title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1041
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils
link: https://peerj.com/articles/10017
last-modified: 2020-10-13
description: Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.
creator: Raden Pramesa Narakusumo
creator: Alexander Riedel
creator: Joan Pons
uri: https://doi.org/10.7717/peerj.10017
license: https://creativecommons.org/licenses/by-nc/4.0/
rights: ©2020 Narakusumo et al.

title: Utilising one minute and four minute recovery when employing the resistance training contrast method does not negatively affect subsequent jump performance in the presence of concurrent training
link: https://peerj.com/articles/10031
last-modified: 2020-10-13
description: BackgroundLittle is known about contrast training and post-activation performance enhancement (PAPE) in a same day concurrent training model. The aim of the current study was to examine the use of two short duration (1-min and 4-min) recovery periods on drop jump performance in same day concurrently trained athletes.MethodsTen professional Australian Rules footballers (age, 20.6 ± 1.9 yr; height, 184.8 ± 6.9 cm; body mass, 85.8 ± 8.4 kg) completed two resistance training sessions with different PAPE recovery durations; 1-min and 4-min, 1 h following a field-based endurance session. Baseline (pre) drop jumps were compared to post-test maximal drop jumps, performed after each set of three squats (where each participant was encouraged to lift as heavy as they could), to determine changes between 1-min and 4-min recovery periods. Data were analysed by fitting a mixed model (significance was set at P ≤ 0.05). Corrected Hedges’ g standardised effect sizes ±95% confidence limits were calculated using group means ± SDs.ResultsThere were no significant differences between baseline and experimental sets 1, 2 and 3 for reactive strength index (RSI), flight time, and total and relative impulse for either recovery duration. However, for contact time, 1-min baseline was significantly different from set 2 (mean difference; 95% CI [0.029; 0.000–0.057 s], P = 0.047, ES; 95% CI [−0.27; −1.20 to 0.66]). For RSI and flight time, 1-min was significantly higher than 4-min (RSI: 0.367; 0.091 to 0.642, P = 0.010, ES; 95% CI [0.52; −0.37 to 1.42]; flight time: 0.033; 0.003 to 0.063 s, P = 0.027, ES; 95% CI [0.86; −0.06 to 1.78]).DiscussionShort recovery periods of 1-min may be a time-efficient form of prescribing strength-power exercise in contrast loading schemes. Longer recovery periods do not appear to benefit immediate, subsequent performance.
creator: Dean Ritchie
creator: Justin W.L. Keogh
creator: Peter Reaburn
creator: Jonathan D. Bartlett
uri: https://doi.org/10.7717/peerj.10031
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Ritchie et al.

title: Plastome structure and adaptive evolution of Calanthe s.l. species
link: https://peerj.com/articles/10051
last-modified: 2020-10-13
description: Calanthe s.l. is the most diverse group in the tribe Collabieae (Orchidaceae), which are pantropical in distribution. Illumina sequencing followed by de novo assembly was used in this study, and the plastid genetic information of Calanthe s.l. was used to investigate the adaptive evolution of this taxon. Herein, the complete plastome of five Calanthe s.l. species (Calanthe davidii, Styloglossum lyroglossa, Preptanthe rubens, Cephalantheropsis obcordata, and Phaius tankervilliae) were determined, and the two other published plastome sequences of Calanthe s.l. were added for comparative analyses to examine the evolutionary pattern of the plastome in the alliance. The seven plastomes ranged from 150,181 bp (C. delavayi) to 159,014 bp (C. davidii) in length and were all mapped as circular structures. Except for the three ndh genes (ndhC, ndhF, and ndhK) lost in C. delavayi, the remaining six species contain identical gene orders and numbers (115 gene). Nucleotide diversity was detected across the plastomes, and we screened 14 mutational hotspot regions, including 12 non-coding regions and two gene regions. For the adaptive evolution investigation, three species showed positive selected genes compared with others, C. obcordata (cemA), S. lyroglossa (infA, ycf1 and ycf2) and C. delavayi (nad6 and ndhB). Six genes were under site-specific positive selection in Calanthe s.l., namely, accD, ndhB, ndhD, rpoC2, ycf1, and ycf2, most of which are involved in photosynthesis. These results, including the new plastomes, provide resources for the comparative plastome, breeding, and plastid genetic engineering of orchids and flowering plants.
creator: Yanqiong Chen
creator: Hui Zhong
creator: Yating Zhu
creator: Yuanzhen Huang
creator: Shasha Wu
creator: Zhongjian Liu
creator: Siren Lan
creator: Junwen Zhai
uri: https://doi.org/10.7717/peerj.10051
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Chen et al.

