Assessing anthropogenic risk to sea otters (Enhydra lutris nereis) for reintroduction into San Francisco Bay
Southern sea otters have been actively managed for their conservation and recovery since listing on the federal Endangered Species Act in 1977. Still, they remain constrained to a geographically small area on the central coast of California relative to their former coast-wide range, with population numbers far below those of the estimated optimal sustainable population size. Species managers have discussed reintroducing southern sea otters into parts of their historic range to facilitate sustained population growth and geographic range expansion. San Francisco Bay (SFB), historically home to several thousand sea otters, is one location identified as a candidate release site for these reintroductions. The return of sea otters to SFB could bring benefits to local ecosystem restoration and tourism, in addition to spurring sea otter population growth to meet recovery goals. However, this is a highly urbanized estuary, so sea otters could also be exposed to serious anthropogenic threats that would challenge a successful reintroduction. In light of these potential detriments we performed a spatially-explicit risk assessment to analyze the suitability of SFB for southern sea otter reintroduction. We looked at threats to sea otters specific to SFB, including: the impacts of vessel traffic from commercial shipping, high-speed ferries, and recreational vessels; environmental contaminants of methylmercury and polychlorinated biphenyls; major oil spills; and commercial fishing. Factors that influenced the relative threat imposed by each stressor included the spatio-temporal extent and intensity of the stressor and its mitigation potential. Our analysis revealed the complex spatial and temporal variation in risk distribution across the SFB. The type and magnitude of anthropogenic risk was not uniformly distributed across the study area. For example, the central SFB housed the greatest cumulative risk, where a high degree of vessel traffic and other stressors occurred in conjunction. The individual stressors that contributed to this risk score varied across different parts of the study area as well. Whereas vessel traffic, particularly of fast ferries, was a high scoring risk factor in in the north and central bay, in the south bay it was environmental contaminants that caused greater risk potential. To help identify areas within the study area that managers might want to target for release efforts, the spatially-explicit risk map revealed pockets of SFB that could provide both suitable habitat and relatively low overall risk. However in some cases these were adjacent or in close proximity to identified high-risk portions of habitat in SFB. This predictive suitability and risk assessment can be used by managers to consider the spatial distribution of potential threats, and risk abatement that may be necessary for sea otters to re-occupy their historic home range in SFB.
Spatial and Geographic Information Science
Rudebusch et al. (2020) Assessing anthropogenic risk to sea otters (Enhydra lutris nereis) for reintroduction into San Francisco Bay. PeerJ 8:e10241 https://doi.org/10.7717/peerj.10241
Predicting disease occurrence of cabbage Verticillium wilt in monoculture using species distribution modeling
Background Although integrated pest management (IPM) is essential for conservation agriculture, this method can be inadequate for severely infected fields. The ability to predict the potential occurrence of severe infestation of soil-borne disease would enable farmers to adopt suitable methods for high-risk areas, such as soil disinfestation, and apply other options for lower risk areas. Recently, researchers have used species distribution modeling (SDM) to predict the occurrence of target plant and animal species based on various environmental variables. In this study, we applied this technique to predict and map the occurrence probability of a soil-borne disease, Verticillium wilt, using cabbage as a case study. Methods A disease survey assessing the distribution of Verticillium wilt in cabbage fields in Tsumagoi village (central Honshu, Japan) was conducted two or three times annually from 1997 to 2013. Road density, elevation and topographic wetness index (TWI) were selected as explanatory variables for disease occurrence potential. A model of occurrence probability of Verticillium wilt was constructed using the MaxEnt software for SDM analysis. As the disease survey was mainly conducted in an agricultural area, the area was weighted as “Bias Grid” and area except for the agricultural area was set as background. Results Grids with disease occurrence showed a high degree of coincidence with those with a high probability occurrence. The highest contribution to the prediction of disease occurrence was the variable road density at 97.1%, followed by TWI at 2.3%, and elevation at 0.5%. The highest permutation importance was road density at 93.0%, followed by TWI at 7.0%, while the variable elevation at 0.0%. This method of predicting disease probability occurrence can help with disease monitoring in areas with high probability occurrence and inform farmers about the selection of control measures.
