title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=682 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Novel lncRNAs with diagnostic or prognostic value screened out from breast cancer via bioinformatics analyses link: https://peerj.com/articles/13641 last-modified: 2022-07-14 description: BackgroundRecent studies have shown that long non-coding RNAs (lncRNAs) may play key regulatory roles in many malignant tumors. This study investigated the use of novel lncRNA biomarkers in the diagnosis and prognosis of breast cancer.Materials and MethodsThe database subsets of The Cancer Genome Atlas (TCGA) by RNA-seq for comparing analysis of tissue samples between breast cancer and normal control groups were downloaded. Additionally, anticoagulant peripheral blood samples were collected and used in this cohort study. The extracellular vesicles (EVs) from the plasma were extracted and sequenced, then analyzed to determine the expressive profiles of the lncRNAs, and the cancer-related differentially expressed lncRNAs were screened out. The expressive profiles and associated downstream-mRNAs were assessed using bioinformatics (such as weighted correlation network analysis (WGCNA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) enrichments, Receiver-Operating Characteristic (ROC) curve and survival analysis, etc.) to investigate the diagnostic and prognostic values of these EV lncRNAs and their effectors.ResultsIn this study, 41 breast cancer-related lncRNAs were screen out from two datasets of tissue and fresh collected plasma samples of breast cancer via the transcriptomic and bioinformatics techniques. A total of 19 gene modules were identified with WGCNA analysis, of which five modules were significantly correlated with the clinical stage of breast cancer, including 28 lncRNA candidates. The ROC curves of these lncRNAs revealed that the area under the curve (AUC) of all candidates were great than 70%. However, eight lncRNAs had an AUC >70%, indicating that the combined one has a good diagnostic value. In addition, the results of survival analysis suggested that two lncRNAs with low expressive levels may indicate the poor prognosis of breast cancer. By tissue sample verification, C15orf54, AL157935.1, LINC01117, and SNHG3 were determined to have good diagnostic ability in breast cancer lesions, however, there was no significant difference in the plasma EVs of patients. Moreover, survival analysis data also showed that AL355974.2 may serve as an independent prognostic factor and as a protective factor.ConclusionA total of five lncRNAs found in this study could be developed as biomarkers for breast cancer patients, including four diagnostic markers (C15orf54, AL157935.1, LINC01117, and SNHG3) and a potential prognostic marker (AL355974.2). creator: Hongxian Wang creator: Lirong Shu creator: Nan Niu creator: Chenyang Zhao creator: Shuqi Lu creator: Yanhua Li creator: Huanyu Wang creator: Yao Liu creator: Tianhui Zou creator: Jiawei Zou creator: Xiaoqin Wu creator: Yun Wang uri: https://doi.org/10.7717/peerj.13641 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Low-level nutrient enrichment during thermal stress delays bleaching and ameliorates calcification in three Hawaiian reef coral species link: https://peerj.com/articles/13707 last-modified: 2022-07-14 description: Terrestrial-based nutrient pollution has emerged as one of the most detrimental factors to coral health in many reef habitats. Recent studies have shown that excessive dissolved inorganic nutrients can reduce coral thermal tolerance thresholds and even exacerbate bleaching during thermal stress, yet the effects of minor nutrient enrichment under heat stress have not been extensively studied. In this study, Lobactis scutaria, Montipora capitata, and Pocillopora acuta colonies under heated conditions (~30.5 °C) were exposed to low and balanced nitrogen and phosphorous concentrations over a 31-day heating period. Coral colonies were collected from Kāne‘ohe Bay, O‘ahu, which has a unique history of nutrient pollution, and held in mesocosms that allowed for environmental manipulation yet are also influenced by local field conditions. Principal findings included delays in the bleaching of nutrient-enriched heated colonies as compared to heated-only colonies, in addition to relatively greater calcification rates and lower proportions of early-stage paling. Species-specific outcomes were prevalent, with L. scutaria demonstrating no difference in calcification with enrichment under heat stress. By the end of the heating stage, however, many heated colonies were at least partially impacted by bleaching or mortality. Despite this, our findings suggest that low levels of