Multi-omic dissection of the cold resistance traits of white water lily.

The white water lily (Nymphaea candida), exemplifying nature's resilience, thrives in the high-altitude terrains of Xinjiang, China, serving as an ideal model for investigating cold adaptation mechanisms in aquatic plants. This study meticulously elucidates the complex cold adaptation mechanisms of the white water lily through a comprehensive and integrated methodological approach. We discovered that the water lily undergoes ecodormancy in winter, retaining high cellular viability and growth potential. During overwintering, the white water lily demonstrates effective resource reallocation, a process facilitated by morphological adjustments, thereby strengthening its resistance to cold temperatures. This enhancement is achieved particularly through the compartmentalization of large vacuoles, the accumulation of osmoregulatory substances, and an increased antioxidant capacity. We established the first exhaustive full-length transcriptome for the white water lily. A subsequent comprehensive analysis of the transcriptome, phytohormones, and metabolome uncovered a multifaceted regulatory network orchestrating cold adaptation. Our research spotlights phytohormone signaling, amino acid metabolism, and circadian rhythms as key elements in the water lily's defense against cold. The results emphasize the critical role of nitrogen metabolism, especially amino acid-related pathways, during cold stress. Metabolite profiling revealed the importance of compounds like myo-inositol and L-proline in enhancing cold tolerance. Remarkably, our study demonstrates that the white water lily notably diminishes the utilization of unsaturated fatty acids in its temperature regulation strategies. In conclusion, this research substantially enriches our understanding of the white water lily's intricate cold adaptation mechanisms, offering new perspectives on the adaptive strategies of aquatic plants and potential applications in agricultural advancement.

A nanoparticle-based molecular beacon for directly detecting attomolar small RNA from plasma without purification.

Molecular beacons (MBs) are DNA-based probes that detect DNA or RNA fragments and hold promise for monitoring diseases and studying protein-nucleic acid interactions. MBs usually use fluorescent molecules as fluorophores for reporting the target detection event. However, the fluorescence of the traditional fluorescent molecules can bleach and even be interfered with the background autofluorescence, reducing the detection performance. Hence, we propose to develop a nanoparticle-based MB (NPMB) that uses upconversion nanoparticles (UCNPs) as a fluorophore, which can be excited by near-infrared light to avoid background autofluorescence and thus enables us to detect small RNA from complicated clinical samples such as plasma. Specifically, we employ a DNA hairpin structure, with one segment complementary to the target RNA, to position a quencher (gold nanoparticles, Au NPs) and the UCNP fluorophore in close proximity, leading to the quenching of the fluorescence of UCNPs in the absence of a target nucleic acid. Only when the hairpin structure is complementary with the detection target, will the hairpin structure be destroyed to separate Au NPs and UCNPs, resulting in the instant recovery of the fluorescence signal of UCNPs and the consequent ultrasensitive detection of the target concentrations. The NPMB has an ultra-low background signal because UCNPs can be excited with NIR light with a wavelength longer than the emitted visible light. We demonstrate that the NPMB can successfully detect a small (22-nt) RNA (using a microRNA cancer biomarker, miR-21, as an example) and a small single-stranded DNA (complementing the cDNA of miR-21) in aqueous solutions from 1 aM to 1 pM, with the linear detection range being 10 aM to 1 pM for the former and 1 aM to 100 fM for the latter. We further show that the NPMB can be used to detect unpurified small RNA (miR-21) in clinical samples such as plasma with the same detection region. Our work suggests that the NPMB is a promising label-free and purification-free method for detecting small nucleic acid biomarkers in clinical samples with a detection limit as low as the aM level.

3D Bacterial flagella as both synthetic biotemplates and ultrathin spacers for enhanced inter-particle coupling and solar energy harvesting.

Linear light-absorbing nanomaterials are ideal for film-based solar harvesting applications as they form porous structures that can maximize the absorption and minimize the reflection of the solar light. Conventional 1D nanochains of plasmonic nanoparticle assemblies can achieve significantly broadened optical absorption through surface plasmon coupling, but their optical bands are still not broad enough to absorb through the solar spectrum and thus are not efficient solar absorbers. Here we discovered first by simulation that 3D structured nanochains of plasmonic nanoparticles presented a remarkably increased optical broadening effect and much longer redshift of the optical peaks due to the enhanced inter-particle coupling effect. Then we fabricated 3D nanochains by assembling gold nanoparticles (AuNPs) around 14 nm ultrathin bionanofibers, the bacterial flagella. The ultrathin biotemplates enabled the 3D arrangement of 50 nm AuNPs along the nanofiber with a very small inter-particle gap, allowing the strong coupling of surface plasmons in a 3D manner. Consistent with the theoretical prediction, the 3D nanochains, when assembled into films, could effectively convert nearly the full spectrum of solar energy into heat, which was further efficiently converted into electricity through a thermoelectric generation unit. Our work represents a nanobiomaterial approach to highly efficient solar thermal power generation.

