Enabling structure-based drug discovery utilizing predicted models.

High-quality predicted structures enable structure-based approaches to an expanding number of drug discovery programs. We propose that by utilizing free energy perturbation (FEP), predicted structures can be confidently employed to achieve drug design goals. We use structure-based modeling of hERG inhibition to illustrate this value of FEP.

Structural and Functional Analysis of a ß2-Adrenergic Receptor Complex with GRK5.

The phosphorylation of agonist-occupied G-protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) functions to turn off G-protein signaling and turn on arrestin-mediated signaling. While a structural understanding of GPCR/G-protein and GPCR/arrestin complexes has emerged in recent years, the molecular architecture of a GPCR/GRK complex remains poorly defined. We used a comprehensive integrated approach of cross-linking, hydrogen-deuterium exchange mass spectrometry (MS), electron microscopy, mutagenesis, molecular dynamics simulations, and computational docking to analyze GRK5 interaction with the ß2-adrenergic receptor (ß2AR). These studies revealed a dynamic mechanism of complex formation that involves large conformational changes in the GRK5 RH/catalytic domain interface upon receptor binding. These changes facilitate contacts between intracellular loops 2 and 3 and the C terminus of the ß2AR with the GRK5 RH bundle subdomain, membrane-binding surface, and kinase catalytic cleft, respectively. These studies significantly contribute to our understanding of the mechanism by which GRKs regulate the function of activated GPCRs. PAPERCLIP.

Illuminating protein space with a programmable generative model.

Three billion years of evolution has produced a tremendous diversity of protein molecules1, but the full potential of proteins is likely to be much greater. Accessing this potential has been challenging for both computation and experiments because the space of possible protein molecules is much larger than the space of those likely to have functions. Here we introduce Chroma, a generative model for proteins and protein complexes that can directly sample novel protein structures and sequences, and that can be conditioned to steer the generative process towards desired properties and functions. To enable this, we introduce a diffusion process that respects the conformational statistics of polymer ensembles, an efficient neural architecture for molecular systems that enables long-range reasoning with sub-quadratic scaling, layers for efficiently synthesizing three-dimensional structures of proteins from predicted inter-residue geometries and a general low-temperature sampling algorithm for diffusion models. Chroma achieves protein design as Bayesian inference under external constraints, which can involve symmetries, substructure, shape, semantics and even natural-language prompts. The experimental characterization of 310 proteins shows that sampling from Chroma results in proteins that are highly expressed, fold and have favourable biophysical properties. The crystal structures of two designed proteins exhibit atomistic agreement with Chroma samples (a backbone root-mean-square deviation of around 1.0 Å). With this unified approach to protein design, we hope to accelerate the programming of protein matter to benefit human health, materials science and synthetic biology.

N6-methyladenosine in poly(A) tails stabilize VSG transcripts.

RNA modifications are important regulators of gene expression1. In Trypanosoma brucei, transcription is polycistronic and thus most regulation happens post-transcriptionally2. N6-methyladenosine (m6A) has been detected in this parasite, but its function remains unknown3. Here we found that m6A is enriched in 342 transcripts using RNA immunoprecipitation, with an enrichment in transcripts encoding variant surface glycoproteins (VSGs). Approximately 50% of the m6A is located in the poly(A) tail of the actively expressed VSG transcripts. m6A residues are removed from the VSG poly(A) tail before deadenylation and mRNA degradation. Computational analysis revealed an association between m6A in the poly(A) tail and a 16-mer motif in the 3' untranslated region of VSG genes. Using genetic tools, we show that the 16-mer motif acts as a cis-acting motif that is required for inclusion of m6A in the poly(A) tail. Removal of this motif from the 3' untranslated region of VSG genes results in poly(A) tails lacking m6A, rapid deadenylation and mRNA degradation. To our knowledge, this is the first identification of an RNA modification in the poly(A) tail of any eukaryote, uncovering a post-transcriptional mechanism of gene regulation.

Structural and electronic transformations of GeSe2 glass under high pressures studied by X-ray absorption spectroscopy.

