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Bioengineering of air-filled protein nanoparticles by genetic and chemical functionalization.(Journal of nanobiotechnology, Springer Science and Business Media LLC, 2023-03-25) [Article]Background: Various bacteria and archaea, including halophilic archaeon Halobacterium sp. NRC-1 produce gas vesicle nanoparticles (GVNPs), a unique class of stable, air-filled intracellular proteinaceous nanostructures. GVNPs are an attractive tool for biotechnological applications due to their readily production, purification, and unique physical properties. GVNPs are spindle- or cylinder-shaped, typically with a length of 100 nm to 1.5 μm and a width of 30–250 nm. Multiple monomeric subunits of GvpA and GvpC proteins form the GVNP shell, and several additional proteins are required as minor structural or assembly proteins. The haloarchaeal genetic system has been successfully used to produce and bioengineer GVNPs by fusing several foreign proteins with GvpC and has shown various applications, such as biocatalysis, diagnostics, bioimaging, drug delivery, and vaccine development. Results: We demonstrated that native GvpC can be removed in a low salt buffer during the GVNP purification, leaving the GvpA-based GVNP's shell intact and stable under physiological conditions. Here, we report a genetic engineering and chemical modification approach for functionalizing the major GVNP protein, GvpA. This novel approach is based on combinatorial cysteine mutagenesis within GvpA and genetic expansion of the N-terminal and C-terminal regions. Consequently, we generated GvpA single, double, and triple cysteine variant libraries and investigated the impact of mutations on the structure and physical shape of the GVNPs formed. We used a thiol–maleimide chemistry strategy to introduce the biotechnological relevant activity by maleimide-activated streptavidin–biotin and maleimide-activated SpyTag003-SpyCatcher003 mediated functionalization of GVNPs. Conclusion: The merger of these genetic and chemical functionalization approaches significantly extends these novel protein nanomaterials' bioengineering and functionalization potential to assemble catalytically active proteins, biomaterials, and vaccines onto one nanoparticle in a modular fashion.
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Efficient in planta production of amidated antimicrobial peptides that are active against drug-resistant ESKAPE pathogens(Nature Communications, Springer Science and Business Media LLC, 2023-03-16) [Article]Antimicrobial peptides (AMPs) are promising next-generation antibiotics that can be used to combat drug-resistant pathogens. However, the high cost involved in AMP synthesis and their short plasma half-life render their clinical translation a challenge. To address these shortcomings, we report efficient production of bioactive amidated AMPs by transient expression of glycine-extended AMPs in Nicotiana benthamiana line expressing the mammalian enzyme peptidylglycine α-amidating mono-oxygenase (PAM). Cationic AMPs accumulate to substantial levels in PAM transgenic plants compare to nontransgenic N. benthamiana. Moreover, AMPs purified from plants exhibit robust killing activity against six highly virulent and antibiotic resistant ESKAPE pathogens, prevent their biofilm formation, analogous to their synthetic counterparts and synergize with antibiotics. We also perform a base case techno-economic analysis of our platform, demonstrating the potential economic advantages and scalability for industrial use. Taken together, our experimental data and techno-economic analysis demonstrate the potential use of plant chassis for large-scale production of clinical-grade AMPs.
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The Microbial Growth Potential of Antiscalants used in Seawater Desalination(Water Research, Elsevier BV, 2023-02-25) [Article]20 years since the first report on the biofouling potential of chemicals used for scale control, still, antiscalants with high bacterial growth potential are used in practice. Evaluating the bacterial growth potential of commercially available antiscalants is therefore essential for a rational selection of these chemicals. Previous antiscalant growth potential tests were conducted in drinking water or seawater inoculated with model bacterial species which do not represent natural bacterial communities. To reflect better on the conditions of desalination systems, we investigated the bacterial growth potential of eight different antiscalants in natural seawater and an autochthonous bacterial population as inoculum. The antiscalants differed strongly in their bacterial growth potential varying from ≤ 1 to 6 μg easily biodegradable C equivalents/mg antiscalant. The six phosphonate-based antiscalants investigated showed a broad range of growth potential, which depended on their chemical composition, whilst the biopolymer and the synthetic carboxylated polymers-based antiscalants showed limited or no significant bacterial growth. Moreover, nuclear magnetic resonance (NMR) scans enabled antiscalant fingerprinting, identifying components and contaminants, providing a rapid and sensitive characterization, and opening opportunities for rational selection of antiscalants for biofouling control.
