least be considered when informing such decisions.
Wassermann et al. (2018) Reassessing public opinion of captive cetacean attractions with a photo elicitation survey. PeerJ 6:e5953 https://doi.org/10.7717/peerj.5953
De novo annotation of the transcriptome of the Northern Wheatear (Oenanthe oenanthe)
We have sequenced a partial transcriptome of the Northern Wheatear (Oenanthe oenanthe), a species with one of the longest migrations on Earth. The transcriptome was constructed de novo using RNA-Seq sequence data from the pooled mRNA of six different tissues: brain, muscle, intestine, liver, adipose tissue and skin. The samples came from nine captive-bred wheatears collected at three different stages of the endogenous autumn migratory period: (1) lean birds prior the onset of migration, (2) during the fattening stage and (3) individuals at their migratory body mass plateau, when they have almost doubled their lean body mass. The sample structure used to build up the transcriptome of the Northern Wheatears concerning tissue composition and time guarantees the future survey of the regulatory genes involved in the development of the migratory phenotype. Through the pre-migratory period, birds accomplish outstanding physical and behavioural changes that involve all organ systems. Nevertheless, the molecular mechanisms through which birds synchronize and control hyperphagia, fattening, restlessness increase, immunity boosting and tuning the muscles for such endurance flight are still largely unknown. The use of RNA-Seq has emerged as a powerful tool to analyse complex traits on a broad scale, and we believe it can help to characterize the migratory phenotype of wheatears at an unprecedented level. The primary challenge to conduct quantitative transcriptomic studies in non-model species is the availability of a reference transcriptome, which we have constructed and described in this paper. The cDNA was sequenced by pyrosequencing using the Genome Sequencer Roche GS FLX System; with single paired-end reads of about 400 bp. We estimate the total number of genes at 15,640, of which 67% could be annotated using Turkey and Zebra Finch genomes, or protein sequence information from SwissProt and NCBI databases. With our study, we have made a first step towards understanding the migratory phenotype regarding gene expression of a species that has become a model to study birds long-distance migrations.
Frias-Soler et al. (2018) De novo annotation of the transcriptome of the Northern Wheatear (Oenanthe oenanthe). PeerJ 6:e5860 https://doi.org/10.7717/peerj.5860
Exploratory investigation of region level risk factors of Ebola Virus Disease in West Africa
Background Ebola Virus Disease (EVD) is a highly infectious disease that has produced over 25,000 cases in the past 50 years. While many past outbreaks resulted in relatively few cases, the 2014 outbreak in West Africa was the most deadly occurrence of EVD to date, producing over 15,000 confirmed cases. Objective In this study, we investigated population level predictors of EVD risk at the regional level in Sierra Leone, Liberia, and Guinea. Methods Spatial and descriptive analyses were conducted to assess distribution of EVD cases. Choropleth maps showing the spatial distribution of EVD risk across the study area were generated in ArcGIS. Poisson and negative binomial models were then used to investigate population and regional predictors of EVD risk. Results Results indicated that the risk of EVD was significantly lower in areas with higher proportions of: (a) the population living in urban areas, (b) households with a low quality or no toilets, and (c) married men working in blue collar jobs. However, risk of EVD was significantly higher in areas with high mean years of education. Conclusions The identified significant predictors of high risk were associated with areas with higher levels of urbanization. This may be due to higher population densities in the more urban centers and hence higher potential of infectious contact. However, there is need to better understand the role of urbanization and individual contact structure in an Ebola outbreak. We discuss shortcomings in available data and emphasize the need to consider spatial scale in future data collection and epidemiological studies.
