ATP biosensor reveals microbial energetic dynamics and facilitates bioproduction.

Adenosine-5'-triphosphate (ATP), the primary energy currency in cellular processes, drives metabolic activities and biosynthesis. Despite its importance, understanding intracellular ATP dynamics' impact on bioproduction and exploiting it for enhanced bioproduction remains largely unexplored. Here, we harness an ATP biosensor to dissect ATP dynamics across different growth phases and carbon sources in multiple microbial strains. We find transient ATP accumulations during the transition from exponential to stationary growth phases in various conditions, coinciding with fatty acid (FA) and polyhydroxyalkanoate (PHA) production in Escherichia coli and Pseudomonas putida, respectively. We identify carbon sources (acetate for E. coli, oleate for P. putida) that elevate steady-state ATP levels and boost FA and PHA production. Moreover, we employ ATP dynamics as a diagnostic tool to assess metabolic burden, revealing bottlenecks that limit limonene bioproduction. Our results not only elucidate the relationship between ATP dynamics and bioproduction but also showcase its value in enhancing bioproduction in various microbial species.

Pathological features-based targeted delivery strategies in IBD therapy: A mini review.

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is characterized by a complex and dysfunctional immune response. Currently, IBD is incurable, and patients with IBD often need to take drugs for life. However, as the traditional systemic treatment strategies for IBD do not target the site of inflammation, only limited efficacy can be obtained from them. Moreover, the possibility of serious side effects stemming from the systemic administration or redistribution of drugs in the body is high when conventional drug formulations are used. Therefore, a targeted drug-delivery system for IBD should be considered. Based on the pathological features related to IBD, the new targeted drug-delivery strategy can directly transfer the drug to the inflammatory site, thus enhancing the accumulation of the drugs and reducing side effects. This article reviews the pathological features of IBD and the application of the IBD-targeted delivery system based on different pathological features, and discusses the challenges and new prospects in this field.

ROS-triggered nanoinducer based on dermatan sulfate enhances immunogenic cell death in melanoma.

Due to its complexity, diversity and heterogeneity, melanoma is a kind of malignant tumor. It has been proved that the enhancement of anti-tumor immune response such as immunogenic cell death (ICD) is an important therapeutic strategy. In previous studies, we confirmed that dermatan sulfate (DS) from skin tissue could specifically homing to melanoma B16F10 cells. In this study, we propose a nanoinducer (DOX/ADS NP) based on a functional DS for melanoma. This nanosystem is composed of DS as framework, aromatic thioketal derivative (ATK) as functional grafting unit and doxorubicin (DOX) designed as an ICD inducer. Through the intermolecular interaction between DOX and ATK, DOX/ADS NP with specific-homing, high-loading and ROS-triggering release was obtained via self-assemble. Compared with free DOX and non-functionalized nanomedicine, DOX/ADS NP could release DOX into B16F10 cells better, and strongly induce the translocation of calreticulin (CRT) to the cell membrane. CRT is a marker of ICD, also as a "eat me" signal to stimulate the maturation and antigen presentation of dendritic cells. Therefore, a series of subsequent immune responses were activated: maturation of dendritic cells, T cells proliferation, increased tumor-infiltrating CTLs and the ratio of CTLs to Tregs, and up-regulated cytotoxic cytokine expression. In conclusion, DOX/ADS NP promoted ICD-associated immune response through more specific targeting effect and sensitive responsive DOX release, achieving better inhibitory effect on melanoma than free DOX and other nanoformulation. This biomimetic ICD nanoinducer based on DS is expected to provide new strategies and references for the treatment of melanoma.

Amyloids as Building Blocks for Macroscopic Functional Materials: Designs, Applications and Challenges.

Amyloids are self-assembled protein aggregates that take cross-ß fibrillar morphology. Although some amyloid proteins are best known for their association with Alzheimer's and Parkinson's disease, many other amyloids are found across diverse organisms, from bacteria to humans, and they play vital functional roles. The rigidity, chemical stability, high aspect ratio, and sequence programmability of amyloid fibrils have made them attractive candidates for functional materials with applications in environmental sciences, material engineering, and translational medicines. This review focuses on recent advances in fabricating various types of macroscopic functional amyloid materials. We discuss different design strategies for the fabrication of amyloid hydrogels, high-strength materials, composite materials, responsive materials, extracellular matrix mimics, conductive materials, and catalytic materials.