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Enhanced Photoresponsivity UV-C Photodetectors Using a p–n Junction Based on Ultra-Wide-Band Gap Sn-Doped β-Ga2O3 Microflake/MnO Quantum Dots(ACS Applied Materials & Interfaces, American Chemical Society (ACS), 2023-02-21) [Article]Solar-blind self-powered UV-C photodetectors suffer from low performance, while heterostructure-based devices require complex fabrication and lack p-type wide band gap semiconductors (WBGSs) operating in the UV-C region (<290 nm). In this work, we mitigate the aforementioned issues by demonstrating a facile fabrication process for a high-responsivity solar-blind self-powered UV-C photodetector based on a p–n WBGS heterojunction structure, operating under ambient conditions. Here, heterojunction structures based on p-type and n-type ultra-wide band gap WBGSs (i.e. both are characterized by energy gap ≥4.5 eV) are demonstrated for the first time; mainly p-type solution-processed manganese oxide quantum dots (MnO QDs) and n-type Sn-doped β-Ga2O3 microflakes. Highly crystalline p-type MnO QDs are synthesized using cost-effective and facile pulsed femtosecond laser ablation in ethanol (FLAL), while the n-type Ga2O3 microflakes are prepared by exfoliation. The solution-processed QDs are uniformly dropcasted on the exfoliated Sn-doped β-Ga2O3 microflakes to fabricate a p–n heterojunction photodetector, resulting in excellent solar-blind UV-C photoresponse characteristics (with a cutoff at ∼265 nm) being demonstrated. Further analyses using XPS demonstrate the good band alignment between p-type MnO QDs and n-type β-Ga2O3 microflakes with a type-II heterojunction. Superior photoresponsivity (922 A/W) is obtained under bias, while the self-powered responsivity is ∼86.9 mA/W. The fabrication strategy adopted in this study will provide a cost-effective means for the development of flexible and highly efficient UV-C devices suitable for energy-saving large-scale fixable applications.
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Maximizing Active Fe Species in ZSM-5 Zeolite Using Organic-Template-Free Synthesis for Efficient Selective Methane Oxidation(Journal of the American Chemical Society, American Chemical Society (ACS), 2023-02-14) [Article]The selective oxidation of CH4 in the aqueous phase to produce valuable chemicals has attracted considerable attention due to its mild reaction conditions and simple process. As the most widely studied catalyst for this reaction, Fe-ZSM-5 demonstrates high intrinsic activity and selectivity; however, Fe-ZSM-5 prepared using conventional methods has a limited number of active Fe sites, resulting in low CH4 conversion per unit mass of the catalyst. This study reports a facile organic-template-free synthesis strategy that enables the incorporation of more Fe into the zeolite framework with a higher dispersion degree compared to conventional synthesis methods. Because framework Fe incorporated in this way is more readily transformed into isolated extra-framework Fe species under thermal treatment, the overall effect is that Fe-ZSM-5 prepared using this method (Fe-HZ5-TF) has 3 times as many catalytically active sites as conventional Fe-ZSM-5. When used for the selective oxidation of CH4 with 0.5 M H2O2 at 75 °C, Fe-HZ5-TF produced a record-high C1 oxygenate yield of 109.4 mmol gcat-1 h-1 (a HCOOH selectivity of 91.1%), surpassing other catalysts reported to date. Spectroscopic characterization and density functional theory calculations revealed that the active sites in Fe-HZ5-TF are mononuclear Fe species in the form of [(H2O)3Fe(IV)═O]2+ bound to Al pairs in the zeolite framework. This differs from conventional Fe-ZSM-5, where binuclear Fe acts as the active site. Analysis of the catalyst and product evolution during the reaction suggests a radical-driven pathway to explain CH4 activation at the mononuclear Fe site and subsequent conversion to C1 oxygenates.
