Expanding walls and shrinking beaches: loss of natural coastline in Okinawa Island, Japan
Okinawa is the largest and most populated island of the Ryukyu Archipelago in southern Japan and is renowned for its natural resources and beauty. Similar as to what has been happening in the rest of the country, Okinawa Island has been affected by an increasing amount of development and construction work. The trend has been particularly acute after reversion to Japanese sovereignty in 1972, following 27 years of post-war American administration. A coastline once characterized by extended sandy beaches surrounded by coral reefs now includes tracts delimited by seawalls, revetments, and other human-made hardening structures. Additionally, part of coastal Okinawa Island was obtained by land-filling shallow ocean areas (land reclamation). Nevertheless, the current extension of the artificial coastline, as well as the level of fragmentation of the natural coastline are unclear, due to the lack of both published studies and easily accessible and updated datasets. The aims of this research were to quantify the extension of coastline alterations in Okinawa Island, including the amount of land-filling performed over the last 41 years, and to describe the coastlines that have been altered the most as well as those that are still relatively pristine. The analyses were performed using a reference map of Okinawa Island based on GIS vector data extracted from the OpenStreetMap (OSM) coastline dataset (average node distance for Okinawa Island = 24 m), in addition to satellite and aerial photography from multiple providers. We measured 431.8 km of altered coastline, equal to about 63% of the total length of coastline in Okinawa Island. Habitat fragmentation is also an issue as the remaining natural coastline was broken into 239 distinct tracts (mean length = 1.05 km). Finally, 21.03 km2 of the island’s surface were of land reclaimed over the last 41 years. The west coast has been altered the most, while the east coast is in relatively more natural conditions, particularly the northern part, which has the largest amount of uninterrupted natural coastline. Given the importance of the ecosystem services that coastal and marine ecosystems provide to local populations of subtropical islands, including significant economic income from tourism, conservation of remaining natural coastlines should be given high priority.
Spatial and Geographic Information Science
Masucci et al. (2019) Expanding walls and shrinking beaches: loss of natural coastline in Okinawa Island, Japan. PeerJ 7:e7520 https://doi.org/10.7717/peerj.7520
Crucial lncRNAs associated with adipocyte differentiation from human adipose-derived stem cells based on co-expression and ceRNA network analyses
Background Injection of adipose-derived stem cells (ASCs) is a promising treatment for facial contour deformities. However, its treatment mechanisms remain largely unknown. The study aimed to explain the molecular mechanisms of adipogenic differentiation from ASCs based on the roles of long noncoding RNAs (lncRNAs). Methods Datasets of mRNA–lncRNA (GSE113253) and miRNA (GSE72429) expression profiling were collected from Gene Expression Omnibus database. The differentially expressed genes (DEGs), lncRNAs (DELs) and miRNAs (DEMs) between undifferentiated and adipocyte differentiated human ASCs were identified using the Linear Models for Microarray Data method. DELs related co-expression and competing endogenous RNA (ceRNA) networks were constructed. Protein–protein interaction (PPI) analysis was performed to screen crucial target genes. Results A total of 748 DEGs, 17 DELs and 51 DEMs were identified. A total of 13 DELs and 279 DEGs with Pearson correlation coefficients > 0.9 and p-value < 0.01 were selected to construct the co-expression network. A total of 151 interaction pairs among 112 nodes (10 DEMs; eight DELs; 94 DEGs) were obtained to construct the ceRNA network. By comparing the lncRNAs and mRNAs in two networks, five lncRNAs (SNHG9, LINC02202, UBAC2-AS1, PTCSC3 and myocardial infarction associated transcript (MIAT)) and 32 genes (i.e., such as phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), protein tyrosine phosphatase receptor type B (PTPRB)) were found to be shared. PPI analysis demonstrated PIK3R1 , forkhead box O1 (FOXO1; a transcription factor) and estrogen receptor 1 (ESR1) were hub genes, which could be regulated by the miRNAs that interacted with the above five lncRNAs, such as LINC02202-miR-136-5p-PIK3R1, LINC02202-miR-381-3p-FOXO1 and MIAT-miR-18a-5p-ESR1. LINC02202 also could directly co-express with PIK3R1. Furthermore, PTPRB was predicted to be modulated by co-expression with LINC01119. Conclusion MIAT, LINC02202 and LINC01119 may be potentially important, new lncRNAs associated with adipogenic differentiation of ASCs. They may be involved in adipogenesis by acting as a ceRNA or co-expressing with their targets.