title: An efficient sorghum protoplast assay for transient gene expression and gene editing by CRISPR/Cas9
link: https://peerj.com/articles/10077
last-modified: 2020-10-13
description: Protoplasts are commonly used in genetic and breeding research. In this study, the isolation of sorghum protoplasts was optimized and applied to transient gene expression and editing by CRISPR/Cas9. The protoplast was most viable in 0.5 M mannitol, which was the highest of three concentrations after 48- and 72-hours treatments. Using this method we can derive an average of 1.6×106 cells which vary from 5 to 22 nm in size. The average transfection of the protoplasts was 68.5% using the PEG-mediated method. The subcellular assays located Sobic.002G279100-GFP and GFP proteins in the cell compartments as predicted bioinformatically. Two CRISPR/Cas9 plasmids were transfected into sorghum protoplasts to screen for an appropriate sgRNA for gene editing. One plasmid can correctly edit the target region using a single protoplast cell as template DNA. Our results indicated that the protoplast assays as optimized are suitable for transient gene expression and sgRNA screening in CRISPR/Cas9 gene editing procedures.
creator: Ruirui Meng
creator: Chenchen Wang
creator: Lihua Wang
creator: Yanlong Liu
creator: Qiuwen Zhan
creator: Jiacheng Zheng
creator: Jieqin Li
uri: https://doi.org/10.7717/peerj.10077
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Meng et al.

title: Integrating multiple microarray dataset analysis and machine learning methods to reveal the key genes and regulatory mechanisms underlying human intervertebral disc degeneration
link: https://peerj.com/articles/10120
last-modified: 2020-10-13
description: Intervertebral disc degeneration (IDD), a major cause of lower back pain, has multiple contributing factors including genetics, environment, age, and loading history. Bioinformatics analysis has been extensively used to identify diagnostic biomarkers and therapeutic targets for IDD diagnosis and treatment. However, multiple microarray dataset analysis and machine learning methods have not been integrated. In this study, we downloaded the mRNA, microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA) expression profiles (GSE34095, GSE15227, GSE63492GSE116726, GSE56081 and GSE67566) associated with IDD from the GEO database. Using differential expression analysis and recursive feature elimination, we extracted four optimal feature genes. We then used the support vector machine (SVM) to make a classification model with the four optimal feature genes. The ROC curve was used to evaluate the model’s performance, and the expression profiles (GSE63492, GSE116726, GSE56081, and GSE67566) were used to construct a competitive endogenous RNA (ceRNA) regulatory network and explore the underlying mechanisms of the feature genes. We found that three miRNAs (hsa-miR-4728-5p, hsa-miR-5196-5p, and hsa-miR-185-5p) and three circRNAs (hsa_circRNA_100723, hsa_circRNA_104471, and hsa_circRNA_100750) were important regulators with more interactions than the other RNAs across the whole network. The expression level analysis of the three datasets revealed that BCAS4 and SCRG1 were key genes involved in IDD development. Ultimately, our study proposes a novel approach to determining reliable and effective targets in IDD diagnosis and treatment.
creator: Hongze Chang
creator: Xiaolong Yang
creator: Kemin You
creator: Mingwei Jiang
creator: Feng Cai
creator: Yan Zhang
creator: Liang Liu
creator: Hui Liu
creator: Xiaodong Liu
uri: https://doi.org/10.7717/peerj.10120
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Chang et al.

