Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing.

A major challenge in genetics is to identify genetic variants driving natural phenotypic variation. However, current methods of genetic mapping have limited resolution. To address this challenge, we developed a CRISPR-Cas9-based high-throughput genome editing approach that can introduce thousands of specific genetic variants in a single experiment. This enabled us to study the fitness consequences of 16,006 natural genetic variants in yeast. We identified 572 variants with significant fitness differences in glucose media; these are highly enriched in promoters, particularly in transcription factor binding sites, while only 19.2% affect amino acid sequences. Strikingly, nearby variants nearly always favor the same parent's alleles, suggesting that lineage-specific selection is often driven by multiple clustered variants. In sum, our genome editing approach reveals the genetic architecture of fitness variation at single-base resolution and could be adapted to measure the effects of genome-wide genetic variation in any screen for cell survival or cell-sortable markers.

CDCA5-EEF1A1 interaction promotes progression of clear cell renal cell carcinoma by regulating mTOR signaling.

BACKGROUND: Cell division cycle associated 5 (CDCA5) plays ontogenetic role in various human cancers. However, its specific function and regulatory mechanism in ccRCC remain uncertain. METHODS: Immunohistochemistry and western blots were performed to investigate the expression of CDCA5 in ccRCC tissues. Genetic knockdown and upregulation of CDCA5 were performed to investigate its functional roles in ccRCC proliferation, migration, apoptosis and sunitinib resistance. Furthermore, Co-IP assay and LC-MS/MS were performed to investigate the underlying mechanisms. RESULTS: We found that CDCA5 expression is frequently upregulated in ccRCC tumors and is associated with poor prognosis of ccRCC patients. Functionally, CDCA5 promotes proliferation, migration, and sunitinib resistance, while inhibiting apoptosis in ccRCC cells. In vivo mouse xenograft model confirms that silencing of CDCA5 drastically inhibits the growth of ccRCC. Mechanistically, we discovered that CDCA5 interacts with Eukaryotic Translation Elongation Factor 1 Alpha 1 (EEF1A1) to regulate mTOR signaling pathway, thereby promoting ccRCC progression. CONCLUSIONS: Taken together, our results demonstrate the significant role of CDCA5 in ccRCC progression. The findings may provide insights for the development of new treatment strategies targeting CDCA5 for ccRCC patients.

Screening of astaxanthin-overproducing Xanthophyllomyces dendrorhous strains via iterative ARTP mutagenesis and cell sorting by flow cytometry.

AIMS: The astaxanthin-producing yeast Xanthophyllomyces dendrorhous is widely used in aquaculture. Due to the production of carotenoid, this yeast shows visible color; however, high-throughput approaches for identification of astaxanthin-overproducing strains remain rare. METHODS AND RESULTS: This study verified an effective approach to identify astaxanthin-overproducing mutants of X. dendrorhous by flow cytometry (FCM) and cell sorting. First, the mutant libraries were generated by atmospheric and room-temperature plasma (ARTP) mutagenesis. Second, a highly direct correlation between the concentrations of intracellular astaxanthin and the levels of emitting fluorescence was constructed by testing a variety of astaxanthin-contained populations via FCM and cell sorting. Third, iterative cell sorting efficiently improves the identification of astaxanthin-overproducing strains. Finally, two mutants producing 4.96 mg astaxanthin g-1 DCW (dry cell weight) and 5.30 mg astaxanthin g-1 DCW were obtained, which were 25.3% and 33.8% higher than that of the original strain, respectively. CONCLUSIONS: This study demonstrated that iterative ARTP mutagenesis along with cell sorting by FCM is effective for identifying astaxanthin-overproduction strains.

Salicylic Acid's impact on Sedum alfredii growth and cadmium tolerance: Comparative physiological, transcriptomic, and metabolomic study.

