High-throughput PRIME-editing screens identify functional DNA variants in the human genome.

Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and single-base resolution manner remains challenging. Here, we develop a pooled prime-editing screen method, PRIME, that can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated single-base resolution analysis. Next, we applied PRIME to functionally characterize 1,304 genome-wide association study (GWAS)-identified non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate that PRIME is capable of characterizing genetic variants at single-base resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.

Revealing genomic heterogeneity and commonality: A penalized integrative analysis approach accounting for the adjacency structure of measurements.

Advancements in high-throughput genomic technologies have revolutionized the field of disease biomarker identification by providing large-scale genomic data. There is an increasing focus on understanding the relationships among diverse patient groups with distinct disease subtypes and characteristics. Complex diseases exhibit both heterogeneity and shared genomic factors, making it essential to investigate these patterns to accurately detect markers and comprehensively understand the diseases. Integrative analysis has emerged as a promising approach to address this challenge. However, existing studies have been limited by ignoring the adjacency structure of genomic measurements, such as single nucleotide polymorphisms (SNPs) and DNA methylations. In this study, we propose a structured integrative analysis method that incorporates a spline type penalty to accommodate this adjacency structure. We utilize a fused lasso type penalty to identify both heterogeneity and commonality across the groups. Extensive simulations demonstrate its superiority compared to several direct competing methods. The analysis of The Cancer Genome Atlas melanoma data with DNA methylation measurements and GENEVA diabetes data with SNP measurements exhibit that the proposed analysis lead to meaningful findings with better prediction performance and higher selection stability.

The Plasmodium vivax MSP1P-19 is involved in binding of reticulocytes through interactions with the membrane proteins band3 and CD71.

The parasite Plasmodium vivax preferentially invades human reticulocytes. Its merozoite surface protein 1 paralog (PvMSP1P), particularly the 19-kDa C-terminal region (PvMSP1P-19), has been shown to bind to reticulocytes, and this binding can be inhibited by antisera obtained by PvMSP1P-19 immunization. The molecular mechanism of interactions between PvMSP1P-19 and reticulocytes during P. vivax invasion, however, remains unclear. In this study, we analyzed the ability of MSP1P-19 to bind to different concentrations of reticulocytes and confirmed its reticulocyte preference. LC-MS analysis was used to identify two potential reticulocyte receptors, band3 and CD71, that interact with MSP1P-19. Both PvMSP1P-19 and its sister taxon Plasmodium cynomolgi MSP1P-19 were found to bind to the extracellular loop (loop 5) of band3, where the interaction of MSP1P-19 with band3 was chymotrypsin sensitive. Antibodies against band3-P5, CD71, and MSP1P-19 reduced the binding activity of PvMSP1P-19 and Plasmodium cynomolgi MSP1P-19 to reticulocytes, while MSP1P-19 proteins inhibited Plasmodium falciparum invasion in vitro in a concentration-dependent manner. To sum up, identification and characterization of the reticulocyte receptor is important for understanding the binding of reticulocytes by MSP1P-19.

Oncolytic Newcastle disease virus induced degradation of YAP through E3 ubiquitin ligase PRKN to exacerbate ferroptosis in tumor cells.

Ferroptosis, a form of programmed cell death characterized by iron-dependent lipid peroxidation, has recently gained considerable attention in the field of cancer therapy. There is significant crosstalk between ferroptosis and several classical signaling pathways, such as the Hippo pathway, which suppresses abnormal growth and is frequently aberrant in tumor tissues. Yes-associated protein 1 (YAP), the core effector molecule of the Hippo pathway, is abnormally expressed and activated in a variety of malignant tumor tissues. We previously proved that the oncolytic Newcastle disease virus (NDV) activated ferroptosis to kill tumor cells. NDV has been used in tumor therapy; however, its oncolytic mechanism is not completely understood. In this study, we demonstrated that NDV exacerbated ferroptosis in tumor cells by inducing ubiquitin-mediated degradation of YAP at Lys90 through E3 ubiquitin ligase parkin (PRKN). Blocking YAP degradation suppressed NDV-induced ferroptosis by suppressing the expression of Zrt/Irt-like protein 14 (ZIP14), a metal ion transporter that regulates iron uptake. These findings demonstrate that NDV exacerbated ferroptosis in tumor cells by inducing YAP degradation. Our study provides new insights into the mechanism of NDV-induced ferroptosis and highlights the critical role that oncolytic viruses play in the treatment of drug-resistant cancers.IMPORTANCEThe oncolytic Newcastle disease virus (NDV) is being developed for use in cancer treatment; however, its oncolytic mechanism is still not completely understood. The Hippo pathway, which is a tumor suppressor pathway, is frequently dysregulated in tumor tissues due to aberrant yes-associated protein 1 (YAP) activation. In this study, we have demonstrated that NDV degrades YAP to induce ferroptosis and promote virus replication in tumor cells. Notably, NDV was found to induce ubiquitin-mediated degradation of YAP at Lys90 through E3 ubiquitin ligase parkin (PRKN). Our study reveals a new mechanism by which NDV induces ferroptosis and provides new insights into NDV as an oncolytic agent for cancer treatment.