balanced nutrient enrichment may serve as a mitigative force during thermal events. Further field-based studies will be required to assess these results in different reef habitats. creator: Ji Hoon J. Han creator: Matthew P. Stefanak creator: Ku‘ulei S. Rodgers uri: https://doi.org/10.7717/peerj.13707 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Han et al. title: ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17 link: https://peerj.com/articles/13710 last-modified: 2022-07-14 description: BackgroundThe auxin indole-3-acetic acid (IAA) is a type of endogenous plant hormone with a low concentration in plants, but it plays an important role in their growth and development. The AUX/IAA gene family was found to be an early sensitive auxin gene with a complicated way of regulating growth and development in plants. The regulation of root growth and development by AUX/IAA family genes has been reported in Arabidopsis, rice and maize.ResultsIn this study, subcellular localization indicated that ZmIAA1-ZmIAA6 primarily played a role in the nucleus. A thermogram analysis showed that AUX/IAA genes were highly expressed in the roots, which was also confirmed by the maize tissue expression patterns. In maize overexpressing ZmIAA5, the length of the main root, the number of lateral roots, and the stalk height at the seedling stage were significantly increased compared with those of the wild type, while the EMS mutant zmiaa5 was significantly reduced. The total number of roots and the dry weight of maize overexpressing ZmIAA5 at the mature stage were also significantly increased compared with those of the wild type, while those of the mutant zmiaa5 was significantly reduced. Yeast one-hybrid experiments showed that ZmTCP15/16/17 could specifically bind to the ZmIAA5 promoter region. Bimolecular fluorescence complementation and yeast two-hybridization indicated an interaction between ZmIAA5 and ZmARF5.ConclusionsTaken together, the results of this study indicate that ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17. creator: Feiyang Yang creator: Yutian Shi creator: Manli Zhao creator: Beijiu Cheng creator: Xiaoyu Li uri: https://doi.org/10.7717/peerj.13710 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: Association between IL-1A and IL-1B gene polymorphisms with peri-implantitis in a Portuguese population—a pilot study link: https://peerj.com/articles/13729 last-modified: 2022-07-14 description: BackgroundScientific evidence indicates that biological complications in dental implants tend to be concentrated in a subset of individuals, which seems to imply that the host response may play a determining role in implant success. Over the last few decades, several polymorphisms have been studied. Polymorphisms in the interleukin (IL) 1 gene cluster have been associated with periodontitis. There are some similar features in the sequence of immunopathological events in peri-implant and periodontal infections. We aimed to investigate if individuals carrying the genetic single nucleotide polymorphism (SNP) in the IL-1A (rs1800587) and IL-1B (rs1143634) genes are more susceptible to develop peri-implantitis.MethodsA cross-sectional analytic pilot study was conducted in 20 Caucasian Portuguese subjects divided into two groups: 10 subjects with peri-implantitis and 10 subjects with peri-implant health (control group). Samples containing cells from the buccal mucosa were stored at −20 °C and later submitted to the DNA extraction process. Genetic analysis was performed using the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Data were analyzed by using descriptive and inferential statistical methodologies.ResultsFor the IL-1A (−889) gene polymorphism, it was observed that the mutated allele was present in a higher percentage in the peri-implantitis group compared to the control group (30% vs 15% respectively, Fisher’s exact test, p = 0.45). For the IL-1B (+3954) gene polymorphism, it was also observed that the altered allele was present in a higher percentage in the disease group compared to the control group (35% vs 10% respectively, Fisher’s exact test, p = 0.13). The positive genotype (at least one allele with nucleotide sequence changed in both genes) was detected in six patients, five belonging to the disease group and one to the health group.ConclusionsRegarding IL-1 gene polymorphisms, there was no statistically significant difference between the health and disease group, however a trend should be highlighted, showing a potential link between the IL-1 genotype and peri-implantitis. More studies are needed to clarify the role of genetic polymorphisms in the development of peri-implantitis. creator: José Maria Cardoso creator: Ana