Exogenous hormones influence Brassica napus leaf cuticular wax deposition and cuticle function
Background Cuticular waxes cover plant surface and play important roles in protecting plants from abiotic and biotic stresses. The variations of wax deposition and chemical compositions under changing environments have been shown to be related to plant adaptations. However, it is still not clear whether the wax depositions could be adjusted to increase plant adaptations to stressed conditions. Methods In this study, exogenous methyl jasmonate (MeJA), the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) and salicylic acid (SA) were applied to test their effects on cuticular wax deposition in two Brassica napus cultivars, Zhongshuang 9 (ZS9, low wax coverage ) and Yuyou 19 (YY19, high wax coverage). Next, we measured the water loss rate and the transcriptional expression of genes involved in wax biosynthesis as well as genes related to disease defense. Results Seven wax compound classes, including fatty acids, aldehydes, alkanes, secondary alcohols, ketones, and unbranched as well as branched primary alcohols, were identified in B. napus leaf wax mixtures. MeJA, SA and ACC treatments had no significant effect on total wax amounts in YY19, whereas ACC reduced total wax amounts in ZS9. Overall, hormone treatments led to an increase in the amounts of aldehydes and ketones, and a decrease of secondary alcohol in ZS9, whereas they led to a decrease of alkane amounts and an increase of secondary alcohol amounts in YY19. Concomitantly, both cultivars also exhibited different changes in cuticle permeability, with leaf water loss rate per 15 min increased from 1.57% (averaged across treatments) at 1.57% (averaged across treatments) at 15 min to 3.12% at 30 min for ZS9 (except for ACC treated plant) and decreased for YY19. MeJA-treated plants of both cultivars relatively had higher water loss rate per 15 min when compared to other treatments. Conclusion. Our findings that B. napus leaf wax composition and cuticle permeability are altered by exogenous SA, MeJA and ACC suggest that the hormone treatments affect wax composition, and that the changes in wax profiles would cause changes in cuticle permeability.
Yuan et al. (2020) Exogenous hormones influence Brassica napus leaf cuticular wax deposition and cuticle function. PeerJ 8:e9264 https://doi.org/10.7717/peerj.9264
Contributions of Latin American researchers in the understanding of the novel coronavirus outbreak: a literature review
This article aimed to give the visibility of Latin American researchers’ contributions to the comprehension of COVID-19; our method was a literature review. Currently, the world is facing a health and socioeconomic crisis caused by the novel coronavirus, SARS-CoV-2, and its disease COVID-19. Therefore, in less than 4 months, researchers have published a significant number of articles related to this novel virus. For instance, a search focused on the Scopus database on 10 April 2020, showed 1,224 documents published by authors with 1,797 affiliations from 80 countries. A total of 25.4%, 24.0% and 12.6% of these national affiliations were from China, Europe and the USA, respectively, making these regions leaders in COVID-19 research. In the case of Latin America, on 10 April 2020, we searched different databases, such as Scopus, PubMed and Web of Science, finding that the contribution of this region was 2.7 ± 0.6% of the total publications found. In other words, we found 153 publications related to COVID-19 with at least one Latin American researcher. We summarized and processed the information from these 153 publications, finding active participation in topics like medical, social and environmental considerations, bioinformatics and epidemiology.
© 2020 Fiesco-Sepúlveda and Serrano-Bermúdez
Fiesco-Sepúlveda et al. (2020) Contributions of Latin American researchers in the understanding of the novel coronavirus outbreak: a literature review. PeerJ 8:e9332 https://doi.org/10.7717/peerj.9332
Clonal diversity and genetic variation of the sedge Carex nigra in an alpine fen depend on soil nutrients
In this study we analysed the impact of water regime and soil nutrients on the clonal diversity and genetic variation of the sedge Carex nigra in a central alpine fen. For our analysis, we established 16 study plots randomly distributed over the fen. We determined the exact elevation of each plot as an indicator for the water regime and measured the content of phosphorous and potassium in the soil of each plot. Clonal diversity and genetic variation of C. nigra were assessed with nuclear microsatellites using leaf material collected in 20 subplots along a diagonal cross within each study plot. The influence of water regime and soil mineral nutrients on clonal diversity and genetic variation was estimated by Bayesian multiple regression. Our study revealed a clear impact of soil nutrient conditions on clonal diversity and genetic variation of C. nigra, which increased with the concentration of phosphorous and decreased with the concentration of potassium. Key background to these findings seems to be the relative offspring success from generative as compared to clonal propagation. Phosphorous acquisition is essential during seedling establishment. Clonal diversity and genetic variation increase, therefore, at sites with higher phosphorous contents due to more successful recruitment. High levels of clonal diversity and genetic variation at sites of low potassium availability may in contrast be mainly caused by increased plant susceptibility to abiotic stress under conditions of potassium deficiency, which brings about more gaps in C. nigra stands and favors the ingrowth from other clones or recruitment from seeds.
