lncRNA MALAT1 mediates osteogenic differentiation of bone mesenchymal stem cells by sponging miR-129-5p
Background Bone mesenchymal stem cells (BMSCs) have good osteogenic differentiation potential and have become ideal seed cells in bone tissue engineering. However, the osteogenic differentiation ability of BMSCs gradually weakens with age, and the regulatory mechanism is unclear. Method We conducted a bioinformatics analysis, dual-luciferase reporter (DLR) experiment, and RNA binding protein immunoprecipitation (RIP) to explore the hub genes that may affect BMSC functions. Results The expression level of long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (Malat1) was significantly higher in the BMSCs from elderly than younger mice, while miR-129-5p showed the opposite trend. The results of alkaline phosphatase staining, quantitative reverse transcription PCR and western blot experiments indicated that inhibiting the expression of Malat1 inhibits the osteogenic differentiation of BMSCs. This effect can be reversed by reducing the expression of miR-129-5p. Additionally, DLR and RIP experiments confirmed that Malat1 acts as a sponge for miR-129-5p. Conclusion Overall, our study findings indicated that lncRNA Malat1 may play a critical role in maintaining the osteoblast differentiation potential of BMSCs by sponging miR-129-5p.
Yin et al. (2022) lncRNA MALAT1 mediates osteogenic differentiation of bone mesenchymal stem cells by sponging miR-129-5p. PeerJ 10:e13355 https://doi.org/10.7717/peerj.13355
Foliar nutrient concentrations of six northern hardwood species responded to nitrogen and phosphorus fertilization but did not predict tree growth
Foliar chemistry can be useful for diagnosing soil nutrient availability and plant nutrient limitation. In northern hardwood forests, foliar responses to nitrogen (N) addition have been more often studied than phosphorus (P) addition, and the interactive effects of N and P addition have rarely been described. In the White Mountains of central New Hampshire, plots in ten forest stands of three age classes across three sites were treated annually beginning in 2011 with 30 kg N ha−1 y−1 or 10 kg P ha−1 y−1 or both or neither–a full factorial design. Green leaves of American beech (Fagus grandifolia Ehrh.), pin cherry (Prunus pensylvanica L.f.), red maple (Acer rubrum L.), sugar maple (A. saccharum Marsh.), white birch (Betula papyrifera Marsh.), and yellow birch (B. alleghaniensis Britton) were sampled pre-treatment and 4–6 years post-treatment in two young stands (last cut between 1988–1990), four mid-aged stands (last cut between 1971–1985) and four mature stands (last cut between 1883–1910). In a factorial analysis of species, stand age class, and nutrient addition, foliar N was 12% higher with N addition (p < 0.001) and foliar P was 45% higher with P addition (p < 0.001). Notably, P addition reduced foliar N concentration by 3% (p = 0.05), and N addition reduced foliar P concentration by 7% (p = 0.002). When both nutrients were added together, foliar P was lower than predicted by the main effects of N and P additions (p = 0.08 for N × P interaction), presumably because addition of N allowed greater use of P for growth. Foliar nutrients did not differ consistently with stand age class (p ≥ 0.11), but tree species differed (p ≤ 0.01), with the pioneer species pin cherry having the highest foliar nutrient concentrations and the greatest responses to nutrient addition. Foliar calcium (Ca) and magnesium (Mg) concentrations, on average, were 10% (p < 0.001) and 5% lower (p = 0.01), respectively, with N addition, but were not affected by P addition (p = 0.35 for Ca and p = 0.93 for Mg). Additions of N and P did not affect foliar potassium (K) concentrations (p = 0.58 for N addition and p = 0.88 for P addition). Pre-treatment foliar N:P ratios were high enough to suggest P limitation, but trees receiving N (p = 0.01), not P (p = 0.64), had higher radial growth rates from 2011 to 2015. The growth response of trees to N or P addition was not explained by pre-treatment foliar N, P, N:P, Ca, Mg, or K.
