Molecular characterization of bacterial leaf streak resistance in hard winter wheat
Bacterial leaf streak (BLS) caused by Xanthomonas campestris pv. translucens is one of the major bacterial diseases threatening wheat production in the United States Northern Great Plains (NGP) region. It is a sporadic but widespread wheat disease that can cause significant loss in grain yield and quality. Identification and characterization of genomic regions in wheat that confer resistance to BLS will help track resistance genes/QTLs in future wheat breeding. In this study, we evaluated a hard winter wheat association mapping panel (HWWAMP) containing 299 hard winter wheat lines from the US hard winter wheat growing region for their reactions to BLS. We observed a range of BLS responses among the lines, importantly, we identified ten genotypes that showed a resistant reaction both in greenhouse and field evaluation. ­Genome-wide association analysis with 15,990 SNPs was conducted using an exponentially compressed mixed linear model. Five genomic regions (p < 0.001) that regulate the resistance to BLS were identified on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS. The QTLs Q.bls.sdsu-1AL, Q.bls.sdsu-1BS, Q.bls.sdsu-3AL, Q.bls.sdsu-4AL, and Q.bls.sdsu-7AS explain a total of 42% of the variation. In silico analysis of sequences in the candidate regions on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS identified 10, 25, 22, eight, and nine genes, respectively with known plant defense-related functions. Comparative analysis with rice showed two syntenic regions in rice that harbor genes for bacterial leaf streak resistance. The ten BLS resistant genotypes and SNP markers linked to the QTLs identified in our study could facilitate breeding for BLS resistance in winter wheat.
Ramakrishnan et al. (2019) Molecular characterization of bacterial leaf streak resistance in hard winter wheat. PeerJ 7:e7276 https://doi.org/10.7717/peerj.7276
Multi-scale relationship between land use/land cover types and water quality in different pollution source areas in Fuxian Lake Basin
The spatial-temporal evolution of land use and land cover (LULC) and its multi-scale impact on the water environment is becoming highly significant in the LULC research field. The current research results show that the more significant scale impact on LULC and water quality in the whole basin and the riparian buffer scale is unclear. A consensus has not been reached about the optimal spatial scale problem in the relationship between the LULC and water quality. The typical lake basin of the Fuxian Lake watershed was used as the research area and the scale relationship between the LULC and water quality was taken as the research object. High resolution remote sensing images, archival resources of surveying, mapping and geographic information, and the monitoring data of water quality were utilized as the main data sources. Remote sensing and Geometric Information Technology were applied. A multi-scale object random forest algorithm (MSORF) was used to raise the classification accuracy of the high resolution remote sensing images from 2005 to 2017 in the basin and the multi-scale relationship between the two was discussed using the Pearson correlation analysis method. From 2005 to 2017, the water quality indicators (Chemical Oxygen Demand (COD), Total Phosphorous (TP), Total Nitrogen (TN)) of nine rivers in the lake’s basin and the Fuxian Lake center were used as response variables and the LULC type in the basin was interpreted as the explanation variable. The stepwise selection method was used to establish a relationship model for the water quality of the water entering the lake and the significance of the LULC type was established at p < 0.05.The results show that in the seven spatial scales, including the whole watershed, sub-basin, and the riparian buffer zone (100 m, 300 m, 500 m, 700 m, and 1,000 m): (1) whether it is in the whole basin or buffer zone of different pollution source areas, impervious surface area (ISA), or other land and is positively correlated with the water quality and promotes it; (2) forestry and grass cover is another important factor and is negatively correlated with water quality; (3) cropping land is not a major factor explaining the decline in water quality; (4) the 300 m buffer zone of the river is the strongest spatial scale for the LULC type to affect the Chemical Oxygen Demand (COD). Reasonable planning for the proportion of land types in the riparian zone and control over the development of urban land in the river basin is necessary for the improvement of the urban river water quality. Some studies have found that the relationship between LULC and water quality in the 100 m buffer zone is more significant than the whole basin scale. While our study is consistent with the results of research conducted by relevant scholars in Aibi Lake in Xinjiang, and Erhai and Fuxian Lakes in Yunnan. Thus, it may be inferred that for the plateau lake basin, the 300 m riparian buffer is the strongest spatial scale for the LULC type to affect COD.
