Salt and osmotic stress can improve the editing efficiency of CRISPR/Cas9-mediated genome editing system in potato
CRISPR/Cas9-mediated genome editing technology has been widely used for the study of gene function in crops, but the differences between species have led to widely varying genome editing efficiencies. The present study utilized a potato hairy root genetic transformation system and incorporated a rapid assay with GFP as a screening marker. The results clearly demonstrated that salt and osmotic stress induced by NaCl (10 to 50 mM) and mannitol (50 to 200 mM) treatments significantly increased the positive rates of genetic transformation mediated by A. rhizogenes and the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato. However, it was observed that the regeneration of potato roots was partially inhibited as a result. The analysis of CRISPR/Cas9-mediated mutation types revealed that chimeras accounted for the largest proportion, ranging from 62.50% to 100%. Moreover, the application of salt and osmotic stress resulted in an increased probability of null mutations in potato. Notably, the highest rate of null mutations, reaching 37.5%, was observed at a NaCl concentration of 10 mM. Three potential off-target sites were sequenced and no off-targeting was found. In conclusion, the application of appropriate salt and osmotic stress significantly improved the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato, with no observed off-target effects. However, there was a trade-off as the regeneration of potato roots was partially inhibited. Overall, these findings present a new and convenient approach to enhance the genome editing efficiency of the CRISPR/Cas9-mediated gene editing system in potato.
Ye et al. (2023) Salt and osmotic stress can improve the editing efficiency of CRISPR/Cas9-mediated genome editing system in potato. PeerJ 11:e15771 https://doi.org/10.7717/peerj.15771
Expression and correlation of COX-2 and NUCB1 in colorectal adenocarcinoma
Objective To investigate the expression and correlation of COX-2 and NUCB1 in colorectal adenocarcinoma and adjacent tissues. Methods The expression of COX-2 and NUCB1 and their effects on prognosis were predicted using bioinformatics. Immunohistochemistry was used to identify the expression of two molecules in 56 cases of colorectal adenocarcinoma and the surrounding tissues. The expression of two molecules and their association with clinicopathological variables were examined using the chi-square test. The association between COX-2 and NUCB1 was investigated using the Spearman correlation test. Results The STRING database revealed that COX-2 and NUCB1 were strongly linked. According to the UALCAN and HPA database, COX-2 was upregulated while NUCB1 was downregulated in colorectal adenocarcinoma, both at the protein and gene levels. The OS times for COX-2 and NUCB1 high expression, however, exhibited the same patterns. The rate of positive COX-2 immunohistochemical staining in cancer tissues was 69.64% (39/56), which was significantly higher than the rate in healthy tissues 28.57% (16/56). NUCB1 was expressed positively in cancer tissues at a rate of 64.29% (36/56) compared to just 19.64% (11/56) in neighboring tissues. The positive expression levels of COX-2 and NUCB1 were both closely related to clinical stage, differentiation degree, and lymphatic metastases (P < 0.05). In colorectal cancer, COX-2 and NUCB1 expression were significantly correlated (rs = 0.6312, P < 0.001). Conclusion Both COX-2 and NUCB1 are overexpressed and significantly associated in colorectal adenocarcinoma.
Zhang et al. (2023) Expression and correlation of COX-2 and NUCB1 in colorectal adenocarcinoma. PeerJ 11:e15774 https://doi.org/10.7717/peerj.15774
The tetrapod fauna of the upper Permian Naobaogou Formation of China: 10. Jimusaria monanensis sp. nov. (Dicynodontia) shows a unique epipterygoid
Jimusaria is the first reported Chinese dicynodont, previously only known from Xinjiang. Here we refer two specimens from the Naobaogou Formation, Nei Mongol, China to Jimusaria based on the following features: squamosal separated from supraoccipital by tabular, tabular contacting opisthotic, sharp and thin lateral dentary shelf expanding anteriorly into a thick swelling, nasals fused as single element, rod-like medial bar formed by footplate of epipterygoid connecting to the parabasisphenoid and periotic medially. A new species, J. monanensis, is named based on the diagnostic characters on these two specimens such as distinct caniniform buttress lacking posteroventral furrow, naso-frontal suture forming an anterior directed sharp angle, and converging ventral ridges on posterior portion of anterior pterygoid rami. In Jimusaria, the epipterygoid posteromedially contacts the parabasisphenoid and the periotic as a rod-like bar, a unique morphology unknown in any other dicynodonts. This structure probably increases the stability of the palatal complex. A similar structure might also appear in other dicynodonts as a cartilage connection. The new occurrence of Jimusaria increases the diversity of the tetrapod assemblage from the Naobaogou Formation, and further strengthens the connection between the tetrapod faunas from Nei Mongol and Xinjiang. Based on the current record, Jimusaria is one of the few tetrapod genera which survived in the end-Permian mass extinction.