Ikeda et al. (2020) Predicting disease occurrence of cabbage Verticillium wilt in monoculture using species distribution modeling. PeerJ 8:e10290 https://doi.org/10.7717/peerj.10290
Analysis of genes and underlying mechanisms involved in foam cells formation and atherosclerosis development
Background Foam cells (FCs) play crucial roles in the process of all stages of atherosclerosis. Smooth muscle cells (SMCs) and macrophages are the major sources of FCs. This study aimed to identify the common molecular mechanism in these two types of FCs. Methods GSE28829, GSE43292, GSE68021, and GSE54666 were included to identify the differentially expressed genes (DEGs) associated with FCs derived from SMCs and macrophages. Gene Ontology biological process (GO-BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed by using the DAVID database. The co-regulated genes associated with the two origins of FCs were validated (GSE9874), and their expression in vulnerable atherosclerosis plaques (GSE120521 and GSE41571) was assessed. Results A total of 432 genes associated with FCs derived from SMCs (SMC-FCs) and 81 genes associated with FCs derived from macrophages (M-FCs) were identified, and they were mainly involved in lipid metabolism, inflammation, cell cycle/apoptosis. Furthermore, three co-regulated genes associated with FCs were identified: GLRX, RNF13, and ABCA1. These three common genes showed an increased tendency in unstable or ruptured plaques, although in some cases, no statistically significant difference was found. Conclusions DEGs related to FCs derived from SMCs and macrophages have contributed to the understanding of the molecular mechanism underlying the formation of FCs and atherosclerosis. GLRX, RNF13, and ABCA1 might be potential targets for atherosclerosis treatment.
Zhang et al. (2020) Analysis of genes and underlying mechanisms involved in foam cells formation and atherosclerosis development. PeerJ 8:e10336 https://doi.org/10.7717/peerj.10336
Third molar agenesis in modern humans with and without agenesis of other teeth
Background The number of teeth in the human dentition is of interest both from developmental and evolutionary aspects. The present case-control study focused on the formation of third molars in modern humans aiming to shed more light on the most variable tooth class in the dentition. Materials and Methods For this reason, we investigated third molar formation in a sample of 303 individuals with agenesis of teeth other than third molars (agenesis group) and compared it to a sex and age matched control group of 303 individuals without agenesis of teeth other than third molars. Results The prevalence of third molar agenesis in the agenesis group was 50.8%, which is significantly higher than the 20.5% in the control group (p < 0.001). The chance of a missing third molar in the agenesis group was increased by 38.3% (p < 0.001), after controlling for the agenesis in other teeth factor. When considering the amount of missing third molars per individual, a clear tendency towards more missing third molars was evident in the agenesis group compared to the control group. The frequency of bilaterally missing third molars in the agenesis group was 29% in the maxilla, as well as in the mandible, which is about three times higher than the frequency of unilaterally missing third molars (p < 0.001). In the control group, bilaterally missing third molars occurred in 8.6% in the maxilla and 8.9% in the mandible. Conclusion The present results indicate that genetic factors involved in tooth agenesis affect also the dentition as a whole. Furthermore, the third molars are more vulnerable to factors involved in agenesis of other teeth and they are more often affected as a whole. These findings seem to be associated with the evolutionary trend in humans towards reduced molar number.