Selectively Suppressing Tumor Angiogenesis for Targeted Breast Cancer Therapy by Genetically Engineered Phage.

Antiangiogenesis is a promising approach to cancer therapy but is limited by the lack of tumor-homing capability of the current antiangiogenic agents. Angiogenin, a protein overexpressed and secreted by tumors to trigger angiogenesis for their growth, has never been explored as an antiangiogenic target in cancer therapy. Here it is shown that filamentous fd phage, as a biomolecular biocompatible nanofiber, can be engineered to become capable of first homing to orthotopic breast tumors and then capturing angiogenin to prevent tumor angiogenesis, resulting in targeted cancer therapy without side effects. The phage is genetically engineered to display many copies of an identified angiogenin-binding peptide on its side wall and multiple copies of a breast-tumor-homing peptide at its tip. Since the tumor-homing peptide can be discovered and customized virtually toward any specific cancer by phage display, the angiogenin-binding phages are thus universal "plug-and-play" tumor-homing cancer therapeutics.

Hierarchical Ordered Assembly of Genetically Modifiable Viruses into Nanoridge-in-Microridge Structures.

Hierarchically assembled nanomaterials can find a variety of applications in medicine, energy, and electronics. Here, an automatically controlled dip-pulling method is developed and optimized to generate an unprecedented ordered nano-to-micro hierarchical nanoridge-in-microridge (NiM) structure from a bacteria-specific human-safe virus, the filamentous phage with or without genetically displaying a foreign peptide. The NiM structure is pictured as a window blind with each lath (the microridge) made of parallel phage bundles (the nanoridges). It is independent of the substrate materials supporting it. Surprisingly, it can induce the bidirectional differentiation of stem cells into neurons and astrocytes within a short timeframe (only 8 d) not seen before, which is highly desired because both neurons and astrocytes are needed simultaneously in treating neurodegenerative diseases. Since phages can direct tissue regeneration, template materials formation, sense molecules, and build electrodes, the NiM structures displaying different peptides and on varying materials hold promise in many technologically important fields.

Guiding nanomaterials to tumors for breast cancer precision medicine: from tumor-targeting small-molecule discovery to targeted nanodrug delivery.

Precision medicine emphasizes patient-specific formulation for treatment of diseases, especially cancer. However, in targeted cancer treatment, because the expression level of tumor receptors in each patient varies even for the same type of cancer, the ligand/receptor-mediated approach does not seem promising for precision medicine. In this work, we demonstrated our strategy of using a phage display technique for breast cancer precision medicine. Using in vivo biopanning, we first selected an MCF-7 breast tumor-targeting peptide, then tested the effectiveness of the as-selected peptide in tumor homing and finally conjugated the peptide to a model photothermal drug, namely, gold nanorods, to achieve enhanced cancer killing efficacy. The peptides identified by the phage display technique can guide the drug to the tumors without the need to know the exact receptors on the tumor. This approach requires significantly less effort to explore patient-specific targeting molecules for precision medicine.

Tuning photothermal properties of gold nanodendrites for in vivo cancer therapy within a wide near infrared range by simply controlling their degree of branching.

Although dendritic nanoparticles have been prepared by many different methods, control over their degree of branching (DB) is still impossible, preventing us from understanding the effect of the DB on the properties of the nanodendrites as cancer therapeutics. Herein, we developed a novel seed-mediated method to prepare gold nanodendrites (AuNDs) in an organic solvent using long chain amines as a structural directing agent. We discovered that the DB could be tuned facilely by simply adjusting synthetic parameters, such as the solvent type, the type and concentration of the long chain amines. We found that DB tuning resulted in dramatic tunability in the optical properties in the near infrared (NIR) range, which led to significantly different performance in the photothermal cancer therapy. Our in vitro and in vivo studies revealed that AuNDs with a higher DB were more efficient in photothermal tumor destruction under a lower wavelength NIR irradiation. In contrast, those with a lower DB performed better in tumor destruction under a higher wavelength NIR irradiation, indicating that AuNDs of even lower DB should have even better photothermal cancer therapy efficiency within the second NIR window. Thus, the tunable optical properties of AuNDs in the NIR range allow us to selectively determine a suitable laser wavelength for the best cancer therapeutic performance.

Ultrasensitive rapid detection of human serum antibody biomarkers by biomarker-capturing viral nanofibers.

