Soil organic carbon estimation using remote sensing data-driven machine learning
Soil organic carbon (SOC) is a crucial component of the global carbon cycle, playing a significant role in ecosystem health and carbon balance. In this study, we focused on assessing the surface SOC content in Shandong Province based on land use types, and explored its spatial distribution pattern and influencing factors. Machine learning methods including random forest (RF), extreme gradient boosting (XGBoost), and support vector machine (SVM) were employed to estimate the surface SOC content in Shandong Province using diverse data sources like sample data, remote sensing data, socio-economic data, soil texture data, topographic data, and meteorological data. The results revealed that the SOC content in Shandong Province was 8.78 g/kg, exhibiting significant variation across different regions. Comparing the model error and correlation coefficient, the XGBoost model showed the highest prediction accuracy, with a coefficient of determination (R²) of 0.7548, root mean square error (RMSE) of 7.6792, and relative percentage difference (RPD) of 1.1311. Elevation and Clay exhibited the highest explanatory power in clarifying the surface SOC content in Shandong Province, contributing 21.74% and 13.47%, respectively. The spatial distribution analysis revealed that SOC content was higher in forest-covered mountainous regions compared to cropland-covered plains and coastal areas. In conclusion, these findings offer valuable scientific insights for land use planning and SOC conservation.
Spatial and Geographic Information Science
Chen et al. (2024) Soil organic carbon estimation using remote sensing data-driven machine learning. PeerJ 12:e17836 https://doi.org/10.7717/peerj.17836
Creation of complex reef structures through coral restoration does not affect associated fish populations on a remote, well-protected, Caribbean reef
Coral reef ecosystems are facing severe degradation due to anthropogenic activities at both local and global scales. In response, extensive restoration efforts are underway, aiming to bolster coral cover and enhance reef fish communities to foster facilitation between fish and corals. This reciprocal relationship is anticipated to improve overall restoration efficacy and enhance coral reef resilience in the face of global warming. Here, we investigate the impact of coral restoration using out-planted Acropora cervicornis colonies attached to raised domes on the associated fish community on the isolated, well-protected reef of Little Cayman Island in the Central Caribbean. Surveys were conducted immediately preceding out-planting, five days later, and 85 days later to capture temporal changes in the fish community. After 85 days of out-planting, there were no changes in fish biomass, abundance, or species richness for the entire fish community. This pattern was consistent for selected fish functional groups. Additionally, no significant differences were observed in the fish community before outplanting, five days after out-planting, or 85 days after out-planting of restoration domes. Our results underscore the limited impact of coral restoration for influencing fish communities in the isolated and highly protected reef of Little Cayman over an 85-day period. Consequently, our findings have implications for using coral restoration as a mechanism to enhance fish populations, particularly in marginally disturbed regions where structural complexity has not been lost. Future restoration programs should therefore incorporate local knowledge of environmental history and restoration needs along with an increased data-driven understanding of the intricate interaction between fish and coral populations to be successful.
Johnson et al. (2024) Creation of complex reef structures through coral restoration does not affect associated fish populations on a remote, well-protected, Caribbean reef. PeerJ 12:e17855 https://doi.org/10.7717/peerj.17855
Short-term microplastic effects on marine meiofauna abundance, diversity and community composition
Background Due to the copious disposal of plastics, marine ecosystems receive a large part of this waste. Microplastics (MPs) are solid particles smaller than 5 millimeters in size. Among the plastic polymers, polystyrene (PS) is one of the most commonly used and discarded. Due to its density being greater than that of water, it accumulates in marine sediments, potentially affecting benthic communities. This study investigated the ingestion of MP and their effect on the meiofauna community of a sandy beach. Meiofauna are an important trophic link between the basal and higher trophic levels of sedimentary food webs and may therefore be substantially involved in trophic transfer of MP and their associated compounds. Methods We incubated microcosms without addition of MP (controls) and treatments contaminated with PS MP (1-µm) in marine sediments at three nominal concentrations (103, 105, 107particles/mL), for nine days, and sampled for meiofauna with collections every three days. At each sampling time, meiofauna were collected, quantified and identified to higher-taxon level, and ingestion of MP was quantified under an epifluorescence microscope. Results Except for Tardigrada, all meiofauna taxa (Nematoda, turbellarians, Copepoda, Nauplii, Acari and Gastrotricha) ingested MP. Absorption was strongly dose dependent, being highest at 107 particles/mL, very low at 105 particles/mL and non-demonstrable at 103 particles/mL. Nematodes accumulated MP mainly in the intestine; MP abundance in the intestine increased with increasing incubation time. The total meiofauna density and species richness were significantly lower at the lowest MP concentration, while at the highest concentration these parameters were very similar to the control. In contrast, Shannon-Wiener diversity and evenness were greater in treatments with low MP concentration. However, these results should be interpreted with caution because of the low meiofauna abundances at the lower two MP concentrations. Conclusion At the highest MP concentration, abundance, taxonomic diversity and community structure of a beach meiofauna community were not significantly affected, suggesting that MP effects on meiofauna are at most subtle. However, lower MP concentrations did cause substantial declines in abundance and diversity, in line with previous studies at the population and community level. While we can only speculate on the underlying mechanism(s) of this counterintuitive response, results suggest that further research is needed to better understand MP effects on marine benthic communities.
