Five decades of change in somatic growth of Pacific hake from Puget Sound and Strait of Georgia
Declines in fish body size have been reported in many populations and these changes likely have important ramifications for the sustainability of harvested species and ecosystem function. Pacific hake, Merluccius productus, have shown declines in size over the last several decades for populations located in Puget Sound (PS), Washington, USA, and Strait of Georgia (SoG), British Columbia, Canada. To examine this decrease in size, we used archived otoliths from both populations to assess when the decrease in somatic growth occurred and explored what factors and processes might explain the decline, including otolith microchemistry to infer the environment experienced by fish at different ages. Results indicated that substantial changes in juvenile somatic growth have occurred across decades. The divergence in body size occurred in the second summer, whereby SoG fish grew, on average, 18% more than PS fish. Within the PS population, somatic growth differed significantly among fish that hatched in the 1980s, 1990s, and 2010s, such that the more recently hatched fish grew 26% more in their first summer and 71% less in their second summer relative to those that hatched in the 1980s. In comparison, growth of SoG fish did not differ between those that hatched in 1970s and 1990s. For both populations growth in the first and third summer was positively and negatively related, respectively, to the abundance of harbor seals, while growth in the first and second summer was negatively related to salinity. Overall, this study highlights the complicated nature of Pacific hake population recovery under dynamic, and typically uncontrollable, variation in biotic and abiotic conditions.
Chittaro et al. (2022) Five decades of change in somatic growth of Pacific hake from Puget Sound and Strait of Georgia. PeerJ 10:e13577 https://doi.org/10.7717/peerj.13577
Assessing availability of European plant protection product data: an example evaluating basic area treated
Besides the benefits of plant protection products (PPPs) for agricultural production, there is an increasing acknowledgement of the associated potential environmental risks. Here, we examine the feasibility of summarizing the extent of PPP usage at the country level, using Ireland as a case study, as well as at the European level. We used the area over which PPPs are applied (basic area) as an example variable that is relevant to initially assess the geographic extent of environmental risk. In Irish agricultural systems, which are primarily grass-based, herbicides fluroxypyr and glyphosate are the most widely applied active substances (ASs) in terms of basic area, followed by the fungicides chlorothalonil and prothioconazole that are closely associated with arable crops. Although all EU countries are subject to Regulation (EC) No 1185/2009, which sets the obligation of PPP usage data reporting at the national level, we only found usable data that met our criteria for Estonia, Germany, Finland, and Spain (4 of 30 countries reviewed). Overall, the most widely applied fungicide and herbicide in terms of basic area were prothioconazole (20%, 7% and 5% of national cultivated areas of Germany, Estonia and Ireland) and glyphosate (11%, 8% and 5% of national cultivated areas of Spain, Estonia and Ireland) respectively, although evaluations using application frequency may result in the observation of different trends. Several recommendations are proposed to tackle current data gaps and deficiencies in accessibility and usability of pesticide usage data across the EU in order to better inform environmental risk assessment and promote evidence-based policymaking.
Environmental Contamination and Remediation
López-Ballesteros et al. (2022) Assessing availability of European plant protection product data: an example evaluating basic area treated. PeerJ 10:e13586 https://doi.org/10.7717/peerj.13586
Seeds harvested during mowing from semi-natural grasslands as an ad hoc but effective solution for grassland restoration
Species-rich grasslands formed by local ecotypes of native species provide numerous ecosystem services both in rural areas as well as urban grasslands. Nonetheless, their area is still too small, making grasslands one of the most frequently restored habitats. Successful restoration requires high-quality seed material, which is expensive and often not easy to acquire. In this study, we tested the potential of seeds accidentally collected during the mowing of a semi-natural grassland for grassland restoration. We tested seed purity, species composition, and germination capability in both laboratory and field conditions. Ninety percent of the collected material consisted of pure seeds of numerous species. Their germination capability was relatively low but still sufficient for successful grassland restoration under a typical seed density/mass per unit area seeding ratio. The germination capacity was the highest in the first two weeks after sowing and increased with overwintering seed storage. The results suggested that the seeds could be successfully used for species-rich grassland restoration. In terms of advantages, the seed mixture had a low cost and contained native species seeds representing local ecotypes. In terms of disadvantages, there was a relatively low amount of seed material and an inability to plan the time of seed harvesting. Thus, the use of the accidentally collected seeds can be considered an effective but rather ad hoc solution.
