Comparison of different selection traits for identification of phosphorus use efficient lines in mungbean
Phosphorus (P) is one of the major constraints for crop growth and development, owing to low availability and least mobility in many tropical soil conditions. Categorization of existing germplasm under P deficient conditions is a prerequisite for the selection and development of P efficient genotypes in the mungbean. In the present investigation, 36 diverse genotypes were categorized for phosphorus use efficiency traits using four different techniques for identification of phosphorus use efficient mungbean genotypes. The studied genotypes were categorized for P efficiency based on efficiency, responsiveness, and stress tolerance score of genotypes under normal and low P conditions. The mean values of traits, root dry mass, root to shoot ratio, and P utilization efficiency are significantly higher under low P conditions indicating the high responsiveness of traits to P deficiency. The presence of significant interaction between genotypes and P treatment indicates the evaluated genotypes were significantly affected by P treatment for studied traits. The total P uptake showed significant and positive correlations with root dry mass, shoot dry mass, total dry mass,and P concentration under both P regimes. Out of the four techniques used for the categorization of genotypes for P efficiency, three techniques revealed that the genotype PUSA 1333, followed by Pusa Vishal, PUSA 1031, and Pusa Ratna is efficient. The categorization based on stress tolerance score is the finest way to study variation and for the selection of contrasting genotypes for P efficiency. The identified P efficient genotypes would be valuable resources for genetic enhancement of P use efficiency in mungbean breeding.
Reddy et al. (2021) Comparison of different selection traits for identification of phosphorus use efficient lines in mungbean. PeerJ 9:e12156 https://doi.org/10.7717/peerj.12156
Genetic effects of long-term captive breeding on the endangered pygmy hog
Long-term captive populations often accumulate genetic changes that are detrimental to their survival in the wild. Periodic genetic evaluation of captive populations is thus necessary to identify deleterious changes and minimize their impact through planned breeding. Pygmy hog (Porcula salvania) is an endangered species with a small population inhabiting the tall sub-Himalayan grasslands of Assam, India. A conservation breeding program of pygmy hog from six founders has produced a multi-generational captive population destined for reintroduction into the wild. However, the impact of conservation breeding on its genetic diversity remained undocumented. Here, we evaluate temporal genetic changes in 39 pygmy hogs from eight consecutive generations of a captive population using genome-wide SNPs, mitochondrial genomes, and MHC sequences, and explore the relationship between genetic diversity and reproductive success. We find that pygmy hog harbors a very low genome-wide heterozygosity (H) compared to other members of the Suidae family. However, within the captive population we find excess heterozygosity and a significant increase in H from the wild-caught founders to the individuals in subsequent generations due to the selective pairing strategy. The MHC and mitochondrial nucleotide diversities were lower in captive generations compared to the founders with a high prevalence of low-frequency MHC haplotypes and more unique mitochondrial genomes. Further, even though no signs of genetic inbreeding were observed from the estimates of individual inbreeding coefficient F and between individuals (FIS) in each generation, the kinship coefficient showed a slightly increasing trend in the recent generations, due to a relatively smaller non-random sample size compared to the entire captive population. Surprisingly, male pygmy hogs that had higher heterozygosity also showed lower breeding success. We briefly discuss the implications of our findings in the context of breeding management and recommend steps to minimize the genetic effects of long-term captive breeding.