Pressure-induced transformations in an archetypal chalcogenide glass (GeSe2) have been investigated up to 157 GPa by X-ray absorption spectroscopy (XAS) and molecular dynamics (MD) simulations. Ge and Se K-edge XAS data allowed simultaneous tracking of the correlated local structural and electronic changes at both Ge and Se sites. Thanks to the simultaneous analysis of extended X-ray absorption fine structure (EXAFS) signals of both edges, reliable quantitative information about the evolution of the first neighbor Ge-Se distribution could be obtained. It also allowed to account for contributions of the Ge-Ge and Se-Se bond distributions (chemical disorder). The low-density to high-density amorphous-amorphous transformation was found to occur within 10 to 30 GPa pressure range, but the conversion from tetrahedral to octahedral coordination of the Ge sites is completed above [Formula: see text] 80 GPa. No convincing evidence of another high-density amorphous state with coordination number larger than six was found within the investigated pressure range. The number of short Ge-Ge and Se-Se "wrong" bonds was found to increase upon pressurization. Experimental XAS results are confirmed by MD simulations, indicating the increase of chemical disorder under high pressure.

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.

The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/.

Cryogels Composites: Recent Improvement in Bone Tissue Engineering.

Autogenous bone grafts have long been considered the optimal choice for bone reconstruction due to their excellent biocompatibility and osteogenic properties. However, their limited availability and associated donor site morbidity have led to exploration of alternative bone substitutes. Cryogels, with their interconnected porosity, shape recovery, and enhanced mass transport capabilities, have emerged as a promising polymer-based solution. By incorporating bioactive glasses and nanofillers, cryogel composites offer bioactivity, cost-efficiency, and easy cell integration. This approach not only enhances bone regeneration but also underscores the broader role of nanotechnology in regenerative medicine. This mini-review discusses the advancement of organic-inorganic composites, focusing on biopolymeric cryogels and inorganic elements for reinforcement. We highlight how cryogels can be integrated into minimally invasive procedures, reducing patient distress and complications, and advanced 3D-printing techniques that enable further customization of these materials to mimic bone tissue architecture, offering potential for patient-specific treatments.

Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.

A knowledge-based grouping of genes into pathways or functional units is essential for describing and understanding cellular complexity. However, it is not always clear a priori how and at what level of specificity functionally interconnected genes should be partitioned into pathways, for a given application. Here, we assess and compare nine existing and two conceptually novel functional classification systems, with respect to their discovery power and generality in gene set enrichment testing. We base our assessment on a collection of nearly 2000 functional genomics datasets provided by users of the STRING database. With these real-life and diverse queries, we assess which systems typically provide the most specific and complete enrichment results. We find many structural and performance differences between classification systems. Overall, the well-established, hierarchically organized pathway annotation systems yield the best enrichment performance, despite covering substantial parts of the human genome in general terms only. On the other hand, the more recent unsupervised annotation systems perform strongest in understudied areas and organisms, and in detecting more specific pathways, albeit with less informative labels.

Magnetoelastic Coupling Evidence by Anisotropic Crossed Thermal Expansion in Magnetocaloric RSrCoFeO6 (R = Sm, Eu) Double Perovskites.

