Biochemical indices, gene expression, and SNPs associated with salinity adaptation in juvenile chum salmon (Oncorhynchus keta) as determined by comparative transcriptome analysis
Chum salmon (Oncorhynchus keta) migrate from freshwater to saltwater, and incur developmental, physiological and molecular adaptations as the salinity changes. The molecular regulation for salinity adaptation in chum salmon is currently not well defined. In this study, 1-g salmon were cultured under 0 (control group, D0), 8‰ (D8), 16‰ (D16), and 24‰ (D24) salinity conditions for 42 days. Na+/K+-ATPase and Ca2+/Mg2+-ATPase activities in the gill first increased and then decreased in response to higher salinity environments where D8 exhibited the highest Na+/K+ATPase and Ca2+/Mg2+-ATPase activity and D24 exhibited the lowest. Alkaline phosphatase (AKP) activity was elevated in all salinity treatment groups relative to controls, while no significant difference in acid phosphatase (ACP) activity was observed across treatment groups. De novo transcriptome sequencing in the D0 and D24 groups using RNA-Seq analysis identified 187,836 unigenes, of which 2,143 were differentially expressed in response to environmental salinity (71 up-regulated and 2,072 down-regulated). A total of 56,020 putative single nucleotide polymorphisms (SNPs) were also identified. The growth, development, osmoregulation and maturation factors of N-methyl-D-aspartate receptors (nmdas) expressed in memory formation, as well as insulin-like growth factor 1 (igf-1) and igf-binding proteins (igfbps) were further investigated using targeted qRT-PCR. The lowest expression of all these genes occurred in the low salinity environments (D8 or D16), while their highest expression occurred in the high salinity environments (D24). These results provide preliminary insight into salinity adaptation in chum salmon and a foundation for the development of marker-assisted breeding for this species.
Li et al. (2022) Biochemical indices, gene expression, and SNPs associated with salinity adaptation in juvenile chum salmon (Oncorhynchus keta) as determined by comparative transcriptome analysis. PeerJ 10:e13585 https://doi.org/10.7717/peerj.13585
Environment and density-dependency explain the fine-scale aggregation of tree recruits before and after thinning in a mixed forest of Southern Europe
Thinning in forest management primarily reduces the density of trees and alters the patchiness and spatial complexity of environmental factors and individual interactions between plant recruits. At fine spatial scales, little is known about the relative weight of ecological processes affecting tree regeneration before and after thinning events. Here we studied the density and aggregation of tree recruits in fully-mapped plots located in mixed forests in Northern Iberian Peninsula (Southern Europe) for over four years, which comprises one year before and three years after a thinning event. We applied spatial point-pattern analyses to examine (a) the aggregation of recruits, and their association with trees and (b) the relative effect of both environmental (i.e., the patchiness of the local environment) and density-dependent factors (i.e., the aggregation of trees and/or recruits) to predict the density, aggregation, and survival of recruits. We found, in thinning plots, that recruits were less dense, their aggregation pattern was more heterogeneous, were distributed randomly in respect of trees and their survival was almost unaffected by the tree proximity. By contrast, recruits in control plots were denser, were only aggregated at distances lower than 1.0 m, were closer to trees, and such closer distance to trees affected negatively in their survival. Independently of the treatment, the aggregation of recruits was chiefly determined by the density-dependent factors at less than 1.0 m and environmental factors at distances beyond that proximity. Overall, our results suggest that thinning affected the aggregation of recruits at two spatial scales: (a) by favoring the tree-recruit and recruit-recruit facilitation at less than 1.0 m and (b) by modifying spatial heterogeneity of the environment at distances beyond that proximity.
Rodríguez-Pérez et al. (2022) Environment and density-dependency explain the fine-scale aggregation of tree recruits before and after thinning in a mixed forest of Southern Europe. PeerJ 10:e13892 https://doi.org/10.7717/peerj.13892
Study on the cultivation of seedlings using buds of potato (Solanum tuberosum L.)
