Transcriptome analysis of the liver of Eospalax fontanierii under hypoxia
Hypoxia can induce cell damage, inflammation, carcinogenesis, and inhibit liver regeneration in non-adapted species. Because of their excellent hypoxia adaptation features, subterranean rodents have been widely studied to clarify the mechanism of hypoxia adaptation. Eospalax fontanierii, which is a subterranean rodent found in China, can survive for more than 10 h under 4% O2 without observable injury, while Sprague-Dawley rats can survive for less than 6 h under the same conditions. To explore the potential mechanism of hypoxia responses in E. fontanierii, we performed RNA-seq analysis of the liver in E. fontanierii exposed to different oxygen levels (6.5% 6h, 10.5% 44h, and 21%). Based on the bioinformatics analysis, 39,439 unigenes were assembled, and 56.78% unigenes were annotated using public databases (Nr, GO, Swiss-Prot, KEGG, and Pfam). In total, 725 differentially expressed genes (DEGs) were identified in the response to hypoxia; six with important functions were validated by qPCR. Those DEGs were mainly involved in processes related to lipid metabolism, steroid catabolism, glycolysis/gluconeogenesis, and the AMPK and PPAR signaling pathway. By analyzing the expression patterns of important genes related to energy associated metabolism under hypoxia, we found that fatty acid oxidation and gluconeogenesis were increased, while protein synthesis and fatty acid synthesis were decreased. Furthermore, the upregulated expression of specific genes with anti-apoptosis or anti-oxidation functions under hypoxia may contribute to the mechanism by which E. fontanierii tolerates hypoxia. Our results provide an understanding of the response to hypoxia in E. fontanierii, and have potential value for biomedical studies.
Hao et al. (2021) Transcriptome analysis of the liver of Eospalax fontanierii under hypoxia. PeerJ 9:e11166 https://doi.org/10.7717/peerj.11166
Soil microbial diversity in organic and non-organic pasture systems
Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.
Acharya et al. (2021) Soil microbial diversity in organic and non-organic pasture systems. PeerJ 9:e11184 https://doi.org/10.7717/peerj.11184
The rise in climate change-induced federal fishery disasters in the United States
Commercial, recreational, and indigenous fisheries are critical to coastal economies and communities in the United States. For over three decades, the federal government has formally recognized the impact of fishery disasters via federal declarations. Despite these impacts, national syntheses of the dynamics, impacts, and causes of fishery disasters are lacking. We developed a nationwide Federal Fishery Disaster database using National Oceanic and Atmospheric Administration (NOAA) fishery disaster declarations and fishery revenue data. From 1989-2020, there were 71 federally approved fishery disasters (eleven are pending), which spanned every federal fisheries management region and coastal state in the country. To date, we estimate fishery disasters resulted in $2B (2019 USD) in Congressional allocations, and an additional, conservative estimate of $3.2B (2019 USD) in direct revenue loss. Despite this scale of impact, the disaster assistance process is largely ad hoc and lacks sufficient detail to properly assess allocation fairness and benefit. Nonetheless, fishery disasters increased in frequency over time, and the causes of disasters included a broad range of anthropogenic and environmental factors, with a recent shift to disasters now almost exclusively caused by extreme environmental events (e.g., marine heatwaves, hurricanes, and harmful algal blooms). Nationwide, 84.5% of fishery disasters were either partially or entirely attributed to extreme environmental events. As climate change drives higher rates of such extreme events, and as natural disaster assistance requests reach an all-time high, the federal system for fisheries disaster declaration and mitigation must evolve in order to effectively protect both fisheries sustainability and societal benefit.
Bellquist et al. (2021) The rise in climate change-induced federal fishery disasters in the United States. PeerJ 9:e11186 https://doi.org/10.7717/peerj.11186
The antimicrobial activity of silver acetate against Acinetobacter baumannii in a Galleria mellonella infection model
Background The increasing prevalence of bacterial infections that are resistant to antibiotic treatment has caused the scientific and medical communities to look for alternate remedies aimed at prevention and treatment. In addition to researching novel antimicrobials, there has also been much interest in revisiting some of the earliest therapies used by man. One such antimicrobial is silver; its use stretches back to the ancient Greeks but interest in its medicinal properties has increased in recent years due to the rise in antibiotic resistance. Currently antimicrobial silver is found in everything from lunch boxes to medical device implants. Though much is claimed about the antimicrobial efficacy of silver salts the research in this area is mixed. Methods Herein we investigated the efficacy of silver acetate against a carbapenem resistant strain of Acinetobacter baumannii to determine the in vitro activity of this silver salt against a World Health Organisation designated category I critical pathogen. Furthermore, we use the Galleria mellonella larvae model to assess toxicity of the compound and its efficacy in treating infections in a live host. Results We found that silver acetate can be delivered safely to Galleria at medically relevant and antimicrobial levels without detriment to the larvae and that administration of silver acetate to an infection model significantly improved survival. This demonstrates the selective toxicity of silver acetate for bacterial pathogens but also highlights the need for administration of well-defined doses of the antimicrobial to provide an efficacious treatment.
