title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=645
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: On the move: spatial ecology and habitat use of red fox in the Trans-Himalayan cold desert
link: https://peerj.com/articles/13967
last-modified: 2022-09-15
description: Red fox (Vulpes vulpes) is the most widespread wild carnivore globally, occupying diverse habitats. The species is known for its adaptability to survive in dynamic anthropogenic landscapes. Despite being one of the most extensively studied carnivores, there is a dearth of information on red fox from the Trans-Himalayan region. We studied the home range sizes of red fox using the different estimation methods: minimum convex polygon (MCP), kernel density estimator (KDE), local convex hull (LoCoH) and Brownian-bridge movement model (BBMM). We analysed the daily movement and assessed the habitat selection with respect to topographic factors (ruggedness, elevation and slope), environmental factor (distance to water) and anthropogenic factors (distance to road and human settlements). We captured and GPS-collared six red fox individuals (three males and three females) from Chiktan and one female from Hemis National Park, Ladakh, India. The collars were programmed to record GPS fixes every 15-min. The average BBMM home range estimate (95% contour) was 22.40 ± 12.12 SD km2 (range 3.81–32.93 km2) and the average core area (50% contour) was 1.87 ± 0.86 SD km2 (range 0.55–2.69 km2). The estimated average daily movement of red fox was 17.76 ± 8.45 SD km/d (range 10.91–34.22 km/d). Red fox significantly selected lower elevations with less rugged terrain and were positively associated with water. This is the first study in the Trans-Himalayan landscape which aims to understand the daily movement of red fox at a fine temporal scale. Studying the movement and home range sizes helps understand the daily energetics and nutritional requirements of red fox. Movement information of a species is important for the prioritisation of areas for conservation and can aid in understanding ecosystem functioning and landscape management.
creator: Hussain S. Reshamwala
creator: Pankaj Raina
creator: Zehidul Hussain
creator: Shaheer Khan
creator: Rodolfo Dirzo
creator: Bilal Habib
uri: https://doi.org/10.7717/peerj.13967
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Reshamwala et al.

title: Transcriptomic analysis and physiological characteristics of exogenous naphthylacetic acid application to regulate the healing process of oriental melon grafted onto squash
link: https://peerj.com/articles/13980
last-modified: 2022-09-15
description: The plant graft healing process is an intricate development influenced by numerous endogenous and environmental factors. This process involves the histological changes, physiological and biochemical reactions, signal transduction, and hormone exchanges in the grafting junction. Studies have shown that applying exogenous plant growth regulators can effectively promote the graft healing process and improve the quality of grafted plantlets. However, the physiological and molecular mechanism of graft healing formation remains unclear. In our present study, transcriptome changes in the melon and cucurbita genomes were analyzed between control and NAA treatment, and we provided the first view of complex networks to regulate graft healing under exogenous NAA application. The results showed that the exogenous NAA application could accelerate the graft healing process of oriental melon scion grafted onto squash rootstock through histological observation, increase the SOD, POD, PAL, and PPO activities during graft union development and enhance the contents of IAA, GA3, and ZR except for the IL stage. The DEGs were identified in the plant hormone signal-transduction, phenylpropanoid biosynthesis, and phenylalanine metabolism through transcriptome analysis of CK vs. NAA at the IL, CA, and VB stage by KEGG pathway enrichment analysis. Moreover, the exogenous NAA application significantly promoted the expression of genes involved in the hormone signal-transduction pathway, ROS scavenging system, and vascular bundle formation.
creator: Chuanqiang Xu
creator: Fang Wu
creator: Jieying Guo
creator: Shuan Hou
creator: Xiaofang Wu
creator: Ying Xin
uri: https://doi.org/10.7717/peerj.13980
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Xu et al.