With the acceleration of industrialization, Cd pollution has emerged as a major threat to soil ecosystem health and food safety. Hyperaccumulating plants like Sedum alfredii Hance are considered to be used as part of an effective strategy for the ecological remediation of Cd polluted soils. This study delved deeply into the physiological, transcriptomic, and metabolomic responses of S. alfredii under cadmium (Cd) stress when treated with exogenous salicylic acid (SA). We found that SA notably enhanced the growth of S. alfredii and thereby increased absorption and accumulation of Cd, effectively alleviating the oxidative stress caused by Cd through upregulation of the antioxidant system. Transcriptomic and metabolomic data further unveiled the influence of SA on photosynthesis, antioxidant defensive mechanisms, and metal absorption enrichment pathways. Notably, the interactions between SA and other plant hormones, especially IAA and JA, played a central role in these processes. These findings offer us a comprehensive perspective on understanding how to enhance the growth and heavy metal absorption capabilities of hyperaccumulator plants by regulating plant hormones, providing invaluable strategies for future environmental remediation efforts.

Transition pathways connecting crystals and quasicrystals.

Due to structural incommensurability, the emergence of a quasicrystal from a crystalline phase represents a challenge to computational physics. Here, the nucleation of quasicrystals is investigated by using an efficient computational method applied to a Landau free-energy functional. Specifically, transition pathways connecting different local minima of the Lifshitz-Petrich model are obtained by using the high-index saddle dynamics. Saddle points on these paths are identified as the critical nuclei of the 6-fold crystals and 12-fold quasicrystals. The results reveal that phase transitions between the crystalline and quasicrystalline phases could follow two possible pathways, corresponding to a one-stage phase transition and a two-stage phase transition involving a metastable lamellar quasicrystalline state, respectively.

Mechanism of Mulberry Leaves and Black Sesame in Alleviating Slow Transit Constipation Revealed by Multi-Omics Analysis.

Traditional Chinese medicine (TCM) possesses the potential of providing good curative effects with no side effects for the effective management of slow transit constipation (STC), an intestinal disease characterized by colonic dyskinesia. Mulberry leaves (Morus alba L.) and black sesame (Sesamum indicum L.), referred to as SH, are processed and conditioned as per standardized protocols. SH has applications as food and medicine. Accordingly, we investigated the therapeutic potential of SH in alleviating STC. The analysis of SH composition identified a total of 504 compounds. The intervention with SH significantly improved intestinal motility, reduced the time for the first black stool, increased antioxidant activity, and enhanced water content, thereby effectively alleviating colon damage caused by STC. Transcriptome analysis revealed the SH in the treatment of STC related to SOD1, MUC2, and AQP1. The analysis of 16S rRNA gene sequences indicated notable differences in the abundance of 10 bacteria between the SH and model. Metabolomic analysis further revealed that SH supplementation increased the levels of nine metabolites associated with STC. Integrative analysis revealed that SH modulated amino acid metabolism, balanced intestinal flora, and targeted key genes (i.e., SOD1, MUC2, AQP1) to exert its effects. SH also inhibited the AQP1 expression and promoted SOD1 and MUC2 expression.

Effectiveness of risk-based caries management among Chinese preschool children: a randomized controlled single-blind trial.

BACKGROUND: Early childhood caries (ECC) remain a serious oral health problem on a global scale. Risk-based caries management (RBCM) implemented in some parts of the world has been effective in preventing ECC. However, there is a lack of prospective research on the application of RBCM among Chinese children, and little is known about its effectiveness. The purpose of this study was to evaluate the effectiveness of RBCM in preventing caries among children aged 3-5 years in Wanzhou District, Chongqing Municipality, China. METHODS: Three- to five-year-old children from four kindergartens in Wanzhou were randomly selected for baseline dental examination and caries risk assessment (CRA) and randomly assigned to the experimental group (EG) or the control group (CG) according to the kindergarten. The EG received caries prevention measures of different intensities based on the child's caries risk level. The CG received full-mouth fluoride twice a year according to standard prevention, regardless of their caries risk. One year later, another dental examination and CRA were conducted, to observe changes in the decayed, missing, and filled teeth (dmft) index and caries risk, and to analyze potential factors that may affect the incidence of new caries. RESULTS: Complete data were collected from 291 children (EG, N = 140, 84.8%; CG, N = 181, 83.4%). A total of 25.7% of the EG and 50.3% of the CG children developed new caries, with newly added dmft scores of 0.54 ± 1.12 and 1.32 ± 1.72, respectively (P < 0.05). Multivariate logistic regression indicated that children living in rural areas, assigned to the CG, and rated as high-risk at baseline were more likely to develop new caries (P < 0.05). The proportion of children with an increased caries risk in the EG was significantly lower than that in the CG (P < 0.05). CONCLUSIONS: RBCM effectively prevented new caries in 3- to 5-year-old Wanzhou children and reduced the proportion of children at increased risk of caries. It is an effective approach for preventing ECC. CLINICAL TRIAL REGISTRATION: This trial was registered in the Chinese Clinical Trials Register. The registration number was ChiCTR230067551 (11/01/2023).

