Transcriptome analysis of Chelidonium majus elaiosomes and seeds provide insights into fatty acid biosynthesis
Background Elaiosomes are specialized fleshy and edible seed appendages dispersed by ants. Lipids are the primary components of elaiosomes. Chelidonium majus is a well-known plant, the seeds of which are dispersed by ants. Previous studies have identified the presence of primary fatty acids in its elaiosomes and seeds. However, the molecular mechanisms underlying fatty acid biosynthesis in elaiosomes remain unknown. Methods In order to gain a comprehensive transcriptional profile of the elaiosomes and seeds of C. majus, and understand the expression patterns of genes associated with fatty acid biosynthesis, four different developmental stages, including the flower-bud (Ch01), flowering (Ch02), young seed (Ch03), and mature seed (Ch04) stages, were chosen to perform whole-transcriptome profiling through the RNA-seq technology (Illumina NGS sequencing). Results A total of 63,064 unigenes were generated from 12 libraries. Of these, 7,323, 258, and 11,540 unigenes were annotated with 25 Cluster of Orthologous Groups, 43 Gene Ontology terms, and 373 Kyoto Encyclopedia of Genes and Genomes pathways, respectively. In addition, 322 genes were involved in lipid transport and metabolism, and 508 genes were involved in the lipid metabolism pathways. A total of 41 significantly differentially expressed genes (DEGs) involved in the lipid metabolism pathways were identified, most of which were upregulated in Ch03 compared to Ch02, indicating that fatty acid biosynthesis primarily occurs during the flowering to the young seed stages. Of the DEGs, acyl-ACP thioesterases, acyl carrier protein desaturase (DESA1), and malonyl CoA-ACP transacylase were involved in palmitic acid synthesis; stearoyl-CoA desaturase and DESA1 were involved in oleic acid synthesis, and acyl-lipid omega-6 desaturase was involved in linoleic acid synthesis.
Wu et al. (2019) Transcriptome analysis of Chelidonium majus elaiosomes and seeds provide insights into fatty acid biosynthesis. PeerJ 7:e6871 https://doi.org/10.7717/peerj.6871
Effects of species-dominated patches on soil organic carbon and total nitrogen storage in a degraded grassland in China
Background Patchy vegetation is a very common phenomenon due to long-term overgrazing in degraded steppe grasslands, which results in substantial uncertainty associated with soil carbon (C) and nitrogen (N) dynamics because of changes in the amount of litter accumulation and nutrition input into soil. Methods We investigated soil C and N stocks beneath three types of monodominant species patches according to community dominance. Stipa krylovii patches, Artemisia frigida patches, and Potentilla acaulis patches represent better to worse vegetation conditions in a grassland in northern China. Results The results revealed that the soil C stock (0–40 cm) changed significantly, from 84.7 to 95.7 Mg ha−1, and that the soil organic carbon content (0–10 cm) and microbial biomass carbon (0–10 and 10–20 cm) varied remarkably among the different monodominant species communities (P < 0.05). However, soil total nitrogen and microbial biomass nitrogen showed no significant differences among different plant patches in the top 0–20 cm of topsoil. The soil C stocks under the P. acaulis and S. krylovii patches were greater than that under the A. frigida patch. Our study implies that accurate estimates of soil C and N storage in degenerated grassland require integrated analyses of the concurrent effects of differences in plant community composition.