Purohit et al. (2021) Genetic effects of long-term captive breeding on the endangered pygmy hog. PeerJ 9:e12212 https://doi.org/10.7717/peerj.12212
Event-related potentials evoked by skin puncture reflect activation of Aβ fibers: comparison with intraepidermal and transcutaneous electrical stimulations
Background Recently, event-related potentials (ERPs) evoked by skin puncture, commonly used for blood sampling, have received attention as a pain assessment tool in neonates. However, their latency appears to be far shorter than the latency of ERPs evoked by intraepidermal electrical stimulation (IES), which selectively activates nociceptive Aδ and C fibers. To clarify this important issue, we examined whether ERPs evoked by skin puncture appropriately reflect central nociceptive processing, as is the case with IES. Methods In Experiment 1, we recorded evoked potentials to the click sound produced by a lance device (click-only), lance stimulation with the click sound (click+lance), or lance stimulation with white noise (WN+lance) in eight healthy adults to investigate the effect of the click sound on the ERP evoked by skin puncture. In Experiment 2, we tested 18 heathy adults and recorded evoked potentials to shallow lance stimulation (SL) with a blade that did not reach the dermis (0.1 mm insertion depth); normal lance stimulation (CL) (1 mm depth); transcutaneous electrical stimulation (ES), which mainly activates Aβ fibers; and IES, which selectively activates Aδ fibers when low stimulation current intensities are applied. White noise was continuously presented during the experiments. The stimulations were applied to the hand dorsum. In the SL, the lance device did not touch the skin and the blade was inserted to a depth of 0.1 mm into the epidermis, where the free nerve endings of Aδ fibers are located, which minimized the tactile sensation caused by the device touching the skin and the activation of Aβ fibers by the blade reaching the dermis. In the CL, as in clinical use, the lance device touched the skin and the blade reached a depth of 1 mm from the skin surface, i.e., the depth of the dermis at which the Aβ fibers are located. Results The ERP N2 latencies for click-only (122 ± 2.9 ms) and click+lance (121 ± 6.5 ms) were significantly shorter than that for WN+lance (154 ± 7.1 ms). The ERP P2 latency for click-only (191 ± 11.3 ms) was significantly shorter than those for click+lance (249 ± 18.6 ms) and WN+lance (253 ± 11.2 ms). This suggests that the click sound shortens the N2 latency of the ERP evoked by skin puncture. The ERP N2 latencies for SL, CL, ES, and IES were 146 ± 8.3, 149 ± 9.9, 148 ± 13.1, and 197 ± 21.2 ms, respectively. The ERP P2 latencies were 250 ± 18.2, 251 ± 14.1, 237 ± 26.3, and 294 ± 30.0 ms, respectively. The ERP latency for SL was significantly shorter than that for IES and was similar to that for ES. This suggests that the penetration force generated by the blade of the lance device activates the Aβ fibers, consequently shortening the ERP latency. Conclusions Lance ERP may reflect the activation of Aβ fibers rather than Aδ fibers. A pain index that correctly and reliably reflects nociceptive processing must be developed to improve pain assessment and management in neonates.
Shiroshita et al. (2021) Event-related potentials evoked by skin puncture reflect activation of Aβ fibers: comparison with intraepidermal and transcutaneous electrical stimulations. PeerJ 9:e12250 https://doi.org/10.7717/peerj.12250
WIN 55,212-2 shows anti-inflammatory and survival properties in human iPSC-derived cardiomyocytes infected with SARS-CoV-2
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can infect several organs, especially impacting respiratory capacity. Among the extrapulmonary manifestations of COVID-19 is myocardial injury, which is associated with a high risk of mortality. Myocardial injury, caused directly or indirectly by SARS-CoV-2 infection, can be triggered by inflammatory processes that lead to damage to the heart tissue. Since one of the hallmarks of severe COVID-19 is the “cytokine storm”, strategies to control inflammation caused by SARS-CoV-2 infection have been considered. Cannabinoids are known to have anti-inflammatory properties by negatively modulating the release of pro-inflammatory cytokines. Herein, we investigated the effects of the cannabinoid agonist WIN 55,212-2 (WIN) in human iPSC-derived cardiomyocytes (hiPSC-CMs) infected with SARS-CoV-2. WIN did not modify angiotensin-converting enzyme II protein levels, nor reduced viral infection and replication in hiPSC-CMs. On the other hand, WIN reduced the levels of interleukins six, eight, 18 and tumor necrosis factor-alpha (TNF-α) released by infected cells, and attenuated cytotoxic damage measured by the release of lactate dehydrogenase (LDH). Our findings suggest that cannabinoids should be further explored as a complementary therapeutic tool for reducing inflammation in COVID-19 patients.