Reisch et al. (2020) Clonal diversity and genetic variation of the sedge Carex nigra in an alpine fen depend on soil nutrients. PeerJ 8:e8887 https://doi.org/10.7717/peerj.8887
A new aggressive xenograft model of human colon cancer using cancer-associated fibroblasts
Background Colorectal cancer is the second leading cause of cancer death. Almost half of the patients present recurrence within 5 years after the treatment of the primary tumor, the majority, with metastasis. On the other hand, in the search for new animal models that simulate metastatic cancer, it has been suggested that fibroblasts immersed in the peritumoral stroma (cancer-associated fibroblasts (CAFs)), play a relevant role in the development of cancer. The objective of this study was to identify an adequate animal model to study metastatic colon cancer and the application of new treatments. Methods Human CAFs and normal fibroblasts (NF) for transplant and culture were obtained from surgical fresh samples of patients with adenocarcinoma of sigmoid colon. Stromal cell purity was evaluated by morphology and immunostaining with vimentin (VIM) as a fibroblast marker and anti-proColXIα1 as a specific human CAF marker. Phenotypic characterization of cultured stromal cells was performed by co-staining with mesenchymal and epithelial cell markers. For identification in mice, human CAFs were labeled with the PKH26 red fluorescence dye. Cell line HT-29 was used as tumor cells. Transplant in the head of the pancreas of 34 SCID mice was performed in four different groups, as follows: I. 150,000 CAFS (n = 12), IIa. 1.5 million HT29 cells (n = 7), IIb. 150,000 NF+1.5 million HT29 cells (n = 5), III. 150,000 CAFS+1.5 million HT29 cells (n = 10). After euthanasia performed one month later, histological analysis was made using hematoxylin–eosin and anti-proColXIα1. A histopathological score system based on three features (tumor volume, desmoplasia and number of metastasized organs) was established to compare the tumor severity. Results The CAFs and NF cultured were proColXIα1+/VIM+, proColXIα1/alphaSMA+ and proColXIα1+/CK19+ in different proportions without differences among them, but the CAFs growth curve was significantly larger than that of the NF (p < 0.05). No tumor developed in those animals that only received CAFs. When comparing group II (a + b) vs. group III, both groups showed 100% hepatic metastases. Median hepatic nodules, tumor burden, lung metastases and severity score were bigger in group III vs group II (a + b), although without being significant, except in the case of the median tumor volume, that was significantly higher in group III (154.8 (76.9–563.2) mm3) vs group II (46.7 (3.7–239.6) mm3), p = 0.04. A correlation was observed between the size of the tumor developed in the pancreas and the metastatic tumor burden in the liver and with the severity score. Conclusion Our experiments demonstrate that cultured CAFs have a higher growth than NF and that when human CAFs are associated to human tumor cells, larger tumors with liver and lung metastases are generated than if only colon cancer cells with/without NF are transplanted. This emphasizes the importance of the tumor stroma, and especially the CAFs, in the development of cancer.
Fernando-Macías et al. (2020) A new aggressive xenograft model of human colon cancer using cancer-associated fibroblasts. PeerJ 8:e9045 https://doi.org/10.7717/peerj.9045
Culicidae-centric metabarcoding through targeted use of D2 ribosomal DNA primers
A practical limitation to many metabarcoding initiatives is that sampling methods tend to collect many non-target taxa, which become “amplicon noise” that can saturate Next Generation Sequencing results and lead to both financial and resource inefficiencies. An available molecular tool that can significantly decrease these non-target amplicons and decrease the need for pre-DNA-extraction sorting of bycatch is the design of PCR primers tailored to the taxa under investigation. We assessed whether the D2 extension segment of the 28S ribosomal operon can limit this shortcoming within the context of mosquito (Culicidae) monitoring. We designed PCR primers that are fully conserved across mosquitos and exclude from amplification most other taxa likely to be collected with current sampling apparatuses. We show that, given enough sequencing depth, D2 is an effective marker for the detection of mosquito sequences within mock genomic DNA pools. As few as 3,050 quality-filtered Illumina reads were able to recover all 17 species in a bulk pool containing as little as 0.2% of constituent DNA from single taxa. We also mixed these mosquito DNA pools with high concentrations of non-Culicidae bycatch DNA and show that the component mosquito species are generally still recoverable and faithful to their original relative frequencies. Finally, we show that there is little loss of fidelity in abundance parameters when pools from degraded DNA samples were sequenced using the D2 primers.
