Analysis of the HD-Zip I transcription factor family in Salvia miltiorrhiza and functional research of SmHD-Zip12 in tanshinone synthesis
Background The homeodomain-leucine zipper I (HD-Zip I) transcription factor is a plant-specific protein that plays an essential role in the abiotic stress response of plants. Research on the HD-Zip I family in Salvia miltiorrhiza is still lacking. Methods and Results In this study, a total of 25 SmHD-Zip I proteins were identified. Their characterizations, phylogenetic relationships, conserved motifs, gene structures, and cis-elements were analyzed comprehensively using bioinformatics methods. Expression profiling revealed that SmHD-Zip I genes exhibited distinctive tissue-specific patterns and divergent responses to ABA, PEG, and NaCl stresses. SmHD-Zip12 responded the most strongly to ABA, PEG, and NaCl, so it was used for transgenic experiments. The overexpression of SmHD-Zip12 significantly increased the content of cryptotanshinone, dihydrotanshinone I, tanshinone I, and tanshinone IIA by 2.89-fold, 1.85-fold, 2.14-fold, and 8.91-fold compared to the wild type, respectively. Moreover, in the tanshinone biosynthetic pathways, the overexpression of SmHD-Zip12 up-regulated the expression levels of SmAACT, SmDXS, SmIDS, SmGGPPS, SmCPS1, SmCPS2, SmCYP76AH1, SmCYP76AH3, and SmCYP76AK1 compared with the wild type. Conclusions This study provides information the possible functions of the HD-Zip I family and lays a theoretical foundation for clarifying the functional mechanism of the SmHD-Zip12 gene in regulating the synthesis of tanshinone in S. miltiorrhiza.
Bai et al. (2023) Analysis of the HD-Zip I transcription factor family in Salvia miltiorrhiza and functional research of SmHD-Zip12 in tanshinone synthesis. PeerJ 11:e15510 https://doi.org/10.7717/peerj.15510
Disclosing the native blueberry rhizosphere community in Portugal—an integrated metagenomic and isolation approach
Backgorund The production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop’s resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices. Methods In this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms. Results Results showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants. Discussion This work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops.
Gomes et al. (2023) Disclosing the native blueberry rhizosphere community in Portugal—an integrated metagenomic and isolation approach. PeerJ 11:e15525 https://doi.org/10.7717/peerj.15525
A preliminary study of the salivary microbiota of young male subjects before, during, and after acute high-altitude exposure
Background The microbial community structure in saliva differs at different altitudes. However, the impact of acute high-altitude exposure on the oral microbiota is unclear. This study explored the impact of acute high-altitude exposure on the salivary microbiome to establish a foundation for the future prevention of oral diseases. Methods. Unstimulated whole saliva samples were collected from 12 male subjects at the following three time points: one day before entering high altitude (an altitude of 350 m, pre-altitude group), seven days after arrival at high altitude (an altitude of 4,500 m, altitude group) and seven days after returning to low altitude (an altitude of 350 m, post-altitude group). Thus, a total of 36 saliva samples were obtained. 16S rRNA V3-V4 region amplicon sequencing was used to analyze the diversity and structure of the salivary microbial communities, and a network analysis was employed to investigate the relationships among salivary microorganisms. The function of these microorganisms was predicted with a Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Results In total, there were 756 operational taxonomic units (OTUs) identified, with 541, 613, and 615 OTUs identified in the pre-altitude, altitude, and post-altitude groups, respectively. Acute high-altitude exposure decreased the diversity of the salivary microbiome. Prior to acute high-altitude exposure, the microbiome mainly consisted of Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria. After altitude exposure, the relative abundance of Streptococcus and Veillonella increased, and the relative abundance of Prevotella, Porphyromonas, and Alloprevotella decreased. The relationship among the salivary microorganisms was also affected by acute high-altitude exposure. The relative abundance of carbohydrate metabolism gene functions was upregulated, while the relative abundance of coenzyme and vitamin metabolism gene functions was downregulated. Conclusion Rapid high-altitude exposure decreased the biodiversity of the salivary microbiome, changing the community structure, symbiotic relationships among species, and abundance of functional genes. This suggests that the stress of acute high-altitude exposure influenced the stability of the salivary microbiome.
