title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1025
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Genome-wide discovery and characterization of long noncoding RNAs in African oil palm (Elaeis guineensis Jacq.)
link: https://peerj.com/articles/9585
last-modified: 2020-11-02
description: Long noncoding RNAs (lncRNAs) are an important class of genes and play important roles in a range of biological processes. However, few reports have described the identification of lncRNAs in oil palm. In this study, we applied strand specific RNA-seq with rRNA removal to identify 1,363 lncRNAs from the equally mixed tissues of oil palm spear leaf and six different developmental stages of mesocarp (8–24 weeks). Based on strand specific RNA-seq data and 18 released oil palm transcriptomes, we systematically characterized the expression patterns of lncRNA loci and their target genes. A total of 875 uniq target genes for natural antisense lncRNAs (NAT-lncRNA, 712), long intergenic noncoding RNAs (lincRNAs, 92), intronic-lncRNAs (33), and sense-lncRNAs (52) were predicted. A majority of lncRNA loci (77.8%–89.6%) had low expression in 18 transcriptomes, while only 89 lncRNA loci had medium to high expression in at least one transcriptome. Coexpression analysis between lncRNAs and their target genes indicated that 6% of lncRNAs had expression patterns positively correlated with those of target genes. Based on single nucleotide polymorphism (SNP) markers derived from our previous research, 6,882 SNPs were detected for lncRNAs and 28 SNPs belonging to 21 lncRNAs were associated with the variation of fatty acid contents. Moreover, seven lncRNAs showed expression patterns positively correlated expression pattern with those of genes in de novo fatty acid synthesis pathways. Our study identified a collection of lncRNAs for oil palm and provided clues for further research into lncRNAs that may regulate mesocarp development and lipid metabolism.
creator: Wei Xia
creator: Yajing Dou
creator: Rui Liu
creator: Shufang Gong
creator: Dongyi Huang
creator: Haikuo Fan
creator: Yong Xiao
uri: https://doi.org/10.7717/peerj.9585
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Xia et al.

title: Static and dynamic alterations in the amplitude of low-frequency fluctuation in patients with amyotrophic lateral sclerosis
link: https://peerj.com/articles/10052
last-modified: 2020-11-02
description: BackgroundStatic changes in local brain activity in patients suffering from amyotrophic lateral sclerosis (ALS) have been studied. However, the dynamic characteristics of local brain activity are poorly understood. Whether dynamic alterations could differentiate patients with ALS from healthy controls (HCs) remains unclear.MethodsA total of 54 patients with ALS (mean age = 48.71 years, male/female = 36/18) and 54 (mean age = 48.30 years, male/female = 36/18) HCs underwent magnetic resonance imaging scans. To depict static alterations in cortical activity, amplitude of low-frequency fluctuations (ALFF) which measures the total power of regional activity was computed. Dynamic ALFF (d-ALFF) from all subjects was calculated using a sliding-window approach. Statistical differences in ALFF and d-ALFF between both groups were used as features to explore whether they could differentiate ALS from HC through support vector machine method.ResultsIn contrast with HCs, patients with ALS displayed increased ALFF in the right inferior temporal gyrus and bilateral frontal gyrus and decreased ALFF in the left middle occipital gyrus and left precentral gyrus. Furthermore, patients with ALS demonstrated lower d-ALFF in widespread regions, including the right lingual gyrus, left superior temporal gyrus, bilateral precentral gyrus, and left paracentral lobule by comparison with HCs. In addition, the ALFF in the left superior orbitofrontal gyrus had a tendency of correlation with ALSFRS-R score and disease progression rate. The classification performance in distinguishing ALS was higher with both features of ALFF and d-ALFF than that with a single approach.ConclusionsDecreased dynamic brain activity in the precentral gyrus, paracentral gyrus, lingual gyrus, and temporal regions was found in the ALS group. The combined ALFF and d-ALFF could distinguish ALS from HCs with a higher accuracy than ALFF and d-ALFF alone. These findings may provide important evidence for understanding the neuropathology underlying ALS.
creator: Xujing Ma
creator: Fengmei Lu
creator: Heng Chen
creator: Caihong Hu
creator: Jiao Wang
creator: Sheng Zhang
creator: Shuqin Zhang
creator: Guiran Yang
creator: Jiuquan Zhang
uri: https://doi.org/10.7717/peerj.10052
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Ma et al.

