Development of droplet digital Polymerase Chain Reaction assays for the detection of long-finned (Anguilla dieffenbachii) and short-finned (Anguilla australis) eels in environmental samples
Freshwater eels are ecologically, and culturally important worldwide. The New Zealand long-finned eel (Anguilla dieffenbachii) and short-finned eel (Anguilla australis) are apex predators, playing an important role in ecosystem functioning of rivers and lakes. Recently, there has been a national decline in their populations due to habitat destruction and commercial harvest. The emergence of targeted environmental DNA detection methodologies provides an opportunity to enhance information about their past and present distributions. In this study we successfully developed species-specific droplet digital Polymerase Chain Reaction (ddPCR) assays to detect A. dieffenbachii and A. australis DNA in water and sediment samples. Assays utilized primers and probes designed for regions of the mitochondrial cytochrome b and 16S ribosomal RNA genes in A. dieffenbachii and A. australis, respectively. River water samples (n = 27) were analyzed using metabarcoding of fish taxa and were compared with the ddPCR assays. The presence of A. dieffenbachii and A. australis DNA was detected in a greater number of water samples using ddPCR in comparison to metabarcoding. There was a strong and positive correlation between gene copies (ddPCR analyses) and relative eel sequence reads (metabarcoding analyses) when compared to eel biomass. These ddPCR assays provide a new method for assessing spatial distributions of A. dieffenbachii and A. australis in a range of environments and sample types.
Thomson-Laing et al. (2021) Development of droplet digital Polymerase Chain Reaction assays for the detection of long-finned (Anguilla dieffenbachii) and short-finned (Anguilla australis) eels in environmental samples. PeerJ 9:e12157 https://doi.org/10.7717/peerj.12157
Evaluation of the molluscicidal activities of arylpyrrole on Oncomelania hupensis, the intermediate host of Schistosoma japonicum
The snail Oncomelania hupensis is the only intermediate host of the highly invasive parasite Schistosoma japonicum. Molluscicide is often used to curb transmission of S. japonicum. Niclosamide, the only World Health Organization (WHO) recognized molluscicide, presents major drawbacks, including high cost and toxicity towards aquatic animals. In the present study, a number of aryl pyrrole derivatives (ADs) were synthesized to serve as potential molluscicides and were tested on O. hupensis. To uncover the underlying mechanisms, adenosine triphosphate (ATP) and adenosine diphosphate (ADP) levels were assessed in the soft body of ADs-exposed O. hupensis, using high performance liquid chromatography (HPLC). The effect of C6 on key points of energy metabolism (the activities of complexes I, III, IV and the membrane potential) was determined. We demonstrated that the Compound 6 (C6, 4-bromo-1-(bromomethyl)-2-(4-chlorophenyl)-5-(trifluoromethyl)-1H-pyrrole-3-carbonitrile) exerted the strongest molluscicidal activity against adult O. hupensis at LC50 of 0.27, 0.19, and 0.13 mg/L for 24, 48, and 72 h respectively. Moreover, we found that the bromide on the pyrrole ring of C6 was essential for molluscicidal activity. Furthermore, the ATP content reduced from 194.46 to 139.75 μg/g after exposure to 1/2 LC50, and reduced to 93.06 μg/g after exposure to LC50. ADP, on the other hand, remained the same level before and after C6 exposure. We found that C6, at 1/2 LC50, reduced the membrane potential of O. hupensis, while no significant changes were observed in the activities of complexes I, III, and IV. C6 was identified with excellent activities on O. hupensis. The obtained structure−activity relationship and action mechanism study results should be useful for further compound design and development.
Xing et al. (2021) Evaluation of the molluscicidal activities of arylpyrrole on Oncomelania hupensis, the intermediate host of Schistosoma japonicum. PeerJ 9:e12209 https://doi.org/10.7717/peerj.12209
Effect of control measures on the pattern of COVID-19 Epidemics in Japan
Background COVID-19 has spread worldwide since its emergence in 2019. In contrast to many other countries with epidemics, Japan differed in that it avoided lockdowns and instead asked people for self-control. A travel campaign was conducted with a sizable budget, but the number of PCR tests was severely limited. These choices may have influenced the course of the epidemic. Methods The increase or decrease in the classes of SARS-CoV-2 variants was estimated by analyzing the published sequences with an objective multivariate analysis. This approach observes the samples in multiple directions, digesting complex differences into simpler forms. The results were compared over time with the number of confirmed cases, PCR tests, and overseas visitors. The kinetics of infection were analyzed using the logarithmic growth rate. Results The declared states of emergency failed to alter the movement of the growth rate. Three epidemic peaks were caused by domestically mutated variants. In other countries, there are few cases in which multiple variants have peaked. However, due to the relaxation of immigration restrictions, several infective variants have been imported from abroad and are currently competing for expansion, creating the fourth peak. By April 2021, these foreign variants exceeded 80%. The chaotic situation in Japan will continue for some time, in part because no effort has been made to identify asymptomatic carriers, and details of the vaccination program are undecided.
