Complex characterization of oat (Avena sativa L.) lines obtained by wide crossing with maize (Zea mays L.)
Background The oat × maize addition (OMA) lines are used for mapping of the maize genome, the studies of centromere-specific histone (CENH3), gene expression, meiotic chromosome behavior and also for introducing maize C4 photosynthetic system to oat. The aim of our study was the identification and molecular-cytogenetic characterization of oat × maize hybrids. Methods Oat DH lines and oat × maize hybrids were obtained using the wide crossing of Avena sativa L. with Zea mays L. The plants identified as having a Grande-1 retrotransposon fragment, which produced seeds, were used for genomic in situ hybridization (GISH). Results A total of 138 oat lines obtained by crossing of 2,314 oat plants from 80 genotypes with maize cv. Waza were tested for the presence of maize chromosomes. The presence of maize chromatin was indicated in 66 lines by amplification of the PCR product (500 bp) generated using primers specific for the maize retrotransposon Grande-1. Genomic in situ hybridization (GISH) detected whole maize chromosomes in eight lines (40%). All of the analyzed plants possessed full complement of oat chromosomes. The number of maize chromosomes differed between the OMA lines. Four OMA lines possessed two maize chromosomes similar in size, three OMA—one maize chromosome, and one OMA—four maize chromosomes. In most of the lines, the detected chromosomes were labeled uniformly. The presence of six 45S rDNA loci was detected in oat chromosomes, but none of the added maize chromosomes in any of the lines carried 45S rDNA locus. Twenty of the analyzed lines did not possess whole maize chromosomes, but the introgression of maize chromatin in the oat chromosomes. Five of 66 hybrids were shorter in height, grassy type without panicles. Twenty-seven OMA lines were fertile and produced seeds ranging in number from 1–102 (in total 613). Sixty-three fertile DH lines, out of 72 which did not have an addition of maize chromosomes or chromatin, produced seeds in the range of 1–343 (in total 3,758). Obtained DH and OMA lines were fertile and produced seeds. Discussion In wide hybridization of oat with maize, the complete or incomplete chromosomes elimination of maize occur. Hybrids of oat and maize had a complete set of oat chromosomes without maize chromosomes, and a complete set of oat chromosomes with one to four retained maize chromosomes.
Skrzypek et al. (2018) Complex characterization of oat (Avena sativa L.) lines obtained by wide crossing with maize (Zea mays L.). PeerJ 6:e5107 https://doi.org/10.7717/peerj.5107
Differing responses of red abalone (Haliotis rufescens) and white abalone (H. sorenseni) to infection with phage-associated Candidatus Xenohaliotis californiensis
The Rickettsiales-like prokaryote and causative agent of Withering Syndrome (WS)—Candidatus Xenohaliotis californiensis (Ca. Xc)—decimated black abalone populations along the Pacific coast of North America. White abalone—Haliotis sorenseni—are also susceptible to WS and have become nearly extinct in the wild due to overfishing in the 1970s. Candidatus Xenohaliotis californiensis proliferates within epithelial cells of the abalone gastrointestinal tract and causes clinical signs of starvation. In 2012, evidence of a putative bacteriophage associated with Ca. Xc in red abalone—Haliotis rufescens—was described. Recently, histologic examination of animals with Ca. Xc infection in California abalone populations universally appear to have the phage-containing inclusions. In this study, we investigated the current virulence of Ca. Xc in red abalone and white abalone at different environmental temperatures. Using a comparative experimental design, we observed differences over time between the two abalone species in mortality, body condition, and bacterial load by quantitative real time PCR (qPCR). By day 251, all white abalone exposed to the current variant of Ca. Xc held in the warm water (18.5 °C) treatment died, while red abalone exposed to the same conditions had a mortality rate of only 10%, despite a relatively heavy bacterial burden as determined by qPCR of posterior esophagus tissue and histological assessment at the termination of the experiment. These data support the current status of Ca. Xc as less virulent in red abalone, and may provide correlative evidence of a protective phage interaction. However, white abalone appear to remain highly susceptible to this disease. These findings have important implications for implementation of a white abalone recovery program, particularly with respect to the thermal regimes of locations where captively-reared individuals will be outplanted.