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Highly Selective Photoelectroreduction of Carbon Dioxide to Ethanol over Graphene/Silicon Carbide Composites.(Angewandte Chemie (International ed. in English), Wiley, 2023-02-14) [Article]Using sunlight to produce valuable chemicals and fuels from carbon dioxide (CO2), i.e., artificial photosynthesis (AP) is a promising strategy to achieve solar energy storage and a negative carbon cycle. However, selective synthesis of C2 compounds with a high CO2 conversion rate remains challenging for current AP technologies. We performed CO2 photoelectroreduction over a graphene/silicon carbide (SiC) catalyst under simulated solar irradiation with ethanol (C2H5OH) selectivity of > 99% and a CO2 conversion rate of up to 17.1 mmol∙gcat-1·h-1 with sustained performance. Experimental and theoretical investigations indicated an optimal interfacial layer to facilitate the transfer of photogenerated electrons from the SiC substrate to the few-layer graphene overlayer, which also favored an efficient CO2 to C2H5OH conversion pathway.
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One-year outdoor operation of monolithic perovskite/silicon tandem solar cells(Cell Reports Physical Science, Elsevier BV, 2023-02-06) [Article]Perovskite/silicon tandem solar cells have gained significant attention as a viable commercial solution for ultra-high-efficiency photovoltaics. Ongoing research efforts focus on improving device performance, stability, and upscaling. Yet, paradoxically, their outdoor behavior remains largely unexplored. Here, we describe their performance over a complete calendar year outdoors in the area of the Red Sea coast of Saudi Arabia, which represents a hot and humid environment. After 1 year, our test device retains 80% of its initial power conversion efficiency. Further, we find three critical factors affecting current matching: the module temperature; deviations of the local, actual solar spectrum from the AM1.5G standard, which dictates optical design requirements of the subcells; and module soiling due to a spectrally non-uniform transmission of light through the accumulated dust. Overall, our results underline the promise of perovskite/silicon tandem solar cells as a future high-performance technology, yet device tailoring toward targeted deployment may be desired to achieve maximum energy yields.
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Elucidation of the alternating copolymerization mechanism of epoxides or aziridines with cyclic anhydrides in the presence of halide salts(Angewandte Chemie, Wiley, 2023-02-03) [Article]Organic halide salts in combination with metal or Lewis acids are the most common and essential catalysts in ring-opening copolymerizations (ROCOP). However, the role of organic halide salts was neglected. Here, we have uncovered the complex behavior of organic halide in ROCOP of epoxides or aziridines with cyclic anhydrides. Coordination of the chain-end cations, electron-withdrawing effect, leaving ability of halide atoms, chain-end basicity/nucleophilicity, and terminal steric hindrance cause three types of side reactions: single-site transesterification, substitution, and elimination. Understanding the complex functions of organic halide salts in ROCOP led us to develop highly active and selective aminocyclopropenium chlorides as catalysts/initiators. Adjustable H-bonding interactions of aminocyclopropenium with propagating anions and epoxides create chain-end coordination processes that generate highly reactive carboxylate and highly selective alkoxide chain ends.
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Improving classification of correct and incorrect protein-protein docking models by augmenting the training set(Bioinformatics Advances, Oxford University Press (OUP), 2023-02-02) [Article]Motivation: Protein-protein interactions drive many relevant biological events, such as infection, replication, and recognition. To control or engineer such events, we need to access the molecular details of the interaction provided by experimental 3D structures. However, such experiments take time and are expensive; moreover, the current technology cannot keep up with the high discovery rate of new interactions. Computational modeling, like protein-protein docking, can help to fill this gap by generating docking poses. Protein-protein docking generally consists of two parts, sampling and scoring. The sampling is an exhaustive search of the tridimensional space. The caveat of the sampling is that it generates a large number of incorrect poses, producing a highly unbalanced dataset. This limits the utility of the data to train machine learning classifiers. Results: Using weak supervision, we developed a data augmentation method that we named hAIkal. Using hAIkal, we increased the labeled training data to train several algorithms. We trained and obtained different classifiers; the best classifier has 81% accuracy and 0.51 MCC on the test set, surpassing the state-of-the-art scoring functions.
