title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=632 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: IQGAP3 in clear cell renal cell carcinoma contributes to drug resistance and genome stability link: https://peerj.com/articles/14201 last-modified: 2022-10-18 description: BackgroundClear cell renal clear cell carcinoma (ccRCC) is resistant to most chemotherapeutic drugs and the molecular mechanisms have not been fully revealed. Genomic instability and the abnormal activation of bypass DNA repair pathway is the potential cause of tumor resistance to radiotherapy and chemotherapy. IQ-motif GTPase activating protein 3 (IQGAP3) regulates cell migration and intercellular adhesion. This study aims to analysis the effects of IQGAP3 expression on cell survival, genome stability and clinical prognosis in ccRCC.MethodsMultiple bioinformatics analysis based on TCGA database and IHC analysis on clinical specimens were included. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot (WB) were used to determine protein expression level. MTT assay and 3D spheroid cell growth assay were used to assess cell proliferation and drug resistance in RNAi transfected ccRCC cells. Cell invasion capacity was evaluated by transwell assay. The influence of IQGAP3 on genome instability was revealed by micronuclei number and γ H2AX recruitment test.ResultsThe highly expressed IQGAP3 in multiple subtypes of renal cell carcinoma has a clear prognostic value. Deletion of IQGAP3 inhibits cell growth in 3D Matrigel. IQGAP3 depletion lso increases accumulated DNA damage, and improves cell sensitivity to ionizing radiation and chemotherapeutic drugs. Therefore, targeting DNA damage repair function of IQGAP3 in tumorigenesis can provide ideas for the development of new targets for early diagnosis. creator: Wen Li creator: Zhifeng Wang creator: Hanlin Wang creator: Jian Zhang creator: Xiaobin Wang creator: Shaojun Xing creator: Si Chen uri: https://doi.org/10.7717/peerj.14201 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Quantitative real-time PCR analysis of bacterial biomarkers enable fast and accurate monitoring in inflammatory bowel disease link: https://peerj.com/articles/14217 last-modified: 2022-10-18 description: Inflammatory bowel diseases (IBD) affect millions of people worldwide with increasing incidence. Ulcerative colitis (UC) and Crohn’s disease (CD) are the two most common IBDs. There is no definite cure for IBD, and response to treatment greatly vary among patients. Therefore, there is urgent need for biomarkers to monitor therapy efficacy, and disease prognosis. We aimed to test whether qPCR analysis of common candidate bacteria identified from a patient’s individual fecal microbiome can be used as a fast and reliable personalized microbial biomarker for efficient monitoring of disease course in IBD. Next generation sequencing (NGS) of 16S rRNA gene region identified species level microbiota profiles for a subset of UC, CD, and control samples. Common high abundance bacterial species observed in all three groups, and reported to be associated with IBD are chosen as candidate marker species. These species, and total bacteria amount are quantified in all samples with qPCR. Relative abundance of anti-inflammatory, beneficial Faecalibacterium prausnitzii, Akkermansia muciniphila, and Streptococcus thermophilus was significantly lower in IBD compared to control samples. Moreover, the relative abundance of the examined common species was correlated with the severity of IBD disease. The variance in qPCR data was much lower compared to NGS data, and showed much higher statistical power for clinical utility. The qPCR analysis of target common bacterial species can be a powerful, cost and time efficient approach for monitoring disease status and identify better personalized treatment options for IBD patients. creator: Efe Sezgin creator: Gamze Terlemez creator: Berkay Bozkurt creator: Göksel Bengi creator: Hale Akpinar creator: İlker Büyüktorun uri: https://doi.org/10.7717/peerj.14217 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sezgin et al. title: Comprehensive screening of low nitrogen tolerant maize based on multiple traits at the seedling stage link: https://peerj.com/articles/14218 last-modified: 2022-10-18 description: BackgroundPlants tolerant to low nitrogen are a quantitative trait affected by many factors, and the different parameters were used for stress-tolerant plant screening