title: In vitro anti-diabetic effects and phytochemical profiling of novel varieties of Cinnamomum zeylanicum (L.) extracts
link: https://peerj.com/articles/10070
last-modified: 2020-11-02
description: BackgroundDiabetes mellitus type 2 (DMT2) is a leading metabolic disorder in the world. Anti-diabetic actions of phytochemicals from various medicinal herbs have been explored as an alternative therapy in the management of DMT2 due to adverse effects of synthetic drugs used in allopathic medicine. α-amylase and α-glucosidase inhibitory potential and phytochemical profiling were investigated in aqueous extracts of two new Cinnamomum zeylanicum accessions, namely C. zeylanicum Sri Wijaya (SW), C. zeylanicum Sri Gemunu (SG) and commercially available C. zeylanicum (CC).MethodsMicrowave Digestion (MD), Pressurized Water Extraction (PWE), Steam Distillation (SD), Solvent Extraction (SE), Decoction Water Extraction (DWE) and Infusion Water Extraction (IWE) methods were used to prepare Cinnamon quill extracts. Total phenolic content (TPC, Folin-Ciocalteu method) and Proanthocyanidin content (PC, vanillin assay), α-amylase and α-glucosidase inhibition of Cinnamon extracts were determined spectrophotometrically. The α-amylase and α-glucosidase inhibition were reported in terms of IC50 value. The phytochemical profiling was accomplished by GC-MS technique.Results and DiscussionLowest IC50 values were observed in PWE and DWE of SW. The highest PC and TPC were also observed in PWE and DWE of SW. Pressured water and decoctions are promising methods for the extraction of antidiabetic constituents from cinnamon. Benzoic acid, cinnamyl alcohol, benzyl alcohol, and 4-Allyl-2,6-dimethoxyphenol were identified as major compounds in SW extracts. These compounds are believed to be responsible for strong enzyme inhibitory activity of the extracts.ConclusionsThis is the first study to explore the use of pressured and decoctions water to extract anti-diabetic phytochemicals from cinnamon. The extensive metabolite profiling of novel SW and SG extracts and comparison of that with commercially available CC are reported for the first time in this study. The C. zeylanicum, SW accession holds some promise in the management of diabetes.
creator: W.A. Niroshani M. Wariyapperuma
creator: Sagarika Kannangara
creator: Yasanandana S. Wijayasinghe
creator: Sri Subramanium
creator: Bimali Jayawardena
uri: https://doi.org/10.7717/peerj.10070
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Wariyapperuma et al.

