The MdCBF1/2-MdTST1/2 module regulates sugar accumulation in response to low temperature in apple.

Soluble sugar content is a key component in controlling fruit flavor, and its accumulation in fruit is largely determined by sugar metabolism and transportation. When the diurnal temperature range is greater, the fleshy fruits accumulated more soluble sugars and become more sweeter. However, the molecular mechanism underlying this response remains largely unknown. In this study, we verified that low-temperature treatment promoted soluble sugar accumulation in apple fruit and found that this was due to the upregulation of the Tonoplast Sugar Transporter genes MdTST1/2. A combined strategy using assay for transposase-accessible chromatin (ATAC) sequencing and gene expression and cis-acting elements analyses, we identified two C-repeat Binding Factors, MdCBF1 and MdCBF2, that were induced by low temperature and that might be upstream transcription factors of MdTST1/2. Further studies established that MdCBF1/2 could bind to the promoters of MdTST1/2 and activate their expression. Overexpression of MdCBF1 or MdCBF2 in apple calli and fruit significantly upregulated MdTST1/2 expression and increased the concentrations of glucose, fructose, and sucrose. Suppression of MdTST1 and/or MdTST2 in an MdCBF1/2-overexpression background abolished the positive effect of MdCBF1/2 on sugar accumulation. In addition, simultaneous silencing of MdCBF1/2 downregulated MdTST1/2 expression and apple fruits failed to accumulate more sugars under low-temperature conditions, indicating that MdCBF1/2-mediated sugar accumulation was dependent on MdTST1/2 expression. Hence, we concluded that the MdCBF1/2-MdTST1/2 module is crucial for sugar accumulation in apples in response to low temperatures. Our findings provide mechanistic components coordinating the relationship between low temperature and sugar accumulation as well as new avenues to improve fruit quality.

Unlocking the dark matter: noncoding RNAs and RNA modifications in cardiac aging.

Cardiac aging is a multifaceted process that encompasses structural and functional alterations culminating in heart failure. As the elderly population continues to expand, there is a growing urgent need for interventions to combat age-related cardiac functional decline. Noncoding RNAs have emerged as critical regulators of cellular and biochemical processes underlying cardiac disease. This review summarizes our current understanding of how noncoding RNAs function in the heart during aging, with particular emphasis on mechanisms of RNA modification that control their activity. Targeting noncoding RNAs as potential novel therapeutics in cardiac aging is also discussed.

Ultra-secure storage and analysis of genetic data for the advancement of precision medicine.

Cloud computing provides the opportunity to store the ever-growing genotype-phenotype data sets needed to achieve the full potential of precision medicine. However, due to the sensitive nature of this data and the patchwork of data privacy laws across states and countries, additional security protections are proving necessary to ensure data privacy and security. Here we present SQUiD, a secure queryable database for storing and analyzing genotype-phenotype data. With SQUiD, genotype-phenotype data can be stored in a low-security, low-cost public cloud in the encrypted form, which researchers can securely query without the public cloud ever being able to decrypt the data. We demonstrate the usability of SQUiD by replicating various commonly used calculations such as polygenic risk scores, cohort creation for GWAS, MAF filtering, and patient similarity analysis both on synthetic and UK Biobank data. Our work represents a new and scalable platform enabling the realization of precision medicine without security and privacy concerns.

Molecular phylogeny of the family Rhabdiasidae (Nematoda: Rhabditida), with morphology, genetic characterization and mitochondrial genomes of Rhabdias kafunata and R. bufonis.

