title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=686 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genetic population structure and reproductive system of two invasive Asian earthworms, Amynthas tokioensis and Amynthas agrestis link: https://peerj.com/articles/13622 last-modified: 2022-07-13 description: 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. creator: Maryam Nouri-Aiin creator: Samantha Connolly creator: Cheryl Keough creator: Annie Jean Smigelsky creator: Yiyi Wen creator: Jeremy Howland creator: Jos. J. Schall creator: Josef H. Görres uri: https://doi.org/10.7717/peerj.13622 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nouri-Aiin et al. title: Changes in the core species of the ant-plant network of oak forest converted to grassland: replacement of its ant functional groups link: https://peerj.com/articles/13679 last-modified: 2022-07-13 description: 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. creator: Mariana Cuautle creator: Cecilia Díaz-Castelazo creator: Citlalli Castillo-Guevara creator: Carolina Guadalupe Torres Lagunes uri: https://doi.org/10.7717/peerj.13679 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cuautle et al. title: Oxygen uptake efficiency slope in healthy normal weight young males: an applicable framework for calculation and interpretation link: https://peerj.com/articles/13709 last-modified: 2022-07-13 description: BackgroundThe 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.ObjectiveWe 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.MethodsIn 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.ResultsVery 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. creator: Lavinia Falcioni creator: Laura Guidetti creator: Carlo Baldari creator: Maria Chiara Gallotta creator: Marco Meucci uri: https://doi.org/10.7717/peerj.13709 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Falcioni et al. title: Are aerosol control devices effective in preventing the spread of dental aerosol? link: https://peerj.com/articles/13714 last-modified: 2022-07-13 description: BackgroundIn 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.MethodsClosed 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.ResultsThe 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).ConclusionsAlthough 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. creator: Elif Seher Böke creator: Ali Keleş creator: Cangül Keskin creator: Yeliz Tanrıverdi Çaycı creator: Tugba Turk uri: https://doi.org/10.7717/peerj.13714 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Böke et al. title: Insights into mobile genetic elements and the role of conjugative plasmid in transferring aminoglycoside resistance in extensively drug-resistant Acinetobacter baumannii AB329 link: https://peerj.com/articles/13718 last-modified: 2022-07-13 description: 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. creator: Supat Khongfak creator: Rapee Thummeepak creator: Udomluk Leungtongkam creator: Kannipa Tasanapak creator: Aunchalee Thanwisai creator: Sutthirat Sitthisak uri: https://doi.org/10.7717/peerj.13718 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Khongfak et al. title: JMJD3 suppresses tumor progression in oral tongue squamous cell carcinoma patients receiving surgical resection link: https://peerj.com/articles/13759 last-modified: 2022-07-13 description: BackgroundJumonji 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.MethodsWe 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.ResultsThe 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.ConclusionOur study showed that high expression of JMJD3 is a good prognostic factor in OTSCC patients who underwent surgical resection. creator: Yen-Hao Chen creator: Chang-Han Chen creator: Chih-Yen Chien creator: Yan-Ye Su creator: Sheng-Dean Luo creator: Shau-Hsuan Li uri: https://doi.org/10.7717/peerj.13759 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: Short physical performance battery as a predictor of mortality in community-dwelling older adults: a longitudinal study in the Brazilian Amazon region link: https://peerj.com/articles/13630 last-modified: 2022-07-12 description: BackgroundThe 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.MethodLongitudinal 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%.ResultsOlder 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.ConclusionsThe 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. creator: Caroline de Fátima Ribeiro Silva creator: Daniela Gonçalves Ohara creator: Areolino Pena Matos creator: Ana Carolina Pereira Nunes Pinto creator: Maycon Sousa Pegorari uri: https://doi.org/10.7717/peerj.13630 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Silva et al. title: CD14 and CD26 from serum exosomes are associated with type 2 diabetes, exosomal Cystatin C and CD14 are associated with metabolic syndrome and atherogenic index of plasma link: https://peerj.com/articles/13656 last-modified: 2022-07-12 description: BackgroundExosomes are microvesicles that actively participate in signaling mechanisms and depending on their content can contribute to the development of different pathologies, such as diabetes and cardiovascular disease.ObjectiveThe aim of this study was to evaluate the association of cystatin C, CD26, and CD14 proteins in serum exosomes from patients with Type 2 Diabetes (T2D), metabolic syndrome (MetS), and atherogenic index of plasma (AIP).MethodsSerum exosomes were isolated by ultracentrifugation from 147 individuals with and without diabetes. Both anthropometric and metabolic parameters were registered from everyone. The levels of exosomal proteins cystatin C, CD26, and CD14 were quantified by ELISA. The association between protein levels and T2D or atherogenic risk factors was analyzed by linear regression and generalized regression models.ResultsWe observed a significant correlation of increased glucose with elevated levels of Cystatin C, and an effect of T2D on the levels of CD26 (β = 45.8 pg/µg; p = 0.001) and CD14 (β = 168 pg/µg; p < 0.001) compared to subjects without T2D. CD14 was significantly related to T2D, metabolic syndrome, glucose, and the Atherogenic Index of Plasma (AIP). Additionally, we observed a significant effect of metabolic syndrome MetS on the increase