de França et al. (2024) Short-term microplastic effects on marine meiofauna abundance, diversity and community composition. PeerJ 12:e17641 https://doi.org/10.7717/peerj.17641
Genome-wide analysis of cellulose synthase (CesA) and cellulose synthase-like (Csl) proteins in Cannabis sativa L
The cellulose and hemicellulose components of plant cell walls are synthesized by the cellulose synthase (CESA) and cellulose synthase-like (CSL) gene families and regulated in response to growth, development, and environmental stimuli. In this study, a total of 29 CESA/CSL family members were identified in Cannabis sativa and were grouped into seven subfamilies (CESA, CSLA, CSLB, CSLC, CSLD, CSLE and CSLG) according to phylogenetic relationships. The CESA/CESA proteins of C. sativa were closely related phylogenetically to the members of the subfamily of other species. The CESA/CSL subfamily members of C. sativa have unique gene structures. In addition, the expressions of four CESA and 10 CsCSL genes in flower, leaf, root, and stem organs of cannabis were detected using RT-qPCR. The results showed that CESA and CSL genes are expressed at varying levels in several organs. This detailed knowledge of the structural, evolutionary, and functional properties of cannabis CESA/CSL genes will provide a basis for designing advanced experiments for genetic manipulation of cell wall biogenesis to improve bast fibers and biofuel production.
Sipahi et al. (2024) Genome-wide analysis of cellulose synthase (CesA) and cellulose synthase-like (Csl) proteins in Cannabis sativa L. PeerJ 12:e17821 https://doi.org/10.7717/peerj.17821
Life history strategy of Tubastraea spp. corals in an upwelling area on the Southwest Atlantic: growth, fecundity, settlement, and recruitment
Over the past few decades, corals of the genus Tubastraea have spread globally, revealing themselves to be organisms of great invasive capacity. Their constant expansion on the Brazilian coast highlights the need for studies to monitor the invasion process. The growth, fecundity, settlement, and data on the coverage area of three co-occurring Tubastraea species in the 2015–2016 period were related to temperature variation and light irradiance on the rocky shores of Arraial do Cabo, Rio de Janeiro. Hence, this study sought to understand and compare the current invasion scenario and characteristics of the life history strategy of sun coral species based on environmental variables, considering the uniqueness of this upwelling area in the southwestern Atlantic. For that, we evaluate the fecundity, settlement, and growth rates of corals by carrying out comparative studies between species over time and correlating them with the variables temperature and irradiance, according to seasonality. Field growth of colonies was measured every two months during a sample year. Monthly collections were performed to count reproductive oocytes to assess fecundity. Also, quadrats were scrapped from an area near a large patch of sun coral to count newly attached coral larvae and used years later to assess diversity and percentage coverage. Results showed that corals presented greater growth during periods of high thermal amplitude and in months with below-average temperatures. Only Tubastraea sp. had greater growth and polyp increase in areas with higher light incidence, showing a greater increase in total area compared to all the other species analyzed. Despite the observed affinity with high temperatures, settlement rates were also higher during the same periods. Months with low thermal amplitude and higher temperature averages presented high fecundity. While higher water temperature averages showed an affinity with greater coral reproductive activity, growth has been shown to be inversely proportional to reproduction. Our study recorded the most significant coral growth for the region, an increase in niche, high annual reproductive activity, and large area coverage, showing the ongoing adaptation of the invasion process in the region. However, lower temperatures in the region affect these corals’ reproductive activity and growth, slowing down the process of introduction into the region. To better understand the advantages of these invasion strategies in the environment, we must understand the relationships between them and the local community that may be acting to slow down this colonization process.