Li et al. (2019) Multi-scale relationship between land use/land cover types and water quality in different pollution source areas in Fuxian Lake Basin. PeerJ 7:e7283 https://doi.org/10.7717/peerj.7283
Shoot and root traits of summer maize hybrid varieties with higher grain yields and higher nitrogen use efficiency at low nitrogen application rates
Breeding high-yielding and nitrogen-efficient maize (Zea mays L.) hybrid varieties is a strategy that could simultaneously solve the problems of resource shortages and environmental pollution. We conducted a 2-year field study using four nitrogen application rates (0, 150, 225, and 300 kg N hm−2) and two maize hybrid varieties (ZD958 and QS101) to understand the plant traits related to high grain yields and high nitrogen use efficiency (NUE). We found that ZD958 had a higher grain yield and nitrogen accumulation in the shoots at harvest as well as a higher NUE at lower nitrogen application rates (0 and 150 kg hm–2) than QS101. The grain yields and NUE were almost identical for the two hybrid varieties at nitrogen application rates of 225 and 300 kg N hm–2. Compared with QS101, ZD958 had higher above-ground and below-ground biomass amounts, a deeper root distribution, longer root length, root active absorption area, greater grain filling rate, and higher photosynthetic NUE than QS101 at lower nitrogen application rates. Our results showed that ZD958 can maintain a higher grain yield at lower nitrogen rates in a similar manner to N-efficient maize hybrid varieties. The selection of hybrids such as ZD958 with a deeper root distribution and higher photosynthetic NUE can increase the grain yield and NUE under low nitrogen conditions.
Su et al. (2019) Shoot and root traits of summer maize hybrid varieties with higher grain yields and higher nitrogen use efficiency at low nitrogen application rates. PeerJ 7:e7294 https://doi.org/10.7717/peerj.7294
The Tsushima leopard cat exhibits extremely low genetic diversity compared with the Korean Amur leopard cat: Implications for conservation
We examined genetic diversity of the wild Tsushima leopard cat—a regional population of the Amur leopard cat—using microsatellite markers. In addition, we compared genetic diversity of the Tsushima leopard cat with that of the Korean population of Amur leopard cat. Although bias should be considered when applying cross-species amplification, the Tsushima leopard cat showed a lower index of molecular genetic diversity than did the Korean population. These results were consistent with those obtained using other genetic markers, such as mitochondrial DNA and Y chromosome sequences. This low genetic diversity of the wild Tsushima leopard cat may be derived from the founding population. Furthermore, our results suggest that the captive populations held in Japanese zoos may show extremely low genetic diversity, leading to difficulties in genetic management of the Tsushima leopard cat. Moreover, the two regional populations were clearly separated using these marker sets. In the present study, we demonstrated that the genetic diversity of the Tsushima leopard cat is extremely low compared with that of the continental regional population. Importantly, the Japanese captive population for ex situ conservation was derived from a founding population with extremely low genetic diversity; hence, we assume that both the captive and wild populations showed extremely low genetic diversities. Our findings emphasize the need to develop carefully considered management strategies for genetic conservation.
Ito et al. (2019) The Tsushima leopard cat exhibits extremely low genetic diversity compared with the Korean Amur leopard cat: Implications for conservation. PeerJ 7:e7297 https://doi.org/10.7717/peerj.7297
Establishing an ecological security pattern for urban agglomeration, taking ecosystem services and human interference factors into consideration
The assessment of ecological security patterns is a topic of conversation in landscape ecology in recent years. However, ecosystem services and human activities are seldom considered comprehensively in the assessment of ecological security patterns. The present study employs the Beijing–Tianjin–Hebei urban agglomeration as a study area, and uses ecological services to determine the ecological sources. The importance of ecological sources is classified based on logical coding and functional types of ecological services. The research combines regional characteristics to select and quantitatively calculate three human disturbance factors: soil erosion sensitivity, geological hazard sensitivity, and night lighting. Then the basic surface resistance of land use to limit migration is modified and ecological corridors are identified by combining these three disturbance factors. The results indicate that the sources of water production, soil and water conservation, and carbon fixation are mainly provided in mountainous areas, recreation sources are mostly distributed in the plains, and these ecological sources improve the maintenance of ecological corridors. The modification of resistance surfaces significantly changes the length of ecological corridors in Tianjin, Tangshan, Cangzhou, and Beijing, and the modified resistance surface improves the recognition of ecological corridors. This study provides a new research framework for identifying the ecological security patterns of urban agglomerations and provides scientific guidance related to ecological protection and urban planning for the Beijing−Tianjin−Hebei urban agglomeration.
