Mutational spectra of SARS-CoV-2 isolated from animals
Coronaviruses are ubiquitous and infect a wide spectrum of animals and humans. The newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a worldwide pandemic. To address the role that animals may play in the evolution of SARS-CoV-2, the full genome sequences of SARS-CoV-2 isolated from animals were compared with SARS-CoV-2 human isolates from the same clade and geographic region. Phylogenetic analysis of SARS-CoV-2 isolated from the cat, dog, mink, mouse, and tiger revealed a close relationship with SARS-CoV-2 human isolates from the same clade and geographic region with sequence identities of 99.94–99.99%. The deduced amino acid sequence of spike (S) protein revealed the presence of a furin cleavage site (682RRAR▾685), which did not differ among all SARS-CoV-2 isolates from animals and humans. SARS-CoV-2 isolates from minks exhibited two amino acid substitutions (G261D, A262S) in the N-terminal domain of S protein and four (L452M, Y453F, F486L, N501T) in the receptor-binding motif (RBM). In the mouse, the S protein had two amino acid substitutions, one in the RBM (Q498H) and the other (N969S) in the heptad repeat 1. SARS-CoV-2 isolated from minks furtherly exhibited three unique amino acid substitutions in the nucleocapsid (N)protein. In the cat, two unique amino acid substitutions were discovered in the N (T247I) and matrix (T175M) proteins. Additionally, SARS-CoV-2 isolated from minks possessed sixteen, four, and two unique amino acid substitutions in the open reading frame 1ab (ORF1ab), ORF3a, and ORF6, respectively. Dog and cat SARS-CoV-2 isolates showed one and seven unique amino acid substitutions in ORF1ab, respectively. Further studies may be necessary to determine the pathogenic significance of these amino acid substitutions to understand the molecular epidemiology and evolution of SARS-CoV-2.
Elaswad et al. (2020) Mutational spectra of SARS-CoV-2 isolated from animals. PeerJ 8:e10609 https://doi.org/10.7717/peerj.10609
Psychosocial variables and quality of life during the COVID-19 lockdown: a correlational study on a convenience sample of young Italians
Background In 2020, to limit the spread of Coronavirus (COVID-19), many countries, including Italy, have issued a lengthy quarantine period for the entire population. For this reason lifestyle has changed, bringing inevitable repercussions to the Quality of Life (QoL). The present study aims to identify which psychosocial variables predict behaviors capable of affecting the QoL during the lockdown period, potentially highlighting factors that might promote well-being and health in the Italian population during the epidemic. Methods Between 27 April 2020 and 11 May 2020, we administered a web-survey to a sample of young Italian people (age M = 21.2; SD = 3.5; female = 57.7% of the sample). Employing variance-based structural equation modeling, we attempted to identify whether social connectedness, social support, and loneliness were variables predictive of the QoL of young Italians. We also sought to identify specific psychological factors, such as symbolic threat, realistic threat, and the threat from potentially contaminated objects, was correlated to COVID-19 fear and whether engaging in particular behaviors was likely to improve the QoL. Results Our results suggest that social connectedness and loneliness are significant predictors of QoL, while social support did not have a significant effect on QoL. Furthermore, we observed that symbolic and realistic threats and the threat from potentially contaminated objects are significant and positive predictors of COVID-19 fear. Moreover, COVID-19 fear had significant and positive relationships with the carrying out of specific behaviors, such as creative activities during the isolation period and that this related to affirming individuals’ country-specific identity. Finally, COVID-19 fear is a significant predictor of behavioral factors related to the adherence to public health advice in line with national guidance regarding the containment of COVID-19; this factor, however, did not correlate with QoL. Conclusion Our results suggest the importance of social context and psychological factors to help devise intervention strategies to improve the QoL during lockdown from epidemic events and, in particular, support the importance of promoting social communication and accurate information about the transmission of the virus.
Lardone et al. (2020) Psychosocial variables and quality of life during the COVID-19 lockdown: a correlational study on a convenience sample of young Italians. PeerJ 8:e10611 https://doi.org/10.7717/peerj.10611
Optimal voluntary and mandatory insect repellent usage and emigration strategies to control the chikungunya outbreak on Reunion Island
In 2005, a chikungunya virus outbreak devastated the tropical island of Reunion, infecting a third of the total population. Motivated by the Reunion Island case study, we investigate the theoretic potential for two intervention measures under both voluntary and mandatory protocols to control a vector-borne disease when there is risk of the disease becoming endemic. The first measure uses insect repellent to prevent mosquito bites, while the second involves emigrating to the neighboring Mauritius Island to avoid infection. There is a threshold on the cost of using repellent above which both voluntary and mandatory regimes find it optimal to forgo usage. Below that threshold, mandatory usage protocols will eradicate the disease; however, voluntary adoption leaves the disease at a small endemic level. Emigrating from the island to avoid infection results in a tragedy-of-the-commons effect: while being potentially beneficial to specific susceptible individuals, the remaining islanders paradoxically face a higher risk of infection. Mandated relocation of susceptible individuals away from the epidemic is viable only if the cost of this relocation is several magnitudes lower than the cost of infection. Since this assumption is unlikely to hold for chikungunya, it is optimal to discourage such emigration for the benefit of the entire population. An underlying assumption about the conservation of human-vector encounter rates in mosquito biting behavior informs our conclusions and may warrant additional experimental verification.
