Rewiring native post-transcriptional global regulators to achieve designer, multi-layered genetic circuits.

As synthetic biology expands, creating "drag-and-drop" regulatory tools that can achieve diverse regulatory outcomes are paramount. Herein, we develop a approach for engineering complex post-transcriptional control by rewiring the Carbon Storage Regulatory (Csr) Network of Escherichia coli. We co-opt native interactions of the Csr Network to establish post-transcriptional logic gates and achieve complex bacterial regulation.

Teaching troubleshooting skills to graduate students.

Troubleshooting is an important part of experimental research, but graduate students rarely receive formal training in this skill. In this article, we describe an initiative called Pipettes and Problem Solving that we developed to teach troubleshooting skills to graduate students at the University of Texas at Austin. An experienced researcher presents details of a hypothetical experiment that has produced unexpected results, and students have to propose new experiments that will help identify the source of the problem.

Transcriptional regulation of living materials via extracellular electron transfer.

Engineered living materials combine the advantages of biological and synthetic systems by leveraging genetic and metabolic programming to control material-wide properties. Here, we demonstrate that extracellular electron transfer (EET), a microbial respiration process, can serve as a tunable bridge between live cell metabolism and synthetic material properties. In this system, EET flux from Shewanella oneidensis to a copper catalyst controls hydrogel cross-linking via two distinct chemistries to form living synthetic polymer networks.

Synthesis of bioengineered heparin chemically and biologically similar to porcine-derived products and convertible to low MW heparin.

Heparins have been invaluable therapeutic anticoagulant polysaccharides for over a century, whether used as unfractionated heparin or as low molecular weight heparin (LMWH) derivatives. However, heparin production by extraction from animal tissues presents multiple challenges, including the risk of adulteration, contamination, prion and viral impurities, limited supply, insecure supply chain, and significant batch-to-batch variability. The use of animal-derived heparin also raises ethical and religious concerns, as well as carries the risk of transmitting zoonotic diseases.

CsrA selectively modulates sRNA-mRNA regulator outcomes.

Post-transcriptional regulation, by small RNAs (sRNAs) as well as the global Carbon Storage Regulator A (CsrA) protein, play critical roles in bacterial metabolic control and stress responses. The CsrA protein affects selective sRNA-mRNA networks, in addition to regulating transcription factors and sigma factors, providing additional avenues of cross talk between other stress-response regulators. Here, we expand the known set of sRNA-CsrA interactions and study their regulatory effects.

CsrA Shows Selective Regulation of sRNA-mRNA Networks.

Post-transcriptional regulation, by small RNAs (sRNAs) as well as the global Carbon Storage Regulator A (CsrA) protein, play critical roles in bacterial metabolic control and stress responses. The CsrA protein affects selective sRNA-mRNA networks, in addition to regulating transcription factors and sigma factors, providing additional avenues of cross talk between other stress-response regulators. Here, we expand the known set of sRNA-CsrA interactions and study their regulatory effects.

RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR.

Ribonucleoproteins (RNPs) are RNA-protein complexes utilized natively in both prokaryotes and eukaryotes to regulate essential processes within the cell. Over the past few years, many of these native systems have been adapted to provide control over custom genetic targets. Engineered RNP-based control systems allow for fine-tune regulation of desired targets, by providing customizable nucleotide-nucleotide interactions.

Production of 1-octanol in Escherichia coli by a high flux thioesterase route.

1-octanol is a valuable molecule in the chemical industry, where it is used as a plasticizer, as a precursor in the production of linear low-density polyethylene (LLDPE), and as a growth inhibitor of tobacco plant suckers. Due to the low availability of eight-carbon acyl chains in natural lipid feedstocks and the selectivity challenges in petrochemical routes to medium-chain fatty alcohols,1-octanol sells for the highest price among the fatty alcohol products. As an alternative, metabolic engineers have pursued sustainable 1-octanol production via engineered microbes.

Metabolic engineering of β-oxidation to leverage thioesterases for production of 2-heptanone, 2-nonanone and 2-undecanone.

