title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=353 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data link: https://peerj.com/articles/17101 last-modified: 2024-03-15 description: BackgroundStructural variant (SV) calling from DNA sequencing data has been challenging due to several factors, including the ambiguity of short-read alignments, multiple complex SVs in the same genomic region, and the lack of “truth” datasets for benchmarking. Additionally, caller choice, parameter settings, and alignment method are known to affect SV calling. However, the impact of FASTQ read order on SV calling has not been explored for long-read data.ResultsHere, we used PacBio DNA sequencing data from 15 Caenorhabditis elegans strains and four Arabidopsis thaliana ecotypes to evaluate the sensitivity of different SV callers on FASTQ read order. Comparisons of variant call format files generated from the original and permutated FASTQ files demonstrated that the order of input data affected the SVs predicted by each caller. In particular, pbsv was highly sensitive to the order of the input data, especially at the highest depths where over 70% of the SV calls generated from pairs of differently ordered FASTQ files were in disagreement. These demonstrate that read order sensitivity is a complex, multifactorial process, as the differences observed both within and between species varied considerably according to the specific combination of aligner, SV caller, and sequencing depth. In addition to the SV callers being sensitive to the input data order, the SAMtools alignment sorting algorithm was identified as a source of variability following read order randomization.ConclusionThe results of this study highlight the sensitivity of SV calling on the order of reads encoded in FASTQ files, which has not been recognized in long-read approaches. These findings have implications for the replication of SV studies and the development of consistent SV calling protocols. Our study suggests that researchers should pay attention to the input order sensitivity of read alignment sorting methods when analyzing long-read sequencing data for SV calling, as mitigating a source of variability could facilitate future replication work. These results also raise important questions surrounding the relationship between SV caller read order sensitivity and tool performance. Therefore, tool developers should also consider input order sensitivity as a potential source of variability during the development and benchmarking of new and improved methods for SV calling. creator: Kyle J. Lesack creator: James D. Wasmuth uri: https://doi.org/10.7717/peerj.17101 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lesack and Wasmuth title: An ELISA-based method for Galleria mellonella apolipophorin-III quantification link: https://peerj.com/articles/17117 last-modified: 2024-03-15 description: Mammalian models, such as murine, are used widely in pathophysiological studies because they have a high degree of similarity in body temperature, metabolism, and immune response with humans. However, non-vertebrate animal models have emerged as alternative models to study the host-pathogen interaction with minimal ethical concerns. Galleria mellonella is an alternative model that has proved useful in studying the interaction of the host with either bacteria or fungi, performing drug testing, and assessing the immunological response to different microorganisms. The G. mellonella immune response includes cellular and humoral components with structural and functional similarities to the immune effectors found in higher vertebrates, such as humans. An important humoral effector stimulated during infections is apolipophorin III (apoLp-III), an opsonin characterized by its lipid and carbohydrate-binding properties that participate in lipid transport, as well as immunomodulatory activity. Despite some parameters, such as the measurement of phenoloxidase activity, melanin production, hemocytes counting, and expression of antimicrobial peptides genes are already used to assess the G. mellonella immune response to pathogens with different virulence degrees, the apoLp-III quantification remains to be a parameter to assess the immune response in this invertebrate. Here, we propose an immunological tool based on an enzyme-linked immunosorbent assay that allows apoLp-III quantification in the hemolymph of larvae challenged with pathogenic agents. We tested the system with hemolymph coming from larvae infected with Escherichia coli, Candida albicans, Sporothrix schenckii, Sporothrix globosa, and Sporothrix brasiliensis. The results revealed significantly higher concentrations of apoLp-III when each microbial species was inoculated, in comparison with untouched