Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes
Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.
Chen et al. (2019) Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes. PeerJ 7:e7480 https://doi.org/10.7717/peerj.7480
Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)
Background VQ proteins, the plant-specific transcription factors, are involved in plant development and multiple stresses; however, only few articles systematic reported the VQ genes in soybean. Methods In total, we identified 75 GmVQ genes, which were classified into 7 groups (I-VII). Conserved domain analysis indicated that VQ gene family members all contain the VQ domains. VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed that cis-elements related to stress responses, phytohormone responses and controlling physical as well as reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were showed expressing in nine tissues, suggesting their putative function in many aspects of plant growth and development as well as response to stress in Glycine max. Results This study aims to understand the roles of VQ genes in various development processes and their expression patterns in responses to stimuli. Our results provide basic information in identification and classification of GmVQ genes. Further experimental analysis will allows us to know the functions of GmVQs participation in plant growth and stress responses.
Wang et al. (2019) Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max). PeerJ 7:e7509 https://doi.org/10.7717/peerj.7509
Delivery of targeted gene therapies using a hybrid cryogel-coated prosthetic vascular graft
Objectives The success of prosthetic vascular grafts in the management of peripheral arterial disease is frequently limited by the development of anastomotic neointimal hyperplasia (ANIH), with the host response to prosthetic grafts beginning soon after implantation. To address this, we combine a platform of polyethylene terephthalate (PET) fabric with an applied cryogel layer containing biologic agents to create a bioactive prosthetic graft system, with the ability to deliver therapeutics targeting modulators of the ANIH-associated transcriptome response, along with antithrombotic agents. Methods Hybrid graft materials were synthesized by cryopolymerization of methacrylated alginate and heparin onto electrospun (ePET), knitted PET (kPET), or woven PET (wPET). Arg-Gly-Asp (RGD) peptides were added to increase cell adhesion. Scanning electron microscopy (SEM) was used to study the microstructure at 1 day, and 2, 4, and 8 weeks. Physical properties such as swelling ratio, pore connectivity, shape recovery, and stiffness were evaluated. Human aortic endothelial cell (HAoEC) adherence was visualized using confocal microscopy after 24 hours and proliferation was evaluated with a resazurin-based assay for 7 days. Confocal microscopy was used to assess delivery of adeno-associated virus (AAV-GFP) after incubation of hybrid grafts with HAoECs. Heparin activity of the materials was measured using an anti-Xa assay. Results SEM demonstrated large interconnected pores throughout the entire structure for all graft types, with minimal degradation of the cryogel after 8 weeks. Hybrid materials showed a trend towards increased shape recovery, increased stiffness, decreased swelling ratio, and no difference in pore connectivity. HAoECs incorporated, adhered, and proliferated over 7 days on all materials. HAoECs were successfully transduced with AAV-GFP from the hybrid graft materials. Anti-Xa assay confirmed continued activity of heparin from all materials for over 7 days. Conclusions We have developed a bioactive prosthetic graft system with a cryogel coating capable of delivering biologic agents with antithrombotic activity. By applying the cryogel and selected agents onto PET prior to graft implantation, this study sets the stage for the system to be individualized and tailored to the patient, with bioengineering and targeted gene therapy strategies dovetailing to create an improved prosthetic graft adaptable to emerging knowledge and technologies.