in different investigations. But there is no agreement on the use of these indicators. Therefore, a method that can integrate different parameters to evaluate stress tolerance is urgently needed.MethodsSix maize genotypes were subject to low nitrogen stress for twenty days. Then seventeen traits of the six maize genotypes related to nitrogen were investigated. Nitrogen tolerance coefficient (NTC) was calculated as low nitrogen traits to high nitrogen traits. Then principal component analysis was conducted based on the NTC. Based on fuzzy mathematics theory, a D value (decimal comprehensive evaluation value) was introduced to evaluate maize tolerant to low nitrogen.ResultsThree maize (SY998, GEMS42-I and GEMS42-II) with the higher D value have better growth and higher nitrogen accumulation under low nitrogen conditions. In contrast, Ji846 with the lowest D value has the lowest nitrogen accumulation and biomass in response to nitrogen limitation. These results indicated that the D value could help to screen low nitrogen tolerant maize, given that the D value was positively correlated with low nitrogen tolerance in maize seedlings.ConclusionsThe present study introduced the D value to evaluate stress tolerance. The higher the D value, the greater tolerance of maize to low nitrogen stress. This method may reduce the complexity of the investigated traits and enhance the accuracy of stress-tolerant evaluation. In addition, this method not only can screen potentially tolerant germplasm for low-nitrogen tolerance quickly, but also can comprise the correlated traits as many as possible to avoid the one-sidedness of a single parameter. creator: Jianjia Miao creator: Fei Shi creator: Wei Li creator: Ming Zhong creator: Cong Li creator: Shuisen Chen uri: https://doi.org/10.7717/peerj.14218 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Miao et al. title: Identification and functional analysis of PIN family genes in Gossypium barbadense link: https://peerj.com/articles/14236 last-modified: 2022-10-18 description: BackgroundPIN proteins are an important class of auxin polar transport proteins that play an important regulatory role in plant growth and development. However, their characteristics and functions have not been identified in Gossypium barbadense.MethodsPIN family genes were identified in the cotton species G. barbadense, Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum, and detailed bioinformatics analyses were conducted to explore the roles of these genes in G. barbadense using transcriptome data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) technology. Functional verification of the genes was performed using virus-induced gene silencing (VIGS) technology.ResultsA total of 138 PIN family genes were identified in the four cotton species; the genes were divided into seven subgroups. GbPIN gene family members were widely distributed on 20 different chromosomes, and most had repeated duplication events. Transcriptome analysis showed that some genes had differential expression patterns in different stages of fiber development. According to ‘PimaS-7’ and ‘5917’ transcript component association analysis, the transcription of five genes was directly related to endogenous auxin content in cotton fibers. qRT-PCR analysis showed that the GbPIN7 gene was routinely expressed during fiber development, and there were significant differences among materials. Transient silencing of the GbPIN7 gene by VIGS led to significantly higher cotton plant growth rates and significantly lower endogenous auxin content in leaves and stems. This study provides comprehensive analyses of the roles of PIN family genes in G. barbadense and their expression during cotton fiber development. Our results will form a basis for further PIN auxin transporter research. creator: Yilei Long creator: Quanjia Chen creator: Yanying Qu creator: Pengfei Liu creator: Yang Jiao creator: Yongsheng Cai creator: Xiaojuan Deng creator: Kai Zheng uri: https://doi.org/10.7717/peerj.14236 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Long et al. title: Artificial light at night correlates with seabird groundings: mapping city lights near a seabird breeding hotspot link: https://peerj.com/articles/14237 last-modified: 2022-10-18 description: Artificial light at night (ALAN) is a growing conservation concern for seabirds, which can become disoriented and grounded by lights from buildings, bridges and boats. Many fledgling