Aragão et al. (2021) WIN 55,212-2 shows anti-inflammatory and survival properties in human iPSC-derived cardiomyocytes infected with SARS-CoV-2. PeerJ 9:e12262 https://doi.org/10.7717/peerj.12262
Biochemical and transcriptomic analyses reveal that critical genes involved in pigment biosynthesis influence leaf color changes in a new sweet osmanthus cultivar ‘Qiannan Guifei’
Background Osmanthus fragrans (Oleaceae) is one of the most important ornamental plant species in China. Many cultivars with different leaf color phenotypes and good ornamental value have recently been developed. For example, a new cultivar ‘Qiannan Guifei’, presents a rich variety of leaf colors, which change from red to yellow-green and ultimately to green as leaves develop, making this cultivar valuable for landscaping. However, the biochemical characteristics and molecular mechanisms underlying leaf color changes of these phenotypes have not been elucidated. It has been hypothesized that the biosynthesis of different pigments in O. fragrans might change during leaf coloration. Here, we analyzed transcriptional changes in genes involved in chlorophyll (Chl), flavonoid, and carotenoid metabolic pathways and identified candidate genes responsible for leaf coloration in the new cultivar ‘Qiannan Guifei’. Methods Leaf samples were collected from ‘Qiannan Guifei’ plants at the red (R), yellow-green (YG) and green (G) leaf stages. We compared the different-colored leaves via leaf pigment concentrations, chloroplast ultrastructure, and transcriptomic data. We further analyzed differentially expressed genes (DEGs) involved in the Chl, flavonoid, and carotenoid metabolic pathways. In addition, we used qRT-PCR to validate expression patterns of the DEGs at the three stages. Results We found that, compared with those at the G stage, chloroplasts at the R and YG stages were less abundant and presented abnormal morphologies. Pigment analyses revealed that the leaves had higher flavonoid and anthocyanin levels at the R stage but lower Chl and carotenoid concentrations. Similarly, Chl and carotenoid concentrations were lower at the YG stage than at the G stage. By using transcriptomic sequencing, we further identified 61 DEGs involved in the three pigment metabolic pathways. Among these DEGs, seven structural genes (OfCHS, OfCHI, OfF3H, OfDFR, OfANS, OfUGT andOf3AT) involved in the flavonoid biosynthesis pathway were expressed at the highest level at the R stage, thereby increasing the biosynthesis of flavonoids, especially anthocyanins. Six putativeOfMYB genes, including three flavonoid-related activators and three repressors, were also highly expressed at the R stage, suggesting that they might coordinately regulate the accumulation of flavonoids, including anthocyanins. Additionally, expressions of the Chl biosynthesis-related genes OfHEMA, OfCHLG and OfCAO and the carotenoid biosynthesis-related genes OfHYB and OfZEP were upregulated from the R stage to the G stage, which increased the accumulation of Chl and carotenoids throughout leaf development. In summary, we screened the candidate genes responsible for the leaf color changes of ‘Qiannan Guifei’, improved current understanding of the regulatory mechanisms underlying leaf coloration and provided potential targets for future leaf color improvement in O. fragrans.
Cui et al. (2021) Biochemical and transcriptomic analyses reveal that critical genes involved in pigment biosynthesis influence leaf color changes in a new sweet osmanthus cultivar ‘Qiannan Guifei’. PeerJ 9:e12265 https://doi.org/10.7717/peerj.12265
Prognostic model of AU-rich genes predicting the prognosis of lung adenocarcinoma
Background AU-rich elements (ARE) are vital cis-acting short sequences in the 3’UTR affecting mRNA stability and translation. The deregulation of ARE-mediated pathways can contribute to tumorigenesis and development. Consequently, ARE-genes are promising to predict prognosis of lung adenocarcinoma (LUAD) patients. Methods Differentially expressed ARE-genes between LUAD and adjacent tissues in TCGA were investigated by Wilcoxon test. LASSO and Cox regression analyses were performed to identify a prognostic genetic signature. The genetic signature was combined with clinicopathological features to establish a prognostic model. LUAD patients were divided into high- and low-risk groups by the model. Kaplan–Meier curve, Harrell’s concordance index (C-index), calibration curves and decision curve analyses (DCA) were used to assess the model. Function enrichment analysis, immunity and tumor mutation analyses were performed to further explore the underlying molecular mechanisms. GEO data were used for external validation. Results Twelve prognostic genes were identified. The gene riskScore, age and stage were independent prognostic factors. The high-risk group had worse overall survival and was less sensitive to chemotherapy and radiotherapy (P < 0.01). C-index and calibration curves showed good performance on survival prediction in both TCGA (1, 3, 5-year ROC: 0.788, 0.776, 0.766) and the GSE13213 validation cohort (1, 3, 5-year ROC: 0.781, 0.811, 0.734). DCA showed the model had notable clinical net benefit. Furthermore, the high-risk group were enriched in cell cycle, DNA damage response, multiple oncological pathways and associated with higher PD-L1 expression, M1 macrophage infiltration. There was no significant difference in tumor mutation burden (TMB) between high- and low-risk groups. Conclusion ARE-genes can reliably predict prognosis of LUAD and may become new therapeutic targets for LUAD.