A dermatan sulfate-functionalized biomimetic nanocarrier for melanoma targeted chemotherapy.

Melanoma is a malignant tumor of melanocytes that is a serious threat to human health. Dermatan sulfate (DS) is a natural glycosaminoglycan. Inspired by the origin of DS, we report a DS-functionalized biomimetic chitosan nanocarrier (DCNP) for melanoma targeted chemotherapy. DS can anchor to the surface of the chitosan nanocarrier (CNP) by forming amide bond. The SN38/DCNP can rapidly release the anti-tumor drug under acidic conditions. The functionalization of DS not only promoted the specific uptake behavior of melanoma cells, but also up-regulated cleaved caspase-3 and PARP promote tumor cell apoptosis. In vivo model, DCNP reduced the non-specific distribution of SN38 in the circulation and other tissues, while shows superior tumor targeting ability. SN38/DCNP significantly inhibit tumor growth and improved the survival rate. Moreover, SN38/DCNP has a milder myelosuppressive effect. The above results indicated that DS could be used as an excellent targeting unit for the treatment of melanoma.

A Multifunctional Nanotherapy for Targeted Treatment of Colon Cancer by Simultaneously Regulating Tumor Microenvironment.

Colitis-associated colon cancer (CAC) is a widely recognized cancer, while treatment with the existing chemotherapeutic drugs affords limited clinical benefits. Herein we proposed a site-specific, combination nanotherapy strategy for targeted treatment of CAC by the oral route. Methods: A reactive oxygen species (ROS)-responsive and hydrogen peroxide-eliminating material OCD was synthesized, which was further produced into a functional nanoparticle (OCD NP). The antioxidative stress and anti-inflammatory effects of OCD NP were examined by in vitro and in vivo experiments. By packaging an anticancer drug camptothecin-11 (CPT-11) into OCD NP, a ROS-responsive nanotherapy CPT-11/OCD NP was obtained, and its antitumor activity was evaluated by both in vitro and in vivo studies. Preliminary safety studies were also performed for CPT-11/OCD NP in mice. Results: OCD NP significantly attenuated oxidative stress and inhibited inflammatory response in different cells and mice with induced colitis. CPT-11/OCD NP could selectively release drug molecules under intestinal pH conditions and at high levels of ROS. In C26 murine colon carcinoma cells, this nanotherapy showed significantly higher antitumor activity compared to free CPT-11 and a non-responsive CPT-11 nanotherapy. Correspondingly, oral delivery of CPT-11/OCD NP notably inhibited tumorigenesis and tumor growth in mice with induced CAC. By combination therapy with the nanovehicle OCD NP in the inflammatory phase, more desirable therapeutic effects were achieved. Furthermore, CPT-11/OCD NP displayed excellent safety profile for oral administration at a dose that is 87.3-fold higher than that employed in therapeutic studies. Conclusions: Anticancer nanotherapies derived from intrinsic anti-inflammatory nanocarriers are promising for targeted combination treatment of inflammation-associated tumors by simultaneously shaping pro-inflammatory microenvironment toward a relatively normal niche sensitive to chemotherapy.

Fibril Self-Assembly of Amyloid-Spider Silk Block Polypeptides.

Because of their association with debilitating diseases and their potential applications in developing novel bionanomaterials, highly ordered amyloid fibrils have recently received considerable attention. While many studies have thus far focused on amyloid fibrils made with short peptides containing just one steric zipper-forming segment of native amyloid proteins, the self-assembly of proteins containing multiple steric zipper-forming segments has been rarely explored. Here we develop a strategy to create four block polypeptides, each containing 16 repeats of a zipper-forming segment from four different amyloid morphological classes. All four block polypeptides self-assemble into fibrils that display the cross-ß structure characteristic of amyloids. These amyloid-spider silk block polypeptides displayed fast self-assembly kinetics, and their fibrils exhibited high thermal stability. These novel synthetic amyloids provide insights into the self-assembly of proteins containing multiple zipper-forming segments, and our approach of creating block polypeptide fibrils could be used to expand the capability of amyloid-based bionanomaterials.