Konishi (2021) Effect of control measures on the pattern of COVID-19 Epidemics in Japan. PeerJ 9:e12215 https://doi.org/10.7717/peerj.12215
Heterogeneity in conservation of multifunctional partner enzymes with meiotic importance, CDK2 kinase and BRCA1 ubiquitin ligase
The evolution of proteins can be accompanied by changes not only to their amino acid sequences, but also their structural and spatial molecular organization. Comparison of the protein conservation within different taxonomic groups (multifunctional, or highly specific) allows to clarify their specificity and the direction of evolution. Two multifunctional enzymes, cyclin-dependent kinase 2 (CDK2) and BRCA1 ubiquitin ligase, that are partners in some mitotic and meiotic processes were investigated in the present work. Two research methods, bioinformatics and immunocytochemical, were combined to examine the conservation levels of the two enzymes. It has been established that CDK2 is a highly conserved protein in different taxonomic lineages of the eukaryotic tree. Immunocytochemically, a conserved CDK2 pattern was revealed in the meiotic autosomes of five rodent species and partially in domestic turkey and clawed frog. Nevertheless, variable CDK2 distribution was detected at the unsynapsed segments of the rodent X chromosomes. BRCA1 was shown to be highly conserved only within certain mammalian taxa. It was also noted that in those rodent nuclei, where BRCA1 specifically binds to antigens, asynaptic regions of sex chromosomes were positive. BRCA1 staining was not always accompanied by specific binding, and a high nonspecificity in the nucleoplasm was observed. Thus, the studies revealed different conservation of the two enzymes at the level of protein structure as well as at the level of chromosome behavior. This suggests variable rates of evolution due to both size and configuration of the protein molecules and their multifunctionality.
Matveevsky et al. (2021) Heterogeneity in conservation of multifunctional partner enzymes with meiotic importance, CDK2 kinase and BRCA1 ubiquitin ligase. PeerJ 9:e12231 https://doi.org/10.7717/peerj.12231
The modeled distribution of corals and sponges surrounding the Salas y Gómez and Nazca ridges with implications for high seas conservation
The Salas y Gómez and Nazca ridges are two adjacent seamount chains off the west coast of South America that collectively contain more than 110 seamounts. The ridges support an exceptionally rich diversity of benthic and pelagic communities, with the highest level of endemism found in any marine environment. Despite some historical fishing in the region, the seamounts are relatively pristine and represent an excellent conservation opportunity to protect a global biodiversity hotspot before it is degraded. One obstacle to effective spatial management of the ridges is the scarcity of direct observations in deeper waters throughout the region and an accompanying understanding of the distribution of key taxa. Species distribution models are increasingly used tools to quantify the distributions of species in data-poor environments. Here, we focused on modeling the distribution of demosponges, glass sponges, and stony corals, three foundation taxa that support large assemblages of associated fauna through the creation of complex habitat structures. Models were constructed at a 1 km2 resolution using presence and pseudoabsence data, dissolved oxygen, nitrate, phosphate, silicate, aragonite saturation state, and several measures of seafloor topography. Highly suitable habitat for each taxa was predicted to occur throughout the Salas y Gómez and Nazca ridges, with the most suitable habitat occurring in small patches on large terrain features such as seamounts, guyots, ridges, and escarpments. Determining the spatial distribution of these three taxa is a critical first step towards supporting the improved spatial management of the region. While the total area of highly suitable habitat was small, our results showed that nearly all of the seamounts in this region provide suitable habitats for deep-water corals and sponges and should therefore be protected from exploitation using the best available conservation measures.