Zhang et al. (2019) Effects of species-dominated patches on soil organic carbon and total nitrogen storage in a degraded grassland in China. PeerJ 7:e6897 https://doi.org/10.7717/peerj.6897
Effect of meteorological factors on influenza-like illness from 2012 to 2015 in Huludao, a northeastern city in China
Background This study aims to describe the epidemiological patterns of influenza-like illness (ILI) in Huludao, China and seek scientific evidence on the link of ILI activity with weather factors. Methods Surveillance data of ILI cases between January 2012 and December 2015 was collected in Huludao Central Hospital, meteorological data was obtained from the China Meteorological Data Service Center. Generalized additive model (GAM) was used to seek the relationship between the number of ILI cases and the meteorological factors. Multiple Smoothing parameter estimation was made on the basis of Poisson distribution, where the number of weekly ILI cases was treated as response, and the smoothness of weather was treated as covariates. Lag time was determined by the smallest Akaike information criterion (AIC). Smoothing coefficients were estimated for the prediction of the number of ILI cases. Results A total of 29, 622 ILI cases were observed during the study period, with children ILI cases constituted 86.77%. The association between ILI activity and meteorological factors varied across different lag periods. The lag time for average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity were 2, 2, 1, 1 and 0 weeks, respectively. Average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity could explain 16.5%, 9.5%, 18.0%, 15.9% and 7.7% of the deviance, respectively. Among the temperature indexes, the minimum temperature played the most important role. The number of ILI cases peaked when minimum temperature was around −13 °C in winter and 18 °C in summer. The number of cases peaked when the relative humidity was equal to 43% and then began to decrease with the increase of relative humidity. When the humidity exceeded 76%, the number of ILI cases began to rise. Conclusions The present study first analyzed the relationship between meteorological factors and ILI cases with special consideration of the length of lag period in Huludao, China. Low air temperature and low relative humidity (cold and dry weather condition) played a considerable role in the epidemic pattern of ILI cases. The trend of ILI activity could be possibly predicted by the variation of meteorological factors.
Bai et al. (2019) Effect of meteorological factors on influenza-like illness from 2012 to 2015 in Huludao, a northeastern city in China. PeerJ 7:e6919 https://doi.org/10.7717/peerj.6919
Combining UAV-based hyperspectral imagery and machine learning algorithms for soil moisture content monitoring
Soil moisture content (SMC) is an important factor that affects agricultural development in arid regions. Compared with the space-borne remote sensing system, the unmanned aerial vehicle (UAV) has been widely used because of its stronger controllability and higher resolution. It also provides a more convenient method for monitoring SMC than normal measurement methods that includes field sampling and oven-drying techniques. However, research based on UAV hyperspectral data has not yet formed a standard procedure in arid regions. Therefore, a universal processing scheme is required. We hypothesized that combining pretreatments of UAV hyperspectral imagery under optimal indices and a set of field observations within a machine learning framework will yield a highly accurate estimate of SMC. Optimal 2D spectral indices act as indispensable variables and allow us to characterize a model’s SMC performance and spatial distribution. For this purpose, we used hyperspectral imagery and a total of 70 topsoil samples (0–10 cm) from the farmland (2.5 × 104 m2) of Fukang City, Xinjiang Uygur AutonomousRegion, China. The random forest (RF) method and extreme learning machine (ELM) were used to estimate the SMC using six methods of pretreatments combined with four optimal spectral indices. The validation accuracy of the estimated method clearly increased compared with that of linear models. The combination of pretreatments and indices by our assessment effectively eliminated the interference and the noises. Comparing two machine learning algorithms showed that the RF models were superior to the ELM models, and the best model was PIR (R2val = 0.907, RMSEP = 1.477, and RPD = 3.396). The SMC map predicted via the best scheme was highly similar to the SMC map measured. We conclude that combining preprocessed spectral indices and machine learning algorithms allows estimation of SMC with high accuracy (R2val = 0.907) via UAV hyperspectral imagery on a regional scale. Ultimately, our program might improve management and conservation strategies for agroecosystem systems in arid regions.