Huynh et al. (2019) Delivery of targeted gene therapies using a hybrid cryogel-coated prosthetic vascular graft. PeerJ 7:e7377 https://doi.org/10.7717/peerj.7377
Twisted tale of the tiger: the case of inappropriate data and deficient science
Publications in peer-reviewed journals are often looked upon as tenets on which future scientific thought is built. Published information is not always flawless and errors in published research should be expediently reported, preferably by a peer-review process. We review a recent publication by Gopalaswamy et al. (10.1111/2041-210X.12351) that challenges the use of “double sampling” in large-scale animal surveys. Double sampling is often resorted to as an established economical and practical approach for large-scale surveys since it calibrates abundance indices against absolute abundance, thereby potentially addressing the statistical shortfalls of indices. Empirical data used by Gopalaswamy et al. (10.1111/2041-210X.12351) to test their theoretical model, relate to tiger sign and tiger abundance referred to as an Index-Calibration experiment (IC-Karanth). These data on tiger abundance and signs should be paired in time and space to qualify as a calibration experiment for double sampling, but original data of IC-Karanth show lags of (up to) several years. Further, data points used in the paper do not match the original sources. We show that by use of inappropriate and incorrect data collected through a faulty experimental design, poor parameterization of their theoretical model, and selectively picked estimates from literature on detection probability, the inferences of this paper are highly questionable. We highlight how the results of Gopalaswamy et al. were further distorted in popular media. If left unaddressed, the paper of Gopalaswamy et al. could have serious implications on statistical design of large-scale animal surveys by propagating unreliable inferences.
Qureshi et al. (2019) Twisted tale of the tiger: the case of inappropriate data and deficient science. PeerJ 7:e7482 https://doi.org/10.7717/peerj.7482
Investigating safety profiles of human papillomavirus vaccine across group differences using VAERS data and MedDRA
Background The safety of vaccines is a critical factor in maintaining public trust in national vaccination programs. This study aimed to evaluate the safety profiles of human papillomavirus (HPV) vaccines with regard to the distribution of adverse events (AE) across gender and age, and the correlations across various AEs using the Food and Drug Administration/Centers for Disease Control and Prevention Vaccine Adverse Event Reporting System (VAERS). Methods For analyses, 27,348 patients aged between 9 and 25 years old with at least one AE reported in VAERS between the year of 2006 and 2017 were included. AEs were summarized into two levels: the lower level preferred term (PT) and higher level system organ classes (SOCs) based on the structure of Medical Dictionary for Regulatory Activities (MedDRA). A series of statistical analyses were applied on both levels of AEs. Zero-truncated Poisson regression and multivariate logistic regression models were first developed to assess the rate and risk of SOCs across age groups and genders. Pairwise Pearson correlation analyses and hierarchical clustering analyses were then conducted to explore the interrelationships and clustering pattern among AEs. Results We identified 27,337 unique HPV vaccine reports between 2006 and 2017. Disproportional reporting of AEs was observed across age and gender in 21 SOCs (p < 0.05). The correlation analyses found most SOCs demonstrate weak positive correlations except for five pairs which were negatively correlated: skin and subcutaneous tissue disorders + injury poisoning and procedural complications; skin and subcutaneous tissue disorders + nervous system disorders; Skin and subcutaneous tissue disorders + pregnancy, puerperium and perinatal conditions; nervous system disorders + pregnancy, puerperium and perinatal conditions; pregnancy, puerperium and perinatal conditions + general disorders and administration site conditions. Nervous system disorders had the most AEs which contributed to 12,448 (46%) cases. In the further analyses of correlations between PT in nervous system disorders, the three most strongly correlated AEs were psychiatric disorders (r = 0.35), gastrointestinal disorders (r = 0.215), and musculoskeletal and connective tissue disorders (r = 0.261). We observed an inter-SOCs correlation of the PTs among AE pairs by nervous system disorders/psychiatric disorders/gastrointestinal disorders/musculoskeletal and connective tissue disorders. Conclusions The analyses revealed a different distribution pattern of AEs across gender and age subgroups in 21 SOC level AEs. Correlation analyses and hierarchical clustering analyses further revealed several correlated patterns across various AEs. However, findings from this study should be interpreted with caution. Further clinical studies are needed to understand the heterogeneity of AEs reporting across subgroups and the biological pathways among the statistically correlated AEs.
