title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=372 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Mitochondrial and nuclear gene sequencing confirms the presence of the invasive sea anemone Diadumene lineata (Verrill, 1869) (Cnidaria: Actiniaria) in Argentina link: https://peerj.com/articles/16479 last-modified: 2023-11-27 description: BackgroundDiadumene lineata is one of the most widespread sea anemone species worldwide. Although this species has been reported a few times on the Argentine coast since 2004, its identification has traditionally been based on external morphological characteristics, and in most cases no voucher specimens are available to support previous records.MethodsIn this study, we obtained DNA sequences of two mitochondrial markers (12S and 16S) and two nuclear markers (18S and 28S) from specimens of D. lineata collected in two locations on the Argentine coast separated by almost 800 km. Additionally, we conducted an analysis of the morphology, as well as the types and size ranges of cnidae, using specimens collected at three different locations along the Argentine coast. Furthermore, since introduced populations of D. lineata are presumably ephemeral and only reproduce asexually outside their native range, we examined the internal anatomy of representatives from the Argentine coast for gametogenic tissue as an indication of whether they might be capable of sexual reproduction.ResultsDNA data support our morphological identification, including cnidae analyses, of the specimens as D. lineata. Furthermore, all specimens examined were determined to be sterile.DiscussionGenetic sequence comparisons, phylogenetic reconstruction, and cnidae data support the identification of individuals of D. lineata from Mar Chiquita and Garipe Beach, confirming the presence of the species on the Argentine coast using both morphological and molecular tools. The absence of fertile specimens suggests that each sampled population is likely reproducing only by asexual reproduction and possibly composed of clones. The presence of an additional category of longer p-mastigophores B2a in the actinopharynx and filaments, as well as holotrichs in the column, is also reported.ConclusionsFor the first time, we have confirmed the presence of D. lineata in Argentina through molecular data. Additionally, our findings indicate that the analyzed specimens are sterile, suggesting that this species is not engaging in sexual reproduction in the studied localities. It is crucial to continue monitoring the populations of D. lineata along the Argentine coast to assess whether they establish sexual reproduction, expand their distribution range or disappear, or potentially cause any harm to local species or alterations in benthic communities. creator: Ricardo González Muñoz creator: Daniel Lauretta creator: María Cielo Bazterrica creator: Francisco Alejandro Puente Tapia creator: Agustín Garese creator: Gregorio Bigatti creator: Pablo E. Penchaszadeh creator: Betina Lomovasky creator: Fabián H. Acuña uri: https://doi.org/10.7717/peerj.16479 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 González Muñoz et al. title: Sirtuin 1 alleviates alcoholic liver disease by inhibiting HMGB1 acetylation and translocation link: https://peerj.com/articles/16480 last-modified: 2023-11-27 description: BackgroundAlcoholic liver disease (ALD) encompasses a spectrum of liver disorders resulting from prolonged alcohol consumption and is influenced by factors such as oxidative stress, inflammation, and apoptosis. High Mobility Group Box 1 (HMGB1) plays a pivotal role in ALD due to its involvement in inflammation and immune responses. Another key factor, Sirtuin 1 (SIRT1), an NAD+-dependent deacetylase, is known for its roles in cellular stress responses and metabolic regulation. Despite individual studies on HMGB1 and SIRT1 in ALD, their specific molecular interactions and combined effects on disease advancement remain incompletely understood.MethodsAlcohol-induced liver injury (ALI) models were established using HepG2 cells and male C57BL/6 mice. HMGB1 and SIRT1 expressions were assessed at the mRNA and protein levels usingreverse transcription-quantitative polymerase chain reaction, western blot, and immunofluorescence staining. The physical interaction between HMGB1 and SIRT1 was investigated using co-immunoprecipitation and immunofluorescence co-expression analyses. Cellular viability was evaluated using the CCK-8 assay.ResultsIn patients with clinical ALI, HMGB1 mRNA levels were elevated, while SIRT1 expression was reduced, indicating a negative correlation between the two. ALI models were successfully established in cells and mice, as evidenced by increased markers of cellular and liver damage. HMGB1 acetylation and translocation were observed in both ALI cells and mouse models. Treatment with the SIRT1 agonist, SRT1720, reversed the upregulation of HMGB1 acetylation, nuclear translocation, and release in the