Plasmodium yoelii surface-related antigen (PySRA) modulates the host pro-inflammatory responses via binding to CD68 on macrophage membrane.

Malaria, one of the major infectious diseases in the world, is caused by the Plasmodium parasite. Plasmodium antigens could modulate the inflammatory response by binding to macrophage membrane receptors. As an export protein on the infected erythrocyte membrane, Plasmodium surface-related antigen (SRA) participates in the erythrocyte invasion and regulates the immune response of the host. This study found that the F2 segment of P. yoelii SRA activated downstream MAPK and NF-κB signaling pathways by binding to CD68 on the surface of the macrophage membrane and regulating the inflammatory response. The anti-PySRA-F2 antibody can protect mice against P. yoelii, and the pro-inflammatory responses such as IL-1ß, TNF-α, and IL-6 after infection with P. yoelii are attenuated. These findings will be helpful for understanding the involvement of the pathogenic mechanism of malaria with the exported protein SRA.

Rational Synthesis of Functionalized Covalent Organic Frameworks via Four-Component Reaction.

The construction of function-oriented covalent organic frameworks (COFs) remains a challenge as it requires simultaneous consideration of diversified structures, robust linkage, and tailorable functionalities. Herein, we report the rational synthesis of functionalized COFs via a four-component reaction strategy. Through the four-component Debus-Radziszewski reaction, 11 N-substituted imidazole-based COFs with diversified structures were facilely constructed from readily available building blocks. By forming the N-substituted imidazole linkage, these synthesized COFs displayed ultrastability toward strong acids and base. Moreover, the four components reaction allows the rational synthesis of COFs with tailorable functionalities. As an example, the phosphonate-functionalized COF (LZU-530) was rationally constructed for the efficient adsorption of uranium(VI). The uranium(VI) uptake of LZU-530 reaches up to 95 mg·g-1 in 2 M HNO3, which is the highest uptake of the existing organic porous materials under such harsh conditions. Our results highlight the use of multicomponent reaction for the rational synthesis of robust and functionalized COFs toward targeted applications.

Advanced patient-specific microglia cell models for pre-clinical studies in Alzheimer's disease.

BACKGROUND: Alzheimer's disease (AD) is an incurable neurodegenerative disorder with a rapidly increasing prevalence worldwide. Current approaches targeting hallmark pathological features of AD have had no consistent clinical benefit. Neuroinflammation is a major contributor to neurodegeneration and hence, microglia, the brain's resident immune cells, are an attractive target for potentially more effective therapeutic strategies. However, there is no current in vitro model system that captures AD patient-specific microglial characteristics using physiologically relevant and experimentally flexible culture conditions. METHODS: To address this shortcoming, we developed novel 3D Matrigel-based monocyte-derived microglia-like cell (MDMi) mono-cultures and co-cultures with neuro-glial cells (ReNcell VM). We used single-cell RNA sequencing (scRNAseq) analysis to compare the transcriptomic signatures of MDMi between model systems (2D, 3D and 3D co-culture) and against published human microglia datasets. To demonstrate the potential of MDMi for use in personalized pre-clinical strategies, we generated and characterized MDMi models from sixteen AD patients and matched healthy controls, and profiled cytokine responses upon treatment with anti-inflammatory drugs (dasatinib and spiperone). RESULTS: MDMi in 3D exhibited a more branched morphology and longer survival in culture compared to 2D. scRNAseq uncovered distinct MDMi subpopulations that exhibit higher functional heterogeneity and best resemble human microglia in 3D co-culture. AD MDMi in 3D co-culture showed altered cell-to-cell interactions, growth factor and cytokine secretion profiles and responses to amyloid-ß. Drug testing assays revealed patient- and model-specific cytokine responses. CONCLUSION: Our study presents a novel, physiologically relevant and AD patient-specific 3D microglia cell model that opens avenues towards improving personalized drug development strategies in AD.