Zhou et al. (2023) A preliminary study of the salivary microbiota of young male subjects before, during, and after acute high-altitude exposure. PeerJ 11:e15537 https://doi.org/10.7717/peerj.15537
Construction and validation of a novel IGFBP3-related signature to predict prognosis and therapeutic decision making for Hepatocellular Carcinoma
Background IGFBP3 plays a pivotal role in carcinogenesis by being anomalously expressed in some malignancies. However, the clinical value of IGFBP3 and the role of IGFBP3-related signature in HCC remain unclear. Methods Multiple bioinformatics methods were used to determine the expression and diagnostic values of IGFBP3. The expression level of IGFBP3 was validated by RT-qPCR and IHC. A IGFBP3-related risk score (IGRS) was built via correlation analysis and LASSO Cox regression analysis. Further analyses, including functional enrichment, immune status of risk groups were analyzed, and the role of IGRS in guiding clinical treatment was also evaluated. Results IGFBP3 expression was significantly downregulated in HCC. IGFBP3 expression correlated with multiple clinicopathological characteristics and demonstrated a powerful diagnostic capability for HCC. In addition, a novel IGRS signature was developed in TCGA, which exhibited good performance for prognosis prediction and its role was further validated in GSE14520. In TCGA and GSE14520, Cox analysis also confirmed that the IGRS could serve as an independent prognostic factor for HCC. Moreover, a nomogram with good accuracy for predicting the survival of HCC was further formulated. Additionally, enrichment analysis showed that the high-IGRS group was enriched in cancer-related pathways and immune-related pathways. Additionally, patients with high IGRS exhibited an immunosuppressive phenotype. Therefore, patients with low IGRS scores may benefit from immunotherapy. Conclusions IGFBP3 can act as a new diagnostic factor for HCC. IGRS signature represents a valuable predictive tool in the prognosis prediction and therapeutic decision making for Hepatocellular Carcinoma.
Chen et al. (2023) Construction and validation of a novel IGFBP3-related signature to predict prognosis and therapeutic decision making for Hepatocellular Carcinoma. PeerJ 11:e15554 https://doi.org/10.7717/peerj.15554
Electrochemical biosensors in healthcare services: bibliometric analysis and recent developments
Biosensors are nowadays being used in various fields including disease diagnosis and clinical analysis. The ability to detect biomolecules associated with disease is vital not only for accurate diagnosis of disease but also for drug discovery and development. Among the different types of biosensors, electrochemical biosensor is most widely used in clinical and health care services especially in multiplex assays due to its high susceptibility, low cost and small in size. This article includes comprehensive review of biosensors in medical field with special emphasis on electrochemical biosensors for multiplex assays and in healthcare services. Also, the publications on electrochemical biosensors are increasing rapidly; therefore, it is crucial to be aware of any latest developments or trends in this field of research. We used bibliometric analyses to summarize the progress of this research area. The study includes global publication counts on electrochemical biosensors for healthcare along with various bibliometric data analyses by VOSviewer software. The study also recognizes the top authors and journals in the related area, and determines proposal for monitoring research.
Yunus et al. (2023) Electrochemical biosensors in healthcare services: bibliometric analysis and recent developments. PeerJ 11:e15566 https://doi.org/10.7717/peerj.15566
Assessment of health promotion behavior and associated factors among the northern Saudi adolescent population: a cross-sectional study
Background and Aim Health promotions among the adolescent population have a significant role in achieving the 2030 sustainable development goals of the World Health Organization. The COVID-19 pandemic has led to several devastating impacts on the health, economic, social, and healthcare systems, and adolescents’ health promotions are no exception. We assessed health promotion behaviors and associated factors among the adolescent population of northern Saudi Arabia (KSA). Methods We used the Arabic version of the adolescent health promotion scale (AHPS-40) among the 400-adolescent population. The AHPS-40 assessed six domains of adolescent health behavior: nutrition, social support, health responsibility, life appreciation, exercise, and stress management. We applied the Chi-square test to identify the associated factors of adolescent health promotion activities and the logistic regression test to find the predictors for overall health promotion categories. Results Of the studied participants, the mean ± SD of the total AHPS-40 was 103.31 ± 18.78. The nutrition domain of the AHPS-40 was significantly associated with the age group (p = 0.002), and the social support domain was significantly related to fathers’ (p = 0.022) and mothers’ education (p = 0.006). The exercise domain of AHPS-40 was significantly associated with age group (p = 0.018) and school level (p = 0.026). Gender was significantly associated with most of the six domains. Furthermore, more than half (52.7%) of them had a low health promotion behavior, which was significantly associated with gender (adjusted odds ratio = 1.59, 95% CI of AOR = 1.04 –2.45, p = 0.032). Conclusion Our study results suggest improving health promotion behaviors by instituting awareness-raising and health promotion intervention programs for adolescent groups. Furthermore, we recommend a focused, exploratory, mixed-method survey among the adolescents of other regions of KSA to identify the region-specific adolescent’s health promotion behaviors.
