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BMC Plant Biology Jun 2024In acidic soils, aluminum (Al) toxicity inhibits the growth and development of plant roots and affects nutrient and water absorption, leading to reduced yield and...
In acidic soils, aluminum (Al) toxicity inhibits the growth and development of plant roots and affects nutrient and water absorption, leading to reduced yield and quality. Therefore, it is crucial to investigate and identify candidate genes for Al tolerance and elucidate their physiological and molecular mechanisms under Al stress. In this study, we identified a new gene OsAlR3 regulating Al tolerance, and analyzed its mechanism from physiological, transcriptional and metabolic levels. Compared with the WT, malondialdehyde (MDA) and hydrogen peroxide (HO) content were significantly increased, superoxide dismutase (SOD) activity and citric acid (CA) content were significantly decreased in the osalr3 mutant lines when exposed to Al stress. Under Al stress, the osalr3 exhibited decreased expression of antioxidant-related genes and lower organic acid content compared with WT. Integrated transcriptome and metabolome analysis showed the phenylpropanoid biosynthetic pathway plays an important role in OsAlR3-mediated Al tolerance. Exogenous CA and oxalic acid (OA) could increase total root length and enhance the antioxidant capacity in the mutant lines under Al stress. Conclusively, we found a new gene OsAlR3 that positively regulates Al tolerance by promoting the chelation of Al ions through the secretion of organic acids, and increasing the expression of antioxidant genes.
Topics: Aluminum; Oryza; Antioxidants; Gene Expression Regulation, Plant; Plant Proteins; Citric Acid; Plant Roots; Genes, Plant
PubMed: 38937693
DOI: 10.1186/s12870-024-05298-9 -
BMC Medical Informatics and Decision... Jun 2024Theories, models and frameworks (TMFs) are useful when implementing, evaluating and sustaining healthcare evidence-based interventions. Yet it can be challenging to...
BACKGROUND
Theories, models and frameworks (TMFs) are useful when implementing, evaluating and sustaining healthcare evidence-based interventions. Yet it can be challenging to identify an appropriate TMF for an implementation project. We developed and tested the usability of an online tool to help individuals who are doing or supporting implementation practice activities to identify appropriate models and/or frameworks to inform their work.
METHODS
We used methods guided by models and evidence on implementation science and user-centered design. Phases of tool development included applying findings from a scoping review of TMFs and interviews with 24 researchers/implementers on barriers and facilitators to identifying and selecting TMFs. Based on interview findings, we categorized the TMFs by aim, stage of implementation, and target level of change to inform the tool's algorithm. We then conducted interviews with 10 end-users to test the usability of the prototype tool and administered the System Usability Scale (SUS). Usability issues were addressed and incorporated into the tool.
RESULTS
We developed Find TMF, an online tool consisting of 3-4 questions about the user's implementation project. The tool's algorithm matches key characteristics of the user's project (aim, stage, target change level) with characteristics of different TMFs and presents a list of candidate models/frameworks. Ten individuals from Canada or Australia participated in usability testing (mean SUS score 84.5, standard deviation 11.4). Overall, participants found the tool to be simple, easy to use and visually appealing with a useful output of candidate models/frameworks to consider for an implementation project. Users wanted additional instruction and guidance on what to expect from the tool and how to use the information in the output table. Tool improvements included incorporating an overview figure outlining the tool steps and output, displaying the tool questions on a single page, and clarifying the available functions of the results page, including adding direct links to the glossary and to complementary tools.
CONCLUSIONS
Find TMF is an easy-to-use online tool that may benefit individuals who support implementation practice activities by making the vast number of models and frameworks more accessible, while also supporting a consistent approach to identifying and selecting relevant TMFs.
Topics: Humans; Internet; Models, Theoretical; Implementation Science
PubMed: 38937692
DOI: 10.1186/s12911-024-02580-6 -
BMC Plant Biology Jun 2024Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast...
BACKGROUND
Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known.
RESULTS
Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively.
CONCLUSIONS
The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.