On the maximization of entropy in the process of thermalization of highly multimode nonlinear beams.

We present a direct experimental confirmation of the maximization of entropy which accompanies the thermalization of a highly multimode light beam, upon its nonlinear propagation in standard graded-index (GRIN) optical fibers.

Circ_0000069 promotes the development of hepatocellular carcinoma by regulating CCL25.

BACKGROUND: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths globally, influenced by aberrant circRNA expression. Investigating circRNA-miRNA-mRNA interactions can unveil underlying mechanisms of HCC and identify potential therapeutic targets. METHODS: In this study, we conducted differential analyses of mRNAs, miRNAs, and circRNAs, and established their relationships using various databases such as miRanda, miRDB, and miTarBase. Additionally, functional enrichment and immune infiltration analyses were performed to evaluate the roles of key genes. We also conducted qPCR assays and western blotting (WB) to examine the expression levels of circRNA, CCL25, and MAP2K1 in both HCC cells and clinical samples. Furthermore, we utilized overexpression and knockdown techniques for circ_0000069 and conducted wound healing, transwell invasion assays, and a tumorigenesis experiment to assess the migratory and invasive abilities of HCC cells. RESULTS: Our findings revealed significant differential expression of 612 upregulated genes and 1173 downregulated genes in HCC samples compared to normal liver tissue. Additionally, 429 upregulated circRNAs and 453 downregulated circRNAs were identified. Significantly, circ_0000069 exhibited upregulation in HCC tissues and cell lines. The overexpression of circ_0000069 notably increased the invasion and migration capacity of Huh7 cells, whereas the downregulation of circ_0000069 reduced this capability in HepG2 cells. Furthermore, this effect was counteracted by CCL25 silencing or overexpression, separately. Animal studies further confirmed that the overexpression of hsa_circ_0000069 facilitated tumor growth in xenografted nude mice, while the inhibition of CCL25 attenuated this effect. CONCLUSION: Circ_0000069 appears to promote HCC progression by regulating CCL25, suggesting that both circ_0000069 and CCL25 can serve as potential therapeutic targets.

Ultra-high b-value DWI accurately identifies isocitrate dehydrogenase genotypes and tumor subtypes of adult-type diffuse gliomas.

OBJECTIVES: To distinguish isocitrate dehydrogenase (IDH) genotypes and tumor subtypes of adult-type diffuse gliomas based on the fifth edition of the World Health Organization classification of central nervous system tumors (WHO CNS5) in 2021 using standard, high, and ultra-high b-value diffusion-weighted imaging (DWI). MATERIALS AND METHODS: This prospective study enrolled 70 patients with adult-type diffuse gliomas who underwent multiple b-value DWI. Apparent diffusion coefficient (ADC) values including ADCb500/b1000, ADCb500/b2000, ADCb500/b3000, ADCb500/b4000, ADCb500/b6000, ADCb500/b8000, and ADCb500/b10000 in tumor parenchyma (TP) and contralateral normal-appearing white matter (NAWM) were calculated. The ADC ratios of TP/NAWM were assessed for correlations with IDH genotypes, tumor subtypes, and Ki-67 status; diagnostic performances were compared. RESULTS: All ADCs were significantly higher in IDH mutant gliomas than in IDH wild-type gliomas (p < 0.01 for all); ADCb500/b8000 had the highest area under the curve (AUC) of 0.866. All ADCs were significantly lower in glioblastoma than in astrocytoma (p < 0.01 for all). ADCs other than ADCb500/b1000 were significantly lower in glioblastoma than in oligodendroglioma (p < 0.05 for all). ADCb500/b8000 and ADCb500/b10000 were significantly higher in oligodendroglioma than in astrocytoma (p = 0.034 and 0.023). The highest AUCs were 0.818 for ADCb500/b6000 when distinguishing glioblastoma from astrocytoma, 0.979 for ADCb500/b8000 and ADCb500/b10000 when distinguishing glioblastoma from oligodendroglioma, and 0.773 for ADCb500/b10000 when distinguishing astrocytoma from oligodendroglioma. Additionally, all ADCs were negatively correlated with Ki-67 status (p < 0.05 for all). CONCLUSION: Ultra-high b-value DWI can reliably separate IDH genotypes and tumor subtypes of adult-type diffuse gliomas using WHO CNS5 criteria. CLINICAL RELEVANCE STATEMENT: Ultra-high b-value diffusion-weighted imaging can accurately distinguish isocitrate dehydrogenase genotypes and tumor subtypes of adult-type diffuse gliomas, which may facilitate personalized treatment and prognostic assessment for patients with glioma. KEY POINTS: • Ultra-high b-value diffusion-weighted imaging can accurately distinguish subtle differences in water diffusion among biological tissues. • Ultra-high b-value diffusion-weighted imaging can reliably separate isocitrate dehydrogenase genotypes and tumor subtypes of adult-type diffuse gliomas. • Compared with standard b-value diffusion-weighted imaging, high and ultra-high b-value diffusion-weighted imaging demonstrate better diagnostic performances.