seabirds, especially Procellariiformes such as petrels and shearwaters, are susceptible to light pollution. The Hauraki Gulf, a seabird hotspot located near Tāmaki Makaurau/Auckland, Aotearoa—New Zealand’s largest urban city, with a considerable amount of light pollution and regularly documented events of seabird groundings. We aim to identify the characteristics of locations especially prone to seabird groundings. We used an online database of seabirds taken to a wildlife rescue facility by the public to map 3 years of seabird groundings and test for correlations between seabird groundings and the natural night sky brightness. We found that areas with lower amounts of natural night sky brightness and greater light pollution often had a higher number of seabirds grounded. Further, we identified important seasonal patterns and species differences in groundings. Such differences may be a by-product of species ecology, visual ecology and breeding locations, all of which may influence attraction to lights. In general, seabird groundings correlate with the brightness of the area and are species-specific. Groundings may not be indicative of human or seabird population abundance considering some areas have a lower human population with high light levels and had high amounts of seabird groundings. These findings can be applied worldwide to mitigate groundings by searching and targeting specific brightly lit anthropogenic structures. Those targeted structures and areas can then be the focus of light mitigation efforts to reduce seabird groundings. Finally, this study illustrates how a combination of community science, and a concern for seabirds grounded from light attraction, in addition to detailed animal welfare data and natural night sky brightness data can be a powerful, collaborative tool to aid global conservation efforts for highly-at-risk animals such as seabirds. creator: Ariel-Micaiah Heswall creator: Lynn Miller creator: Ellery J. McNaughton creator: Amy L. Brunton-Martin creator: Kristal E. Cain creator: Megan R. Friesen creator: Anne C. Gaskett uri: https://doi.org/10.7717/peerj.14237 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Heswall et al. title: Terrien, a metabolite made by Aspergillus terreus, has activity against Cryptococcus neoformans link: https://peerj.com/articles/14239 last-modified: 2022-10-18 description: Antimicrobial compounds, including antibiotics, have been a cornerstone of modern medicine being able to both treat infections and prevent infections in at-risk people, including those who are immune-compromised and those undergoing routine surgical procedures. Their intense use, including in people, animals, and plants, has led to an increase in the incidence of resistant bacteria and fungi, resulting in a desperate need for novel antimicrobial compounds with new mechanisms of action. Many antimicrobial compounds in current use originate from microbial sources, such as penicillin from the fungus Penicillium chrysogenum (renamed by some as P. rubens). Through a collaboration with Aotearoa New Zealand Crown Research Institute Manaaki Whenua–Landcare Research we have access to a collection of thousands of fungal cultures known as the International Collection of Microorganisms from Plants (ICMP). The ICMP contains both known and novel species which have not been extensively tested for their antimicrobial activity. Initial screening of ICMP isolates for activity against Escherichia coli and Staphylococcus aureus directed our interest towards ICMP 477, an isolate of the soil-inhabiting fungus, Aspergillus terreus. In our investigation of the secondary metabolites of A. terreus, through extraction, fractionation, and purification, we isolated nine known natural products. We evaluated the biological activity of selected compounds against various bacteria and fungi and discovered that terrein (1) has potent activity against the important human pathogen Cryptococcus neoformans. creator: Melissa Cadelis creator: Alex Grey creator: Shara van de Pas creator: Soeren Geese creator: Bevan S. Weir creator: Brent Copp creator: Siouxsie Wiles uri: https://doi.org/10.7717/peerj.14239 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cadelis et al. title: Fecal fungal microbiota alterations associated with clinical phenotypes in Crohn’s disease in southwest China link: https://peerj.com/articles/14260 last-modified: 2022-10-18 description: Although previous studies reported that