Scheiwiller et al. (2020) Third molar agenesis in modern humans with and without agenesis of other teeth. PeerJ 8:e10367 https://doi.org/10.7717/peerj.10367
Increased copy number of syncytin-1 in the trophectoderm is associated with implantation of the blastocyst
Background A key step in embryo implantation is the adhesion to and invasion of the endometrium by the blastocyst trophectoderm. The envelope proteins of HERV-W and -FRD (human endogenous retrovirus-W and -FRD), syncytin-1 and syncytin-2, are mainly distributed in the placenta, and play important roles in the development of the placenta. The placenta originates from the trophectoderm of the blastocyst. It is unclear whether the envelope proteins of HERV-W and -FRD have an effect on the development of the trophectoderm and whether they have any association with the implantation of the blastocyst. Methods The whole-genome amplification products of the human blastocyst trophectoderm were used to measure the copy number of syncytin-1 and syncytin-2 using real time qPCR. In addition, clinical data associated with the outcome of pregnancies was collected, and included age, body mass index (BMI), basic follicle stimulating hormone(bFSH), rate of primary infertility and oligo-astheno-teratospermia, the thickness of the endometrium on the day of endometrial transformation, the levels of estrogen and progestin on the transfer day, the days and the morphological scores of the blastocysts. The expression of mRNA and the copy numbers of syncytin-1 and syncytin-2 in H1 stem cells, and in differentiated H1 cells, induced by BMP4, were measured using real time qPCR. Results The relative copy number of syncytin-1 in the pregnant group (median: 424%, quartile: 232%–463%, p < 0.05) was significantly higher than in the non-pregnant group (median: 100%, quartile: 81%–163%). There was a correlation (rs = 0.681, p < 0.001) between the copy number of syncytin-1 and blastocyst implantation after embryo transfer. As the stem cells differentiated, the expression of NANOG mRNA decreased, and the expression of caudal type homeobox 2(CDX2) and β-human chorionic gonadotropin (β-hCG) mRNAs increased. Compared to the undifferentiated cells, the relative expression of the syncytin-1 mRNA was 1.63 (quartile: 0.59–6.37, p > 0.05), 3.36 (quartile: 0.85–14.80, p > 0.05), 10.85 (quartile: 3.39–24.46, p < 0.05) and 67.81 (quartile: 54.07–85.48, p < 0.05) on day 1, 3, 5 and 7, respectively, after the differentiation. The relative expression of syncytin-2 was 5.34 (quartile: 4.50–10.30), 7.90 (quartile: 2.46–14.01), 57.44 (quartile: 38.35–103.87) and 344.76 (quartile: 267.72–440.10) on day 1, 3, 5 and 7, respectively, after the differentiation (p < 0.05). The copy number of syncytin-1 increased significantly during differentiation. Conclusion Preceding the transfer of frozen embryos, the increased copy number of syncytin-1 in the blastocyst trophectoderm was associated with good outcomes of pregnancies.
Guo et al. (2020) Increased copy number of syncytin-1 in the trophectoderm is associated with implantation of the blastocyst. PeerJ 8:e10368 https://doi.org/10.7717/peerj.10368
MiR-26a-5p inhibits GSK3β expression and promotes cardiac hypertrophy in vitro
Background The role of miR-26a-5p expression in cardiac hypertrophy remains unclear. Herein, the effect of miR-26a-5p on cardiac hypertrophy was investigated using phenylephrine (PE)-induced cardiac hypertrophy in vitro and in a rat model of hypertension-induced hypertrophy in vivo. Methods The PE-induced cardiac hypertrophy models in vitro and vivo were established. To investigate the effect of miR-26a-5p activation on autophagy, the protein expression of autophagosome marker (LC3) and p62 was detected by western blot analysis. To explore the effect of miR-26a-5p activation on cardiac hypertrophy, the relative mRNA expression of cardiac hypertrophy related mark GSK3β was detected by qRT-PCR in vitro and vivo. In addition, immunofluorescence staining was used to detect cardiac hypertrophy related mark α-actinin. The cell surface area was measured by immunofluorescence staining. The direct target relationship between miR-26a-5p and GSK3β was confirmed by dual luciferase report. Results MiR-26a-5p was highly expressed in PE-induced cardiac hypertrophy. MiR-26a-5p promoted LC3II and decreased p62 expression in PE-induced cardiac hypertrophy in the presence or absence of lysosomal inhibitor. Furthermore, miR-26a-5p significantly inhibited GSK3β expression in vitro and in vivo. Dual luciferase report results confirmed that miR-26a-5p could directly target GSK3β. GSK3β overexpression significantly reversed the expression of cardiac hypertrophy-related markers including ANP, ACTA1 and MYH7. Immunofluorescence staining results demonstrated that miR-26a-5p promoted cardiac hypertrophy related protein α-actinin expression, and increased cell surface area in vitro and in vivo. Conclusion Our study revealed that miR-26a-5p promotes myocardial cell autophagy activation and cardiac hypertrophy by regulating GSK3β, which needs further research.