Developing a Cas9-based tool to engineer native plasmids in Synechocystis sp. PCC 6803.

The oxygenic photosynthetic bacterium Synechocystis sp. PCC 6803 (S6803) is a model cyanobacterium widely used for fundamental research and biotechnology applications. Due to its polyploidy, existing methods for genome engineering of S6803 require multiple rounds of selection to modify all genome copies, which is time-consuming and inefficient. In this study, we engineered the Cas9 tool for one-step, segregation-free genome engineering. We further used our Cas9 tool to delete three of seven S6803 native plasmids. Our results show that all three small-size native plasmids, but not the large-size native plasmids, can be deleted with this tool. To further facilitate heterologous gene expression in S6803, a shuttle vector based on the native plasmid pCC5.2 was created. The shuttle vector can be introduced into Cas9-containing S6803 in one step without requiring segregation and can be stably maintained without antibiotic pressure for at least 30 days. Moreover, genes encoded on the shuttle vector remain functional after 30 days of continuous cultivation without selective pressure. Thus, this study provides a set of new tools for rapid modification of the S6803 genome and for stable expression of heterologous genes, potentially facilitating both fundamental research and biotechnology applications using S6803.

Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on 13C-metabolic flux analysis.

We engineered a fatty acid overproducing Escherichia coli strain through overexpressing tesA ("pull") and fadR ("push") and knocking out fadE ("block"). This "pull-push-block" strategy yielded 0.17 g of fatty acids (C12­C18) per gram of glucose (equivalent to 48% of the maximum theoretical yield) in batch cultures during the exponential growth phase under aerobic conditions. Metabolic fluxes were determined for the engineered E. coli and its control strain using tracer ([1,2-13C]glucose) experiments and 13C-metabolic flux analysis. Cofactor (NADPH) and energy (ATP) balances were also investigated for both strains based on estimated fluxes. Compared to the control strain, fatty acid overproduction led to significant metabolic responses in the central metabolism: (1) Acetic acid secretion flux decreased 10-fold; (2) Pentose phosphate pathway and Entner­Doudoroff pathway fluxes increased 1.5- and 2.0-fold, respectively; (3) Biomass synthesis flux was reduced 1.9-fold; (4) Anaplerotic phosphoenolpyruvate carboxylation flux decreased 1.7-fold; (5) Transhydrogenation flux converting NADH to NADPH increased by 1.7-fold. Real-time quantitative RT-PCR analysis revealed the engineered strain increased the transcription levels of pntA (encoding the membrane-bound transhydrogenase) by 2.1-fold and udhA (encoding the soluble transhydrogenase) by 1.4-fold, which is in agreement with the increased transhydrogenation flux. Cofactor and energy balances analyses showed that the fatty acid overproducing E. coli consumed significantly higher cellular maintenance energy than the control strain. We discussed the strategies to future strain development and process improvements for fatty acid production in E. coli.

Evidence of iron cyanides as supplementary nitrogen source to rice seedlings.

The effect of iron cyanides on activities of nitrate reductase (NR) and glutamine synthetase (GS) of plants was investigated. Young rice seedlings (Oryza sativa L. cv. XZX 45) were grown in the nutrient solutions containing KNO(3) or NH(4)Cl and treated with ferro-cyanide [K(4)Fe(CN)(6)] or ferri-cyanide [K(3)Fe(CN)(6)]. Total cyanide and free cyanide in solutions and in plant materials were analyzed. Activities of NR and GS in different parts of plants were assayed in vivo. Results indicated that all rice seedlings exposed to either ferro- or ferri-cyanide showed positive growth. The phyto-assimilation rates of both iron cyanide species by rice seedlings were positively correlated to the doses supplied. Seedlings grown on NO(3)(-) showed significantly higher assimilatory potential for both ferro- and ferri-cyanide than those on NH(4)(+). Rice seedlings grown on NH(4)(+)-containing nutrient solution accumulated more cyanide in plant materials, majority being in roots rather than shoots, than these grown on NO(3)(-)-containing nutrient solution, suggesting that the presence of ammonium (NH(4)(+)) in the nutrient solution caused a negative impact on botanical assimilation of both iron cyanides. Sensitivity of NR and GS in rice seedlings exposed to ferro- and ferri-cyanide was identical, where conspicuous effects were only observed at the highest concentration supplied. The evidence offered here suggests that both iron cyanides can be a supplementary source of nitrogen to plant nutrition.