Alruwaili et al. (2023) Assessment of health promotion behavior and associated factors among the northern Saudi adolescent population: a cross-sectional study. PeerJ 11:e15567 https://doi.org/10.7717/peerj.15567
The use of wireless sensors in the neonatal intensive care unit: a study protocol
Background Continuous monitoring of vital signs and other biological signals in the Neonatal Intensive Care Unit (NICU) requires sensors connected to the bedside monitors by wires and cables. This monitoring system presents challenges such as risks for skin damage or infection, possibility of tangling around the patient body, or damage of the wires, which may complicate routine care. Furthermore, the presence of cables and wires can act as a barrier for parent-infant interactions and skin to skin contact. This study will investigate the use of a new wireless sensor for routine vital monitoring in the NICU. Methods Forty-eight neonates will be recruited from the Montreal Children’s Hospital NICU. The primary outcome is to evaluate the feasibility, safety, and accuracy of a wireless monitoring technology called ANNE® One (Sibel Health, Niles, MI, USA). The study will be conducted in 2 phases where physiological signals will be acquired from the standard monitoring system and the new wireless monitoring system simultaneously. In phase 1, participants will be monitored for 8 h, on four consecutive days, and the following signals will be obtained: heart rate, respiratory rate, oxygen saturation and skin temperature. In phase 2, the same signals will be recorded, but for a period of 96 consecutive hours. Safety and feasibility of the wireless devices will be assessed. Analyses of device accuracy and performance will be accomplished offline by the biomedical engineering team. Conclusion This study will evaluate feasibility, safety, and accuracy of a new wireless monitoring technology in neonates treated in the NICU.
Senechal et al. (2023) The use of wireless sensors in the neonatal intensive care unit: a study protocol. PeerJ 11:e15578 https://doi.org/10.7717/peerj.15578
Divergence of wastewater SARS-CoV-2 and reported laboratory-confirmed COVID-19 incident case data coincident with wide-spread availability of at-home COVID-19 antigen tests
Concentrations of SARS-CoV-2 RNA in wastewater settled solids from publicly owned treatment works (POTWs) historically correlated strongly with laboratory confirmed incident COVID-19 case data. With the increased availability of at-home antigen tests since late 2021 and early 2022, laboratory test availability and test seeking behavior has decreased. In the United States, the results from at-home antigen tests are not typically reportable to public health agencies and thus are not counted in case reports. As a result, the number of reported laboratory-confirmed incident COVID-19 cases has decreased dramatically, even during times of increased test positivity rates and wastewater concentrations of SARS-CoV-2 RNA. Herein, we tested whether the correlative relationship between wastewater concentrations of SARS-CoV-2 RNA and reported laboratory-confirmed COVID-19 incidence rate has changed since 1 May 2022, a point in time immediately before the onset of the BA.2/BA.5 surge, the first surge to begin after at-home antigen test availability was high in the region. We used daily data from three POTWs in the Greater San Francisco Bay Area of California, USA for the analysis. We found that although there is a significant positive association between wastewater measurements and incident rate data collected after 1 May 2022, the parameters describing the relationship are different than those describing the relationship between the data collected prior to 1 May 2022. If laboratory test seeking or availability continues to change, the relationship between wastewater and reported case data will continue to change. Our results suggest, assuming SARS-CoV-2 RNA shedding remains relatively stable among those infected with the virus as different variants emerge, that wastewater concentrations of SARS-CoV-2 RNA can be used to estimate COVID-19 cases as they would have been during the time when laboratory testing availability and test seeking behavior were at a high (here, before 1 May 2022) using the historical relationship between SARS-CoV-2 RNA and COVID-19 case data.