Background Potato, a vegetable crop grown worldwide, has many uses, a short growth period, a large market demand and high economic benefits. The loss of potato seediness due to traditional potato growing methods is becoming increasingly evident, and research on new ways of growing potatoes is particularly important. Bud planting technology has the advantages of more reproduction, faster growth, and simplified maintenance of crop plants under cultivation. Methods In this study, a bud planting method was adopted for the cultivation of potato seedlings. Specifically, we assessed different types of treatments for the production of high-quality buds and seedlings of potato. A total of four disease-free potato varieties (Fujin, Youjin, Zhongshu 4, and Feiwuruita) were selected, potato buds with three different lengths (3 cm, 5 cm, and 7 cm) were considered the T1, T2, and T3 treatments, and terminal buds, middle buds, and tail buds were used as the T4, T5, and T6 treatments. A nutrient pot experiment was performed following a randomized complete block design (RCBD) with three replicates and a natural control (CK) treatment. Cultivation was performed with the common horticultural practices of weeding and hoeing applied as needed. The photosynthetic indices, physiological indices, growth indices and quality of potato seedlings and quality of potato buds were measured at two-week intervals, and yield indices were measured when the final crop was harvested 14 weeks after planting. Results and Conclusions Cultivation of seedlings from potato buds of different lengths increased the reproduction coefficient and reduced the number of seed potatoes needed for cultivation. All morphological, physiological, and yield indices showed positive trends. A potato bud length of 7 cm was optimal for raising seedlings. Moreover, buds located at the terminal of the potato yielded seedlings with the best quality. In conclusion, we recommend that our proven bud planting technique be adopted at the commercial level, which could support good crop production with maximum yield.
Wang et al. (2022) Study on the cultivation of seedlings using buds of potato (Solanum tuberosum L.). PeerJ 10:e13804 https://doi.org/10.7717/peerj.13804
Genome-wide identification of the trehalose-6-phosphate synthase gene family in sweet orange (Citrus sinensis) and expression analysis in response to phytohormones and abiotic stresses
Background Trehalose-6-phosphate synthase (TPS) is an essential enzyme for synthesizing trehalose and is a significant regulator of plant development and stress response. Sweet orange (Citrus sinensis) is an economically important fruit tree crop and a common transgenic material. At present, little information is available about the TPS gene family in sweet orange. Methods The TPS gene family were identified from sweet orange genome by bioinformatics analysis. Additionally, the expression of CisTPS genes was analyzed under phytohormones and abiotic stresses by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR). Results Here, eight TPS genes were identified and were found to be randomly distributed in five sweet orange chromosomes. TPS and trehalose-6-phosphate phosphatase (TPP) domains were observed in all CisTPS proteins. The phylogenetic tree showed that CisTPS genes were divided into two subfamilies, and genes in each subfamily had conserved intron structures and motif compositions. The cis-acting elements of CisTPS genes suggested their roles in phytohormone and stress responses. All CisTPS genes were ubiquitously expressed in roots, leaves, and stems, and six members were highly expressed in roots. Expression profiles showed that CisTPS genes exhibited tissue specificity and were differentially expressed in response to phytohormones and abiotic stresses. This study lays a foundation for revealing the functions of the TPS gene family in trehalose regulation in sweet orange, and provides a valuable reference for this gene family in other plants.