Tang et al. (2020) MiR-26a-5p inhibits GSK3β expression and promotes cardiac hypertrophy in vitro. PeerJ 8:e10371 https://doi.org/10.7717/peerj.10371
Different analysis strategies of 16S rRNA gene data from rodent studies generate contrasting views of gut bacterial communities associated with diet, health and obesity
Background One of the main functions of diet is to nurture the gut microbiota and this relationship affects the health of the host. However, different analysis strategies can generate different views on the relative abundance of each microbial taxon, which can affect our conclusions about the significance of diet to gut health in lean and obese subjects. Here we explored the impact of using different analysis strategies to study the gut microbiota in a context of diet, health and obesity. Methods Over 15 million 16S rRNA gene sequences from published studies involving dietary interventions in obese laboratory rodents were analyzed. Three strategies were used to assign the 16S sequences to Operational Taxonomic Units (OTUs) based on the GreenGenes reference OTU sequence files clustered at 97% and 99% similarity. Results Different strategies to select OTUs influenced the relative abundance of all bacterial taxa, but the magnitude of this phenomenon showed a strong study effect. Different taxa showed up to 20% difference in relative abundance within the same study, depending on the analysis strategy. Very few OTUs were shared among the samples. ANOSIM test on unweighted UniFrac distances showed that study, sequencing technique, animal model, and dietary treatment (in that order) were the most important factors explaining the differences in bacterial communities. Except for obesity status, the contribution of diet and other factors to explain the variability in bacterial communities was lower when using weighted UniFrac distances. Predicted functional profile and high-level phenotypes of the microbiota showed that each study was associated with unique features and patterns. Conclusions The results confirm previous findings showing a strong study effect on gut microbial composition and raise concerns about the impact of analysis strategies on the membership and composition of the gut microbiota. This study may be helpful to guide future research aiming to investigate the relationship between diet, health, and the gut microbiota.
Garcia-Mazcorro et al. (2020) Different analysis strategies of 16S rRNA gene data from rodent studies generate contrasting views of gut bacterial communities associated with diet, health and obesity. PeerJ 8:e10372 https://doi.org/10.7717/peerj.10372
Investigation of acute-phase proteins and cytokines response in goats with contagious caprine pleuropneumonia with special reference to their diagnostic accuracy
Acute-phase proteins (APPs) have always had valued diagnostic potentialities in response to infection. This study aimed to evaluate the diagnostic accuracy of selected APPs and proinflammatory cytokines (PIC) in goats with contagious caprine pleuropneumonia (CCPP) under field conditions. Moreover, to highlight the role of tested biomarkers in CCPP pathogenesis. Fifty-eight goats (38 confirmed cases with CCPP and 20 healthy controls) were involved in this investigation. C-reactive protein (CRP), procalcitonin (PCT), haptoglobin (HP), fibrinogen (Fb), serum amyloid A (SAA), selected PIC (IL1-α, IL1-β, IL-6, interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α)) levels were investigated in serum samples from all goats under investigation. Latex agglutination test was used for diagnosis of goats with CCPP. For microbiological investigations, nasopharyngeal swabs (from all goats), lung tissues and pleural fluids (from only necropsied goats) were collected. This study revealed that all tested parameters have a high to moderate degree of diagnostic performance for CCPP. Magnitudes of increase in levels of APPs (CRP, HP and SAA) were stronger than PIC, IFN-γ, Fb and PCT. All tested parameters showed high diagnostic accuracy (AUROC >90%), except HP (AUROC = 87.3%) and IFN-γ (AUROC = 78.8%) showed moderate accuracy in differentiation of goats with and without CCPP infection. For detecting goats with and without CCPP infection, HP had the lowest sensitivity (Se = 81.6%) and Fb had the lowest specificity (Sp = 85.0%) among the APPs parameters tested. However, PCT showed the highest Se (100%) and Sp (95.0%) to detect goats with and without CCPP infection among tested parameters. Conclusively, this study endorses the significance of selected APPs and PIC as additional screening diagnostic parameters for naturally occurring CCPP in goats. However, it does not replace traditional methods for diagnosis of CCPP in goats. Furthermore, APPs and PIC have an important role in disease pathogenesis in goats.