SMAD4 regulates the progression of cholangiocarcinoma by modulating the expression of STING1.

SMAD4 is a tumour suppressor and an important regulator of tumour immune scape which is downregulated in cholangiocarcinoma (CCA). STING1 is a vital sensing factor of abnormal DNA; however, the correlation between SMAD4 and STING1 and the role of the SMAD4-STING1 interaction in the progression of CCA have not yet been evaluated. Public database was analysed to reveal the expression of SMAD4 and STING1. A cohort comprising 50 iCCA, 113 pCCA and 119 dCCA patients was assembled for the study. Immunohistochemistry was employed to evaluate the expression levels of STING1 and SMAD4. In vitro transwell and CCK8 assays, along with luciferase reporter assay, were conducted to analyse the potential regulatory mechanisms of SMAD4 on the expression of STING1. Expression of SMAD4 and STING1 were downregulated in CCA tumours and STING1 expression correlated with SMAD4 expression. The overexpression of SMAD4 was found to suppress the migration, invasion and proliferation capabilities of CCA cells; whereas, the knockdown of SMAD4 enhanced these abilities. Furthermore, it was observed that SMAD4 translocated into the nucleus following TGF-ß1 stimulation. Knockdown of SMAD4 resulted in the inhibition of STING1 transcriptional activity, whereas the overexpression of SMAD4 promoted the transcriptional activity of STING1. Clinically, low STING1 and SMAD4 expression indicated poor prognosis in CCA, and simultaneously low expression of STING1 and SMAD4 predicts poorer patient survival. SMAD4 regulates the expression of STING1 through its transcription regulating function. Dual low expression of STING1 and SMAD4 had more power in predicting patient survival. These results indicate that SMAD4-silenced CCA may downregulate its STING1 expression to adapt to the immune system.

Physiological ß-amyloid clearance by the liver and its therapeutic potential for Alzheimer's disease.

Cerebral amyloid-ß (Aß) accumulation due to impaired Aß clearance is a pivotal event in the pathogenesis of Alzheimer's disease (AD). Considerable brain-derived Aß is cleared via transporting to the periphery. The liver is the largest organ responsible for the clearance of metabolites in the periphery. Whether the liver physiologically clears circulating Aß and its therapeutic potential for AD remains unclear. Here, we found that about 13.9% of Aß42 and 8.9% of Aß40 were removed from the blood when flowing through the liver, and this capacity was decreased with Aß receptor LRP-1 expression down-regulated in hepatocytes in the aged animals. Partial blockage of hepatic blood flow increased Aß levels in both blood and brain interstitial fluid. The chronic decline in hepatic Aß clearance via LRP-1 knockdown specific in hepatocytes aggravated cerebral Aß burden and cognitive deficits, while enhancing hepatic Aß clearance via LRP-1 overexpression attenuated cerebral Aß deposition and cognitive impairments in APP/PS1 mice. Our findings demonstrate that the liver physiologically clears blood Aß and regulates brain Aß levels, suggesting that a decline of hepatic Aß clearance during aging could be involved in AD development, and hepatic Aß clearance is a novel therapeutic approach for AD.

Phase Behavior of Binary Blends of Diblock Copolymers: Progress and Opportunities.

The phase behavior of binary blends of diblock copolymers has been examined extensively in the past decades. Experimental and theoretical studies have demonstrated that mixing two different block copolymers provides an efficient and versatile route to regulate their self-assembled morphologies. A good understanding of the principles governing the self-assembly of block copolymer blends has been obtained from the study of A1B1/A2B2 diblock copolymer blends. The second (A2B2) diblocks could act synergistically as fillers and cosurfactants to regulate the domain size and interfacial properties, resulting in the formation of ordered phases not found in the parent (A1B1 or A2B2) diblock copolymer melts. The study of A1B1/A2B2 block copolymer blends further provides a solid foundation for future research on more complex block copolymer blends.