The efficacy and safety of continuous blood purification in neonates with septic shock and acute kidney injury: a two-center retrospective study.

To investigate the efficacy and safety of continuous blood purification (CBP) in neonates with septic shock and acute kidney injury (AKI). This retrospective study was conducted at two tertiary care children's hospitals between January 2015 and May 2022. A total of 26 neonates with septic shock and AKI were included in this study, with a mortality rate of 50%. Fourteen neonates (53.8%) received continuous veno-venous hemodiafiltration, and 12 (46.2%) received continuous veno-venous hemofiltration. Compared with the indices before CBP, urine output increased 12 h after CBP initiation (P = 0.003) and serum creatinine decreased (P = 0.019). After 24 h of CBP, blood urea nitrogen had decreased (P = 0.006) and mean arterial pressure had increased (P = 0.007). At the end of CBP, the vasoactive-inotropic score and blood lactate were decreased (P = 0.035 and 0.038, respectively) and PH was increased (P = 0.015). Thrombocytopenia was the most common complication of CBP.  Conclusion: CBP can efficiently maintain hemodynamic stability, improve renal function, and has good safety in neonates with septic shock and AKI. However, the mortality rate remains high, and whether CBP improves the prognosis of neonates with septic shock and AKI remains unclear. What is Known: • Over 50% of children with septic shock have severe AKI, of which 21.6% required CBP. • The clinical application of CBP in septic shock has attracted increasing attention. What is New: • CBP can efficiently maintain hemodynamic stability, improve renal function, and has good safety in neonates with septic shock and AKI. • The mortality rate in neonates with septic shock and AKI receiving CBP remains high.

Low serum hepcidin levels in women with polycystic ovary syndrome: evidence from meta-analysis.

BACKGROUND: Iron metabolism plays a significant role in the development of metabolic disorders in women with polycystic ovary syndrome (PCOS). Despite the importance of hepcidin, a key iron regulator, current research on serum hepcidin levels in PCOS patients shows conflicting results. METHODS: PubMed, Embase, Web of Science, Cochrane Library and the China National Knowledge Infrastructure (CNKI) database were systematically searched from their inception to 9 September 2023. The search aimed to identify studies in English and Chinese that examined hepcidin levels in women with PCOS compared to healthy control subjects. Standardized mean differences (SMDs) with corresponding 95% confidence intervals (95% CIs) were calculated to evaluate the difference in serum hepcidin levels between women with and without PCOS. RESULTS: The meta-analysis included a total of 10 eligible studies, which encompassed 499 PCOS patients and 391 control subjects. The pooled analysis revealed a significant reduction in serum hepcidin levels among the PCOS patients compared to the healthy controls (SMD = -3.49, 95% CI: -4.68 to -2.30, p < .05). There was no statistically significant difference in serum hepcidin levels between PCOS patients with a body mass index (BMI) < 25 and those with a BMI ≥ 25 (p > .05). CONCLUSION: The serum hepcidin levels of women with PCOS were significantly lower than those of healthy controls, which suggests that serum hepcidin could be a potential biomarker for PCOS.