Evidence of kinetic control of ligand binding and staged product release in MurA (enolpyruvyl UDP-GlcNAc synthase)-catalyzed reactions .

MurA (enolpyruvyl UDP-GlcNAc synthase) catalyzes the first committed step in peptidoglycan biosynthesis. In this study, MurA-catalyzed breakdown of its tetrahedral intermediate (THI), with a k(cat)/K(M) of 520 M(-1) s(-1), was far slower than the normal reaction, and 3 x 10(5)-fold slower than the homologous enzyme, AroA, reacting with its THI. This provided kinetic evidence of slow binding and a conformationally constrained active site. The MurA cocrystal structure with UDP-N-acetylmuramic acid (UDP-MurNAc), a potent inhibitor, and phosphite revealed a new "staged" MurA conformation in which the Arg397 side chain tracked phosphite out of the catalytic site. The closed-to-staged transition involved breaking eight MurA.ligand ion pairs, and three intraprotein hydrogen bonds helping hold the active site loop closed. These were replaced with only two MurA.UDP-MurNAc ion pairs, two with phosphite, and seven new intraprotein ion pairs or hydrogen bonds. Cys115 appears to have an important role in forming the staged conformation. The staged conformation appears to be one step in a complex choreography of release of the product from MurA.

Spectral tuning of azobenzene photoswitches for biological applications.

Longer switching wavelengths and good photochemical yields and stabilities of the cis isomers in reducing aqueous environments are achieved by introducing 2,2'-aminoalkyl substituents into 4,4'-diamido-substituted azobenzenes. The products are thus suitable for photocontrol of biomolecular structures in intracellular environments, such as switching between two peptide configurations (see picture).

Structure-based approach to the photocontrol of protein folding.

Photoswitchable proteins offer exciting prospects for remote control of biochemical processes. We propose a general approach to the design of photoswitchable proteins based on the introduction of a photoswitchable intramolecular cross-linker. We chose, as a model, a FynSH3 domain for which the free energy of folding is less than the energy available from photoisomerization of the cross-linker. Taking the experimentally determined structure of the folded protein as a starting point, mutations were made to introduce pairs of Cys residues so that the distance between Cys sulfur atoms matches the ideal length of the cis form, but not the trans form, of the cross-linker. When the trans cross-linker was introduced into this L3C-L29C-T47AFynSH3 mutant, the protein was destabilized so that folded and unfolded forms coexisted. Irradiation of the cross-linker to produce the cis isomer recovered the folded, active state of the protein. This work shows that structure-based introduction of switchable cross-linkers is a feasible approach for photocontrol of folding/unfolding of globular proteins.

Synthesis and characterization of a long, rigid photoswitchable cross-linker for promoting peptide and protein conformational change.