Clara Ribeiro creator: Constança Palos creator: Luis Proença creator: Susana Noronha creator: Ricardo Castro Alves uri: https://doi.org/10.7717/peerj.13729 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cardoso et al. title: Minimally invasive versus traditional inverted “L” approach for posterior cruciate ligament avulsion fractures: a retrospective study link: https://peerj.com/articles/13732 last-modified: 2022-07-14 description: PurposeTo evaluate the clinical efficacy of a minimally invasive arthroscopic approach and to compare it with the traditional inverted “L” approach for the treatment of posterior cruciate ligament (PCL) avulsion fractures.MethodsFrom January 2016 to January 2020, the clinical data from patients with PCL avulsion fracture of the tibial insertion were analyzed retrospectively. They were divided into two groups based on surgical approaches: minimally invasive approach group (n = 15) and traditional inverted “L” group (n = 15 cases). The operation time, incision length, intraoperative blood loss, hospitalization time and complications were all recorded and compared between the two groups. The fracture healing time, knee range of motion (ROM), and residual relaxation degree were compared between the two groups after regular follow-up. The International Knee Documentation Committee (IKDC) and Lysholm scores were used to assess knee joint function.ResultsThere were no significant differences between the two groups in terms of gender, age, side, body mass index, cause of injury, Meyers McKeever classification and time from injury to operation (P > 0.05). The incision length and intraoperative bleeding in the minimally invasive group were significantly lower (P < 0.05) than those in the traditional group. There were no significant differences between the two groups in terms of operative time, fracture healing time, or residual relaxation (P > 0.05). The Lachman test and posterior drawer test were both negative, and there were no postoperative complications. The VAS pain score within 2 weeks and ROM within 4 weeks in the minimally invasive group were significantly better (P < 0.05) than those in the traditional inverted “L” approach group. The knee joint stability of both groups was good 12 months after surgery, and there were no significant differences in IKDC score, Lysholm score and ROM (P > 0.05) between the two groups.ConclusionThe minimally invasive approaches for the treatment of PCL avulsion fractures provide adequate exposure without the surgical complications associated with traditional open surgical approaches. The procedure is safe, fast and minimally invasive, and does not need a long learning curve. creator: Yao Zhao creator: Huihui Guo creator: Liang Gao creator: Chang Liu creator: Xinzhong Xu creator: Wendan Cheng uri: https://doi.org/10.7717/peerj.13732 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhao et al. title: Land use affects the response of soil moisture and soil temperature to environmental factors in the loess hilly region of China link: https://peerj.com/articles/13736 last-modified: 2022-07-14 description: Changes in soil moisture and soil temperature result from the combined effects of several environmental factors. Scientific determination of the response characteristics of soil moisture and soil temperature to environmental factors is critical for adjusting the sloping land use structure and improving the ecological environment in China’s loess hilly region. Soybean sloping fields, maize terraced fields, jujube orchards, and grasslands in the loess hilly region were selected as the research areas. The change in characteristics of soil moisture and soil temperature, as well as their interactions and statistical relationships with meteorological factors, were analyzed using continuously measured soil moisture, soil temperature, and meteorological factors. The results revealed that air temperature and humidity were the main controlling factors affecting soil moisture changes in the 0–60 cm soil layer of soybean sloping fields and grasslands in the normal precipitation year (2014) and the dry year (2015). Humidity and wind speed were the main meteorological factors affecting soil moisture changes in the maize terraced field. Air temperature had a significant negative effect on soil moisture in the jujube orchard. Soil moisture and soil temperature were all negatively correlated under the four sloping land use types. In normal precipitation years, atmospheric humidity had the greatest direct and comprehensive effect on soil moisture in soybean sloping fields, maize terraced fields, and grasslands; soil temperature had a relatively large impact on soil moisture in jujube orchards. The