Intraspecific variability in the filter mesh size of suspension feeding organisms: the case of invasive Ponto-Caspian corophiids (Crustacea: Amphipoda)
Suspension feeders play pivotal roles in the nutrient cycling of almost all aquatic ecosystems. Since sufficiently large differences in the filter mesh size (FMS) can lead to different food web positions, the inter- and intraspecific variability of this trait might be of community-level importance. The aim of this study was to quantify the range of FMS variation within the three invasive Ponto-Caspian Chelicorophium species based on a large material representing various conditions (1,224 specimens from 40 samples across Central Europe), characterize the components of variation within populations, identify the main factors determining intraspecific differences, and reveal how intraspecific variation affects the FMS overlaps among species. The FMS of the most widespread invader, C. curvispinum, varied within the broadest range (between 2.34–8.28 μm, compared to 2.51–5.97 μm in C. robustum and 1.08–3.23 μm in C. sowinskyi); nevertheless, the contribution of intraspecific plasticity to the invasion success of the species is not evident based on the present study. The within-individual variability of FMS increased with the individual mean of the trait and decreased with body size; however, it showed little differences among samples. The among-individual variation within samples could be partitioned into components related to body size (ontogenetic niche shift/differences among cohorts) and sex (ecological sexual dimorphism) as well as a seemingly random component (individual specialization), varying widely in extent and relative contributions. The FMS of C. curvispinum was significantly larger in the presence of C. sowinskyi than in allopatry, likely reflecting character displacement; however, it did not show further increase when C. robustum was also present. Similar differences could not be observed in C. sowinskyi. The FMS ranges of C. curvispinum and C. robustum never overlapped with that of C. sowinskyi in co-occurrence despite the considerable intraspecific differences among sites, suggesting that their interaction can be seen as a clear case of niche differentiation by food particle size. On the contrary, the strong overlaps observed between C. curvispinum and C. robustum indicate that other factors might play the primary role in their coexistence. The studied species appear to be suitable model organisms for identifying the drivers and mechanisms of FMS variability.
Borza (2021) Intraspecific variability in the filter mesh size of suspension feeding organisms: the case of invasive Ponto-Caspian corophiids (Crustacea: Amphipoda). PeerJ 9:e11245 https://doi.org/10.7717/peerj.11245
Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples
Background Hoary bats (Lasiurus cinereus) are among the bat species most commonly killed by wind turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of changing census population size if other factors affecting Ne are stable. Methods We used the NeEstimator package to derive effective breeding population size (Nb) estimates for two temporally spaced cohorts: 93 hoary bats collected in 2009–2010 and an additional 93 collected in 2017–2018. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers. Results Analysis of the reference genome with psmc suggested at least a doubling of Ne in the last 100,000 years, likely exceeding Ne = 10,000 in the Holocene. Allele and genotype frequency analyses confirmed that the two cohorts were comparable, although some samples had unusually high or low observed heterozygosities. Additionally, the older cohort had lower mean coverage and greater variability in coverage, and batch effects of sampling locality were observed that were consistent with sample degradation. We therefore excluded samples with low coverage or outlier heterozygosity, as well as loci with sequence coverage far from the mode value, from the final data set. Prior to excluding these outliers, contemporary Nb estimates were significantly higher in the more recent cohort, but this finding was driven by high values for the 2018 sample year and low values for all other years. In the reduced data set, Nb did not differ significantly between cohorts. We found base substitutions to be strongly biased toward cytosine to thymine or the complement, and further partitioning loci by substitution type had a strong effect on Nb estimates. Minor allele frequency and base quality bias thresholds also had strong effects on Nb estimates. Instability of Nb with respect to common data filtering parameters and empirically identified factors prevented robust comparison of the two cohorts. Given that confidence intervals frequently included infinity as the stringency of data filtering increased, contemporary trends in Nb of North American hoary bats may not be tractable with the linkage disequilibrium method, at least using the protocol employed here.
