Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest
Background The delimitation of cryptic species is a challenge for biodiversity conservation. Anurans show high cryptic diversity levels, and molecular species delimitation methods could help identify putative new species. Additionally, species delimitation approaches can provide important results for cryptic species conservation, with integrative methods adding robustness to results. Ischnocnema manezinho was described from Santa Catarina Island (SCI), southern Brazil. More recently, some inventories indicated continental populations supposedly similar in morphology to it. If these records are confirmed as I. manezinho, it would likely change its endangered status on National Red List, removing the species from conservation agendas. We investigated the threatened frog Ischnocnema manezinho, to evaluate if the continental populations belong to this species or if they form an undescribed species complex. Methods We used coalescent, distance, and allele-sharing-based species delimitation methods and integrative analyses of morphometric and bioacoustics traits to test evolutionary independence between I. manezinho from SCI, Arvoredo Island, and continental populations. Results Ischnocnema manezinho is restricted to Santa Catarina Island, while the five remaining lineages should be further investigated through a taxonomic review. Our results point to a small geographic range of Ischnocnema manezinho. Additionally, the species occurs in isolated fragments of forest in SCI surrounded by expanding urban areas, confirming its status as Endangered. Thus, the protection and monitoring of I. manezinho and the taxonomic description of the continental and Arvoredo Island candidate species should be priorities.
Oswald et al. (2023) Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest. PeerJ 11:e15393 https://doi.org/10.7717/peerj.15393
PFI-3 induces vasorelaxation with potency to reduce extracellular calcium influx in rat mesenteric artery
Background PFI-3 is a small-molecule inhibitor that targets the bromodomains (BRDs) of Brahma-related gene 1 (BRG1). This monomeric compound, which has high selectivity and potent cellular effects, has recently been developed. Although PFI-3 has been reported as a potential therapeutic agent targeting thrombomodulin, its role in the regulation of vascular function remains unknown. Therefore, we aimed to investigate the impact of PFI-3 on arterial vessel tone. Methods A microvascular tension measurement device (DMT) was utilized to identify alterations in vascular tension within the mesenteric artery. To detect variations in cytosolic [Ca2+]i, a Fluo-3/AM fluorescent probe and fluorescence microscope were employed. Additionally, whole-cell patch clamp techniques were utilized to evaluate the activity of L-type voltage-dependent calcium channels (VDCCs) in cultured arterial smooth muscle cells (A10 cells). Results PFI-3 exerted a dose-dependent relaxation effect on rat mesenteric arteries with both intact and denuded endothelium after phenylephrine (PE)- and high-K+-induced constriction. PFI-3-induced vasorelaxation was not affected by the presence of L-NAME/ODQ or K+ channel blockers (Gli/TEA). PFI-3 abolished Ca2+-induced contraction on endothelium-denuded mesenteric arteries preincubated by PE in Ca2+-free solution. Incubation with TG had no impact on PFI-3-induced vasorelaxation pre-contracted by PE. PFI-3 reduced Ca2+-induced contraction on endothelium-denuded mesenteric arteries pre-incubated by KCl (60 mM) in Ca2+-free solution. PFI-3 declined extracellular calcium influx in A10 cells detected by Fluo-3/AM fluorescent probe and fluorescence microscope. Furthermore, we observed that PFI-3 decreased the current densities of L-type VDCC by whole-cell patch clamp techniques. Conclusions PFI-3 blunted PE and high K+-induced vasoconstriction independent of endothelium on rat mesenteric artery. The vasodilatory effect of PFI-3 may be attributed to its inhibition of VDCCs and receptor-operated calcium channels (ROCCs) on vascular smooth muscle cells (VSMCs).
