Integration of persistent Laplacian and pre-trained transformer for protein solubility changes upon mutation

Protein mutations can significantly influence protein solubility, which results in altered protein functions and leads to various diseases. Despite of tremendous effort, machine learning prediction of protein solubility changes upon mutation remains a challenging task as indicated by the poor scores of normalized Correct Prediction Ratio (CPR). Part of the challenge stems from the fact that there is no three-dimensional (3D) structures for the wild-type and mutant proteins. This work integrates persistent Laplacians and pre-trained Transformer for the task. The Transformer, pretrained with hunderds of millions of protein sequences, embeds wild-type and mutant sequences, while persistent Laplacians track the topological invariant change and homotopic shape evolution induced by mutations in 3D protein structures, which are rendered from AlphaFold2. The resulting machine learning model was trained on an extensive data set labeled with three solubility types. Our model outperforms all existing predictive methods and improves the state-of-the-art up to 15%

Rhizosphere microbe populations but not root traits induced by drought in Populus euphratica males

Funding Information: This work was supported by the National Natural Science Foundation of China (Grant No. U1803231). Publisher Copyright: © 2023, Higher Education Press.How sex-related root traits and soil microbes and their interactions respond to drought remains unclear. Here, we investigated how fine root traits and the composition of rhizosphere microbial communities in Populus euphratica females and males respond to drought in concert in 17-year-old plantations. Females increased specific root length (SRL) in response to drought. However, males showed no changes in their roots but significant increases in arbuscular mycorrhizal hyphal biomass and population of Gram-negative bacteria in the rhizosphere. Also, fungal symbiotroph communities associated with root systems in males differed from those in females under drought. We further demonstrated that the Gram-positive to Gram-negative bacteria ratios positively correlated with the SRL, while fungi to bacteria ratios were negatively correlated. Meanwhile, the relative abundance of symbiotrophs was negatively correlated with the SRL, while saprotroph abundance was positively correlated. Nevertheless, the relative abundance of symbiotrophs was positively correlated with the root carbon content (RCC). These findings indicate that microbial responses to drought depend highly upon the sex of the plant and microbial group and are related to root trait adjustments to drought. This discovery also highlights the role of plant-microbial interactions in the ecosystems of P. euphratica forest plantations.Peer reviewe

Association between gut microbiota and benign prostatic hyperplasia: a two-sample mendelian randomization study

BackgroundRecent researches have shown a correlation between the gut microbiota (GM) and various diseases. However, it remains uncertain whether the relationship between GM and benign prostatic hyperplasia (BPH) is causal.MethodsWe carried out a two-sample Mendelian randomization (MR) analysis, utilizing data from the most extensive GM-focused genome-wide association study by the MiBioGen consortium, with a sample size of 13,266. Data for BPH, encompassing 26,358 cases and 110,070 controls, were obtained from the R8 release of the FinnGen consortium. We employed multiple techniques, such as inverse variance weighted (IVW), constrained maximum likelihood and model averaging methods, maximum likelihood, MR-Pleiotropy RESidual Sum and Outlier (MRPRESSO),MR-Egger, and weighted median methods, to investigate the causal relationship between GM and BPH. To evaluate the heterogeneity among the instrumental variables, Cochran’s Q statistics were employed. Additionally, the presence of horizontal pleiotropy was assessed through the application of both MR-Egger and MR-PRESSO tests. The direction of causality was scrutinized for robustness using the MR-Steiger directionality test. A reverse MR analysis examined the GM previously linked to BPH through a causal relationship in the forward MR assessment.ResultsAccording to the analysis conducted using IVW,Eisenbergiella (odds ratio [OR]=0.92, 95% confidence interval [CI]: 0.85–0.99,P=0.022) and Ruminococcaceae (UCG009) (OR=0.88, 95% CI: 0.79–0.99, P=0.027) were found to reduce the risk of BPH, while Escherichia shigella (OR=1.19, 95% CI: 1.05–1.36, P=0.0082) appeared to increase it. The subsequent reverse MR analysis revealed that the three GM were not significantly influenced by BPH, and there was no noticeable heterogeneity or horizontal pleiotropy among the instrumental variables.Conclusion: These results indicated a causal relationship between Eisenbergiella, Ruminococcaceae (UCG009), and Escherichia shigella and BPH. Further randomized controlled trials are needed to explore more comprehensively the roles and operational mechanisms of these GM in relation to BPH

Electrospun chitosan-graft-poly (ɛ-caprolactone)/poly (ɛ-caprolactone) nanofibrous scaffolds for retinal tissue engineering