Nervonic acid and its sphingolipids: Biological functions and potential food applications.

Nervonic acid, a 24-carbon fatty acid with only one double bond at the 9th carbon (C24:1n-9), is abundant in the human brain, liver, and kidney. It not only functions in free form but also serves as a critical component of sphingolipids which participate in many biological processes such as cell membrane formation, apoptosis, and neurotransmission. Recent studies show that nervonic acid supplementation is not only beneficial to human health but also can improve the many medical conditions such as neurological diseases, cancers, diabetes, obesity, and their complications. Nervonic acid and its sphingomyelins serve as a special material for myelination in infants and remyelination patients with multiple sclerosis. Besides, the administration of nervonic acid is reported to reduce motor disorder in mice with Parkinson's disease and limit weight gain. Perturbations of nervonic acid and its sphingolipids might lead to the pathogenesis of many diseases and understanding these mechanisms is critical for investigating potential therapeutic approaches for such diseases. However, available studies about this aspect are limited. In this review, relevant findings about functional mechanisms of nervonic acid have been comprehensively and systematically described, focusing on four interconnected functions: cellular structure, signaling, anti-inflammation, lipid mobilization, and their related diseases.

[Advances in traditional Chinese medicine treatment of non-alcoholic fatty liver disease via farnesoid X receptor].

Non-alcoholic fatty liver disease(NAFLD) is a chronic metabolic condition with rapidly increasing incidence, becoming a public health issue of worldwide concern. Studies have shown that farnesoid X receptor(FXR)-based modulation of downstream targets can improve liver function and metabolic status in the patients with NAFLD and may be a potential drug target for treating this di-sease. Great progress has been achieved in the development of drugs targeting FXR for the treatment of NAFLD. A number of studies have explored the traditional Chinese medicine and their active ingredients for the treatment of NAFLD via FXR considering the high safety and efficacy and mild side effects. This paper systematically describes the mechanism of traditional Chinese medicines in the treatment of NAFLD via FXR and the downstream targets, aiming to provide precise targets for the drug development and clinical treatment of NAFLD.

Overexpression of SSR2 promotes proliferation of liver cancer cells and predicts prognosis of patients with hepatocellular carcinoma.

Signal Sequence Receptor Subunit 2 (SSR2) is a key endoplasmic reticulum gene involved in protein folding and processing. Previous studies found that it was upregulated in several cancers, but its precise role in hepatocellular carcinoma (HCC) remains unclear. To have a better understanding of this gene in HCC, we examined the expression of SSR2 in HCC tissues by analysing The Cancer Genome Atlas (TCGA) data and immunohistochemistry. We also assessed the association between SSR2 expression and clinicopathological characteristics of HCC patients and patient survival. Potential function of SSR2 was predicted through GSEA and protein-protein interaction analysis. MTT, flowcytometry, transwell and a nude mice xenograft model were employed to investigate the biological functions in vivo and in vitro. The results showed that the expression of SSR2 was significantly increased in HCC tissues, and SSR2 expression was associated with several clinical characteristics. In addition, patients with higher SSR2 expression had poorer survival. Enrichment analysis suggested that SSR2 was probably involved in biological process or signalling pathways related to G2/M checkpoint, passive transmembrane transporter activity, ATF2_S_UP. V1_UP and ncRNA metabolic process. Further experimental study showed that SSR2 knockdown inhibited cell proliferation, migration and invasion ability and promoted apoptosis and cell cycle arrest in vitro. Moreover, downregulation of SSR2 also repressed the growth of HepG2 cells in vivo. In conclusion, our study suggests that SSR2 may act as an oncogene in HCC.

Intersubject correlation analysis reveals the plasticity of cerebral functional connectivity in the long-term use of social media.