Topics: Phylogeny; Genome, Mitochondrial; Lauraceae; Genome, Plant
PubMed: 38937691
DOI: 10.1186/s12870-024-05050-3 -
BMC Plant Biology Jun 2024Ichang papeda (Citrus ichangensis), a wild perennial plant of the Rutaceae family, is a cold-hardy plant. WRKY transcription factors are crucial regulators of plant...
BACKGROUND
Ichang papeda (Citrus ichangensis), a wild perennial plant of the Rutaceae family, is a cold-hardy plant. WRKY transcription factors are crucial regulators of plant growth and development as well as abiotic stress responses. However, the WRKY genes in C. ichangensis (CiWRKY) and their expression patterns under cold stress have not been thoroughly investigated, hindering our understanding of their role in cold tolerance.
RESULTS
In this study, a total of 52 CiWRKY genes identified in the genome of C. ichangensis were classified into three main groups and five subgroups based on phylogenetic analysis. Comprehensive analyses of motif features, conserved domains, and gene structures were performed. Segmental duplication plays a significant role in the CiWRKY gene family expansion. Cis-acting element analysis revealed the presence of various stress-responsive elements in the promoters of the majority of CiWRKYs. Gene ontology (GO) analysis and protein-protein interaction predictions indicate that the CiWRKYs exhibit crucial roles in regulation of both development and stress response. Expression profiling analysis demonstrates that 14 CiWRKYs were substantially induced under cold stress. Virus-induced gene silencing (VIGS) assay confirmed that CiWRKY31, one of the cold-induced WRKYs, functions positively in regulation of cold tolerance.
CONCLUSION
Sequence and protein properties of CiWRKYs were systematically analyzed. Among the 52 CiWRKY genes 14 members exhibited cold-responsive expression patterns, and CiWRKY31 was verified to be a positive regulator of cold tolerance. These findings pave way for future investigations to understand the molecular functions of CiWRKYs in cold tolerance and contribute to unravelling WRKYs that may be used for engineering cold tolerance in citrus.
Topics: Transcription Factors; Citrus; Cold-Shock Response; Plant Proteins; Phylogeny; Gene Expression Regulation, Plant; Genome, Plant; Gene Expression Profiling; Genes, Plant; Cold Temperature
PubMed: 38937686
DOI: 10.1186/s12870-024-05320-0 -
BMC Genomics Jun 2024The Alpine Merino is a new breed of fine-wool sheep adapted to the cold and arid climate of the plateau in the world. It has been popularized in Northwest China due to...
BACKGROUND
The Alpine Merino is a new breed of fine-wool sheep adapted to the cold and arid climate of the plateau in the world. It has been popularized in Northwest China due to its superior adaptability as well as excellent production performance. Those traits related to body weight, wool yield, and wool fiber characteristics, which are economically essential traits in Alpine Merino sheep, are controlled by QTL (Quantitative Trait Loci). Therefore, the identification of QTL and genetic markers for these key economic traits is a critical step in establishing a MAS (Marker-Assisted Selection) breeding program.
RESULTS
In this study, we constructed the high-density genetic linkage map of Alpine Merino sheep by sequencing 110 F generation individuals using WGR (Whole Genome Resequencing) technology. 14,942 SNPs (Single Nucleotide Polymorphism) were identified and genotyped. The map spanned 2,697.86 cM, with an average genetic marker interval of 1.44 cM. A total of 1,871 high-quality SNP markers were distributed across 27 linkage groups, with an average of 69 markers per LG (Linkage Group). Among them, the smallest genetic distance is 19.62 cM for LG2, while the largest is 237.19 cM for LG19. The average genetic distance between markers in LGs ranged from 0.24 cM (LG2) to 3.57 cM (LG17). The marker density in the LGs ranged from LG14 (39 markers) to LG1 (150 markers).
CONCLUSIONS
The first genetic map of Alpine Merino sheep we constructed included 14,942 SNPs, while 46 QTLs associated with body weight, wool yield and wool fiber traits were identified, laying the foundation for genetic studies and molecular marker-assisted breeding. Notably, there were QTL intervals for overlapping traits on LG4 and LG8, providing potential opportunities for multi-trait co-breeding and further theoretical support for selection and breeding of ultra-fine and meaty Alpine Merino sheep.
