Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data
Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation.
Seabra et al. (2021) Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data. PeerJ 9:e11425 https://doi.org/10.7717/peerj.11425
Development of landscape conservation value map of Jeju island, Korea for integrative landscape management and planning using conservation value of landscape typology
Understanding landscape as a socio-ecological system where systematic interactions occur among diverse ecosystems and human society is necessary for a sustainable landscape and resource management. However, many countries with rapid economic growth, including South Korea, depend on conventional planning and policy decisions to meet increasing demands for the use of specific natural resources. Such resource-oriented planning and policy which neglect considerations for the surrounding landscape can result in conflicts of interest and regulation. We designed a landscape conservation value (LCV) map of Jeju Island, Korea to overcome rising managerial and policy issues with the provision of systematic perspectives of landscape. With a consideration for natural and human-modified characteristics of the landscape, we used landform and land cover data to create fundamental landscape types. Then, the LCV was assigned to each type by a board of landscape experts. Within a study region, we observed relatively high values in registered protected areas and unique landscapes, and areas where high and low values are aligned. The resultant LCV map can identify areas that potentially require an integrated approach to prevent adverse effects caused by a conventional approach.
Spatial and Geographic Information Science
Jun et al. (2021) Development of landscape conservation value map of Jeju island, Korea for integrative landscape management and planning using conservation value of landscape typology. PeerJ 9:e11449 https://doi.org/10.7717/peerj.11449
Oyster farms are the main spawning grounds of the black sea bream Acanthopagrus schlegelii in Hiroshima Bay, Japan
Understanding the anthropogenic impact of oyster farms is essential for the management and conservation of marine fishes. In Japan, Hiroshima Bay is the region with the most intense oyster farming and thus suitable to study the impact of these farms. Here, we surveyed spherical planktonic eggs of the black sea bream Acanthopagrus schlegelii, one of the most abundant fish in the Bay. Our survey was performed at fourteen stations which included places with oyster farms and historical spawning grounds. We found the highest egg densities in four stations, one with historical spawning aggregations and three with major oyster farms. Besides, surveys at the innermost part of Hiroshima Bay, where two major rivers discharge, showed a low density of eggs indicating that black sea bream avoids spawning in low salinity areas. Our study suggests that oyster farms benefit spawners of black sea bream by providing more food sources than historical spawning grounds for efficient spawning. Yet, whether oyster farms represent a full advantage for the species remains unclear, particularly because they are known to host jellyfishes that prey on eggs and limit water flow that can influence the survival of fish eggs.
Kawai et al. (2021) Oyster farms are the main spawning grounds of the black sea bream Acanthopagrus schlegelii in Hiroshima Bay, Japan. PeerJ 9:e11475 https://doi.org/10.7717/peerj.11475
Myocardial contrast echocardiography assessment of mouse myocardial infarction: comparison of kinetic parameters with conventional methods
This study explores the use of a minimally invasive assessment of myocardial infarction (MI) in mice using myocardial contrast echocardiography (MCE). The technique uses existing equipment and software readily available to the average researcher. C57/BL6 mice were randomized to either MI or sham surgery and evaluated using MCE at 1- or 2-weeks post-surgery. Size-isolated microbubbles were injected via retro-orbital catheter where their non-linear characteristics were utilized to produce the two-dimensional parameters of Wash-in-Rate and the Peak Enhancement, indicative of relative myocardial perfusion and blood volume, respectively. Three-dimensional cardiac reconstructions allowed the calculation of the Percent Agent, interpreted as the vascularity of the entire myocardium. These MCE parameters were compared to conventional assessments including M-Mode, strain analysis, and 2,3,5-Triphenyltetrazolium chloride (TTC) staining. Except for the Wash-in-Rate 2-week cohort, all MCE parameters were able to differentiate sham-operated versus MI animals and correlated with TTC staining (P < 0.05). MCE parameters were also able to identify MI group animals which failed to develop infarctions as determined by TTC staining. This study provides basic validation of these MCE parameters to detect MI in mice complementary to conventional methods while providing additional hemodynamic information in vivo.