title: Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings: a feasibility study
link: https://peerj.com/articles/10196
last-modified: 2020-10-13
description: As the world’s economies come out of the lockdown imposed by the COVID-19 pandemic, there is an urgent need for technologies to mitigate COVID-19 transmission in confined spaces such as buildings. This feasibility study looks at one such technology, upper-room ultraviolet (UV) air disinfection, that can be safely used while humans are present in the room space, and which has already proven its efficacy as an intervention to inhibit the transmission of airborne diseases such as measles and tuberculosis. Using published data from various sources, it is shown that the SARS-CoV-2 virus, the causative agent of COVID-19, is highly likely to be susceptible to UV-C damage when suspended in air, with a UV susceptibility constant likely to be in the region 0.377–0.590 m2/J, similar to that for other aerosolised coronaviruses. As such, the UV-C flux required to disinfect the virus is expected to be acceptable and safe for upper-room applications. Through analysis of expected and worst-case scenarios, the efficacy of the upper-room UV-C approach for reducing COVID-19 transmission in confined spaces (with moderate but sufficient ceiling height) is demonstrated. Furthermore, it is shown that with SARS-CoV-2, it should be possible to achieve high equivalent air change rates using upper-room UV air disinfection, suggesting that the technology might be particularly applicable to poorly ventilated spaces.
creator: Clive B. Beggs
creator: Eldad J. Avital
uri: https://doi.org/10.7717/peerj.10196
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Beggs and Avital

title: Soil carbon, nitrogen and phosphorus ecological stoichiometry shifts with tree species in subalpine plantations
link: https://peerj.com/articles/9702
last-modified: 2020-10-12
description: Understanding ecological stoichiometric characteristics of soil nutrient elements, such as carbon (C), nitrogen (N) and phosphorus (P) is crucial to guide ecological restoration of plantations in ecologically vulnerable areas, such as alpine and subalpine regions. However, there has been only a few related studies, and thus whether and how different tree species would affect soil C:N:P ecological stoichiometry remains unclear. We compared soil C:N:P ecological stoichiometry of Pinus tabulaeformis, Larix kaempferi and Cercidiphyllum japonicum to primary shrubland in a subalpine region. We observed strong tree-specific and depth-dependent effects on soil C:N:P stoichiometry in subalpine plantations. In general, the C:N, C:P and N:P of topsoil (0–10 cm) are higher than subsoil (>10 cm) layer at 0–30 cm depth profiles. The differences in C:N, N:P and C:P at the topsoil across target tree species were significantly linked to standing litter stock, tree biomass/total aboveground biomass and Margalef’s index of plant community, respectively, whereas the observed variations of C:N, N:P and C:P ratio among soil profiles are closely related to differences in soil bulk density, soil moisture, the quantity and quality of aboveground litter inputs as well as underground fine root across plantations examined. Our results highlight that soil nutrients in plantation depend on litter quantity and quality of selected tree species as well as soil physical attributes. Therefore, matching site with trees is crucial to enhance ecological functioning in degraded regions resulting from human activity.
creator: Kaibin Qi
creator: Xueyong Pang
creator: Bing Yang
creator: Weikai Bao
uri: https://doi.org/10.7717/peerj.9702
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Qi et al.

title: Genetic characterization of feline panleukopenia virus from dogs in Vietnam reveals a unique Thr101 mutation in VP2
link: https://peerj.com/articles/9752
last-modified: 2020-10-12
description: BackgroundCanine parvovirus type 2 (CPV-2) and feline parvovirus (FPV) are known as the main causes of several serious diseases and have a severe impact on puppies and kittens, respectively. FPV and new CPV-2 variants are all able to infect cats, causing diseases indistinguishable from feline panleukopenia. However, FPV only replicates efficiently in feline cells in vitro and replicates in dogs in the thymus and bone marrow without being shed in feces. In our previous study, the genotypes of six parvoviral isolates were unable to be identified using a SimpleProbe® real-time PCR assay.MethodsIn the present study, we characterized previously unidentified FPV-like viruses isolated from dogs in Vietnam. The six isolates were utilized to complete VP2 gene sequencing and to conduct phylogenetic analyses.ResultsSequence analysis of the six parvoviral strains identified the species as being similar to FPV. Phylogenetic analysis demonstrated that the complete VP2 genes of the strains are similar to those of FPV. The FPV-like strains contain a Thr101 mutation in the VP2 protein, which is different from prototype FPV strains.DiscussionOur data provide evidence for the existence of changes in the charge, protein contact potential and molecular surface of the core of the receptor-binding size with an Ile101 to Thr101 mutation. This is also the first study to provide reliable evidence that FPV may be a threat to the Vietnamese dog population.
creator: Minh Hoang
creator: Cheng-Nan Wu
creator: Chuen-Fu Lin
creator: Huong Thanh Thi Nguyen
creator: Van Phan Le
creator: Ming-Tang Chiou
creator: Chao-Nan Lin
uri: https://doi.org/10.7717/peerj.9752
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Hoang et al.