Li et al. (2023) PFI-3 induces vasorelaxation with potency to reduce extracellular calcium influx in rat mesenteric artery. PeerJ 11:e15407 https://doi.org/10.7717/peerj.15407
Identifying C1QB, ITGAM, and ITGB2 as potential diagnostic candidate genes for diabetic nephropathy using bioinformatics analysis
Background Diabetic nephropathy (DN), the most intractable complication in diabetes patients, can lead to proteinuria and progressive reduction of glomerular filtration rate (GFR), which seriously affects the quality of life of patients and is associated with high mortality. However, the lack of accurate key candidate genes makes diagnosis of DN very difficult. This study aimed to identify new potential candidate genes for DN using bioinformatics, and elucidated the mechanism of DN at the cellular transcriptional level. Methods The microarray dataset GSE30529 was downloaded from the Gene Expression Omnibus Database (GEO), and the differentially expressed genes (DEGs) were screened by R software. We used Gene Ontology (GO), gene set enrichment analysis (GSEA), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis to identify the signal pathways and genes. Protein-protein interaction (PPI) networks were constructed using the STRING database. The GSE30122 dataset was selected as the validation set. Receiver operating characteristic (ROC) curves were applied to evaluate the predictive value of genes. An area under curve (AUC) greater than 0.85 was considered to be of high diagnostic value. Several online databases were used to predict miRNAs and transcription factors (TFs) capable of binding hub genes. Cytoscape was used for constructing a miRNA-mRNA-TF network. The online database ‘nephroseq’ predicted the correlation between genes and kidney function. The serum level of creatinine, BUN, and albumin, and the urinary protein/creatinine ratio of the DN rat model were detected. The expression of hub genes was further verified through qPCR. Data were analyzed statistically using Student’s t-test by the ‘ggpubr’ package. Results A total of 463 DEGs were identified from GSE30529. According to enrichment analysis, DEGs were mainly enriched in the immune response, coagulation cascades, and cytokine signaling pathways. Twenty hub genes with the highest connectivity and several gene cluster modules were ensured using Cytoscape. Five high diagnostic hub genes were selected and verified by GSE30122. The MiRNA-mRNA-TF network suggested a potential RNA regulatory relationship. Hub gene expression was positively correlated with kidney injury. The level of serum creatinine and BUN in the DN group was higher than in the control group (unpaired t test, t = 3.391, df = 4, p = 0.0275, r = 0.861). Meanwhile, the DN group had a higher urinary protein/creatinine ratio (unpaired t test, t = 17.23, df = 16, p < 0.001, r = 0.974). QPCR results showed that the potential candidate genes for DN diagnosis included C1QB, ITGAM, and ITGB2. Conclusions We identified C1QB, ITGAM and ITGB2 as potential candidate genes for DN diagnosis and therapy and provided insight into the mechanisms of DN development at transcriptome level. We further completed the construction of miRNA-mRNA-TF network to propose potential RNA regulatory pathways adjusting disease progression in DN.