Thielen et al. (2021) Myocardial contrast echocardiography assessment of mouse myocardial infarction: comparison of kinetic parameters with conventional methods. PeerJ 9:e11500 https://doi.org/10.7717/peerj.11500
Neuromedin U and neurotensin may promote the development of the tumour microenvironment in neuroblastoma
Stage 4S neuroblastoma, as defined by the International Neuroblastoma Staging System committee (INSS), is known to regress spontaneously and have a more favourable outcome compared with stage 4 tumours. Comparing the molecular differences between these two stages may provide insights into the progression of neuroblastoma. Our study aimed to explore the molecular differences in the tumour microenvironment (TME) between INSS stage 4S and stage 4 tumours to provide an insight into the mechanisms underlying the biological processes of neuroblastoma. We downloaded the datasets GSE120572 and GSE73517 from the GEO database and pre-processed them using the limma package. CIBERSORT deconvolution agorithm was applied to analyse the differences in 22 infiltrating immune leukocyte subsets between the two stages. We used gene ontology (GO) enrichment analysis to determine the biological process (BP) annotation of differentially expressed genes (DEGs) using the online WebGestalt tool. Hub genes were determined in the STRING database and Cytoscape, and the expression of these genes was verified in the Oncomine database. Then these critical genes were performed survival analysis in TARGET database. We further validated the hub genes using a transwell assay and wound healing assay to detect the function of the genes in the neuroblastoma cell line SK-N-BE(2). GO analysis revealed that the 216 DEGs between stage 4S and stage 4 were enriched in aggressive biological processes. Neuromedin U (NMU) and neurotensin (NTS), which were significantly associated with patients’ overall survival rate, were verified to be elevated in stage 4, and to promote the proliferation and invasion of the SK-N-BE(2) cell. Tumour infiltrating leukocyte analysis showed a high infiltration of regulatory T cells and type 2 tumour-associated macrophages in stage 4 but not in stage 4S. Results of gene co-expression correlation, and the results of previous studies, suggest that NMU and NTS may play certain roles in modulating TME, thus facilitating the progression of neuroblastoma.
Yang et al. (2021) Neuromedin U and neurotensin may promote the development of the tumour microenvironment in neuroblastoma. PeerJ 9:e11512 https://doi.org/10.7717/peerj.11512
Promoting effect of rapamycin on osteogenic differentiation of maxillary sinus membrane stem cells
Background Stem cells located in the maxillary sinus membrane can differentiate into osteocytes. Our study aimed to evaluate the effect of rapamycin (RAPA) on the osteogenic differentiation of maxillary sinus membrane stem cells (MSMSCs). Methods Colony-forming unit assay, immunophenotype identification assay, and multi-differentiation assay confirmed characteristics of MSMSCs obtained from SD rats. Transmission electron microscopy (TEM) and flow cytometry (FCM) identified the initial autophagic level of MSMSCs induced by RAPA. Real-time quantitative PCR (qPCR) evaluated subsequent autophagic levels and osteogenic differentiation. Alkaline phosphatase (ALP) activity assay and alizarin red staining (ARS) evaluated subsequent osteogenic differentiation. We performed a histological examination to clarify in vivo osteogenesis with ectopic bone mass from BALB/c nude mice. Results MSMSCs possessed an active proliferation and multi-differentiation capacity, showing a phenotype of mesenchymal stem cells. The autophagic level increased with increasing RAPA (0, 10, 100, 1,000 nM) and decreased over time. ALP activity and calcium nodules forming in four RAPA-treated groups on three-time points (7, 14, 21 d) showed significant differences. Col1a1, Runx2, and Spp1 expressed most in 100 nM RAPA group on 7 and 14 d. Osteogenesis-related genes except for Ibsp expression between four groups tended to be consistent on 21 d. 100 nM and 10 nM RAPA-treated groups showed more bone formation in vivo. Conclusion RAPA can promote osteogenic differentiation of MSMSCs, indicating a possible relationship between osteogenic differentiation and autophagy.
Lin et al. (2021) Promoting effect of rapamycin on osteogenic differentiation of maxillary sinus membrane stem cells. PeerJ 9:e11513 https://doi.org/10.7717/peerj.11513
Structural variation and evolution of chloroplast tRNAs in green algae
As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the Ψ-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. Based on the constructed phylogenetic tree, mutations were found to accompany the evolution of the Green algae chloroplast tRNA. Moreover, chloroplast tRNAs of Chlorophyceae are consistent with those of monocotyledons and gymnosperms in terms of evolutionary patterns, sharing a common multi-phylogenetic pattern and rooted in a rich common ancestor. Sequence alignment and systematic analysis of tRNA in chloroplast genome of Chlorophyceae, clarified the characteristics and rules of tRNA changes, which will promote the evolutionary relationship of tRNA and the origin and evolution of chloroplast.
Qi et al. (2021) Structural variation and evolution of chloroplast tRNAs in green algae. PeerJ 9:e11524 https://doi.org/10.7717/peerj.11524
T-complex protein 1 subunit zeta-2 (CCT6B) deficiency induces murine teratospermia
Background The CCT complex is an important mediator of microtubule assembly and intracellular protein folding. Owing to its high expression in spermatids, CCT knockdown can disrupt spermatogenesis. In the present report, we therefore evaluated the in vivo functionality of the testis-specific CCT complex component CCT6B using a murine knockout model system. Methods A CRISPR/Cas9 approach was used to generate Cct6b−/− mice, after which candidate gene expression in these animals was evaluated via qPCR and Western blotting. Testicular and epididymal phenotypes were assessed through histological and immunofluorescent staining assays, while a computer-assisted sperm analyzer was employed to assess semen quality. Results Cct6b−/− mice were successfully generated, and exhibited no differences in development, fertility, appearance, testis weight, or sperm counts relative to control littermates. In addition, no differences in spermatogenesis were detected when comparingCct6b+/+ and Cct6b−/− testes. However, when progressive motility was analyzed, the ratio of normal sperm was significantly decreased in Cct6b−/− male mice, with nuclear base bending being the primary detected abnormality. In addition, slight decreases in Cct4 and Cct7 expression were detected. Conclusion These data indicated that CCT6B is an important regulator of murine spermatogenesis, with the loss of this protein resulting in CCT complex dysfunction, providing a foundation for further studies.