Owing to the limitations of cross-sectional studies, it is unclear whether social media induce brain changes, or if individuals with certain biological traits are more likely to use social media. Functional connectivity (FC) can reflect cerebral functional plasticity, and if social media can influence cerebral FC, then the FC of light social media users should be more similar to that of heavy users after they "heavily" used social media for a long period. We combined longitudinal study design and intersubject correlation (ISC) analysis to investigate this similarity. Thirty-five heavy and 21 light social media users underwent cognitive tests and functional MRIs. The 21 light social media users underwent another functional MRI scan after completing an additional four-week social media task. We conducted the ISC at the group, individual, and brain-region levels to investigate the similarity of FC and locate the brain regions most affected by social media. The FC of light social media users was more similar to that of heavy social media users after they completed the four-week social media task. Then, social media had an impact on half of the brain, involving almost all brain networks. Finally, cerebral FC that mostly affected by social media was associated with selective attention. We concluded that the impact of social media use on cerebral functional connectivity changes is revealed by ISC method and longitudinal design, which may provide guidance for clinical practice. The methods used in the current research could also be applied to similar domains.

[Prevention and treatment of non-alcoholic fatty liver disease by regulation of mitochondrial function with Chinese medicine].

Non-alcoholic fatty liver disease(NAFLD), as a metabolic stress liver injury disease, is one of the most common chronic liver diseases, which seriously threatens people's health. The pathogenesis of NAFLD is very complex. A large number of studies show that the hepatic mitochondrial dysfunction leads to the disorder of hepatic glucose and lipid metabolism, oxidative stress, and inflammation, thus inducing hepatocyte apoptosis, which plays an important role in the progression of NAFLD. In recent years, researchers have begun to focus on developing drugs that slowed the progression of NAFLD by regulating the hepatic mitochondrial function. Chinese medicine has a good curative effect on the treatment of NAFLD, with the advantages of high safety and few side effects. Various studies have shown that Chinese medicine prevented and treated NAFLD by regulating the mitochondrial function. Therefore, this paper summarized the relationship between NAFLD and mitochondria, and the mechanism of Chinese medicine(single Chinese medicine, Chinese medicine monomer, and Chinese medicine compound prescription) in the prevention and treatment of NAFLD by regulating mitochondrial function. This paper is expected to provide references for clinical application of traditional Chinese medicine in the treatment of NAFLD by regulating mitochondrial function.

Origins of low-symmetry phases in asymmetric diblock copolymer melts.

Cooling disordered compositionally asymmetric diblock copolymers leads to the formation of nearly spherical particles, each containing hundreds of molecules, which crystallize upon cooling below the order-disorder transition temperature (TODT). Self-consistent field theory (SCFT) reveals that dispersity in the block degrees of polymerization stabilizes various Frank-Kasper phases, including the C14 and C15 Laves phases, which have been accessed experimentally in low-molar-mass poly(isoprene)-b-poly(lactide) (PI-PLA) diblock copolymers using thermal processing strategies. Heating and cooling a specimen containing 15% PLA above and below the TODT from the body-centered cubic (BCC) or C14 states regenerates the same crystalline order established at lower temperatures. This memory effect is also demonstrated with a specimen containing 20% PLA, which recrystallizes to either C15 or hexagonally ordered cylinders (HEXC) upon heating and cooling. The process-path-dependent formation of crystalline order shapes the number of particles per unit volume, n/V, which is retained in the highly structured disordered liquid as revealed by small-angle X-ray scattering (SAXS) experiments. We hypothesize that symmetry breaking during crystallization is governed by the particle number density imprinted in the liquid during ordering at lower temperature, and this metastable liquid is kinetically constrained from equilibrating due to prohibitively large free energy barriers for micelle fusion and fission. Ordering at fixed n/V is enabled by facile chain exchange, which redistributes mass as required to meet the multiple particle sizes and packing associated with specific low-symmetry Frank-Kasper phases. This discovery exposes universal concepts related to order and disorder in self-assembled soft materials.

Plasma miR-6089 as potential diagnostic biomarker for retinoblastoma.

