A miRNome analysis at the early postmortem interval
The postmortem interval (PMI) is the time elapsing since the death of an individual until the body is examined. Different molecules have been analyzed to better estimate the PMI with variable results. The miRNAs draw attention in the forensic field to estimate the PMI as they can better support degradation. In the present work, we analyzed the miRNome at early PMI in rats’ skeletal muscle using the Affymetrix GeneChip™ miRNA 4.0 microarrays. We found 156 dysregulated miRNAs in rats’ skeletal muscle at 24 h of PMI, out of which 84 were downregulated, and 72 upregulated. The miRNA most significantly downregulated was miR-139-5p (FC = −160, p = 9.97 × 10−11), while the most upregulated was rno-miR-92b-5p (FC = 241.18, p = 2.39 × 10−6). Regarding the targets of these dysregulated miRNAs, the rno-miR-125b-5p and rno-miR-138-5p were the miRNAs with more mRNA targets. The mRNA targets that we found in the present study participate in several biological processes such as interleukin secretion regulation, translation regulation, cell growth, or low oxygen response. In addition, we found a downregulation of SIRT1 mRNA and an upregulation of TGFBR2 mRNA at 24 h of PMI. These results suggest there is an active participation of miRNAs at early PMI which could be further explored to identify potential biomarkers for PMI estimation.
Guardado-Estrada et al. (2023) A miRNome analysis at the early postmortem interval. PeerJ 11:e15409 https://doi.org/10.7717/peerj.15409
Improving taxonomic classification of marine zooplankton by molecular approach: registration of taxonomically verified 18S and 28S rRNA gene sequences
Background Zooplankton plays an important role in the marine ecosystem. A high level of taxonomic expertise is necessary for accurate species identification based on morphological characteristics. As an alternative method to morphological classification, we focused on a molecular approach using 18S and 28S ribosomal RNA (rRNA) gene sequences. This study investigates how the accuracy of species identification by metabarcoding improves when taxonomically verified sequences of dominant zooplankton species are added to the public database. The improvement was tested by using natural zooplankton samples. Methods rRNA gene sequences were obtained from dominant zooplankton species from six sea areas around Japan and registered in the public database for improving the accuracy of taxonomic classifications. Two reference databases with and without newly registered sequences were created. Comparison of detected OTUs associated with single species between the two references was done using field-collected zooplankton samples from the Sea of Okhotsk for metabarcoding analysis to verify whether or not the newly registered sequences improved the accuracy of taxonomic classifications. Results A total of 166 sequences in 96 species based on the 18S marker and 165 sequences in 95 species based on the 28S marker belonging to Arthropoda (mostly Copepoda) and Chaetognatha were registered in the public database. The newly registered sequences were mainly composed of small non-calanoid copepods, such as species belonging to Oithona and Oncaea. Based on the metabarcoding analysis of field samples, a total of 18 out of 92 OTUs were identified at the species level based on newly registered sequences in the data obtained by the 18S marker. Based on the 28S marker, 42 out of 89 OTUs were classified at the species level based on taxonomically verified sequences. Thanks to the newly registered sequences, the number of OTUs associated with a single species based on the 18S marker increased by 16% in total and by 10% per sample. Based on the 28S marker, the number of OTUs associated with a single species increased by 39% in total and by 15% per sample. The improved accuracy of species identification was confirmed by comparing different sequences obtained from the same species. The newly registered sequences had higher similarity values (mean >0.003) than the pre-existing sequences based on both rRNA genes. These OTUs were identified at the species level based on sequences not only present in the Sea of Okhotsk but also in other areas. Discussion The results of the registration of new taxonomically verified sequences and the subsequent comparison of databases based on metabarcoding data of natural zooplankton samples clearly showed an increase in accuracy in species identification. Continuous registration of sequence data covering various environmental conditions is necessary for further improvement of metabarcoding analysis of zooplankton for monitoring marine ecosystems.