Georgian et al. (2021) The modeled distribution of corals and sponges surrounding the Salas y Gómez and Nazca ridges with implications for high seas conservation. PeerJ 9:e11972 https://doi.org/10.7717/peerj.11972
New free-living nematode species and records (Chromadorea: Plectida and Desmodorida) from the edge and axis of Kermadec Trench, Southwest Pacific Ocean
One new nematode species is described and two new species records are provided from the edge (6,080 m depth) and axis (7,132 m) of Kermadec Trench, Southwest Pacific. Leptolaimus hadalis sp. nov. is characterised by medium body 587–741 μm long, labial region not offset from body contour, inconspicuous labial sensilla, amphid located 12–19 μm from anterior end, female without supplements, male with four tubular precloacal supplements (alveolar supplements absent), tubular supplements almost straight with dentate tip, arcuate spicules and weakly cuticularized dorsal gubernacular apophyses strongly bent distally. In a previously published ecological survey of Kermadec Trench, L. hadalis sp. nov. was the most abundant species in a core obtained at 8,079 m water depth and third most abundant species in a core obtained at 7,132 m, while only one individual was found at 6,096 m depth, and none at 9,175 m depth (Leduc & Rowden, 2018). Alaimella aff. cincta and Desmodora aff. pilosa are recorded for the first time from the Southwest Pacific region. Prior to the present study, Alaimella had only been recorded from coastal locations and from the Weddell sea to a depth of 2,000 m. The record of Desmodora aff. pilosa at 6,080 m depth is the deepest record of a Desmodora species to date, although unidentified Desmodora specimens have been found as deep as 6,300 m in the South Sandwich Trench. The morphology of the Kermadec Trench Alaimella aff. cincta and Desmodora aff. pilosa specimens bear a strong resemblance to their respective type populations from the Northern Hemisphere, but further morphological and molecular data are required to ascertain whether they in fact represent distinct species.
Leduc (2021) New free-living nematode species and records (Chromadorea: Plectida and Desmodorida) from the edge and axis of Kermadec Trench, Southwest Pacific Ocean. PeerJ 9:e12037 https://doi.org/10.7717/peerj.12037
Quantitative trait locus mapping analysis of multiple traits when using genotype data with potential errors
Background Quantitative trait locus (QTL) analysis aims to locate and estimate the effects of the genes influencing quantitative traits and infer the relationship between gene variants and changes in phenotypic characteristics using statistical methods. Some methods have been developed to map QTLs of multiple traits in the case of no genotype error in a given dataset. However, practical genetic data that people use may contain some potential errors because of the limitations of biotechnology. Common genetic data correction methods can only reduce errors, but cannot calculate the degree of error. In this paper, we propose a QTL mapping strategy for multiple traits in the presence of genotype errors. Methods The additive effect, dominant effect, recombination rate, error rate, and other parameters of QTLs can be simultaneously obtained using this new method in the framework of multiple-interval mapping. Results Our simulation results show that the accuracy of parameter estimation can be improved by considering the errors of marker genotypes during the analysis of genetic data. Real data analysis also shows that the new method proposed in this paper can map the QTLs of multiple traits more accurately.
Tong et al. (2021) Quantitative trait locus mapping analysis of multiple traits when using genotype data with potential errors. PeerJ 9:e12187 https://doi.org/10.7717/peerj.12187
Bilateral back squat strength is increased during a 3-week undulating resistance training program with and without variable resistance in DIII collegiate football players
Background Optimizing training adaptations is of the utmost importance for the strength and conditioning professional. The pre-season of any sport is particularly important to ensure preparedness of the athletes. In DIII Collegiate Football pre-season consists of approximately 3 weeks. The abbreviated time of the pre-season increases the importance of optimizing training using safe methods, including alternative loading strategies. The purpose of the current study was to determine if a 3-week variable resistance training VRT during an undulating (UL) resistance training program elicited a greater increase in back squat strength compared to traditional loading methods. Methods and Materials Forty DIII Football players (age range: 18–25 years) participated in a 3-week UL bilateral back squat (BBS) program. Both groups performed the BBS 3 times per week with a minimum of 24 hours between exercise sessions. The control group (C) (n = 20) (height = 182.3 + 5.1 cm, body mass: pre = 102.8 ± 17.7 kg, post = 104.1 ± 17.8 kg) used traditional loading methods (i.e., Olympic weights only) and the experimental group (E) (n = 20) (height = 180.7 ± 8.0 cm, body mass: pre = 100.3 ± 27.1 kg, post = 101.0 ± 27.7 kg) used traditional loading methods and variable resistance (i.e., resistance bands). The variable resistance accounted for approximately 20% of the total resistance while 80% of the resistance was supplied by traditional loading methods. Results When all data was pooled, subjects had a significant increase (p < 0.05) in 1-RM BBS from pre (154.2 + 26.1 kg) to post (166.8 + 26.2 kg), with a percent increase of 8.13% at the completion of the 3-week training program. There was no significant difference (p > 0.05) between the C and E groups for muscular strength, muscular power, or vertical jump. Volume-loads were not significantly (p > 0.05) different between groups for any of the weeks (C: Week 1 = 858.1 + 101.3, Week 2 = 588.6 + 69.2, Week 3 = 332.5 + 38.9, Total = 1179.2 + 209.4 vs. E: Week 1 = 835.2 + 179.7, Week 2 = 572.2 + 123.4, Week 3 = 323.5 + 68.8, Total = 1730.9 + 371.8) or for the pre-season as a whole. Conclusion A traditional UL resistance training program and training program with variable resistance are both effective methods at increasing back squat strength during 3 weeks of training. Resistance band variable resistance (VR) does not enhance training effects within a 3-week mesocycle greater than traditional resistance.