Spatial and Geographic Information Science
Ge et al. (2019) Combining UAV-based hyperspectral imagery and machine learning algorithms for soil moisture content monitoring. PeerJ 7:e6926 https://doi.org/10.7717/peerj.6926
Cytotoxic and apoptosis-inducing effects of wildtype and mutated Hydra actinoporin-like toxin 1 (HALT-1) on various cancer cell lines
Background Hydra actinoporin like toxin -1 (HALT-1), is a small 18.5 kDa pore forming toxin derived from Hydra magnipapillata which has been shown to elicit strong haemolytic and cytolytic activity when in contact with cell membranes. Due to its cytotoxic potency, HALT-1 was further investigated for its potential as a toxin moiety candidate in immunotoxin developmental efforts, ideally as a form of targeted therapy against cancer. Methods In this study, wtHALT-1 (wild type) and its Y110A mutated binding domain counterpart (mHALT-1) were produced and evaluated for their cytotoxic and apoptotic effects on various cancer cell lines. A total of seven different tumour and non-tumour cell lines including HeLa, HepG2, SW-620, MCF-7, CCD841CoN, NHDF and HCT116 were used. Immunofluorescence assays were used to observe membrane binding and localization changes between both HALT-1 recombinant proteins based on 6xHis-tag detection. Result Based on MTT data, mHALT-1 demonstrated a significant reduction of 82% ± 12.21% in cytotoxic activity across all cell lines after the membrane recognition domain had been mutated in comparison to the wtHALT-1. Annexin V FITC/PI assay data also indicated that HeLa, HepG2 and MCF-7 demonstrated an apoptosis-mediated cell death after being treated with wtHALT-1. Additionally, a notable difference between wtHALT-1 and mHALT-1 binding affinity was clearly observed where emission of green fluorescence along the cell membrane was observed only in wtHALT-1 treated cells. Discussion These results suggest that mHALT-1 (Y110A) can be potentially developed as a toxin-moiety candidate for the development of future immunotoxins against various human cell-based diseases.
Ng et al. (2019) Cytotoxic and apoptosis-inducing effects of wildtype and mutated Hydra actinoporin-like toxin 1 (HALT-1) on various cancer cell lines. PeerJ 7:e6639 https://doi.org/10.7717/peerj.6639
Century-scale changes in phytoplankton phenology in the Gulf of Maine
The phenology of major seasonal events is an important indicator of climate. We analyzed multiple datasets of in situ chlorophyll measurements from the Gulf of Maine dating back to the early 20th century in order to detect climate-scale changes in phenology. The seasonal cycle was consistently characterized by a two-bloom pattern, with spring and autumn blooms. The timing of both spring and autumn blooms has shifted later in the year at rates ranging from ∼1 to 9 days per decade since 1960, depending on the phenology metric, and trends only emerged at time scales of >40 years. Bloom phenology had only weak correlations with major climate indices. There were stronger associations between bloom timing and physical and chemical variables. Autumn bloom initiation correlated strongly with surface temperature and salinity, and spring bloom with nutrients. A later spring bloom also correlated with an increased cohort of Calanus finmarchicus, suggesting broader ecosystem implications of phytoplankton phenology.
Record et al. (2019) Century-scale changes in phytoplankton phenology in the Gulf of Maine. PeerJ 7:e6735 https://doi.org/10.7717/peerj.6735
Two new species of parasitic copepods from the genera Nothobomolochus and Unicolax (Cyclopoida: Bomolochidae) from Australian waters
A 2016 collaborative survey of commercial fish parasites in Moreton Bay, Queensland, Australia led to the discovery of two new species of parasitic copepods belonging to the family Bomolochidae. Females of Nothobomolochus johndaveorum n. sp. were found attached to the gill filaments of Gerres subfasciatus and Gerres oyena. The new species most closely resembles N. leiognathicola and N. quadriceros. All 3 species possess 3 modified setae on the first antennulary segment that are approximately the same length and have a robust seta on the second antennulary segment adjacent to the 3 modified setae giving a superficial appearance of 4 modified setae on the antennule. The new species can be distinguished from these two species in its possession of longer inner setae on the first two endopodal segments of leg 4: the seta on endopodal segment 1 extends past the midline of the distal segment in the new species vs to the proximal margin of the distal segment in the other two species, and the seta on segment 2 extends well beyond the distal margin of the endopod in the new species vs just to the margin in the other two species. Females and males of Unicolax longicrus n. sp. were found in the nasal sinuses of Sillago maculata and Sillago ciliata. The new species differs from 6 of its 7 congeners in having a leg 4 exopod formula of II, I, 4 rather than II, I, 3 or II, I, 5. The new species resembles U. anonymous in this feature, but differs in its possession of a leg 5 that is relatively longer and less wide, and, whereas U. anonymous possesses inner and outer distal spines on leg 5 that are approximately the same length, those of the new species are relatively longer and asymmetrical. Unicolax longicrus n. sp. is unique among its congeners in its possession of a leg 4 with highly elongated endopodal segments 2 and 3, from which its name is derived. In addition to describing the two new species, host and locality reports for all species of Nothobomolochus and Unicolax are reviewed.