Chen et al. (2019) Crucial lncRNAs associated with adipocyte differentiation from human adipose-derived stem cells based on co-expression and ceRNA network analyses. PeerJ 7:e7544 https://doi.org/10.7717/peerj.7544
Design, synthesis and antimicrobial activities of novel 1,3,5-thiadiazine-2-thione derivatives containing a 1,3,4-thiadiazole group
A series of novel 1,3,5-thiadiazine-2-thione derivatives containing a 1,3,4-thiadiazole group was designed and synthesized. The structures of all the compounds were well characterized using 1H NMR, 13C NMR and high-resolution mass spectrometer, and further confirmed by the X-ray diffraction analysis of 8d. The antimicrobial activities of all the target compounds against Xanthomonas oryzae pv. oryzicola, X. oryzae pv. oryzae, Rhizoctonia solani and Fusarium graminearum were evaluated. The in vitro antimicrobial bioassays indicated that some title compounds exhibited noteworthy antimicrobial effects against the above strains. Notably, the compound N-(5-(ethylthio)-1,3,4-thiadiazol-2-yl)-2-(5-methyl-6-thioxo-1,3,5-thiadiazinan-3-yl)acetamide (8a) displayed obvious antibacterial effects against X. oryzae pv. oryzicola and X. oryzae pv. oryzae at 100 μg/mL with the inhibition rates of 30% and 56%, respectively, which was better than the commercial bactericide thiodiazole-copper. In addition, the anti-R. solani EC50 value of 8a was 33.70 μg/mL, which was more effective than that of the commercial fungicide hymexazol (67.10 μg/mL). It was found that the substitutes in the 1,3,5-thiadiazine-2-thione and the 1,3,4-thiadiazole rings played a vital role in the antimicrobial activities of the title compounds. More active title compounds against phytopathogenic microorganisms might be obtained via further structural modification.
Yan et al. (2019) Design, synthesis and antimicrobial activities of novel 1,3,5-thiadiazine-2-thione derivatives containing a 1,3,4-thiadiazole group. PeerJ 7:e7581 https://doi.org/10.7717/peerj.7581
Sensitive and rapid detection of Ortleppascaris sinensis (Nematoda: Ascaridoidea) by loop-mediated isothermal amplification
Ortleppascaris sinensis is the dominant nematode species infecting the gastrointestinal tract of the captive Chinese alligator, a critically endangered species. Gastrointestinal nematode infection may cause a loss of appetite, growth, a development disorder, and even mortality in alligators, especially young ones. This research first establishment a loop-mediated isothermal amplification (LAMP) assay in rapidly identifying O. sinensis, upon the basis of the complete internal transcribed spacers (ITS) gene. Eight sets of primers were designed for recognition of the unique conserved ITS gene sequences, and one set was selected to be the most suitable primer for rapid detection. The specific as well as the sensitive features of the most appropriate primer in LAMP reactions for O. sinensis, and feces specimens of Chinese alligators suffering from O. sinensis were determined. Turbidity monitoring and Te Visual Reagent methods were used for determining negative and positive consequences. According to this study, amplification and visualization of the target DNA could be realized through two detection approaches during 50 min at 65 °C isothermal temperature. The sensitivity of LAMP was a detecting limitation of 3.46 pg/µl DNA. No cross-reactions were found between O. sinensis and any other of the nine heterologous nematode parasites, which shows the outstanding specific features of the primers. The LAMP assay could also perform a detection of target DNA of O. sinensis in the feces samples of Chinese alligators. This LAMP assay is useful for directly detecting O. sinensis in the Chinese alligator breeding centers, particularly due to its rapidity, simplicity and low cost.