title: Interactions of semiconductor Cd-based quantum dots and Cd2+ with gut bacteria isolated from wild Salmo trutta fry
link: https://peerj.com/articles/14025
last-modified: 2022-09-15
description: BackgroundWith the rapid development of nanotechnology, more and more nanoproducts are being released into the environment where they may both pose ecological risks and be toxic to living organisms. The ecotoxicological impact of quantum dots (QDs), a class of nanoparticles (NPs), on aquatic organisms is becoming an emerging issue, this due to their nano-specific properties, to the physico-chemical transformation in the environment and to the possible release of toxic metals from their structure such as Cd.MethodsIn this work, (i) spectroscopic measurements of commercially available Cd-based QDs (CdSe/ZnS-COOH) were made at various pH values (5.0 and 7.0) to study their interactions (at a concentration of 4 nm) with various strains of Gram-positive and Gram-negative gut bacteria after short-term exposure and (ii) the antibacterial efficacy of QDs and Cd2+ (at a concentration 0.09–3.56 mM) against gut bacteria isolated from wild freshwater Salmo trutta fry was studied at different temperatures (15 °C and 25 °C) and pH values (5.0 and 7.0) by applying a well-established disc diffusion assay.ResultsTwenty-six gut bacterial isolates from wild Salmo trutta fry were identified as Aeromonas spp., A. popoffii, A. salmonicida, A. sobria, Carnobacterium maltaromaticum, Buttiauxella sp., Listeria sp., Microbacterium sp., Shewanella putrefaciens and Serratia sp. Cd-based (CdSe/ZnS-COOH) QDs at a concentration of 4 nm were found to be stable in aqueous media (with pH 7.0) or starting to form aggregates (at pH 5.0), thus, apparently, did not release heavy metals (HMs) into the media over 48 h in conditions of light or dark and did not show antibacterial efficacy on the gut bacteria isolated from wild Salmo trutta fry after short-term (9 h and 48 h) incubations. Cd2+ was found to produce significant dose-dependent toxic effects on bacterial growth, and the size of the inhibition zones on some of the tested strains significantly correlated with temperature. The most sensitive and the most resistant to Cd2+ were the Gram-positive bacteria, for which the minimum inhibitory concentration (MIC) values of Cd2+ were 0.09–0.27 mM and 3.11–3.29 mM respectively and varied significantly between the tested temperatures (15 °C and 25 °C). The MIC values of Cd2+ for the Gram-negative bacteria (18 out of 22 strains) ranged from 0.44 to 0.71 mM and did not differ significantly between the tested temperatures. Among the selected Gram-positive and Gram-negative strains, those with the higher sensitivity towards Cd2+ also revealed relatively stronger signals of QDs photoluminescence (PL) when transferred after incubation into fresh medium without QDs. In addition, the formation of endogenous metalloporphyrins observed spectroscopically in some bacterial strains indicates certain differences in metabolic activity that may play a protective role against potential oxidative damage.
creator: Renata Butrimienė
creator: Agnė Kalnaitytė
creator: Emilija Januškaitė
creator: Saulius Bagdonas
creator: Živilė Jurgelėnė
creator: Dalius Butkauskas
creator: Tomas Virbickas
creator: Danguolė Montvydienė
creator: Nijolė Kazlauskienė
creator: Vesta Skrodenytė-Arbačiauskienė
uri: https://doi.org/10.7717/peerj.14025
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Butrimienė et al.

title: CAV1 alleviated CaOx stones formation via suppressing autophagy-dependent ferroptosis
link: https://peerj.com/articles/14033
last-modified: 2022-09-15
description: BackgroundCalcium oxalate (CaOx) is the most common type of kidney stone, but the mechanism of CaOx stones formation remains unclear. The injury of renal cells such as ferroptosis and autophagy has been considered a basis for stones formation.MethodsWe conducted transmission electron microscope (TEM), reactive oxygen species (ROS), malondialdehyde (MDA), glutathione (GSH), and C11-BODIPY analysis to explore whether CaOx could induce autophagy-dependent ferroptosis in vivo and in vitro. To explore the possible mechanism, we conducted bioinformatic analysis of patients with or without CaOx stones, Western blot and qPCR were used to identify the different genes we found in bioinformatic analysis.ResultsIn our study, we found that CaOx could induce autophagy-dependent ferroptosis no matter in vivo or in vitro, which might finally lead to urolithiasis. Bioinformatic analysis of the GSE73680 dataset indicated that the expression of caveolin-1 (CAV1) was higher in control patients than CaOx stone patients, the STRING database indicated that CAV1 might interact with low density lipoprotein receptro-related protein 6 (LRP6), Gene Set Enrichment Analysis (GSEA) showed that the WNT pathway positively associated with the control group while negatively related to the stone group, and LRP6 was the core gene of the WNT pathway. Western blot found that CAV1, LRP6, and Wnt/β-Catenin were decreased in Human Kidney2 (HK2) cells stimulated with CaOx. Furthermore, the WNT pathway was considered to be involved in autophagy and ferroptosis.ConclusionsWe presumed that CAV1 could ameliorate autophagy-dependent ferroptosis through the LRP6/Wnt/β-Catenin axis, and finally alleviate CaOx stone formation.
creator: Yuanyuan Yang
creator: Senyuan Hong
creator: Yuchao Lu
creator: Qing Wang
creator: Shaogang Wang
creator: Yang Xun
uri: https://doi.org/10.7717/peerj.14033
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Yang et al.