Perera et al. (2022) Seeds harvested during mowing from semi-natural grasslands as an ad hoc but effective solution for grassland restoration. PeerJ 10:e13621 https://doi.org/10.7717/peerj.13621
Genetic population structure and reproductive system of two invasive Asian earthworms, Amynthas tokioensis and Amynthas agrestis
The invasive Asian earthworms, Amynthas tokioensis and A. agrestis, have been successful in entering North American forests in recent decades, with significant damage to both soils and above-ground environments. This success could be driven in part by a polyploid genetic system and parthenogenetic reproduction, often suggested as benefits for invasive species. Therefore, we assessed the genetic population structure, genetic diversity, and reproductive system of both species using morphological traits and panels of microsatellite markers. A total of 216 A. tokioensis and 196 A. agrestis from six sites in Vermont USA were analyzed. Although all worms were morphologically hermaphroditic, all the A. agrestis lacked the male pore (the structure allowing pass of sperm between individuals), and only 19% of the A. tokioensis possessed the male pore. All A. tokioensis earthworms were triploid (scored for three alleles for at least 1 locus, and usually several), and A. agrestis was a mix of triploid and diploid individuals. Notable was the high proportion (80%) of A. agrestis earthworms that were diploid at one site. There was clearly clonal reproduction, with identical seven- locus genotypes observed for earthworms from each site, with as many as 45 individuals with the identical genotype at one site. However, the earthworms were also genetically diverse, with 14 genotypes observed for A. tokioensis and 54 for A. agrestis, and with many singleton genotypes (a single individual). Most genotypes (71% for A. tokioensis and 92% for A. agrestis) were found at a single site. The greatest number of genotypes was found at a commercial nursery where fully 23/26 A. agrestis earthworms were singleton genotypes. As expected for the pattern of private clone alleles at sites, several measures of geographic genetic differentiation were positive, and as expected for triploid systems, an AMOVA analysis showed high within-individual genetic diversity. The paradox of clear clonal reproduction, but with a great number of genotypes for each species, and the mix of triploid and diploid individuals could be explained if the worms have been sexually reproductive, with the switch to the uniparental system only recently (or even if sexual reproduction is episodic). Last, a large number of microsatellite loci were recovered for each species and there sequence and suggested PCR primers are provided for free use by other researchers.
Nouri-Aiin et al. (2022) Genetic population structure and reproductive system of two invasive Asian earthworms, Amynthas tokioensis and Amynthas agrestis. PeerJ 10:e13622 https://doi.org/10.7717/peerj.13622
Changes in the core species of the ant-plant network of oak forest converted to grassland: replacement of its ant functional groups
Land-use change in terrestrial environments is one of the main threats to biodiversity. The study of ant-plant networks has increased our knowledge of the diversity of interactions and structure of these communities; however, little is known about how land-use change affects ant-plant networks. Here we determine whether the change in land use, from native oak forest to induced grassland, affected the network properties of ant-plant networks in a temperate forest in Mexico. We hypothesize that the disturbed vegetation will be more nested and generalized due to the addition of generalist species to the network. The oak forest network comprises 47 plant species and 11 ant species, while the induced grassland network has 35 and 13, respectively. Floral nectar was the resource used most intensely by the ants in both vegetation types. The ant-plant network of the induced grassland was significantly more nested and generalist than that of the oak forest; however, none of the networks were nested when considering the frequency of interaction. In both vegetation types, the ants were more specialized than the plants, and niche overlap was low. This could be related to the dominant species present in each type of vegetation: Prenolepis imparis in the oak forest and Camponotus rubrithorax in the grassland. The central core of cold climate ant species in the oak forest was replaced by a central core of subordinate Camponotini and tropical specialists in the induced grassland. These results suggest that the increase in nestedness and generalization in the grassland may be related to the loss of the cold climate specialists from the core of the oak forest network. Our findings provide evidence that land-use change increases the level of generalization in the ant-plant interaction networks of temperate forests.
