title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=368 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Alveolar antral artery: cone beam computed tomography study and clinical context link: https://peerj.com/articles/16439 last-modified: 2023-11-30 description: PurposeAnastomosis between posterior superior alveolar artery and infraorbital artery can go through bony canal in the lateral wall of the maxilla. This artery is called alveolar antral artery. It can complicate lateral sinus lift procedure by bleeding and hemosinus formation or bone graft wash out. The artery can also go in soft tissues where is not visible on cone beam computed tomography. In previous studies, the relation of this artery to sinus floor or alveolar process was measured. These structures are highly unstable during lifetime and after tooth loss. The aim of this study is to study presence and relations of bony canal in the lateral maxillary wall, to characterize the group of patients which is more likely to have bone canal in the lateral maxilla. The aim and the novelty of this study is the describing of the relationship of the bony canal to the more stable structure of hard palate and describing the relation of presence of bony canal on width of maxillary sinus, and to facilitate the prediction of presence of the alveolar antral artery.MaterialsThe cone beam computed tomography scans of the patients (251 in number) of the university hospital were examined for presence of alveolar antral artery (148 was fulfilled inclusion criteria), patient were characterized by gender, age, and sinus type (wide, average, narrow). The diameter of the bony canal and its relation to the level of sinus floor and hard palate were measured.ResultsThe cone beam computed tomography scans of 148 patients, out of it 55 man (37,2%) and 93 women (62,8%). Bony canal containing alveolar anastomosis was found in 69 cases (57,0%). Presence of the bony canal in the lateral wall of maxillae showed statistical probability depending on age with p = 0, 064 according to Mann-Whitney test. The older patients have more likely the bony canal. The presence of the alveolar antral artery was found more likely in the wide sinuses. The hard palate level can serve as a prediction point of alveolar antral artery only in first molar and second premolar region. In accordance with previous studies the width of bony canal is significantly higher in group of man (p = 0, 015). There was found a correlation between smaller distance of bony canal from sinus floor in the presence of teeth (p = 0, 067). After tooth loss the distance between sinus floor and bony canal increases, but the distance of bony canal to hard palate level stays constant. This can be explained hypothetically so that periodontal ligaments and root surface acts as a barrier for sinus pneumatization.ConclusionLateral sinus lifting in some cases can be unenviable, the knowledge about alveolar antral artery anatomy can reduce the risk of arterial bleeding. The cone-beam computed tomography is a routine examination prior to augmentation surgery and therefore the data obtained from it has an impact on clinical practice. creator: Ján Staněk creator: Kateřina Machálková creator: Magdalena Staňková creator: Jana Zapletalová creator: Tat’ána Kocurová uri: https://doi.org/10.7717/peerj.16439 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Staněk et al. title: Amlodipine and lufenuron as repurposing drugs against Sporothrix brasiliensis link: https://peerj.com/articles/16443 last-modified: 2023-11-30 description: BackgroundSporotrichosis caused by Sporothrix brasiliensis is a globally emerging infectious disease with limited therapeutic options. Thus, we aimed to evaluate the in vitro activity of amlodipine (AML) and lufenuron (LUF) alone and their interaction with itraconazole (ITZ), the first-choice drug against S. brasiliensis.MethodsTwenty clinical isolates of S. brasiliensis from two hyperendemic regions were tested through a microdilution assay to evaluate the minimal inhibitory concentration (MIC) and minimal fungicidal concentration (MFC) of AML and LUF. Checkerboard assay was performed with 10 isolates for both drug interactions with ITZ.ResultsAML showed inhibitory and fungicidal activity against all isolates included, with MIC values ranging from 32 to 256 µg/mL, and MFC from 64 to 256 µg/mL. However, none of the S. brasiliensis isolates were inhibited by the highest soluble concentration of LUF (MIC >64 µg/mL for all strains). Synergic interaction of AML and LUF with ITZ occurred in 50% and 40% of the isolates tested, without any antagonistic effects.ConclusionBoth repurposing drugs evaluated in our study showed a promising in vitro activity, especially in synergy with ITZ against S. brasiliensis, warranting future in vivo investigations regarding its activity. creator: Vanice Rodrigues Poester creator: Jéssica Estefania Dávila Hidalgo creator: Lara Severo Jardim creator: Mariana Rodrigues Trápaga creator: Vanessa Brito de Souza Rabello creator: Rodrigo Almeida-Paes creator: Rosely Maria Zancope-Oliveira creator: Melissa Orzechowski Xavier uri: https://doi.org/10.7717/peerj.16443 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Poester et al. title: Morphology and molecular phylogeny of Neolentinus in northern China link: https://peerj.com/articles/16470 last-modified: 2023-11-30 description: Neolentinus is a significant genus, belonging to Gloeophyllaceae, with important economic and ecological values, which are parasites on decaying wood of broad-leaf or coniferous trees, and will cause brown rot. However, the taxonomic study is lagging behind to other groups of macrofungi, especially in China. In view of this, we conducted morphological and molecular phylogenetic studies on this genus. We have discovered new types of cheilocystidia and with extremely long lamellae in Neolentinus, and, thus proposed it as a new species—Neolentinus longifolius. At the same time, we clarified the distribution of Neolentinus cyathiformis in China and provided a detailed description. Moreover, we also described two common species, viz. Neolentinus lepideus and Neolentinus adhaerens. All the species are described based on the Chinese collections. The key to the reported species of Neolentinus from China is provided. And the phylogeny of Neolentinus from China is reconstructed based on DNA sequences of multiple loci including the internal transcribed spacer (ITS) regions, the large subunit nuclear ribosomal RNA gene (nLSU), and the translation elongation factor 1-α gene (tef-1α). In addition, full morphological descriptions, illustrations, color photographs, taxonomic notes, and all the available sequences of Neolentinus species are provided. creator: Lei Yue creator: Yong-lan Tuo creator: Zheng-xiang Qi creator: Jia-jun Hu creator: Ya-jie Liu creator: Xue-fei Li creator: Ming-hao Liu creator: Bo Zhang creator: Shu-Yan Liu creator: Yu Li uri: https://doi.org/10.7717/peerj.16470 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yue et al. title: Role of Pink1-mediated mitophagy in adenomyosis link: https://peerj.com/articles/16497 last-modified: 2023-11-30 description: Abstract BackgroundRecent studies indicate that endometrial hypoxia plays a critical role in adenomyosis (AM) development. Mitochondria are extremely sensitive to hypoxic damage, which can result in both morphological and functional impairment. Mitophagy is a crucial mechanism for preserving mitochondrial quality by selectively removing damaged mitochondria, thus ensuring the proper functioning of the entire mitochondrial network. In response to hypoxia, PINK1 is activated as a regulator of mitophagy, but its role in AM requires further study.ObjectiveTo explore the potential mechanism of mitophagy mediated by PINK1 in the pathogenesis of AM.MethodThe study compared PINK1, Parkin, OPTIN, P62, and NDP52 protein expression levels in patients with or without AM using clinical specimens and an AM mouse model. Pathological changes were compared using HE staining. Immunofluorescence and western blot were used to detect protein expression levels. Endometrial stromal cells (ESC) were isolated and examined for mitophagy, protein expression level, and cell invasion ability.ResultsBoth the endometrial tissue from patients with AM and AM ESC displayed an upregulation of protein levels for PINK1, Parkin, OPTIN, P62, and NDP52 when compared with the control group. Then, HE staining confirmed the successful establishment of the AM mouse model. Moreover, the ultrastructural analysis using transmission electron microscopy revealed that AM mice’s endometrial glandular epithelial and stromal cells had exhibited swollen, deformed, and reduced mitochondria along with an increase in the number of lysosomes and mitochondrial autophagosomes. The protein levels of PINK1, Parkin, OPTIN, P62, and NDP52 in uterine tissue from AM mice were noticeably increased, accompanied by a considerable upregulation of ROS levels compared to the control group. In addition, cells in the AM group showed remarkably elevated mitophagy and invasion potentials compared to the control group. In contrast, the cell invasion ability decreased following PINK1 knockdown using the RNA interference technique.ConclusionThe high levels of PINK1-mediated mitophagy have been found in AM. The upregulation in mitophagy contributes to mitochondrial damage, which may result in the abnormal invasion characteristic of AM. creator: Minmin Chen creator: Wei Wang creator: Xianyun Fu creator: Yongli Yi creator: Kun Wang creator: Meiling Wang uri: https://doi.org/10.7717/peerj.16497 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Circular RNA hsa_circ_0051246 acts as a microRNA-375 sponge to promote the progression of gastric cancer stem cells via YAP1 link: https://peerj.com/articles/16523 