Vater et al. (2018) Differing responses of red abalone (Haliotis rufescens) and white abalone (H. sorenseni) to infection with phage-associated Candidatus Xenohaliotis californiensis. PeerJ 6:e5104 https://doi.org/10.7717/peerj.5104
Dry season diet composition of four-horned antelope Tetracerus quadricornis in tropical dry deciduous forests, Nepal
It is essential to assess the feeding strategies of threatened species during resource-scarce seasons to understand their dietary niche breadth and inform appropriate habitat management measures. In this study, we examined the diet composition of four-horned antelope (FHA) Tetracerus and quadricornis, one of the least studied ungulate species, in Banke National Park, Nepal. A total of 53 fresh pellet groups were collected between December 2015 and January 2016 and analyzed using micro-histological fecal analysis technique. First, we prepared 133 micro-histological photographs of different parts of 64 reference plant species. Then we compared 1,590 fragments of 53 fecal samples with photographs of reference plants to assess the percentage of occurrence of different plant species in FHA diet. A total of 30 plant species belonging to 18 different families were identified in fecal samples. Chi-square goodness of fit tests showed that FHA appeared not to feed all plant uniformly. Out of 1,520 identified fragments in fecal samples, 1,300 were browse species and 220 were grass species. Browse represented 85.5% of the identified plant fragments, suggesting that FHA might be adopting a browser strategy at least during winter when grasses are low in abundance and their nutritive quality is poor. Tree species had the highest contribution in the diet (46.55%) followed by shrubs (24.52%). The family Gramineae was consumed in the highest proportion (27.68%) followed by Euphorbiaceae (11.95%). Overall, our results suggest that FHA has the feeding plasticity to adapt to resource fluctuation. Based on the findings of this study, we recommend that dicot plant species—particularly fruit trees and shrubs, which are the major source of nutrients for FHA during resource-lean, dry season—be conserved and natural regeneration of these taxa be promoted.
Oli et al. (2018) Dry season diet composition of four-horned antelope Tetracerus quadricornis in tropical dry deciduous forests, Nepal. PeerJ 6:e5102 https://doi.org/10.7717/peerj.5102
Mulch and groundcover effects on soil temperature and moisture, surface reflectance, grapevine water potential, and vineyard weed management
The objectives of this research were to identify alternatives to glyphosate for intra-row (under-trellis) vineyard floor management and to evaluate the potential for intra-row and inter-row (alleyway) groundcovers to reduce vegetative vigor of ‘Marquette’ grapevines (Vitis spp.) in a southeast Nebraska vineyard. The experiment was a randomized factorial design with five intra-row treatments (crushed glass mulch [CG], distillers’ grain mulch [DG], creeping red fescue [CRF], non-sprayed control [NSC], and glyphosate [GLY]) and three inter-row treatments (creeping red fescue [CRF], Kentucky bluegrass [KB], and resident vegetation [RV]). Treatments were established in 2010–2011 and measurements were conducted during 2012 and 2013 on 5- and 6-year-old vines. Soil temperatures were mostly higher under mulches and lower under intra-row groundcovers, compared to GLY. Weed cover in CG, DG, and CRF treatments was the same or less than GLY. At most sampling dates, inter-row soil moisture was lowest under KB. Intra-row soil moisture was highest under DG mulch and lowest under CRF and NSC; CG had the same or lower soil moisture than GLY. Surprisingly, we did not detect differences in mid-day photosynthetically active radiation (PAR) reflectance, despite visual differences among the intra-row treatments. Mid-day vine water potential did not differ among treatments. We concluded it is not necessary to maintain a bare soil strip under established vines in this region, where soil fertility and moisture are non-limiting.