Mannix-Fisher et al. (2021) The antimicrobial activity of silver acetate against Acinetobacter baumannii in a Galleria mellonella infection model. PeerJ 9:e11196 https://doi.org/10.7717/peerj.11196
Stable isotope and fatty acid analyses reveal significant differences in trophic niches of smooth hammerhead Sphyrna zygaena (Carcharhiniformes) among three nursery areas in northern Humboldt Current System
Fishery pressure on nursery areas of smooth hammerhead in northern Peruvian coast have become a serious threat to sustainability of this resource. Even though, some management actions focused on conservation of the smooth hammerhead populations were proposed in recent years, their scientific foundations are often limited, and biomass of smooth hammerhead in Peruvian waters continues to decrease. To inform management and conservation, this study aims to evaluate the trophic niche of smooth hammerhead juveniles from three nursery areas in the northern Peruvian coast using stable isotope and fatty acid analyses. First, we compared the environmental characteristics of each nursery area (i.e., sea surface temperature and chlorophyll-a concentration) and concluded that nursery areas differed significantly and consistently in sea surface temperature. Subsequently, we evaluated isotopic composition of carbon and nitrogen and fatty acid profiles of muscle and liver tissues collected from juvenile smooth hammerhead from each nursery area. We found that juvenile smooth hammerhead captured in San José were enriched in heavier 13C and 15N isotopes compared to those captured in Máncora and Salaverry. Furthermore, the broadest isotopic niches were observed in juveniles from Máncora, whereas isotopic niches of juveniles from Salaverry and San José were narrower. This difference is primarily driven by the Humboldt Current System and associated upwelling of cold and nutrient rich water that drives increased primary production in San José and, to a less extent, in Salaverry. Compared to smooth hammerhead juveniles from Máncora, those from San José and Salaverry were characterised by higher essential fatty acid concentrations related to pelagic and migratory prey. We conclude that smooth hammerhead juveniles from three nursery areas in the northern Peruvian coast differ significantly in their trophic niches. Thus, management and conservation efforts should consider each nursery area as a unique juvenile stock associated with a unique ecosystem and recognize the dependence of smooth hammerhead recruitment in San José and Salaverry on the productivity driven by the Humboldt Current System.
Segura-Cobeña et al. (2021) Stable isotope and fatty acid analyses reveal significant differences in trophic niches of smooth hammerhead Sphyrna zygaena (Carcharhiniformes) among three nursery areas in northern Humboldt Current System. PeerJ 9:e11283 https://doi.org/10.7717/peerj.11283
Effects of different resistance training frequencies on body composition and muscular performance adaptations in men
Background The aim of this study was to compare the effects of 8 weeks resistance training (RT) with two sessions versus four sessions per week under volume load-equated conditions on body composition, maximal strength, and explosive actions performance in recreationally trained men. Methods Thirty-five healthy young men participated in the study and were randomly divided into a two sessions per-week RT (RT2, n = 12), four sessions per-week RT (RT4, n = 13) or a control group (CG, n = 10). All subjects were evaluated for thigh, chest and arm circumference, countermovement jump (CMJ), medicine ball throw (MBT), 1-repetition maximum (1RM) leg press, bench press, arm curl, muscular endurance (i.e., 60% of 1RM to failure) for leg press, and bench press at pre, mid (week 4) and post an 8-week training intervention. Results A two-way analysis of variance with repeated measures (3 [group] × 3 [time]) revealed that both training groups increased chest and thigh circumferences, strength and explosive actions performance tests in comparison to CG following 8 weeks of training (p = 0.01 to 0.04). Group × time interactions were also noted in 1RM bench press (effects size [ES] = 1.07 vs. 0.89) and arm curl (ES = 1.15 vs. 0.89), with greater gains for RT4 than RT2 (p = 0.03). Conclusion RT improved muscle strength, explosive actions performance and markers of muscle size in recreationally trained men; however, four sessions of resistance training per week produced greater gains in muscular strength for the upper body measures (i.e., 1RM bench press and arm curl) when compared to two sessions per week under volume-equated conditions.
Arazi et al. (2021) Effects of different resistance training frequencies on body composition and muscular performance adaptations in men. PeerJ 9:e10537 https://doi.org/10.7717/peerj.10537
Photoperiod induced the pituitary differential regulation of lncRNAs and mRNAs related to reproduction in sheep
The pituitary is a vital endocrine organ that regulates animal seasonal reproduction by controlling the synthesis and secretion of the hormone. The change of photoperiod is the key factor affecting the function of the pituitary in animals, but the mechanism is unclear. Here, we studied the transcriptomic variation in pars distalis (PD) of the pituitary between short photoperiod (SP) and long photoperiod (LP) using RNA sequencing based on the OVX+E2 sheep. 346 differentially expressed (DE) lncRNAs and 186 DE-mRNA were found in the PD. Moreover, function annotation analysis indicated that the reproductive hormones and photoperiod response-related pathways including aldosterone synthesis and secretion, insulin secretion, thyroid hormone synthesis, and circadian entrainment were enriched. The interaction analysis of mRNA-lncRNA suggested that MSTRG.240648, MSTRG.85500, MSTRG.32448, and MSTRG.304959 targeted CREB3L1 and DUSP6, which may be involved in the photoperiodic regulation of the PD. These findings provide resources for further study on the seasonal reproductive in ewes.