Jia et al. (2019) Investigating safety profiles of human papillomavirus vaccine across group differences using VAERS data and MedDRA. PeerJ 7:e7490 https://doi.org/10.7717/peerj.7490
Effects of digging by a native and introduced ecosystem engineer on soil physical and chemical properties in temperate grassy woodland
Temperate grasslands and woodlands are the focus of extensive restoration efforts worldwide. Reintroduction of locally extinct soil-foraging and burrowing animals has been suggested as a means to restore soil function in these ecosystems. Yet little is known about the physical and chemical effects of digging on soil over time and how these effects differ between species of digging animal, vegetation types or ecosystems. We compared foraging pits of a native reintroduced marsupial, the eastern bettong (Bettongia gaimardi) and that of the exotic European rabbit (Oryctolagus cuniculus). We simulated pits of these animals and measured pit dimensions and soil chemical properties over a period of 2 years. We showed that bettong and rabbit pits differed in their morphology and longevity, and that pits had a strong moderating effect on soil surface temperatures. Over 75% of the simulated pits were still visible after 2 years, and bettong pits infilled faster than rabbit pits. Bettong pits reduced diurnal temperature range by up to 25 °C compared to the soil surface. We did not find any effects of digging on soil chemistry that were consistent across vegetation types, between bettong and rabbit pits, and with time since digging, which is contrary to studies conducted in arid biomes. Our findings show that animal foraging pits in temperate ecosystems cause physical alteration of the soil surface and microclimatic conditions rather than nutrient changes often observed in arid areas.
Ross et al. (2019) Effects of digging by a native and introduced ecosystem engineer on soil physical and chemical properties in temperate grassy woodland. PeerJ 7:e7506 https://doi.org/10.7717/peerj.7506
Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors
Heat shock protein 70 (Hsp70) plays an essential role in plant growth and development, as well as stress response. Rapeseed (Brassica napus L.) originated from recently interspecific hybridization between Brassica rapa and Brassica oleracea. In this study, a total of 47 Hsp70 genes were identified in B. napus (AnAnCnCn genome), including 22 genes from An subgenome and 25 genes from Cn subgenome. Meanwhile, 29 and 20 Hsp70 genes were explored in B. rapa (ArAr genome) and B. oleracea (CoCo genome), respectively. Based on phylogenetic analysis, 114 Hsp70 proteins derived from B. napus, B. rapa, B. oleracea and Arabidopsis thaliana, were divided into 6 subfamilies containing 16 Ar-An and 11 Co-Cn reliable orthologous pairs. The homology and synteny analysis indicated whole genome triplication and segmental duplication may be the major contributor for the expansion of Hsp70 gene family. Intron gain of BnHsp70 genes and domain loss of BnHsp70 proteins also were found in B. napus, associating with intron evolution and module evolution of proteins after allopolyploidization. In addition, transcriptional profiles analyses indicated that expression patterns of most BnHsp70 genes were tissue-specific. Moreover, Hsp70 orthologs exhibited different expression patterns in the same tissue and Cn subgenome biased expression was observed in leaf. These findings contribute to exploration of the evolutionary adaptation of polyploidy and will facilitate further application of BnHsp70 gene functions.
Liang et al. (2019) Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors. PeerJ 7:e7511 https://doi.org/10.7717/peerj.7511
Movement velocity can be used to estimate the relative load during the bench press and leg press exercises in older women
Background Movement velocity has been proposed as an effective tool to prescribe the load during resistance training in young healthy adults. This study aimed to elucidate whether movement velocity could also be used to estimate the relative load (i.e., % of the one-repetition maximum (1RM)) in older women. Methods A total of 22 older women (age = 68.2 ± 3.6 years, bench press 1RM = 22.3 ± 4.7 kg, leg press 1RM = 114.6 ± 15.9 kg) performed an incremental loading test during the free-weight bench press and the leg press exercises on two separate sessions. The mean velocity (MV) was collected with a linear position transducer. Results A strong linear relationship between MV and the relative load was observed for the bench press (%1RM = −130.4 MV + 119.3; r2 = 0.827, standard error of the estimate (SEE) = 6.10%1RM, p < 0.001) and leg press exercises (%1RM = −158.3 MV + 131.4; r2 = 0.913, SEE = 5.63%1RM, p < 0.001). No significant differences were observed between the bench press and leg press exercises for the MV attained against light-medium relative loads (≤70%1RM), while the MV associated with heavy loads (≥80%1RM) was significantly higher for the leg press. Conclusions These results suggest that the monitoring of MV could be useful to prescribe the loads during resistance training in older women. However, it should be noted that the MV associated with a given %1RM is significantly lower in older women compared to young healthy individuals.