BACKGROUND: The family Rhabdiasidae (Nematoda: Rhabditida) is a globally distributed group of nematode parasites, with over 110 species parasitic mainly in amphibians and reptiles. However, the systematic position of the family Rhabdiasidae in the order Rhabditida remains unsolved, and the evolutionary relationships among its genera are still unclear. Moreover, the present knowledge of the mitochondrial genomes of rhabdiasids remains limited. METHODS: Two rhabdiasid species: Rhabdias kafunata Sata, Takeuchi & Nakano, 2020 and R. bufonis (Schrank, 1788) collected from the Asiatic toad Bufo gargarizans Cantor (Amphibia: Anura) in China, were identified based on morphology (light and scanning electron microscopy) and molecular characterization (sequencing of the nuclear 28S and ITS regions and mitochondrial cox1 and 12S genes). The complete mitochondrial genomes of R. kafunata and R. bufonis were also sequenced and annotated for the first time. Moreover, phylogenetic analyses based on the amino acid sequences of 12 protein-coding genes (PCGs) of the mitochondrial genomes were performed to clarify the systematic position of the family Rhabdiasidae in the order Rhabditida using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses based on the 28S + ITS sequences, were also inferred to assess the evolutionary relationships among the genera within Rhabdiasidae. RESULTS: The detailed morphology of the cephalic structures, vulva and eggs in R. kafunata and R. bufonis was revealed using scanning electron microscopy (SEM) for the first time. The characterization of 28S and ITS regions of R. kafunata was reported for the first time. The mitogenomes of R. kafunata and R. bufonis are 15,437 bp and 15,128 bp long, respectively, and both contain 36 genes, including 12 PCGs (missing atp8). Comparative mitogenomics revealed that the gene arrangement of R. kafunata and R. bufonis is different from all of the currently available mitogenomes of nematodes. Phylogenetic analyses based on the ITS + 28S data showed Neoentomelas and Kurilonema as sister lineages, and supported the monophyly of Entomelas, Pneumonema, Serpentirhabdias and Rhabdias. Mitochondrial phylogenomic results supported Rhabdiasidae as a member of the superfamily Rhabditoidea in the suborder Rhabditina, and its occurrance as sister to the family Rhabditidae. CONCLUSIONS: The complete mitochondrial genome of R. kafunata and R. bufonis were reported for the first time, and two new gene arrangements of mitogenomes in Nematoda were revealed. Mitogenomic phylogenetic results indicated that the family Rhabdiasidae is a member of Rhabditoidea in Rhabditina, and is closely related to Rhabditidae. Molecular phylogenies based on the ITS + 28S sequence data supported the validity of Kurilonema, and showed that Kurilonema is sister to Neoentomelas. The present phylogenetic results also indicated that the ancestors of rhabdiasids seem to have initially infected reptiles, then spreading to amphibians.

Probiotic and intra-nasal oxytocin combination therapy on autonomic function and gut-brain axis signaling in young children and teens with autism spectrum disorder.

Autonomic dysfunction has been widely studied in individuals with autism spectral disorder (ASD); however, the autonomic response to probiotic and oxytocin (OT) combination intervention has not yet been explored. We conducted the present study that includes 35 individuals with ASD aged 3-20 years to explore autonomic responses to daily Lactobacillus plantarum probiotic supplementation and OT nasal spray treatment both alone and in combination. We identified significant improvements in autonomic indices from subjects receiving combination treatment relative to those receiving placebo. Parameters that were observed to improve following combination treatment are time domain metrics of heart rate variability (HRV), including the root mean square of successive differences between normal heartbeats (RMSSD), standard deviation of normal-to-normal R-R intervals (SDNN), and proportion of the number of pairs of adjacent NN intervals that differ by more than 50ms (pNN50, p < 0.05). Furthermore, individuals that received either probiotics or OT alone demonstrated fewer changes in RMSSD, pNN50, and SDNN. Several parameters that demonstrated significant improvements in combination therapy were found to be correlated with baseline levels of OT (LF power: r = -0.86, p = 0.024; mean HR: r = 0.89, p = 0.012). Additionally, Social Responsiveness Scale (SRS) raw total scores (mean HR, r = 0.86, p = 0.024) and Aberrant Behavior Checklist (ABC) raw total scores (mean HR r = 0.94, p = 0.017) were correlated with mean heart rate (HR) and HRV-derived parameters. These results provide further evidence of synergy of probiotic and OT combination and help us gain a better understanding of the role of the gut-brain axis in ASD phenotypes and pathogenesis.