ethyl alcohol (EtOH) group. Furthermore, SIRT1 significantly attenuated ALI. Importantly, in vivo binding was confirmed between SIRT1 and HMGB1.ConclusionsSIRT1 alleviates HMGB1 acetylation and translocation, thereby ameliorating ALI. creator: Juan Fu creator: Wei Deng creator: Jun Ge creator: Shengqi Fu creator: Panpan Li creator: Huazhi Wu creator: Jiao Wang creator: Yi Gao creator: Hui Gao creator: Tao Wu uri: https://doi.org/10.7717/peerj.16480 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Fu et al. title: Context of substance initiation among urban Native Americans: an exploratory retrospective case-control study link: https://peerj.com/articles/16482 last-modified: 2023-11-27 description: BackgroundAddiction is a significant problem among many Native American groups but has rarely been examined in urban populations. In particular, little is known about the context in which urban Native Americans first use substances. This study compares cases (people with a history of addiction) to controls (people without a history of addiction) on demographics, substance use history, context of first substance use, and polysubstance use. In addition, this appears to be the first study to overcome the lack of Native American professionals by employing and training lay community members to identify criteria of substance use disorders in survey participants. Employing community members helped foster trust that enabled the revelation of sensitive and often illegal activity. As a result, the investigators were able to recruit participants who likely would not have engaged with traditional researchers.MethodsThe trained Native American lay research assistants recruited community members and administered surveys. They first asked questions regarding the criteria for substance use disorders. Individuals who were determined to have met criteria for a substance use disorder in the past were classified as cases (n = 38) and those who never met such criteria were classified as controls (n = 42). They then asked demographic, substance use, and polysubstance use questions. Lastly, eight cases and eight controls were randomly selected for a second interview by a licensed drug and alcohol counselor (LDAC) who conducted a blinded assessment regarding the presence or absence of a history of a substance use disorder.ResultsBoth groups reported a relatively young age of first substance use (age 16 years for cases and age 15 years for controls). Alcohol was the first substance most commonly used in both groups. Controls reported first benzodiazepine use at a younger age than cases but no other significant differences were found. Both groups reported first obtaining their first drug from family, friends, or at home (rather than a party, bar, or store). Most commonly, the location of their first use of drugs occurred at a friend’s home, a party, a bar, or school rather than at their own home. Cases were marginally more likely to report that their first drug use occurred with a friend rather than with a family member when compared with controls. The majority of both groups reported that their first drug use occurred with other Native Americans rather than with non-Native Americans. Polysubstance use was common in both groups (43–45%). There were no significant differences between the groups regarding polysubstance use. The LDAC arrived at the same determination as the trained research assistants on all eight cases and eight controls. creator: Nicholas Guenzel creator: Hongying Daisy Dai creator: Lyndsay Dean uri: https://doi.org/10.7717/peerj.16482 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guenzel et al. title: Clinicopathologic features and prognosis of 71 patients with gastric cancer and disseminated intravascular coagulation link: https://peerj.com/articles/16527 last-modified: 2023-11-27 description: BackgroundGastric cancer consists of solid tumors with a tendency for disseminated intravascular coagulation (DIC). DIC is rare in patients with stomach cancer, and there have been few studies on this condition. We aimed to perform comprehensive analyses of the prognosis and clinicopathologic characteristics of stomach cancer patients with DIC.MethodsBetween June 2006 and March 2020, 14,016 patients at Fujian Cancer Hospital were diagnosed with stomach cancer. We reviewed their medical records and found that 105 of these patients were diagnosed with DIC. After excluding patients who were lost to follow-up, 71 patients with DIC remained. The clinical data were retrospectively analyzed to observe clinical characteristics and prognostic factors, and the Kaplan–Meier survival analysis was performed. Prognostic variables were investigated by the Cox proportional hazards method.ResultsThe median age was 54 (range, 21–83) years, and 38 patients (53.5%) were male. The histological category was poorly differentiated gastric cancer in 58 patients (81.7%). Eleven patients (15.5%) developed DIC after curative gastric