Levy et al. (2018) Exploratory investigation of region level risk factors of Ebola Virus Disease in West Africa. PeerJ 6:e5888 https://doi.org/10.7717/peerj.5888
Chondrogenic differentiation of adipose-derived mesenchymal stem cells induced by L-ascorbic acid and platelet rich plasma on silk fibroin scaffold
Articular cartilage is an avascular tissue with limited regenerative property. Therefore, a defect or trauma in articular cartilage due to disease or accident can lead to progressive tissue deterioration. Cartilage tissue engineering, by replacing defective cartilage tissue, is a method for repairing such a problem. In this research, three main aspects—cell, biomaterial scaffold, and bioactive factors—that support tissue engineering study were optimized. Adipose-derived mesenchymal stem cells (ADSC) that become cartilage were grown in an optimized growth medium supplemented with either platelet rich plasma (PRP) or L-ascorbic acid (LAA). As the characterization result, the ADSC used in this experiment could be classified as Mesenchymal Stem Cell (MSC) based on multipotency analysis and cell surface marker analysis. The biomaterial scaffold was fabricated from the Bombyx morii cocoon using silk fibroin by salt leaching method and was engineered to form different sizes of pores to provide optimized support for cell adhesion and growth. Biocompatibility and cytotoxicity evaluation was done using MTT assay to optimize silk fibroin concentration and pore size. Characterized ADSC were grown on the optimized scaffold. LAA and PRP were chosen as bioactive factors to induce ADSC differentiation to become chondrocytes. The concentration optimization of LAA and PRP was analyzed by cell proliferation using MTT assay and chondrogenic differentiation by measuring glycosaminoglycan (GAG) using Alcian Blue at 605 nm wavelength. The optimum silk fibroin concentration, pore size, LAA concentration, and PRP concentration were used to grow and differentiate characterized ADSC for 7, 14, and 21 days. The cell morphology on the scaffold was analyzed using a scanning electron microscope (SEM). The result showed that the ADSC could adhere on plastic, express specific cell surface markers (CD73, CD90, and CD105), and could be differentiated into three types of mature cells. The silk fibroin scaffold made from 12% w/v concentration formed a 500 µm pore diameter (SEM analysis), and was shown by MTT assay to be biocompatible and to facilitate cell growth. The optimum concentrations of the bioactive factors LAA and PRP were 50 µg/mL and 10%, respectively. GAG analysis with Alcian Blue staining suggested that PRP induction medium and LAA induction medium on 12% w/v scaffold could effectively promote not only cell adhesion and cell proliferation but also chondrogenic differentiation of ADSC within 21 days of culture. Therefore, this study provides a new approach to articular tissue engineering with a combination of ADSC as cell source, LAA and PRP as bioactive factors, and silk fibroin as a biocompatible and biodegradable scaffold.
Barlian et al. (2018) Chondrogenic differentiation of adipose-derived mesenchymal stem cells induced by L-ascorbic acid and platelet rich plasma on silk fibroin scaffold. PeerJ 6:e5809 https://doi.org/10.7717/peerj.5809
Recommended nitrogen fertilization enhances soil carbon sequestration in China’s monsoonal temperate zone
China consumes more than one-third of the world’s nitrogen (N) fertilizer, and an increasing amount of N fertilizer has been applied over the past decades. Although N fertilization can increase the carbon sequestration potentials of cropland in China, the quantitative effects of different N fertilizer application levels on soil carbon changes have not been evaluated. Therefore, a 12-year cultivation experiment was conducted under three N fertilizer application levels (no N fertilizer input, the recommended N fertilizer input after soil testing, and the estimated additional fertilizer input) to estimate the effect of N addition on soil carbon changes in the root layer (0–80 cm) and non-root layer (80–200 cm) using a within-study meta-analysis method. The results showed significant declines in the soil inorganic carbon (SIC) in the root layers and significant growth in the SIC in the non-root layers under N fertilizer input. The soil organic carbon (SOC) in the root layers and the non-root layer significantly decreased under all the treatments. In addition, the recommended N fertilizer application level significantly increased the SOC and soil total carbon stocks compared with the future N fertilizer application level and no N input, while the future N fertilization significantly decreased the SIC and soil total carbon compared with no N input. The results suggest that N fertilization can rearrange the soil carbon distribution over the entire soil profile, and the recommended N fertilization rather than excess N input can increase the soil carbon stock, which suggests that the national soil testing program in China can improve the soil carbon sequestration potential.