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Riemannian Geometry for Scientific Visualization(ACM, 2023-01-31) [Conference Paper]This tutorial introduces the most important basics of Riemannian geometry and related concepts with a specific focus on applications in scientific visualization. The main concept in Riemannian geometry is the presence of a Riemannian metric on a differentiable manifold, comprising a second-order tensor field that defines an inner product in each tangent space that varies smoothly from point to point. Technically, the metric is what allows defining and computing distances and angles in a coordinate-independent manner. However, even more importantly, it in a sense is really the major structure (on top of topological considerations) that defines the space where scientific data, such as scalar, vector, and tensor fields live.
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Metabolic biomarkers in cancer(Elsevier, 2023-01-27) [Book Chapter]Over the course of years healthcare systems have utilized various “-omics” approaches to prognose, diagnose, and evaluate the treatment efficacy of cancer diseases. Metabolomics is one of the latest prominent additions to the -omics approaches, characterized by its versatile methodology. Owing to constant improvements in the field, metabolomics aims to provide a faster and a more accurate diagnosis, as well as personalized and optimal strategies of treatment. In recent years, a growing number of studies have utilized metabolomics approach to find new disease-related biomarkers of cancer diseases. Here we present the summary of recent advances in biomarker discovery for various types of cancers such as leukemia, ovarian, lung, breast, and liver cancers as well as cancer-related cachexia.
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Evaluation of next generation of high-order compressible fluid dynamic solvers on the cloud computing for complex industrial flows(Array, Elsevier BV, 2022-12-09) [Article]Industrially relevant computational fluid dynamics simulations frequently require vast computational resources that are only available to governments, wealthy corporations, and wealthy institutions. Thus, in many contexts and realities, high-performance computing grids and cloud resources on demand should be evaluated as viable alternatives to conventional computing clusters. In this work, we present the analysis of the time-to-solution and cost of an entropy stable collocated discontinuous Galerkin (SSDC) compressible computational fluid dynamics framework on Ibex, the on-premises cluster at KAUST, and the Amazon Web Services Elastic Compute Cloud for complex compressible flows. SSDC is a prototype of the next generation computational fluid dynamics frameworks developed following the road map established by the NASA CFD vision 2030. We simulate complex flow problems using high-order accurate fully-discrete entropy stable algorithms. In terms of time-to-solution, the Amazon Elastic Compute Cloud delivers the best performance, with the Graviton2 processors based on the Arm architecture being the fastest. However, the results also indicate that the Ibex nodes based on the AMD Rome architecture deliver good performance, close to those observed for the Amazon Elastic Compute Cloud. Furthermore, we observed that computations performed on the Ibex on-premises cluster are currently less expensive than those performed in the cloud. Our findings could be used to develop guidelines for selecting high-performance computing cloud resources to simulate realistic fluid flow problems.
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Long-term warming increased richness in the asymmetric mutualism between bacteria and microalgae(Authorea, Inc., 2022-11-18) [Preprint]Microalgae, the ocean's primary producers, have proven a large capacity for adaptation, but the implications for species interactions are rarely examined. In a 2-year experiment, we exposed the marine diatom Chaetoceros tenuissmus to warming and examined the responses of its mutualistic bacterial community. The diatom adapted to warming by increasing its temperature optimum and maximum growth rate, whereas the microbiota increased its maximum growth rate without changing its temperature optimum. Rhodobacteria dominated the diatom-associated communities at ambient temperatures and this dominance did not diminish under warming conditions. Extinctions occurred in low-abundance genera, but under warming conditions, new partners appeared. The warming consortium was stable when transplanted to ambient temperatures, indicating a strong association. Duration of exposure to temperature appeared relevant, highlighting the consequences of short-warming events. Our results agree with predictions that long-term evolution of asymmetric mutualistic associations increases strength and diversity, particularly under warming.