last-modified: 2023-11-30 description: BackgroundGastric cancer (GC) stem cells play an important role in GC progression. Circular RNAs (circRNAs) act as microRNA (miRNA) sponges and inhibit the biological function of miRNAs in GC cytoplasm. MiRNAs also participate in GC progress. circ_0051246 was shown to be associated with miR-375 after analyzing GC microarray data GSE78091 and GSE83521. The oncoprotein Yes-associated protein 1 (YAP1) is targeted by miR-375 and can be inactivated via the Hippo tumor suppressor pathway. Due to insufficient research on circ_0051246, this study aimed to investigate its relationship with miR-375 and YAP1 in cancer stem cells (CSCs).MethodsSGC-7901 CSCs were used to establish knockdown/overexpression models of circ_0051246, miR-375, and YAP1. Malignant phenotypes of CSCs were assessed using Cell Counting Kit 8, colony/sphere formation, 5-Ethynyl-2′-deoxyuridine assay, flow cytometry, Transwell, and wound healing assays. To detect the interactions between circ_0051246, miR-375, and YAP1 in CSCs, a dual-luciferase reporter assay and fluorescence in situ hybridization were performed. In addition, 24 BALB/c nude mice were used to establish orthotopic xenograft tumor models. Four groups of mice were injected with CSCs (1 × 106 cells/100 µL) with circ_0051246 knockdown, miR-375 overexpression, or their respective control cells, and tumor progression and gene expression were observed by hematoxylin-eosin staining, immunohistochemistry. Western blot and quantitative real-time PCR were utilized to examine protein and gene expression, respectively.ResultsCirc_0051246 silencing reduced viability, promoted apoptosis, and inhibited proliferation, migration and invasion of CSCs. The functional effects of miR-375 mimics were comparable to those of circ_0051246 knockdown; however, the opposite was observed after miR-375 inhibitors treatment of CSCs. Furthermore, circ_0051246-overexpression antagonized the miR-375 mimics’ effects on CSCs. Additionally, YAP1 overexpression promoted CSC features, such as self-renewal, migration, and invasion, inhibited apoptosis and E-cadherin levels, and upregulated the expression of N-cadherin, vimentin, YAP1, neurogenic locus notch homolog protein 1, and jagged canonical notch ligand 1. Conversely, YAP1-silenced produced the opposite effect. Moreover, miR-375 treatment antagonized the malignant effects of YAP1 overexpression in CSCs. Importantly, circ_0051246 knockdown and miR-375 activation suppressed CSC tumorigenicity in vivo.ConclusionThis study highlights the promotion of circ_0051246-miR-375-YAP1 axis activation in GC progression and provides a scientific basis for research on the molecular mechanism of CSCs. creator: Minghui Deng creator: Yefeng Xu creator: Yongwei Yao creator: Yiqing Wang creator: Qingying Yan creator: Miao Cheng creator: YunXia Liu uri: https://doi.org/10.7717/peerj.16523 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Deng et al. title: Water-use characteristics of Syzygium antisepticum and Adinandra integerrima in a secondary forest of Khao Yai National Park in Thailand with implications for environmental management link: https://peerj.com/articles/16525 last-modified: 2023-11-30 description: BackgroundSoutheast Asia has experienced widespread deforestation and change in land use. Consequently, many reforestation projects have been initiated in this region. However, it is imperative to carefully choose the tree species for planting, especially in light of the increasing climate variability and the potential alteration of plantation on the watershed water balance. Thus, the information regarding water-use characteristics of various tree species and sizes is critical in the tree species selection for reforestation.MethodsWe estimated tree water use (T) of dominant species including Syzygium antisepticum and Adinandra integerrima, hereafter Sa and Ai, respectively, in a secondary tropical forest in Khao Yai National Park, Thailand, using sap flow data, and compared T between species and size classes. Additionally, we evaluated the responses of T of both species in each size class to environmental factors including soil moisture and vapor pressure deficit (VPD).ResultsResults showed consistently higher T in Sa compared to Ai across ranges of VPD and soil moisture. Under low soil moisture, T of Sa responded to VPD, following a saturating exponential pattern while Ai maintained T across different VPD levels, irrespective of tree size. No responses of T to VPD were observed in either species when soil water was moderate. When soil moisture was high, T of both species significantly increased and saturated at high VPD, albeit the responses were less sensitive in large trees. Our results imply that Ai may be suitable for reforestation in water-limited areas where droughts frequently occur to minimize reforestation impact on water availability to downstream ecosystems. In contrast, Sa