title: Assessment of autonomous nerve system through non-linear heart rate variability outcomes in sedentary healthy adults
link: https://peerj.com/articles/10178
last-modified: 2020-11-02
description: BackgroundHeart rate variability (HRV) is a psycho-physiological phenomenon with broad health implications. Different data analysis methods have been used to assess the autonomic nervous system activity, but the validation of new indexes that accurately describe its balance through non-invasive methods (i.e., HRV analysis) is of clinical interest. This study aimed: (i) to evaluate the association of the Stress Score (SS) and the Sympathetic/Parasympathetic Ratio (S/PS) with time domain and frequency domain analysis of HRV, and (ii) to set reference values of SS and S/PS in sedentary healthy adults.MethodsA total of 156 sedentary healthy adults (38.4 ± 15.57 years old, 81 women), aged were involved in this study. HRV was measured for 15 min in a supine position at rest. SS and S/PS were calculated from the non-linear HRV analyses based on Poincare Plot.ResultsStress Score showed a non-linear negative power-law relationship with SDNN (β = −0.969; R2 = 0.963; P < 0.001), RMSSD (β = −0.867; R2 = 0.722; P < 0.001), high frequency (β = −0.834; R2 = 0.752; P =< 0.001), low frequency (β = −0.627; R2 = 0.330; P < 0.001), SD1 (β = −0.867; R2 = 0.722; P < 0.001) and SD2 (β = −1.000; R2 > 0.999; P < 0.001). There was observed a negative cubic relationship between SS with PNN50 (β = −1.972; R2 = 0.644; P < 0.001). A linear regression model was conducted between SS with Ratio Low/High Frequency (β = 0.026; R2 < 0.001; P = 0.750). Non-linear power-law regression models were built between S/PS and SDNN (β = −0.990; R2 = 0.981; P < 0.001), RMSSD (β = −0.973; R2 = 0.939; P < 0.001), high frequency (β = −0.928; R2 = 0.970; P < 0.001), low frequency (β = −2.344; R2 = 0.557; P < 0.001), SD1 (β = −0.973; R2 = 0.939; P < 0.001) and SD2 (β = −0.611; R2 = 0.908; P < 0.001). A non-linear negative regression model was built between S/PS and PNN50 (β = −3.412; R2 = 0.868; P < 0.001). A linear regression model was conducted between S/PS and SD2/SD1 (β = 0.075; R2 = 0.006; P < 0.001).ConclusionOur results support the use of SS as a sympathetic activity marker, and S/PS as an indicator of the sympathetic and parasympathetic activity of the autonomic nervous system in sedentary healthy adults.
creator: Gines Navarro-Lomas
creator: Alejandro De-la-O
creator: Lucas Jurado-Fasoli
creator: Manuel J. Castillo
creator: Pedro Femia
creator: Francisco J. Amaro-Gahete
uri: https://doi.org/10.7717/peerj.10178
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Navarro-Lomas et al.

title: Transcriptome and gene expression analysis of Rhynchophorus ferrugineus (Coleoptera: Curculionidae) during developmental stages
link: https://peerj.com/articles/10223
last-modified: 2020-11-02
description: BackgroundRed palm weevil, Rhynchophorus ferrugineus Olivier, is one of the most destructive pests harming palm trees. However, genomic resources for R. ferrugineus are still lacking, limiting the ability to discover molecular and genetic means of pest control.MethodsIn this study, PacBio Iso-Seq and Illumina RNA-seq were used to generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th-instar larva, adult) to increase the understanding of the life cycle and molecular characteristics of the pest.ResultsSequencing generated 625,983,256 clean reads, from which 63,801 full-length transcripts were assembled with N50 of 3,547 bp. Expression analyses revealed 8,583 differentially expressed genes (DEGs). Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mainly related to the peroxisome pathway which associated with metabolic pathways, material transportation and organ tissue formation. In summary, this work provides a valuable basis for further research on the growth and development, gene expression and gene prediction, and pest control of R. ferrugineus.
creator: Hongjun Yang
creator: Danping Xu
creator: Zhihang Zhuo
creator: Jiameng Hu
creator: Baoqian Lu
uri: https://doi.org/10.7717/peerj.10223
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Yang et al.