Cuautle et al. (2022) Changes in the core species of the ant-plant network of oak forest converted to grassland: replacement of its ant functional groups. PeerJ 10:e13679 https://doi.org/10.7717/peerj.13679
Oxygen uptake efficiency slope in healthy normal weight young males: an applicable framework for calculation and interpretation
Background The oxygen uptake efficiency slope (OUES) is considered a reliable indicator of cardiorespiratory fitness in young and clinical populations who cannot achieve maximal effort during a graded exercise test. However, OUES accuracy depends on the data points used for its calculation and it is still not clear if the submaximal OUES can accurately assess CRF in healthy young males. Objective We investigated the association between peak oxygen uptake and peak and submaximal OUES, and the agreement between submaximal OUES and peak OUES in male adolescents and young adults. Methods In this cross-sectional, observational study, fifty normal weight healthy participants (age 14–22 years, peak oxygen uptake 43.8 ± 7.3 mL·min−1·kg−1) performed a graded exercise test on a cycle ergometer and pulmonary gas exchange was assessed using breath-by-breath analysis. Peak oxygen uptake, and oxygen consumption at the aerobic and at the anaerobic threshold were determined as the 30-s average of the oxygen consumption values. Peak OUES (up to peak) and submaximal OUES (up to the aerobic and anaerobic thresholds) were calculated from the logarithmic relation between oxygen consumption and pulmonary ventilation. Results Very strong correlations were observed between peak oxygen uptake and peak OUES (r = 0.80–0.88) while fair-to-very strong correlations were observed between the peak oxygen uptake and the two submaximal OUES (r = 0.32–0.81). The level of agreement between peak OUES and OUES up to the anaerobic threshold (r = 0.89–0.93; Typical percentage error 6%; Intraclass correlation coefficient = 0.89–0.93) was greater than the one between the peak oxygen uptake with OUES up to the aerobic threshold (r = 0.39–0.56; Typical percentage error 15%; Intraclass correlation coefficient = 0.38–0.56). Conclusions . The peak OUES is a better indicator of aerobic fitness than the OUES up to the anaerobic threshold in healthy, young males. The OUES up to the anaerobic threshold is a valid alternative to peak OUES.
Falcioni et al. (2022) Oxygen uptake efficiency slope in healthy normal weight young males: an applicable framework for calculation and interpretation. PeerJ 10:e13709 https://doi.org/10.7717/peerj.13709
Are aerosol control devices effective in preventing the spread of dental aerosol?
Background In dental clinics, aerosols produced from dental instruments have become a matter of concern following breakout of coronavirus disease 19 (COVID-19) evolving into a pandemic. This study compared aerosol reduction systems and in terms of their ability to reduce Enterococcus faecalis (E. faecalis) contaminated aerosol in a simulated dental office set-up. Methods Closed clinic model with manikin and mandibular molar typodont was simulated. For 10 min, the air and water dispersed by the rotating bur mounted on an aerator was contaminated by pouring the suspension containing 1–3 × 108 CFU/mL E. faecalis directly on the bur. During and after the procedures, the air within the cabin was also sampled. CFU count was recorded and scored. The mean CFU scores obtained from agar plate count and air sampling device was compared using Kruskal–Wallis H test among groups with 5% significance threshold. Results The use of WS Aerosol Defender device led to greater CFU scores on the agars levelled to patient’s chest compared to other directions (p = 0.001). Combined use of VacStation and WS Aerosol Defender resulted in significantly decreased CFU score in the air samples compared to experimental and positive control groups (p = 0 < 0.05). Conclusions Although the devices prevented the spread of aerosol around the patient to some extent, they could not completely eliminate the contaminated aerosol load in the cabin environment.
Böke et al. (2022) Are aerosol control devices effective in preventing the spread of dental aerosol?. PeerJ 10:e13714 https://doi.org/10.7717/peerj.13714
Insights into mobile genetic elements and the role of conjugative plasmid in transferring aminoglycoside resistance in extensively drug-resistant Acinetobacter baumannii AB329
Acinetobacter baumannii is a major cause of nosocomial infection, and the incidence of extensively drug-resistant A. baumannii (XDRAB) infections has dramatically increased worldwide. In this study, we aimed to explore the complete genome sequence of XDRAB 329, ST1166/98 (Oxford/Pasteur), which is an outbreak clone from a hospital in Thailand. Whole-genome sequencing (WGS) was performed using short-read Illumina and long-read PacBio sequencing, and a conjugation assay of its plasmid was performed. The complete genome sequence of A. baumannii AB329 revealed a circular chromosome 3,948,038 bp in length with 39% GC content. Antibiotic resistance genes (ARGs), including beta-lactam resistance (blaOXA-51, blaADC-25, blaOXA-23, blaTEM-1D), aminoglycoside resistance (aph(3′)-Ia, aph(3″)-Ib, aph(6)-Id, armA), tetracycline resistance (tet(B), tet (R)), macrolide resistance (mph(E), msr(E)), and efflux pumps, were found. Mobile genetic elements (MGEs) analysis of A. baumannii AB329 revealed two plasmids (pAB329a and pAB329b), three prophages, 19 genomic islands (GIs), and 33 insertion sequences (ISs). pAB329a is a small circular plasmid of 8,731 bp, and pAB329b is a megaplasmid of 82,120 bp. aph(3′)-VIa was detected in pAB329b, and a major facilitator superfamily (MFS) transporter was detected in the prophage. Acinetobacter baumannii resistance island 4 (AbaR4) harboring tetracycline and aminoglycoside resistance was detected in the genome of A. baumannii AB329. pAB329b, which belongs to Rep-type GR6 (plasmid lineage LN_1), is a conjugative plasmid with the ability to transfer an aminoglycoside resistance gene to sodium azide-resistant A. baumannii. This study provides insights into the features of the MGEs of XDRAB, which are the main reservoir and source of dissemination of ARGs.