A promising therapy for retinal diseases is to employ biodegradable scaffolds to deliver retinal progenitor cells (RPCs) for repairing damaged or diseased retinal tissue. In the present study, cationic chitosan-graft-poly(ɛ-caprolactone)/polycaprolactone (CS-PCL/PCL) hybrid scaffolds were successfully prepared by electrospinning. Characterization of the obtained nanofibrous scaffolds indicated that zeta-potential, fiber diameter, and the content of amino groups on their surface were closely correlated with the amount of CS-PCL in CS-PCL/PCL scaffolds. To assess the cell–scaffold interaction, mice RPCs (mRPCs) were cultured on the electrospun scaffolds for 7 days. In-vitro proliferation assays revealed that mRPCs proliferated faster on the CS-PCL/PCL (20/80) scaffolds than the other electrospun scaffolds. Scanning electron microscopy and the real-time quantitative polymerase chain reaction results showed that mRPCs grown on CS-PCL/PCL (20/80) scaffolds were more likely to differentiate towards retinal neurons than those on PCL scaffolds. Taken together, these results suggest that CS-PCL/PCL(20/80) scaffolds have potential application in retinal tissue engineering

Transcriptional regulation of PEN-2, a key component of the γ-secretase complex, by CREB

Gamma-secretase, which is responsible for the intramembranous cleavage of Alzheimer's P-amyloid precursor protein (APP), the signaling receptor Notch, and many other substrates, is a multiprotein complex consisting of at least four components: presenilin (PS), nicastrin, APH-1, and PEN-2. Despite the fact that PEN-2 is known to mediate endoproteolytic cleavage of full-length PS and APH-1 and nicastrin are required for maintaining the stability of the complex, the detailed physiological function of each component remain elusive. Unlike that of PS, the transcriptional regulation of PEN-2, APH-1, and nicastrin has not been investigated. Here, we characterized the upstream regions of the human PEN-2 gene and identified a 238-bp fragment located 353 bp upstream of the translational start codon as the key region necessary for the promoter activity. Further analysis revealed a CREB binding site located in the 238-bp region that is essential for the transcriptional activity of the PEN-2 promoter. Mutation of the CREB site abolished the transcriptional activity of the PEN-2 promoter. Electrophoretic mobility shift assays and chromatin immunoprecipitation analysis showed the binding of CREB to the PEN-2 promoter region both in vitro and in vivo. Activation of the CREB transcriptional factor by forskolin dramatically promoted the expression of PEN-2 mRNA and protein, whereas the other components of the gamma-secretase complex remained unaffected. Forskolin treatment slightly increases the secretion of soluble APP alpha and A beta without affecting Notch cleavage. These results demonstrate that expression of PEN-2 is regulated by CREB and suggest that the specific control of PEN-2 expression may imply additional physiological functions uniquely assigned to PEN-2

Increasing yield potential through manipulating of an ARE1 ortholog related to nitrogen use efficiency in wheat by CRISPR/Cas9.

peer reviewedWheat (Triticum aestivum L.) is a staple food crop consumed by more than 30% of world population. Nitrogen (N) fertilizer has been applied broadly in agriculture practice to improve wheat yield to meet the growing demands for food production. However, undue N fertilizer application and the low N use efficiency (NUE) of modern wheat varieties are aggravating environmental pollution and ecological deterioration. Under nitrogen-limiting conditions, the rice (Oryza sativa) abnormal cytokinin response1 repressor1 (are1) mutant exhibits increased NUE, delayed senescence and consequently, increased grain yield. However, the function of ARE1 ortholog in wheat remains unknown. Here, we isolated and characterized three TaARE1 homoeologs from the elite Chinese winter wheat cultivar ZhengMai 7698. We then used CRISPR/Cas9-mediated targeted mutagenesis to generate a series of transgene-free mutant lines either with partial or triple-null taare1 alleles. All transgene-free mutant lines showed enhanced tolerance to N starvation, and showed delayed senescence and increased grain yield in field conditions. In particular, the AABBdd and aabbDD mutant lines exhibited delayed senescence and significantly increased grain yield without growth defects compared to the wild-type control. Together, our results underscore the potential to manipulate ARE1 orthologs through gene editing for breeding of high-yield wheat as well as other cereal crops with improved NUE

Effects of Dioscorea polystachya \u27yam gruel\u27 on the cognitive function of diabetic rats with focal cerebral ischemia-reperfusion injury via the gut-brain axis