Spatial and Geographic Information Science
Wang et al. (2019) Establishing an ecological security pattern for urban agglomeration, taking ecosystem services and human interference factors into consideration. PeerJ 7:e7306 https://doi.org/10.7717/peerj.7306
Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China
Background Distinguishing among species in the genus Lepista is difficult because of their similar morphologies. Methods To identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: internal transcribed spacer (ITS), the intergenic spacer (IGS), nuclear ribosomal RNA subunit, mitochondrial small subunit rDNA, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra- and inter-specific variations. Results The results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades.
Wang et al. (2019) Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China. PeerJ 7:e7307 https://doi.org/10.7717/peerj.7307
Predicting the potential distribution of the Asian citrus psyllid, Diaphorina citri (Kuwayama), in China using the MaxEnt model
Background Citrus huanglongbing (HLB) is a destructive disease of citrus and a major threat to the citrus industry around the world. This disease accounts for substantial economic losses in China every year. Diaphorina citri Kuwayama is one of the major vectors by which citrus HLB is spread under natural conditions in China. Research is needed to identify the geographic distribution of D. citri and its major areas of occurrence and to formulate measures for early warning, monitoring, and control of this pest and citrus HLB. Methods In this study, the ecological niche modelling software MaxEnt (maximum entropy model) was combined with ArcGIS (a geographic information system) to predict the potential geographic distribution of D. citri in China. Key environmental factors and the appropriate ranges of their values were also investigated. Results Our results show that the training data provided a good forecast (AUCmean = 0.988). The highly suitable areas for D. citri in China are mainly concentrated to the south of the Yangtze River, and the total area is 139.83 × 104 km2. The area of the moderately suitable areas is 27.71 × 104 km2, with a narrower distribution than that of the highly suitable area. The important environmental factors affecting the distribution of D. citri were min temperature of coldest month, mean temperature of coldest quarter, precipitation of wettest quarter, mean temperature of warmest quarter, precipitation of warmest quarter, max temperature of warmest month, and temperature seasonality. These results provide a valuable theoretical basis for risk assessments and control of D. citri. Discussion The predicted results showed that there were highly suitable areas for D. citri in Chongqing, Hubei, Anhui, and Jiangsu. Therefore, the possibility exists for the further spread of D. citri in China in the future. Extreme temperature variables, especially the min temperature of the coldest month, play an important role in the distribution of D. citri and are most closely related to the distribution of D. citri.
Wang et al. (2019) Predicting the potential distribution of the Asian citrus psyllid, Diaphorina citri (Kuwayama), in China using the MaxEnt model. PeerJ 7:e7323 https://doi.org/10.7717/peerj.7323
Upregulation of SPOCK2 inhibits the invasion and migration of prostate cancer cells by regulating the MT1-MMP/MMP2 pathway
Background It is known that secreted protein acidic and cysteine rich (osteonectin), cwcv and kazal-like domains proteoglycan 2 (SPOCK2) plays a significant role in the development and progression of several human cancers; however, the role of SPOCK2 in prostate cancer (PCa) remains unclear. This study aimed to find the role and mechanism of SPOCK2 in the development and progression of PCa. Methods The messenger ribonucleic acid (mRNA) expression of SPOCK2 in PCa tissue was detected by real-time polymerase chain reaction (PCR). Upregulation of the SPOCK2 gene was achieved using the DU145 and LNCaP cells by transfecting the cells with SPOCK2 recombinant fragment. Cell invasion and migration ability were detected by transwell chamber and wound healing assay. The expression of membrane-type 1 matrix metalloproteinase (MT1-MMP) and matrix metalloproteinase 2 (MMP2) in the cells was detected by Western Blot and zymography gel assay. Results The mRNA level of SPOCK2 was significantly lower in the PCa tissue compared to benign prostate hyperplasia. Upregulation of SPOCK2 inhibited cell invasion and migration in DU145 and LNCaP cells, inhibited the expression of MT1-MMP and MMP2 and, inhibited activation of MMP2 in DU145 and LNCaP cells. Conclusion SPOCK2 is associated with the progression of PCa. Upregulation of SPOCK2 can inhibit PCa cell invasion and metastasis by decreasing MT1-MMP and MMP2 gene expression and decreasing MMP2 protein activation.