Klein et al. (2020) Optimal voluntary and mandatory insect repellent usage and emigration strategies to control the chikungunya outbreak on Reunion Island. PeerJ 8:e10151 https://doi.org/10.7717/peerj.10151
A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment
Background The importance of the inland fisheries sector in food security as a provider of much-needed protein and income supplier has been highlighted. This is especially the case in poor rural communities in developing countries. Inland capture fisheries in Thailand are in place nationwide in rivers, lakes, swamps and reservoirs. The clown featherback (Chitala ornata) is popularly consumed and is an economically important fish in Thailand which is often used in food products such as fish balls and fish cakes. Along with other fish species, the clown featherback is one of fish of inland fisheries at Phayao Lake. Recent fish surveys from 2016-2018 at Phayao Lake using netting and electrofishing found that the number of clown featherback have been reducing since 2016 and could not be detected at all by 2018. This is despite the fact that there are still reports of their presence in the lake from locals. Methods We developed an eDNA-based method for detection of the clown featherback in Phayao Lake as an alternative tool. Water samples were collected in three different sampling months (February, June and September) at six sites located in the lake. Species-specific primers and the probe were designed to amplify a 183 bp fragment of the cytB region of the clown featherback. Results eDNA of the clown featherback can be detected in all different sampling months and sites. Concentration of the clown featherback found in Prayao Lake showed no difference over sampling month but between collecting sites. This proves that eDNA based survey is a sensitive and useful tool for monitoring and surveying the clown featherback at any time of the year.
Osathanunkul et al. (2020) A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment. PeerJ 8:e10338 https://doi.org/10.7717/peerj.10338
The effect of decay and lexical uncertainty on processing long-distance dependencies in reading
To make sense of a sentence, a reader must keep track of dependent relationships between words, such as between a verb and its particle (e.g. turn the music down). In languages such as German, verb-particle dependencies often span long distances, with the particle only appearing at the end of the clause. This means that it may be necessary to process a large amount of intervening sentence material before the full verb of the sentence is known. To facilitate processing, previous studies have shown that readers can preactivate the lexical information of neighbouring upcoming words, but less is known about whether such preactivation can be sustained over longer distances. We asked the question, do readers preactivate lexical information about long-distance verb particles? In one self-paced reading and one eye tracking experiment, we delayed the appearance of an obligatory verb particle that varied only in the predictability of its lexical identity. We additionally manipulated the length of the delay in order to test two contrasting accounts of dependency processing: that increased distance between dependent elements may sharpen expectation of the distant word and facilitate its processing (an antilocality effect), or that it may slow processing via temporal activation decay (a locality effect). We isolated decay by delaying the particle with a neutral noun modifier containing no information about the identity of the upcoming particle, and no known sources of interference or working memory load. Under the assumption that readers would preactivate the lexical representations of plausible verb particles, we hypothesised that a smaller number of plausible particles would lead to stronger preactivation of each particle, and thus higher predictability of the target. This in turn should have made predictable target particles more resistant to the effects of decay than less predictable target particles. The eye tracking experiment provided evidence that higher predictability did facilitate reading times, but found evidence against any effect of decay or its interaction with predictability. The self-paced reading study provided evidence against any effect of predictability or temporal decay, or their interaction. In sum, we provide evidence from eye movements that readers preactivate long-distance lexical content and that adding neutral sentence information does not induce detectable decay of this activation. The findings are consistent with accounts suggesting that delaying dependency resolution may only affect processing if the intervening information either confirms expectations or adds to working memory load, and that temporal activation decay alone may not be a major predictor of processing time.
