A new framework for exploratory network mediator analysis in omics data.

Omics methods are widely used in basic biology and translational medicine research. More and more omics data are collected to explain the impact of certain risk factors on clinical outcomes. To explain the mechanism of the risk factors, a core question is how to find the genes/proteins/metabolites that mediate their effects on the clinical outcome. Mediation analysis is a modeling framework to study the relationship between risk factors and pathological outcomes, via mediator variables. However, high-dimensional omics data are far more challenging than traditional data: (1) From tens of thousands of genes, can we overcome the curse of dimensionality to reliably select a set of mediators? (2) How do we ensure that the selected mediators are functionally consistent? (3) Many biological mechanisms contain nonlinear effects. How do we include nonlinear effects in the high-dimensional mediation analysis? (4) How do we consider multiple risk factors at the same time? To meet these challenges, we propose a new exploratory mediation analysis framework, medNet, which focuses on finding mediators through predictive modeling. We propose new definitions for predictive exposure, predictive mediator, and predictive network mediator, using a statistical hypothesis testing framework to identify predictive exposures and mediators. Additionally, two heuristic search algorithms are proposed to identify network mediators, essentially subnetworks in the genome-scale biological network that mediate the effects of single or multiple exposures. We applied medNet on a breast cancer data set and a metabolomics data set combined with food intake questionnaire data. It identified functionally consistent network mediators for the exposures' impact on the outcome, facilitating data interpretation.

Silk-protein-based gradient hydrogels with multimode reprogrammable shape changes for biointegrated devices.

Biocompatible and morphable hydrogels capable of multimode reprogrammable, and adaptive shape changes are potentially useful for diverse biomedical applications. However, existing morphable systems often rely on complicated structural designs involving cumbersome and energy-intensive fabrication processes. Here, we report a simple electric-field-activated protein network migration strategy to reversibly program silk-protein hydrogels with controllable and reprogrammable complex shape transformations. The application of a low electric field enables the convergence of net negatively charged protein cross-linking networks toward the anode (isoelectric point plane) due to the pH gradient generated in the process, facilitating the formation of a gradient network structure and systems suitable for three-dimensional shape change. These tunable protein networks can be reprogrammed or permanently fixed by control of the polymorphic transitions. We show that these morphing hydrogels are capable of conformally interfacing with biological tissues by programming the shape changes and a bimorph structure consisting of aligned carbon nanotube multilayers and the silk hydrogels was assembled to illustrate utility as an implantable bioelectronic device for localized low-voltage electrical stimulation of the sciatic nerve in a rabbit.

Angle-Multiplexed 3D Photonic Superstructures with Multi-Directional Switchable Structural Color for Information Transformation, Storage, and Encryption.

Creating photonic crystals that can integrate and switch between multiple structural color images will greatly advance their utility in dynamic information transformation, high-capacity storage, and advanced encryption, but has proven to be highly challenging. Here, it is reported that by programmably integrating newly developed 1D quasi-periodic folding structures into a 3D photonic crystal, the generated photonic superstructure exhibits distinctive optical effects that combine independently manipulatable specular and anisotropic diffuse reflections within a versatile protein-based platform, thus creating different optical channels for structural color imaging. The polymorphic transition of the protein format allows for the facile modulation of both folding patterns and photonic lattices and, therefore, the superstructure's spectral response within each channel. The capacity to manipulate the structural assembly of the superstructure enables the programmable encoding of multiple independent patterns into a single system, which can be decoded by the simple adjustment of lighting directions. The multifunctional utility of the photonic platform is demonstrated in information processing, showcasing its ability to achieve multimode transformation of information codes, multi-code high-capacity storage, and high-level numerical information encryption. The present strategy opens new pathways for achieving multichannel transformable imaging, thereby facilitating the development of emerging information conversion, storage, and encryption media using photonic crystals.

Exploring the neuroprotection of the combination of astragaloside A, chlorogenic acid and scutellarin in treating chronic cerebral ischemia via network analysis and experimental validation.