Hu et al. (2023) Identifying C1QB, ITGAM, and ITGB2 as potential diagnostic candidate genes for diabetic nephropathy using bioinformatics analysis. PeerJ 11:e15437 https://doi.org/10.7717/peerj.15437
A low-tech method for monitoring survival and growth of coral transplants at a boutique restoration site
Background Coral reef restoration projects are becoming a popular corporate environmental responsibility activity at hotel resorts. Such involvement of private businesses offers the potential to expand restoration into a new socioeconomic sector. However, the scarcity of user-friendly monitoring methods for hotel staff, but robust enough to detect changes over time, hinders the ability to quantify the success or failure of the restoration activity. Here, we present a monitoring method of easy application by hotel staff, without scientific training, using the standard resources available at a hotel resort. Methods Survival and growth of coral transplants were evaluated over 1 year at a boutique coral reef restoration site. The restoration was tailored to the needs of a hotel resort in Seychelles, Indian Ocean. A total of 2,015 nursery-grown corals of branching (four genera, 15 species), massive (16 genera, 23 species), and encrusting (seven genera, seven species) growth types were transplanted to a 1–3 m deep degraded patch reef. A unique cement mix was used to transplant corals onto the hard substrate. On the north side of each coral selected for monitoring, we attached an 8.2 cm × 8.2 cm reflective tile. We used reflective tiles instead of numbered tags due to the expected amount of biofouling growing on the tag surface. Every coral was recorded with top view photography (perpendicular to the plane of coral attachment), with the reflective square in the field of view. We drafted a map of the site to facilitate navigation and re-sighting of the monitored colonies. Then, we developed a simple monitoring protocol for hotel staff. Using the map, and the reflective tiles, the divers located the coral colonies, recorded status (alive, dead, bleaching), and took a photograph. We measured the two-dimensional coral planar area and the change in colony size over time using contour tissue measurements of photographs. Results The monitoring method was robust enough to detect the expected survival of coral transplants, with encrusting and massive corals outperforming branching corals. Survival of encrusting and massive corals was higher (50%–100%) than branching corals (16.6%–83.3%). The change in colony size was 10.1 cm2 ± 8.8 (SE). Branching coral survivors grew faster than massive/encrusting corals. A comprehensive approach to the boutique restoration monitoring experiment would have included comparisons with a control patch reef with a similar species composition to the coral transplants. However, the ability to monitor such a control site, in addition to the restoration site, was beyond the logistic capabilities of the hotel staff, and we were limited to monitoring survival and growth within the restoration site. We conclude that science-based boutique coral reef restoration, tailored to the needs of a hotel resort, combined with a simple monitoring method, can provide a framework for involving hotels as partners in coral reef restoration worldwide.
Frias-Torres et al. (2023) A low-tech method for monitoring survival and growth of coral transplants at a boutique restoration site. PeerJ 11:e15062 https://doi.org/10.7717/peerj.15062
minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data
Here, we present the R package, minSNPs. This is a re-development of a previously described Java application named Minimum SNPs. MinSNPs assembles resolution-optimised sets of single nucleotide polymorphisms (SNPs) from sequence alignments such as genome-wide orthologous SNP matrices. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to determine all sequences from all other sequences, i.e., to maximise diversity. MinSNPs encompasses functions that facilitate rapid and flexible SNP mining, and clear and comprehensive presentation of the results. The minSNPs’ running time scales in a linear fashion with input data volume and the numbers of SNPs and SNPs sets specified in the output. MinSNPs was tested using a previously reported orthologous SNP matrix of Staphylococcus aureus and an orthologous SNP matrix of 3,279 genomes with 164,335 SNPs assembled from four S. aureus short read genomic data sets. MinSNPs was shown to be effective for deriving discriminatory SNP sets for potential surveillance targets and in identifying SNP sets optimised to discriminate isolates from different clonal complexes. MinSNPs was also tested with a large Plasmodium vivax orthologous SNP matrix. A set of five SNPs was derived that reliably indicated the country of origin within three south-east Asian countries. In summary, we report the capacity to assemble comprehensive SNP matrices that effectively capture microbial genomic diversity, and to rapidly and flexibly mine these entities for optimised marker sets.