larvae, or inoculated with phosphate-buffered saline. We also demonstrated that the apoLp-III levels correlated with the strains’ virulence, which was already reported. To our knowledge, this is one of the first attempts to quantify apoLp-III, using a quick and easy-to-use serological technique. creator: Uriel Ramírez-Sotelo creator: Laura C. García-Carnero creator: José A. Martínez-Álvarez creator: Manuela Gómez-Gaviria creator: Héctor Manuel Mora-Montes uri: https://doi.org/10.7717/peerj.17117 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ramírez-Sotelo et al. title: Assessing the professional quality of life in the context of pediatric care link: https://peerj.com/articles/17120 last-modified: 2024-03-15 description: BackgroundThis study examines the professional quality of life (ProQOL), including compassion satisfaction (CS) and compassion fatigue (CF), burnout (BO) and secondary traumatic stress (STS) among registered nurses in the context of pediatric care in Riyadh city in Saudi Arabia.MethodsThis study utilised a random multistage sampling method and a survey to collect data from 250 participants on personal characteristics, work-related aspects, lifestyle, and professional quality of life.ResultsThe study participants were all female. Only 2.0% were under 25, with 27.2% aged between 25 and 30 years, 24.0% aged between 31 and 35, and 26.4% over 40 years old. The majority, 74%, were non-Saudis. The participants reported low compassion satisfaction (CS) and compassion fatigue (CF) levels. The CS, burnout (BO), and secondary traumatic stress (STS) scores were 3.23 ± 0.764, 2.75 ± 0.68, and 2.69 ± 0.54, respectively. The study found a significant difference in ProQOL level based on factors such as age, nationality, previous experience, department, shift length, overtime work, state of overtime (mandatory versus optional), and salary.ConclusionsWorking with vulnerable groups poses unique challenges for pediatric nurses. The nationality, salary, and state of overtime were found to be significantly different when compared to CS scores. Additionally, age, department, previous experience, shift length, and overtime work were very different compared to CF scores. However, lifestyle factors did not affect CS and CF scores significantly.ImplicationsTo improve their well-being and interest in activities, pediatric nurses should practice self-compassion and utilise available educational resources such as workshops. They should also strive to achieve a work-life balance and adopt healthy habits to reduce CF. creator: Manal F. Alharbi creator: Aljawharah M. Alkhamshi uri: https://doi.org/10.7717/peerj.17120 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Alharbi and Alkhamshi title: Chigno/CG11180 and SUMO are Chinmo-interacting proteins with a role in Drosophila testes somatic support cells link: https://peerj.com/articles/16971 last-modified: 2024-03-14 description: Stem cells are critical for replenishment of cells lost to death, damage or differentiation. Drosophila testes are a key model system for elucidating mechanisms regulating stem cell maintenance and differentiation. An intriguing gene identified through such studies is the transcription factor, chronologically inappropriate morphogenesis (Chinmo). Chinmo is a downstream effector of the Jak-STAT signaling pathway that acts in testis somatic stem cells to ensure maintenance of male stem cell fate and sexual identity. Defects in these processes can lead to infertility and the formation of germ cell tumors. While Chinmo’s effect on testis stem cell behavior has been investigated in detail, there is still much to be learned about its structure, function, and interactions with other proteins. Using a two-hybrid screen, we find that Chinmo interacts with itself, the small ubiquitin-like modifier SUMO, the novel protein CG11180, and four other proteins (CG4318, Ova (ovaries absent), Taf3 (TBP-associated factor 3), and CG18269). Since both Chinmo and CG11180 contain sumoylation sites and SUMO-interacting motifs (SIMs), we analyzed their interaction in more detail. Using site-directed mutagenesis of a unique SIM in CG11180, we demonstrate that Chinmo’s interaction with CG11180 is SUMO-dependent. Furthermore, to assess the functional relevance of both SUMO and CG11180, we performed RNAi-mediated knockdown of both proteins in somatic cells of the Drosophila testis. Using this approach, we find that CG11180 and SUMO are required in somatic cells of adult testes, and that reduction of either protein causes formation of germ cell tumors. Overall, our work suggests that SUMO may be involved in the interaction of Chinmo and CG11180 and that these genes are required in somatic cells of the adult Drosophila testis. Consistent with the CG11180 