Double perovskite oxides, characterized by their tunable magnetic properties and robust interconnection between the lattice and magnetic degrees of freedom, present an enticing foundation for advanced magnetic refrigeration materials. Herein, we delve into the influence of rare-earth elements on RSrCoFeO6 (R = Sm, Eu) disordered double perovskites by examining their structural, electronic, magnetic, and magnetocaloric properties. Temperature-dependent synchrotron X-ray diffraction analysis confirmed the stability of the orthorhombic phase (Pnma) across a wide temperature range. X-ray photoemission spectroscopy revealed that both Sm and Eu are in the 3+ state, whereas multiple states for Co2+/3+ and Fe3+/4+ are identified. The magnetic investigation and magnetocaloric effect (MCE) analysis brought to light the presence of a long-range antiferromagnetic (AFM) order with a second-order phase transition (SOPT) in both samples. The maximum magnetic entropy change ΔSMmax was approximately 0.9 J/kg K for both samples at applied field 0-7 T, manifesting prominently above Neel temperatures TN ≈ 93 K (Sm) and 84 K (Eu). Nevertheless, different relative cooling powers (RCP) of 112.6 J/kg (Sm) and 95.5 J/kg (Eu) were observed. A detailed analysis of the temperature-dependent lattice parameters shed light on a distinct magnetocaloric effect across the magnetic transition temperature, unveiling an anisotropic thermal expansion [αV = 1.41 × 10-5 K-1 (Sm) and αV = 1.54 × 10-5 K-1 (Eu)] wherein the thermal expansion axial ratio αbSm/αbEu = 0.61 became lower with increasing temperature, which suggests that the Eu sample experiences a greater thermal expansion in the b-axis direction. At the atomic bonding level, the evidence for magnetoelastic coupling around the magnetic transition temperatures TN was found through the anomalies along the average Co/Fe-O bond distance, formal valence, octahedral distortion, as well as an anisotropic lattice expansion.

Unveiling the Structural Properties, Optical Behavior, and Thermoelectric Performance of 2D CsSn2Br5 Halide Obtained by Mechanochemistry.

Metal halide perovskites with a two-dimensional structure are utilized in photovoltaics and optoelectronics. High-crystallinity CsSn2Br5 specimens have been synthesized via ball milling. Differential scanning calorimetry curves show melting at 553 K (endothermic) and recrystallization at 516 K (exothermic). Structural analysis using synchrotron X-ray diffraction data, collected from 100 to 373 K, allows for the determination of Debye model parameters. This analysis provides insights into the relative Cs-Br and Sn-Br chemical bonds within the tetragonal structure (space group: I4/mcm), which remains stable throughout the temperature range studied. Combined with neutron data, X-N techniques permit the identification of the Sn2+ lone electron pair (5s2) in the two-dimensional framework, occupying empty space opposite to the four Sn-Br bonds of the pyramidal [SnBr4] coordination polyhedra. Additionally, diffuse reflectance UV-vis spectroscopy unveils an indirect optical gap of approximately ∼3.3 eV, aligning with the calculated value from the B3LYP-DFT method (∼3.2 eV). The material exhibits a positive Seebeck coefficient as high as 6.5 × 104 µV K-1 at 350 K, which evolves down to negative values of -3.0 × 103 µV K-1 at 550 K, surpassing values reported for other halide perovskites. Notably, the thermal conductivity remains exceptionally low, between 0.32 and 0.25 W m-1 K-1.

An acute bout of resistance exercise increases BDNF in hippocampus and restores the long-term memory of insulin-resistant rats.

A sedentary lifestyle, inadequate diet, and obesity are substantial risk factors for Type 2 diabetes mellitus (T2DM) development. A major picture of T2DM is insulin resistance (IR), which causes many impairments in brain physiology, such as increased proinflammatory state and decreased brain-derived neurotrophic factor (BDNF) concentration, hence reducing cognitive function. Physical exercise is a non-pharmacological tool for managing T2DM/IR and its complications. Thus, this study investigated the effects of IR induction and the acute effects of resistance exercise (RE) on memory, neurotrophic, and inflammatory responses in the hippocampus and prefrontal cortex of insulin-resistant rats. IR was induced by a high-fat diet and fructose-rich beverage. Insulin-resistant rats performed acute resistance exercise (IR.RE; vertical ladder climb at 50-100% of the maximum load) or rest (IR.REST; 20 min). Cognitive parameters were assessed by novel object recognition (NOR) tasks, and biochemical analyses were performed to assess BDNF concentrations and inflammatory profile in the hippocampus and prefrontal cortex. Insulin-resistant rats had 20% worse long-term memory (LTM) (p < 0.01) and lower BDNF concentration in the hippocampus (-14.6%; p < 0.05) when compared to non-insulin-resistant rats (CON). An acute bout of RE restored LTM (-9.7% pre vs. post; p > 0.05) and increased BDNF concentration in the hippocampus (9.1%; p < 0.05) of insulin-resistant rats compared to REST. Thus, an acute bout of RE can attenuate the adverse effects of IR on memory and neurotrophic factors in rats, representing a therapeutic tool to alleviate the IR impact on the brain.