Shi et al. (2023) The tetrapod fauna of the upper Permian Naobaogou Formation of China: 10. Jimusaria monanensis sp. nov. (Dicynodontia) shows a unique epipterygoid. PeerJ 11:e15783 https://doi.org/10.7717/peerj.15783
The weathering process of carbonatite: weathering time
Soil formation by rock weathering is driven by a combination of parent material, climate, organisms, topography, and time. Among these soil-forming factors, time plays a pivotal role in the weathering of carbonatite but it is a challenging factor to study quantitatively. A method for determining the weathering duration of carbonatite based on its weathering characteristics over a century-scale time period has not been clearly established. In this study, we selected abandoned carbonatite tombstones commonly found in the karst region of southwest China for investigation, using the date when the tombstones were erected as the onset of weathering. Chemical weathering indices were used to evaluate the weathering degree of different oxide contents produced by the carbonatite weathering process. In order to explore the weathering characteristics over time, the relationship between weathering duration and weathering degree was established. The results showed the following: (1) magnesium (Mg), aluminum (Al), silicon (Si), iron (Fe), titanium (Ti) are gradually enriched in the carbonatite regolith, and calcium (Ca) is gradually reduced. (2) The chemical indices of alteration (CIA), leaching coefficient (Lc), alumina-to-calcium ratio (AC) and mobiles index (Imob) can be successfully used for evaluation of the weathering degree of the carbonatite in different weathering time periods. (3) During the weathering of carbonatite, the weathering rate is a logarithmic function of time. Our research shows that over a period of more than 100 years of weathering, the carbonatite weathering process is characterized by fast weathering rates and low weathering degree in the early stages, but slow weathering rates in the later stages.
Chen et al. (2023) The weathering process of carbonatite: weathering time. PeerJ 11:e15793 https://doi.org/10.7717/peerj.15793
Green synthesis of silver nanoparticles using Ocimum sanctum Linn. and its antibacterial activity against multidrug resistant Acinetobacter baumannii
The biosynthesis of nanoparticles using the green route is an effective strategy in nanotechnology that provides a cost-effective and environmentally friendly alternative to physical and chemical methods. This study aims to prepare an aqueous extract of Ocimum sanctum (O. sanctum)-based silver nanoparticles (AgNPs) through the green route and test their antibacterial activity. The biosynthesized silver nanoparticles were characterised by colour change, UV spectrometric analysis, FTIR, and particle shape and size morphology by SEM and TEM images. The nanoparticles are almost spherical to oval or rod-shaped with smooth surfaces and have a mean particle size in the range of 55 nm with a zeta potential of −2.7 mV. The antibacterial activities of AgNPs evaluated against clinically isolated multidrug-resistant Acinetobacter baumannii (A. baumannii) showed that the AgNPs from O. sanctum are effective in inhibiting A. baumannii growth with a zone of inhibition of 15 mm in the agar well diffusion method and MIC and MBC of 32 µg/mL and 64 µg/mL, respectively. The SEM images of A. baumannii treated with AgNPs revealed damage and rupture in bacterial cells. The time-killing assay by spectrophotometry revealed the time- and dose-dependent killing action of AgNPs against A. baumannii, and the assay at various concentrations and time intervals indicated a statistically significant result in comparison with the positive control colistin at 2 µg/mL (P < 0.05). The cytotoxicity test using the MTT assay protocol showed that prepared nanoparticles of O. sanctum are less toxic against human cell A549. This study opens up a ray of hope to explore the further research in this area and to improve the antimicrobial activities against multidrug resistant bacteria.