Unraveling the correlations between microbial communities and metabolic profiles of strong-flavor Jinhui Daqu with different storage periods.

Daqu is a saccharification agent required for fermenting Baijiu, a popular Chinese liquor. Our objective was to investigate the relationships between physicochemical indices, microbial community diversity, and metabolite profiles of strong-flavor Jinhui Daqu during different storage periods. During different storage periods of Jinhui Daqu, we combined Illumina MiSeq sequencing and non-target sequencing techniques to analyze dynamic changes of the microbial community and metabolite composition, established a symbiotic network and explored the correlation between dominant microorganisms and differential metabolites in Daqu. Fungal community diversity in 8d_Daqu was higher than that in 45d_Daqu and 90d_Daqu, whereas bacterial community diversity was higher in 90d_Daqu. Twelve bacterial and four fungal genera were dominant during storage of Daqu. Bacillus, Leuconostoc, Kroppenstedtia, Lactococcus, Thermomyces and Wickerhamomyces decreased as the storage period increased. Differences of microbiota structure led to various metabolic pathways, and 993 differential metabolites were found in all Daqu samples. Differential microorganisms were significantly related to key metabolites. Major metabolic pathways involved in the formation of amino acids and lipids, such as l-arogenate and hydroxyproline, were identified. Interactions between moisture, acidity, and microbes may drive the succession of the microbial community, which further affects the formation of metabolites.

Spinal muscle characteristics during three different types of locomotion activities among college students with idiopathic scoliosis.

BACKGROUND CONTEXT: Physical activities such as walking and climbing stairs are pervasive in human daily life. Individuals with scoliosis frequently encounter dysfunction in their muscle recruitment. Multiple studies have corroborated the presence of muscle dysfunction in individuals diagnosed with scoliosis. However, there is currently a noteworthy research gap regarding the exploration of changes in muscle characteristics and disparities from those observed in individuals without scoliosis during everyday activities, specifically stair climbing. PURPOSE: This study aims to examine the unique patterns of muscle activity during daily life in individuals with scoliosis and distinguish the specific differences between scoliosis patients and the healthy controls. The findings of this study are significantly important for the future accurate assessment of scoliosis and the development of rehabilitation treatment plans. STUDY DESIGN: Case-control study. SAMPLE SIZE: Twenty eight idiopathic scoliosis patients and twenty eight controls. OUTCOME MEASURES: Root Mean Square(RMS), Maximum Voluntary Isometric Contraction(MVIC)%, RMS ratio(RMS convex / RMS concave). METHODS: The surface electromyography (sEMG) device used in this study was the Delsys Trigno, with a sampling frequency of 1500 Hz. It recorded the activation level, peak contraction, and average activation level of the erector spinae (at T6, T10, and L3 levels), gluteus maximus, gluteus medius, external oblique, and rectus abdominis muscles during three different types of locomotion for both the 28 individuals with idiopathic scoliosis and the 28 control participants. RESULTS: The movement patterns of the idiopathic scoliosis patients significantly differ from those of the normal population during level walking and ascending or descending stairs. In level walking, there is an asymmetry in the activation levels of the T6 and L3 erector spinae muscles, with lower activation on the convex side compared to the concave side. Similarly, during stair ascent, the activation of the T6 and T10 erector spinae muscles is asymmetric, with higher activation on the convex side than the concave side. Moreover, during stair descent, the activation of the T6 erector spinae muscle is asymmetric, with higher activation on the convex side than the concave side. CONCLUSIONS: During level walking and stair activities, idiopathic scoliosis patients exhibit pronounced abnormal movement patterns that significantly differ from those of the control group. Under different activity conditions such as level walking, ascending and descending stairs, idiopathic scoliosis patients demonstrate abnormal muscle activation in different segments of the spine. It is crucial for clinicians to prioritize the symmetry of muscle activation in the spinal region of idiopathic scoliosis patients and consider incorporating symmetry training for these muscles.

Machine learning-based analysis of heavy metal contamination in Chinese lake basin sediments: Assessing influencing factors and policy implications.