© 2020 Pang et al. Published by IMR press. Focal cerebral ischemia-reperfusion injury is closely related to hyperglycemia and gut microbiota imbalance, while gut microbiota contributes to the regulation of brain function through the gut-brain axis. Previous studies in patients with diabetes have found that \u27yam gruel\u27 is a classic medicated diet made from Dioscorea polystachya, increases the content of Bifidobacterium, regulates oxidative stress, and reduces fasting blood glucose levels. The research reported here investigated the effects of \u27yam gruel\u27 on the cognitive function of streptozotocin-induced diabetic rats with focal cerebral ischemia-reperfusion injury and explored the mechanism underlying the role of the gut-brain axis in this process. \u27Yam gruel\u27 was shown to improve cognitive function as indicated by increased relative content of probiotic bacteria, and short-chain fatty acids in the intestinal tract and cerebral cortex reduced oxidative stress and inflammatory response and promotion of the expression of neurotransmitters and brain-derived neurotrophic factor. Thus, it is concluded that \u27yam gruel\u27 has a protective effect on cognitive function via a mechanism related to the gut-brain axis

Validation of a Disability Assessment Tool Based on the International Classification of Functioning, Disability, and Health in the Chinese Context

Background:The common standards of disability assessment for long-term care (LTC) insurance are currently absent. The International Classification of Functioning, Disability and Health (ICF) was designed for a better description of health and functioning, which could fill the demand gap for the standards of disability assessment and be a promising tool for the development of LTC insurance system.ObjectivesTo validate a disability assessment scale for disabled elderly individuals based on the ICF for LTC in the Chinese context.MethodsThe present study is a cross-sectional study. A disability assessment tool based on the ICF was developed by referring to other assessment tools and an expert consensus meeting in the initial phase of the study. The developed tool was used to evaluate 1,610 elderly individuals in the LTC institutions. The Cronbach's α coefficient and split-half reliability were applied to test the internal consistency of the tool, while the Interclass correlation coefficients (ICCs) were used to evaluate the interrater reliability (IRR). Factor analysis was performed to verify the construct validity of the tool. The scores from the Medical Outcomes Short Form-12 (SF-12) were correlated with that from the disability assessment tool, to assess the criterion-related validity.ResultsThe Cronbach's α coefficient and split-half reliability of the disability assessment tool were 0.969 and 0.877, respectively. The ICCs of the sum scale was 0.85, and the ICCs of each of the 20 items in the scale ranged from 0.78 to 0.94. The items were divided into three factors through analysis, which is consistent with the structure expectation. The scores of each item and the sum score of the disability assessment scale were negatively correlated with the scores of the physical and psychological fields in SF-12 (p < 0.001). Overall, the data indicated that the tool was characterized by good internal consistency, IRR, construct validity, and criterion-related validity.ConclusionsThe disability assessment tool based on the ICF is a reliable and valid tool for the collection of information on functioning across various LTC settings. The information of disability provided evidence for the distribution of LTC service and guided the development of LTC insurance standards

Oriental melon roots metabolites changing response to the pathogen of Fusarium oxysporum f. sp. melonis mediated by Trichoderma harzianum

IntroductionTrichoderma spp. is a recognized bio-control agent that promotes plant growth and enhances resistance against soil-borne diseases, especially Fusarium wilt. It is frequently suggested that there is a relationship between resistance to melon wilt and changes in soil microbiome structures in the rhizosphere with plant metabolites. However, the exact mechanism remains unclear.MethodThis study aims to investigate the effects of Trichoderma application on the metabolic pathway of oriental melon roots in response to Fusarium oxysporum f. sp. melonis in a pot experiment. The experiment consisted of three treatments, namely water-treated (CK), FOM-inoculated (KW), and Trichoderma-applied (MM) treatments, that lasted for 25 days. Ultra-performance liquid chromatography-electron spray ionization-mass spectrometry (UPLC-ESI-MS) was used to analyze the compounds in melon roots.ResultsThe results show that Trichoderma harzianum application resulted in a reduction in the severity of oriental melon Fusarium wilt. A total of 416 distinct metabolites, categorized into four groups, were detected among the 886 metabolites analyzed. Additionally, seven differential metabolites were identified as key compounds being accumulated after inoculation with Fusarium oxysporum f. sp. melonis (FOM) and Trichoderma. The mechanism by which Trichoderma enhanced melon's resistance to Fusarium wilt was primarily associated with glycolysis/gluconeogenesis, phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and the biosynthesis of cofactors pathway. In comparison with the treatments of CK and MM, the KW treatment increased the metabolites of flavone and flavonol biosynthesis, suggesting that oriental melon defended against pathogen infection by increasing flavonol biosynthesis in the KW treatment, whereas the application of Trichoderma harzianum decreased pathogen infection while also increasing the biosynthesis of glycolysis/gluconeogenesis and biosynthesis of cofactors pathway, which were related to growth. This study also aims to enhance our understanding of how melon responds to FOM infection and the mechanisms by which Trichoderma harzianum treatment improves melon resistance at the metabolic level