Khongfak et al. (2022) Insights into mobile genetic elements and the role of conjugative plasmid in transferring aminoglycoside resistance in extensively drug-resistant Acinetobacter baumannii AB329. PeerJ 10:e13718 https://doi.org/10.7717/peerj.13718
JMJD3 suppresses tumor progression in oral tongue squamous cell carcinoma patients receiving surgical resection
Background Jumonji domain-containing-3 (JMJD3) is reported to be a histone H3 lysine 27 (H3K27) demethylase and a tumor suppressor gene. The present study designed to investigate the crucial role of JMJD3 in oral tongue squamous cell carcinoma (OTSCC) patients who received surgical resection. Methods We enrolled a total of 156 OTSCC patients receiving surgical resection, including 73 patients (47%) with high expression of JMJD3 and 83 patients (53%) harboring low expression of JMJD3. Two OTSCC cell lines, SAS and Cal 27, were used to explore the modulation of cancer. GSK-J4, a potent inhibitor of JMJD3, was used to treat the two OTSCC cell lines. The Chi-square test was performed to examine between-group differences in categorical variables; the Kaplan–Meier method was used to investigate survival outcome in univariate analysis, and the Cox regression model was used for multivariate analysis. Results The median follow-up period was 59.2 months and he five-year disease-free survival (DFS) and overall survival (OS) rates were 46.2% and 50.0%, respectively. Better five-year DFS (59% versus 35%) and five-year OS (63% versus 39%) were mentioned in patients with high expression of JMJD3 compared to those with low expression of JMJD3. High expression of JMJD3 was significantly associated with superior DFS and OS in the univariate and multivariate analyses. Following successful inhibition of JMJD3 by GSK-J4, western blotting analysis showed the decreased expression of Rb and p21. Conclusion Our study showed that high expression of JMJD3 is a good prognostic factor in OTSCC patients who underwent surgical resection.
Chen et al. (2022) JMJD3 suppresses tumor progression in oral tongue squamous cell carcinoma patients receiving surgical resection. PeerJ 10:e13759 https://doi.org/10.7717/peerj.13759
Short physical performance battery as a predictor of mortality in community-dwelling older adults: a longitudinal study in the Brazilian Amazon region
Background The Short Physical Performance Battery (SPPB) is an instrument for assessing physical performance widely used in research among the elderly in multiple settings. We did not find Brazilian longitudinal studies that aimed to analyze the predictive capacity and accuracy of the SPPB among community-dwelling older adults and no systematic reviews were found on the accuracy of the SPPB in predicting mortality in community- dwelling older adults. This study aimed to analyze the capacity and accuracy of the SPPB for predicting mortality in community-dwelling older adults, as well as to determine cut-off points for men and women. Method Longitudinal observational study conducted with 411 (70.1 ± 7.25 years) community-dwelling older adults, between 2017 and 2020 (37.7 ± 6.24 months). Physical performance was evaluated using the SPPB and information on the all-cause mortality rate was also recorded. Multivariate Cox regression analyses and curves were performed using the Kaplan–Meier method. Receiver Operating Characteristic (ROC) curves were constructed, with the parameters of area under the ROC curve (AUC) to determine cutoff points for discriminating mortality, considering a significance level of 5% (p < 0.05) and 95% confidence interval (CI) 95%. Results Older adults with very low and low physical performance in the SPPB, showed higher risks of mortality (HR = 9.67; 95% CI [1.20–77.65]; HR = 4.06; 95% CI [1.09–15.01]), respectively. In the subtest’s analysis, older adults with low performance in the balance (HR = 0.54; 95% CI [0.36–0.81]) and gait speed tests (HR = 0.50; 95% CI [0.33–0.76]) showed greater risks of dying. The same was reproduced for categories in each test (participants that scored 2 points in the balance test had an HR = 5.86; 95% CI [1.84–18.61] and 2 points in the gait speed test, HR = 5.07; 95% CI [1.76–14.58]. The cutoff point ≤ 9 in the SPPB set the discriminator criterion for mortality in older people of both sexes. Conclusions The SPPB, as well as the balance and gait speed subtests were predictors of mortality, and the SPPB is accurate in predicting mortality among community-dwelling older adults.
Silva et al. (2022) Short physical performance battery as a predictor of mortality in community-dwelling older adults: a longitudinal study in the Brazilian Amazon region. PeerJ 10:e13630 https://doi.org/10.7717/peerj.13630