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Formic Acid Dehydrogenation via an Active Ruthenium Pincer Catalyst Immobilized on Tetra-Coordinated Aluminum Hydride Species Supported on Fibrous Silica Nanospheres(ACS Catalysis, American Chemical Society (ACS), 2022-11-08) [Article]The demand for harmless and efficient energy sources is remarkably expanding, particularly after the increased awareness of global warming, greenhouse gas emissions, immense fossil fuel consumption, and so forth. Formic acid is considered a potential candidate as an energy carrier for reversible hydrogen storage owing to its decomposition to hydrogen (H2) and carbon dioxide (CO2) in the presence of suitable catalysts. However, selective and efficient decomposition of formic acid using classical heterogeneous catalysis is still challenging because most heterogeneous catalysts which are known are ill defined. Herein, we report a promising heterogeneous approach toward formic acid dehydrogenation using a ruthenium PN3P pincer complex, [Ru–H(CO) (tBuPN3P)] (I), immobilized on a fibrous silica nanosphere, KCC-1, with a strong Lewis acid character [(≡Si–O–Si≡) (≡Si–O−)2Al–H]. The resulting heterogeneous catalyst, [Ru(H) (CO) (tBuPN3P)]@[(≡Si–O–Si≡) (≡Si–O−)2Al–H] (III), has been fully characterized by advanced solid-state characterization techniques. In this compound, Al is tetrahedrally coordinated. It is a single-site catalyst which exhibits good stability toward water, high pressures, and high temperatures as well as good activity in formic acid dehydrogenation. An excellent turnover number of 600,000 and a recyclability of up to 45 cycles are observed.
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A personal, reference quality, fully annotated genome from a Saudi individual(Cold Spring Harbor Laboratory, 2022-11-08) [Preprint]We have used multiple sequencing approaches to sequence the genome of a volunteer from Saudi Arabia. We use the resulting data to generate a de novo assembly of the genome, and use different computational approaches to refine the assembly. As a consequence, we provide a continguous assembly of the complete genome of an individual from Saudi Arabia for all chromosomes except chromosome Y, and label this assembly KSA001. We transferred genome annotations from reference genomes and predicted genome features using methods from Artificial Intelligence to fully annotate KSA001, and we make all primary sequencing data, the assembly, and the genome annotations freely available in public databases using the FAIR data principles.
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Ultra-Efficient Optical Gain and Lasing in MDACl2-Doped Perovskite Thin Films(Chemistry of Materials, American Chemical Society (ACS), 2022-10-25) [Article]Solution-processed perovskite materials have been enticing candidates for optical gain and lasing media because of their low cost, remarkable color purity, facile bandgap tunability, and high absorption cross-section. However, it is difficult, if not impossible, for them to highly amplify light with stable operations because they experience severe non-radiative emission losses due to their high density of surface and bulk defect centers and irregular composition. Here, we report that incorporating 5% of methylenediammonium dichloride (MDACl2) into mixed perovskite systems leads to a drastic reduction in the density of iodide interstitials and surface recombination losses. Subsequently, we record that MDA-treated, cavity-free thin perovskite films exhibit very photostable and ultra-low threshold amplified spontaneous emission of <6 μJ/cm2, approximately 30 times lower than the untreated films. Moreover, an ultra-high optical gain of 1000 cm–1 is successfully achieved, representing the highest reported gain for cavity-free perovskite films. These results are fully supported by extensive high-level density functional theory calculations and ultrafast transient absorption measurements. These findings will serve as a benchmark for the design and fabrication of low-threshold, high amplification perovskite media for lasers and light emission applications.
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Are hierarchical zeolites good catalysts for Methane Dehydroaromatization? A critical analysis(Catalysis Today, Elsevier BV, 2022-10-14) [Article]The socioeconomic dependence on natural gas must be reduced to comply with the stricter carbon emissions requirements. However, avoiding natural gas from the future energy mix is easier said than done. To bridge this gap, lignocellulosic biomass-derived biomethane (aka. “renewable natural gas”) represents an elegant solution to this contemporary problem. Owing to the increased industrial interest in hierarchically structured zeolites for biomethane valorization, through this work, we explore the technical feasibility and challenges associated with methane dehydroaromatization over Mo-loaded on both microporous and hierarchical zeolite ZSM-5. Hierarchical zeolites were prepared using inexpensive and environmentally benign glucose as a secondary organic structure directing agent, leading to two shapes (coffins and hexagonal bars) with comparable physicochemical properties. Although a similar catalytic performance was obtained over (nano-sized) microporous and hexagonal bar-derived zeolites, coffin-shaped zeolite catalysts led to lower activity and slower deactivation. Herein, catalyst deactivation was governed by inter- and intra-particle diffusional properties.