Topics: Animals; Quantitative Trait Loci; Body Weight; Wool; Chromosome Mapping; Polymorphism, Single Nucleotide; Sheep; Genetic Linkage; Genetic Markers; Whole Genome Sequencing; Phenotype; Sheep, Domestic; Genotype
PubMed: 38937677
DOI: 10.1186/s12864-024-10535-4 -
Communications Biology Jun 2024Aggregation of the human islet amyloid polypeptide (hIAPP) contributes to the development and progression of Type 2 Diabetes (T2D). hIAPP aggregates within a few hours...
Aggregation of the human islet amyloid polypeptide (hIAPP) contributes to the development and progression of Type 2 Diabetes (T2D). hIAPP aggregates within a few hours at few micromolar concentration in vitro but exists at millimolar concentrations in vivo. Natively occurring inhibitors of hIAPP aggregation might therefore provide a model for drug design against amyloid formation associated with T2D. Here, we describe the combined ability of low pH, zinc, and insulin to inhibit hIAPP fibrillation. Insulin dose-dependently slows hIAPP aggregation near neutral pH but had less effect on the aggregation kinetics at acidic pH. We determine that insulin alters hIAPP aggregation in two manners. First, insulin diverts the aggregation pathway to large nonfibrillar aggregates with ThT-positive molecular structure, rather than to amyloid fibrils. Second, soluble insulin suppresses hIAPP dimer formation, which is an important early aggregation event. Further, we observe that zinc significantly modulates the inhibition of hIAPP aggregation by insulin. We hypothesize that this effect arose from controlling the oligomeric state of insulin and show that hIAPP interacts more strongly with monomeric than oligomeric insulin.
Topics: Islet Amyloid Polypeptide; Hydrogen-Ion Concentration; Humans; Zinc; Insulin; Protein Aggregates; Diabetes Mellitus, Type 2; Kinetics; Amyloid; Protein Aggregation, Pathological
PubMed: 38937578
DOI: 10.1038/s42003-024-06388-y -
Scientific Reports Jun 2024The association of postpartum cardiac reverse remodeling (RR) with urinary proteome, particularly in pregnant women with cardiovascular (CV) risk factors who show...
The association of postpartum cardiac reverse remodeling (RR) with urinary proteome, particularly in pregnant women with cardiovascular (CV) risk factors who show long-term increased risk of cardiovascular disease and mortality is unknown. We aim to profile the urinary proteome in pregnant women with/without CV risk factors to identify proteins associated with postpartum RR. Our study included a prospective cohort of 32 healthy and 27 obese and/or hypertensive and/or diabetic pregnant women who underwent transthoracic echocardiography, pulse-wave-velocity, and urine collection at the 3rd trimester and 6 months postpartum. Shotgun HPLC-MS/MS profiled proteins. Generalized linear mixed-effects models were used to identify associations between urinary proteins and left ventricle mass (LVM), a surrogate of RR. An increase in arterial stiffness was documented from 3rd trimester to 6 months after delivery, being significantly elevated in women with CV risk factors. In addition, the presence of at least one CV risk factor was associated with worse LVM RR. We identified 6 and 11 proteins associated with high and low LVM regression, respectively. These proteins were functionally linked with insulin-like growth factor (IGF) transport and uptake regulation by IGF binding-proteins, platelet activation, signaling and aggregation and the immune system's activity. The concentration of IGF-1 in urine samples was associated with low LVM regression after delivery. Urinary proteome showed a predicting potential for identifying pregnant women with incomplete postpartum RR.
Topics: Humans; Female; Pregnancy; Adult; Proteome; Postpartum Period; Ventricular Remodeling; Prospective Studies; Biomarkers; Vascular Stiffness; Echocardiography; Risk Factors
PubMed: 38937573
DOI: 10.1038/s41598-024-65612-1 -
Scientific Reports Jun 2024Marine Heatwaves (MHWs) can directly influence survival of marine fishes, particularly for early life stages, including age-0 juveniles during their residence in coastal...