knockdown phenotype in male testes, and to underscore its connection to Chinmo, we propose the name Chigno (Childless Gambino) for CG11180. creator: Leanna Rinehart creator: Wendy E. Stewart creator: Natalie Luffman creator: Matthew Wawersik creator: Oliver Kerscher uri: https://doi.org/10.7717/peerj.16971 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Rinehart et al. title: The impact of sprint interval training versus moderate intensity continuous training on blood pressure and cardiorespiratory health in adults: a systematic review and meta-analysis link: https://peerj.com/articles/17064 last-modified: 2024-03-14 description: BackgroundAlthough aerobic exercise is the primary modality recommended for the treatment of hypertension, it remains unclear whether high-intensity all-out sprint interval training (SIT) can result in greater reductions of blood pressure (BP) and cardiorespiratory health. This systematic review aims to compare the impact of SIT versus Moderate-intensity continuous training (MICT) on improvements in resting systolic blood pressure (SBP), diastolic blood pressure (DBP) and maximal oxygen uptake (VO2 max) among adults.MethodsWe conducted a systematic search of three online databases (PubMed, Embase, and Web of Science) from January 2000 to July 2023 to identify randomized controlled trials that compared the chronic effects of SIT versus MICT on BP in participants with high or normal blood pressure. We extracted information on participant characteristics, exercise protocols, BP outcomes, and intervention settings. Furthermore, the changes in VO2 max between the two groups were analyzed using a meta-analysis. The pooled results were presented as weighted means with 95% confidence intervals (CI).ResultsOut of the 1,874 studies initially were found, eight were included in this review, totaling 169 participants. A significant decrease in SBP (MD = −2.82 mmHg, 95% CI [−4.53 to −1.10], p = 0.08, I2 =45%) was observed in the SIT group compared to before the training, but no significant decrease in DBP (MD = −0.75 mmHg, 95% CI [−1.92 to 0.42], p = 0.16, I2 = 33%) was observed. In contrast, both SBP (MD = −3.00 mmHg, 95% CI [−5.31 to −0.69], p = 0.68, I2 = 0%) and DBP (MD = −2.11 mmHg, 95% CI [−3.63 to −0.60], p = 0.72, I2 = 0%) significantly decreased in the MICT group with low heterogeneity. No significant difference was found in resting SBP and DBP between SIT and MICT after the intervention. Both SIT and MICT significantly increased VO2 peak, with SIT resulting in a mean difference (MD) of 1.75 mL/kg/min (95% CI [0.39–3.10], p = 0.02, I2 = 61%), and MICT resulting in a mean difference of 3.10 mL/kg/min (95% CI [1.03–5.18], p = 0.007, I2 = 69%). MICT was more effective in improving VO2 peak (MD = −1.36 mL/kg/min, 95% CI [−2.31 to 0.40], p = 0.56, I2 = 0%). Subgroup analysis of duration and single sprint time showed that SIT was more effective in reducing SBP when the duration was ≥8 weeks or when the sprint time was <30 s.ConclusionOur meta-analysis showed that SIT is an effective intervention in reducing BP and improving cardiorespiratory fitness among adults. Consequently, SIT can be used in combination with traditional MICT to increase the variety, utility, and time efficiency of exercise prescriptions for different populations. creator: Weibao Liang creator: Chuannan Liu creator: Xujie Yan creator: Yu Hou creator: Guan Yang creator: Jianmin Dai creator: Songtao Wang uri: https://doi.org/10.7717/peerj.17064 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liang et al. title: Plant growth regulators mitigate oxidative damage to rice seedling roots by NaCl stress link: https://peerj.com/articles/17068 last-modified: 2024-03-14 description: The aim of this experiment was to investigate the effects of exogenous sprays of 5-aminolevulinic acid (5-ALA) and 2-Diethylaminoethyl hexanoate (DTA-6) on the growth and salt tolerance of rice (Oryza sativa L.) seedlings. This study was conducted in a solar greenhouse at Guangdong Ocean University, where ‘Huanghuazhan’ was selected as the test material, and 40 mg/L 5-ALA and 30 mg/L DTA-6 were applied as foliar sprays at the three-leaf-one-heart stage of rice, followed by treatment with 0.3% NaCl (W/W) 24 h later. A total of six treatments were set up as follows: (1) CK: control, (2) A: 40 mg⋅ L−1 5-ALA, (3) D: 30 mg⋅ L−1 DTA-6, (4) S: 0.3% NaCl, (5) AS: 40 mg⋅ L−1 5-ALA + 0.3% NaCl, and (6) DS: 30 mg⋅ L−1 DTA-6+0.3% NaCl. Samples were taken at 1, 4, 7, 10, and 13 d after NaCl treatment to determine the morphology and physiological and biochemical indices of rice roots. The results showed that NaCl stress significantly inhibited rice growth; disrupted the antioxidant system; increased the rates of malondialdehyde, hydrogen