Engineering natural based nanocomposite inks via interface interaction for extrusion 3D printing.

Nanocomposites and low-viscous materials lack translation in additive manufacturing technologies due to deficiency in rheological requirements and heterogeneity of their preparation. This work proposes the chemical crosslinking between composing phases as a universal approach for mitigating such issues. The model system is composed of amine-functionalized bioactive glass nanoparticles (BGNP) and light-responsive methacrylated bovine serum albumin (BSAMA) which further allows post-print photocrosslinking. The interfacial interaction was conducted by 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide crosslinking agent and N-Hydroxysuccinimide between BGNP-grafted amines and BSAMA's carboxylic groups. Different chemical crosslinking amounts and percentages of BGNP in the nanocomposites were tested. The improved interface interactions increased the elastic and viscous modulus of all formulations. More pronounced increases were found with the highest crosslinking agent amounts (4 % w/v) and BGNP concentrations (10 % w/w). This formulation also displayed the highest Young's modulus of the double-crosslinked construct. All composite formulations could effectively immobilize the BGNP and turn an extremely low viscous material into an appropriate inks for 3d printing technologies, attesting for the systems' tunability. Thus, we describe a versatile methodology which can successfully render tunable and light-responsive nanocomposite inks with homogeneously distributed bioactive fillers. This system can further reproducibly recapitulate phases of other natures, broadening applicability.

Exposure to nicotine and withdrawal in Wistar rats: an electrophysiological study.

INTRODUCTION: Throughout the world, smoking is one of the principal causes of preventable death. Nicotine, the primary active component of tabacco, acts as a psychostimulant and modulates the electrical activity of a number of the areas of the brain involved in addiction. Abstinence from nicotine will also impact the functional state of the brain, which is reflected in symptoms of craving and susceptibility to relapse. In addition, given the increase in the sympathetic tone of the heart and pulse rate promoted by nicotine, its consumption can contribute to tachyarrhythmia. METHODS: The present study investigated the electroencephalographic (EEG) and electrocardiographic (ECG) patterns of Wistar rats submitted to acute or chronic exposure to nicotine, followed by withdrawal for 24 or 48 hours, and the re-administration (or not) of nicotine, to simulate episodes of relapse. RESULTS: The EEG data revealed an increase in all types of brainwaves, with emphasis on high-frequency (alpha, beta, and gamma) brain oscillations following both acute and chronic exposure to nicotine (14 days), whereas in withdrawal, there was a predominancy of delta waves. When exposure to nicotine was reinstated after withdrawal, the observed EEG profile was similar to that found in chronic exposure. The electrocardiogram reads showed that both acute and chronic exposure to nicotine caused abnormalities in the atrioventricular conduction and that, while these changes improve with substance withdrawal, relapse can worsen these parameters. CONCLUSIONS: The results of this study indicate that high-frequency brainwaves are correlated with nicotine dependence, while slow brain oscillations are consistent with drug craving, and episodes of nicotine relapse can reproduce brain activity patterns linked to dependence. Finally, exposure to nicotine predisposes the individual to heart rhythm abnormalities, which are attenuated by withdrawal, but may nevertheless be restored rapidly with re-exposure to the substance. IMPLICATIONS: This study demonstrated that nicotine increases high-frequency brain oscillations, which is associated with addiction, whereas withdrawal elevates the delta wave power, suggesting craving. Re-exposure to nicotine following withdrawal restores rapidly the EEG profile of chronic dependence. In addition, nicotine has deleterious impacts on cardiac activity, which are linked to fatal arrhythmias. This implies that stopping smoking is beneficial for the amelioration of the alterations in heart rhythm caused by nicotine addiction. This study elucidates the functional states of the brain and heart during both sporadic and chronic nicotine use, and the electrophysiological explanation for substance dependence and drug relapse after craving episodes.

Electric-field-tuned topological phase transition in ultrathin Na3Bi.