Zhao et al. (2019) Sensitive and rapid detection of Ortleppascaris sinensis (Nematoda: Ascaridoidea) by loop-mediated isothermal amplification. PeerJ 7:e7607 https://doi.org/10.7717/peerj.7607
Identification of Flap endonuclease 1 as a potential core gene in hepatocellular carcinoma by integrated bioinformatics analysis
Hepatocellular carcinoma (HCC) is a common yet deadly form of malignant cancer. However, the specific mechanisms involved in HCC diagnosis have not yet fully elucidated. Herein, we screened four publically available Gene Expression Omnibus (GEO) expression profiles (GSE14520, GSE29721, GSE45267 and GSE60502), and used them to identify 409 differentially expressed genes (DEGs), including 142 and 267 up- and down-regulated genes, respectively. The DAVID database was used to look for functionally enriched pathways among DEGs, and the STRING database and Cytoscape platform were used to generate a protein-protein interaction (PPI) network for these DEGs. The cytoHubba plug-in was utilized to detect 185 hub genes, and three key clustering modules were constructed with the MCODE plug-in. Gene functional enrichment analyses of these three key clustering modules were further performed, and nine core genes including BIRC5, DLGAP5, DTL, FEN1, KIAA0101, KIF4A, MCM2, MKI67, and RFC4, were identified in the most critical cluster. Subsequently, the hierarchical clustering and expression of core genes in TCGA liver cancer tissues were analyzed using the UCSC Cancer Genomics Browser, and whether elevated core gene expression was linked to a poor prognosis in HCC patients was assessed using the GEPIA database. The PPI of the nine core genes revealed an interaction between FEN1, MCM2, RFC4, and BIRC5. Furthermore, the expression of FEN1 was positively correlated with that of three other core genes in TCGA liver cancer tissues. FEN1 expression in HCC and other tumor types was assessed with the FIREBROWSE and ONCOMINE databases, and results were verified in HCC samples and hepatoma cells. FEN1 levels were also positively correlated with tumor size, distant metastasis and vascular invasion. In conclusion, we identified nine core genes associated with HCC development, offering novel insight into HCC progression. In particular, the aberrantly elevated FEN1 may represent a potential biomarker for HCC diagnosis and treatment.
Li et al. (2019) Identification of Flap endonuclease 1 as a potential core gene in hepatocellular carcinoma by integrated bioinformatics analysis. PeerJ 7:e7619 https://doi.org/10.7717/peerj.7619
Dendrobium alkaloids decrease Aβ by regulating α- and β-secretases in hippocampal neurons of SD rats
Background Alzheimer’s disease (AD) is the primary cause of dementia in the elderly. The imbalance between production and clearance of amyloid β (Aβ) is a very early, often initiating factor in AD. Dendrobium nobile Lindl. alkaloids (DNLA) extracted from a Chinese medicinal herb, which have been shown to have anti-aging effects, protected against neuronal impairment in vivo and in vitro. Moreover, we confirmed that DNLA can improve learning and memory function in elderly normal mice, indicating that DNLA has potential health benefits. However, the underlying mechanism is unclear. Therefore, we further explored the effect of DNLA on neurons, which is closely related to learning and memory, based on Aβ. Methods We exposed cultured hippocampal neurons to DNLA to investigate the effect of DNLA on Aβ in vitro. Cell viability was evaluated by MTT assays. Proteins were analyzed by Western blot analysis. Results The cell viability of hippocampal neurons was not changed significantly after treatment with DNLA. But DNLA reduced the protein expression of amyloid precursor protein (APP), disintegrin and metalloprotease 10 (ADAM10), β-site APP cleaving enzyme 1 (BACE1) and Aβ1–42 of hippocampal neurons in rats and increased the protein expression of ADAM17. Conclusions DNLA decreases Aβ by regulating α- and β-secretase in hippocampal neurons of SD rats.