should be planted in regions with abundant and reliable water resources. However, a mixed species plantation should be generally considered to increase forest resilience to increasing climate variation. creator: Ratchanon Ampornpitak creator: Anuttara Nathalang creator: Pantana Tor-ngern uri: https://doi.org/10.7717/peerj.16525 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ampornpitak et al. title: Niraparib restrains prostate cancer cell proliferation and metastasis and tumor growth in mice by regulating the lncRNA MEG3/miR-181-5p/GATA6 pathway link: https://peerj.com/articles/16314 last-modified: 2023-11-29 description: BackgroundPoly (ADP-ribose) polymerase (PARP) inhibitors (PARPi), have gained approval for treating patients with castration-resistant prostate cancer (CRPC). Maternally expressed gene 3 (MEG3), a long non-coding RNA (lncRNA), plays a role in inhibiting tumorigenesis through regulating DNA repair genes. This study aimed to investigate the association between the anti-prostate cancer (PCa) effect of niraparib, a representative PARPi, and MEG3 expression, as well as explore the downstream pathway involved.MethodsThe levels of MEG3, miR-181-5p, GATA binding protein 6 (GATA6) in clinical samples from PCa patients were accessed by RT-qPCR. PC3 cells were treated with niraparib, and the expression of MEG3, miR-181-5p, GATA6 expression was tested. PC3 cell proliferation, migration, and invasion were tested by CCK-8, wound healing, and Transwell assays, respectively. The bindings between miR-181-5p and MEG3/GATA6 were determined by dual-luciferase reporter gene assay. Furthermore, rescue experiments were conducted to investigate the underlying mechanism of MEG3/miR-181-5p/GATA6 axis in PCa progression. Additionally, mice were injected with PC3 cells transfected with sh-MEG3 and treated with niraparib, and the xenograft tumor growth was observed.ResultsMEG3 and GATA6 were upregulated and miR-181-5p was downregulated in PCa patients. Niraparib treatment substantially upregulated MEG3 and GATA6, and downregulated miR-181-5p expression in PCa cells. Niraparib effectively restrained PC3 cell proliferation, migration, and invasion. MiR-181-5p targeted to MEG3, and the inhibitory effects of MEG3 overexpression on PC3 cell proliferation and metastasis were abrogated by miR-181-5p overexpression. Moreover, GATA6 was identified as a target of miR-181-5p, and GATA6 silencing abolished the inhibitory effects of miR-181-5p inhibition on PC3 cell proliferation and metastasis. Besides, MEG3 silencing could abrogate niraparib-mediated tumor growth inhibition in mice.ConclusionsNiraparib restrains prostate cancer cell proliferation and metastasis and tumor growth in mice by regulating the lncRNA MEG3/miR-181-5p/GATA6 pathway. creator: Ji Cheng creator: Yi Sun creator: Huacai Zhao creator: Wei Ren creator: Dan Gao creator: Zhigang Wang creator: Wei Lv creator: Qingchuan Dong uri: https://doi.org/10.7717/peerj.16314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cheng et al. title: Interactive bioacoustic playback as a tool for detecting and exploring nonhuman intelligence: “conversing” with an Alaskan humpback whale link: https://peerj.com/articles/16349 last-modified: 2023-11-29 description: Here we report on a rare and opportunistic acoustic turn-taking with an adult female humpback whale, known as Twain, in Southeast Alaska. Post hoc acoustic and statistical analyses of a 20-min acoustic exchange between the broadcast of a recorded contact call, known as a ‘whup/throp’, with call responses by Twain revealed an intentional human-whale acoustic (and behavioral) interaction. Our results show that Twain participated both physically and acoustically in three phases of interaction (Phase 1: Engagement, Phase 2: Agitation, Phase 3: Disengagement), independently determined by blind observers reporting on surface behavior and respiratory activity of the interacting whale. A close examination of both changes to the latency between Twain’s calls and the temporal matching to the latency of the exemplar across phases indicated that Twain was actively engaged in the exchange during Phase 1 (Engagement), less so during Phase 2 (Agitation), and disengaged during Phase 3 (Disengagement). These results, while preliminary, point to several key considerations for effective playback design, namely the importance of salient, dynamic and adaptive playbacks, that should be utilized in experimentation with whales and other interactive nonhuman species. creator: Brenda McCowan creator: Josephine Hubbard creator: Lisa Walker creator: Fred Sharpe creator: Jodi Frediani creator: Laurance Doyle uri: https://doi.org/10.7717/peerj.16349 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 McCowan et al. title: An ecological transcriptome approach to capture the molecular and physiological mechanisms of mass flowering in Shorea curtisii link: https://peerj.com/articles/16368 