OBJECTIVE: The purpose of this study was to screen target miRNA related to RB and explore the expression levels of target miRNA in RB and its potential value of diagnosis. METHODS: The Affymetrix GeneChip miRNA 4.0 Array was used to screen the differential miRNAs in the plasma of 5 RB patients before and after intravenous chemotherapy, and the most significant down-regulated miRNA was selected for target miRNA. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is used to verify the expression levels of plasma target miRNA in 30 RB patients. Then, qRT-PCR was performed to further verify the expression of target miRNA in plasma of RB patients and RB tumor tissues. Finally, receiver-operating-characteristic (ROC) curve and the area under the ROC curve (AUC) were used to evaluate the diagnostic power of plasma target miRNA. RESULTS: The miRNA Array obtain 8 core miRNAs, 1 up-regulated and 7 down-regulated, of which miR-6089 was the most significantly down-regulated. Plasma miR-6089 levels were significantly up-regulated in RB patients. Besides, in RB tumor tissues, miR-6089 levels were also obviously up-regulated. After intravenous chemotherapy, the expression of plasma miR-6089 was significantly decreased. Furthermore, ROC curve analysis showed that miR-6089 in the plasma had a good sensitivity and specificity for distinguishing RB from the healthy control group. CONCLUSIONS: MiR-6089 may be considered as a novel potential diagnostic biomarker for RB. TRIAL REGISTRATION NUMBER: ChiCTR2000040154; date of registration: 2020/11/22; retrospectively registered.

Pathways connecting two opposed bilayers with a fusion pore: a molecularly-informed phase field approach.

A phase field model with two phase fields, representing the concentration and the head-tail separation of amphiphilic molecules, respectively, has been constructed using an extension of the Ohta-Kawasaki model (Macromolecules, 1986, 19, 2621-2632). It is shown that this molecularly-informed phase field model is capable of producing various self-assembled amphiphilic aggregates, such as bilayers, vesicles and micelles. Furthermore, pathways connecting two opposed bilayers with a fusion pore are obtained by using a combination of the phase field model and the string method. Multiple fusion pathways, including a classical pathway and a leaky pathway, have been obtained depending on the initial separation of the two bilayers. The study shed light on the understanding of the membrane fusion pathways and, more importantly, laid a foundation for further investigation of more complex membrane morphologies and transitions.

Acute conduction recurrence of mitral isthmus: Incidence, clinical characteristics, and implications.

BACKGROUND: Data on the incidence, clinical characteristics, and implications of acute conduction recurrence during mitral isthmus (MI) ablation are scarce. METHODS: MI ablation was performed in patients with atrial fibrillation. After confirming bidirectional conduction block, the acute conduction recurrence of MI was systematically evaluated. Clinical and electrophysiological characteristics were analyzed. RESULTS: A total of 66 consecutive patients in whom bidirectional conduction block of MI was achieved were prospectively enrolled in a single center. Acute conduction recurrence of MI developed in 12 (18.2%) patients within 14.2 ± 11.5 minutes after the confirmation of bidirectional conduction block. There were two recurrent conduction breakthrough sites of MI along the course of the great cardiac vein (4.5 ± 3.5 min) in two patients and 11 along the course of the ligament of Marshall (LOM) (16.0 ± 11.6 min, P = .035) in 11 patients. LOM accounted for most (84.6%, 11/13) acute MI conduction recurrence. MI length, total ablation time, and procedure time for MI were greater in patients with acute conduction recurrence than in those without acute conduction recurrence. During follow-up, arrhythmia recurrences were less observed in patients with acute conduction when compared to patients without acute conduction recurrence (0% vs 26.4%, P = .055). CONCLUSION: Acute conduction recurrence, predominantly due to recurrent LOM conduction, was a common phenomenon during MI ablation, and its evaluation should therefore be the focus to improve MI ablation efficacy and durability.

Elastic properties of self-assembled bilayer membranes: Analytic expressions via asymptotic expansion.

Bilayer membranes self-assembled from amphiphilic molecules are ubiquitous in biological and soft matter systems. The elastic properties of bilayer membranes are essential in determining the shape and structure of bilayers. A novel method to calculate the elastic moduli of the self-assembled bilayers within the framework of the self-consistent field theory is developed based on an asymptotic expansion of the order parameters in terms of the bilayer curvature. In particular, the asymptotic expansion method is used to derive analytic expressions of the elastic moduli, which allows us to design more efficient numerical schemes. The efficiency of the proposed method is illustrated by a model system composed of flexible amphiphilic chains dissolved in hydrophilic polymeric solvents.