Watanabe et al. (2023) Improving taxonomic classification of marine zooplankton by molecular approach: registration of taxonomically verified 18S and 28S rRNA gene sequences. PeerJ 11:e15427 https://doi.org/10.7717/peerj.15427
MFAP2 enhances cisplatin resistance in gastric cancer cells by regulating autophagy
Background Cisplatin (CDDP) is of importance in cancer treatment and widely used in advanced gastric cancer (GC). However, its clinical usage is limited due to its resistance, and the regulatory mechanism of CDDP resistance in GC has not yet been fully elucidated. In this study, we first conducted a comprehensive study to investigate the role of MFAP2 through bioinformatics analysis. Methods The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were applied to downloadgene expression data and clinicopathologic data, and the differentially expressed genes (DEGs) were further analyzed. Then, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and survival analysis were conducted. Furthermore, according to the clinicopathological characteristics of TCGA, clinical correlation analysis was conducted, and a receiver operating characteristic curve (ROC) was plotted. Results We revealed that FAP, INHBA and MFAP2 were good diagnostic factors of GC. However, the mechanism of MFAP2 in GC remains elusive, especially in the aspect of chemotherapy resistance. We developed the CDDP-resistant cell line, and found that MFAP2 was upregulated in CDDP-resistant cells, and MFAP2-knockdown improved CDDP sensitivity. Finally, we found that MFAP2 enhanced CDDP resistance by inducing autophagy in drug-resistant cell lines. Conclusions The above results suggested that MFAP2 could affect the chemotherapy resistance by altering the level of autophagy in GC patients as a potential therapeutic target.
Li et al. (2023) MFAP2 enhances cisplatin resistance in gastric cancer cells by regulating autophagy. PeerJ 11:e15441 https://doi.org/10.7717/peerj.15441
Alterations in gene expressions of Caco-2 cell responses to LPS and ploy(I:C) stimulation
The intestinal epithelium barrier serves as a highly dynamic immunologic frontier in the defense against invading pathogenic bacteria and viruses. Hence, understanding of the complicated underlying relationship between enteric pathogens and the intestinal epithelium barrier is vital for developing strategies to improve the intestinal health of farm animals. To this end, Caco-2 cells were stimulated by 1 µg/ml lipopolysaccharide (LPS) for 24 h and 5 µg/ml polyinosinic-polycytidylic acid (ploy(I:C)) for 4 h to imitate bacterial and viral infection processes, respectively. The specific alterations in gene expression of Caco-2 cells after stimulation were characterized by transcriptome sequencing. Seventy differentially expressed genes (DEGs) were identified under LPS exposure, and 17 DEGs were observed under ploy(I:C) exposure. We found that most DEGs were specific, and only one common DEG SPAG7 was observed. Gene Ontology (GO) annotation analysis indicated that all DEGs identified in the different treatments were mainly derived from GO terms related to the maintenance of cellular homeostasis. Moreover, specific DEGs such as SLC39A10, MT2A, and MT1E regulated by LPS treatment, while IFIT2 and RUNX2 mediated by ploy(I:C) treatment, which are derived from immune function modulation related GO terms, were confirmed by both transcriptome sequencing and qRT-PCR. In addition, both transcriptome sequencing and qRT-PCR results verified that LPS specifically down-regulated the DEGs INHBE and ARF6, which are involved in inflammation responses related to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway including the TGF-beta signaling pathways and the Ras signaling pathway. Ploy(I:C) uniquely suppressed the DEGs GABARAP and LAMTOR3, which participated in viral replication-associated pathways including autophagy and mTOR signaling pathway.
Qin et al. (2023) Alterations in gene expressions of Caco-2 cell responses to LPS and ploy(I:C) stimulation. PeerJ 11:e15459 https://doi.org/10.7717/peerj.15459
Endophytic fungus Biscogniauxia petrensis produces antibacterial substances
Widespread drug resistance and limited antibiotics challenge the treatment of pathogenic bacteria, which leads to a focus on searching for new antimicrobial lead compounds. We found the endophytic fungus Biscogniauxia petrensis MFLUCC14-0151 from the medicinal plant Dendrobium harveyanum had antibacterial activity for the first time. This work aimed to reveal the capacity of Biscogniauxia petrensis MFLUCC14-0151 against foodborne pathogenic bacteria and identify its bioactive substances. Bioassay-guided isolation led to the discovery of six infrequent active monomers, including (10R)-Xylariterpenoid B (1), Xylariterpenoid C (2), Tricycloalternarene 1b (3), Tricycloalternarene 3b (4), Funicin (5) and Vinetorin (6) from MFLUCC14-0151 for the first time. The results of antibacterial tests showed that (10R)-Xylariterpenoid B and Xylariterpenoid C exhibited inhibitory activities against Streptococcus agalactiae with MIC values ranging from 99.21 to 100.00 μM, and against Streptococcus aureus with MIC values ranging from 49.60 to 50.00 μM. Tricycloalternarene 1b and Tricycloalternarene 3b showed inhibitory effects on Streptococcus agalactiae with MIC values ranging from 36.13 to 75.76 μM. Unexpectedly, Funicin and Vinetorin exhibited remarkable antagonistic activities against Streptococcus agalactiae with MIC values of 10.35 and 10.21 μM, respectively, and against Streptococcus aureus with MIC values of 5.17 and 20.42 μM, respectively. In conclusion, we suggest that the isolated compounds Funicin and Vinetorin may be promising lead compounds for natural antibacterial agents.
