A digital mapping application for quantifying and displaying air temperatures at high spatiotemporal resolutions in near real-time across Australia
Surface air temperature (Ta) required for real-time environmental modelling applications should be spatially quantified to capture the nuances of local-scale climates. This study created near real-time air temperature maps at a high spatial resolution across Australia. This mapping is achieved using the thin plate spline interpolation in concert with a digital elevation model and ‘live’ recordings garnered from 534 telemetered Australian Bureau of Meteorology automatic weather station (AWS) sites. The interpolation was assessed using cross-validation analysis in a 1-year period using 30-min interval observation. This was then applied to a fully automated mapping system—based in the R programming language—to produce near real-time maps at sub-hourly intervals. The cross-validation analysis revealed broad similarities across the seasons with mean-absolute error ranging from 1.2 °C (autumn and summer) to 1.3 °C (winter and spring), and corresponding root-mean-square error in the range 1.6 °C to 1.7 °C. The R2 and concordance correlation coefficient (Pc ) values were also above 0.8 in each season indicating predictions were strongly correlated to the validation data. On an hourly basis, errors tended to be highest during the late afternoons in spring and summer from 3 pm to 6 pm, particularly for the coastal areas of Western Australia. The mapping system was trialled over a 21-day period from 1 June 2020 to 21 June 2020 with majority of maps completed within 28-min of AWS site observations being recorded. All outputs were displayed in a web mapping application to exemplify a real-time application of the outputs. This study found that the methods employed would be highly suited for similar applications requiring real-time processing and delivery of climate data at high spatiotemporal resolutions across a considerably large land mass.
Spatial and Geographic Information Science
Webb et al. (2020) A digital mapping application for quantifying and displaying air temperatures at high spatiotemporal resolutions in near real-time across Australia. PeerJ 8:e10106 https://doi.org/10.7717/peerj.10106
COVID-19: molecular and serological detection methods
Since COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared as a pandemic disease by the World Health Organization in early 2020, many countries, organizations and companies have tried to find the best way to diagnose the virus and contain its spreading. SARS-CoV-2 is a positive-sense single RNA (+ssRNA) coronavirus and mainly spreads through droplets, respiratory secretions, and direct contact. The early detection of the virus plays a central role in lowering COVID19 incidents and mortality rates. Thus, finding a simple, accurate, cheap and quick detection approach for SARS-CoV-2 at early stage of the viral infection is urgent and at high demand all around the world. The Food and Drug Administration and other health agencies have declared Emergency Use Authorization to develop diagnostic methods for COVID-19 and fulfill the demand. However, not all developed methods are appropriate and selecting a suitable method is challenging. Among all detection methods, rRT-PCR is the gold standard method. Unlike molecular methods, serological methods lack the ability of early detection with low accuracy. In this review, we summarized the current knowledge about COVID-19 detection methods aiming to highlight the advantages and disadvantages of molecular and serological methods.
Dhamad et al. (2020) COVID-19: molecular and serological detection methods. PeerJ 8:e10180 https://doi.org/10.7717/peerj.10180
The highly rearranged mitochondrial genomes of three economically important scale insects and the mitochondrial phylogeny of Coccoidea (Hemiptera: Sternorrhyncha)
The mitochondrial genomes (mitogenomes) of scale insects are less known in comparison to other insects, which hinders the phylogenetic and evolutionary studies of Coccoidea and higher taxa. Herein, the complete mitogenomes of Unaspis yanonensis, Planococcus citri and Ceroplastes rubens were sequenced for Coccoidea. The 15,220-bp long mitogenome of U. yanonensis contained the typical set of 37 genes including 13 PCGs, 22 tRNA genes and two rRNA genes; the 15,549-bp long mitogenome of P. citri lacked the tRNA gene trnV; the 15,387-bp long mitogenome of C. rubens exhibited several shortened PCGs and lacked five tRNA genes. The mitochondrial gene arrangement of the three mitogenomes was different from other scale insects and Drosophila yakuba. Most PCGs used standard ATN (ATA, ATT, ATC and ATG) start codons and complete TAN (TAA or TAG) termination codons. The ND4L had the highest evolutionary rate but COX1 and CYTB were the lowest. Most tRNA genes had cloverleaf secondary structures, whereas the reduction of dihydrouridine (DHU) arms and TψC arms were detected. Tandem repeats, stem-loop (SL) structures and poly-[TA]n stretch were found in the control regions (CRs) of the three mitogenomes. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) showed identical results, both supporting the inner relationship of Coccoidea as Coccidae + (Pseudococcidae + Diaspididae).