title: Physiological aspects and energetic contribution in 20s:10s high-intensity interval exercise at different intensities
link: https://peerj.com/articles/9791
last-modified: 2020-10-12
description: BackgroundOne of the most popular high-intensity interval exercises is the called “Tabata Protocol”. However, most investigations have limitations in describing the work intensity, and this fact appears to be due to the protocol unfeasibility. Furthermore, the physiological demands and energetic contribution during this kind of exercise remain unclear.MethodsEight physically active students (21.8 ± 3.7 years) and eight well-trained cycling athletes (27.8 ± 6.4 years) were enrolled. In the first visit, we collected descriptive data and the peak power output (PPO). On the next three visits, in random order, participants performed interval training with the same time structure (effort:rest 20s:10s) but using different intensities (115%, 130%, and 170% of PPO). We collected the number of sprints, power output, oxygen consumption, blood lactate, and heart rate.ResultsThe analysis of variance for multivariate test (number of sprints, power output, blood lactate, peak heart rate and percentage of maximal heart rate) showed significant differences between groups (F = 9.62; p = 0.001) and intensities (F = 384.05; p < 0.001), with no interactions (F = 0.94; p = 0.57). All three energetic contributions and intensities were different between protocols. The higher contribution was aerobic, followed by alactic and lactic. The aerobic contribution was higher at 115%PPO, while the alactic system showed higher contribution at 130%PPO. In conclusion, the aerobic system was predominant in the three exercise protocols, and we observed a higher contribution at lower intensities.
creator: Gabriel V. Protzen
creator: Charles Bartel
creator: Victor S. Coswig
creator: Paulo Gentil
creator: Fabricio B. Del Vecchio
uri: https://doi.org/10.7717/peerj.9791
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2020 Protzen et al.

title: Genomic signatures of globally enhanced gene duplicate accumulation in the megadiverse higher Diptera fueling intralocus sexual conflict resolution
link: https://peerj.com/articles/10012
last-modified: 2020-10-12
description: Gene duplication is an important source of evolutionary innovation. To explore the relative impact of gene duplication during the diversification of major insect model system lineages, we performed a comparative analysis of lineage-specific gene duplications in the fruit fly Drosophila melanogaster (Diptera: Brachycera), the mosquito Anopheles gambiae (Diptera: Culicomorpha), the red flour beetle Tribolium castaneum (Coleoptera), and the honeybee Apis mellifera (Hymenoptera). Focusing on close to 6,000 insect core gene families containing maximally six paralogs, we detected a conspicuously higher number of lineage-specific duplications in Drosophila (689) compared to Anopheles (315), Tribolium (386), and Apis (223). Based on analyses of sequence divergence, phylogenetic distribution, and gene ontology information, we present evidence that an increased background rate of gene duplicate accumulation played an exceptional role during the diversification of the higher Diptera (Brachycera), in part by providing enriched opportunities for intralocus sexual conflict resolution, which may have boosted speciation rates during the early radiation of the megadiverse brachyceran subclade Schizophora.
creator: Riyue Bao
creator: Markus Friedrich
uri: https://doi.org/10.7717/peerj.10012
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2020 Bao and Friedrich