title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=705 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genomic insights into Lactobacillus gasseri and Lactobacillus paragasseri link: https://peerj.com/articles/13479 last-modified: 2022-06-07 description: BackgroundAntimicrobial and antifungal species are essential members of the healthy human microbiota. Several different species of lactobacilli that naturally inhabit the human body have been explored for their probiotic capabilities including strains of the species Lactobacillus gasseri. However, L. gasseri (identified by 16S rRNA gene sequencing) has been associated with urogenital symptoms. Recently a new sister taxon of L. gasseri was described: L. paragasseri. L. paragasseri is also posited to have probiotic qualities.MethodsHere, we present a genomic investigation of all (n = 79) publicly available genome assemblies for both species. These strains include isolates from the vaginal tract, gastrointestinal tract, urinary tract, oral cavity, wounds, and lungs.ResultsThe two species cannot be distinguished from short-read sequencing of the 16S rRNA as the full-length gene sequences differ only by two nucleotides. Based upon average nucleotide identity (ANI), we identified 20 strains deposited as L. gasseri that are in fact representatives of L. paragasseri. Investigation of the genic content of the strains of these two species suggests recent divergence and/or frequent gene exchange between the two species. The genomes frequently harbored intact prophage sequences, including prophages identified in strains of both species. To further explore the antimicrobial potential associated with both species, genome assemblies were examined for biosynthetic gene clusters. Gassericin T and S were identified in 46 of the genome assemblies, with all L. paragasseri strains including one or both bacteriocins. This suggests that the properties once ascribed to L. gasseri may better represent the L. paragasseri species. creator: Adriana Ene creator: Natalie Stegman creator: Alan Wolfe creator: Catherine Putonti uri: https://doi.org/10.7717/peerj.13479 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ene et al. title: Explaining detection heterogeneity with finite mixture and non-Euclidean movement in spatially explicit capture-recapture models link: https://peerj.com/articles/13490 last-modified: 2022-06-07 description: Landscape structure affects animal movement. Differences between landscapes may induce heterogeneity in home range size and movement rates among individuals within a population. These types of heterogeneity can cause bias when estimating population size or density and are seldom considered during analyses. Individual heterogeneity, attributable to unknown or unobserved covariates, is often modelled using latent mixture distributions, but these are demanding of data, and abundance estimates are sensitive to the parameters of the mixture distribution. A recent extension of spatially explicit capture-recapture models allows landscape structure to be modelled explicitly by incorporating landscape connectivity using non-Euclidean least-cost paths, improving inference, especially in highly structured (riparian & mountainous) landscapes. Our objective was to investigate whether these novel models could improve inference about black bear (Ursus americanus) density. We fit spatially explicit capture-recapture models with standard and complex structures to black bear data from 51 separate study areas. We found that non-Euclidean models were supported in over half of our study areas. Associated density estimates were higher and less precise than those from simple models and only slightly more precise than those from finite mixture models. Estimates were sensitive to the scale (pixel resolution) at which least-cost paths were calculated, but there was no consistent pattern across covariates or resolutions. Our results indicate that negative bias associated with ignoring heterogeneity is potentially severe. However, the most popular method for dealing with this heterogeneity (finite mixtures) yielded potentially unreliable point estimates of abundance that may not be comparable across surveys, even in data sets with 136–350 total detections, 3–5 detections per individual, 97–283 recaptures, and 80–254 spatial recaptures. In these same study areas with high sample sizes, we expected that landscape features would not severely constrain animal movements and modelling non-Euclidian distance would not consistently improve inference. Our results suggest caution in applying non-Euclidean SCR models when there is no clear landscape covariate that is known to strongly influence the movement of the focal species, and in applying finite mixture models except when abundant data are available. creator: Robby R. Marrotte creator: Eric J. Howe creator: Kaela B. Beauclerc creator: Derek Potter creator: Joseph M. Northrup uri: https://doi.org/10.7717/peerj.13490 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Marrotte et al. title: Microfluidics-assisted electrospinning of aligned nanofibers for modeling intestine barriers link: https://peerj.com/articles/13513 last-modified: 2022-06-07 description: During electrospinning, the fibers deposited on the collector are usually randomly oriented in a disordered form. Researchers hope to generate periodic structures to expand the application of electrospinning, including improving the sensing