Stone et al. (2020) The effect of decay and lexical uncertainty on processing long-distance dependencies in reading. PeerJ 8:e10438 https://doi.org/10.7717/peerj.10438
Digitizing abdominal palpation with a pressure measurement and positioning device
An abdominal physical examination is one of the most important tools in evaluating patients with acute abdominal pain. We focused on palpation, in which assessment is made according to the patient’s response and force feedback. Since palpation is performed manually by the examiner, the uniformity of force and location is difficult to achieve during examinations. We propose an integrated system to quantify palpation pressure and location. A force sensor continuously collects pressure data, while a camera locates the precise position of contact. The system recorded, displayed average and maximum pressure by creating a pressure/time curve for computer-aided diagnosis. Compared with previous work on pressure sensors of quantifying abdominal palpation, our proposed system is the integrated approach to measure palpation force and track the corresponding position at the same time, for further diagnosis. In addition, we only make use of a sensing device and a general web camera, rather than commercial algometry and infrared cameras used in the previous work. Based on our clinical trials, the statistics of palpation pressure values and the corresponding findings are also reported. We performed abdominal palpation with our system for twenty-three healthy participants, including fourteen males and nine females. We applied two grades of force on the abdomen (light and deep) by four-quadrant and nine-region schemes, record the value of pressure and location. In the four-quadrant scheme, the average pressures of abdominal palpation with light and deep force levels were 0.506(N) and 0.552(N), respectively. In the nine-region scheme, the average pressures were 0.496(N) and 0.577(N), respectively. Two episodes of contact dermal reaction were identified. According to our experiment statistics, there is no significant difference in the force level between the four-quadrant and nine-region scheme. Our results have the potential to be used as a reference guide while designing digital abdominal palpation devices.
Hsu et al. (2020) Digitizing abdominal palpation with a pressure measurement and positioning device. PeerJ 8:e10511 https://doi.org/10.7717/peerj.10511
Distribution and species diversity of the floating green macroalgae and micro-propagules in the Subei Shoal, southwestern Yellow Sea
Massive floating green macroalgae have formed harmful green tides in the Yellow Sea since 2007. To study the early development and the associated environmental factors for the green tide, a field survey was carried out in the Subei Shoal, southwestern Yellow Sea. Multiple species were identified in both floating green macroalgae and micro-propagules , while their abundances showed distinct spatial variations. The floating macroalgal biomass was widespread in the northern Subei Shoal and most abundant at 34°N. Ulva prolifera dominated (91.2% in average) the floating macroalgae, and the majority (88.5%) of U. prolifera was the ‘floating type’. In comparison, the micro-propagules were most abundant around the aquaculture rafts, and decreased significantly with the distance to the rafts. The dominant species of micro-propagules was U. linza (48.5%), followed by U. prolifera (35.1%). Their distinct distribution patterns and species diversity suggested little direct contribution of micro-propagules for the floating macroalgae. The spatial variation of the floating macroalgae was probably a combined result from the biomass source and environmental factors, while the abundance of micro-propagules was closely associated with the rafts. A positive correlation between the floating macroalgae and DO was observed and suggested active photosynthesis of the initial biomass in Subei Shoal. This study revealed specific distributional pattern and relationships among the floating macroalgae, micro-propagules and the environmental factors in the source region, which helps understanding the early blooming dynamics of the green tides in Yellow Sea.
Miao et al. (2020) Distribution and species diversity of the floating green macroalgae and micro-propagules in the Subei Shoal, southwestern Yellow Sea. PeerJ 8:e10538 https://doi.org/10.7717/peerj.10538
Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery
Background Panulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region. Methods This study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus. Results Using a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5′ ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3′ ETS (287 bp). A total of 1,281 SSRs were identified.
Baeza (2020) Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery. PeerJ 8:e10554 https://doi.org/10.7717/peerj.10554
bmd: an R package for benchmark dose estimation
The benchmark dose (BMD) methodology is used to derive a hazard characterization measure for risk assessment in toxicology or ecotoxicology. The present paper’s objective is to introduce the R extension package bmd, which facilitates the estimation of BMD and the benchmark dose lower limit for a wide range of dose-response models via the popular package drc. It allows using the most current statistical methods for BMD estimation, including model averaging. The package bmd can be used for BMD estimation for binomial, continuous, and count data in a simple set up or from complex hierarchical designs and is introduced using four examples. While there are other stand-alone software solutions available to estimate BMDs, the package bmd facilitates easy estimation within the established and flexible statistical environment R. It allows the rapid implementation of available, novel, and future statistical methods and the integration of other statistical analyses.
Jensen et al. (2020) bmd: an R package for benchmark dose estimation. PeerJ 8:e10557 https://doi.org/10.7717/peerj.10557
Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas
Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA, USA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and three adjacent genes are collectively similar to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of large modular toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though fleas in wild populations mostly harbor wCfeT alone. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism.
Driscoll et al. (2020) Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas. PeerJ 8:e10646 https://doi.org/10.7717/peerj.10646