Gautam et al. (2023) Green synthesis of silver nanoparticles using Ocimum sanctum Linn. and its antibacterial activity against multidrug resistant Acinetobacter baumannii. PeerJ 11:e15590 https://doi.org/10.7717/peerj.15590
Large-sized fossil hamsters from the late Middle Pleistocene Locality 2 of Shanyangzhai, China, and discussion on the validity of Cricetinus and C. varians (Rodentia: Cricetidae)
A detailed morphological description and comparative study were conducted on numerous large-sized hamster remains collected from the late Middle Pleistocene Locality 2 of Shanyangzhai (Syz 2), Hebei Province, China. The comparisons reveal that these fossils are highly similar to the extant Tscherskia triton in size and morphology, including the small degree of alternating between the main opposite cusps on M1-3, the presence of axioloph on M3, and mesolophids on m1-2 that are present but seldom reach the lingual margin of the teeth, among other features. However, minor differences between the two still exist. Consequently, all these fossils are designated as a chronosubspecies of the extant species, T. triton varians comb. nov. The skull and molar morphologies of Cricetinus varians and T. triton were meticulously compared to resolve the long-standing debate regarding the validity of Cricetinus Zdansky, 1928 and C. varians Zdansky, 1928. The findings indicate that the differences between the two are slight; as a result, C. varians can only be considered a chronosubspecies of T. triton, i.e., T. triton varians comb. nov., and Cricetinus should be recognized as a junior synonym of Tscherskia. We tentatively propose that, among the seven species once referred to Cricetinus, C. europaeus, C. gritzai, C. janossyi, and C. koufosi should be reassigned to Tscherskia, while C. beremendensis should be transferred to Allocricetus, and C. mesolophidos to Neocricetodon. Excluding Tscherskia sp. from the Late Pliocene Youhe fauna, there are no reliable Tscherskia fossils in China earlier than the Middle Pleistocene. Based on the current evidence, Tscherskia may have originated from Neocricetodon during the Early Pliocene in Europe and subsequently spread to Asia. T. triton is its sole surviving representative, which now exclusively inhabits East Asia.
Xie et al. (2023) Large-sized fossil hamsters from the late Middle Pleistocene Locality 2 of Shanyangzhai, China, and discussion on the validity of Cricetinus and C. varians (Rodentia: Cricetidae). PeerJ 11:e15604 https://doi.org/10.7717/peerj.15604
The effect of rhythm training on the motor coordination abilities of 8–12-year-old freestyle swimmers
This study aims to evaluate the effect of rhythm training in the early coordination development and to find out its role in the transfer of specific performance in young swimmers. Eighty young swimmers aged eight to twelve were divided randomly into a control group (CON, n = 40, M/F=17/23) or an experimental group (EXP, n = 40, M/F=19/21). A total of 72 swimmers completed all the training programs and tests included in this study (CON, n = 35, M/F=15/20; EXP, n = 37, M/F=16/21). The training programme lasted 12 weeks. During the study period, all groups participated in the same swimming training program with the control group participating six times a week, and the experimental group participating four times a week with an additional two rhythm trainings each week. The height, weight, walking backwards ability, jumping sideways ability, and 25 m freestyle were measured for each participant and an index of coordination was analyzed from recordings of the participant’s 25 m freestyle. The results indicated that participation in rhythm training resulted in improved general motor and swimming-specific coordination among the swimmers, but the results varied by number of years of sport-specific training experience. The swimmers with more training experience improved more in swimming-specific coordination but less in general motor coordination. This study strengthens the evidence for the effectiveness of early rhythm training in swimmers, indicating that it is feasible to design programs to address general and sport-specific coordination in young athletes.
Yin et al. (2023) The effect of rhythm training on the motor coordination abilities of 8–12-year-old freestyle swimmers. PeerJ 11:e15667 https://doi.org/10.7717/peerj.15667
Effects of extracts from various parts of invasive Solidago species on the germination and growth of native grassland plant species
Allelopathy is an important factor influencing whether an invasive plant species can become successfully established in a new range through disrupting the germination and growth of native plant species. Goldenrods (Solidago species) are one of the most widespread invasive taxa in Central Europe of North American origin. Owing to their high environmental impact and wide distribution range, invasive Solidago species should be controlled in Europe, and the areas invaded by them should be restored. Numerous studies have reported the allelopathic effects of Solidago gigantea and Solidago canadensis, but the results are inconsistent regarding differences in the allelopathic effects of particular plant parts and in the sensitivity to Solidago allelopathic effects among native species as well as between the two invasive species themselves. In this study, we aimed to analyse the effect of water extracts from S. canadensis and S. gigantea parts (roots, rhizomes, stems, leaves, and inflorescences) on the germination and initial growth of seedlings of 13 grassland species that typically grow in Central Europe. The tested grassland species differed in susceptibility to Solidago allelopathy, with the most resistant species being Schedonorus pratensis, Lolium perenne, Trifolium pratense, Daucus carota and Leucanthemum vulgare. The inhibitory effect of 10% water extracts from leaves and flowers were stronger than those from rhizomes, roots, and stems without leaves, regardless of the Solidago species. Our study results imply that reducing the allelopathic effect of Solidago during habitat restoration requires removal of the aboveground parts, including fallen leaves. The allelopathic effects of roots and rhizomes seem to be of secondary importance.