properties of electronic and photonic devices, improving the mechanical properties of solid polymer composites and directional growth of human tissues. Here, we propose a technique to control the preparation of aligned foodborne nanofibers by placing dielectric polymers on microfluidic devices, which does not require the use of metal collectors. This study was conducted by introduced PEDOT:PSS polymer as a ground collector to prepare aligned foodborne nanofibers directly on the microfluidic platform. The fluidity of the electrolytic polymer collector makes it possible to shape the grounding collector according to the shape of the microcavity, thus forming a space adjustable nanofiber membrane with a controllable body. The simplicity of dismantling the collector also enables it extremely simple to obtain a complete electrospun fiber membrane without any additional steps. In addition, nanofibers can be easily stacked into a multi-layer structure with controllable hierarchical structures. The Caco-2 cells that grow on the device formed a compact intestinal epithelial layer that continuously expresses the tightly bound protein ZO-1. This intestinal barrier, which selectively filters small molecules, has a higher level of TEER, reproducing intestinal filtration functions similar to those of in vivo models. This method provides new opportunities for the design and manufacture of various tissue scaffolds, photonic and electronic sensors. creator: Wentao Su creator: Miao Zhang creator: Wenbo Wei creator: Haitao Wang creator: Wei Zhang creator: Zhongyu Li creator: Mingqian Tan creator: Zongzheng Chen uri: https://doi.org/10.7717/peerj.13513 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Su et al. title: Microplastic pollution at Qilianyu, the largest green sea turtle nesting grounds in the northern South China Sea link: https://peerj.com/articles/13536 last-modified: 2022-06-07 description: Microplastics, new persistent pollutants, have recently attracted considerable attention. When present in beach sediments, microplastics may adversely affect the nesting and hatching of sea turtles on beaches. In this study, we investigate microplastic pollution at Qilianyu (northeastern Xisha Islands), the largest known nesting ground for green sea turtles (Chelonia mydas) in China. We found that the average abundance of microplastics in the beach surface sediments was 338.44 ± 315.69 thousand pieces·m−3 or 1,353.78 ± 853.68 pieces·m−2, with foam and fragments as the main microplastic type identified. The microplastic particles were categorised as small and were predominantly within the 0.05–1 mm size category. Most microplastic particles were white (71.31%). Polystyrene and polyethylene were found to be the most common forms of plastic present. Microplastic pollution was not only observed on the beach surface but also at the bottom of nests approximately 60 cm may be harmful to the incubation of sea turtle eggs. We suggest removing plastic litter, especially small pieces of plastic, on beaches to reduce the threat of microplastic pollution to marine life, including sea turtles. Furthermore, the foam used in aquaculture should be recovered and replaced before it becomes fragmented due to age. In addition, regional cooperation between stakeholders in the South China Sea should be strengthened to collectively promote the reduction and cleanup of marine litter. creator: Ting Zhang creator: Liu Lin creator: Deqin Li creator: Jichao Wang creator: Yunteng Liu creator: Rui Li creator: Shannan Wu creator: Haitao Shi uri: https://doi.org/10.7717/peerj.13536 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Measuring the developmental function of peer review: a multi-dimensional, cross-disciplinary analysis of peer review reports from 740 academic journals link: https://peerj.com/articles/13539 last-modified: 2022-06-07 description: Reviewers do not only help editors to screen manuscripts for publication in academic journals; they also serve to increase the rigor and value of manuscripts by constructive feedback. However, measuring this developmental function of peer review is difficult as it requires fine-grained data on reports and journals without any optimal benchmark. To fill this gap, we adapted a recently proposed quality assessment tool and tested it on a sample of 1.3 million reports submitted to 740 Elsevier journals in 2018–2020. Results showed that the developmental standards of peer review are shared across areas of research, yet with remarkable differences. Reports submitted to social science and economics journals show the highest developmental standards. Reports from junior reviewers, women and reviewers from Western Europe are generally more developmental than those from senior, men and reviewers working in academic institutions outside Western regions. Our findings suggest that increasing the standards of peer review at journals requires effort to assess interventions and measure practices with context-specific and multi-dimensional frameworks. creator: Daniel Garcia-Costa creator: Flaminio Squazzoni creator: Bahar Mehmani creator: Francisco Grimaldo uri: https://doi.org/10.7717/peerj.13539 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Garcia-Costa et al. title: Storage media and RNA extraction approaches substantially influence the recovery and integrity of livestock fecal microbial RNA link: https://peerj.com/articles/13547 last-modified: 2022-06-07 description: BackgroundThere