Bernot et al. (2019) Two new species of parasitic copepods from the genera Nothobomolochus and Unicolax (Cyclopoida: Bomolochidae) from Australian waters. PeerJ 7:e6858 https://doi.org/10.7717/peerj.6858
Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae)
A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.
Niu et al. (2019) Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae). PeerJ 7:e6866 https://doi.org/10.7717/peerj.6866
Coupling and metabolic analysis of urbanization and environment between two resource-based cities in North China
Background The complex relationship between urbanization and environment in resource-based cities is of increasing concern. Methods As typical examples of rapid economic growth, obvious urbanization, and successful transformed production models, the cities of Dongying and Binzhou in Yellow River Delta High-tech Economic Zone were chosen for research. First, this study examines the coupling relationship between urbanization and the environment over the last seventeen years using the coupling degree model. Second, the emergy analysis method is used to further study the energy metabolism and environmental load in the two cities to reveal these couplings. Results Dongying and Binzhou were well-coupled and the coupling coordination degree was in the stage of mild coordination coupling showing an upward trend. The total metabolic energy of the two cities increased yearly from 2000 to 2016, and the emergy extroversion ratio data showed the cities’ dependence on external elements such as continuously increased imported resources. The total emergy used in the two cities showed an upward trend during 2000 and 2016, while the emergy per capita consumption increased significantly, suggesting that the society’s energy efficiency improved. During the same period, the environmental loading ratio increased gradually, and the elements causing the environmental load shifted from internal to external. Discussion The study shows that the factors of environmental load in developing cities are gradually shifting from internal to external, which is vital to understanding the impact of urban transformation and upgrading of resource-based cities on the environment.
Chen et al. (2019) Coupling and metabolic analysis of urbanization and environment between two resource-based cities in North China. PeerJ 7:e6869 https://doi.org/10.7717/peerj.6869
How can we augment the few that remain? Using stable population dynamics to aid reintroduction planning of an iteroparous species
Restoration of depleted populations is an important method in biological conservation. Reintroduction strategies frequently aim to restore stable, increasing, self-sustaining populations. Knowledge of asymptotic system dynamics may provide advantage in selecting reintroduction strategies. We introduce interactive software that is designed to identify strategies for release of females that are immediately aligned with stable population dynamics from species represented by 2-, 3-, 4-, and 5-stage life history strategies. The software allows managers to input a matrix of interest, the desired number of breeding females, and the desired management timeline, and calls upon stable population theory to give release strategies that are in concert with both stable population status and the management goals. We demonstrate how the software can aid in assessing various strategies ahead of a hypothetical restoration. For the purpose of demonstration of the tool only, we use published vital rates of an ungulate species, but remark that the selection of species for demonstration is not central to the use of this tool. Adaption of this tool to real-life restorations of any 2-, 3-, 4-, or 5-stage iteroparous species may aid in understanding how to minimize undesirable recovery complications that may naturally arise from transient population dynamics. The software is freely available at: https//cwhl.vet.cornell.edu/tools/stapopd.
Hanley et al. (2019) How can we augment the few that remain? Using stable population dynamics to aid reintroduction planning of an iteroparous species. PeerJ 7:e6873 https://doi.org/10.7717/peerj.6873