Pedro et al. (2020) Culicidae-centric metabarcoding through targeted use of D2 ribosomal DNA primers. PeerJ 8:e9057 https://doi.org/10.7717/peerj.9057
Simultaneous determination of phenolic metabolites in Chinese citrus and grape cultivars
Background As the major bioactive compounds in citrus and grape, it is significant to use the contents of flavonoids and phenolic acids as quality evaluation criteria to provide a better view of classifying the quality and understanding the potential health benefits of each fruit variety. Methods A total of 15 varieties of citrus and 12 varieties of grapes were collected from Fujian, China. High-performance liquid chromatography method was used for the simultaneous determination of 17 phenolic compounds, including gallic acid, chlorogenic acid, caffeic acid, syringic acid, ρ-coumaric acid, ferulic acid, benzoic acid, salicylic acid, catechin, epicatechin, resveratrol, rutin, naringin, hesperidin, quercetin, nobiletin and tangeritin in the peels of citrus and grape cultivars. Further, the cultivars of citrus and grape were classified using principal component analysis (PCA) and hierarchical cluster analysis (HCA). Results A thorough separation of the 17 compounds was achieved within 100 min. The tested method exhibited good linearity (the limits of detection and limits of quantification were in the range of 0.03–1.83 µg/mL and 0.09–5.55 µg/mL, respectively), precision (the relative standard deviations of repeatability were 1.02–1.97%), and recovery (92.2–102.82%) for all the compounds, which could be used for the simultaneous determination of phenolic compounds in citrus and grape. Hesperidin (12.93–26,160.98 µg/g DW) and salicylic acid (5.35–751.02 µg/g DW) were the main flavonoids and phenolic acids in 15 citrus varieties, respectively. Besides, the hesperidin (ND to 605.48 µg/g DW) and salicylic acid (ND to 1,461.79 µg/g DW) were found as the highest flavonoid and the most abundant phenolic acid in grapes, respectively. A total of 15 citrus and 12 grape samples were classified into two main groups by PCA and HCA with strong consistency.
Chen et al. (2020) Simultaneous determination of phenolic metabolites in Chinese citrus and grape cultivars. PeerJ 8:e9083 https://doi.org/10.7717/peerj.9083
Isolation, characterization, and cryopreservation of collared peccary skin-derived fibroblast cell lines
Background Biobanking of cell lines is a promising tool of support for wildlife conservation. In particular, the ability to preserve fibroblast cell lines derived from collared peccaries is of significance as these wild mammals are unique to the Americas and play a large role in maintaining the ecosystem. We identified collared peccary fibroblasts by immunofluorescence and evaluated their morphology, growth and adherence capacity. Further, we monitored the viability and metabolic activity of the fibroblasts to determine the effects of passage number and cryopreservation on establishment of cell lines. Methods Skin biopsies were collected from the peripheral ear region from five adult animals in captivity. Initially, cells were isolated from fragments and cultured in the Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and 2% antibiotic–antimycotic solution under a controlled atmosphere (38.5 °C, 5% CO2). We evaluated the maintenance of primary cells for morphology, adherence capacity of explants, explants in subconfluence, cell growth and absence of contamination. Moreover, we identified the fibroblast cells by immunofluorescence. Additionally, to evaluate the influence of the number of passages (first, third and tenth passage) and cryopreservation on establishment of cell lines, fibroblasts were analysed for the viability, metabolic activity, population doubling time (PDT), levels of reactive oxygen species (ROS), and mitochondrial membrane potential (ΔΨm). Results All explants (20/20) adhered to the dish in 2.4 days ± 0.5 with growth around the explants in 4.6 days ± 0.7, and subconfluence was observed within 7.8 days ± 1.0. Moreover, by morphology and immunocytochemistry analyses, cells were identified as fibroblasts which presented oval nuclei, a fusiform shape and positive vimentin staining. No contamination was observed after culture without antibiotics and antifungals for 30 days. While there was no difference observed for cell viability after the passages (first vs. third: P = 0.98; first vs. tenth: P = 0.76; third vs. tenth: P = 0.85), metabolic activity was found to be reduced in the tenth passage (23.2 ± 12.1%) when compared to that in the first and third passage (100.0 ± 24.4%, P = 0.006). Moreover, the cryopreservation did not influence the viability (P = 0.11), metabolic activity (P = 0.77), or PDT (P = 0.11). Nevertheless, a greater ΔΨm (P = 0.0001) was observed for the cryopreserved cells (2.12 ± 0.14) when compared to that in the non-cryopreserved cells (1.00 ± 0.05). Additionally, the cryopreserved cells showed greater levels of intracellular ROS after thawing (1.69 ± 0.38 vs. 1.00 ± 0.22, P = 0.04). Conclusions This study is the first report on isolation, characterization and cryopreservation of fibroblasts from collared peccaries. We showed that adherent cultures were efficient for obtaining fibroblasts, which can be used as donor cells for nuclei for species cloning and other applications.