The electric-field-induced quantum phase transition from topological to conventional insulator has been proposed as the basis of a topological field effect transistor1-4. In this scheme, 'on' is the ballistic flow of charge and spin along dissipationless edges of a two-dimensional quantum spin Hall insulator5-9, and 'off' is produced by applying an electric field that converts the exotic insulator to a conventional insulator with no conductive channels. Such a topological transistor is promising for low-energy logic circuits4, which would necessitate electric-field-switched materials with conventional and topological bandgaps much greater than the thermal energy at room temperature, substantially greater than proposed so far6-8. Topological Dirac semimetals are promising systems in which to look for topological field-effect switching, as they lie at the boundary between conventional and topological phases3,10-16. Here we use scanning tunnelling microscopy and spectroscopy and angle-resolved photoelectron spectroscopy to show that mono- and bilayer films of the topological Dirac semimetal3,17 Na3Bi are two-dimensional topological insulators with bulk bandgaps greater than 300 millielectronvolts owing to quantum confinement in the absence of electric field. On application of electric field by doping with potassium or by close approach of the scanning tunnelling microscope tip, the Stark effect completely closes the bandgap and re-opens it as a conventional gap of 90 millielectronvolts. The large bandgaps in both the conventional and quantum spin Hall phases, much greater than the thermal energy at room temperature (25 millielectronvolts), suggest that ultrathin Na3Bi is suitable for room-temperature topological transistor operation.

Modifications to the parasitological technique of Rugai increase the diagnostic sensitivity for strongyloidiasis.

Strongyloidiasis is a neglected tropical disease caused mainly by Strongyloides stercoralis, a nematode that can persist for decades in the human host with a very low parasitic burden and without specific symptoms. Hence, it is difficult to diagnose and control. Larval concentration and culture methods with fecal samples show higher sensitivity for the diagnosis of Strongyloides-infected individuals; however, these techniques are not routinely used, primarily due to the challenges associated with processing a substantial volume of fecal samples. In the current study, we comparatively evaluated the sensitivity and applicability of modifications made to the Rugai parasitological method for the diagnosis of strongyloidiasis in fecal samples of experimentally infected rats and in 68 individuals from an urban community close to Maceió, Brazil. The presence and quantity of parasite larvae in the feces were comparatively evaluated using different parasitological techniques. In the experimental model, we demonstrated that the modified Rugai technique (RMOD) allowed for significantly higher recovery of larvae than the original Rugai technique (RO). Moreover, the sediment was cleaner and easier to evaluate using optical microscopy. Compared to other parasitological techniques, such as agar-plate culture (A-PC) and spontaneous sedimentation (SS), the RMOD technique showed higher sensitivity in the detection of larvae in all infected groups and presented comparatively better performance, especially in rats with a low parasite burden. In the human population, among the 68 stool samples evaluated, Strongyloides larvae were detected in the feces of six individuals with an estimated prevalence of 8.82%. However, the performance of each parasitological method was remarkably different. SS identified Strongyloides larvae in only two individuals and A-PC in three, whereas RMOD was able to identify six infected individuals, resulting in sensitivities of 33.3%, 50%, and 100%, respectively. In conclusion, the modifications introduced to the Rugai technique resulted in improved sensitivity for the detection of Strongyloides spp. infections, especially in stool samples with a low parasite burden, in comparison with other routinely used parasitological techniques.

Functional and morphological evaluation of the trapezius muscle after spinal accessory nerve transfer to brachial plexus nerves.