direct and comprehensive effects of soil temperature on soil moisture under all sloping land use types were the largest and most negative in the dry year. Air temperature had a high correlation with soil temperature in the 0–60 cm soil layer under the four sloping land use types, and the grey relational grade decreased as the soil layer deepened. The coefficient of determination between the 0–20 cm soil temperature and air temperature in the maize terraced field was low, indicating a weak response to air temperature. The above findings can serve as a scientific foundation for optimizing sloping land use structures and maximizing the efficient and sustainable utilization of sloping land resources in China’s loess hilly region. creator: Min Tang creator: Wanning Li creator: Xiaodong Gao creator: Pute Wu creator: Hongchen Li creator: Qiang Ling creator: Chao Zhang uri: https://doi.org/10.7717/peerj.13736 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tang et al. title: Acoustic and vibrational signaling in true katydid Nesoecia nigrispina: three means of sound production in one species link: https://peerj.com/articles/13749 last-modified: 2022-07-14 description: The males of Mexican katydids Nesoecia nigrispina (Stal, 1873) produce calling songs and protest sounds using the typical stridulatory apparatus, situated, as in most of the other Ensifera, at the bases of the tegmina. It includes a stridulatory file on the upper tegmen and a plectrum on the lower one. The calling sounds, which are of two types (fast and slow), are two-syllabic series, with a repetition rate fluctuate within 3–4.5 s−1 (fast) and 1.2–2 s−1 (slow). After tactile stimulation, males produce protest signals in the form of short trills of uniform syllable duration. The syllable repetition rate is higher than that of the calling sounds: 7.7 s−1. The frequency spectra of these signals have maxima in the band of 14–15 kHz. However, in addition to the sounds described, both males and females are capable of producing protest signals of the second type, with the help of another sound apparatus, namely the hind wings. Apparently, the sound is produced by the friction of the hind wings on the lower tegmen. The dominant frequencies in the frequency spectra of these sounds are 40–60 kHz. In adults of both sexes and older nymphs, in response mainly to tactile stimulation, short clicks are recorded, which they produce, apparently, by the mandibles. Thus, N. nigrispina seems to have the most extensive acoustic repertoire among pseudophyllines and three means of emitting sound signals. Tremulatory substrate-borne vibrations are produced by individuals of both sexes during courtship and by males completing the calling signal cycle and after copulation. It is possible that vibrational signals are an additional factor in the reproductive isolation of sympatric species, since the calling sound signals in representatives of the genus Nesoecia are similar and exhibit considerable variability. The type and parameters of the calling signal used by the female during recognizing a conspecific mate remain unclear. creator: Olga S. Korsunovskaya creator: Rustem D. Zhantiev uri: https://doi.org/10.7717/peerj.13749 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Korsunovskaya and Zhantiev title: Synthesis of geological data and comparative phylogeography of lowland tetrapods suggests recent dispersal through lowland portals crossing the Eastern Andean Cordillera link: https://peerj.com/articles/13186 last-modified: 2022-07-13 description: Vicariance is the simplest explanation for divergence between sister lineages separated by a potential barrier, and the northern Andes would seem to provide an ideal example of a vicariant driver of divergence. We evaluated the potential role of the uplift of the Eastern Cordillera (EC) of the Colombian Andes and the Mérida Andes (MA) of Venezuela as drivers of vicariance between lowland populations co-distributed on both flanks. We synthesized published geological data and provided a new reconstruction showing that the EC-MA grew from north to south, reaching significant heights and separating drainages and changing sediment composition by 38–33 million years ago (Ma). A few lowland passes across the EC-MA may have reached their current heights (~1,900 m a.s.l.) at 3–5 Ma. We created a comparative phylogeographic data set for 37 lineages of lowland tetrapods. Based on molecular phylogenetic analyses, most divergences between sister populations or species across the EC-MA occurred during Pliocene and the Quaternary and a few during the latest Miocene, and coalescent simulations rejected synchronous divergence for most groups. Divergence times were on