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
A noninvasive flexible conformal sensor for accurate real-time monitoring of local cerebral edema based on electromagnetic induction
Cerebral edema (CE) is a non-specific pathological swelling of the brain secondary to any type of neurological injury. The real-time monitoring of focal CE mostly found in early stage is of great significance to reduce mortality and disability. Magnetic Induction Phase Shift (MIPS) is expected to achieve non-invasive continuous monitoring of CE. However, most existing MIPS sensors are made of hard materials which makes it difficult to accurately retrieve CE information. In this article, we designed a conformal two-coil structure and a single-coil structure, and studied their sensitivity map using finite element method (FEM). After that, the conformal MIPS sensor that is preferable for local CE monitoring was fabricated by flexible printed circuit (FPC). Next, physical experiments were conducted to investigate its performance on different levels of simulated CE solution volume, measurement distance, and bending. Subsequently, 14 rabbits were chosen to establish CE model and another three rabbits were selected as controls. The 24-hour MIPS real-time monitoring experiments was carried out to verify that the feasibility. Results showed a gentler attenuation trend of the conformal two-coil structure, compared with the single-coil structure. In addition, the novel flexible conformal MIPS sensor has a characteristic of being robust to bending according to the physical experiments. The results of animal experiments showed that the sensor can be used for CE monitoring. It can be concluded that this flexible conformal MIPS sensor is desirable for local focusing measurement of CE and subsequent multidimensional information extraction for predicting model. Also, it enables a much more comfortable environment for long-time bedside monitoring.
Chen et al. (2020) A noninvasive flexible conformal sensor for accurate real-time monitoring of local cerebral edema based on electromagnetic induction. PeerJ 8:e10079 https://doi.org/10.7717/peerj.10079
Attention behaviours but not pain-related behaviours are modified by the presence of a twin in lambs undergoing castration by rubber ring
The social context of social species such as sheep can modify their physiological and behavioural responses to stressors, through social buffering and social facilitation. Social buffering can lead to amelioration of stress, while social facilitation can lead to stress responses in an observer animal in the presence of a conspecific in distress. The current study investigated twin lambs undergoing ring castration, grouped either homogeneously with a castrated lamb (actor), or heterogeneously with a non-castrated lamb (observer) to examine the impact of social grouping on behavioural responses. Each lamb was scored for two classes of behaviour: pain-related behaviours and postures that are putatively related to the response to castration; and attentional behaviours directed at its twin. Thus, each lamb participated in the experiment as an actor exhibiting pain-related behaviours and postures, and as an observer of its twin. When behaviours of lambs were assessed as actors, there was a significant (P < 0.05) effect of castration but no significant effect of social grouping on expression of pain-related behaviours. When behaviours of lambs were assessed as observers, homogeneous grouping of castrated lambs increased attention towards the other twin in comparison to non-castrated lambs grouped homogeneously or lambs grouped heterogeneously (P < 0.01). Non-castrated lambs grouped homogeneously demonstrated significantly lower numbers of head direction changes (P < 0.001) and lower number of ear posture changes (P < 0.05) than heterogeneously grouped or castrated lambs. This study indicates that social attention between twin lambs is not clearly dependent on pain status of the actor lamb. It suggests that in order for the observer lamb to provide significant attention to the actor lamb displaying pain-related behaviour, the observer lamb also needs to be experiencing pain concurrently. Furthermore, there is some evidence that the presence of pain-related behaviours can lead to increased attention to the surrounding environment in non-castrated lambs. Understanding the effect of concurrent experience and varying social context assists us to improve our understanding of results of other experiments on pain-related behavioural responses.
Cho et al. (2020) Attention behaviours but not pain-related behaviours are modified by the presence of a twin in lambs undergoing castration by rubber ring. PeerJ 8:e10081 https://doi.org/10.7717/peerj.10081
Mathematical achievement: the role of spatial and motor skills in 6–8 year-old children
Several studies have tried to establish the factors that underlie mathematical ability across development. Among them, spatial and motor abilities might play a relevant role, but no studies jointly contemplate both types of abilities to account for mathematical performance. The present study was designed to observe the roles of spatial and motor skills in mathematical performance. A total of 305 children aged between 6 and 8 years took part in this study. A generalized linear regression model with mathematical performance as a dependent variable was performed. Results revealed that Block design (as a visuospatial reasoning measure) accounted for mathematical performance, especially among 6- and 7-year-olds but not in 8-year-olds. After controlling for the effect of the block design, mental rotation and manual dexterity predicted mathematical performance. These findings highlight the role of underlying cognitive (spatial) and motor abilities in supporting mathematical achievement in primary school children.
Fernández-Méndez et al. (2020) Mathematical achievement: the role of spatial and motor skills in 6–8 year-old children. PeerJ 8:e10095 https://doi.org/10.7717/peerj.10095