Hong et al. (2022) Foliar nutrient concentrations of six northern hardwood species responded to nitrogen and phosphorus fertilization but did not predict tree growth. PeerJ 10:e13193 https://doi.org/10.7717/peerj.13193
Nickel mine soil is a potential source for soybean plant growth promoting and heavy metal tolerant rhizobia
Mine soil is not only barren but also contaminated by some heavy metals. It is unclear whether some rhizobia survived under extreme conditions in the nickel mine soil. Therefore, this study tries to isolate some effective soybean plant growth promoting and heavy metal resistant rhizobia from nickel mine soil, and to analyze their diversity. Soybean plants were used to trap rhizobia from the nickel mine soil. A total of 21 isolates were preliminarily identified as rhizobia, which were clustered into eight groups at 87% similarity level using BOXA1R-PCR fingerprinting technique. Four out of the eight representative isolates formed nodules on soybean roots with effectively symbiotic nitrogen-fixing and plant growth promoting abilities in the soybean pot experiment. Phylogenetic analysis of 16S rRNA, four housekeeping genes (atpD-recA-glnII-rpoB) and nifH genes assigned the symbiotic isolates YN5, YN8 and YN10 into Ensifer xinjiangense and YN11 into Rhizobium radiobacter, respectively. They also showed different tolerance levels to the heavy metals including cadmium, chromium, copper, nickel, and zinc. It was concluded that there were some plant growth promoting and heavy metal resistant rhizobia with the potential to facilitate phytoremediation and alleviate the effects of heavy metals on soybean cultivation in nickel mine soil, indicating a novel evidence for further exploring more functional microbes from the nickel mine soil.
Environmental Contamination and Remediation
Liu et al. (2022) Nickel mine soil is a potential source for soybean plant growth promoting and heavy metal tolerant rhizobia. PeerJ 10:e13215 https://doi.org/10.7717/peerj.13215
Strategic decision making and prediction differences in autism
Background Several theories in autism posit that common aspects of the autism phenotype may be manifestations of an underlying differentiation in predictive abilities. The present study investigates this hypothesis in the context of strategic decision making in autistic participants compared to a control group. Method Autistic individuals (43 adults, 35 male) and a comparison group (42 adults, 35 male) of age and gender matched individuals, played a modified version of the prisoner’s dilemma (PD) task where they were asked, if capable, to predict their opponents’ move. The predictive performance of the two groups was assessed. Results Overall, participants in the autism group had a significantly lower number of correct predictions. Moreover, autistic participants stated, significantly more frequently than the comparison group, that they were unable to make a prediction. When attempting a prediction however, the success ratio did not differ between the two groups. Conclusions These findings indicate that there is a difference in prediction performance between the two groups. Although our task design does not allow us to identify whether this difference is due to difficulty to form a prediction or a reluctance in registering one, these findings could justify a role for prediction in strategic decision making during the PD task.
Mantas et al. (2022) Strategic decision making and prediction differences in autism. PeerJ 10:e13328 https://doi.org/10.7717/peerj.13328
Changes in primary metabolites and volatile organic compounds in cotton seedling leaves exposed to silver ions and silver nanoparticles revealed by metabolomic analysis
In the area of climate change, nanotechnology provides handy tools for improving crop production and assuring sustainability in global agricultural system. Due to excellent physiological and biochemical properties, silver nanoparticles (AgNPs) have been widely studied for potential use in agriculture. However, there are concerns about the mechanism of the toxic effects of the accumulation of AgNPs on crop growth and development. In this study, the impacts of AgNPs on cotton (Gossypium hirsutum) seedlings were evaluated by integrating physiological and comprehensive metabolomic analyses. Potting-soil-grown, two-week-old cotton seedlings were foliar-exposed to 5 mg/plant AgNP or 0.02 mg/plant Ag+ (equivalent to the free Ag+ released from AgNPs). Primary metabolites and volatile organic compounds (VOCs) were identified by gas chromatography–mass spectrometry (GC-MS) and solid-phase microextraction (SPME) GC-MS, respectively. AgNPs inhibited the photosynthetic capacity of the cotton leaves. The metabolic spectrum analysis identified and quantified 73 primary metabolites and 45 VOCs in cotton leaves. Both treatments significantly changed the metabolite profiles of plant leaves. Among the primary metabolites, AgNPs induced marked changes in amino acids, sugars and sugar alcohols. Among the VOCs, 13 volatiles, mainly aldehydes, alkanes and terpenoids, were specifically altered only in response to AgNPs. In summary, our study showed that the comprehensive influence of AgNPs on primary metabolites and VOCs was not merely attributed to the released Ag+ but was caused by AgNP-specific effects on cotton leaves. These results provide important knowledge about the physiological and chemical changes in cotton leaves upon exposure to AgNPs and offer a new insight for supporting the sustainable use of AgNPs in agriculture.
Yang et al. (2022) Changes in primary metabolites and volatile organic compounds in cotton seedling leaves exposed to silver ions and silver nanoparticles revealed by metabolomic analysis. PeerJ 10:e13336 https://doi.org/10.7717/peerj.13336
DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera)
Background The hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy. Methods A morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies. Results Sequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally.