Marcos-Pardo et al. (2019) Movement velocity can be used to estimate the relative load during the bench press and leg press exercises in older women. PeerJ 7:e7533 https://doi.org/10.7717/peerj.7533
Anxiety-like behavior and whole-body cortisol responses to components of energy drinks in zebrafish (Danio rerio)
The current study investigated the independent and combined effects of caffeine and taurine on anxiety-like behavior and neuroendocrine responses in adult zebrafish (Danio rerio). Caffeine (1,3,7-trimethylpurine-2,6-dione), the world’s most commonly used psychoactive drug, acts as an adenosine receptor blocker and a mild central nervous system stimulant. However, excessive use of caffeine is associated with heightened anxiety levels. Taurine (2-aminoethanesulfonic acid), a semi-essential amino acid synthesized within the human brain, has been hypothesized to play a role in regulating anxiolytic behavior. Caffeine and taurine are two common additives in energy drinks and are often found in high concentrations in these beverages. However, few studies have investigated the interaction of these two chemicals with regards to anxiety measures. A suitable vertebrate to examine anxiety-like behavior and physiological stress responses is the zebrafish, which has shown promise due to substantial physiological and genetic homology with humans. Anxiety-like behavior in zebrafish can be determined by analyzing habituation to novelty when fish are placed into a novel tank and scototaxis (light avoidance) behavior in the light-dark test. Stress-related neuroendocrine responses can be measured in zebrafish by analyzing whole-body cortisol levels. The goal of this study was to determine if exposure to caffeine, taurine, or a combination of the two compounds altered anxiety-like behavior and whole-body cortisol levels in zebrafish relative to control. Zebrafish were individually exposed to either caffeine (100 mg/L), taurine (400 mg/L), or both for 15 min. Zebrafish in the control group were handled in the same manner but were only exposed to system tank water. After treatment, fish were transferred to the novel tank test or the light-dark test. Behavior was tracked for the first 6 min in the novel tank and 15 min in the light-tark test. Fifteen min after introduction to the behavioral task, fish were euthanized for the analysis of whole-body cortisol levels. The results demonstrate that caffeine treatment decreased the amount of exploration in the top of the novel tank and increased scototaxis behavior in the light-dark test, which supports the established anxiogenic effect of acute exposure to caffeine. Taurine alone did not alter basal levels of anxiety-like behavioral responses nor ameliorated the anxiogenic effects of caffeine on behavior when the two compounds were administered concurrently. None of the drug treatments altered basal levels of whole-body cortisol. The current results of this study suggest that, at least at this dose and time of exposure, taurine does not mitigate the anxiety-producing effects of caffeine when administered in combination, such as with energy drink consumption.
Alia et al. (2019) Anxiety-like behavior and whole-body cortisol responses to components of energy drinks in zebrafish (Danio rerio). PeerJ 7:e7546 https://doi.org/10.7717/peerj.7546
A revision of the Neotropical caddisfly genus Ascotrichia Flint, 1983 (Trichoptera, Hydroptilidae)
A revision of the microcaddisfly genus Ascotrichia (Trichoptera, Hydroptilidae) is provided, including a generic diagnosis, illustrations, and descriptions of males. This genus is endemic to the Neotropical region and has been recorded from countries in northern South America. Adults of the genus are notable within the family for the contrasting black and green hairs on the forewings. A total of six species are treated, three described as new: Ascotrichia adirecta sp. n. (Brazil), A. hystricosa sp. n. (Brazil), and A. simoma sp. n. (Brazil).
Thomson (2019) A revision of the Neotropical caddisfly genus Ascotrichia Flint, 1983 (Trichoptera, Hydroptilidae). PeerJ 7:e7560 https://doi.org/10.7717/peerj.7560