Hoon et al. (2023) minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data. PeerJ 11:e15339 https://doi.org/10.7717/peerj.15339
Supplementation of PUFA extracted from microalgae for the development of chicken patties
In recent years, there has been a growing interest in development of a diverse range of foods that are enriched with omega-3 fatty acids. It is widely recognized that through dietary interventions, the lipid fraction of food can be modified to enhance its nutritional content. This study is aimed to develop chicken patties enriched with poly unstaurated fatty acids (PUFAs) extracted from microalgae aurintricarboxylic acid (ATA) concentration of 0% (T0), 1% (T1), 2% (T2), and 3% (T3). All treatments were stored at −18 °C for one month and analysed at an interval of 0, 10, 20, and 30 days to assess the effect of PUFAs supplementation on physicochemical, oxidative, microbiological and organoleptic properties of chicken patties. The results revealed that moisture content was significantly increased during the storage; the maximum moisture was observed in T0 (67.25% ± 0.03) on day 0, while the minimun was found in T3 (64.69% ± 0.04) on day 30. Supplemenatation of PUFAs in chicken patties significantly enhanced the fat content of the product the highest fat content was observed for T3 (9.7% ± 0.06. An increase in PUFAs concentration led to a significant increase in thiobarbituric acid reactive substances (TBARS). TBARS were increased from 1.22 ± 0.43 at 0 days to 1.48 ± 0.39 at 30 days of storage. The PUFAs incorporation negatively effected sensory acceptance of the product ranging from (8.41 ± 0.17 to 7.28 ± 0.12). However, the sensory scores were in acceptable range for supplemented patties as compared to control sample. Treatment T3 depicted the highest nutritional content. The sensory and physiochemical analysis of supplemented patties suggested that PUFAs extracted from microalgae can be used as a functional ingredient in the preparation various meat products particularly chicken meta patties. However, antioxidants should be added to to prevent lipid oxidation in the product.
Dr et al. (2023) Supplementation of PUFA extracted from microalgae for the development of chicken patties. PeerJ 11:e15355 https://doi.org/10.7717/peerj.15355
Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau
In the extreme alpine climate of the Qinghai-Tibet Plateau (QTP), plant growth and reproduction are limited by extremely cold temperatures, low soil moisture, and scarce nutrient availability. The root-associated microbiome indirectly promotes plant growth and plays a role in the fitness of plants on the QTP, particularly in Tibetan medicinal plants. Despite the importance of the root-associated microbiome, little is known about the root zone. This study used high-throughput sequencing to investigate two medicinal Meconopsis plants, M. horridula and M. integrifolia, to determine whether habitat or plant identity had a more significant impact on the microbial composition of the roots. The fungal sequences were obtained using ITS-1 and ITS-2, and bacterial sequences were obtained using 16S rRNA. Different microbial patterns were observed in the microbial compositions of fungi and bacteria in the root zones of two Meconopsis plants. In contrast to bacteria, which were not significantly impacted by plant identity or habitat, the fungi in the root zone were significantly impacted by plant identity, but not habitat. In addition, the synergistic effect was more significant than the antagonistic effect in the correlation between fungi and bacteria in the root zone soil. The fungal structure was influenced by total nitrogen and pH, whereas the structure of bacterial communities was influenced by soil moisture and organic matter. Plant identity had a greater influence on fungal structure than habitat in two Meconopsis plants. The dissimilarity of fungal communities suggests that more attention should be paid to fungi-plant interactions.
Chen et al. (2023) Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau. PeerJ 11:e15361 https://doi.org/10.7717/peerj.15361
Spatio-temporal evolution and prediction of carbon storage in Kunming based on PLUS and InVEST models
Carbon storage is a critical ecosystem service provided by terrestrial environmental systems that can effectively reduce regional carbon emissions and is critical for achieving carbon neutrality and carbon peak. We conducted a study in Kunming and analyzed the land utilization data for 2000, 2010, and 2020. We assessed the features of land utilization conversion and forecasted land utilization under three development patterns in 2030 on the basis of the Patch-generating Land Use Simulation (PLUS) model. We used the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model to estimate changes in carbon storage trends under three development scenarios in 2000, 2010, 2020, and 2030 and the impact of socioeconomic and natural factors on carbon storage. The results of the study indicated that (1) carbon storage is intimately associated with land utilization practices. Carbon storage in Kunming in 2000, 2010, and 2020 was 1.146 × 108 t, 1.139 × 108 t, and 1.120 × 108 t, respectively. During the 20 years, forest land decreased by 142.28 km2, and the decrease in forest land area caused a loss of carbon storage. (2) Carbon storage in 2030 was predicted to be 1.102 × 108 t, 1.136 × 108 t, and 1.105 × 108 t, respectively, under the trend continuation scenario, eco-friendly scenario, and comprehensive development scenario, indicating that implementing ecological protection and cultivated land protection measures can facilitate regional ecosystem carbon storage restoration. (3) Impervious surfaces and vegetation have the greatest influence on carbon storage for the study area. A spatial global and local negative correlation was found between impervious surface coverage and ecosystem carbon storage. A spatial global and local positive correlation was found between NDVI and ecosystem carbon storage. Therefore, ecological and farmland protection policies need to be strengthened, the expansion of impervious surfaces should be strictly controlled, and vegetation coverage should be improved.