Huang et al. (2019) Dendrobium alkaloids decrease Aβ by regulating α- and β-secretases in hippocampal neurons of SD rats. PeerJ 7:e7627 https://doi.org/10.7717/peerj.7627
Differential mechanisms underlying responses of soil bacterial and fungal communities to nitrogen and phosphorus inputs in a subtropical forest
Atmospheric nitrogen (N) deposition and phosphorus (P) addition both can change soil bacterial and fungal community structure with a consequent impact on ecosystem functions. However, which factor plays an important role in regulating responses of bacterial and fungal community to N and P enrichments remains unclear. We conducted a manipulative experiment to simulate N and P inputs (10 g N · m−2 · yr−1 NH4NO3 or 10 g P · m−2 · yr−1 NaH2PO4) and compared their effects on soil bacterial and fungal species richness and community composition. The results showed that the addition of N significantly increased NH4+ and Al3+ by 99.6% and 57.4%, respectively, and consequently led to a decline in soil pH from 4.18 to 3.75 after a 5-year treatment. P addition increased Al3+ and available P by 27.0% and 10-fold, respectively, but had no effect on soil pH. N addition significantly decreased bacterial species richness and Shannon index and resulted in a substantial shift of bacterial community composition, whereas P addition did not. Neither N nor P addition changed fungal species richness, Shannon index, and fungal community composition. A structural equation model showed that the shift in bacterial community composition was related to an increase in soil acid cations. The principal component scores of soil nutrients showed a significantly positive relationship with fungal community composition. Our results suggest that N and P additions affect soil bacterial and fungal communities in different ways in subtropical forest. These findings highlight how the diversity of microbial communities of subtropical forest soil will depend on future scenarios of anthropogenic N deposition and P enrichment, with a particular sensitivity of bacterial community to N addition.
Li et al. (2019) Differential mechanisms underlying responses of soil bacterial and fungal communities to nitrogen and phosphorus inputs in a subtropical forest. PeerJ 7:e7631 https://doi.org/10.7717/peerj.7631
Two new species of Notodasus Fauchald, 1972 (Annelida: Capitellidae) from the Central Indo-Pacific region
Notodasus Fauchald, 1972 is a small genus of the polychaete family Capitellidae, including 10 described species worldwide. The genus is unusual in the Central Indo-Pacific, and there is no taxonomic record of Notodasus in this region. In this study, two new species of Notodasus are described and illustrated, namely Notodasus celebensis sp. nov. and N. chinensis sp. nov. The former species, collected from the mixed-species seagrass beds in the Indonesian island of Sulawesi, is mainly characterized by the longitudinally striated epithelium on thoracic segments and the completely separated notopodial lobes. The latter species, obtained from coastal waters off southern China, differs from its congeners with the following characters: tessellated epithelium present on anterior thorax as well as on the dorsum of chaetigers 11 and 12, notopodial lobes fused and chaetal fascicles almost touching each other on anterior abdomen, and branchial pores evident from anterior abdomen. Comparisons are made with closely related species in this paper, and a revised key is provided to all described Notodasus species. The descriptions of the two new species represent the first record of Notodasus in this region and expand the geographical distribution of the genus.