title: Analysis of road traffic injuries and casualties in China: a ten-year nationwide longitudinal study
link: https://peerj.com/articles/14046
last-modified: 2022-09-15
description: BackgroundRoad traffic injuries (RTIs) are a serious global problem, and a huge challenge for both economic development and public health.MethodsThis longitudinal study was based on the national data from Chinese authorities. Descriptive analysis was utilized to analyze the prevalence and trend of RTIs among different types, groups and regions. In addition, ridge regression or/and curve regression were also used to explore the relationship between those possible influencing factors and RTIs.ResultsFrom 2010 to 2019, the death toll from motor vehicle accidents (MVAs) decreased firstly and then increased, while the death toll from non-MVAs continued to rise since 2012, and the death toll from pedestrian and occupant accidents fluctuated only a little. The mortality rate of MVA was relatively stable from 2010 to 2012, and declined from 2013. The mortality rate of motor vehicle accidents was higher in rural than urban, the same to male compared with female. The results of ridge regression showed that gross domestic product (GDP)-per-capita, total population, number of health personnel and car ownership were positively correlated with the death toll of non-MVAs (P < 0.05). Additionally, the results of curve regression suggested that the quadratic or cubic relationship between each factor and the number of MVAs was well fitted, while only partially fitted in fatalities.ConclusionsIn recent years, RTIs in China show different trends, and the problem of non-motor vehicle traffic injuries has been neglected which should be paid more attention. Moreover, according to the new trends and traffic conditions in RTIs revealed in this study, it is necessary to formulate targeted intervention measures establish a multi-faceted comprehensive safety system to reduce the disease burden of RTIs as well as the total injuries.
creator: Miao Qi
creator: Xiuli Hu
creator: Xiahong Li
creator: Xue Wang
creator: Xiuquan Shi
uri: https://doi.org/10.7717/peerj.14046
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Qi et al.

title: Correlation and agreement of regional cerebral oxygen saturation measured from sensor sites at frontal and temporal areas in adult patients undergoing cardiovascular anesthesia
link: https://peerj.com/articles/14058
last-modified: 2022-09-15
description: BackgroundThe function and viability of the brain depend on adequate oxygen supply. A decrease in cerebral blood supply causing cerebral desaturation may lead to many neurological complications. Direct measurement of regional cerebral oxygen saturation (rScO2) assists in early detection and management. Near-infrared spectroscopy (NIRS) has been introduced for measuring rScO2. A pair of sensors are attached to the right and left forehead. However, there are some situations where the forehead of the patient is not accessible for sensor attachment (e.g., neurosurgery involving the frontal area; a bispectral index (BIS) sensor already attached, or a wound to the forehead); therefore, alternate sites for sensor attachment are required. The temporal area was proposed as an alternate site. The objective of this study was to assess the correlation and agreement of rScO2 measured at the forehead vs. the temporal area.MethodsAdult patients undergoing cardiothoracic or vascular surgery were monitored for rScO2 using two pairs of ForeSight sensors. The first pair (A1 and A2) were attached to the right and left forehead, while the second pair (B1 and B2) were attached to the right and left temporal area. The rScO2 values measured from A1 vs. B1 and A2 vs. B2 were assessed for correlation and agreement using the Bland-Altman analysis.ResultsData from 19 patients with 14,364 sets of data were analyzed. The data from A1 vs. B1 and A2 vs. B2 showed moderate positive correlation (r = 0.627; P < 0.0001 and r = 0.548; P < 0.0001). The biases of A1 vs. B1 and A2 vs. B2 were −2.3% (95% CI [−2.5 to −2.2]; P < 0.0001) and 0.7% (95% CI [0.6–0.8]; P < 0.0001). The lower and upper limits of agreement of A1 vs. B1 were −17.5% (95% CI [−17.7 to −17.3]) and 12.8% (95% CI [12.6–13.0]). The lower and upper limits of agreement of A2 vs. B2 were −14.6% (95% CI [−14.8 to −14.4]) and 16.0% (95% [CI 15.8–16.3]).ConclusionsThe rScO2 values measured from sensors at the frontal and temporal areas show a moderate correlation with sufficiently good agreement. The temporal area may be an alternative to the frontal area for cerebral oximetry monitoring.
creator: Sirirat Tribuddharat
creator: Kriangsak Ngamsaengsirisup
creator: Phatcharakamon Mahothorn
creator: Thepakorn Sathitkarnmanee
uri: https://doi.org/10.7717/peerj.14058
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Tribuddharat et al.