Borges et al. (2020) Isolation, characterization, and cryopreservation of collared peccary skin-derived fibroblast cell lines. PeerJ 8:e9136 https://doi.org/10.7717/peerj.9136
Identification of DEGs and transcription factors involved in H. pylori-associated inflammation and their relevance with gastric cancer
Background Previous studies have indicated that chronic inflammation linked to H. pylori infection is the leading causes for gastric cancer (GC). However, the exact mechanism is not entirely clear until now. Purpose To identify the key molecules and TFs involved in H. pylori infection and to provide new insights into H. pylori-associated carcinogenesis and lay the groundwork for the prevention of GC. Results GO and KEGG analysis revealed that the DEGs of Hp+-NAG were mainly associated with the immune response, chemokine activity, extracellular region and rheumatoid arthritis pathway. The DEGs of Hp+-AG-IM were related to the apical plasma membrane, intestinal cholesterol absorption, transporter activity and fat digestion and absorption pathway. In Hp+-NAG network, the expression of TNF, CXCL8, MMP9, CXCL9, CXCL1, CCL20, CTLA4, CXCL2, C3, SAA1 and FOXP3, JUN had statistical significance between normal and cancer in TCGA database. In Hp+-AG-IM network the expression of APOA4, GCG, CYP3A4, XPNPEP2 and FOXP3, JUN were statistically different in the comparison of normal and cancer in TCGA database. FOXP3 were negatively associated with overall survival, and the association for JUN was positive. Conclusion The current study identified key DEGs and their transcriptional regulatory networks involved in H. pylori-associated NAG, AG-IM and GC and found that patients with higher expressed FOXP3 or lower expressed JUN had shorter overall survival time. Our study provided new directions for inflammation-associated oncogenic transformation involved in H. pylori infection.
Yin et al. (2020) Identification of DEGs and transcription factors involved in H. pylori-associated inflammation and their relevance with gastric cancer. PeerJ 8:e9223 https://doi.org/10.7717/peerj.9223
Incorporating reef fish avoidance behavior improves accuracy of species distribution models
Species distribution models (SDMs) are used to interpret and map fish distributions based on habitat variables and other drivers. Reef fish avoidance behavior has been shown to vary in the presence of divers and is primarily driven by spearfishing pressure. Diver avoidance behavior or fish wariness may spatially influence counts and other descriptive measures of fish assemblages. Because fish assemblage metrics are response variables for SDMs, measures of fish wariness may be useful as predictors in SDMs of fishes targeted by spearfishing. We used a diver operated stereo-video system to conduct fish surveys and record minimum approach distance (MAD) of targeted reef fishes inside and outside of two marine reserves on the island of Oʻahu in the main Hawaiian Islands. By comparing MAD between sites and management types we tested the assumption that it provides a proxy for fish wariness related to spearfishing pressure. We then compared the accuracy of SDMs which included MAD as a predictor with SDMs that did not. Individual measures of MAD differed between sites though not management types. When included as a predictor, MAD averaged at the transect level greatly improved the accuracy of SDMs of targeted fish biomass.
Spatial and Geographic Information Science
Stamoulis et al. (2020) Incorporating reef fish avoidance behavior improves accuracy of species distribution models. PeerJ 8:e9246 https://doi.org/10.7717/peerj.9246
Addressing initialisation uncertainty for end-to-end ecosystem models: application to the Chatham Rise Atlantis model
Ecosystem models require the specification of initial conditions, and these initial conditions have some level of uncertainty. It is important to allow for uncertainty when presenting model results, because it reduces the risk of errant or non-representative results. It is crucial that model results are presented as an envelope of what is likely, rather than presenting only one instance. We perturbed the initial conditions of the Chatham Rise Atlantis model and analysed the effect of this uncertainty on the model’s dynamics by comparing the model outputs resulting from many initial condition perturbations. At the species group level, we found some species groups were more sensitive than others, with lower trophic level species groups generally more sensitive to perturbations of the initial conditions. We recommend testing for robust system dynamics by assessing the consistency of ecosystem indicators in response to fishing pressure under perturbed initial conditions. In any set of scenarios explored using complex end-to-end ecosystem models, we recommend that associated uncertainty analysis be included with perturbations of the initial conditions.
McGregor et al. (2020) Addressing initialisation uncertainty for end-to-end ecosystem models: application to the Chatham Rise Atlantis model. PeerJ 8:e9254 https://doi.org/10.7717/peerj.9254