Yang et al. (2021) T-complex protein 1 subunit zeta-2 (CCT6B) deficiency induces murine teratospermia. PeerJ 9:e11545 https://doi.org/10.7717/peerj.11545
High PHD Finger Protein 19 (PHF19) expression predicts poor prognosis in colorectal cancer: a retrospective study
Background Colorectal cancer (CRC) is the third most common cancer all around the world, and it seriously threats human health. PHF19 has been proved to be closely related to the prognosis of patients in a variety of malignant tumors, but the effect of PHF19 on the prognosis evaluation of CRC patients has not been confirmed. Methods In our study, we used GEO, TCGA database and IHC to verify the PHF19 expression in CRC samples. Survival analysis of PHF19 based on TCGA, GEO series, and our own CRC sample were performed. Cox regression was performed to reveal the relationship between PHF19 and prognosis. Co-expression was performed to find genes related to PHF19 expression. GO/KEGG enrichment analysis and GSEA analysis were used to confirm the most relevant signal pathway to PHF19. Next, cell experiments were performed to verify the effect of PHF19 on the proliferation, invasion and metastasis of CRC. Then, Western blot was used to verify the protein expression of the above two phenotypes. Finally, tumor formation experiments in nude mice were used to verify the role of PHF19 of tumor proliferation in vivo. Results We found that PHF19 was significantly over-expressed in tumors compared with normal tissues. Kaplan–Meier (K–M) analysis indicated that high PHF19 in CRC associated with poor overall survival (OS) in CRC patients. Clinical correlation analysis showed that high expression of PHF19 was closely related to t umor progression in CRC patients, especially infiltration and metastasis. Bioinformatics revealed that PHF19 might affect tumor malignant phenotype by regulating the cell cycle in CRC. CCK-8 and clonal formation experiment showed that the proliferative ability of tumor cells was promoted. Flow cytometry showed that the cell cycle accelerated the transition from G1 to S phase. Western blot found that Cyclin D1, CDK4, and CDK6 expression were up-regulated. Transwell and wound-healing experiment found that invasive and migratory abilities was promoted after the over-expression of PHF19. Western blot showed that the expression of key proteins of Epithelial-Mesenchymal Transition (EMT) changed. Tumor formation experiments in nude mice showed that overexpression of PHF19 could promote tumor proliferation in vivo. Conclusion Our research proved that PHF19 could be an independent prognostic factor for CRC, PHF19 promoted the proliferative ability and the invasion and metastasis of CRC by up-regulating the expression of key molecules related to cell cycle and EMT pathway in vitro, promoting tumor proliferation in vivo.
Li et al. (2021) High PHD Finger Protein 19 (PHF19) expression predicts poor prognosis in colorectal cancer: a retrospective study. PeerJ 9:e11551 https://doi.org/10.7717/peerj.11551
Changes in the stoichiometry of Castanopsis fargesii along an elevation gradient in a Chinese subtropical forest
Elevation is important for determining the nutrient biogeochemical cycle in forest ecosystems. Changes in the ecological stoichiometry of nutrients along an elevation gradient can be used to predict how an element cycle responds in the midst of global climate change. We investigated changes in concentrations of and relationships between nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) in the leaves and roots of the dominant tree species, Castanopsis fargesii, along an elevation gradient (from 500 to 1,000 m above mean sea level) in a subtropical natural forest in China. We analyzed correlations between C. fargesii’s above-ground biomass and stoichiometry with environmental factors. We also analyzed the soil and plant stoichiometry of this C. fargesii population. Our results showed that leaf N decreased while leaf K and Ca increased at higher elevations. Meanwhile, leaf P showed no relationship with elevation. The leaf N:P indicated that C. fargesii was limited by N. Elevation gradients contributed 46.40% of the total variance of ecological stoichiometry when assessing environmental factors. Our research may provide a theoretical basis for the biogeochemical cycle along with better forest management and fertilization for this C. fargesii population.
Liu et al. (2021) Changes in the stoichiometry of Castanopsis fargesii along an elevation gradient in a Chinese subtropical forest. PeerJ 9:e11553 https://doi.org/10.7717/peerj.11553