resection. Sixty patients (84.5%) had DIC at the initial presentation of gastric cancer or developed DIC when the tumor progressed during treatment. Fifty-one patients (71.8%) had bleeding symptoms, and 43 (60.6%) patients had comorbidities at the time of DIC diagnosis. Among the 71 patients, 42 (59.2%) had multiple metastatic patterns. Twenty-one (29.6%) patients received chemotherapy. The median overall survival (OS) was 57.0 days (95% confidence interval [CI] [33.1–80.9] days). Tumor status (P = 0.000) and treatment (P = 0.003) were found to be significant variables associated with OS by univariate analysis. Multivariate analysis showed that tumor status (P = 0.000) and treatment (P = 0.000) had independent effects on OS.ConclusionsGastrointestinal bleeding, multiple metastatic patterns and comorbidities at diagnosis with DIC are common in patients with gastric cancer complicated with DIC. Patients with poorly differentiated gastric cancer are more likely to develop DIC. Treatment and tumor status are separate risk variables for the survival of gastric cancer patients with DIC.DIC patients without tumors have a good prognosis and can be cured by appropriate etiological correction and symptomatic treatment. Chemotherapy can improve the prognosis of DIC patients with tumors. creator: Ling Chen creator: Jing Lin creator: Yu Chen creator: Jiami Yu creator: Xiaojie Wang uri: https://doi.org/10.7717/peerj.16527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chen et al. title: Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs link: https://peerj.com/articles/16381 last-modified: 2023-11-24 description: Sponges are widely spread organisms in the tropical reefs of the American Northwest-Atlantic Ocean, they structure ecosystems and provide services such as shelter, protection from predators, and food sources to a wide diversity of both vertebrates and invertebrates species. The high diversity of sponge-associated fauna can generate complex networks of species interactions over small and large spatial-temporal gradients. One way to start uncovering the organization of the sponge host-guest complex networks is to understand how the accumulated geographic area, the sponge morphology and, sponge taxonomy contributes to the connectivity of sponge species within such networks. This study is a meta-analysis based on previous sponge host-guest literature obtained in 65 scientific publications, yielding a total of 745 host-guest interactions between sponges and their associated fauna across the Caribbean Sea and the Gulf of Mexico. We analyzed the sponge species contribution to network organization in the Northwest Tropical Atlantic coral reefs by using the combination of seven complementary species-level descriptors and related this importance with three main traits, sponge-accumulated geographic area, functional sponge morphology, and sponges’ taxonomy bias. In general, we observed that sponges with a widespread distribution and a higher accumulated geographic area had a greater network structural contribution. Similarly, we also found that Cup-like and Massive functional morphologies trend to be shapes with a greater contribution to the interaction network organization compared to the Erect and Crust-like morphos. Lastly, we did not detect a taxonomy bias between interaction network organization and sponges’ orders. These results highlight the importance of a specific combination of sponge traits to promote the diversity of association between reef sponges and their guest species. creator: Antar Mijail Pérez-Botello creator: Wesley Dáttilo creator: Nuno Simões uri: https://doi.org/10.7717/peerj.16381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Pérez Botello et al. title: Environmental dissemination of respiratory viruses: dynamic interdependencies of respiratory droplets, aerosols, aerial particulates, environmental surfaces, and contribution of viral re-aerosolization link: https://peerj.com/articles/16420 last-modified: 2023-11-24 description: During the recent pandemic of COVID-19 (SARS-CoV-2), influential public health agencies such as the World Health Organization (WHO) and the U.S. Centers for Disease Control and Prevention (CDC) have favored the view that SARS CoV-2 spreads predominantly via droplets. Many experts in aerobiology have openly opposed that stance, forcing a vigorous debate on the topic. In this review, we discuss the various proposed modes of viral transmission, stressing the interdependencies between droplet, aerosol, and fomite spread. Relative humidity and temperature prevailing determine the rates at which respiratory aerosols and droplets emitted from an expiratory event (sneezing, coughing, etc.) evaporate to form smaller droplets or aerosols, or experience hygroscopic growth. Gravitational settling of droplets may result in contamination of environmental surfaces (fomites). Depending upon human, animal and mechanical activities in the occupied space indoors, viruses