Jin (2018) Recommended nitrogen fertilization enhances soil carbon sequestration in China’s monsoonal temperate zone. PeerJ 6:e5983 https://doi.org/10.7717/peerj.5983
Influencing factors and health risk assessment of microcystins in the Yongjiang river (China) by Monte Carlo simulation
The Yongjiang river is a large, shallow, hyper-trophic, freshwater river in Guangxi, China. To investigate the presence of microcystin-RR, microcystin-LR, and microcystin-YR (MC-RR, MC-LR, and MC-YR) in the Yongjiang river and describe their correlation with environmental factors, as well as, assess health risk using Monte Carlo simulation, 90 water samples were collected at three sample points from March to December 2017. Results showed that during the monitoring period, total concentrations of MC-RR (TMC-RR), MC-YR (TMC-YR), and MC-LR (TMC-LR) varied from 0.0224 to 0.3783 μg/L, 0.0329 to 0.1433 μg/L, and 0.0341 to 0.2663 μg/L, respectively. Total phosphorus (TP) content appeared to be related to TMC-LR and the total concentrations of microcystins (TMCs), while pH and total nitrogen (TN)/TP ratio appeared to be related to TMC-RR and TMC-YR, respectively. Using the professional health risk assessment software @Risk7.5, the risks of dietary intake of microcystins (MCs), including the carcinogenic risk and non-carcinogenic risk, were evaluated. It was found that the carcinogenic risk of MC-RR from drinking water was higher than MC-LR and MC-YR, and the presence of MCs would lead to high potential health risks, especially in children. The carcinogenic risk of MC-RR to children was >1 × 10−4, the maximum allowance level recommended by the US Environmental Protection Agency; as for adults, it was >5 × 10−5, the maximum allowance level recommended by the International Commission on Radiological Protection. The non-carcinogenic hazard index (HI) of MC-RR, MC-YR, and MC-LR increased successively, indicating that MC-LR was more hazardous to human health than MC-YR and MC-RR, but its HI was <1. This suggests that MCs pose less risk to health. However, it is necessary to strengthen the protection and monitoring of drinking water source for effective control of water pollution and safeguarding of human health.
Xiao et al. (2018) Influencing factors and health risk assessment of microcystins in the Yongjiang river (China) by Monte Carlo simulation. PeerJ 6:e5955 https://doi.org/10.7717/peerj.5955
An emerging viral pathogen truncates population age structure in a European amphibian and may reduce population viability
Infectious diseases can alter the demography of their host populations, reducing their viability even in the absence of mass mortality. Amphibians are the most threatened group of vertebrates globally, and emerging infectious diseases play a large role in their continued population declines. Viruses belonging to the genus Ranavirus are responsible for one of the deadliest and most widespread of these diseases. To date, no work has used individual level data to investigate how ranaviruses affect population demographic structure. We used skeletochronology and morphology to evaluate the impact of ranaviruses on the age structure of populations of the European common frog (Rana temporaria) in the UK. We compared ecologically similar populations that differed most notably in their historical presence or absence of ranavirosis (the acute syndrome caused by ranavirus infection). Our results suggest that ranavirosis may truncate the age structure of R. temporaria populations. One potential explanation for such a shift might be increased adult mortality and subsequent shifts in the life history of younger age classes that increase reproductive output earlier in life. Additionally, we constructed population projection models which indicated that such increased adult mortality could heighten the vulnerability of frog populations to stochastic environmental challenges.