Neural Projection Filter: Learning Unknown Dynamics Driven by Noisy Observations.

In this article, we propose the novel neural stochastic differential equations (SDEs) driven by noisy sequential observations called neural projection filter (NPF) under the continuous state-space models (SSMs) framework. The contributions of this work are both theoretical and algorithmic. On the one hand, we investigate the approximation capacity of the NPF, i.e., the universal approximation theorem for NPF. More explicitly, under some natural assumptions, we prove that the solution of the SDE driven by the semimartingale can be well approximated by the solution of the NPF. In particular, the explicit estimation bound is given. On the other hand, as an important application of this result, we develop a novel data-driven filter based on NPF. Also, under certain condition, we prove the algorithm convergence; i.e., the dynamics of NPF converges to the target dynamics. At last, we systematically compare the NPF with the existing filters. We verify the convergence theorem in linear case and experimentally demonstrate that the NPF outperforms existing filters in nonlinear case with robustness and efficiency. Furthermore, NPF could handle high-dimensional systems in real-time manner, even for the 100 -D cubic sensor, while the state-of-the-art (SOTA) filter fails to do it.

SerpinB1 is required for Rev-erbα-mediated protection against acute lung injury induced by lipopolysaccharide-in mice.

BACKGROUND AND PURPOSE: Acute lung injury (ALI) is a serious, life-threatening inflammation of the lungs that still lacks effective treatment. We previously showed that serine protease inhibitor B1 (SerpinB1) protects against ALI induced by orthotopic autologous liver transplantation. However, the role of SerpinB1 in lipopolysaccharide (LPS)-induced ALI and its regulatory mechanisms are not known. EXPERIMENTAL APPROACH: Wild-type (WT) and SerpinB1 knockout (KO) mice were treated with intratracheal LPS stimulation to induce ALI. Some of the WT and KO mice were injected i.p. with melatonin, a rhythm-related protein Rev-erbα agonist. The circadian rhythm in WT mice was disrupted by exposing mice to 24 h of continuous dark or light conditions after intratracheal LPS. Neutrophils were isolated from alveolar lavage fluid of WT and KO mice, and from human peripheral blood. Neutrophils were treated with LPS and melatonin. KEY RESULTS: Disruption of circadian rhythm by either 24-h dark or light conditions exacerbated LPS-induced ALI and decreased expression of Rev-erbα and SerpinB1 protein in lung, whereas melatonin treatment increased SerpinB1 expression and attenuated LPS-induced ALI in WT mice, but not in KO mice. In isolated neutrophils, Rev-erbα was co-localized with SerpinB1 and bound to its promoter to trigger SerpinB1 transcription. Furthermore, LPS stimulation increased formation of neutrophil extracellular traps, which was reversed by melatonin treatment in neutrophils from WT mice, but not from KO mice. CONCLUSION AND IMPLICATIONS: In mice, SerpinB1 is rhythmically regulated by Rev-erbα, and its down-regulation exacerbates LPS-induced ALI by inducing formation of neutrophil extracellular traps.

Injury Site Specific Xenon Delivered by Platelet Membrane-Mimicking Hybrid Microbubbles to Protect Against Acute Kidney Injury via Inhibition of Cellular Senescence.