Liu et al. (2022) Genome-wide identification of the trehalose-6-phosphate synthase gene family in sweet orange (Citrus sinensis) and expression analysis in response to phytohormones and abiotic stresses. PeerJ 10:e13934 https://doi.org/10.7717/peerj.13934
A retrospective study of real-world effectiveness and safety of rivaroxaban in patients with non-valvular atrial fibrillation and venous thromboembolism in Saudi Arabia
Background Real-world evidence on factor Xa inhibitor (rivaroxaban) prescribing patterns, safety, and efficacy in patients with non-valvular atrial fibrillation (NVAF) and venous thromboembolism (VTE) is rare. Herein, we sought to examine the above outcomes in the largest academic center in the Kingdom of Saudi Arabia (KSA). Methods This is a retrospective observational study designed to examine the prescribing pattern, safety and real-world effectiveness of the factor Xa inhibitor rivaroxaban in patients with NVAF and VTE. Data on rivaroxaban prescriptions were collected and analyzed. Bleeding outcomes were defined as per the International Society on Thrombosis and Hemostasis (ISTH) definition. Results A total of 2,316 patients taking rivaroxaban recruited through several departments of King Saud University Medical City (KSUMC). The mean age was 61 years (±17.8) with 55% above the age of 60 and 58% were females. Deep vein thrombosis and pulmonary embolism (VTE) was the most prevalent reason for prescribing rivaroxaban, followed by NVAF. A total daily dosage of 15 mg was given to 23% of the patients. The incidence rate of recurrent thrombosis and recurrent stroke was 0.2%. Furthermore, rivaroxaban had a 0.04 percent incidence rate of myocardial infarction. Half of the patients with recurrent thrombosis and stroke were taking 15 mg per day. The incidence rate of major bleeding was 1.1%. More over half of the patients who experienced significant bleeding were taking rivaroxaban at a dosage of 20 mg per day. According to the HAS-BLED Score (>2 score), 48 percent of patients who experienced significant bleeding had a high risk of bleeding. Non-major bleeding occurred in 0.6% of cases. Similarly, 40% of patients with non-major bleeding were taking rivaroxaban at a dosage of 20 mg per day. According to the HAS-BLED Score, just 6.6% of these individuals had a high risk of bleeding. 93.4% of the patients, on the other hand, were at intermediate risk. Conclusion The prescription of rivaroxaban in this real-life cohort study differs from the prescribing label and the outcomes of a phase 3 randomised clinical trial. However, for individuals with VTE and NVAF, the 20 mg dose looked to be more efficacious than the pivotal trial outcomes. Furthermore, among patients with VTE and NVAF, rivaroxaban was linked to a decreased incidence of safety events such as recurrent thrombosis, recurrent stroke, MI, major bleeding, and non-major haemorrhage in a real-world environment.
Alosaimi et al. (2022) A retrospective study of real-world effectiveness and safety of rivaroxaban in patients with non-valvular atrial fibrillation and venous thromboembolism in Saudi Arabia. PeerJ 10:e13974 https://doi.org/10.7717/peerj.13974
Semi-field evaluation of human landing catches versus human double net trap for estimating human biting rate of Anopheles minimus and Anopheles harrisoni in Thailand
Background Whilst the human landing catch (HLC) technique is considered the ‘gold standard’ for estimating human-biting rates, it is labor-intensive and fraught with potential risk of exposure to infectious mosquito bites. This study evaluated the feasibility and performance of an alternative method, the human double net trap (HDNT) relative to HLC for monitoring host-seeking malaria vectors of the Anopheles minimus complex in a semi-field system (SFS). Methods HDNT and HLC were positioned in two rooms, 30 m apart at both ends of the SFS. Two human volunteers were rotated between both traps and collected released mosquitoes (n = 100) from 6:00 pm till 6:00 am. Differences in Anopheles mosquito densities among the trapping methods were compared using a generalized linear model based on a negative binomial distribution. Results There were 82.80% (2,136/2,580) of recaptures of wild-caught and 94.50% (2,835/3,000) of laboratory-reared mosquitoes that were molecularly identified as An. harrisoni and An. minimus, respectively. Mean density of An. harrisoni was significantly lower in HNDT (15.50 per night, 95% CI [12.48–18.52]) relative to HLC (25.32 per night (95% CI [22.28–28.36]), p < 0.001). Similarly, the mean density of a laboratory strain of An. minimus recaptured in HDNT was significantly lower (37.87 per night, 95% CI [34.62–41.11]) relative to HLC (56.40 per night, 95% CI [55.37–57.43]), p < 0.001. Relative sampling efficiency analysis showed that HLC was the more efficient trap in collecting the An. minimus complex in the SFS. Conclusion HDNT caught proportionately fewer An. minimus complex than HLC. HDNT was not sensitive nor significantly correlated with HLC, suggesting that it is not an alternative method to HLC.