title: Cancer, platelet distribution width, and total protein levels as predictors of rebleeding in upper gastrointestinal bleeding
link: https://peerj.com/articles/14061
last-modified: 2022-09-15
description: BackgroundRebleeding is associated with poor outcomes in upper gastrointestinal bleeding (UGIB). Identifying predictors of rebleeding can assist in risk assessment. The aim of the study is to investigate the factors affecting rebleeding in patients with UGIB admitted to the emergency department.MethodsThis retrospective, observational, cross-sectional study was conducted on patients with UGIB presented to the emergency department. Patients who did not arrest in the first 24 h, who were not diagnosed with GI malignancy, and who were clinically diagnosed with UGIB were included in the study. Patient demographic characteristics, hemodynamic parameters, patient parameters, and bleeding that may affect rebleeding were evaluated. The primary endpoint was rebleeding within 7 days.ResultsThe study included 371 patients. A total of 55 patients (14.8%) had rebleeding within 7 days, and 62 patients (16.7%) presented without bleeding manifestations. Rebleeding rates were higher in those who presented with bloody or coffee-ground vomitus, had a diagnosis of cancer, had blood in their nasogastric tube, and had peptic ulcers due to endoscopy. Mean cell hemoglobin concentration, lymphocyte, albumin, and total protein values of patients with rebleeding were low; red blood cell distribution width, neutrophil count, platelet distribution width (PDW), and neutrophil lymphocyte ratio were high. In-hospital mortality and 30-day mortality values of patients with rebleeding were significantly increased. In the multivariate analysis, cancer, PDW, and total protein levels were statistically significant.ConclusionThe presence of cancer, low total protein level, and high PDW are effective parameters in predicting 7-day rebleeding in patients with UGIB admitted to the emergency department.
creator: Ali Cankut Tatlıparmak
creator: Özlem Dikme
creator: Özgür Dikme
creator: Hakan Topaçoğlu
uri: https://doi.org/10.7717/peerj.14061
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Tatlıparmak et al.

title: miR-378 associated with proliferation, migration and apoptosis properties in A549 cells and targeted NPNT in COPD
link: https://peerj.com/articles/14062
last-modified: 2022-09-15
description: BackgroundmicroRNAs contribute to the development and progression of chronic obstructive pulmonary disease (COPD). However, the underlying molecular mechanisms are largely unclear. The goal of this study was to investigate the roles of miR-378 in alveolar epithelial type II cells and identify molecular mechanisms which contribute to the pathogenesis of COPD.Materials and methodsHuman alveolar epithelial (A549) cells were cultured in Dulbecco’s Modified Eagle Medium. Cell proliferation was studied by using a cell counting kit-8 (CCK-8) and colony formation assays. Cell apoptosis and cell cycle were analyzed by flow cytometry and wound healing and Transwell were used to analyze the cell migration and. We performed bioinformatics analysis including target gene prediction, gene ontology (GO), Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment and construction of protein-protein interaction (PPI) network. The expression of miR-378 and NPNT from publically available expression microarray of COPD lung tissues was analyzed.ResultsOverexpression of miR-378 significantly increases cell proliferation, migration, and suppress apoptosis. GO analysis demonstrated that the miR-378 involved in transcription, vascular endothelial growth factor receptor signaling pathway, phosphatidylinositol 3-kinase signaling, cell migration, blood coagulation, cell shape, protein stabilization and phosphorylation. Pathway enrichment showed that the 1,629 target genes of miR-378 were associated with mTOR, ErbB, TGF-β, MAPK, and FoxO signaling pathways. Notably, miR-378 directly targets Nephronectin in A549 cells, and miR-378 was upregulated while NPNT was downregulated in COPD lung tissue samples.ConclusionsThese findings suggest that miR-378 can regulate the proliferation, migration, and apoptosis of A549 cells and target NPNT. miR-378 increased in COPD lung tissues while NPNT decreased, and might prove a potential target for novel drug therapy.
creator: Guoqing Qian
creator: Qi Liao
creator: Guoxiang Li
creator: Fengying Yin
uri: https://doi.org/10.7717/peerj.14062
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Qian et al.