Liu et al. (2020) The highly rearranged mitochondrial genomes of three economically important scale insects and the mitochondrial phylogeny of Coccoidea (Hemiptera: Sternorrhyncha). PeerJ 8:e9932 https://doi.org/10.7717/peerj.9932
Master regulator genes and their impact on major diseases
Master regulator genes (MRGs) have become a hot topic in recent decades. They not only affect the development of tissue and organ systems but also play a role in other signal pathways by regulating additional MRGs. Because a MRG can regulate the concurrent expression of several genes, its mutation often leads to major diseases. Moreover, the occurrence of many tumors and cardiovascular and nervous system diseases are closely related to MRG changes. With the development in omics technology, an increasing amount of investigations will be directed toward MRGs because their regulation involves all aspects of an organism’s development. This review focuses on the definition and classification of MRGs as well as their influence on disease regulation.
Cai et al. (2020) Master regulator genes and their impact on major diseases. PeerJ 8:e9952 https://doi.org/10.7717/peerj.9952
Increased photosynthesis and grain yields in maize grown with less irrigation water combined with density adjustment in semiarid regions
In order to design a water-saving and high-yield maize planting model suitable for semiarid areas, we conducted trials by combining supplementary irrigation with different planting densities. Three planting densities (L: 52,500, M: 75,000, and H: 97,500 plants ha–1) and four supplementary irrigation modes (NI: no irrigation; IV: 375 m3 ha–1 during the 11-leaf stage; IS: 375 m3 ha–1 in the silking stage; and IVS: 375 m3 ha–1 during both stages) were tested. The irrigation treatments significantly increased the leaf relative water content, but the high planting density significantly decreased the relative water content during the silking and filling stages. After supplementary irrigation during the 11-leaf stage, IV and IVS significantly increased the photosynthetic capacity, but decreased the leaf water use efficiency. IS and IVS significantly increased the photosynthetic capacity after supplementary irrigation in the silking stage over two years. During the filling stage, IV, IS, and IVS increased the two-year average net photosynthetic rate by 17.0%, 27.2%, and 30.3%, respectively. The intercellular CO2 concentration increased as the density increased, whereas the stomatal conductance, transpiration rate, net photosynthetic rate, and leaf water use efficiency decreased, and the high planting density significantly reduced the leaf photosynthetic capacity. The highest grain yield was obtained using the IVS treatment under the medium planting density, but it did not differ significantly from that with the IS treatment. Furthermore, the IVS treatment used two times more water than the IS treatment. Thus, the medium planting density combined with supplementary irrigation during the silking stage was identified as a suitable water-saving planting model to improve the photosynthetic capacity and grain yield, and to cope with drought and water shortages in semiarid regions.
Liu et al. (2020) Increased photosynthesis and grain yields in maize grown with less irrigation water combined with density adjustment in semiarid regions. PeerJ 8:e9959 https://doi.org/10.7717/peerj.9959
Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia
Background The evolutionary history of southern South American organisms has been strongly influenced by Pleistocene climate oscillations. Amphibians are good models to evaluate hypotheses about the influence of these climate cycles on population structure and diversification of the biota, because they are sensitive to environmental changes and have restricted dispersal capabilities. We test hypotheses regarding putative forest refugia and expansion events associated with past climatic changes in the wood frog Batrachyla leptopus distributed along ∼1,000 km of length including glaciated and non-glaciated areas in southwestern Patagonia. Methods Using three mitochondrial regions (D-loop, cyt b, and coI) and two nuclear loci (pomc and crybA1), we conducted multilocus phylogeographic analyses and species distribution modelling to gain insights of the evolutionary history of this species. Intraspecific genealogy was explored with maximum likelihood, Bayesian, and phylogenetic network approaches. Diversification time was assessed using molecular clock models in a Bayesian framework, and demographic scenarios were evaluated using approximate Bayesian computation (ABC) and extended Bayesian skyline plot (EBSP). Species distribution models (SDM) were reconstructed using climatic and geographic data. Results Population structure and genealogical analyses support the existence of four lineages distributed north to south, with moderate to high phylogenetic support (Bootstrap > 70%; BPP > 0.92). The diversification time of B. leptopus’ populations began at ∼0.107 mya. The divergence between A and B lineages would have occurred by the late Pleistocene, approximately 0.068 mya, and divergence between C and D lineages was approximately 0.065 mya. The ABC simulations indicate that lineages coalesced at two different time periods, suggesting the presence of at least two glacial refugia and a postglacial colonization route that may have generated two southern lineages (p = 0.93, type I error: <0.094, type II error: 0.134). EBSP, mismatch distribution and neutrality indexes suggest sudden population expansion at ∼0.02 mya for all lineages. SDM infers fragmented distributions of B. leptopus associated with Pleistocene glaciations. Although the present populations of B. leptopus are found in zones affected by the last glacial maximum (∼0.023 mya), our analyses recover an older history of interglacial diversification (0.107–0.019 mya). In addition, we hypothesize two glacial refugia and three interglacial colonization routes, one of which gave rise to two expanding lineages in the south.