Azobenzene-based photoswitchable compounds can be use to photocontrol a variety of biochemical systems. In some cases, their effectiveness may be limited by the size of the conformational change that the switch undergoes. To produce an azobenzene photoswitch that undergoes a large end-to-end distance change upon isomerization, we synthesized 3,3'-diazene-1,2-diylbis{6-[2-sulfonato-4-(chloroacetylamino)phenylethynyl]benzene sulfonic acid} (DDPBA). This long, rigid, water-soluble, thiol-reactive cross-linker undergoes an end-to-end distance change of approximately 13 A upon isomerization. DDPBA was successfully cross-linked to peptides through cysteine side chains. The photoswitch undergoes trans-to-cis photoisomerization maximally when irradiated at 400 nm, although the efficiency of production of the cis isomer is lower than for simpler azobenzenes. Under steady-state illumination conditions, the percentage of cis form produced increases as temperature increases; approximately 56 % cis is obtained at 60 degrees C. Thermal relaxation occurs with a half-life of approximately 75 min at room temperature. When DDPBA was attached to an alpha-helical peptide with two cysteine residues at i and i+14 positions, an increase in helix content was observed after photoirradiation. When cross-linked to another peptide with two cysteine residues spaced at i and i+21 positions, a decrease in helix content after trans-to-cis isomerization was observed. Due to the small percentage of cis form produced under the experimental conditions, the CD signal changes were small. However, the large structural change upon photoisomerization provided by this cross-linker can potentially be used to photoswitch other biochemical systems.

Synthesis of 3,3'-bis(sulfonato)-4,4'-bis(chloroacetamido)azobenzene and cysteine cross-linking for photo-control of protein conformation and activity.

This protocol describes a procedure for the synthesis of 3,3'-bis(sulfonato)-4,4'-bis(chloroacetamido)azobenzene (BSBCA), a water-soluble, thiol-reactive, photo-switchable cross-linker. In addition, a protocol is outlined for installing the cross-linker in an intramolecular fashion onto proteins bearing two surface-exposed Cys residues. BSBCA is designed to be used as an in vitro activity switch that operates by exerting temporal and reversible photo-control over alpha-helix content within synthetic peptides and recombinant proteins. Synthesis of the cross-linker requires approximately 4.5 d, and cross-linking can be performed in 10-12 h.

sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking.

UNLABELLED: sGAL is a computer program designed to find pairs of sites suitable for introducing chemical cross-links into proteins. sGAL takes a protein structure file in PDB format as input, truncates each residue sequentially to its gamma side chain atom to mimic mutation to Cys, and calculates the exposed surface area of the gamma atom. The user then inputs the minimum and maximum lengths of the cross-linker. sGAL provides as output pairs of residues that would have exposed gamma atom separations that fall within this range. Furthermore, if a line joining the pair of gamma atoms contacts more than a given number of buried atoms, that pair is discarded. In this way, sites for which the protein would sterically interfere with cross-linking are avoided. AVAILABILITY: http://www.chem.utoronto.ca/staff/GAW/links.html; (Surface Racer is also required see: http://monte.biochem.wisc.edu/~tsodikov/surface.html).

[Effect of early intestinal dripping of jianpi tongli Chinese herbs on serum level IL-2, sIL-2R and IL-12 in patients with gastric cancer after operation].

OBJECTIVE: To explore the regulation and clinical significance of intestinal dripping of Jianpi Tongli (JPTL) Chinese herbs on levels of serum cytokines, such as interleukin-2 (IL-2), soluble interleukin-2 receptor (sIL-2R) and interleukin-12 (IL-12) in treating patients with gastric cancer (GC) at early post-operational stage. METHODS: Sixty patients with GC were randomly divided into two groups, i. e. the studied group (n = 30), treated with JPTL Chinese herbs, and the control group (n = 30) treated with normal saline. The medication was started from the 1st day after operation by intestinal dripping daily, 7 days as one course. Levels of IL-2, sIL-2R and IL-12 were observed before and after operation. RESULTS: Significant difference was seen on the 7th day post-operation between the studied and the control group, mainly in aspects of obvious increase of IL-2 and decrease of sIL-2R (P <0.05), no significant difference in IL-12 was found (P >0.05) though there was certain improvement. Compared with pre-operation of the same group, significant difference was found in the studied group in the increased IL-2 and IL-12 and decreased sIL-2R on the 7th day post-operation, while no significant difference in these indexes was found in the control group (P >0.05), though certain improvement was shown. CONCLUSION: Early intestinal dripping of JPTL Chinese herbs to post-operational patients with GC could improve their immune function, which was of important significance in early preventing the severe complications, improving the prognosis, and elevating the survival rate.