INTRODUCTION: The main innervation of the trapezius muscle is provided by the spinal accessory nerve. Several studies describe the contributions of cervical plexus roots to the trapezius muscle innervation, either directly or through connections with the spinal accessory nerve. There is no adequate understanding of how the trapezius muscle is affected after using the spinal accessory nerve in nerve transfer procedures with the usual technique, preserving at least 1 branch for the upper trapezius. METHODS: We evaluated 20 patients with sequelae of traumatic brachial plexus injury who underwent surgical procedures for brachial plexus repair or free muscle transfer, which included the spinal accessory nerve transfer technique and were followed for a minimum of 1 year. The three portions trapezius muscle were evaluated by physical examination, magnetic resonance imaging (analysis of fatty degeneration) and electromyography. RESULTS: In all evaluation methods, the middle and lower portions of the trapezius muscle showed more significant morphological and/or functional impairment than the upper portion, in most cases. There was a statistically significant difference in all the complementary exams results, between the affected side (with sacrifice of the nerve) versus the normal side, in the middle and lower portions of the trapezius muscle. CONCLUSIONS: Physical examination alone is not sufficient to determine the residual functionality of the trapezius muscle. Magnetic resonance imaging and electromyography are useful tools to assess both morphological involvement of the trapezius muscle and nerve conduction impairment of the trapezius muscle, respectively. The results suggest that the middle and lower portions of the trapezius muscle are affected by previous SAN transfer and should be considered with caution for further muscle transfer procedures.

Sustainable synthesis of bionanomaterials using non-native plant extracts for maintaining ecological balance: A computational bibliography analysis.

Biological approaches via biomolecular extracts of bacteria, fungi, or plants have recently been introduced as an alternative approach to synthesizing less or nontoxic nanomaterials, compared to conventional physical and chemical approaches. Among these biological methods, plant-mediated approaches (phytosynthesis) are reported to be highly beneficial for large-scale, nontoxic nanomaterial synthesis. However, plant-mediated synthesis of nanomaterials using native plant extract can lead to bioprospecting issues and deforestation challenges. On the other hand, non-native or invasive plants are non-indigenous to a particular geographic location that can grow and spread rapidly, ultimately disrupting the local and endogenous plant communities or ecosystems. Thus, controlling or eradicating these non-native plants before they damage the ecosystem is necessary. Even though mechanical, chemical, and biological approaches are available to control non-native plants, all these methods possess certain limitations, such as environmental toxicity, disturbance in the nutrient cycle, and loss of genetic integrity. Therefore, non-native plants were recently proposed as a novel sustainable source of phytochemicals for preparing nanomaterials via green chemistry, mainly metallic nanoparticles, as an alternative to native, agriculture-based, or medicinal plants. This work aims to cover a literature gap on plant-mediated bionanomaterial synthesis with an overview and bibliography analysis of non-native plants via novel data mining and advanced visualization tools. In addition, the potential of non-native plants as a sustainable, green chemistry-based alternative for bionanomaterial preparation for maintaining ecological balance, the mechanism of formation via phytochemicals, and their possible applications to promote their control and spread were also discussed. The bibliography analysis revealed that only an average of 4 articles have been published in the last 10 years (2013-2023) on non-native/invasive plants for nanomaterial synthesis, which shows the significance of this article.

The role of computed tomography with external rotation and dorsiflexion in decision making for acute isolated non-displaced posterior malleolar fractures Bartonícek and Rammelt type II: a prospective study.

PURPOSE: Our objective was to evaluate the syndesmotic and fracture instability using conventional ankle computed tomography (CT) with stress maneuvers. METHODS: A consecutive sample of 123 individuals with an ankle sprain was assessed for eligibility. In total, 33 patients met the inclusion criteria. All patients underwent a magnetic resonance imaging (MRI) and CT scan with stress maneuvers (CTSM). The patterns of ligament tears f were classified using West Point grades I, IIA, IIB, III. Mann-Whitney test was used to test the differences in the numerical variables between injured and uninjured syndesmoses. The Spearman correlation tested the strength of the association between the tibial joint surface involved in posterior malleolus fracture and syndesmotic instability. RESULTS: In MRI, two patterns of syndesmotic ligament injury predominated. A completely torn anterior inferior tibiofibular (AITFL) and interosseous tibiofibular ligaments (ITFL) and a completely torn AITFL were combined with a partially torn ITFL. In the neutral phase CTSM and during the stress phase the median difference of the narrowest tibiofibular distance between injured and uninjured syndesmoses was 0.2 mm (P = 0.057) and 2.3 mm (P < 0.0001), respectively. There was no association between the percentage of involvement of the posterior tibial joint surface in the posterior malleolar fracture and syndesmotic instability as measured with CTSM. CONCLUSION: The conventional computed tomography with external rotation and dorsiflexion represents a reproducible and accurate diagnostic option for detecting syndesmosis instability and fracture instability in acute isolated non-displaced posterior malleolar fractures Bartonícek and Rammelt type II. LEVEL OF EVIDENCE: Prospective study among consecutive patients (Diagnosis); Level of evidence, 2.