Nuñez et al. (2020) Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia. PeerJ 8:e9980 https://doi.org/10.7717/peerj.9980
Light quality affects the proliferation of in vitro cultured plantlets of Camellia oleifera Huajin
Background Camellia oleifera is an important oil-yielding woody plant native to China. Tea oil extracted from the seeds is rich in health-beneficial compounds. Huajin is a high-yielding elite variety of C. oleifera, with large fruits and remarkable resilience, widely cultivated in southern China; however, its seedling quality tends to be uneven. At present, techniques such as grafting, and cuttings are primarily adopted to propagate C. oleifera. These approaches are susceptible to environmental constraints owing to the long growth period, resulting in the lack of C. oleifera seedlings. Methods to make the cultivation more economical are warranted; this can be facilitated by tissue culture technology to provide good-quality seedlings in a short time. Methods In vitro cultured plantlets of C. oleifera Huajin were exposed to red light (RL), blue light (BL), red:blue light at a 4:1 ratio (R4:B1), and red:blue light at a 1:4 ratio (R1:B4); white light (WL) was used as the control treatment. To investigate the influence of light spectral quality on the proliferation coefficient, photosynthetic pigments, soluble proteins, plant height, leaf shape, Rubisco enzyme activity, and stomata and leaf anatomical features. Results The highest proliferation coefficient was observed under combined red and blue (4:1) light. In addition, this treatment resulted in the second highest chlorophyll content, the thickest palisade and spongy tissues, and consequently, the thickest leaves. The same treatment resulted in the second highest stomatal density, albeit concomitantly with the smallest average stomatal length and width. Discussion These results indicate that high-quality propagation of Huajin shoots can be achieved by culturing the plants in vitro under a combination of red and blue (4:1) lights. Previous studies have shown that red and blue lights improve rooting and transplanting rates of tissue culture seedlings. Hence, future research should focus on the effect of light quality on rooting and transplanting of tissue culture plantlets of Huajin and its specific molecular mechanisms.
He et al. (2020) Light quality affects the proliferation of in vitro cultured plantlets of Camellia oleifera Huajin. PeerJ 8:e10016 https://doi.org/10.7717/peerj.10016
The tale of springs and streams: how different aquatic ecosystems impacted the mtDNA population structure of two riffle beetles in the Western Carpathians
The Western Carpathians are a particularly interesting part of the Carpathian Arc. According to recent molecular data upon aquatic and terrestrial taxa, this mountain area is an important biodiversity hotspot of Europe. Moreover, the W Carpathians include rich systems of karst springs inhabited by specific fauna, where molecular diversity and phylogeographic patterns are yet to be fully explored. Our study aims to compare population genetic structure and molecular diversity of two related and commonly co-occurring riffle beetles, Elmis aenea (PWJ Müller, 1806) and Limnius perrisi (Dufour, 1843) in the springs and streams of the W Carpathians using the mitochondrial DNA barcoding fragment of the cytochrome c oxidase subunit I gene (COI). The relatively stable thermal and chemical conditions of springs throughout unfavourable climatic settings make these highly specific lotic systems potentially ideal for a long-term survival of some aquatic biota. Populations of both elmid species were relatively homogeneous genetically, with a single dominant haplotype. However, we revealed that E. aenea significantly dominated in the springs, while L. perrisi preferred streams. Relative isolation of the springs and their stable conditions were reflected in significantly higher molecular diversity of the E. aenea population in comparison to L. perrisi. The results of Bayesian Skyline Plot analysis also indicated the exceptional position of springs regarding maintaining the population size of E. aenea. On the other hand, it seems that streams in the W Carpathians provide more effective dispersal channels for L. perrisi, whose population expanded much earlier compared to E. aenea. Present study points out that different demographic histories of these two closely related elmid species are manifested by their different habitat preference and molecular diversity.