Sediments are important heavy metal sinks in lakes, crucial for ensuring water environment safety. Existing studies mainly focused on well-studied lakes, leaving gaps in understanding pollution patterns in specific basins and influencing factors.We compiled comprehensive sediment contamination data from literature and public datasets, including hydro-geomorphological, climatic, soil, landscape, and anthropogenic factors. Using advanced machine learning, we analyzed typical pollution factors to infer potential sources and migration pathways of pollutants and predicted pollution levels in basins with limited data availability. Our analysis of pollutant distribution data revealed that Cd had the most extensive pollution range, with the most severe pollution occurring in the Huaihe and Yangtze River basins. Furthermore, we identified distinct groups of driving factors influencing various heavy metals. Cd, Cr, and Pb were primarily influenced by human activities, while Cu and Ni were affected by both anthropogenic and natural factors, and Zn tended more towards natural sources. Our predictions indicated that, in addition to the typical highly polluted areas, the potential risk of Cd, Cu and Ni is higher in Xinjiang, and in Tibet and Qinghai, the potential risk of Cd, Cr, Cu and Ni is higher. Pb and Zn presented lower risks, except in the Huaihe and Yangtze River Basins. Temperature, wind, precipitation, precipitation rate, and the cation exchange capacity of soil significantly impacted the predictions of heavy metal pollution in sediments, suggesting that particulate migration, rainfall runoff, and soil erosion are likely the main pathways for pollutant migration into sediments. Considering the migration, pathways, and sources of pollutants, we propose strategies such as low-impact development and promoting sustainable transportation to mitigate pollution. This study provides the latest insights into heavy metal pollution in Chinese lake sediments, offering references for policy-making and water resource management.

Metagenomic insights into the mechanism of sophorolipid in facilitating co-anaerobic digestion of mushroom residues and cattle manure: Functional microorganisms and metabolic pathway analysis.

The present study aimed to enhance the co-anaerobic digestion system of mushroom residues and cattle manure by incorporating biosurfactant sophorolipid. Results demonstrated that the addition of 75 mg/L sophorolipid increased cumulative methane production by 33.68%, acetate content by 9-10 times, and the abundance of Methanosarcina by 69.22%. The electroactive microorganisms (Bacteroides, Petrimonas, etc.) were enriched, while the up-regulation of functional genes associated with carbohydrate metabolism and methane metabolism was observed. The metagenomic analysis revealed the significant involvement of inter-microbial communication and extracellular electron transfer in anaerobic digestion. Petrimonas was identified as the predominant host involved in cellular processes and environmental information processing. The supplementation of sophorolipid significantly enhanced its abundance during the late anaerobic digestion period (by 12.30%-64.84%). The results emphasize the crucial function of sophorolipid as biosurfactant in enhancing the efficiency of anaerobic digestion.

Antifungal Activity and Multi-Target Mechanism of Action of Methylaervine on Candida albicans.

The discovery of a lead compound against Candida albicans is urgently needed because of the lack of clinically available antifungal drugs and the increase in drug resistance. Herein, a ß-carboline alkaloid methylaervine (MET) exhibited potential activity against C. albicans (MIC = 16-128 µg/mL), no hemolytic toxicity, and a low tendency to induce drug resistance. An antifungal mechanism study indicated that MET effectively inhibited the biofilm formation and disrupted the mature biofilm. Moreover, filamentation formation and spore germination were also weakened. The electron microscopy analysis revealed that MET could damage the cell structure, including the cell wall, membrane, and cytoplasm. In particular, the permeability and integrity of the cell membrane were destroyed. When it entered the fungi cell, it interfered with the redox homeostasis and DNA function. Overall, MET can inhibit the growth of C. albicans from multiple channels, such as biofilm, filamentation, cell structure, and intracellular targets, which are difficult to mutate at the same time to generate drug resistance. This work provides a promising lead compound for the creation of new antifungal agents against C. albicans.

Glycosylphosphatidylinositol-anchored micronemal antigen (GAMA) interacts with the band 3 receptor to promote erythrocyte invasion by malaria parasites.