Candida albicans (C. albicans) infection causes high mortality rates within cancer patients. Due to the low sensitivity of the current diagnosis systems, a new sensitive detection method is needed for its diagnosis. Toward this end, here we exploited the capability of genetically displaying two functional peptides, one responsible for recognizing the biomarker for the infection (antisecreted aspartyl proteinase 2 IgG antibody) in the sera of cancer patients and another for binding magnetic nanoparticles (MNPs), on a single filamentous fd phage, a human-safe bacteria-specific virus. The resultant phage is first decorated with MNPs and then captures the biomarker from the sera. The phage-bound biomarker is then magnetically enriched and biochemically detected. This method greatly increases the sensitivity and specificity of the biomarker detection. The average detection time for each serum sample is only about 6 h, much shorter than the clinically used gold standard method, which takes about 1 week. The detection limit of our nanobiotechnological method is approximately 1.1 pg/mL, about 2 orders of magnitude lower than that of the traditional antigen-based method, opening up a new avenue to virus-based disease diagnosis.

Nontoxic virus nanofibers improve the detection sensitivity for the anti-p53 antibody, a biomarker in cancer patients.

The presence of anti-p53 antibody in serum is a biomarker for cancer. However, its high sensitivity detection is still an issue in cancer diagnosis. To tackle this challenge, we used fd phage, a human-safe bacteria-specific virus nanofiber that can be mass-produced by infecting host bacteria in an error-free manner, and genetically engineered it to display a peptide capable of recognizing and capturing anti-p53 antibody on its side wall. We employed the resultant phage nanofibers as a capture probe to develop a modified version of the enzyme-linked immunosorbent assay (ELISA) method, termed phage-ELISA. We compared it to the traditional ELISA method for the detection of anti-p53 antibody, p53-ELISA, which uses recombinant wild-type p53 protein to capture anti-p53 antibody. We applied phage-ELISA to detect anti-p53 antibody in an experimental group of 316 patients with various types of malignant tumors. We found that a detection rate of 17.7% (56 positive cases) was achieved by phage-ELISA, which was comparable to the detection rate of 20.6% for p53-ELISA (65 positive cases). However, when both phage and p53 were combined to form antibody-capturing probes for phage/p53-ELISA, a detection rate of 30.4% (96 positive cases) was achieved. Our work showed that owing to the combined capture of the anti-p53 antibody by both phage nanofibers and p53, the phage/p53-ELISA achieved the highest diagnostic accuracy and detection efficiency for the anti-p53 antibody in patients with various types of cancers. Our work suggests that a combination of nanofibers and antigens, both of which capture antibody, could lead to increased detection sensitivity, which is useful for applications in the life sciences, clinical medicine, and environmental sciences.

NIR-induced highly sensitive detection of latent finger-marks by NaYF4:Yb,Er upconversion nanoparticles in a dry powder state.

The most commonly found fingermarks at crime scenes are latent and, thus, an efficient method for detecting latent fingermarks is very important. However, traditional developing techniques have drawbacks such as low detection sensitivity, high background interference, complicated operation, and high toxicity. To tackle this challenge, we employed fluorescent NaYF4:Yb,Er upconversion nanoparticles (UCNPs), which can fluoresce visible light when excited by 980 nm human-safe near-infrared light, to stain the latent fingermarks on various substrate surfaces. The UCNPs were successfully used as a novel fluorescent label for the detection of latent fingermarks with high sensitivity, low background, high efficiency, and low toxicity on various substrates including non-infiltrating materials (glass, marble, aluminum alloy sheets, stainless steel sheets, aluminum foils, and plastic cards), semi-infiltrating materials (floor leathers, ceramic tiles, wood floor, and painted wood), and infiltrating materials such as various types of papers. This work shows that UCNPs are a versatile fluorescent label for the facile detection of fingermarks on virtually any material, enabling their practical applications in forensic sciences.

Mesoporous iron oxide nanoparticles prepared by polyacrylic acid etching and their application in gene delivery to mesenchymal stem cells.

Novel monodisperse mesoporous iron oxide nanoparticles (m-IONPs) were synthesized by a postsynthesis etching approach and characterized by electron microscopy. In this approach, solid iron oxide nanoparticles (s-IONPs) were first prepared following a solvothermal method, and then etched anisotropically by polyacrylic acid to form the mesoporous nanostructures. MTT cytotoxicity assay demonstrated that the m-IONPs have good biocompatibility with mesenchymal stem cells (MSCs). Owing to their mesoporous structure and good biocompatibility, these monodisperse m-IONPs were used as a nonviral vector for the delivery of a gene of vascular endothelial growth factor (VEGF) tagged with a green fluorescence protein (GFP) into the hard-to-transfect stem cells. Successful gene delivery and transfection were verified by detecting the GFP fluorescence from MSCs using fluorescence microscopy. Our results illustrated that the m-IONPs synthesized in this work can serve as a potential nonviral carrier in gene therapy where stem cells should be first transfected and then implanted into disease sites for disease treatment.