Bozáňová et al. (2020) The tale of springs and streams: how different aquatic ecosystems impacted the mtDNA population structure of two riffle beetles in the Western Carpathians. PeerJ 8:e10039 https://doi.org/10.7717/peerj.10039
Neighbourhood socioeconomic characteristics and blood pressure among Jamaican youth: a pooled analysis of data from observational studies
Introduction Neighbourhood characteristics are associated with several diseases, but few studies have investigated the association between neighbourhood and health in Jamaica. We evaluated the relationship between neighbourhood socioeconomic status (SES) and blood pressure (BP) among youth, 15–24 years old, in Jamaica. Methods A pooled analysis was conducted using data from three studies (two national surveys and a birth cohort), conducted between 2005–2008, with individual level BP, anthropometric and demographic data, and household SES. Data on neighbourhood SES were obtained from the Mona Geo-Informatics Institute. Neighbourhood was defined using community boundaries from the Social Development Commission in Jamaica. Community characteristics (poverty, unemployment, dependency ratio, population density, house size, and proportion with tertiary education) were combined into SES scores using principal component analysis (PCA). Multivariable analyses were computed using mixed effects multilevel models. Results Analyses included 2,556 participants (1,446 females; 1,110 males; mean age 17.9 years) from 306 communities. PCA yielded two neighbourhood SES variables; the first, PCA-SES1, loaded highly positive for tertiary education and larger house size (higher value = higher SES); while the second, PCA-SES2, loaded highly positive for unemployment and population density (higher value = lower SES). Among males, PCA-SES1 was inversely associated with systolic BP (β-1.48 [95%CI −2.11, −0.84] mmHg, p < 0.001, for each standard deviation unit increase in PCA-SES1 score) in multivariable model accounting for age, household SES, study, BMI, fasting glucose, physical activity and diet. PCA-SES1 was not significantly associated with systolic BP among females (β −0.48 [−1.62, 0.66], p = 0.410) in a similar model. Associations for PCA-SES2 was assessed using linear splines to account for non-linear effects. The were no significant associations between systolic BP and PCA-SES2 among males. Among females, higher PCA-SES2 (i.e. lower SES) was associated with higher systolic BP at spline 2 [z-score -1 to 0] (β4.09 [1.49, 6.69], p = 0.002), but with lower systolic BP at spline 3 [z-core 0 to 1] (β-2.81 [−5.04, −0.59], p = 0.013). There were no significant associations between diastolic BP and PCA-SES1, but PCA-SES2 showed non-linear associations with diastolic BP particularly among males. Conclusion Higher neighbourhood SES was inversely associated with systolic BP among male Jamaican youth; there were non-linear associations between neighbourhood SES and systolic BP among females and for diastolic BP for both males and females.
Ferguson et al. (2020) Neighbourhood socioeconomic characteristics and blood pressure among Jamaican youth: a pooled analysis of data from observational studies. PeerJ 8:e10058 https://doi.org/10.7717/peerj.10058
Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies
Background Next-generation sequencing (NGS) is a high-throughput technology that has become widely integrated in molecular diagnostics laboratories. Among the large diversity of NGS-based panels, the Trusight Tumor 26 (TsT26) enables the detection of low-frequency variants across 26 genes using the MiSeq platform. Methods We describe the inter-laboratory validation and subsequent clinical application of the panel in 399 patients presenting a range of tumor types, including gastrointestinal (GI, 29%), hematologic (18%), lung (13%), gynecological and breast (8% each), among others. Results The panel is highly accurate with a test sensitivity of 92%, and demonstrated high specificity and positive predictive values (95% and 96%, respectively). Sequencing testing was successful in two-thirds of patients, while the remaining third failed due to unsuccessful quality-control filtering. Most detected variants were observed in the TP53 (28%), KRAS (16%), APC (10%) and PIK3CA (8%) genes. Overall, 372 variants were identified, primarily distributed as missense (81%), stop gain (9%) and frameshift (7%) altered sequences and mostly reported as pathogenic (78%) and variants of uncertain significance (19%). Only 14% of patients received targeted treatment based on the variant determined by the panel. The variants most frequently observed in GI and lung tumors were: KRAS c.35G > A (p.G12D), c.35G > T (p.G12V) and c.34G > T (p.G12C). Conclusions Prior panel validation allowed its use in the laboratory daily practice by providing several relevant and potentially targetable variants across multiple tumors. However, this study is limited by high sample inadequacy rate, raising doubts as to continuity in the clinical setting.
Prieto-Potin et al. (2020) Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies. PeerJ 8:e10069 https://doi.org/10.7717/peerj.10069