Cornman et al. (2021) Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples. PeerJ 9:e11285 https://doi.org/10.7717/peerj.11285
Student health behavior and academic performance
Objective To explore the association between health behaviors and habits of university students and academic achievement. Participants Six hundred fourteen undergraduate students at a state university in the United States. Methods Students were invited over a 2-year period to participate in an anonymous online survey that asked questions concerning a wide range of health behaviors and habits; participants were asked to report their current grade point average (GPA). Standard Least Squares Models were used to examine differences in self-reported GPA across the different health behaviors and habits, with individuals as replicates. Results The study found positive associations between breakfast consumption, physical activity, and strength training and self-reported GPA, and negative associations between the hours of sleep per night, hours worked per week, fast food and energy drinks consumption, and use of marijuana, alcohol and electronic vaping products. Conclusions While there is an association for some of the studied health behaviors and habits with self-reported GPA, the effect sizes for these health behaviors were low. The significant effect of vaping on GPA as well as the increased use reported in this study indicates that the topic should be explored further. Furthermore, students should be educated on the potential positive and negative effects of health behavior choices to help them make better choices.
Reuter et al. (2021) Student health behavior and academic performance. PeerJ 9:e11107 https://doi.org/10.7717/peerj.11107
The physiological response of Ectomycorrhizal fungus Lepista sordida to Cd and Cu stress
Ectomycorrhizal fungi (ECMF) can develop the resistance of host plants to heavy metal stress. However, little is known about the response of ECMF to heavy metal exposure. In this study, the growth and physiological indices of Lepista sordida under Cd and Cu stress were studied. The growth of L. sordida on PDA medium under Cd and Cu stress was observed using scanning electron microscopy (SEM). After the addition of Cd and Cu to the medium, the mycelium started twisting, breaking, sticking together, and even dissolving. In the control group, a good and luxuriant mycelium growth of L. sordida along with the numerous clamp connections was observed. The mycelial biomass decreased with increasing concentrations of heavy metals in a liquid medium. The catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and ascorbate peroxidase (APX) activities were also investigated, and the results showed that the Cd and Cu treatments caused a significant increase in the antioxidant enzyme activities. The contents of soluble protein, soluble sugar, and free proline in L. sordida were investigated, and it was found that the contents initially increased and then decreased with the increasing concentrations of Cd and Cu. However, the content of malondialdehyde (MDA) increased with the increasing concentrations of Cd and Cu. In conclusion, the present study provides a theoretical basis for the better utilization of Ectomycorrhizal fungal resources for the remediation of soil contaminated with heavy metal.
Dachuan et al. (2021) The physiological response of Ectomycorrhizal fungus Lepista sordida to Cd and Cu stress. PeerJ 9:e11115 https://doi.org/10.7717/peerj.11115
A new fossil mantis shrimp and the convergent evolution of a lobster-like morphotype
Eumalacostracan crustaceans all have a more or less stereotypic body organisation in the sense of tagmosis. Originally, this included a head with six segments (ocular segment plus five appendage-bearing segments), a thorax region with eight segments, and a pleon with six segments. Interestingly, despite these restrictions in variability in terms of tagmosis, the morphological diversity within Eumalacostraca is rather high. A group providing representative examples that are commonly known is Decapoda. Decapodan crustaceans include shrimp-like forms, lobster-like forms and crab-like forms. The stem species of Eucarida, the group including Decapoda and Euphausiacea, presumably possessed a rather shrimp-like morphology, quite similar to the stem species of Eumalacostraca. Also two other lineages within Eumalacostraca, namely Hoplocarida (with the mantis shrimps as modern representatives) and Neocarida (with the sister groups Thermosbaenacea and Peracarida) evolved from the shrimp-like body organisation to include a lobster-like one. In this study, we demonstrate that the stepwise evolution towards a lobster morphotype occurred to a certain extent in similar order in these three lineages, Hoplocarida, Eucarida and Peracarida, leading to similar types of derived body organisation. This evolutionary reconstruction is based not only on observations of modern fauna, but especially on exceptionally preserved Mesozoic fossils, including the description of a new species of mantis shrimps bridging the morphological gap between the more ancestral-appearing Carboniferous forms and the more modern-appearing Jurassic forms. With this, Mesozoic eumalacostracans represent an important (if not unique) ‘experimental set-up’ for research on factors leading to convergent evolution, the understanding of which is still one of the puzzling challenges of modern evolutionary theory.