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Three-dimensional hierarchically porous MoS2 foam as high-rate and stable lithium-ion battery anode(Nature Communications, Springer Science and Business Media LLC, 2022-10-12) [Article]Architected materials that actively respond to external stimuli hold tantalizing prospects for applications in energy storage, wearable electronics, and bioengineering. Molybdenum disulfide, an excellent two-dimensional building block, is a promising candidate for lithium-ion battery anode. However, the stacked and brittle two-dimensional layered structure limits its rate capability and electrochemical stability. Here we report the dewetting-induced manufacturing of two-dimensional molybdenum disulfide nanosheets into a three-dimensional foam with a structural hierarchy across seven orders of magnitude. Our molybdenum disulfide foam provides an interpenetrating network for efficient charge transport, rapid ion diffusion, and mechanically resilient and chemically stable support for electrochemical reactions. These features induce a pseudocapacitive energy storage mechanism involving molybdenum redox reactions, confirmed by in-situ X-ray absorption near edge structure. The extraordinary electrochemical performance of molybdenum disulfide foam outperforms most reported molybdenum disulfide-based Lithium-ion battery anodes and state-of-the-art materials. This work opens promising inroads for various applications where special properties arise from hierarchical architecture.
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Sharing of Antimicrobial Resistance Genes between Humans and Food Animals(mSystems, American Society for Microbiology, 2022-10-11) [Article]The prevalence and propagation of antimicrobial resistance (AMR) are serious global public health concerns. The large and the ever-increasing use of antibiotics in livestock is also considered a great concern. The extent of the similarity of acquired antibiotic resistance genes (ARGs) between humans and food animals and the driving factors underlying AMR transfer between them are not clear, although a link between ARGs in both hosts was proposed. To address this question, with swine and chicken as examples of food animals, we analyzed over 1,000 gut metagenomes of humans and food animals from over the world. A relatively high abundance and diversity of ARGs were observed in swine compared with those in humans as a whole. Commensal bacteria, particularly species from Clostridiales, contribute the most ARGs associated with mobile genetic elements (MGEs) and were found in both humans and food animals. Further studies demonstrate that overrepresented MGEs, namely, Tn4451/Tn4453 and TnAs3, are attributed mainly to the sharing between humans and food animals. A member of large resolvase family site-specific recombinases, TnpX, is found in Tn4451/Tn4453 which facilitates the insertions of the transient circular molecule. Although the variance in the transferability of ARGs in humans is higher than that in swine, a higher average transferability was observed in swine than that in humans. In conclusion, the potential antibiotic resistance hot spots with higher transferability in food animals observed in the present study emphasize the importance of surveillance for emerging resistance threats before they spread.
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Cryo-electron structures of the extreme thermostable enzymes Sulfur Oxygenase Reductase and Lumazine Synthase(PLOS ONE, Public Library of Science (PLoS), 2022-10-03) [Article]Thermostable enzymes have the potential for use in a wide variety of biotechnological applications. Cryo-electron microscopy (cryo-EM) enables the imaging of biomolecules in their native aqueous environment. Here, we present high resolution cryo-EM structures of two thermostable enzymes that exhibit multimeric cage-like structures arranged into two different point-group symmetries. First, we determined the structure of the Sulfur Oxygenase Reductase (SOR) enzyme that catalyzes both the oxygenation and disproportionation of elemental sulfur in Archea and is composed of 24 homomeric units each of MW ≃ 35 kDa arranged in octahedral symmetry. The structure of SOR from Acidianus ambivalens (7X9W) was determined at 2.78 Å resolution. The active site of each subunit inside the central nanocompartment is composed of Fe3+ coordinated to two water molecules and the three amino acids (H86, H90 and E114). Second, we determined the structure of Lumazine Synthase (LS) from Aquifex aeolicus (7X7M) at 2.33 Å resolution. LS forms a cage-like structure consisting of 60 identical subunits each of MW ≃ 15 kDa arranged in a strict icosahedral symmetry. The LS subunits are interconnected by ion-pair network. Due to their thermostability and relatively easy purification scheme, both SOR and LS can serve as a model for the catalytic and structural characterization of biocatalysts as well as a benchmark for cryo-EM sample preparation, optimization of the acquisition parameters and 3D reconstruction.