Yan et al. (2022) Semi-field evaluation of human landing catches versus human double net trap for estimating human biting rate of Anopheles minimus and Anopheles harrisoni in Thailand. PeerJ 10:e13865 https://doi.org/10.7717/peerj.13865
Floral ontogeny of Tachigali (Caesalpinioideae, Fabaceae) species
Background The present ontogenetic study reveals variations throughout floral development in three morphologically representative species from the genus Tachigali, allowing a better understanding of floral organs diversity, flower symmetry and their homologies, especially in Fabaceae, a diverse family that exhibits a wide variation in floral architecture. Tachigali (Caesalpinioideae) corresponds to an important Neotropical legumes tree genus with 58 species in Brazil. Species of the genus Sclerolobium Vogel were incorporated in its circumscription, increasing the diversity of its floral morphology. Methods This work aims to perform an ontogenetic study of T. denudata, T. paratyensis and T. spathulipetala, morphologically representative species of Tachigali, in order to describe the floral development and to better comprehend the floral morphology varieties among the species, using scanning electron microscopy. Results We found the studied species to have floral buds with acropetal and helical development along the inflorescence axis; sepals and petals with helical development, varying the position of the primordia in the bud, according to the different species; stamens with unilateral development and carpel with adaxial curvature. These data correspond to original records of Tachigali ontogeny and contribute to an improved understanding of floral morphology and symmetry with data related to the zygomorphic and early development of the sepals and petals.
Marques Casanova et al. (2022) Floral ontogeny of Tachigali (Caesalpinioideae, Fabaceae) species. PeerJ 10:e13975 https://doi.org/10.7717/peerj.13975
The cold-stress responsive gene DREB1A involved in low-temperature tolerance in Xinjiang wild walnut
Background Low-temperatures have the potential to be a serious problem for plants and can negatively affect the normal growth and development of walnuts. DREB1/CBF (Dehydration Responsive Element Binding Protein 1/C-repeat Binding Factor), one of the most direct transcription factors in response to low-temperature stress, may improve the resistance of plants to low-temperatures by regulating their functional genes. However, few studies have been conducted in walnut. The Xinjiang wild walnut is a rare wild plant found in China, with a large number of excellent trait genes, and is hardier than cultivated walnuts in Xinjiang. Methods In this work, we identified all of the DREB1 members from the walnut genome and analyzed their expression levels in different tissues and during low-temperature stress on the Xinjiang wild walnut. The JfDREB1A gene of the Xinjiang wild walnut was cloned and transformed into Arabidopsis thaliana for functional verification. Results There were five DREB1 transcription factors in the walnut genome. Among them, the relative expression level of the DREB1A gene was significantly higher than other members in the different tissues (root, stem, leaf) and was immediately un-regulated under low-temperature stress. The overexpression of the JfDREB1A gene increased the survival rates of transgenic Arabidopsis lines, mainly through maintaining the stability of cell membrane, decreasing the electrical conductivity and increasing the activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). Additionally, the expression levels of cold-inducible genes like AtKIN1, AtERD10, AtRD29A, AtCOR15A and AtCOR47, were significantly increased. These results showed that the JfDREB1A gene may play an important role in the response to cold stress of the Xinjiang wild walnut. This study contributes to our understanding of the molecular mechanism of the Xinjiang wild walnut’s response to low-temperature stress and will be beneficial for developing walnut cultivars with improved cold resistance.