Hlebec et al. (2022) DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera). PeerJ 10:e13213 https://doi.org/10.7717/peerj.13213
Changes in serum amino acid levels in non-small cell lung cancer: a case-control study in Chinese population
Background Previous studies have shown the alteration of amino acid (AA) profile in patients with non-small cell lung cancer (NSCLC). However, there is little data regarding AA profile in NSCLC in Chinese population. The aim of this study was to evaluate AA profile in Chinese NSCLC patients, explore its utility in sample classification and further discuss its related metabolic pathways. Methods The concentrations of 22 AAs in serum samples from 200 patients with NSCLC and 202 healthy controls were determined by liquid chromatography-tandem mass spectrometer (LC-MS/MS). AA levels in different tumor stages and histological types were also discussed. The performance of AA panel in classifying the cases and controls was evaluated in the training data set and validation data set based on the receiver operating characteristic (ROC) curve, and the important metabolic pathways were identified. Results The concentrations of tryptophan (Trp), phenylalanine (Phe), isoleucine (Ile), glycine (Gly), serine (Ser), aspartic acid (Asp), asparagine (Asn), cystein (Cys), glutamic acid (Glu), ornithine (Orn) and citrulline (Cit) were significantly altered in NSCLC patients compared with controls (all P-FDR < 0.05). Among these, four AAs including Asp, Cys, Glu and Orn were substantially up-regulated in NSCLC patients (FC ≥ 1.2). AA levels were significantly altered in patients with late-stage NSCLC, but not in those with early-stage when comparing with healthy controls. In terms of histological type, these AAs were altered in both adenocarcinoma and squamous cell carcinoma. For discrimination of NSCLC from controls, the area under the ROC curve (AUC) was 0.80 (95% CI [0.74–0.85]) in the training data set and 0.79 (95%CI [0.71–0.87]) in the validation data set. The AUCs for early-stage and late-stage NSCLC were 0.75 (95% CI [0.68–0.81]) and 0.86 (95% CI [0.82–0.91]), respectively. Moreover, the model showed a better performance in the classification of squamous cell carcinoma (AUC = 0.90, 95% CI [0.85–0.95]) than adenocarcinoma (AUC = 0.77, 95% CI [0.71–0.82]) from controls. Three important metabolic pathways were involved in the alteration of AA profile, including Gly, Ser and Thr metabolism; Ala, Asp and Glu metabolism; and Arg biosynthesis. Conclusions The levels of several AAs in serum were altered in Chinese NSCLC patients. These altered AAs may be utilized to classify the cases from the controls. Gly, Ser and Thr metabolism; Ala, Asp and Glu metabolism and Arg biosynthesis pathways may play roles in metabolism of the NSCLC patient.
Liu et al. (2022) Changes in serum amino acid levels in non-small cell lung cancer: a case-control study in Chinese population. PeerJ 10:e13272 https://doi.org/10.7717/peerj.13272
Population biological traits of Periophthalmus chrysospilos Bleeker, 1853 in the Vietnamese Mekong Delta
Periophthalmus chrysospilos is an amphibious fish living in mudflats from eastern India to Indonesia, including the Vietnamese Mekong Delta. Population biological traits play an important role in fishery assessment, but understanding is limited for this species. In total 1,031 specimens were caught in two regions covering four provinces, including the TVST (Duyen Hai, Tra Vinh and Tran De, Soc Trang) and BLCM (Dong Hai, Bac Lieu and Dam Doi, Ca Mau). Results found that the sex ratio was close to 1:1. The parameters of the von Bertalanffy in TVST were L∞ = 12.8 cm, K = 0.41 yr−1, t0 = −0.10 yr and in BLCM were 12.7 cm, 0.38 yr−1 and −0.08 yr, respectively. Although the growth coefficient (Φ′) in BLCM (1.79), was lower than that in TVST (1.83), the species shared a similar size at first capture (7.9 cm in TVST and 7.9 cm in BLCM). The species suffered from heavy pressure of fishing in TVST as fishing mortality in TVST (2.32 yr−1) was higher than that in BLCM (1.38 yr−1), leading to the higher total mortality (Z = 3.60 yr−1) in TVST compared to BLCM (Z = 2.59 yr−1). By contrast, the species showed similar natural mortality over both sites (1.20 yr−1 in TVST and 1.22 yr−1 in BLCM). The Periophthalmus chrysospilos population was reasonably exploited because E values (0.64 in TVST and 0.53 in BLCM) were lower than E10 (0.706 in BTTV and 0.705 in STBL). Nonetheless, to avoid the consequences of overfishing, some sustainable fisheries practices should be implemented, such as protecting mangrove forests, restricting fishing during the recruitment period, using appropriate fishing tools and increasing mesh size.