Bastos et al. (2024) Life history strategy of Tubastraea spp. corals in an upwelling area on the Southwest Atlantic: growth, fecundity, settlement, and recruitment. PeerJ 12:e17829 https://doi.org/10.7717/peerj.17829
Immune infiltration and prognosis in gastric cancer: role of NAD+ metabolism-related markers
Background This study endeavored to develop a nicotinamide adenine dinucleotide (NAD+) metabolism-related biomarkers in gastric cancer (GC), which could provide a theoretical foundation for prognosis and therapy of GC patients. Methods In this study, differentially expressed genes (DEGs1) between GC and paraneoplastic tissues were overlapped with NAD+ metabolism-related genes (NMRGs) to identify differentially expressed NMRGs (DE-NMRGs). Then, GC patients were divided into high and low score groups by gene set variation analysis (GSVA) algorithm for differential expression analysis to obtain DEGs2, which was overlapped with DEGs1 for identification of intersection genes. These genes were further analyzed using univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses to obtain prognostic genes for constructing a risk model. Enrichment and immune infiltration analyses further investigated investigate the different risk groups, and qRT-PCR validated the prognostic genes. Results Initially, we identified DE-NMRGs involved in NAD biosynthesis, with seven (DNAJB13, CST2, THPO, CIDEA, ONECUT1, UPK1B and SNCG) showing prognostic significance in GC. Subsequent, a prognostic model was constructed in which the risk score, derived from the expression profiles of these genes, along with gender, emerged as robust independent predictors of patient outcomes in GC. Enrichment analysis linked high-risk patients to synaptic membrane pathways and low-risk to the CMG complex pathway. Tumor immune infiltration analysis revealed correlations between risk scores and immune cell abundance, suggesting a relationship between NAD+ metabolism and immune response in GC. The prognostic significance of our identified genes was validated by qRT-PCR, which confirmed their upregulated expression in GC tissue samples. Conclusion In this study, seven NAD+ metabolism-related markers were established, which is of great significance for the development of prognostic molecular biomarkers and clinical prognosis prediction for gastric cancer patients.
Xing et al. (2024) Immune infiltration and prognosis in gastric cancer: role of NAD+ metabolism-related markers. PeerJ 12:e17833 https://doi.org/10.7717/peerj.17833
Transcription factor NF-E2-related factor 2 plays a critical role in acute lung injury/acute respiratory distress syndrome (ALI/ARDS) by regulating ferroptosis
NRF2 is an important transcription factor that regulates redox homeostasis in vivo and exerts its anti-oxidative stress and anti-inflammatory response by binding to the ARE to activate and regulate the transcription of downstream protective protein genes, reducing the release of reactive oxygen species. Ferroptosis is a novel iron-dependent, lipid peroxidation-driven cell death mode, and recent studies have shown that ferroptosis is closely associated with acute lung injury/acute respiratory distress syndrome (ALI/ARDS). NRF2 is able to regulate ferroptosis through the regulation of the transcription of its target genes to ameliorate ALI/ARDS. Therefore, This article focuses on how NRF2 plays a role in ALI/ARDS by regulating ferroptosis. We further reviewed the literature and deeply analyzed the signaling pathways related to ferroptosis which were regulated by NRF2. Additionally, we sorted out the chemical molecules targeting NRF2 that are effective for ALI/ARDS. This review provides a relevant theoretical basis for further research on this theory and the prevention and treatment of ALI/ARDS. The intended audience is clinicians and researchers in the field of respiratory disease.