title: Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients: Evidence for co-infections
link: https://peerj.com/articles/10246
last-modified: 2020-11-02
description: BackgroundIn December 2019, an ongoing outbreak of pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/ 2019-nCoV) infection was initially reported in Wuhan, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused disease: coronavirus disease 2019 (COVID-19) and declared COVID-19 to be a Public Health Emergency of International Concern (PHEIC). Cellular co-infection is a critical determinant of viral fitness and infection outcomes and plays a crucial role in shaping the host immune response to infections.MethodsIn this study, 68 public next-generation sequencing data from SARS-CoV-2 infected patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Data screening was performed using an alignment-free method based on k-mer mapping and extension, fastv. Taxonomic classification was performed using Kraken 2 on all reads containing one or more virus sequences other than SARS-CoV-2.ResultsSARS-CoV-2 was identified in all except three patients. Influenza type A (H7N9) virus, human immunodeficiency virus, rhabdovirus, human metapneumovirus, Human adenovirus, Human herpesvirus 1, coronavirus NL63, parvovirus, simian virus 40, and hepatitis virus genomes sequences were detected in SARS-CoV-2 infected patients. Besides, a very diverse group of bacterial populations were observed in the samples.
creator: Mohamed A. Abouelkhair
uri: https://doi.org/10.7717/peerj.10246
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Abouelkhair

title: Optimizing and purifying extracellular amylase from soil bacteria to inhibit clinical biofilm-forming bacteria
link: https://peerj.com/articles/10288
last-modified: 2020-11-02
description: BackgroundBacterial biofilms have become a major threat to human health. The objective of this study was to isolate amylase-producing bacteria from soil to determine the overall inhibition of certain pathogenic bacterial biofilms.MethodsWe used serial dilution and the streaking method to obtain a total of 75 positive amylase isolates. The starch-agar plate method was used to screen the amylolytic activities of these isolates, and we used morphological and biochemical methods to characterize the isolates. Optimal conditions for amylase production and purification using Sephadex G-200 and SDS-PAGE were monitored. We screened these isolates’ antagonistic activities and the purified amylase against pathogenic and multi-drug-resistant human bacteria using the agar disk diffusion method. Some standard antibiotics were controlled according to their degree of sensitivity. Finally, we used spectrophotometric methods to screen the antibiofilm 24 and 48 h after application of filtering and purifying enzymes in order to determine its efficacy at human pathogenic bacteria.ResultsThe isolated Bacillus species were Bacillus megaterium (26.7%), Bacillus subtilis (16%), Bacillus cereus (13.3%), Bacillus thuringiesis (10.7%), Bacillus lentus (10.7%), Bacillus mycoides (5.3%), Bacillus alvei (5.3%), Bacillus polymyxa (4%), Bacillus circulans (4%), and Micrococcus roseus (4%). Interestingly, all isolates showed a high antagonism to target pathogens. B. alevi had the highest recorded activity (48 mm) and B. polymyxa had the lowest recorded activity (12 mm) against Staphylococcus aureus (MRSA) and Escherichia coli, respectively. On the other hand, we detected no antibacterial activity for purified amylase. The supernatant of the isolated amylase-producing bacteria and its purified amylase showed significant inhibition for biofilm: 93.7% and 78.8%, respectively. This suggests that supernatant and purified amylase may be effective for clinical and environmental biofilm control.DiscussionOur results showed that soil bacterial isolates such as Bacillus sp. supernatant and its purified amylase are good antibiofilm tools that can inhibit multidrug-resistant former strains. They could be beneficial for pharmaceutical use. While purified amylase was effective as an antibiofilm, the isolated supernatant showed better results.
creator: Rokaia Elamary
creator: Wesam M. Salem
uri: https://doi.org/10.7717/peerj.10288
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Elamary and Salem

title: The current knowledge gap on metallothionein mediated metal-detoxification in Elasmobranchs
link: https://peerj.com/articles/10293
last-modified: 2020-11-02
description: Elasmobranchs are particularly vulnerable to environmental contamination, especially pollutants that may bioaccumulate and biomagnify, throughout the trophic web, such as metals. However, Elasmobranch management and conservation plans are challenging, and this group is often neglected regarding ecotoxicological analyses, particularly concerning metal detoxification mechanisms. This article discusses metallothionein (MT) mediated metal detoxification in Elasmobranchs and reflects on the current knowledge gap in this regard.
creator: Rachel Ann Hauser-Davis
uri: https://doi.org/10.7717/peerj.10293
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Hauser-Davis