Environmental Contamination and Remediation
Boehm et al. (2023) Divergence of wastewater SARS-CoV-2 and reported laboratory-confirmed COVID-19 incident case data coincident with wide-spread availability of at-home COVID-19 antigen tests. PeerJ 11:e15631 https://doi.org/10.7717/peerj.15631
MicroRNA-154-5p suppresses cervical carcinoma growth and metastasis by silencing Cullin2 in vitro and in vivo
Background MicroRNA-154-5p (miR-154-5p) plays a role in tumorigenesis in diverse human malignancies. Nevertheless, little is known about the mechanism by which miR-154-5p alters the growth and metastasis of cervical cancer. This research aimed to analyze the role of miR-154-5p in the pathology of cervical cancer in vitro and in vivo. Methods The level of miR-154-5p in human papillomavirus 16 positive cervical cancer cells was examined by real-time quantitative polymerase chain reaction. Bioinformatics predicted the downstream targets and potential functions of miR-154-5p. Furthermore, lentiviral technology was used to construct SiHa cell lines with stable up- and down-expression levels of miR-154-5p. Its differential expression effects on the progress and metastasis of cervical cancer were analyzed using cell culture and animal models. Results MiR-154-5p showed low expression in cervical cancer cells. Overexpression of miR-154-5p could markedly inhibit the proliferation, migration, and colony formation ability of SiHa cells, concomitantly leading to G1 arrest of the cell cycle, while silencing miR-154-5p triggered the opposite results. Meanwhile, overexpression of miR-154-5p restrained the growth and metastasis of cervical cancer by silencing CUL2 in vivo. Additionally, miR-154-5p reduced CUL2 level, and overexpression of CUL2 influenced the effect of miR-154-5p in cervical cancer. In conclusion, miR-154-5p restrained the growth and metastasis of cervical cancer by directly silencing CUL2.
Li et al. (2023) MicroRNA-154-5p suppresses cervical carcinoma growth and metastasis by silencing Cullin2 in vitro and in vivo. PeerJ 11:e15641 https://doi.org/10.7717/peerj.15641
copLAB gene prevalence and diversity among Trinidadian Xanthomonas spp. black-rot lesion isolates with variable copper resistance profiles
Background There has been limited exploration of copLAB genotypes and associated copper resistance phenotypes in Xanthomonas spp. in the southern Caribbean region. An earlier study highlighted a variant copLAB gene cluster found in one Trinidadian Xanthomonas campestris pv. campestris (Xcc) strain (BrA1), with <90% similarity to previously reported Xanthomonas copLAB genes. With only one report describing this copper resistance genotype, the current study investigated the distribution of the BrA1 variant copLAB gene cluster and previously reported forms of copper resistance genes in local Xanthomonas spp. Methods Xanthomonas spp. were isolated from black-rot infected lesions on leaf tissue from crucifer crops at intensively farmed sites with high agrochemical usage in Trinidad. The identity of morphologically identified isolates were confirmed using a paired primer PCR based screen and 16s rRNA partial gene sequencing. MGY agar amended with CuSO4.5H2O up to 2.4 mM was used to establish MIC’s for confirmed isolates and group strains as sensitive, tolerant, or resistant to copper. Separate primer pairs targeting the BrA1 variant copLAB genes and those predicted to target multiple homologs found in Xanthomonas and Stenotrophomonas spp. were used to screen copper resistant isolates. Select amplicons were sanger sequenced and evolutionary relationships inferred from global reference sequences using a ML approach. Results Only four copper sensitive/tolerant Xanthomonas sp. strains were isolated, with 35 others classed as copper-resistant from a total population of 45 isolates. PCR detection of copLAB genes revealed two PCR negative copper-resistant resistant strains. Variant copLAB genes were only found in Xcc from the original source location of the BrA1 strain, Aranguez. Other copper-resistant strains contained other copLAB homologs that clustered into three distinct clades. These groups were more similar to genes from X. perforans plasmids and Stenotrophomonas spp. chromosomal homologs than reference Xcc sequences. This study highlights the localisation of the BrA1 variant copLAB genes to one agricultural community and the presence of three distinct copLAB gene groupings in Xcc and related Xanthomonas spp. with defined CuSO4.5H2O MIC. Further characterisation of these gene groups and copper resistance gene exchange dynamics on and within leaf tissue between Xcc and other Xanthomonas species are needed as similar gene clusters showed variable copper sensitivity profiles. This work will serve as a baseline for copper resistance gene characterisation in Trinidad and the wider Caribbean region and can be used to boost already lacking resistant phytopathogen management in the region.
Ramnarine et al. (2023) copLAB gene prevalence and diversity among Trinidadian Xanthomonas spp. black-rot lesion isolates with variable copper resistance profiles. PeerJ 11:e15657 https://doi.org/10.7717/peerj.15657