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
Small-fragment, high turnover: soil microenvironment fluctuation effect on tree diversity in a Neotropical montane oak forest
Background Soil microenvironmental variables showed an important key in α and β-tree diversity in Neotropical montane oak forest. Thus, understanding the microenvironment fluctuation at small-fragment effects on tree diversity is crucial in maintaining the montane oak ecosystems. In this study, we hypothesized that within a relatively small-fragment (151.63 ha), tree α and β-diversity fluctuate and specific soil microenvironmental factors could influence tree species diversity to answer three questions: Do tree α and β-diversity differ among transects, even in a short-distance between them? Do microenvironmental variables influence tree diversity composition that occurs within a relict Neotropical montane oak forest? Is there a particular microenvironmental variable influencing tree species-specific? Methods We established four permanent transects during a year in a relict Neotropical montane oak forest, we assessed tree diversity and specific microenvironmental variables (soil moisture, soil temperature, pH, depth litterfall and light incidence). This allowed us to evaluate how microenvironmental variables at small-fragment influence α and β-tree diversity and tree species-specific. Results Our results showed that α-diversity was not different among transects; however, β-diversity of tree species was mostly explained by turnover and soil moisture, soil temperature, and light incidence were the microenvironmental variables that triggered the replacement (i.e., one species by another). Those variables also had effect on tree species-specific: Mexican beech (Fagus mexicana), Quebracho (Quercus delgadoana), Pezma (Cyathea fulva), Aguacatillo (Beilschmiedia mexicana), Pezma (Dicksonia sellowiana var. arachneosa), and Mountain magnolia (Magnolia schiedeana). Discussion Our results confirm our hypothesis related to β-diversity but not with α-diversity; however, the tree community structure of the diversity was similar among transects. Our study represents the first effort to evaluate and link the soil microenvironmental effect on tree α and β-diversity, finding a high replacement in a small-fragment of Neotropical montane oak forest from eastern Mexico.
López-Calvillo et al. (2023) Small-fragment, high turnover: soil microenvironment fluctuation effect on tree diversity in a Neotropical montane oak forest. PeerJ 11:e15415 https://doi.org/10.7717/peerj.15415
Minimizing the variables of voiding spot assay for comparison between laboratories
The voiding spot assay (VSA) is increasingly being adopted as a standard method for assessing mouse urinary function. However, VSA outcomes are highly sensitive to housing environment and procedural parameters. Many variables exist among laboratories, including analytical software, type of daily housing cage, transportation, and the time of the day. Some of these variables, such as the time of VSA and analytical software, have been shown to result in inconsistency and incomparability of data. In this study, we evaluated whether the results of VSA can be compared across laboratories by minimizing these variables. We found that analytical tools between Fiji and MATLAB are in good agreement in the quantification of VSA parameters, especially primary voiding spot (PVS) parameters. Unexpectedly, we found that mice housed in different daily home cages did not alter voiding patterns in a standard VSA cage. Nonetheless, we still recommend acclimation when performing VSA in unfamiliar cages. Notably, mice are highly sensitive to transportation and the time in the morning versus afternoon, which can induce significant changes in voiding patterns. Therefore, a standardized period among laboratories and allowing 2–3 days of rest for mice acclimation after transportation are necessary for VSA. Finally, we performed VSA using identical procedural parameters in two laboratories from two geographical locations to compare the results of VSA and concluded that it is possible to generate limited comparable VSA data, such as PVS volume.
Luo et al. (2023) Minimizing the variables of voiding spot assay for comparison between laboratories. PeerJ 11:e15420 https://doi.org/10.7717/peerj.15420
Virioplankton and virus-induced mortality of prokaryotes in the Kara Sea (Arctic) in summer
Among the Arctic seas, the largest volume of river runoff (~45% of the total river-water inflow into the Arctic Ocean) enters the Siberian Kara Sea. The viral communities of the Kara Sea are important for the functioning of the marine ecosystem. Studies of virus–prokaryote interactions on the Kara Sea shelf have been conducted only in spring and autumn. Here, we investigated the abundance of free viruses, viruses attached to prokaryotes, and pico-sized detrital particles; the morphology (shape and size) of the viruses, viral infection and virus-mediated mortality of prokaryotes in early summer, i.e., during a seasonal ice melting period and maximum inflow of river-water volumes with high concentrations of dissolved and suspended organic carbon. Seawater samples for microbial analyses were collected across the Kara Sea shelf zone on board the Norilskiy Nickel as a research platform from June 29 to July 15, 2018. Abundances of prokaryotes (range (0.6–25.3) × 105 cells mL−1) and free viruses (range (10–117) × 105 viruses mL−1) were correlated (r = 0.63, p = 0.005) with an average virus: prokaryote ratio of 23.9 ± 5.3. The abundance of free viruses and viral-mediated mortality of prokaryotes were significantly higher in early summer than in early spring and autumn. Free viruses with a capsid diameter of 16–304 nm were recorded in the examined water samples. Waters in the Kara Sea shelf contained high concentrations of suspended organic particles 0.25–4.0 µm in size (range (0.6–25.3) × 105 particles mL−1). The proportions of free viruses, viruses attached to prokaryotes, and viruses attached to pico-sized detrital particles were 89.8 ± 6.0%, 2.2 ± 0.6% and 8.0 ± 1.3%, respectively, of the total virioplankton abundance (on average (61.5 ± 6.2) × 105 viruses mL−1). Viruses smaller than 60 nm clearly dominated at all studied sites. The majority of free viruses were not tailed. We estimated that an average of 1.4% (range 0.4–3.5%) of the prokaryote community was visibly infected by viruses, suggesting that a significant proportion of prokaryotic secondary production, 11.4% on average (range 4.0–34.0%), was lost due to viral lysis. There was a negative correlation between the abundance of pico-sized detrital particles and the frequency of visibly infected prokaryotic cells: r = −0.67, p = 0.0008.
Kopylov et al. (2023) Virioplankton and virus-induced mortality of prokaryotes in the Kara Sea (Arctic) in summer. PeerJ 11:e15457 https://doi.org/10.7717/peerj.15457
Determination of the affinity constants for phage display albumin-binding peptides
Background Phage display technology has been established as a powerful screening approach to select ligands or peptides for binding to proteins. Despite rapid growth in the field, there has been a relative dearth of quantitative criteria to measure the effectiveness of the process of phage display screening. Since human serum albumin (HSA) has been extensively studied as a drug carrier to extend the plasma half-life of protein therapeutics, the use of phage display technology is required for identifying albumin-binding peptides as the very promising strategy of albumin-binding against albumin fusion. The construction of albumin-binding drug requires the assessment of a large quantity of HSA-binding peptide (HSA binder) candidates for conjugation with therapeutic proteins. The use of the linear epitope mapping method has allowed researchers to discover many HSA-binding peptides. However, it may be inefficient to select these peptides based on sequence identity via randomly sequencing individual phage clones from enrichment pools. Method Here, a simple assessment method to facilitate phage display selection of HSA-binding peptides was recommended. With experimentally determined phage titer, one can calculate the specificity ratios, the recovery yields and the relative dissociation constants, which are defined as quantitative criteria for panning and characterization of the binding phage fused peptides. Results Consequently, this approach may not only enable more rapid and low-cost phage display screening, but also efficiently reduce pseudo-positive phages selected as HSA binders for conjugation with therapeutic proteins.
Shi (2023) Determination of the affinity constants for phage display albumin-binding peptides. PeerJ 11:e15078 https://doi.org/10.7717/peerj.15078