peroxide, and superoxide anion production; and affected the content of related hormones. Malondialdehyde content, hydrogen peroxide content, and superoxide anion production rate significantly increased from 12.57% to 21.82%, 18.12% to 63.10%, and 7.17% to 56.20%, respectively, in the S treatment group compared to the CK group. Under salt stress, foliar sprays of both 5-ALA and DTA-6 increased antioxidant enzyme activities and osmoregulatory substance content; expanded non-enzymatic antioxidant AsA and GSH content; reduced reactive oxygen species (ROS) accumulation; lowered malondialdehyde content; increased endogenous hormones GA3, JA, IAA, SA, and ZR content; and lowered ABA content in the rice root system. The MDA, H2O2, and O2− contents were reduced from 35.64% to 56.92%, 22.30% to 53.47%, and 7.06% to 20.01%, respectively, in the AS treatment group compared with the S treatment group. In the DS treatment group, the MDA, H2O2, and O2− contents were reduced from 24.60% to 51.09%, 12.14% to 59.05%, and 12.70% to 45.20%. In summary, NaCl stress exerted an inhibitory effect on the rice root system, both foliar sprays of 5-ALA and DTA-6 alleviated damage from NaCl stress on the rice root system, and the effect of 5-ALA was better than that of DTA-6. creator: Yaxin Wang creator: Li-ming Zhao creator: Naijie Feng creator: Dianfeng Zheng creator: Xue Feng Shen creator: Hang Zhou creator: Wenxin Jiang creator: Youwei Du creator: Huimin Zhao creator: Xutong Lu creator: Peng Deng uri: https://doi.org/10.7717/peerj.17068 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Wang et al. title: Generation and characterization of mAb 61H9 against junctional adhesion molecule-a with potent antitumor activity link: https://peerj.com/articles/17088 last-modified: 2024-03-14 description: Junctional adhesion molecule-A (JAM-A) is an adhesion molecule that exists on the surface of certain types of cells, including white blood cells, endothelial cells, and dendritic cells. In this study, the cDNA sequences of JAM-A-Fc were chemically synthesized with optimization for mammalian expression. Afterward, we analyzed JAM-A protein expression through transient transfection in HEK293 cell lines. Mice were immunized with JAM-A-Fc protein, and hybridoma was prepared by fusing myeloma cells and mouse spleen cells. Antibodies were purified from the hybridoma supernatant and four monoclonal strains were obtained and numbered 61H9, 70E5, 71A8, and 74H3 via enzyme-linked immunosorbent assay screening. Immunofluorescence staining assay showed 61H9 was the most suitable cell line for mAb production due to its fluorescence signal being the strongest. Flow cytometric analysis proved that 61H9 possessed high affinity. Moreover, antagonism of JAM-A mAb could attenuate the proliferative, migrative, and invasive abilities of ESCC cells and significantly inhibit tumor growth in mice. By examining hematoxylin-eosin staining mice tumor tissues, we found inflammatory cells infiltrated lightly in the anti-JAM-A group. The expression of BCL-2 and IκBα in the anti-JAM-A group were decreased in mice tumor tissues compared to the control group. Ultimately, a method for preparing high-yield JAM-A-Fc protein was created and a high affinity mAb against JAM-A with an antitumor effect was prepared. creator: Kang Liu creator: Hang Yang creator: Rong Xiong creator: Yunlong Shen creator: Guiqin Song creator: Jinliang Yang creator: Zhenling Wang uri: https://doi.org/10.7717/peerj.17088 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Construction of a predictive model for bone metastasis from first primary lung adenocarcinoma within 3 cm based on machine learning algorithm: a retrospective study link: https://peerj.com/articles/17098 last-modified: 2024-03-14 description: BackgroundAdenocarcinoma, the most prevalent histological subtype of non-small cell lung cancer, is associated with a significantly higher likelihood of bone metastasis compared to other subtypes. The presence of bone metastasis has a profound adverse impact on patient prognosis. However, to date, there is a lack of accurate bone metastasis prediction models. As a result, this study aims to employ machine learning algorithms for predicting the risk of bone metastasis in patients.MethodWe collected a dataset comprising 19,454 cases of solitary, primary lung adenocarcinoma with pulmonary nodules measuring less than 3 cm. These cases were diagnosed between 2010 and 2015 and were sourced from the Surveillance, Epidemiology, and End Results (SEER) database. Utilizing clinical feature indicators, we developed predictive models using seven machine learning algorithms, namely extreme gradient boosting (XGBoost), logistic regression (LR), light gradient boosting machine (LightGBM), Adaptive Boosting (AdaBoost), Gaussian Naive Bayes (GNB), multilayer perceptron (MLP) and support vector machine (SVM).ResultsThe results demonstrated that XGBoost exhibited superior performance among the four algorithms (training set: AUC: 0.913; test set: AUC: 0.853). Furthermore, for convenient application, we created an online scoring system accessible at the following URL: https://www.xsmartanalysis.com/model/predict/?mid=731symbol=7Fr16wX56AR9Mk233917, which is based on the highest performing model.ConclusionXGBoost proves to be an effective algorithm for predicting the occurrence of bone metastasis in patients with solitary, primary lung adenocarcinoma featuring pulmonary nodules below 3 cm in size. Moreover, its robust clinical applicability enhances its potential utility. creator: Yu Zhang creator: Lixia Xiao creator: Lan LYu creator: Liwei Zhang uri: https://doi.org/10.7717/peerj.17098 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Evaluation of different Kabuli chickpea genotypes against Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in relation to biotic and abiotic factors link: https://peerj.com/articles/16944 last-modified: 2024-03-13 description: BackgroundThe chickpea pod borer Helicoverpa armigera (Hübner) is a significant insect pest of chickpea crops, causing substantial global losses.MethodsField experiments were conducted in Central Punjab, Pakistan, to investigate the impact of biotic and abiotic factors on pod borer population dynamics and infestation in nine kabuli chickpea genotypes during two cropping seasons (2020–2021 and 2021–2022). The crops were sown in November in both years, with row-to-row and plant-to-plant distances of 30 and 15 cm, respectively, following a randomized complete block design (RCBD).ResultsResults showed a significant difference among the tested genotypes in trichome density, pod wall thickness, and leaf chlorophyll contents. Significantly lower larval population (0.85 and 1.10 larvae per plant) and percent damage (10.65% and 14.25%) were observed in genotype Noor-2019 during 2020–2021 and 2021–2022, respectively. Pod trichome density, pod wall thickness, and chlorophyll content of leaves also showed significant variation among the tested genotypes. Pod trichome density and pod wall thickness correlated negatively with larval infestation, while chlorophyll content in leaves showed a positive correlation. Additionally, the larval population positively correlated with minimum and maximum temperatures, while relative humidity negatively correlated with the larval population. Study results explore natural enemies as potential biological control agents and reduce reliance on chemical pesticides. creator: Hafiz Muhammad Bilal Yousuf creator: Muhammad Yasin creator: Habib Ali creator: Khalid Naveed creator: Ammara Riaz creator: Amal Mohamed AlGarawi creator: Ashraf Atef Hatamleh creator: Yunfeng Shan uri: https://doi.org/10.7717/peerj.16944 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Muhammad Bilal Yousuf et al. title: Filling the gaps in ecology of tropical tiger beetles (Coleoptera: Cicindelidae): first quantitative data of sexual dimorphism in semi-arboreal Therates from the Philippine biodiversity hotspot link: https://peerj.com/articles/16956 last-modified: 2024-03-13 description: BackgroundSexual dimorphism, driven by sexual selection, leads to varied morphological distinctions in male and female insects, providing insights into selection pressures across species. However, research on the morphometric variability within specific taxa of tiger beetles (Coleoptera: Cicindelidae), particularly arboreal and semi-arboreal species, remains very limited.MethodsWe investigate sexual dimorphism in six semi-arboreal Therates tiger beetle taxa from the Philippines, focusing on morphological traits. We employed morphometric measurements and multivariate analyses to reveal patterns of sexual dimorphism between sexes within the taxa.ResultsOur results indicate significant sexual dimorphism in elytra width, with females consistently displaying broader elytra, potentially enhancing fecundity. Notable sexual size dimorphism was observed in Therates fulvipennis bidentatus and T. coracinus coracinus, suggesting heightened sexual selection pressures on male body size. Ecological factors, mating behavior, and female mate choice might contribute to the observed morphological variation. These findings emphasize the need for further studies to comprehend mating dynamics, mate choice, and ecological influences on morphological variations in semi-arboreal and arboreal tiger beetles. creator: Dale Ann Acal creator: Anna Sulikowska-Drozd creator: Radomir Jaskuła uri: https://doi.org/10.7717/peerj.16956 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Acal et al.