Dinh et al. (2022) Population biological traits of Periophthalmus chrysospilos Bleeker, 1853 in the Vietnamese Mekong Delta. PeerJ 10:e13289 https://doi.org/10.7717/peerj.13289
Change of intestinal microbiota in mice model of bronchopulmonary dysplasia
Background Gut microbiota has been proposed to be related to the pathogenesis of pulmonary diseases such as asthma and lung cancer, according to the gut-lung axis. However, little is known about the roles of gut microbiota in the pathogenesis of bronchopulmonary dysplasia (BPD). This study was designed to investigate the changes of gut microbiota in neonatal mice with BPD. Methods BPD model was induced through exposure to high concentration of oxygen. Hematoxylin and eosin (H&E) staining was utilized to determine the modeling efficiency. Stool samples were collected from the distal colon for the sequencing of V3–V4 regions of 16S rRNA, in order to analyze the gut microbiota diversity. Results Alpha diversity indicated that there were no statistical differences in the richness of gut microbiota between BPD model group and control group on day 7, 14 and 21. Beta diversity analysis showed that there were statistical differences in the gut microbiota on day 14 (R = 0.368, p = 0.021). Linear discriminant analysis effect size (LEfSe) showed that there were 22 markers with statistical differences on day 14 (p < 0.05), while those on day 7 and 21 were 3 and 4, respectively. Functional prediction analysis showed that the top three metabolic pathways were signal transduction (PFDR = 0.037), glycan biosynthesis and metabolism (PFDR = 0.032), and metabolism of terpenoids and polyketides (PFDR = 0.049). Conclusions BPD mice showed disorder of gut microbiota, which may involve specific metabolic pathways in the early stage. With the progression of neonatal maturity, the differences of the gut microbiota between the two groups would gradually disappear.
Fan et al. (2022) Change of intestinal microbiota in mice model of bronchopulmonary dysplasia. PeerJ 10:e13295 https://doi.org/10.7717/peerj.13295
Modification of the association between experience of economic distress during the COVID-19 pandemic and behavioral health outcomes by availability of emergency cash reserves: findings from a nationally-representative survey in Thailand
Background Studies have suggested that economic distress is associated with behavioral health outcomes, while availability of cash reserves for emergencies is associated with a reduction in economic distress. The objective of this study was to assess the extent that the availability of emergency cash reserves modified the association between experience of economic distress during the COVID-19 pandemic and behavioral health outcomes in the general adult population of Thailand. Methods We conducted a nationally-representative phone-based survey in late April 2021. Survey questions included questions on experience of economic distress, and a question on what participants would do to cover a 5,000 Thai Bahts (THB) emergency expense within one week, anxiety and depression screening questions, and questions regarding sleep, exercise, gambling, smoking, and drinking behaviors. We analyzed data using descriptive statistics and multivariate logistic regression analyses with adjustment for complex survey designs, and stratified analyses with assessment of heterogeneity of odds ratios between strata and assessment of additive and multiplicative interactions. Results A total of 1,555 individuals from 15 provinces participated in the survey (participation rate = 68.3%). Approximately 19.6% ± 1.0% of the participants reported that they would cover the 5,000 THB emergency expense only with cash or cash equivalent without resorting to other means. Experience of economic distress was associated with anxiety disorder after adjusting for covariables (Adjusted Odds Ratio (OR) = 2.47; 95% CI [1.45–4.19]). There was no evidence that availability of emergency cash reserves significantly modified the stated association, nor the association between experience of economic distress and other outcomes. However, with regard to anxiety disorder, depressive symptoms and history of gambling in past 30 days, the p-for-trend values (p-for-trend < 0.001) suggested that those with emergency cash reserves had lower prevalence of these outcomes than those without emergency cash reserves. Conclusions The study findings did not support our hypothesis that availability of emergency cash reserves modified the association between experience of economic distress and behavioral health outcomes. Nonetheless, the study findings can serve as potentially useful basic information for relevant stakeholders. Future studies should consider qualitative data collection and longitudinal study design in order to explore these associations at greater depths.
Wichaidit et al. (2022) Modification of the association between experience of economic distress during the COVID-19 pandemic and behavioral health outcomes by availability of emergency cash reserves: findings from a nationally-representative survey in Thailand. PeerJ 10:e13307 https://doi.org/10.7717/peerj.13307