Chronic cerebral ischemia (CCI) primarily causes cognitive dysfunction and other neurological impairments, yet there remains a lack of ideal therapeutic medications. The preparation combination of Astragalus membranaceus (Fisch.) Bunge and Erigeron breviscapus (Vant.) Hand.-Mazz have been utilized to ameliorate neurological dysfunction following cerebral ischemia, but material basis of its synergy remains unclear. The principal active ingredients and their optimal proportions in this combination have been identified through the oxygen and glucose deprivation (OGD) cell model, including astragaloside A, chlorogenic acid and scutellarin (ACS), and its efficacy in enhancing the survival of OGD PC12 cells surpasses that of the combination preparation. Nevertheless, mechanism of ACS against CCI remains elusive. In this study, 63 potential targets of ACS against CCI injury were obtained by network pharmacology, among which AKT1, CASP3 and TNF are the core targets. Subsequent analysis utilizing KEGG and GO suggested that PI3K/AKT pathway may play a crucial role for ACS in ameliorating CCI injury. Then, a right unilateral common carotid artery occlusion (rUCCAO) mouse model and an OGD PC12 cell model were established to replicate the pathological processes of CCI in vivo and in vitro. These models were utilized to explore the anti-CCI effects of ACS and its regulatory mechanisms, particularly focusing on PI3K/AKT pathway. The results showed that ACS facilitated the restoration of cerebral blood flow in CCI mice, enhanced the function of the central cholinergic nervous system, protected against ischemic nerve cell and mitochondrial damage, and improved cognitive function and other neurological impairments. Additionally, ACS upregulated the expression of p-PI3K, p-AKT, p-GSK3ß and Bcl-2, and diminished the expression of Cyto-c, cleaved Caspase-3 and Bax significantly. However, the PI3K inhibitor (LY294002) partially reversed the downregulation of Bax, Cyto-c and cleaved Caspase-3 expression as well as the upregulation of p-AKT/AKT, p-GSK3ß/GSK3ß, and Bcl-2/Bax ratios. These findings suggest that ACS against neuronal damage in cerebral ischemia may be closely related to the activation of PI3K/AKT pathway. These results declared first time ACS may become an ideal candidate drug against CCI due to its neuroprotective effects, which are mediated by the activated PI3K/AKT pathway mitigates mitochondrial damage and prevents cell apoptosis.

Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening.

Mitochondria are key regulators of hematopoietic stem cell (HSC) homeostasis. Our research identifies the transcription factor Nynrin as a crucial regulator of HSC maintenance by modulating mitochondrial function. Nynrin is highly expressed in HSCs under both steady-state and stress conditions. The knockout Nynrin diminishes HSC frequency, dormancy, and self-renewal, with increased mitochondrial dysfunction indicated by abnormal mPTP opening, mitochondrial swelling, and elevated ROS levels. These changes reduce HSC radiation tolerance and promote necrosis-like phenotypes. By contrast, Nynrin overexpression in HSCs diminishes irradiation (IR)-induced lethality. The deletion of Nynrin activates Ppif, leading to overexpression of cyclophilin D (CypD) and further mitochondrial dysfunction. Strategies such as Ppif haploinsufficiency or pharmacological inhibition of CypD significantly mitigate these effects, restoring HSC function in Nynrin-deficient mice. This study identifies Nynrin as a critical regulator of mitochondrial function in HSCs, highlighting potential therapeutic targets for preserving stem cell viability during cancer treatment.

Formation of multilayer through layer-by-layer assembly of starch-based polyanion with divalent metal ion.

The layer-by-layer (LbL) assembly between metal ion and starch-based anion driven by electrostatic interaction was investigated. Multilayer films were obtained from starch-based derivative containing carboxyl groups (SC) with copper or lead ions. It was found that the concentration of metal ion in aqueous solution decreased with increasing the layers. X-ray photoelectron spectroscopy exhibited the content of Cu(II) was higher when the surface was copper-ion-layer than that composed of SC. The surface of the film was smooth and no obvious fault plane was observed on its cross-section, which also indicated that the LbL assembly between starch-based polyanion and metal ion was carried out. Sodium alginate was adopted as another polyanion to conduct the LbL assembly. Part of metal ion was replaced with rhodamine B to fabricate composite multilayer. During such an assembly, the concentration of copper ion in aqueous solution decreased with increasing the layers as well. These phenomena suggested that the LbL assembly between polysaccharide-based polyanion and metal ion was feasible.

A facile physical approach to make chitosan soluble in acid-free water.

We changed the situation that chitosan was only dissolved in diluted acid through mild physical treatment. In viewing of the usual methods to modify chitosan are chemical ones, we established the approach by using a water-soluble chitosan derivative as the model polymer. Its water-solubility was modulated via changing the concentration of solution and varying the precipitants. Such a physical method was adopted to treat chitiosan. One gram chitosan was dissolved in a mixture of 100mL 10% acetic acid and 50mL methanol, and then precipitated from a precipitant consisted of 10mL ethanol and 90mL acetate ester. The treated chitosan became soluble in acid-free water completely, and its solubility was 8.02mg/mL.

Entrapment of carbon dioxide with chitosan-based core-shell particles containing changeable cores.

Water-soluble chitosan-based core-shell particles that contained changeable cores were successfully applied to anchor carbon dioxide. The entrapment capacity of the particles for carbon dioxide (EC) depended on the cores. It was found that EC of the particles contained aqueous cores was higher than that of the beads with water-soluble chitosan gel cores, which was confirmed with thermogravimetric analysis. In addition, calcium ions and sodium hydroxide were introduced within the particles to examine their effect on the entrapment. EC of the particles was enhanced with sodium hydroxide when the cores were WSC gel. The incorporation of calcium ions was helpful for stabilizing carbon dioxide through the formation of calcium carbonate, which was verified with Fourier transform infrared spectra and scanning electron microscopy/energy-dispersive spectrometry. This phenomenon meant the role of calcium ions for fixating carbon dioxide was significant.