title: Changing health compliance through message repetition based on the extended parallel process model in the COVID-19 pandemic
link: https://peerj.com/articles/10318
last-modified: 2020-11-02
description: When people are confronted with health proposals during the coronavirus disease 2019 (COVID-19) pandemic, it has been suggested that fear of COVID-19 can serve protective functions and ensure public health compliance. However, health proposal repetition and its perceived efficacy also influence the behavior intention toward the proposal, which has not yet been confirmed in the COVID-19 context. The present study aims to examine whether the extended parallel process model (EPPM) can be generalized to a naturalistic context like the COVID-19 pandemic. Additionally, we will explore how repetition of a health proposal is involved with the EPPM. In this study, two groups of participants are exposed to the same health proposal related to COVID-19, where one group is exposed once and another group twice. They then fill out a questionnaire consisting of items concerning behavior intention and adapted from the Risk Behavior Diagnosis Scale. Structural equation modeling will be used to determine the multivariate associations between the variables. We predict that repetition of the health proposal will associate with response efficacy (i.e., a belief about the effectiveness of the health proposal in deterring the threat) and perceived susceptibility (i.e., a belief about the risk of experiencing the threat). It is also predicted that following the EPPM, behavior intention will associate with both perceived efficacy of the health proposal, which will underlie response efficacy, and perceived threat of COVID-19, which will underlie perceived susceptibility. We will discuss the process, based on the model, where health message repetition affects behavior intention during the COVID-19 pandemic.
creator: Jingwen Yang
creator: Xue Wu
creator: Kyoshiro Sasaki
creator: Yuki Yamada
uri: https://doi.org/10.7717/peerj.10318
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Yang et al.

title: The efficacy of IL-6 inhibitor Tocilizumab in reducing severe COVID-19 mortality: a systematic review
link: https://peerj.com/articles/10322
last-modified: 2020-11-02
description: BackgroundIn the absence of highly effective antiviral therapies against SARS-CoV-2, it is crucial to counter the known pathophysiological causes of severe COVID-19. Evaluating the efficacy existing drugs may expedite the development of such therapeutics. Severe COVID-19 is largely the result of a dysregulated immune response characterized by lymphocytopenia, neutrophilia and critical hypercytokinemia, or “cytokine storm,” which is largely mediated by the cytokine interleukin-6 (IL-6). The IL-6 inhibitor tocilizumab (TCZ) could potentially suppress the effects of the pro-inflammatory cytokine and thereby lower mortality from the disease. This systematic analysis aimed to investigate and synthesize existing evidence for the efficacy of TCZ in reducing COVID-19 mortality.MethodologyPubMed and SearchWorks searches were performed to locate clinical studies with primary data on TCZ treatment for severe COVID-19. Sixteen case-control studies comparing mortality between TCZ and standard of care (SOC) were identified for quantitative synthesis. The systematic analysis was pre-approved through PROSPERO (CRD42020193479).ResultsCombined mortality for the TCZ-treated and SOC groups were 26.0% and 43.4% respectively. In all but one of the studies, the odds ratio of mortality from COVID-19 pointed towards lower fatality with TCZ vs the SOC. A combined random effects odds ratio calculation yielded an odds ratio of 0.453 (95% CI [0.376–0.547], p < 0.001). Additionally, 18 uncontrolled trials were identified for qualitative analysis producing a raw combined mortality rate of 16.0%.ConclusionsImportant caveats to this research include the lack of prospective randomized control trials and the absence of data from the large COVATA study from the published literature. However, results from this systematic analysis of published research provide positive evidence for the potential efficacy of TCZ to treat severe COVID-19, validating the ethical basis and merit of ongoing randomized controlled clinical trials.
creator: Avi Gurion Kaye
creator: Robert Siegel
uri: https://doi.org/10.7717/peerj.10322
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Kaye and Siegel