Self-Supporting Hyaluronic Acid-Functionalized G-Quadruplex-Based Perfusable Multicomponent Hydrogels Embedded in Photo-Cross-Linkable Matrices for Bioapplications.

Dynamic G-quadruplex supramolecular hydrogels have aroused great interest in a broad range of bioapplications. However, neither the development of native extracellular matrix (ECM)-derived natural biopolymer-functionalized G-quadruplex hydrogels nor their use to create perfusable self-supporting hydrogels has been explored to date, despite their intrinsic potential as carrier vehicles of therapeutic agents, or even living cells in advanced regenerative therapies, or as platforms to enable the diffusion of nutrients and oxygen to sustain long-term cell survival. Herein, we developed a dynamic co-assembling multicomponent system that integrates guanosine (G), 3-aminophenylboronic acid functionalized hyaluronic acid (HA-PBA), and potassium chloride to bioengineer strong, homogeneous, and transparent HA-functionalized G-quadruplex hydrogels with injectable, thermo-reversible, conductive, and self-healing properties. The supramolecular polymeric hydrogels were developed by hydrogen bonding and π-π stacking interactions between G coupled via dynamic covalent boronate ester bonds to HA-PBA and stabilized by K+ ions, as demonstrated by a combination of experiments and molecular dynamics simulations. The intrinsic instability of the self-assembled G-quadruplex structures was used to bioengineer self-supporting perfusable multicomponent hydrogels with interconnected size and shape-tunable hollow microchannels when embedded in 3D methacrylated gelatin supporting matrices. The microchannel-embedded 3D constructs have shown enhanced cell viability when compared to the bulk hydrogels, holding great promise for being use as artificial vessels for enabling the diffusion of nutrients and oxygen essential for cell survival. The proposed approach opens new avenues on the use of ECM-derived natural biopolymer-functionalized dynamic G-quadruplex hydrogels to design next-generation smart systems for being used in tissue regeneration, drug screening, or organ-on-a-chip.

Mapping competitive pathways to terpenoid biosynthesis in Synechocystis sp. PCC 6803 using an antisense RNA synthetic tool.

BACKGROUND: Synechocystis sp. PCC 6803 utilizes pyruvate and glyceraldehyde 3-phosphate via the methylerythritol 4-phosphate (MEP) pathway for the biosynthesis of terpenoids. Considering the deep connection of the MEP pathway to the central carbon metabolism, and the low carbon partitioning towards terpenoid biosynthesis, significant changes in the metabolic network are required to increase cyanobacterial production of terpenoids. RESULTS: We used the Hfq-MicC antisense RNA regulatory tool, under control of the nickel-inducible PnrsB promoter, to target 12 different genes involved in terpenoid biosynthesis, central carbon metabolism, amino acid biosynthesis and ATP production, and evaluated the changes in the performance of an isoprene-producing cyanobacterial strain. Six candidate targets showed a positive effect on isoprene production: three genes involved in terpenoid biosynthesis (crtE, chlP and thiG), two involved in amino acid biosynthesis (ilvG and ccmA) and one involved in sugar catabolism (gpi). The same strategy was applied to interfere with different parts of the terpenoid biosynthetic pathway in a bisabolene-producing strain. Increased bisabolene production was observed not only when interfering with chlorophyll a biosynthesis, but also with carotenogenesis. CONCLUSIONS: We demonstrated that the Hfq-MicC synthetic tool can be used to evaluate the effects of gene knockdown on heterologous terpenoid production, despite the need for further optimization of the technique. Possible targets for future engineering of Synechocystis aiming at improved terpenoid microbial production were identified.