title: Effects of CRISPR/Cas9-mediated stearoyl-Coenzyme A desaturase 1 knockout on mouse embryo development and lipid synthesis
link: https://peerj.com/articles/13945
last-modified: 2022-09-14
description: BackgroundLipid synthesis is an indispensable process during embryo and growth development. Abnormal lipid synthesis metabolism can cause multiple metabolic diseases including obesity and hyperlipidemia. Stearoyl-Coenzyme A desaturase 1 (SCD1) is responsible for catalyzing the synthesis of monounsaturated fatty acids (MUFA) and plays an essential role in lipid metabolism. The aim of our study was to evaluate the effects of SCD1 on embryo development and lipid synthesis in a knockout mice model.MethodsWe used the CRISPR/Cas9 system together with microinjection for the knockout mouse model generation. Ten-week-old female C57BL/6 mice were used for zygote collection. RNase-free water was injected into mouse zygotes at different cell phases in order to select the optimal time for microinjection. Five sgRNAs were designed and in vitro transcription was performed to obtain sgRNAs and Cas9 mRNA. RNase-free water, NC sgRNA/Cas9 mRNA, and Scd1 sgRNA/Cas9 mRNA were injected into zygotes to observe the morula and blastocyst formation rates. Embryos that were injected with Scd1 sgRNA/Cas9 mRNA and developed to the two-cell stage were used for embryo transfer. Body weight, triacylglycerol (TAG), and cholesterol in Scd1 knockout mice serum were analyzed to determine the effects of SCD1 on lipid metabolism.ResultsMicroinjection performed during the S phase presented with the highest zygote survival rate (P < 0.05). Of the five sgRNAs targeted to Scd1, two sgRNAs with relatively higher gene editing efficiency were used for Scd1 knockout embryos and mice generation. Genome sequence modification was observed at Scd1 exons in embryos, and Scd1 knockout reduced blastocyst formation rates (P < 0.05). Three Scd1 monoallelic knockout mice were obtained. In mice, the protein level of SCD1 decreased (P < 0.05), and the body weight and serum TAG and cholesterol contents were all reduced (P < 0.01).
creator: Huibin Tian
creator: Huimin Niu
creator: Jun Luo
creator: Weiwei Yao
creator: Wenchang Gao
creator: Yang Wen
creator: Min Cheng
creator: Anmin Lei
creator: Jinlian Hua
uri: https://doi.org/10.7717/peerj.13945
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Tian et al.

title: Phenotypic spectrum of FGF10-related disorders: a systematic review
link: https://peerj.com/articles/14003
last-modified: 2022-09-14
description: FGF10, as an FGFR2b-specific ligand, plays a crucial role during cell proliferation, multi-organ development, and tissue injury repair. The developmental importance of FGF10 has been emphasized by the identification of FGF10 abnormalities in human congenital disorders affecting different organs and systems. Single-nucleotide variants in FGF10 or FGF10-involving copy-number variant deletions have been reported in families with lacrimo-auriculo-dento-digital syndrome, aplasia of the lacrimal and salivary glands, or lethal lung developmental disorders. Abnormalities involving FGF10 have also been implicated in cleft lip and palate, myopia, or congenital heart disease. However, the exact developmental role of FGF10 and large phenotypic heterogeneity associated with FGF10 disruption remain incompletely understood. Here, we review human and animal studies and summarize the data on FGF10 mechanism of action, expression, multi-organ function, as well as its variants and their usefulness for clinicians and researchers.
creator: Katarzyna Bzdega
creator: Justyna A. Karolak
uri: https://doi.org/10.7717/peerj.14003
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Bzdega and Karolak