Bavougian et al. (2018) Mulch and groundcover effects on soil temperature and moisture, surface reflectance, grapevine water potential, and vineyard weed management. PeerJ 6:e5082 https://doi.org/10.7717/peerj.5082
It’s a matter of design—how pitfall trap design affects trap samples and possible predictions
Background Pitfall traps are commonly used to assess ground dwelling arthropod communities. The effects of different pitfall trap designs on the trapping outcome are poorly investigated however they might affect conclusions drawn from pitfall trap data greatly. Methods We tested four pitfall trap types which have been used in previous studies for their effectiveness: a simple type, a faster exchangeable type with an extended plastic rim plate and two types with guidance barriers (V- and X-shaped). About 20 traps were active for 10 weeks and emptied biweekly resulting in 100 trap samples. Results Pitfall traps with guidance barriers were up to five times more effective than simple pitfall traps and trap samples resulted in more similar assemblage approximations. Pitfall traps with extended plastic rim plates did not only perform poorly but also resulted in distinct carabid assemblages with less individuals of small species and a larger variation. Discussion Due to the obvious trait filtering and resulting altered assemblages, we suggest not to use pitfall traps with extended plastic rim plates. In comprehensive biodiversity inventories, a smaller number of pitfall traps with guidance barriers and a larger number of spatial replicates is of advantage, while due to comparability reasons, the use of simple pitfall traps will be recommended in most other cases.
Boetzl et al. (2018) It’s a matter of design—how pitfall trap design affects trap samples and possible predictions. PeerJ 6:e5078 https://doi.org/10.7717/peerj.5078
Potamopyrgus antipodarum as a potential defender against swimmer’s itch in European recreational water bodies—experimental study
Swimmer’s itch is a re-emerging human disease caused by bird schistosome cercariae, which can infect bathing or working people in water bodies. Even if cercariae fail after penetrating the human skin, they can cause dangerous symptoms in atypical mammal hosts. One of the natural methods to reduce the presence of cercariae in the environment could lie in the introduction of non–host snail species to the ecosystem, which is known as the “dilution” or “decoy” effect. The caenogastropod Potamopyrgus antipodarum—an alien in Europe—could be a good candidate against swimmer’s itch because of its apparent resistance to invasion by European bird schistosome species and its high population density. As a pilot study on this topic, we have carried out a laboratory experiment on how P. antipodarum influences the infestation of the intermediate host Radix balthica (a native lymnaeid) by the bird schistosome Trichobilharzia regenti. We found that the co–exposure of 200 P. antipodarum individuals per one R. balthica to the T. regenti miracidia under experimental conditions makes the infestation ineffective. Our results show that a non–host snail population has the potential to interfere with the transmission of a trematode via suitable snail hosts.
Marszewska et al. (2018) Potamopyrgus antipodarum as a potential defender against swimmer’s itch in European recreational water bodies—experimental study. PeerJ 6:e5045 https://doi.org/10.7717/peerj.5045
Nitrogen addition increases the contents of glomalin-related soil protein and soil organic carbon but retains aggregate stability in a Pinus tabulaeformis forest
Background Glomalin-related soil protein (GRSP) and soil organic carbon (SOC) contribute to the formation and stability of soil aggregates, but the mechanism by which global atmospheric nitrogen (N) deposition changes soil aggregate stability by altering the distribution of GRSP and SOC in different aggregate fractions remains unknown. Methods We used a gradient N addition (0–9 g N m−2 y−1) in Pinus tabulaeformis forest for two years in northeast China and then examined the changes in SOC contents, total GRSP (T-GRSP), and easily extractable GRSP (EE-GRSP) contents in three soil aggregate fractions (macro-aggregate: >250 μm, micro-aggregate: 250–53 μm, and fine material: <53 μm) and their relationship with aggregate stability. Results (1) The soil was dominated by macro-aggregates. Short term N addition had no significant effect on mean weight diameter (MWD) and geometric mean diameter (GMD). (2) GRSP varied among aggregate fractions, and N addition had different effects on the distribution of GRSP in aggregate fractions. The EE-GRSP content in the macro-aggregates increased initially and then decreased with increasing N addition levels, having a peak value of 0.480 mg g−1 at 6 g N m−2 y−1. The micro-aggregates had the lowest EE-GRSP content (0.148 mg g−1) at 6 g N m−2 y−1. Furthermore, the T-GRSP content significantly increased in the aggregate fractions with the N addition levels. (3) The macro-aggregate had the highest SOC content, followed by the micro-aggregate and the fine material had the lowest SOC content. N addition significantly increased the SOC content in all the aggregate fractions. (4) GRSP and SOC contents were not significantly correlated with MWD. Conclusion Glomalin-related soil protein and SOC contents increased by N addition, but this increase did not enhance aggregate stability in short term, and the improvement of stability might depend on binding agents and incubation time.