He et al. (2021) Photoperiod induced the pituitary differential regulation of lncRNAs and mRNAs related to reproduction in sheep. PeerJ 9:e10953 https://doi.org/10.7717/peerj.10953
Identification of a novel autophagy signature for predicting survival in patients with lung adenocarcinoma
Background Lung adenocarcinoma (LUAD) is the most commonhistological lung cancer subtype, with an overall five-year survivalrate of only 17%. In this study, we aimed to identify autophagy-related genes (ARGs) and develop an LUAD prognostic signature. Methods In this study, we obtained ARGs from three databases and downloaded gene expression profiles from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. We used TCGA-LUAD (n = 490) for a training and testing dataset, and GSE50081 (n = 127) as the external validation dataset.The least absolute shrinkage and selection operator (LASSO) Cox and multivariate Cox regression models were used to generate an autophagy-related signature. We performed gene set enrichment analysis (GSEA) and immune cell analysis between the high- and low-risk groups. A nomogram was built to guide the individual treatment for LUAD patients. Results We identified a total of 83 differentially expressed ARGs (DEARGs) from the TCGA-LUAD dataset, including 33 upregulated DEARGs and 50 downregulated DEARGs, both with thresholds of adjusted P < 0.05 and |Fold change| > 1.5. Using LASSO and multivariate Cox regression analyses, we identified 10 ARGs that we used to build a prognostic signature with areas under the curve (AUCs) of 0.705, 0.715, and 0.778 at 1, 3, and 5 years, respectively. Using the risk score formula, the LUAD patients were divided into low- or high-risk groups. Our GSEA results suggested that the low-risk group were enriched in metabolism and immune-related pathways, while the high-risk group was involved in tumorigenesis and tumor progression pathways. Immune cell analysis revealed that, when compared to the high-risk group, the low-risk group had a lower cell fraction of M0- and M1- macrophages, and higher CD4 and PD-L1 expression levels. Conclusion Our identified robust signature may provide novel insight into underlying autophagy mechanisms as well as therapeutic strategies for LUAD treatment.
Duan et al. (2021) Identification of a novel autophagy signature for predicting survival in patients with lung adenocarcinoma. PeerJ 9:e11074 https://doi.org/10.7717/peerj.11074
A novel Tick Carousel Assay for testing efficacy of repellents on Amblyomma americanum L.
Ticks are important vectors of human and veterinary diseases. A primary way ticks gain access to human hosts is by engaging to clothing. Repellents or acaricides sprayed onto fabric are used to deter ticks’ access to human hosts. However, there are a limited amount of standardized laboratory assays that can determine the potency and efficacy of repellents. We present a novel fabric-engagement assay referred to as the ‘Tick Carousel Assay’. This assay utilizes fabric brushing past ticks located on an artificial grass patch and measures tick engagements to fabric over time. After screening a variety of tick species, we used the lone star tick (Amblyomma americanum) to test the efficacy of four commonly used active ingredients in repellents: DEET, Picaridin, IR3535, and Oil of Lemon Eucalyptus. Repellency was tested immediately, after three hours, and six hours post application to fabric. Our data show that each repellent we tested significantly reduced the number of tick engagements to fabric for at least 6 hours. We did not find significant differences in repellent efficacy between the four active ingredients tested directly and three hours after application. After six hours, Oil of Lemon Eucalyptus repelled ticks more than the other active ingredients. We show that our Tick Carousel Assay provides an affordable, repeatable, and standardized way to compare and test repellent efficacy on treated fabrics. Our results confirm that commonly used repellents applied to fabric are an effective way to reduce tick engagement.
Luker et al. (2021) A novel Tick Carousel Assay for testing efficacy of repellents on Amblyomma americanum L.. PeerJ 9:e11138 https://doi.org/10.7717/peerj.11138
Understanding experiments and research practices for reproducibility: an exploratory study
Scientific experiments and research practices vary across disciplines. The research practices followed by scientists in each domain play an essential role in the understandability and reproducibility of results. The “Reproducibility Crisis”, where researchers find difficulty in reproducing published results, is currently faced by several disciplines. To understand the underlying problem in the context of the reproducibility crisis, it is important to first know the different research practices followed in their domain and the factors that hinder reproducibility. We performed an exploratory study by conducting a survey addressed to researchers representing a range of disciplines to understand scientific experiments and research practices for reproducibility. The survey findings identify a reproducibility crisis and a strong need for sharing data, code, methods, steps, and negative and positive results. Insufficient metadata, lack of publicly available data, and incomplete information in study methods are considered to be the main reasons for poor reproducibility. The survey results also address a wide number of research questions on the reproducibility of scientific results. Based on the results of our explorative study and supported by the existing published literature, we offer general recommendations that could help the scientific community to understand, reproduce, and reuse experimental data and results in the research data lifecycle.
Samuel et al. (2021) Understanding experiments and research practices for reproducibility: an exploratory study. PeerJ 9:e11140 https://doi.org/10.7717/peerj.11140