deposited on environmental surfaces may be re-aerosolized (re-suspended) to contribute to aerosols, and can be conveyed on aerial particulate matter such as dust and allergens. The transmission of respiratory viruses may then best be viewed as resulting from dynamic virus spread from infected individuals to susceptible individuals by various physical states of active respiratory emissions, instead of the current paradigm that emphasizes separate dissemination by respiratory droplets, aerosols or by contaminated fomites. To achieve the optimum outcome in terms of risk mitigation and infection prevention and control (IPAC) during seasonal infection peaks, outbreaks, and pandemics, this holistic view emphasizes the importance of dealing with all interdependent transmission modalities, rather than focusing on one modality. creator: M. Khalid Ijaz creator: Syed A. Sattar creator: Raymond W. Nims creator: Stephanie A. Boone creator: Julie McKinney creator: Charles P. Gerba uri: https://doi.org/10.7717/peerj.16420 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ijaz et al. title: Differentiating wild from captive animals: an isotopic approach link: https://peerj.com/articles/16460 last-modified: 2023-11-24 description: BackgroundWildlife farming can be an important but complex tool for conservation. To achieve conservation benefits, wildlife farming should meet a variety of criteria, including traceability conditions to identify the animals’ origin. The traditional techniques for discriminating between wild and captive animals may be insufficient to prevent doubts or misdeclaration, especially when labels are not expected or mandatory. There is a pressing need to develop more accurate techniques to discriminate between wild and captive animals and their products. Stable isotope analysis has been used to identify animal provenance, and some studies have successfully demonstrated its potential to differentiate wild from captive animals. In this literature review, we examined an extensive collection of publications to develop an overall picture of the application of stable isotopes to distinguish between wild and captive animals focusing on evaluating the patterns and potential of this tool.Survey methodologyWe searched peer-reviewed publications in the Web of Science database and the references list from the main studies on the subject. We selected and analyzed 47 studies that used δ13C, δ15N, δ2H, δ18O, and δ34S in tissues from fish, amphibians, reptiles, birds, and mammals. We built a database from the isotope ratios and metadata extracted from the publications.ResultsStudies have been using stable isotopes in wild and captive animals worldwide, with a particular concentration in Europe, covering all main vertebrate groups. A total of 80.8% of the studies combined stable isotopes of carbon and nitrogen, and 88.2% used at least one of those elements. Fish is the most studied group, while amphibians are the least. Muscle and inert organic structures were the most analyzed tissues (46.81% and 42.55%). δ13C and δ15N standard deviation and range were significantly higher in the wild than in captive animals, suggesting a more variable diet in the first group. δ13C tended to be higher in wild fishes and in captive mammals, birds, reptiles, and amphibians. δ15N was higher in the wild terrestrial animals when controlling for diet. Only 5.7% of the studies failed to differentiate wild and captive animals using stable isotopes.ConclusionsThis review reveals that SIA can help distinguish between wild and captive in different vertebrate groups, rearing conditions, and methodological designs. Some aspects should be carefully considered to use the methodology properly, such as the wild and captivity conditions, the tissue analyzed, and how homogeneous the samples are. Despite the increased use of SIA to distinguish wild from captive animals, some gaps remain since some taxonomic groups (e.g., amphibians), countries (e.g., Africa), and isotopes (e.g., δ2H, δ18O, and δ34S) have been little studied. creator: Luiza Brasileiro creator: Rodrigo Ribeiro Mayrink creator: André Costa Pereira creator: Fabio José Viana Costa creator: Gabriela Bielefeld Nardoto uri: https://doi.org/10.7717/peerj.16460 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Brasileiro et al. title: Development of a 5-mRNAsi-related gene signature to predict the prognosis of colon adenocarcinoma link: https://peerj.com/articles/16477 last-modified: 2023-11-24 description: AimTo create a prognosis model based on mRNA-based stem index (mRNAsi) for evaluating the prognostic outcomes of colon adenocarcinoma (COAD).BackgroundGeneration of heterogeneous COAD cells could be promoted by the self-renewal and differentiation potential of cancer stem cells (CSCs). Biomarkers contributing to the development of COAD stem cells remained to be discovered.ObjectiveTo develop and validate an mRNAsi-based risk model for estimating the prognostic outcomes of patients