Spatial and Geographic Information Science
Li et al. (2023) Spatio-temporal evolution and prediction of carbon storage in Kunming based on PLUS and InVEST models. PeerJ 11:e15285 https://doi.org/10.7717/peerj.15285
Transcriptome analysis reveals genes associated with wool fineness in merinos
Hair/wool usually plays an important role in maintaining animal physiological activities, and the economic value of wool cannot be ignored. At present, people set higher demands on wool fineness. Hence, improving wool fineness is the concern of fine wool sheep breeding. Using RNA-Seq to screen the potential candidate genes that associate with wool fineness can provide theoretical references for fine-wool sheep breeding, and also provide us new ideas for further understand the molecular regulation mechanism of hair growth. In this study, we compared the expression pattern difference of genome-wide genes between the skin transcriptomes of Subo and Chinese Merinos. The results showed that, 16 candidate differentially expressed genes (DEGs) (Included: CACNA1S, GP5, LOC101102392, HSF5, SLITRK2, LOC101104661, CREB3L4, COL1A1, PTPRR, SFRP4, LOC443220, COL6A6, COL6A5, LAMA1, LOC114115342 and LOC101116863 genes) that may associate with wool fineness were screened, and these genes were located in signaling pathways that regulate hair follicle development, cycle or hair growth. It is worth noting that, among the 16 DEGs, COL1A1 gene has the highest expression level in Merino skins, and the fold change of LOC101116863 gene is the highest, and the structures of these two genes are both highly conserved in different species. In conclusion, we speculate that these two genes may play a key role in regulating wool fineness and respectively have similar and conserved functions in different species.
Ma et al. (2023) Transcriptome analysis reveals genes associated with wool fineness in merinos. PeerJ 11:e15327 https://doi.org/10.7717/peerj.15327
Morphometric analysis of odontoid process among Arab population: a retrospective cone beam CT study
Objective This study aims to evaluate the feasibility of using cone beam computed tomography (CBCT) scans to assess the odontoid process diameter in the Arab population and to determine whether one or two cortical screws can be used for treating odontoid fractures. Methods The odontoid process of 142 individuals aged 12–75 years, including 72 males (mean age: 35.5) and 70 females (mean age: 36.2), were analyzed using CBCT scans. The sagittal and coronal CBCT views were used to evaluate the antero-posterior (AP) and transverse diameters of the odontoid process. Results Males had substantially bigger transverse and AP diameters of the odontoid process than females (p < 0.05 & P < 0.01 respectively). Among the sample, 97 individuals (67.4%) had external transverse diameter (METD) of less than 9 mm which is slightly bigger than that of Indians and 48 individuals (31.83%) had enough room for two 3.5 mm or two 2.7 mm screws as their METD was more than 9 mm like that of Greek and Turkish. Age had no significant impact on the morphometric measurements of the odontoid process. Conclusion More than sixty percent of the sample had METDs of less than 9 millimeters, indicating that a single 4.5-mm Herbert screw may be suggested for fixing fractured odontoid processes in the Arab population.
Uthman et al. (2023) Morphometric analysis of odontoid process among Arab population: a retrospective cone beam CT study. PeerJ 11:e15411 https://doi.org/10.7717/peerj.15411