Han et al. (2023) Endophytic fungus Biscogniauxia petrensis produces antibacterial substances. PeerJ 11:e15461 https://doi.org/10.7717/peerj.15461
The introduction of an invasive weed was not followed by the introduction of ethnobotanical knowledge: a review on the ethnobotany of Centaurea solstitialis L. (Asteraceae)
Invasive plants are known for their impacts to ecosystems and societies, but their potential cultural use tend to be unexplored. One important mechanism of plant invasion is the use of “allelochemicals” or “novel weapons”: chemical defenses which are new to their invaded habitats and that confer them competitive advantages. However, these chemicals are precisely what confers them ethnobotanical and medicinal properties. We reviewed the literature assessing the biogeography of the cultural uses of the model invasive plant yellow-starthistle (Centaurea solstitialis L.; Asteraceae), and assessed the extent to which the introduction of a weed native to Eurasia into several non-native world regions was paralleled by the spread of cultural uses from its native range. We found that the species was rich in pharmaceutically active compounds and that the species had been traditionally used for medicinal purposes, as raw material, and as food. However, ethnobotanical uses were reported almost exclusively in its native range, with no uses described for the non-native range, apart from honey production in California, Argentina, and Australia. Our study exemplifies how, when plant introductions are not paralleled synchronously by significant human migrations, cultural adoption can be extremely slow, even within the native range of the species. Invasive species can provide real-time insights into the cultural processes by which humans learn to use plants. This case study highlights how biological invasions and cultural expansions can be subjected to different constraints.
Branco et al. (2023) The introduction of an invasive weed was not followed by the introduction of ethnobotanical knowledge: a review on the ethnobotany of Centaurea solstitialis L. (Asteraceae). PeerJ 11:e15489 https://doi.org/10.7717/peerj.15489
Raptor couples mTORC1 and ERK1/2 inhibition by cardamonin with oxidative stress induction in ovarian cancer cells
Background A balance on nutrient supply and redox homeostasis is required for cell survival, and increased antioxidant capacity of cancer cells may lead to chemotherapy failure. Objective To investigate the mechanism of anti-proliferation of cardamonin by inducing oxidative stress in ovarian cancer cells. Methods After 24 h of drug treatment, CCK8 kit and wound healing test were used to detect cell viability and migration ability, respectively, and the ROS levels were detected by flow cytometry. The differential protein expression after cardamonin administration was analyzed by proteomics, and the protein level was detected by Western blotting. Results Cardamonin inhibited the cell growth, which was related to ROS accumulation. Proteomic analysis suggested that MAPK pathway might be involved in cardamonin-induced oxidative stress. Western blotting showed that cardamonin decreased Raptor expression and the activity of mTORC1 and ERK1/2. Same results were observed in Raptor KO cells. Notably, in Raptor KO cells, the effect of cardamonin was weakened. Conclusion Raptor mediated the function of cardamonin on cellular redox homeostasis and cell proliferation through mTORC1 and ERK1/2 pathways.