Han et al. (2022) The cold-stress responsive gene DREB1A involved in low-temperature tolerance in Xinjiang wild walnut. PeerJ 10:e14021 https://doi.org/10.7717/peerj.14021
First photographic evidence of oceanic manta rays (Mobula birostris) at two locations in the Fiji islands
Until the revision of the genus Manta in 2009, when a second manta species (Manta alfredi) was resurrected based on morphological and meristic data, all available records in Fijian literature were recorded as Manta birostris. Subsequently, documented sightings were recorded as M. alfredi. Another reclassification of the genus Manta was undertaken in 2018 when both manta ray species (Manta alfredi, Manta birostris) were moved to Mobula based on phylogenetic analysis. Here, we present the first unequivocal evidence of oceanic manta ray (Mobula birostris) occurrence in Fijian waters. In November 2018, two individuals were sighted foraging in Laucala Bay, a large lagoon adjacent to Suva, the capital city of Fiji. Subsequently, three more individuals were sighted in December 2018, two individuals in July 2020, at least six individuals were observed in November 2021, and eight individuals in May/June 2022, all foraging in the same geographical area. Unique ventral identification patterns could be obtained for nine individuals, and all nine individuals have been re-sighted since first identification, with one individual being documented in 2018, 2020, 2021 and 2022. Two additional individuals were recorded in the Yasawa Island Group in the west of Fiji while passing through and foraging in a channel between Drawaqa and Naviti Island in April and September 2020. We provide photographic identification of ten M. birostris individuals from two sites and discuss our findings in the context of local environmental parameters and other recorded sightings in the South Pacific region. In light of the global extinction risk of M. birostris and the recent reclassification from Vulnerable to Endangered on the Red List of Threatened Species, the expansion of their known distribution range to Fijian waters and the recurrence of individuals over consecutive years in the same location adds valuable information for the development of effective and data-driven conservation strategies.
Gordon et al. (2022) First photographic evidence of oceanic manta rays (Mobula birostris) at two locations in the Fiji islands. PeerJ 10:e13883 https://doi.org/10.7717/peerj.13883
Investigation and research on elderly people’s willingness to combine medical and health care and related factors in coastal cities in eastern China
Background The problem of global aging was becoming increasingly prominent. At present, the empty nest and miniaturization of family structure reduce the function of home-based elderly care. Methods A questionnaire survey was conducted on 347 elderly people in multiple communities and nursing homes in eastern coastal cities of China, and 13 institutional staff members of eight nursing institutions that carried out the medical-nursing integration model were interviewed as the research objects. The survey mainly focuses on the basic characteristics of the elderly, the family support system, and the acceptance of medical care and health care. The influencing factors were screened by t test, univariate analysis and multivariate logistic regression analysis. SPSS software was used to test the reliability and validity of the questionnaire, and the Crobach’s was 0.792, which can be considered that the questionnaire had good internal reliability. The classification of the questionnaire was reasonable, the reliability of the questionnaire was high, and the internal consistency of the scale was high. According to KMO and Bartlett test, KMO = 0.826, χ2 = 853.731, the degree of freedom was 36, and the P value was 0.000. Results The proportion of male and female respondents was 48.1% and 51.9% respectively. Multivariate logistic regression analysis results showed that gender had no statistical significances on the degree of support for combine medical and health care in the elderly (P > 0.05). The results showed that gender, age, marital status, medical insurance type and old-age insurance type had little effect on the support of the combination of medical care and health care for the elderly (P > 0.05). Compared with the control group with education below primary school, the elderly with bachelor’s degree or above are more willing to support the combination of medical care and health (P < 0.05). The registered residence type is more obvious than that of the urban residents (P < 0.05). Compared with the enterprise employees in the control group, the elderly who were employed as migrant workers before retirement were more willing to support the combination of medical care and health (P < 0.05). From the perspective of family monthly income, the elderly with family income ≥10,000 RMB have more obvious support for the combination of medical care and health than the elderly with family monthly income <3,000 RMB in the control group (P < 0.05). In terms of the degree of understanding, the degree of understanding and support in different degrees are significantly higher than that in the control group (P < 0.05). Conclusion Through multivariate logistic regression analysis, education level, registered residence, pre-retirement occupation and family income are more obvious for the elderly to support medical care and health. It is necessary to increase investment in elderly activity centers, actively carry out activities.
Wei et al. (2022) Investigation and research on elderly people’s willingness to combine medical and health care and related factors in coastal cities in eastern China. PeerJ 10:e14004 https://doi.org/10.7717/peerj.14004