Marine Heatwaves (MHWs) can directly influence survival of marine fishes, particularly for early life stages, including age-0 juveniles during their residence in coastal nursery habitats. However, the ability of nurseries to support high fish densities, optimize foraging and growth, and protect against predators may be altered during MHWs. Gulf of Alaska Pacific cod (Gadus macrocephalus) larval, juvenile, and adult abundances declined dramatically following MHW events in 2014-2016 and 2019. To evaluate coastal nursery function during MHWs, we compared diet composition, recent growth, size, condition, and abundance of age-0 juveniles throughout their first summer before, during, and between MHWs. Diet shifted to larger prey during MHWs, particularly mysids, but diet did not appear to influence growth. We observed faster growth rates during MHWs, yet even when accounting for growth, we could not explain the higher body sizes observed in August during MHWs. Together with lower abundance and the near absence of small fish in the nursery by August during MHWs, these patterns highlight potential for size-selection and a reduced ability of nursery habitats to buffer against environmental variability during MHWs, with only a small number of large "super survivors" persisting through the summer.
Topics: Animals; Ecosystem; Alaska; Gadiformes; Larva; Seasons; Body Size
PubMed: 38937554
DOI: 10.1038/s41598-024-63897-w -
A multi-center study on the adaptability of a shared foundation model for electronic health records.NPJ Digital Medicine Jun 2024Foundation models are transforming artificial intelligence (AI) in healthcare by providing modular components adaptable for various downstream tasks, making AI...
Foundation models are transforming artificial intelligence (AI) in healthcare by providing modular components adaptable for various downstream tasks, making AI development more scalable and cost-effective. Foundation models for structured electronic health records (EHR), trained on coded medical records from millions of patients, demonstrated benefits including increased performance with fewer training labels, and improved robustness to distribution shifts. However, questions remain on the feasibility of sharing these models across hospitals and their performance in local tasks. This multi-center study examined the adaptability of a publicly accessible structured EHR foundation model (FM), trained on 2.57 M patient records from Stanford Medicine. Experiments used EHR data from The Hospital for Sick Children (SickKids) and Medical Information Mart for Intensive Care (MIMIC-IV). We assessed both adaptability via continued pretraining on local data, and task adaptability compared to baselines of locally training models from scratch, including a local foundation model. Evaluations on 8 clinical prediction tasks showed that adapting the off-the-shelf FM matched the performance of gradient boosting machines (GBM) locally trained on all data while providing a 13% improvement in settings with few task-specific training labels. Continued pretraining on local data showed FM required fewer than 1% of training examples to match the fully trained GBM's performance, and was 60 to 90% more sample-efficient than training local foundation models from scratch. Our findings demonstrate that adapting EHR foundation models across hospitals provides improved prediction performance at less cost, underscoring the utility of base foundation models as modular components to streamline the development of healthcare AI.
PubMed: 38937550
DOI: 10.1038/s41746-024-01166-w -
Scientific Reports Jun 2024We report the growth of bulk β-GaO crystals based on crystal pulling from a melt using a cold container without employing a precious-metal crucible. Our approach, named...
We report the growth of bulk β-GaO crystals based on crystal pulling from a melt using a cold container without employing a precious-metal crucible. Our approach, named oxide crystal growth from cold crucible (OCCC), is a fusion between the skull-melting and Czochralski methods. The absence of an expensive precious-metal crucible makes this a cost-effective crystal growth method, which is a critical factor in the semiconductor industry. An original construction 0.4-0.5 MHz SiC MOSFET transistor generator with power up to 35 kW was used to successfully grow bulk β-GaO crystals with diameters up to 46 mm. Also, an original diameter control system by generator frequency change was applied. In this preliminary study, the full width at half maximum of the X-ray rocking curve from the obtained β-GaO crystals with diameters ≤ 46 mm was comparable to those of β-GaO produced by edge-defined film fed growth. Moreover, as expected, the purity of the obtained crystals was high because only raw material-derived impurities were detected, and contamination from the process, such as insulation and noble metals, was below the detection limit. Our results indicate that the OCCC technique can be used to produce high-purity bulk β-GaO single crystalline substrate.
PubMed: 38937526
DOI: 10.1038/s41598-024-65420-7