Liu et al. (2019) Upregulation of SPOCK2 inhibits the invasion and migration of prostate cancer cells by regulating the MT1-MMP/MMP2 pathway. PeerJ 7:e7163 https://doi.org/10.7717/peerj.7163
BioDinamica: a toolkit for analyses of biodiversity and biogeography on the Dinamica-EGO modelling platform
Biogeography and macroecology are at the heart of the debate on ecology and evolution. We have developed the BioDinamica package, a suite of user-friendly graphical programs for analysing spatial patterns of biogeography and macroecology. BioDinamica includes analyses of beta-diversity, species richness, endemicity, phylo-diversity, species distribution models, predictive models of biodiversity patterns, and several tools for spatial biodiversity analysis. BioDinamica consists of a sub-library of Dinamica-EGO operators developed by integrating EGO native functions with R scripts. The BioDinamica operators can be assembled to create complex analytical and simulation models through the EGO graphical programming interface. In addition, we make available “Wizard” tutorials for end users. BioDinamica can be downloaded free of charge from the Dinamica EGO submodel store. The tools made available in BioDinamica not only facilitate complex biodiversity analyses, they also help develop state-of-the-art spatial models for biogeography and macroecology studies.
Oliveira et al. (2019) BioDinamica: a toolkit for analyses of biodiversity and biogeography on the Dinamica-EGO modelling platform. PeerJ 7:e7213 https://doi.org/10.7717/peerj.7213
Site specificity and attachment mode of Symcallio and Calliobothrium species (Cestoda: “Tetraphyllidea”) in smoothhound sharks of the genus Mustelus (Carcharhiniformes: Triakidae)
Previous studies suggest that cestodes (i.e., tapeworms) of the sister genera Symcallio and Calliobothrium attach in different specific regions of the spiral intestine of their triakid shark hosts, with species of Symcallio attaching in the anterior region of the spiral intestine and species of Calliobothrium attaching with a broader distribution centered around the middle of the spiral intestine. In the present study, we tested the generality of this pattern of site specificity in two additional species pairs: Symcallio peteri and Calliobothrium euzeti in Mustelus palumbes and S. leuckarti and C. wightmanorum in M. asterias. Finding that these cestodes also exhibit the aforementioned pattern, we investigated a series of functional explanations that might account for this phylogenetically conserved pattern of site specificity. The mucosal surface of the spiral intestine of both shark species was characterized, as were the attachment mechanisms of all four cestode species. Although anatomical differences in mucosal surface were seen along the length of the spiral intestine in both shark species, these differences do not appear to correspond to the attachment mode of these cestodes. We find that while species of Symcallio, like most cestodes, attach using their scolex, species of Calliobothrium attach with their scolex and, to a much greater extent, also with their strobila. Furthermore, attachment of Calliobothrium species appears to be enhanced by laciniations (flap-like extensions on the posterior margins of the proglottids) that interdigitate with elements of the mucosal surface of the spiral intestine. The role of proglottid laciniations in attachment in species of Calliobothrium helps reconcile a number of morphological features that differ between these two closely related cestode genera.
Bernot et al. (2019) Site specificity and attachment mode of Symcallio and Calliobothrium species (Cestoda: “Tetraphyllidea”) in smoothhound sharks of the genus Mustelus (Carcharhiniformes: Triakidae). PeerJ 7:e7264 https://doi.org/10.7717/peerj.7264