suffering from COAD.MethodsSamples were collected from Rectal Adenocarcinoma (TCGA-READ) PanCancer Atlas datasets, The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD), and the GSE87211 dataset. MRNAsi was calculated by one-class logistic regression (OCLR) algorithm. Under the criterion of correlation greater than 0.4, genes related to mRNAsi were screened and clustered. Meanwhile, differentially expressed genes (DEGs) between molecular subtypes were identified to establish a risk model. According to the median risk score value for immunotherapy and results from immune cell infiltration and clinicopathological analyses, clusters and patients were divided into high-RiskScore and low-RiskScore groups. Cell apoptosis and viability were detected by flow cytometer and Cell Counting Kit-8 (CCK-8) assay, respectively.ResultsA negative correlation between mRNAsi and clinical stages was observed. Three clusters of patients (C1, C2, and C3) were defined based on a total of 165 survival-related mRNAsi genes. Specifically, C1 patients had greater immune cell infiltration and a poorer prognosis. A 5-mRNAsi-gene signature (HEYL, FSTL3, FABP4, ADAM8, and EBF4) served as a prediction index for COAD prognosis. High-RiskScore patients had a poorer prognosis and higher level of immune cell infiltration. In addition, the five genes in the signature all showed a high expression in COAD cells. Knocking down HEYL promoted COAD cell apoptosis and inhibited viability.ConclusionOur mRNAsi risk model could better predict the prognosis of COAD patients. creator: Haifu Huang creator: Lin Lu creator: Yaoxuan Li creator: Xiumei Chen creator: Meng Li creator: Meiling Yang creator: Xuewu Huang uri: https://doi.org/10.7717/peerj.16477 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al. title: Assessment of genetic diversity and phylogenetic relationship of local coffee populations in southwestern Saudi Arabia using DNA barcoding link: https://peerj.com/articles/16486 last-modified: 2023-11-24 description: The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts. creator: Habib Khemira creator: Mosbah Mahdhi creator: Muhammad Afzal creator: Mohammed D.Y. Oteef creator: Taieb Tounekti creator: Zarraq AL-Faifi creator: Wail Alsolami uri: https://doi.org/10.7717/peerj.16486 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Khemira et al. title: Antioxidant activity, anti-tyrosinase activity, molecular docking studies, and molecular dynamic simulation of active compounds found in nipa palm vinegar link: https://peerj.com/articles/16494 last-modified: 2023-11-24 description: Tyrosinase is a key enzyme in melanogenesis and its inhibitors have become increasingly because of their potential activity as hypopigmenting agents which have less side effects. Nipa palm vinegar is an aqueous product that is normally used as a food supplement. The aim of this study was to study the determination of antioxidant activity and tyrosinase inhibitory activities of aqueous extract of original nipa palm vinegar (AE O-NPV), nipa palm vinegar powder (NPV-P) and aqueous extract of nipa palm vinegar powder (AE NPV-P) were examined. Nipa palm vinegars were evaluated the phenolic and flavonoid content, and the active compounds which were submitted to molecular docking and molecular dynamic simulation, chemoinformatics, rule of five, skin absorption and toxicity. The highest phenolic and flavonoid contents in the AE O-NPV were 2.36 ± 0.23 mg gallic acid equivalents/g extract and 5.11 ± 0.59 mg quercetin equivalents/g, and the highest ABTS radical cation scavenging activity was also found. The AE O-NPV, NPV-P and AE NPV-P showed anti-mushroom tyrosinase activity. The HPLC analysis showed that there were vanillic acid and three flavonoids (catechin, rutin and quercetin). The molecular docking study revealed that the binding of the vanillic acid and three flavonoids occurred in the active site residues (histidine and other amino acids). Moreover, the number of hydrogen bond acceptors/donors, solubility, polar surface area and bioavailability score of the vanillic acid and three flavonoids were acceptable compared to Lipinski’s Rule of Five. The molecular dynamic simulation showed that vanillic acid interacts with HIS284 through π–π stacking hydrophobic interactions and forms a metal-acceptor interaction with the copper molecule at the tyrosinase active site. All compounds revealed good skin permeability and nontoxicity. Nipa palm vinegar could be a promising source of a new ingredient for tyrosinase inhibition for cosmetics or pharmaceutical products. creator: Moragot Chatatikun creator: Aman Tedasen creator: Nawanwat Chainuwong Pattaranggoon creator: Wilawan Palachum creator: Sirithip Chuaijit creator: Amron Mudpan creator: Supawita Pruksaphanrat creator: Sasirat Sohbenalee creator: Kenshi Yamasaki creator: Wiyada Kwanhian Klangbud uri: https://doi.org/10.7717/peerj.16494 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chatatikun et al.