Lin et al. (2019) Two new species of Notodasus Fauchald, 1972 (Annelida: Capitellidae) from the Central Indo-Pacific region. PeerJ 7:e7638 https://doi.org/10.7717/peerj.7638
Cloning, phylogenetic research, and prokaryotic expression study of the metabolic detoxification gene EoGSTs1 in Empoasca onukii Matsuda
Due to the misuse of chemical pesticides, small green leafhoppers (Empoasca onukii Matsuda) have developed resistance to pesticides, thereby posing a serious problem to the tea industry. Glutathione S-transferases (GSTs) are an important family of enzymes that are involved in pesticide resistance in Empoasca onukii Matsuda. Empoasca onukii GST sigma 1 (EoGSTs1, GenBank: MK443501) is a member of the GST family. In this study, the full-length cDNA of EoGSTs1 was cloned by reverse transcription polymerase chain reaction (qPCR), and its taxonomic identity was examined. Furthermore, we performed bioinformatics and phylogenetic analyses of the gene and structural and functional domain prediction of the protein. The results demonstrate that EoGSTS1 belongs to the Sigma family of GSTs; the full-length EoGSTs1 cDNA is 841 bp with a 624-bp coding region that encodes a 23.68932-kDa protein containing 207 amino acids. The theoretical isoelectric point (IEP) was calculated to be 6.00. Phylogenetic analysis indicates that EoGSTS1 is closely related to the Sub psaltriayangi subfamily of the Cicadoidea superfamily in order Hemiptera, whereas it is distantly related to Periplaneta americana of order Blattodea. Amino acid sequence alignment of EoGSTS1 and GSTs from four other insects of order Hemiptera revealed protein sequence conservation. Tertiary structure analysis and structural domain functional predictions of the protein revealed that EoGSTS1 contains nine α helices and two β sheets with one conserved GST domain. The results of enzyme activity assay showed that recombinant EoGSTs1 (rEoGSTs1) protein had catalytic activity for substrate 1-chloro-2,4-dinitrobenzene (CDNB) and exhibited the highest activity at pH 7 and 25 °C. The Michaelis constant Km of rEoGSTs1 protein was 0.07782 ± 0.01990 mmol/L, and the maximum reaction rate Vmax was 12.15 ± 1.673 µmol/min⋅mg. Our study clarified the taxonomic identity of small green leafhopper EoGSTs1 and revealed some properties of the gene and its encoded protein sequence. According to the catalytic activity of the rEoGSTs1 enzyme on the model substrate CDNB, we infer that it functions in the degradation of exogenous substances.
Zhang et al. (2019) Cloning, phylogenetic research, and prokaryotic expression study of the metabolic detoxification gene EoGSTs1 in Empoasca onukii Matsuda. PeerJ 7:e7641 https://doi.org/10.7717/peerj.7641
Responses of weed community, soil nutrients, and microbes to different weed management practices in a fallow field in Northern China
The long-term use of herbicides to remove weeds in fallow croplands can impair soil biodiversity, affect the quality of agricultural products, and threaten human health. Consequently, the identification of methods that can effectively limit the weed seed bank and maintain fallow soil fertility without causing soil pollution for the next planting is a critical task. In this study, four weeding treatments were established based on different degrees of disturbance to the topsoil: natural fallow (N), physical clearance (C), deep tillage (D), and sprayed herbicide (H). The changes in the soil weed seed banks, soil nutrients, and soil microbial biomass were carefully investigated. During the fallow period, the C treatment decreased the annual and biennial weed seed bank by 34% against pretreatment, whereas the H treatment did not effectively reduce the weed seed bank. The D treatment had positive effects on the soil fertility, increasing the available nitrogen 108% over that found in the N soil. In addition, a pre-winter deep tillage interfered with the rhizome propagation of perennial weeds. The total biomass of soil bacterial, fungal, and actinomycete in H treatment was the lowest among the four treatments. The biomass of arbuscular mycorrhizal fungi in the N treatment was respectively 42%, 35%, and 91%, higher than that in the C, D, and H treatments. An ecological weeding strategy was proposed based on our findings, which called for exhausting seed banks, blocking seed transmission, and taking advantage of natural opportunities to prevent weed growth for fallow lands. This study could provide a theoretical basis for weed management in fallow fields and organic farming systems.
Gu et al. (2019) Responses of weed community, soil nutrients, and microbes to different weed management practices in a fallow field in Northern China. PeerJ 7:e7650 https://doi.org/10.7717/peerj.7650