average slightly but significantly more recent in homeotherms relative to poikilotherms. Because divergence ages are mostly too recent relative to the geological history and too asynchronous relative to each other, divergence across the northern Andes may be better explained by organism-environment interactions concomitant with climate oscillations during the Pleistocene, and/or dispersal across portals through the Andes. creator: Erika Rodriguez-Muñoz creator: Camilo Montes creator: Fernando J. M. Rojas-Runjaic creator: Andrew J. Crawford uri: https://doi.org/10.7717/peerj.13186 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rodriguez-Muñoz et al. title: Postembryonic development of the tracheal system of beetles in the context of aptery and adaptations towards an arid environment link: https://peerj.com/articles/13378 last-modified: 2022-07-13 description: The tracheal system comprises one of the major adaptations of insects towards a terrestrial lifestyle. Many aspects such as the modifications towards wing reduction or a life in an arid climate are still poorly understood. To address these issues, we performed the first three-dimensional morphometric analyses of the tracheal system of a wingless insect, the desert beetle Gonopus tibialis and compared it with a flying beetle (Tenebrio molitor). Our results clearly show that the reduction of the flight apparatus has severe consequences for the tracheal system. This includes the reduction of the tracheal density, the relative volume of the trachea, the volume of the respective spiracles and the complete loss of individual tracheae. At the same time, the reduction of wings in the desert beetle allows modifications of the tracheal system that would be impossible in an animal with a functional flight apparatus such as the formation of a subelytral cavity as a part of the tracheal system, the strong elongation of the digestive tract including its tracheal system or the respiration through a single spiracle. Finally, we addressed when these modifications of the tracheal system take place during the development of the studied beetles. We can clearly show that they develop during pupation while the larvae of both species are almost identical in their tracheal system and body shape. creator: Marcin Raś creator: Benjamin Wipfler creator: Tim Dannenfeld creator: Dariusz Iwan uri: https://doi.org/10.7717/peerj.13378 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Raś et al. title: WASH regulates the oxidative stress Nrf2/ARE pathway to inhibit proliferation and promote apoptosis of HeLa cells under the action of Jolkinolide B link: https://peerj.com/articles/13499 last-modified: 2022-07-13 description: Jolkinolide B (JB), a diterpenoid compound isolated from the roots of Euphorbia fischeriana, has gained research attention for its antitumor effects. In recent years, JB reportedly displayed anti-tumor activity in solid tumors, such as breast, ovarian, and prostate cancer, and leukemia. In this study, we evaluated the effect of JB on HeLa cells with a focus on cell growth inhibition and related mechanisms. HeLa cells were cultured in vitro and divided into a blank control group, HeLa-Scramble (0, 0.25, 0.5 mM), and Wiskott-Aldrich syndrome protein and SCAR homolog (WASH) protein silenced group, HeLa-shWASH (0, 0.25, 0.5 mM). Morphological changes were observed using an inverted microscope. The inhibition rate of cell proliferation was detected using the WST-1 method. Flow cytometry Brdu+PI double standard method was used to detect cell replication ability and FITC+PI double standard method was used to detect cell apoptosis rate. Western blot was used to verify the expression of Nrf2, HO-1, WASH, Bax, Bcl-2, and PCNA. The mRNA expression of cytokines (IL-1α, IL-6, and IL-8) was detected using RT-qPCR. The results showed that JB induced cell apoptosis and arrested cells at the G2/M phase in HeLa-shWASH cells compared with HeLa-Scramble cells (P < 0.05, P < 0.01, respectively). In addition, JB upregulated IL-1α, IL-6, and IL-8 in HeLa-shWASH cells. We conclude that WASH protein participates in JB-induced regulation of the Nrf2/ARE pathway, aggravates inflammatory responses, and promotes cancer cell apoptosis, thus inhibiting the proliferation and invasion abilities of HeLa cells. JB may have anti-tumor effects and potential clinical value for the treatment of cervical cancer. creator: Yu Hong creator: Jicheng Liu creator: Wanying Kong creator: Hui Li creator: Ying Cui creator: Yuchao Liu creator: Zhihui Deng creator: Dezhi Ma creator: Keyong Zhang creator: Jinghui Li creator: Minhui Li uri: https://doi.org/10.7717/peerj.13499 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hong et al.