Zhu et al. (2023) Raptor couples mTORC1 and ERK1/2 inhibition by cardamonin with oxidative stress induction in ovarian cancer cells. PeerJ 11:e15498 https://doi.org/10.7717/peerj.15498
Diagnostic value and characteristic analysis of serum nucleocapsid antigen in COVID-19 patients
Background To date, several types of laboratory tests for coronavirus disease 2019 (COVID-19) diagnosis have been developed. However, the clinical importance of serum severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen (N-Ag) remains to be fully elucidated. In this study, we sought to investigate the value of serum SARS-CoV-2 N-Ag for COVID-19 diagnosis and to analyze N-Ag characteristics in COVID-19 individuals. Methods Serum samples collected from 215 COVID-19 patients and 65 non-COVID-19 individuals were used to quantitatively detect N-Ag via chemiluminescent immunoassay according to the manufacturer’s instructions. Results The sensitivity and specificity of the N-Ag assay were 64.75% (95% confidence interval (95% CI) [55.94–72.66%]) and 100% (95% CI [93.05–100.00%]), respectively, according to the cut-off value recommended by the manufacturer. The receiver operating characteristic (ROC) curve showed a sensitivity of 100.00% (95% CI [94.42–100.00%]) and a specificity of 71.31% (95% CI [62.73–78.59%]). The positive rates and levels of serum SARS-CoV-2 N-Ag were not related to sex, comorbidity status or disease severity of COVID-19 (all P < 0.001). Compared with RT‒PCR, there was a lower positive rate of serum N-Ag for acute COVID-19 patients (P < 0.001). The positive rate and levels of serum SARS-CoV-2 N-Ag in acute patients were significantly higher than those in convalescent patients (all P < 0.001). In addition, the positive rate of serum SARS-CoV-2 N-Ag in acute COVID-19 patients was higher than that of serum antibodies (IgM, IgG, IgA and neutralizing antibodies (Nab)) against SARS-CoV-2 (all P < 0.001). However, the positive rate of serum SARS-CoV-2 N-Ag in convalescent COVID-19 patients was significantly lower than that of antibodies (all P < 0.001). Conclusion Serum N-Ag can be used as a biomarker for early COVID-19 diagnosis based on appropriate cut-off values. In addition, our study also demonstrated the relationship between serum N-Ag and clinical characteristics.
Zhang et al. (2023) Diagnostic value and characteristic analysis of serum nucleocapsid antigen in COVID-19 patients. PeerJ 11:e15515 https://doi.org/10.7717/peerj.15515
Soil organic carbon pools and carbon management index under different land use systems in North western Himalayas
Current study was conducted to evaluate the effect of important land uses and soil depth on soil organic carbon pools viz. total organic carbon, Walkley and black carbon, labile organic carbon, particulate organic carbon, microbial biomass carbon and carbon management index (CMI) in the north Western Himalayas, India. Soil samples from five different land uses viz. forest, pasture, apple, saffron and paddy-oilseed were collected up to a depth of 1 m (0–30, 30–60, 60–90 cm). The results revealed that regardless of soil depth, all the carbon pools differed significantly (p < 0.05) among studied land use systems with maximum values observed under forest soils and lowest under paddy-oilseed soils. Further, upon evaluating the impact of soil depth, a significant (p < 0.05) decline and variation in all the carbon pools was observed with maximum values recorded in surface (0–30 cm) soils and least in sub-surface (60–90 cm) layers. CMI was higher in forest soils and lowest in paddy-oilseed. From regression analysis, a positive significant association (high R-squared values) between CMI and soil organic carbon pools was also observed at all three depths. Therefore, land use changes and soil depth had a significant impact on soil organic carbon pools and eventually on CMI, which is used as deterioration indicator or soil carbon rehabilitation that influences the universal goal of sustainability in the long run.
Mir et al. (2023) Soil organic carbon pools and carbon management index under different land use systems in North western Himalayas. PeerJ 11:e15266 https://doi.org/10.7717/peerj.15266
Bombardiers and assassins: mimetic interactions between unequally defended insects
In defensive mimicry, resemblance between unequally defended species can be parasitic; this phenomenon has been termed quasi-Batesian mimicry. Few studies have used real co-mimics and their predators to test whether the mimetic interactions were parasitic. Here, we investigated the mimetic interaction between two well-defended insect species, the bombardier beetle Pheropsophus occipitalis jessoensis (Coleoptera: Carabidae) and the assassin bug Sirthenea flavipes (Hemiptera: Reduviidae), using their potential predator, the pond frog Pelophylax nigromaculatus (Anura: Ranidae), which coexists with these insect species in the same habitat in Japan. We observed behavioural responses of this frog species (adults and juveniles) to adult Ph. occipitalis jessoensis and adult S. flavipes under laboratory conditions. Among the frogs, 100% and 75% rejected Ph. occipitalis jessoensis and S. flavipes, respectively, suggesting that, compared with the assassin bug S. flavipes, the bombardier beetle Ph. occipitalis jessoensis is more well-defended against frogs. An assassin bug or a bombardier beetle was provided to a frog that had encountered the other insect species. Frogs with a history of assassin bug encounter demonstrated a lower rate of attack toward bombardier beetles. Similarly, frogs with a history of bombardier beetle encounter demonstrated a lower rate of attack toward assassin bugs. Therefore, both the bombardier beetle Ph. occipitalis jessoensis and the assassin bug S. flavipes benefit from the mimetic interaction.
Sugiura et al. (2023) Bombardiers and assassins: mimetic interactions between unequally defended insects. PeerJ 11:e15380 https://doi.org/10.7717/peerj.15380