Deng et al. (2024) Transcription factor NF-E2-related factor 2 plays a critical role in acute lung injury/acute respiratory distress syndrome (ALI/ARDS) by regulating ferroptosis. PeerJ 12:e17692 https://doi.org/10.7717/peerj.17692
Neighborhood structure-guided brain functional networks estimation for mild cognitive impairment identification
The adoption and growth of functional magnetic resonance imaging (fMRI) technology, especially through the use of Pearson’s correlation (PC) for constructing brain functional networks (BFN), has significantly advanced brain disease diagnostics by uncovering the brain’s operational mechanisms and offering biomarkers for early detection. However, the PC always tends to make for a dense BFN, which violates the biological prior. Therefore, in practice, researchers use hard-threshold to remove weak connection edges or introduce l1-norm as a regularization term to obtain sparse BFNs. However, these approaches neglect the spatial neighborhood information between regions of interest (ROIs), and ROI with closer distances has higher connectivity prospects than ROI with farther distances due to the principle of simple wiring costs in resent studies. Thus, we propose a neighborhood structure-guided BFN estimation method in this article. In detail, we figure the ROIs’ Euclidean distances and sort them. Then, we apply the K-nearest neighbor (KNN) to find out the top K neighbors closest to the current ROIs, where each ROI’s K neighbors are independent of each other. We establish the connection relationship between the ROIs and these K neighbors and construct the global topology adjacency matrix according to the binary network. Connect ROI nodes with k nearest neighbors using edges to generate an adjacency graph, forming an adjacency matrix. Based on adjacency matrix, PC calculates the correlation coefficient between ROIs connected by edges, and generates the BFN. With the purpose of evaluating the performance of the introduced method, we utilize the estimated BFN for distinguishing individuals with mild cognitive impairment (MCI) from the healthy ones. Experimental outcomes imply this method attains better classification performance than the baselines. Additionally, we compared it with the most commonly used time series methods in deep learning. Results of the performance of K-nearest neighbor-Pearson’s correlation (K-PC) has some advantage over deep learning.
Liang et al. (2024) Neighborhood structure-guided brain functional networks estimation for mild cognitive impairment identification. PeerJ 12:e17774 https://doi.org/10.7717/peerj.17774
Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar
Background Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and transfer of antibiotic resistance genes (ARGs). Methods This study used metagenomics to identify and compare the abundance of bacterial species and ARGs detected in the gut microbiomes from sympatric humans and wild mouse lemurs in a forest-dominated, roadless region of Madagascar near Ranomafana National Park. We examined the contribution of human geographic location toward differences in ARG abundance and compared the genomic similarity of ARGs between host source microbiomes. Results Alpha and beta diversity of species and ARGs between host sources were distinct but maintained a similar number of detectable ARG alleles. Humans were differentially more abundant for four distinct tetracycline resistance-associated genes compared to lemurs. There was no significant difference in human ARG diversity from different locations. Human and lemur microbiomes shared 14 distinct ARGs with highly conserved in nucleotide identity. Synteny of ARG-associated assemblies revealed a distinct multidrug-resistant gene cassette carrying dfrA1 and aadA1 present in human and lemur microbiomes without evidence of geographic overlap, suggesting that these resistance genes could be widespread in this ecosystem. Further investigation into intermediary processes that maintain drug-resistant bacteria in wildlife settings is needed.
Talbot et al. (2024) Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar. PeerJ 12:e17805 https://doi.org/10.7717/peerj.17805
Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress
Stress-associated proteins (SAPs) are known to play an important role in plant responses to abiotic stresses. This study systematically identified members of the sunflower SAP gene family using sunflower genome data. The genes of the sunflower SAP gene family were analyzed using bioinformatic methods, and gene expression was assessed through fluorescence quantification (qRT-PCR) under salt and drought stress. A comprehensive analysis was also performed on the number, structure, collinearity, and phylogeny of seven Compositae species and eight other plant SAP gene families. The sunflower genome was found to have 27 SAP genes, distributed across 14 chromosomes. The evolutionary analysis revealed that the SAP family genes could be divided into three subgroups. Notably, the annuus variety exhibited amplification of the SAP gene for Group 3. Among the Compositae species, C. morifolium demonstrated the highest number of collinearity gene pairs and the closest distance on the phylogenetic tree, suggesting relative conservation in the evolutionary process. An analysis of gene structure revealed that Group 1 exhibited the most complex gene structure, while the majority of HaSAP genes in Group 2 and Group 3 lacked introns. The promoter analysis revealed the presence of cis-acting elements related to ABA, indicating their involvement in stress responses. The expression analysis indicated the potential involvement of 10 genes (HaSAP1, HaSAP3, HaSAP8, HaSAP10, HaSAP15, HaSAP16, HaSAP21, HaSAP22, HaSAP23, and HaSAP26) in sunflower salt tolerance. The expression of these 10 genes were then examined under salt and drought stress using qRT-PCR, and the tissue-specific expression patterns of these 10 genes were also analyzed. HaSAP1, HaSAP21, and HaSAP23 exhibited consistent expression patterns under both salt and drought stress, indicating these genes play a role in both salt tolerance and drought resistance in sunflower. The findings of this study highlight the significant contribution of the SAP gene family to salt tolerance and drought resistance in sunflower.
Zhang et al. (2024) Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress. PeerJ 12:e17808 https://doi.org/10.7717/peerj.17808