Perera et al. (2023) Effects of extracts from various parts of invasive Solidago species on the germination and growth of native grassland plant species. PeerJ 11:e15676 https://doi.org/10.7717/peerj.15676
Introduction The fast, intuitive and autonomous system 1 along with the slow, analytical and more logical system 2 constitute the dual system processing model of decision making. Whether acting independently or influencing each other both systems would, to an extent, rely on randomness in order to reach a decision. The role of randomness, however, would be more pronounced when arbitrary choices need to be made, typically engaging system 1. The present exploratory study aims to capture the expression of a possible innate randomness mechanism, as proposed by the authors, by trying to isolate system 1 and examine arbitrary decision making in autistic participants with high functioning Autism Spectrum Disorders (ASD). Methods Autistic participants withhigh functioning ASD and an age and gender matched comparison group performed the random number generation task. The task was modified to limit the contribution of working memory and allow any innate randomness mechanisms expressed through system 1, to emerge. Results Utilizing a standard analyses approach, the random number sequences produced by autistic individuals and the comparison group did not differ in their randomness characteristics. No significant differences were identified when the sequences were examined using a moving window approach. When machine learning was used, random sequences’ features could discriminate the groups with relatively high accuracy. Conclusions Our findings indicate the possibility that individual patterns during random sequence production could be consistent enough between groups to allow for an accurate discrimination between the autistic and the comparison group. In order to draw firm conclusions around innate randomness and further validate our experiment, our findings need to be replicated in a bigger sample.
Mantas et al. (2023) Exploring randomness in autism. PeerJ 11:e15751 https://doi.org/10.7717/peerj.15751
Eutrophication trends in the coastal region of the Great Tokyo area based on long-term trends of Secchi depth
Background The coastal ocean’s environment has changed owing to human activity, with eutrophication becoming a global concern. However, oligotrophication occurs locally and decreases fish production. Historically, the Secchi depth has been used as an index of primary productivity. We analyzed the results of over-a-half-century routine observations conducted in Sagami Bay and Tokyo Bay to verify the eutrophication/oligotrophication trend based on Secchi depth observations in a temperate coastal region near the Greater Tokyo area, which is highly affected by human activities. Methods Data recorded in the Kanagawa Prefecture from 1963 to 2018 were used in this study. After quality control, the observation area was divided into Tokyo Bay, the Uraga Channel (outer part of Tokyo Bay), Sagami Bay (northern part), and Sagami Nada (southern part of Sagami Bay) based on temperature and salinity at a depth of 10 m. Because the environmental parameters showed autocorrelation, time-series and correlation analyses were conducted using generalized least squares (GLS) models with a Prais-Winsten estimator. Results The Secchi depth was the shallowest in Tokyo Bay, followed by the Uraga Channel, Sagami Bay, and Sagami Nada, and was deep in winter (December and January), and shallow in summer (July) in all regions. The correlated analyses using the GLS model indicated that the shallowing of Secchi depth was significantly associated with decreases in temperature, salinity, and phosphate concentration. However, time-series analyses using GLS models indicated that the Secchi depth was significantly shallower, except in Tokyo Bay, where the surface temperature was significantly warming and the surface phosphate and nitrite concentrations decreased everywhere. A significant shallowing trend of the Secchi depth was mostly observed during the light-limiting season (January–March). Discussion Correlation analyses suggested the importance of horizontal advective transport, particularly from Tokyo Bay, which has cold and less saline eutrophic water. However, long-term shallowing of the Secchi depth was associated with warming, and changes in salinity were not significant in most months when the Secchi depth trend was significant. Thus, horizontal advection is not the primary cause of long-term eutrophication. Because the eutrophication trend was primarily observed in winter, when light is the major limiting factor of primary production, we concluded that warming provides a better photoenvironment for phytoplankton growth and induces eutrophication. As a decline in anthropogenic nutrient input after 1990s was reported in the investigated area, the long-term eutrophication trend was most likely caused due to global warming, which is another alarming impact resulting from human activities.
Akada et al. (2023) Eutrophication trends in the coastal region of the Great Tokyo area based on long-term trends of Secchi depth. PeerJ 11:e15764 https://doi.org/10.7717/peerj.15764