Sawyer et al. (2021) Bilateral back squat strength is increased during a 3-week undulating resistance training program with and without variable resistance in DIII collegiate football players. PeerJ 9:e12189 https://doi.org/10.7717/peerj.12189
Novel real-time PCR based assays for differentiating fall armyworm strains using four single nucleotide polymorphisms
The fall armyworm, Spodoptera frugiperda, is a polyphagous global pest with a preference for gramineous crops such as corn, sorghum and pasture grasses. This species is comprised of two morphologically identical but genetically distinct host strains known as the corn and rice strains, which can complicate pest management approaches. Two molecular markers are commonly used to differentiate between strains, however, discordance between these markers can lead to inconclusive strain identification. Here, we used double digest restriction site associated DNA sequencing to identify diagnostic single nucleotide polymorphisms (SNPs) with alleles unique to each strain. We then used these strain-specific SNPs to develop four real-time PCR based TaqMan assays to rapidly and reliably differentiate between strains and interstrain hybrids. These assays provide a new tool for differentiating between strains in field-collected samples, facilitating future studies on strain population dynamics and interstrain hybridization rates. Understanding the basic ecology of S. frugiperda strains is necessary to inform future management strategies.
Tessnow et al. (2021) Novel real-time PCR based assays for differentiating fall armyworm strains using four single nucleotide polymorphisms. PeerJ 9:e12195 https://doi.org/10.7717/peerj.12195
Efficacy of 4% articaine vs 2% lidocaine in mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis: a systematic review and meta-analysis
Objective The goal of this systematic review and meta-analysis is to determine the performance of 4% Articaine vs. 2% Lidocaine for mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis (IP). Methods PubMed/MEDLINE, Cochrane Central Register of Controlled Trials, Web of Science, Google Scholar, and Open Gray were used to conduct a thorough literature search. A manual search of the reference lists of the publications found was also carried out. Two reviewers critically evaluated the papers for inclusion and exclusion criteria, and data extraction was done on the selected publications. The Cochrane Collaboration Tool and the Minors checklist were used to assess the quality of the selected studies for randomised controlled trials (RCTs) and non-randomised studies, respectively. The RevMan software was used to perform a meta-analysis of the pooled data and subgroups according to the technique of anaesthetic solution delivery, as well as a sensitivity analysis (P < 0.05). Results A total of twenty-six papers were included in the qualitative synthesis, with twenty-two of them being included in the meta-analysis. There were fifteen studies with a low potential for bias, three with a moderate potential for bias, and seven with a high potential for bias. The combined results of the 19 trials in the tooth level unit revealed that 4% articaine had a success rate 1.37 times greater than 2% lidocaine for mandibular teeth (RR, 1.37; 95% CI [1.17–1.62]; P = 0.0002). For the maxillary buccal infiltration method, the combined results from the three trials revealed that 4% articaine resulted in a success rate 1.06 times greater than 2% lidocaine (RR, 1.06; 95% CI [0.95–1.2]; P = 0.3). Excluding subgroups with a single study in sensitivity analysis for mandibular teeth revealed a substantial improvement in the success rate of the articaine group in treating IP when compared to the lidocaine group. Conclusion The findings of this meta-analysis back up the claim that articaine is more effective than lidocaine in providing anaesthesia in patients with IP. PROSPERO Registration No.: CRD42020204606 (https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020204606).
Miglani et al. (2021) Efficacy of 4% articaine vs 2% lidocaine in mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis: a systematic review and meta-analysis. PeerJ 9:e12214 https://doi.org/10.7717/peerj.12214