El-Deeb et al. (2020) Investigation of acute-phase proteins and cytokines response in goats with contagious caprine pleuropneumonia with special reference to their diagnostic accuracy. PeerJ 8:e10394 https://doi.org/10.7717/peerj.10394
The easternmost occurrence of Mammut pacificus (Proboscidea: Mammutidae), based on a partial skull from eastern Montana, USA
Mammut pacificus is a recently described species of mastodon from the Pleistocene of California and Idaho. We report the easternmost occurrence of this taxon based upon the palate with right and left M3 of an adult male from the Irvingtonian of eastern Montana. The undamaged right M3 exhibits the extreme narrowness that characterizes M. pacificus rather than M. americanum. The Montana specimen dates to an interglacial interval between pre-Illinoian and Illinoian glaciation, perhaps indicating that M. pacificus was extirpated in the region due to habitat shifts associated with glacial encroachment.
McDonald et al. (2020) The easternmost occurrence of Mammut pacificus (Proboscidea: Mammutidae), based on a partial skull from eastern Montana, USA. PeerJ 8:e10030 https://doi.org/10.7717/peerj.10030
Acetate correlates with disability and immune response in multiple sclerosis
Background Gut microbiota has been related to multiple sclerosis (MS) etiopathogenesis. Short-chain fatty acids (SCFA) are compounds derived from microbial metabolism that have a role in gut-brain axis. Objectives To analyse SCFA levels in plasma of MS patients and healthy donors (HD), and the possible link between these levels and both clinical data and immune cell populations. Methods Ninety-five MS patients and 54 HD were recruited. Patients were selected according to their score in the Expanded Disability Status Scale (EDSS) (49 EDSS ≤ 1.5, 46 EDSS ≥ 5.0). SCFA were studied in plasma samples by liquid chromatography-mass spectrometry. Peripheral blood mononuclear cells were studied by flow cytometry. Gender, age, treatments, EDSS and Multiple Sclerosis Severity Score (MSSS) were evaluated at the recruitment. Results Plasma acetate levels were higher in patients than in HD (p = 0.003). Patients with EDSS ≥ 5.0 had higher acetate levels than those with EDSS≤ 1.5 (p = 0.029), and HD (p = 2.97e–4). Acetate levels correlated with EDSS (r = 0.387; p = 1.08e–4) and MSSS (r = 0.265; p = 0.011). In untreated MS patients, acetate levels correlated inversely with CD4+ naïve T cells (r = − 0.550, p = 0.001) and directly with CD8+ IL-17+ cells (r = 0.557; p = 0.001). Conclusions Plasma acetate levels are higher in MS patients than in HD. In MS there exists a correlation between plasma acetate levels, EDSS and increased IL-17+ T cells. Future studies will elucidate the role of SCFA in the disease.
Pérez-Pérez et al. (2020) Acetate correlates with disability and immune response in multiple sclerosis. PeerJ 8:e10220 https://doi.org/10.7717/peerj.10220