Sun et al. (2018) Nitrogen addition increases the contents of glomalin-related soil protein and soil organic carbon but retains aggregate stability in a Pinus tabulaeformis forest. PeerJ 6:e5039 https://doi.org/10.7717/peerj.5039
Specalyzer—an interactive online tool to analyze spectral reflectance measurements
Low-cost phenotyping using proximal sensors is increasingly becoming popular in plant breeding. As these techniques generate a large amount of data, analysis pipelines that do not require expertise in computer programming can benefit a broader user base. In this work, a new online tool Specalyzer is presented that allows interactive analysis of the spectral reflectance data generated by proximal spectroradiometers. Specalyzer can be operated from any web browser allowing data uploading, analysis, interactive plots and exporting by point and click using a simple graphical user interface. Specalyzer is evaluated with case study data from a winter wheat fertilizer trial with two fertilizer treatments. Specalyzer can be accessed online at http://www.specalyzer.org.
Koc et al. (2018) Specalyzer—an interactive online tool to analyze spectral reflectance measurements. PeerJ 6:e5031 https://doi.org/10.7717/peerj.5031
Alpha-mangostin inhibits the migration and invasion of A549 lung cancer cells
Several studies have indicated that α-mangostin exerts anti-metastasis and anti-subsistence effects on several types of cancer cells. Especially, the anti-metastatic effect of α-mangostin on cancer cells is a prospective function in cancer treatment. However, the metastasis process is complicated, and includes migration, invasion, intravasation, and extravasation; thus, the main target of anti-metastatic effect of α-mangostin is not known. In this study, we investigated the effects of α-mangostin on the invasion, subsistence, and migration of lung cancer cells under co-culture conditions with normal cells and regular mono-culture conditions. We found that α-mangostin killed the lung cancer and normal cells in a dose-dependent manner. Furthermore, the alteration in the surface mechanical properties of cells was examined by using atomic force microscopy. Although the α-mangostin concentrations of 5 and 10 µM did not affect the short-term cell viability, they considerably decreased the Young’s modulus of lung cancer cells implying a decline in cell surface actin cytoskeletal properties. Additionally, these concentrations of α-mangostin inhibited the migration of lung cancer cells. In co-culture conditions (cancer cells with normal cells), the invasive activities of cancer cells on normal cells were discernibly observed, and was inhibited after treatment with 5 and 10 µM of α-mangostin. Taken together, α-mangostin suppressed the subsistence of lung cancer cells and displayed anti-metastatic activities by inhibiting the migration and invasion, and reducing the actin cytoskeleton of cancer cells. Our findings suggest that α-mangostin could be a potential therapeutic agent for cancer treatment.
Phan et al. (2018) Alpha-mangostin inhibits the migration and invasion of A549 lung cancer cells. PeerJ 6:e5027 https://doi.org/10.7717/peerj.5027
DNA barcoding of marine fish species from Rongcheng Bay, China
Rongcheng Bay is a coastal bay of the Northern Yellow Sea, China. To investigate and monitor the fish resources in Rongcheng Bay, 187 specimens from 41 different species belonging to 28 families in nine orders were DNA-barcoded using the mitochondrial cytochrome c oxidase subunit I gene (COI). Most of the fish species could be discriminated using this COI sequence with the exception of Cynoglossus joyneri and Cynoglossus lighti. The average GC% content of the 41 fish species was 47.3%. The average Kimura 2-parameter genetic distances within the species, genera, families, and orders were 0.21%, 5.28%, 21.30%, and 23.63%, respectively. Our results confirmed that the use of combined morphological and DNA barcoding identification methods facilitated fish species identification in Rongcheng Bay, and also established a reliable DNA barcode reference library for these fish. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in this area.
Wang et al. (2018) DNA barcoding of marine fish species from Rongcheng Bay, China. PeerJ 6:e5013 https://doi.org/10.7717/peerj.5013