is growing interest in understanding gut microbiome dynamics, to increase the sustainability of livestock production systems and to better understand the dynamics that regulate antibiotic resistance genes (i.e., the resistome). High-throughput sequencing of RNA transcripts (RNA-seq) from microbial communities (metatranscriptome) allows an unprecedented opportunity to analyze the functional and taxonomical dynamics of the expressed microbiome and emerges as a highly informative approach. However, the isolation and preservation of high-quality RNA from livestock fecal samples remains highly challenging. This study aimed to determine the impact of the various sample storage and RNA extraction strategies on the recovery and integrity of microbial RNA extracted from selected livestock (chicken and pig) fecal samples.MethodsFecal samples from pigs and chicken were collected from conventional slaughterhouses. Two different storage buffers were used at two different storage temperatures. The extraction of total RNA was done using four different commercially available kits and RNA integrity/quality and concentration were measured using a Bioanalyzer 2100 system with RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). In addition, RT-qPCR was used to assess bacterial RNA quality and the level of host RNA contamination.ResultsThe quantity and quality of RNA differed by sample type (i.e., either pig or chicken) and most significantly by the extraction kit, with differences in the extraction method resulting in the least variability in pig feces samples and the most variability in chicken feces. Considering a tradeoff between the RNA yield and the RNA integrity and at the same time minimizing the amount of host RNA in the sample, a combination of storing the fecal samples in RNALater at either 4 °C (for 24 h) or −80 °C (up to 2 weeks) with extraction with PM kit (RNEasy Power Microbiome Kit) had the best performance for both chicken and pig samples.ConclusionOur findings provided a further emphasis on using a consistent methodology for sample storage, duration as well as a compatible RNA extraction approach. This is crucial as the impact of these technical steps can be potentially large compared with the real biological variability to be explained in microbiome and resistome studies. creator: Raju Koorakula creator: Mahdi Ghanbari creator: Matteo Schiavinato creator: Gertrude Wegl creator: Juliane C. Dohm creator: Konrad J. Domig uri: https://doi.org/10.7717/peerj.13547 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Koorakula et al. title: Cuticular hydrocarbons as caste-linked cues in Neotropical swarm-founding wasps link: https://peerj.com/articles/13571 last-modified: 2022-06-07 description: Wasps (Vespidae) are important organisms to understand the evolution of social behaviour. Wasps show different levels of sociality, which includes solitary to highly eusocial organisms. In social insect species, queens and workers differ in physiology and morphology. The Neotropical swarm-founding wasps (Epiponini) show a variety of caste syndromes. In this clade, the caste-flexibility is a unique characteristic, in which workers can become queens and swarm to start a new nest. The investigation of the caste system comparing several Epiponini species show a clear-cut morphological distinction between queens and workers, with a morphological continuum between queens and workers. However, whether cuticular hydrocarbons (CHCs) are used as cues for caste recognition in swarm-founding wasps is still unknown. We studied whether CHCs may display caste-linked differences in eleven species of Epiponini wasps and if CHCs differences would follow morphological patterns. Our results suggest that queens and workers of Epiponini wasps are chemically different from each other at two levels, qualitatively and quantitatively, or merely quantitatively. This variation seems to exist regardless of their morphological traits and may be useful to help us understanding how chemical communication evolved differently in these species. creator: Rafael Carvalho da Silva creator: Amanda Prato creator: Ivelize Tannure-Nascimento creator: Cintia Akemi Oi creator: Tom Wenseleers creator: Fabio Nascimento uri: https://doi.org/10.7717/peerj.13571 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 da Silva et al. title: Online e-learning during the COVID-19 lockdown in Trinidad and Tobago: prevalence and associated factors with ocular complaints among schoolchildren aged 11–19 years link: https://peerj.com/articles/13334 last-modified: 2022-06-06 description: BackgroundThe increase in online learning during the pandemic has been linked to various ocular complaints. This study determined the prevalence and factors associated with ocular complaints among schoolchildren aged 12–19 years during the COVID-19 lockdown in Trinidad and Tobago (T&T).MethodsA cross-sectional study was conducted between January and May 2021, during the COVID-19 lockdown in T&T among secondary school students studying remotely. A two-stage cluster sampling method was employed. A modified web-based Computer Vision Syndrome questionnaire was administered to students. Data on demography, duration of digital device use, and ocular complaints were collected, and multilevel logistic regression was used to determine factors associated with ocular complaints among school children, 12–19 years of age in T&T.ResultsA total of 435 schoolchildren (mean age, standard