gut fungal microbiota was associated with Crohn’s disease (CD), only a few studies have focused on the correlation between gut fungi and clinical phenotypes of CD. Here, we aimed to analyze the association between intestinal fungi and the occurrence of CD, disease activity, biological behaviors, and perianal lesions. Stool samples from subjects meeting the inclusion and exclusion criteria were collected for running internal transcribed spacer 2 (ITS2) high-throughput sequencing. Then, correlation analysis was conducted between intestinal fungi and different clinical groups. There were 45 patients with CD and 17 healthy controls (HCs) enrolled. Results showed that two phyla, Rozellomycota and Mortierellomycota, were not present in patients with CD compared to HCs. At the same time, there was a higher abundance of fungal genera and species belonging to the phylum Ascomycota in patients with CD. SparCC network analysis showed fewer interactions among the fungal communities in patients with CD compared to HCs. Exophiala dermatitidis was positively associated with the clinical active stage and platelet count. The genus Candida was with significantly higher abundance in the non-B1 CD group based on the Montreal classification. Clonostachys, Humicola, and Lophiostoma were significantly enriched in patients with CD with perianal lesions. Our results demonstrated that the composition of the intestinal fungal microbiota in patients with CD and HCs was markedly different, some of which might play a pathogenic role in the occurrence of CD and perianal lesions. Exophiala dermatitidis and genus Candida might be associated with active disease stage and type non-B1 CD (CD with intestinal stenosis or penetrating lesions, or both), respectively. creator: Li Zeng creator: Zhe Feng creator: Ma Zhuo creator: Zhonghui Wen creator: Cairong Zhu creator: Chengwei Tang creator: Ling Liu creator: Yufang Wang uri: https://doi.org/10.7717/peerj.14260 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zeng et al. title: Six new species of Pristimantis (Anura: Strabomantidae) from Llanganates National Park and Sangay National Park in Amazonian cloud forests of Ecuador link: https://peerj.com/articles/13761 last-modified: 2022-10-17 description: We describe six new species of rainfrogs of the genus Pristimantis (Strabomantidae) from Amazonian cloud forests in Ecuador. We also present a phylogeny showing the relationships of the new species. The phylogeny is based on mitochondrial genes 16S rRNA (16S), 12 rRNA (12S), NADH-ubiquinone oxidoreductase chain 1 (ND1) and the nuclear gene recombination-activating 1 (RAG1). We also describe the osteology of two of the new species using high-resolution x-ray computed tomography. The new species belong to two clades. The first clade is sister to the subgenus Huicundomantis and includes P. tamia sp. nov., P. miktos, and P. mallii. Pristimantis tamia sp. nov. is morphologically similar to P. miktos, P. mallii, P. martiae, and P. incomptus, but differs from them by lacking vocal slits and tympanic membrane and by having light greenish blue iris. Based in our results we expand the subgenus Huicundomantis to include the P. miktos species group. The second clade is remarkable by being highly divergent and consisting exclusively of new species: P. anaiae sp. nov., P. glendae sp. nov., P. kunam sp. nov., P. resistencia sp. nov., and P. venegasi sp. nov. The new species resemble P. roni, P. yanezi, P. llanganati, P. katoptroides, P. verecundus, and P. mutabilis but can be distinguished from them by lacking vocal slits and tympanic membrane and by having large dark round areas with thin clear borders in the sacral region. All six new species occur in the eastern slopes of the Ecuadorian Andes and are known from a single locality in Llanganates or Sangay National Park. We recommend assigning all of them to the Data Deficient (DD) Red List category. Based in our high-resolution x-ray tomographies, we report the presence of structures that appear to be intercalary elements. This would be the first report of such structures in Terrarana. creator: Jhael A. Ortega creator: Jorge Brito creator: Santiago R. Ron uri: https://doi.org/10.7717/peerj.13761 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ortega et al. title: Species level mapping of a seagrass bed using an unmanned aerial vehicle and deep learning technique link: https://peerj.com/articles/14017 last-modified: 2022-10-17 description: BackgroundSeagrass beds are essential habitats in coastal ecosystems, providing valuable ecosystem services, but are threatened by various climate change and human activities. Seagrass monitoring by remote sensing have been conducted over past decades using satellite and aerial images, which have low resolution to analyze changes in the composition of different seagrass species in the meadows. Recently, unmanned aerial vehicles (UAVs) have allowed us to obtain much higher resolution images, which is promising in observing fine-scale changes in seagrass species composition. Furthermore, image processing techniques based on deep learning can be applied to the discrimination of seagrass species that were difficult based only on color variation. In this study, we conducted mapping of a multispecific seagrass bed in Saroma-ko Lagoon, Hokkaido, Japan, and compared the accuracy of the three discrimination methods of seagrass bed areas and species composition, i.e., pixel-based classification, object-based classification, and the application of deep neural network.MethodsWe set five benthic classes, two seagrass species (Zostera marina and Z. japonica), brown and green macroalgae, and no vegetation for creating a benthic cover map. High-resolution images by UAV photography enabled us to produce a map at fine scales (<1 cm resolution).ResultsThe application of a deep neural network successfully classified the two seagrass species. The accuracy of seagrass bed classification was the highest (82%) when the deep neural network was applied.ConclusionOur results highlighted that a combination of UAV mapping and deep learning could help monitor the spatial extent of seagrass beds and classify their species composition at very fine scales. creator: Satoru Tahara creator: Kenji Sudo creator: Takehisa Yamakita creator: Masahiro Nakaoka uri: https://doi.org/10.7717/peerj.14017 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tahara et al. title: Mobile phone addiction and non-suicidal self-injury among adolescents in China link: https://peerj.com/articles/14057 last-modified: 2022-10-17 description: BackgroundNon-suicidal self-injury (NSSI) has recently widely discussed. Independently, mobile phone addiction (MPA) has also attracted academic attention. A few research have examined the correlation between the two. However, there is inadequate knowledge to characterize this relationship altogether. This study further explores the correlation between MPA and NSSI, specifically repeated and severe NSSI.MethodA population-based cross-sectional survey was conducted among 2,719 adolescents in Lincang, Yunnan. The mobile phone addiction index (MPAI) and the Modified Adolescents Self-Harm Survey (MASHS) were administered in combination. The connection between the MPAI and NSSI, as well as both repeated and severe NSSI, was studied using univariate and multivariate logistic regression models. (The copyright holders have permitted the authors to use the MPAI and the MASHS).ResultsThe prevalence of NSSI was 47.11% (95% CI [36.2–58.0%]), and the detection rate of MPA was 11.11% (95% CI [6.7–18.0%]). The prevalence of NSSI among those with MPA was 4.280 times (95% CI [3.480–5.266]) that of respondents not exhibiting MPA. In addition, all subscales of the MPAI, except for the feeling anxious and lost subscale (FALS), were positively correlated with NSSI. Risk factors, represented by odds ratios, of repeated NSSI with the inability to control cravings subscale (ICCS), the FALS, and the withdrawal and escape subscale (WES) was 1.052 (95% CI [1.032–1.072]), 1.028 (95% CI [1.006–1.051]), and 1.048 (95% CI [1.019–1.078]) respectively. Risk factors of these same three subscales for severe NSSI, had odds ratios of 1.048 (95% CI [1.029–1.068]), 1.033 (95% CI [1.009–1.057]), and 1.045 (95% CI [1.018–1.073]).ConclusionMPA was shown to be a risk factor for NSSI in adolescents. Individuals with high scores on the ICCS, the WES, and the FALS were more prone to experience repeated and severe NSSI. As a result, early assessment using the MPAI to determine the need for intervention can contribute to the prediction and prevention of NSSI. creator: Rui Wang creator: Runxu Yang creator: Hailiang Ran creator: Xiufeng Xu creator: Guangya Yang creator: TianLan Wang creator: Yusan Che creator: Die Fang creator: Jin Lu creator: Yuanyuan Xiao uri: https://doi.org/10.7717/peerj.14057 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al.