Haug et al. (2021) A new fossil mantis shrimp and the convergent evolution of a lobster-like morphotype. PeerJ 9:e11124 https://doi.org/10.7717/peerj.11124
TP53 mutation and MET amplification in circulating tumor DNA analysis predict disease progression in patients with advanced gastric cancer
Background Gastric cancer (GC) is a heterogeneous disease that encompasses various molecular subtypes. The molecular mutation characteristics of circulating tumor DNA (ctDNA) in advanced gastric cancer (AGC), especially the clinical utility of TP53 mutation and MET amplification in ctDNA need to be further explored. Objectives The aim of this study was mainly to assess the clinical utility of TP53 mutation and MET amplification in ctDNA as biomarkers for monitoring disease progression of AGC. Patients and Methods We used multigene NGS-panel technology to study the characteristics of ctDNA gene mutations and screen the key mutant genes in AGC patients. The Kaplan-Meier method was used to calculate the survival probability and log-rank test was used to compare the survival curves of TP53 mutation and MET amplification in ctDNA of AGC patients. The survival time was set from the blood test time to the follow-up time to observe the relationship between the monitoring index and tumor prognosis. Results We performed mutation detection on ctDNA in 23 patients with AGC and identified the top 20 mutant genes. The five most frequently mutated genes were TP53 (55%), EGFR (20%), ERBB2 (20%), MET (15%) and APC (10%). TP53 was the most common mutated gene (55%) and MET had a higher frequency of mutations (15%) in our study. Kaplan-Meier analysis showed that patients with TP53 mutant in ctDNA had shorter overall survival (OS) than these with TP53 wild (P < 0.001). The Allele frequency (AF) of TP53 mutations in patient number 1 was higher in the second time (0.94%) than in the first time (0.36%); the AF of TP53 mutations in patient number 16 was from scratch (0∼0.26%). In addition, the AF of TP53 mutations in patients who survive was relatively low (P = 0.047). Simultaneously, Kaplan-Meier analysis showed that patients with MET amplification also had shorter OS than these with MET without amplification (P < 0.001). Conclusion TP53 and MET are the two common frequently mutant genes in ctDNA of AGC patients.TP53 mutation and MET amplification in ctDNA could predict disease progression of AGC patients.
Li et al. (2021) TP53 mutation and MET amplification in circulating tumor DNA analysis predict disease progression in patients with advanced gastric cancer. PeerJ 9:e11146 https://doi.org/10.7717/peerj.11146
Predicting migration routes for three species of migratory bats using species distribution models
Understanding seasonal variation in the distribution and movement patterns of migratory species is essential to monitoring and conservation efforts. While there are many species of migratory bats in North America, little is known about their seasonal movements. In terms of conservation, this is important because the bat fatalities from wind energy turbines are significant and may fluctuate seasonally. Here we describe seasonally resolved distributions for the three species that are most impacted by wind farms (Lasiurus borealis (eastern red bat), L. cinereus (hoary bat) and Lasionycteris noctivagans (silver-haired bat)) and use these distributions to infer their most likely migratory pathways. To accomplish this, we collected 2,880 occurrence points from the Global Biodiversity Information Facility over five decades in North America to model species distributions on a seasonal basis and used an ensemble approach for modeling distributions. This dataset included 1,129 data points for L. borealis, 917 for L. cinereus and 834 for L. noctivagans. The results suggest that all three species exhibit variation in distributions from north to south depending on season, with each species showing potential migratory pathways during the fall migration that follow linear features. Finally, we describe proposed migratory pathways for these three species that can be used to identify stop-over sites, assess small-scale migration and highlight areas that should be prioritized for actions to reduce the effects of wind farm mortality.
Wieringa et al. (2021) Predicting migration routes for three species of migratory bats using species distribution models. PeerJ 9:e11177 https://doi.org/10.7717/peerj.11177
Evaluation potential of PGPR to protect tomato against Fusarium wilt and promote plant growth
Soilborne fungal diseases are most common among vegetable crops and have major implications for crop yield and productivity. Eco-friendly sustainable agriculture practices that can overcome biotic and abiotic stresses are of prime importance. In this study, we evaluated the ability of plant growth-promoting rhizobacterium (PGPR) Bacillus aryabhattai strain SRB02 to control the effects of tomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (strain KACC40032) and promote plant growth. In vitro bioassays showed significant inhibition of fungal growth by SRB02. Inoculation of susceptible and tolerant tomato cultivars in the presence of SRB02 showed significant protection of the cultivar that was susceptible to infection and promotion of plant growth and biomass production in both of the cultivars. Further analysis of SRB02-treated plants revealed a significantly higher production of amino acids following infection by F. oxysporum. Analysis of plant defense hormones after inoculation by the pathogen revealed a significantly higher accumulation of salicylic acid (SA), with a concomitant reduction in jasmonic acid (JA). These results indicate that B. aryabhattai strain SRB02 reduces the effects of Fusarium wilt disease in tomato by modulating endogenous phytohormones and amino acid levels.