of exosomal Cystatin C and CD14.ConclusionsT2D may contribute to the increase of CD14 protein contained in exosomes, as well as to the predisposition of atherogenic events development due to its relationship with the increase in serum triglyceride concentrations and the AIP score. Finally, the increased levels of CD14 and Cystatin C in exosomes are related to MetS. The analysis of exosome contents of diabetic patients remains an incipient field, so extensive characterization is crucial for their use as biomarkers or to analyze their possible contribution to diabetic complications. creator: Claudia Paola Pérez-Macedonio creator: Eugenia Flores-Alfaro creator: Luz del C. Alarcón-Romero creator: Amalia Vences-Velázquez creator: Natividad Castro-Alarcón creator: Eduardo Martínez-Martínez creator: Monica Ramirez uri: https://doi.org/10.7717/peerj.13656 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Pérez-Macedonio et al. title: Prevalence of HPV genotypes and assessment of their clinical relevance in laryngeal squamous cell carcinoma in a northeastern state of Brazil—a retrospective study link: https://peerj.com/articles/13684 last-modified: 2022-07-12 description: BackgroundA high prevalence and incidence of head and neck tumors make Brazil the country with the third-highest number of cases of these malignant neoplasms. The main risk factors are smoking and alcohol consumption; however, cases related to the human papillomavirus (HPV) have tripled in number, demonstrating a changing disease profile. Studies have reported the prevalence of HPV in laryngeal squamous cell carcinoma (LSCC) to vary between 8% and 83%. The role of HPV as an important causative factor in LSCC remains unclear.MethodsThis retrospective study included 82 patients with LSCC diagnosed between 2014 and 2019 at two oncology hospitals in São Luís, Brazil. Sociodemographic and clinical data, and the histopathologic characteristics of the tumors, were collected directly from medical records. Genetic material was extracted from paraffin-embedded samples using nested polymerase chain reaction (PCR) and automated sequencing for HPV detection and genotyping. The results by social and clinicopathologic variables were then compared using the chi-squared test and multivariate analysis.ResultsSociodemographic analysesdemonstrated that most patients were men (87.8%), brown-skinned (75.6%), and resident in the state capital (53.7%). They generally had a poor education status (53.7%), having only an elementary school education (completed/incomplete), and 51.2% were self-employed in occupations such as farming or fishing. Smoking and alcohol consumption habits were observed in approximately half the patients. With respect to clinical characteristics, 39% of patients exhibited T1/T2 staging, 51.2% had no distant metastasis, and 30.5% had lymph node invasion. HPV DNA was detected in half the samples (50%), with the high oncogenic type 16 being the most prevalent. There was no significant relationship observed between the economic, educational, occupational with the HPV LSCC in the presented data, although multivariate analysis demonstrated that HPV DNA was more likely to be present in T3–T4 tumors (p = 0.002). creator: Charlles Brito creator: Rachel D. Cossetti creator: Diego Agra de Souza creator: Marcos Catanha creator: Pablo de Matos Monteiro creator: Flavia Castello Branco Vidal uri: https://doi.org/10.7717/peerj.13684 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Brito et al. title: Comparative full-length transcriptome analysis by Oxford Nanopore Technologies reveals genes involved in anthocyanin accumulation in storage roots of sweet potatoes (Ipomoea batatas L.) link: https://peerj.com/articles/13688 last-modified: 2022-07-12 description: BackgroundStorage roots of sweet potatoes (Ipomoea batatas L.) with different colors vary in anthocyanin content, indicating different economically agronomic trait. As the newest DNA/RNA sequencing technology, Oxford Nanopore Technologies (ONT) have been applied in rapid transcriptome sequencing for investigation of genes related to nutrient metabolism. At present, few reports concern full-length transcriptome analysis based on ONT for study on the molecular mechanism of anthocyanin accumulation leading to color change of tuberous roots of sweet potato cultivars.ResultsThe storage roots of purple-fleshed sweet potato (PFSP) and white-fleshed sweet potato (WFSP) at different developmental stages were subjected to anthocyanin content comparison by UV-visible spectroscopy as well as transcriptome analysis at ONT MinION platform. UV-visible spectrophotometric measurements demonstrated the anthocyanin content of PFSP was much higher than that of WFSP. ONT RNA-Seq results showed each sample generated average 2.75 GB clean data with Full-Length Percentage (FL%) over 70% and the length of N50 ranged from 1,192 to 1,395 bp, indicating reliable data for transcriptome analysis. Subsequent analysis illustrated intron retention was the most prominent splicing event present in the resulting transcripts. As compared PFSP with WFSP at the relative developmental stages with the highest (PH vs. WH) and the lowest (PL vs. WL) anthocyanin content, 282 and 216 genes were up-regulated and two and 11 genes were down-regulated respectively. The differential expression genes involved in flavonoid biosynthesis pathway include CCoAOMT, PpLDOX, DFR, Cytochrome P450, CHI, and CHS. The genes encoding oxygenase superfamily were significantly up-regulated when compared PFSP with WFSP at the relative developmental stages.ConclusionsComparative full-length transcriptome analysis based on ONT serves as an effective approach to detect the differences in anthocyanin accumulation in the storage roots of different sweet potato cultivars at transcript level, with noting that some key genes can now be closely related to flavonoids biosynthesis. This study helps to improve understanding of molecular mechanism for anthocyanin accumulation in sweet potatoes and also provides a theoretical basis for high-quality sweet potato breeding. creator: Jun Xiong creator: Xiuhua Tang creator: Minzheng Wei creator: Wenjin Yu uri: https://doi.org/10.7717/peerj.13688 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xiong et al.