Inhalation of xenon gas improves acute kidney injury (AKI). However, xenon can only be delivered through inhalation, which causes non-specific distribution and low bioavailability of xenon, thus limiting its clinical application. In this study, xenon is loaded into platelet membrane-mimicking hybrid microbubbles (Xe-Pla-MBs). In ischemia-reperfusion-induced AKI, intravenously injected Xe-Pla-MBs adhere to the endothelial injury site in the kidney. Xe-Pla-MBs are then disrupted by ultrasound, and xenon is released to the injured site. This release of xenon reduced ischemia-reperfusion-induced renal fibrosis and improved renal function, which are associated with decreased protein expression of cellular senescence markers p53 and p16, as well as reduced beta-galactosidase in renal tubular epithelial cells. Together, platelet membrane-mimicking hybrid microbubble-delivered xenon to the injred site protects against ischemia-reperfusion-induced AKI, which likely reduces renal senescence. Thus, the delivery of xenon by platelet membrane-mimicking hybrid microbubbles is a potential therapeutic approach for AKI.

Metformin regulates inflammation and fibrosis in diabetic kidney disease through TNC/TLR4/NF-κB/miR-155-5p inflammatory loop.

BACKGROUND: Type 2 diabetes mellitus (T2DM) is significantly increasing worldwide, and the incidence of its complications is also on the rise. One of the main complications of T2DM is diabetic kidney disease (DKD). The glomerular filtration rate (GFR) and urinary albumin creatinine ratio (UACR) increase in the early stage. As the disease progresses, UACR continue to rise and GFR begins to decline until end-stage renal disease appears. At the same time, DKD will also increase the incidence and mortality of cardiovascular and cerebrovascular diseases. At present, the pathogenesis of DKD is not very clear. Therefore, exploration of the pathogenesis of DKD to find a treatment approach, so as to delay the development of DKD, is essential to improve the prognosis of DKD. AIM: To detect the expression of tenascin-C (TNC) in the serum of T2DM patients, observe the content of TNC in the glomerulus of DKD rats, and detect the expression of TNC on inflammatory and fibrotic factors in rat mesangial cells (RMCs) cultured under high glucose condition, in order to explore the specific molecular mechanism of TNC in DKD and bring a new direction for the treatment of DKD. METHODS: The expression level of TNC in the serum of diabetic patients was detected by enzyme-linked immunosorbent assay (ELISA), the protein expression level of TNC in the glomerular area of DKD rats was detected by immunohistochemistry, and the expression level of TNC in the rat serum was detected by ELISA. Rat glomerular mesangial cells were cultured. Following high glucose stimulation, the expression levels of related proteins and mRNA were detected by Western blot and polymerase chain reaction, respectively. RESULTS: ELISA results revealed an increase in the serum TNC level in patients with T2DM. Increasing UACR and hypertension significantly increased the expression of TNC (P < 0.05). TNC expression was positively correlated with glycosylated haemoglobin (HbA1c) level, body mass index, systolic blood pressure, and UACR (P < 0.05). Immunohistochemical staining showed that TNC expression in the glomeruli of rats with streptozotocin-induced diabetes was significantly increased compared with normal controls (P < 0.05). Compared with normal rats, serum level of TNC in diabetic rats was significantly increased (P < 0.05), which was positively correlated with urea nitrogen and urinary creatinine (P < 0.05). The levels of TNC, Toll-like receptor-4 (TLR4), phosphorylated nuclear factor-κB p65 protein (Ser536) (p-NF-κB p65), and miR-155-5p were increased in RMCs treated with high glucose (P < 0.05). The level of TNC protein peaked 24 h after high glucose stimulation (P < 0.05). After TNC knockdown, the levels of TLR4, p-NF-κB p65, miR-155-5p, connective tissue growth factor (CTGF), and fibronectin (FN) were decreased, revealing that TNC regulated miR-155-5p expression through the TLR4/NF-κB p65 pathway, thereby regulating inflammation (NF-κB p65) and fibrosis (CTGF and FN) in individuals with DKD. In addition, metformin treatment may relive the processes of inflammation and fibrosis in individuals with DKD by reducing the levels of the TNC, p-NF-κB p65, CTGF, and FN proteins. CONCLUSION: TNC can promote the occurrence and development of DKD. Interfering with the TNC/TLR4/NF-κB p65/miR-155-5p pathway may become a new target for DKD treatment.