last-modified: 2023-11-29 description: Climatic factors have commonly been attributed as the trigger of general flowering, a unique community-level mass flowering phenomenon involving most dipterocarp species that forms the foundation of Southeast Asian tropical rainforests. This intriguing flowering event is often succeeded by mast fruiting, which provides a temporary yet substantial burst of food resources for animals, particularly frugivores. However, the physiological mechanism that triggers general flowering, particularly in dipterocarp species, is not well understood largely due to its irregular and unpredictable occurrences in the tall and dense forests. To shed light on this mechanism, we employed ecological transcriptomic analyses on an RNA-seq dataset of a general flowering species, Shorea curtisii (Dipterocarpaceae), sequenced from leaves and buds collected at multiple vegetative and flowering phenological stages. We assembled 64,219 unigenes from the transcriptome of which 1,730 and 3,559 were differentially expressed in the leaf and the bud, respectively. Differentially expressed unigene clusters were found to be enriched with homologs of Arabidopsis thaliana genes associated with response to biotic and abiotic stresses, nutrient level, and hormonal treatments. When combined with rainfall data, our transcriptome data reveals that the trees were responding to a brief period of drought prior to the elevated expression of key floral promoters and followed by differential expression of unigenes that indicates physiological changes associated with the transition from vegetative to reproductive stages. Our study is timely for a representative general flowering dipterocarp species that occurs in forests that are under the constant threat of deforestation and climate change as it pinpoints important climate sensitive and flowering-related homologs and offers a glimpse into the cascade of gene expression before and after the onset of floral initiation. creator: Ahmad Husaini Suhaimi creator: Masaki J. Kobayashi creator: Akiko Satake creator: Ching Ching Ng creator: Soon Leong Lee creator: Norwati Muhammad creator: Shinya Numata creator: Tatsuya Otani creator: Toshiaki Kondo creator: Naoki Tani creator: Suat Hui Yeoh uri: https://doi.org/10.7717/peerj.16368 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Suhaimi et al. title: Assessing lead and cadmium tolerance of Chenopodium ambrosioides during micropropagation: an in-depth qualitative and quantitative analysis link: https://peerj.com/articles/16369 last-modified: 2023-11-29 description: The tolerance of Chenopodium ambrosioides to some heavy metals under in vitro environment was thoroughly investigated. A micropropagation protocol was developed to facilitate the mass production of plants and to identify metals-tolerant species for potential use in the restoration of polluted areas. Nodal explants exhibited callus formation when treated with N6-benzyladenin (BA) (1.5 mg/l) and a combination of BA/α-naphthalene acetic acid (NAA) at concentrations of 1.5/1.0 mg/l on the Murashige and Skoog (MS) medium. The optimal shoot formation was achieved with the callus grown on a medium enriched with 1.5/1.0 mg/l BA/NAA, resulting in an impressive number (21.89) and length (11.79 cm) of shoots. The in vitro shoots were rooted using NAA (1.0 and 1.5 mg/l) and were acclimatized in pots with 71% survival rate. After standardizing micropropagation protocol, the in vitro shoots were subjected to various doses of lead nitrate (Pb(NO3)2 and cadmium chloride (CdCl2). Pb(NO3)2 and CdCl2 in the media let to a reduction in shoot multiplication, decreasing from 18.73 in the control group to 11.31 for Pb(NO3)2 and 13.89 for CdCl2 containing medium. However, Pb(NO3)2 and CdCl2 promoted shoot length from 5.61 in the control to 9.86 on Pb(NO3)2 and 12.51 on CdCl2 containing medium. In the case of Pb(NO3)2 treated shoots, the growth tolerance index (GTI) ranged from117.64% to 194.11%, whereas for CdCl2 treated shoots, the GTI ranged from 188.23% to 264.70%. Shoots treated with high level of Pb(NO3)2induced reddish-purple shoots, while a low level of Pb(NO3)2 induced shoots displayed both green and reddish-purple colors in the same explants. In CdCl2 treated culture, the toxic effects were narrow leaf lamina, elongated petiole and a dark reddish purple coloration. These findings highlight the remarkable potential of C. ambrosioides to maintain growth and organogenesis even in the presence Pb(NO3)2 and CdCl2 on the MS medium, indicating a high degree of metal tolerance. creator: Tour Jan creator: Nasrullah Khan creator: Muhammad Wahab creator: Mohammad K. Okla creator: Mostafa A. Abdel-Maksoud creator: Ibrahim A. Saleh creator: Hashem A. Abu-Harirah creator: Tareq Nayef AlRamadneh creator: Hamada AbdElgawad uri: https://doi.org/10.7717/peerj.16369 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jan et al.