Syed Nabi et al. (2021) Evaluation potential of PGPR to protect tomato against Fusarium wilt and promote plant growth. PeerJ 9:e11194 https://doi.org/10.7717/peerj.11194
NGScloud2: optimized bioinformatic analysis using Amazon Web Services
Background NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services. The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation sequencing data, have made the software obsolete. NGScloud2 is an enhanced and expanded version of NGScloud that permits the access to ad hoc cloud computing infrastructure, scaled according to the complexity of each experiment. Methods NGScloud2 presents major technical improvements, such as the possibility of running spot instances and the most updated AWS instances types, that can lead to significant cost savings. As compared to its initial implementation, this improved version updates and includes common applications for de novo RNAseq analysis, and incorporates tools to operate workflows of bioinformatic analysis of reference-based RNAseq, RADseq and functional annotation. NGScloud2 optimizes the access to Amazon’s large computing infrastructures to easily run popular bioinformatic software applications, otherwise inaccessible to non-specialized users lacking suitable hardware infrastructures. Results The correct performance of the pipelines for de novo RNAseq, reference-based RNAseq, RADseq and functional annotation was tested with real experimental data, providing workflow performance estimates and tips to make optimal use of NGScloud2. Further, we provide a qualitative comparison of NGScloud2 vs. the Galaxy framework. NGScloud2 code, instructions for software installation and use are available at https://github.com/GGFHF/NGScloud2. NGScloud2 includes a companion package, NGShelper that contains Python utilities to post-process the output of the pipelines for downstream analysis at https://github.com/GGFHF/NGShelper.
Mora-Márquez et al. (2021) NGScloud2: optimized bioinformatic analysis using Amazon Web Services. PeerJ 9:e11237 https://doi.org/10.7717/peerj.11237
Antifungal properties of volatile organic compounds produced by Daldinia eschscholtzii MFLUCC 19-0493 isolated from Barleria prionitis leaves against Colletotrichum acutatum and its post-harvest infections on strawberry fruits
Fungal endophytes are microorganisms living symbiotically with a host plant. They can produce volatile organic compounds (VOCs) that have antimicrobial activity. This study aimed to isolate endophytic fungi from Barleria prionitis plants grown in Thailand and to investigate the antifungal properties of their VOCs against Colletotrichum acutatum, a causal agent of anthracnose disease on post-harvest strawberry fruits. A total of 34 endophytic fungi were isolated from leaves of B. prionitis. The VOCs produced from each individual isolate were screened for their antifungal activity against C. acutatum using a dual-culture plate method. From this in vitro screening experiment, the VOCs produced by the endophytic isolate BP11 were found to have the highest inhibition percentage (80.3%) against the mycelial growth of C. acutatum. The endophytic isolate BP11 was molecularly identified as Daldinia eschscholtzii MFLUCC 19-0493. This strain was then selected for an in vivo experiment. Results from the in vivo experiment indicated that the VOCs produced by D. eschscholtzii MFLUCC 19-0493 were able to inhibit infections by C. acutatum on organic fresh strawberry fruits with an average inhibition percentage of 72.4%. The quality of the pathogen-inoculated strawberry fruits treated with VOCs produced by D. eschscholtzii MFLUCC 19-0493 was evaluated. Their fruit firmness, total soluble solids, and pH were found to be similar to the untreated strawberry fruits. Solid phase microextraction-gas chromatographic-mass spectrometric analysis of the VOCs produced by D. eschscholtzii MFLUCC 19-0493 led to the detection and identification of 60 compounds. The major compounds were elemicin (23.8%), benzaldehyde dimethyl acetal (8.5%), ethyl sorbate (6.8%), methyl geranate (6.5%), trans-sabinene hydrate (5.4%), and 3,5-dimethyl-4-heptanone (5.1%). Each major compound was tested for its antifungal activity against C. acutatum using the in vitro assay. While all these selected VOCs showed varying degrees of antifungal activity, elemicin was found to possess the strongest antifungal activity. This work suggests that D. eschscholtzii MFLUCC 19-0493 could be a promising natural preservative for controlling C. acutatum associated anthracnose disease in strawberry fruits during the post-harvest period.
Khruengsai et al. (2021) Antifungal properties of volatile organic compounds produced by Daldinia eschscholtzii MFLUCC 19-0493 isolated from Barleria prionitis leaves against Colletotrichum acutatum and its post-harvest infections on strawberry fruits. PeerJ 9:e11242 https://doi.org/10.7717/peerj.11242