Liu et al. (2021) Prognostic model of AU-rich genes predicting the prognosis of lung adenocarcinoma. PeerJ 9:e12275 https://doi.org/10.7717/peerj.12275
Improving size selectivity of round pot for Charybdis japonica by configuring escape vents in the Yellow Sea, China
Sustainable development of the important economic species, Asian paddle crab (Charybdis japonica), has attracted attention in the coastal waters of the Yellow Sea, China. The commonly used round pots are almost nonselective, resulting in severe bycatch of juveniles. In this study, we explored a method to improve the size selectivity for C. japonica by mounting escape vents on the side panels of each pot. The selectivity of pots with escape vent sizes of 70 mm × 20 mm, 70 mm × 25 mm, 70 mm × 30 mm, and 70 mm × 35 mm was tested using a catch comparison method. The estimated minimum landing size (MLS) of carapace height (27 mm), according to the regulated MLS of carapace length (50 mm), was used as a reference point to explain the results. Significant increases in the size of crabs caught by pots were found with the enlargement of escape vent size (Kruskal–Wallis test, P < 0.01). The pots with 70 mm × 20 mm, 70 mm × 25 mm and 70 mm × 30 mm escape vents released nearly 50%, 75% and 95% of undersized individuals, respectively, and these three types of pots retained approximately 90% of legal-sized individuals compared with the control pots without escape vents. The pots with 70 mm × 35 mm escape vents released nearly all undersized individuals, but they also released most legal-sized individuals. Pots with an escape vent size of 70 mm × 30 mm were recommended for the sustainable development of C. japonica in the Yellow Sea of China. The results of this study reiterate the importance of carapace height for determining the size selectivity, which can serve as a reference to formulate management regulations in the coastal waters of the Yellow Sea, China.
Yu et al. (2021) Improving size selectivity of round pot for Charybdis japonica by configuring escape vents in the Yellow Sea, China. PeerJ 9:e12282 https://doi.org/10.7717/peerj.12282
Analysis of how the spatial and temporal patterns of fire and their bioclimatic and anthropogenic drivers vary across the Amazon rainforest in El Niño and non-El Niño years
In the past two decades, Amazon rainforest countries (Brazil, Bolivia, Colombia, Ecuador, Guyana, Peru and Venezuela) have experienced a substantial increase in fire frequency due to the changes in the patterns of different anthropogenic and climatic drivers. This study examines how both fire dynamics and bioclimatic factors varied based on the season (wet season and dry season) El Niño years across the different countries and ecosystems within the Amazon rainforest. Data from publicly available databases on forest fires (Global Fire Atlas) and bioclimatic, topographic and anthropogenic variables were employed in the analysis. Linear mixed-effect models discovered that year type (El Niño vs. non-El Niño), seasonality (dry vs. wet), land cover and forest strata (in terms of canopy cover and intactness) and their interactions varied across the Amazonian countries (and the different ecosystems) under consideration. A machine learning model, Multivariate Adaptive Regression Spline (MARS), was utilized to determine the relative importance of climatic, topographic, forest structure and human modification variables on fire dynamics across wet and dry seasons, both in El Niño and non-El Niño years. The findings of this study make clear that declining precipitation and increased temperatures have strong impact on fire dynamics (size, duration, expansion and speed) for El Niño years. El Niño years also saw greater fire sizes and speeds as compared to non-El Niño years. Dense and relatively undisturbed forests were found to have the lowest fire activity and increased human impact on a landscape was associated with exacerbated fire dynamics, especially in the El Niño years. Additionally, the presence of grass-dominated ecosystems such as grasslands also acted as a driver of fire in both El Niño and non-El Niño years. Hence, from a conservation perspective, increased interventions during the El Niño periods should be considered.