deviation, 15.2 ± 1.9 years range 12–19 years) responded to the questionnaire. The prevalence of self-reported symptoms of headache, blurred vision, dry eyes, itchy eyes, and double vision were 75.0%, 65.1%; 56.8%; 46.4%; and 33.5%, respectively. Schoolchildren aged 18–19 years, those that used spectacles for correction of their refractive errors, and spent more than 6 h on average on digital devices, reported a high prevalence of any ocular complaints. Analysis also revealed that age (14–15 years) was associated with dry eyes, blurred vision, and headaches, while gender (more prevalently females) was associated with blurred vision and headache. Those that had an eye examination in the last year and schoolchildren that took action to resolve ocular complaints were more likely to experience nearly all ocular complaints.ConclusionsDuring the COVID-19 lockdown, over three in four students in T&T reported ocular complaints from digital devices for online learning. Tailored interventional messages to reduce all forms of ocular complaints should target older students, particularly females, those who laid down when learning online via their devices and people who regularly examine their eyes. creator: Kingsley Ekemiri creator: Ngozika Ezinne creator: Khadeejah Kamalodeen creator: Keomi Pierre creator: Brandon Lalla creator: Onyekachukwu Amiebenomo creator: Diane van Staden creator: Ferial Zeried creator: Chioma Ekemiri creator: Kingsley E. Agho creator: Uchechukwu Levi Osuagwu uri: https://doi.org/10.7717/peerj.13334 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ekemiri et al. title: Cell division cycle associated 2 (CDCA2) upregulation promotes the progression of hepatocellular carcinoma in a p53-dependant manner link: https://peerj.com/articles/13535 last-modified: 2022-06-06 description: BackgroundElevated expression and oncogenic functions of cell division cycle associated 2 (CDCA2), an important mitotic regulator, have been demonstrated in several cancer types, however their involvement in hepatocellular carcinoma (HCC) has not been elucidated, and the underlying molecular mechanism remains unclear. This study aims to determine the role of CDCA2 in HCC and the underlying molecular mechanism.MethodsThe expression of CDCA2 in HCC was studied in 40 pairs of frozen and 48 pairs of paraffin-embedded HCC samples and paracancerous normal samples by qRT-PCR and immunohistochemistry, respectively, and using The Cancer Genome Atlas (TCGA) datasets. The cellular function of CDCA2 was studied in vitro in the HepG2, Huh7 and SK-Hep1 HCC cell lines.ResultsWe found significantly upregulated CDCA2 expression in HCC, which was correlated with higher clinical stage, tumor grade and Glypican-3 (+). High CDCA2 expression was correlated with worse overall survival. CDCA2 promoted the proliferation of HCC cells by promoting G1/S transition through the upregulation and activation of CCND1/CDK4/6 and CCNE1/CDK2, enhanced the clonogenic ability, inhibited apoptosis in a p53/p21-dependent manner by inhibiting the p38 MAPK pathway and activating the JNK/c-Jun pathway, and promoted the migration of p53-mutant Huh7 cells by activating the epithelial-mesenchymal transition. Targeting CDCA2 reduced the chemoresistance of HCC cells to cisplatin. CDCA2 expression was also regulated by cyclophilin J.ConclusionsThis study revealed elevated expression of CDCA2 in HCC, possibly as a result of p53 dysregulation, which was associated with worse prognosis of patients. We confirmed the oncogenic role of CDCA2 in HCC in vitro and revealed some of the underlying molecular mechanisms. This study indicated the potential value of CDCA2 as a future target for the treatment of HCC. creator: Jiahui Wang creator: Xin Liu creator: Hongjin Chu creator: Jian Chen uri: https://doi.org/10.7717/peerj.13535 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Association between fibrinogen/albumin ratio and severity of coronary artery calcification in patients with chronic kidney disease: a retrospective study link: https://peerj.com/articles/13550 last-modified: 2022-06-06 description: AimPrevious studies have shown that the fibrinogen to albumin ratio (FAR) is closely related to the severity and prognosis of coronary atherosclerosis. In this study, we sought to evaluate the association between FAR and the degree of coronary artery calcification (CAC) in patients with chronic kidney disease (CKD).MethodsIn this retrospective study, 218 patients with CKD were stratified into low, medium and high FAR groups according to the tertiles of the FAR values. The CAC scores, clinical information and laboratory test results of the three FAR groups were compared. To explore the relationship between FAR and CAC we conducted binary logistic regression and correlation analyses.ResultsIn the low FAR group, the CAC scores were significantly lower than those in the medium and high FAR groups (P  <  0.001). There was a significant correlation between the FAR and CAC scores (r = 0.510, P  <  0.001). The FAR was an independent predictor of CAC (OR = 1.106, 95% CI [1.004–1.218], P = 0.042).ConclusionIn patients with CKD, the FAR can be considered as an effective predictor of CAC. creator: Yuyu Zhu creator: Shuman Tao creator: Danfeng Zhang creator: Jianping Xiao creator: Xuerong Wang creator: Liang Yuan creator: Haifeng Pan creator: Deguang Wang uri: https://doi.org/10.7717/peerj.13550 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Zhu et al.