Silica-based branched hollow microfibers as a biomimetic extracellular matrix for promoting tumor cell growth in vitro and in vivo.

A novel scaffold composed of loosely branched hollow silica microfibers that has been proven to be highly biocompatible is proposed for the 3D culture of cancer cells. The MCF-7 cancer cells can grow and proliferate freely inside the scaffold in the form of multicellular spheroids. MCF-7 cancer cells cultured on the current 3D silica scaffold retained significantly more oncological characters than those cultured on the conventional 2D substrate and can serve as in vitro tumor model for studying cancer treatment.

Bio-imaging, detection and analysis by using nanostructures as SERS substrates.

Surface-enhanced Raman scattering (SERS) is a phenomenon that occurs on nanoscale-roughed metallic surface. The magnitude of the Raman scattering signal can be greatly enhanced when the scatterer is placed in the very close vicinity of the surface, which enables this phenomenon to be a highly sensitive analytical technique. SERS inherits the general strongpoint of conventional Raman spectroscopy and overcomes the inherently small cross section problem of a Raman scattering. It is a sensitive and nondestructive spectroscopic method for biological samples, and can be exploited either for the delivery of molecular structural information or for the detection of trace levels of analytes. Therefore, SERS has long been regarded as a powerful tool in biomedical research. Metallic nanostructure plays a key role in all the biomedical applications of SERS because the enhanced Raman signal can only be obtained on the surface of a finely divided substrate. This review focuses on progress made in the use of SERS as an analytical technique in bio-imaging, analysis and detection. Recent progress in the fabrication of SERS active nanostructures is also highlighted.

Oil phase evaporation-induced self-assembly of hydrophobic nanoparticles into spherical clusters with controlled surface chemistry in an oil-in-water dispersion and comparison of behaviors of individual and clustered iron oxide nanoparticles.

We report a general method for preparing nanoparticle clusters (NPCs) in an oil-in-water emulsion system mediated by cetyl trimethylammonium bromide (CTAB), where previously only individual nanoparticles were obtained. NPCs of magnetic, metallic, and semiconductor nanoparticles have been prepared to demonstrate the generality of the method. The NPCs were spherical and composed of densely packed individual nanoparticles. The number density of nanoparticles in the oil phase was found to be critical for the formation, morphology, and yield of NPCs. The method developed here is scalable and can produce NPCs in nearly 100% yield at a concentration of 5 mg/mL in water, which is approximately 5 times higher than the highest value reported in the literature. The surface chemistry of NPCs can also be controlled by replacing CTAB with polymers containing different functional groups via a similar procedure. The reproducible production of NPCs with well-defined shapes has allowed us to compare the properties of individual and clustered iron oxide nanoparticles, including magnetization, magnetic moments, and contrast enhancement in magnetic resonance imaging (MRI). We found that, due to their collective properties, NPCs are more responsive to an external magnetic field and can potentially serve as better contrast enhancement agents than individually dispersed magnetic NPs in MRI.

Biomimetic branched hollow fibers templated by self-assembled fibrous polyvinylpyrrolidone structures in aqueous solution.

Branched hollow fibers are common in nature, but to form artificial fibers with a similar branched hollow structure is still a challenge. We discovered that polyvinylpyrrolidone (PVP) could self-assemble into branched hollow fibers in an aqueous solution after aging the PVP solution for about two weeks. On the basis of this finding, we demonstrated two approaches by which the self-assembly of PVP into branched hollow fibers could be exploited to template the formation of branched hollow inorganic fibers. First, inorganic material such as silica with high affinity against the PVP could be deposited on the surface of the branched hollow PVP fibers to form branched hollow silica fibers. To extend the application of PVP self-assembly in templating the formation of hollow branched fibers, we then adopted a second approach where the PVP molecules bound to inorganic nanoparticles (using gold nanoparticles as a model) co-self-assemble with the free PVP molecules in an aqueous solution, resulting in the formation of the branched hollow fibers with the nanoparticles embedded in the PVP matrix constituting the walls of the fibers. Heating the resultant fibers above the glass transition temperature of PVP led to the formation of branched hollow gold fibers. Our work suggests that the self-assembly of the PVP molecules in the solution can serve as a general method for directing the formation of branched hollow inorganic fibers. The branched hollow fibers may find potential applications in microfluidics, artificial blood vessel generation, and tissue engineering.