Spatial and Geographic Information Science
Singh et al. (2021) Analysis of how the spatial and temporal patterns of fire and their bioclimatic and anthropogenic drivers vary across the Amazon rainforest in El Niño and non-El Niño years. PeerJ 9:e12029 https://doi.org/10.7717/peerj.12029
Heronry distribution and site preference dynamics of tree-nesting colonial waterbirds in Tamil Nadu
Anthropogenic disturbance and climate change have significantly affected the distribution of wetlands globally and particularly in Asian countries. Various types of wetlands are harboured across all the biogeographic zones in India. These wetlands provide vital ecological services and are rich in biodiversity. However, anthropogenic pressures continue to be a threat to these wetlands by affecting the flora and fauna that depend on them. Tree-nesting colonial waterbirds are vulnerable to these pressures as their colonies are typically located in wetlands and associated areas. Disturbances to these areas have resulted in the loss or shifting of many heronries. The present study was conducted in the Indian state of Tamil Nadu during the period of 2017–2019 to document the existing and previously unknown heronries of the landscape. A total of 101 heronries were documented in 22 districts. The Little Cormorant was the most dominant species, occurring in 79% of the sites, with relative abundances of 24% and 26% during 2017–2018 and 2018–2019, respectively. A total of 23 tree species were utilized by the birds for nesting and Vachellia nilotica trees were used for nesting in about 25% of the heronries. 19% of the heronries were situated inside protected areas and 81% were located outside protected areas. Out of the 58 active nesting sites reported in 2005, 43 have been lost or are no longer active. Species distribution modelling with presence only data indicated that the sites with a high probability of occurrence were confined to the major waterbodies and rivers. Spatial correlation showed that the heronries were dispersed randomly across the landscape. The population dynamics within heronries and colonial nesting waterbirds’ response to various environmental factors must be monitored continuously to conserve these heronries.
Frank et al. (2021) Heronry distribution and site preference dynamics of tree-nesting colonial waterbirds in Tamil Nadu. PeerJ 9:e12256 https://doi.org/10.7717/peerj.12256
The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket)
This study examines the soil bacterial diversity in the Portulacaria afra-dominated succulent thicket vegetation of the Albany Subtropical Thicket biome; this biome is endemic to South Africa. The aim of the study was to compare the soil microbiomes between intact and degraded zones in the succulent thicket and identify environmental factors which could explain the community compositions. Bacterial diversity, using 16S amplicon sequencing, and soil physicochemistry were compared across three zones: intact (undisturbed and vegetated), degraded (near complete removal of vegetation due to browsing) and restored (a previously degraded area which was replanted approximately 11 years before sampling). Amplicon Sequence Variant (ASV) richness was similar across the three zones, however, the bacterial community composition and soil physicochemistry differed across the intact and degraded zones. We identified, via correlation, the potential drivers of microbial community composition as soil density, pH and the ratio of Ca to Mg. The restored zone was intermediate between the intact and degraded zones. The differences in the microbial communities appeared to be driven by the presence of plants, with plant-associated taxa more common in the intact zone. The dominant taxa in the degraded zone were cosmopolitan organisms, that have been reported globally in a wide variety of habitats. This study provides baseline information on the changes of the soil bacterial community of a spatially restricted and threatened biome. It also provides a starting point for further studies on community composition and function concerning the restoration of degraded succulent thicket ecosystems.
Schagen et al. (2021) The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket). PeerJ 9:e12176 https://doi.org/10.7717/peerj.12176