Glycosylphosphatidylinositol-anchored micronemal antigen (GAMA) is an erythrocyte binding protein known to be involved in malarial parasite invasion. Although anti-GAMA antibodies have been shown to block GAMA attachment to the erythrocyte surface and subsequently inhibit parasite invasion, little is known about the molecular mechanisms by which GAMA promotes the invasion process. In this study, LC-MS analysis was performed on the erythrocyte membrane to identify the specific receptor that interacts with GAMA. We found that ankyrin 1 and the band 3 membrane protein showed affinity for GAMA, and characterization of their binding specificity indicated that both Plasmodium falciparum and Plasmodium vivax GAMA bound to the same extracellular loop of band 3 (loop 5). In addition, we show the interaction between GAMA and band 3 was sensitive to chymotrypsin. Furthermore, antibodies against band 3 loop 5 were able to reduce the binding activity of GAMA to erythrocytes and inhibit the invasion of P. falciparum merozoites into human erythrocytes, whereas antibodies against P. falciparum GAMA (PfGAMA)-Tr3 only slightly reduced P. falciparum invasion. The identification and characterization of the erythrocyte GAMA receptor is a novel finding that identifies an essential mechanism of parasite invasion of host erythrocytes.

DReSS: a method to quantitatively describe the influence of structural perturbations on state spaces of genetic regulatory networks.

Structures of genetic regulatory networks are not fixed. These structural perturbations can cause changes to the reachability of systems' state spaces. As system structures are related to genotypes and state spaces are related to phenotypes, it is important to study the relationship between structures and state spaces. However, there is still no method can quantitively describe the reachability differences of two state spaces caused by structural perturbations. Therefore, Difference in Reachability between State Spaces (DReSS) is proposed. DReSS index family can quantitively describe differences of reachability, attractor sets between two state spaces and can help find the key structure in a system, which may influence system's state space significantly. First, basic properties of DReSS including non-negativity, symmetry and subadditivity are proved. Then, typical examples are shown to explain the meaning of DReSS and the differences between DReSS and traditional graph distance. Finally, differences of DReSS distribution between real biological regulatory networks and random networks are compared. Results show most structural perturbations in biological networks tend to affect reachability inside and between attractor basins rather than to affect attractor set itself when compared with random networks, which illustrates that most genotype differences tend to influence the proportion of different phenotypes and only a few ones can create new phenotypes. DReSS can provide researchers with a new insight to study the relation between genotypes and phenotypes.

Identification of a Novel Coumarins Biosynthetic Pathway in the Endophytic Fungus Fusarium oxysporum GU-7 with Antioxidant Activity.

Coumarins are generally considered to be produced by natural plants. Fungi have been reported to produce coumarins, but their biosynthetic pathways are still unknown. In this study, Fusarium oxysporum GU-7 and GU-60 were isolated from Glycyrrhiza uralensis, and their antioxidant activities were determined to be significantly different. Abundant dipeptide, phenolic acids, and the plant-derived coumarins fraxetin and scopoletin were identified in GU-7 by untargeted metabolomics, and these compounds may account for its stronger antioxidant activity compared to GU-60. Combined with metabolome and RNA sequencing analysis, we identified 24 potentially key genes involved in coumarin biosynthesis and 6 intermediate metabolites. Interestingly, the best hit of S8H, a key gene involved in hydroxylation at the C-8 position of scopoletin to yield fraxetin, belongs to a plant species. Additionally, nondestructive infection of G. uralensis seeds with GU-7 significantly improved the antioxidant activity of seedlings compared to the control group. This antioxidant activity may depend on the biological characteristics of endophytes themselves, as we observed a positive correlation between the antioxidant activity of endophytic fungi and that of their nondestructively infected seedlings. IMPORTANCE Plant-produced coumarins have been shown to play an important role in assembly of the plant microbiomes and iron acquisition. Coumarins can also be produced by some microorganisms. However, studies on coumarin biosynthesis in microorganisms are still lacking. We report for the first time that fraxetin and scopoletin were simultaneously produced by F. oxysporum GU-7 with strong free radical scavenging abilities. Subsequently, we identified intermediate metabolites and key genes in the biosynthesis of these two coumarins. This is the first report on the coumarin biosynthesis pathway in nonplant species, providing new strategies and perspectives for coumarin production and expanding research on new ways for plants to obtain iron.