Campbell et al. (2018) An emerging viral pathogen truncates population age structure in a European amphibian and may reduce population viability. PeerJ 6:e5949 https://doi.org/10.7717/peerj.5949
Soil moisture dynamics under two rainfall frequency treatments drive early spring CO2 gas exchange of lichen-dominated biocrusts in central Spain
Background Biocrusts, communities dominated by mosses, lichens, cyanobacteria, and other microorganisms, largely affect the carbon cycle of drylands. As poikilohydric organisms, their activity time is often limited to short hydration events. The photosynthetic and respiratory response of biocrusts to hydration events is not only determined by the overall amount of available water, but also by the frequency and size of individual rainfall pulses. Methods We experimentally assessed the carbon exchange of a biocrust community dominated by the lichen Diploschistes diacapsis in central Spain. We compared the effect of two simulated precipitation patterns providing the same overall amount of water, but with different pulse sizes and frequency (high frequency: five mm/day vs. low frequency: 15 mm/3 days), on net/gross photosynthesis and dark respiration. Results Radiation and soil temperature, together with the watering treatment, affected the rates of net and gross photosynthesis, as well as dark respiration. On average, the low frequency treatment showed a 46% ± 3% (mean ± 1 SE) lower rate of net photosynthesis, a 13% ± 7% lower rate of dark respiration, and a 24% ± 8% lower rate of gross photosynthesis. However, on the days when samples of both treatments were watered, no differences between their carbon fluxes were observed. The carbon flux response of D. diacapsis was modulated by the environmental conditions and was particularly dependent on the antecedent soil moisture. Discussion In line with other studies, we found a synergetic effect of individual pulse size, frequency, environmental conditions, and antecedent moisture on the carbon exchange fluxes of biocrusts. However, most studies on this subject were conducted in summer and they obtained results different from ours, so we conclude that there is a need for long-term experiments of manipulated precipitation impacts on the carbon exchange of biocrusts. This will enable a more complete assessment of the impacts of climate change-induced alterations in precipitation patterns on biocrust communities.
Baldauf et al. (2018) Soil moisture dynamics under two rainfall frequency treatments drive early spring CO2 gas exchange of lichen-dominated biocrusts in central Spain. PeerJ 6:e5904 https://doi.org/10.7717/peerj.5904
A new microvertebrate assemblage from the Mussentuchit Member, Cedar Mountain Formation: insights into the paleobiodiversity and paleobiogeography of early Late Cretaceous ecosystems in western North America
The vertebrate fauna of the Late Cretaceous Mussentuchit Member of the Cedar Mountain Formation has been studied for nearly three decades, yet the fossil-rich unit continues to produce new information about life in western North America approximately 97 million years ago. Here we report on the composition of the Cliffs of Insanity (COI) microvertebrate locality, a newly sampled site containing perhaps one of the densest concentrations of microvertebrate fossils yet discovered in the Mussentuchit Member. The COI locality preserves osteichthyan, lissamphibian, testudinatan, mesoeucrocodylian, dinosaurian, metatherian, and trace fossil remains and is among the most taxonomically rich microvertebrate localities in the Mussentuchit Member. To better refine taxonomic identifications of isolated theropod dinosaur teeth, we used quantitative analyses of taxonomically comprehensive databases of theropod tooth measurements, adding new data on theropod tooth morphodiversity in this poorly understood interval. We further provide the first descriptions of tyrannosauroid premaxillary teeth and document the earliest North American record of adocid remains, extending the appearance of this ancestrally Asian clade by 5 million years in western North America and supporting studies of pre-Cenomaninan Laurasian faunal exchange across Beringia. The overabundance of mesoeucrocodylian remains at the COI locality produces a comparatively low measure of relative biodiversity when compared to other microvertebrate sites in the Mussentuchit Member using both raw and subsampling methods. Much more microvertebrate research is necessary to understand the roles of changing ecology and taphonomy that may be linked to transgression of the Western Interior Seaway or microhabitat variation.
Avrahami et al. (2018) A new microvertebrate assemblage from the Mussentuchit Member, Cedar Mountain Formation: insights into the paleobiodiversity and paleobiogeography of early Late Cretaceous ecosystems in western North America. PeerJ 6:e5883 https://doi.org/10.7717/peerj.5883