Medium-chain length methyl ketones are potential blending fuels due to their cetane numbers and low melting temperatures. Biomanufacturing offers the potential to produce these molecules from renewable resources such as lignocellulosic biomass. In this work, we designed and tested metabolic pathways in Escherichia coli to specifically produce 2-heptanone, 2-nonanone and 2-undecanone.

Novel Cellulose-Halloysite Hemostatic Nanocomposite Fibers with a Dramatic Reduction in Human Plasma Coagulation Time.

High-performance cellulose-halloysite hemostatic nanocomposite fibers (CHNFs) are fabricated using a one-step wet-wet electrospinning process and evaluated for human plasma coagulation by activated partial thromboplastin time. These novel biocompatible CHNFs exhibit 2.4 times faster plasma coagulation time compared with the industry gold standard QuikClot Combat Gauze (QCG).

Highly Active C-Acyl-ACP Thioesterase Variant Isolated by a Synthetic Selection Strategy.

Microbial metabolism is an attractive route for producing medium chain length fatty acids, e.g., octanoic acid, used in the oleochemical industry.

Biodegradable and Bioactive PCL-PGS Core-Shell Fibers for Tissue Engineering.

Poly(glycerol sebacate) (PGS) has increasingly become a desirable biomaterial due to its elastic mechanical properties, biodegradability, and biocompatibility. Here, we report microfibrous core-shell mats of polycaprolactone (PCL)-PGS prepared using wet-wet coaxial electrospinning. The anticoagulant heparin was immobilized onto the surface of these electrospun fiber mats, and they were evaluated for their chemical, mechanical, and biological properties.

Synthesis of Heparin-Immobilized, Magnetically Addressable Cellulose Nanofibers for Biomedical Applications.

Magnetically responsive heparin-immobilized cellulose nanofiber composites were synthesized by wet-wet electrospinning from a nonvolatile, room-temperature ionic liquid (RTIL), 1-methyl-3-methylimidazolium acetate ([EMIM][Ac]), into an aqueous coagulation bath. Superparamagnetic magnetite (FeO) nanoparticles were incorporated into the fibers to enable the manipulation of both dry and wet nanofiber membranes with an external magnetic field. Three synthetic routes were developed to prepare three distinct types of nanocomposite fibers: cellulose-FeO-heparin monofilament fibers, cellulose-FeO-heparin core-shell fibers with heparin covalently immobilized on the fiber surface, and cellulose -FeO core-shell fibers with heparin physically immobilized on the fiber surface.

Nickel-centred proton reduction catalysis in a model of [NiFe] hydrogenase.

Hydrogen production through water splitting is one of the most promising solutions for the storage of renewable energy. [NiFe] hydrogenases are organometallic enzymes containing nickel and iron centres that catalyse hydrogen evolution with performances that rival those of platinum. These enzymes provide inspiration for the design of new molecular catalysts that do not require precious metals.

Surface modification of a polyethylene film for anticoagulant and anti-microbial catheter.

A functional anticoagulant and anti-bacterial coating for polyethylene (PE) films is described. The stepwise preparation of this nanocomposite surface coating involves O plasma etching of PE film, carbodiimide coupling of cysteamine to the etched PE film, binding of Ag to sulfhydryl groups of cysteamine, and assembly of heparin capped AgNPs on the PE film. The nanocomposite film and its components were characterized by H-nuclear magnetic resonance spectroscopy, attenuated total reflectance-Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and field emission-scanning electron microscopy.

Can natural fibers be a silver bullet? Antibacterial cellulose fibers through the covalent bonding of silver nanoparticles to electrospun fibers.

Natural cotton was dissolved in a room-temperature ionic liquid 1-ethyl-3-methyl acetate and wet-jet electrospun to obtain nanoscale cotton fibers with a substantially reduced diameter-and therefore an increased surface area-relative to natural cotton fibers. The resulting nano-cotton fibers were esterified with trityl-3-mercaptopropionic acid, which after selective de-tritylation afforded nano-cotton fibers containing reactive thiol functionality. Silver nanoparticles that were covalently attached to these sulfhydryl groups were assembled next.

Novel B(Ar')2(Ar'') hetero-tri(aryl)boranes: a systematic study of Lewis acidity.

A series of homo- and hetero-tri(aryl)boranes incorporating pentafluorophenyl, 3,5-bis(trifluoromethyl)phenyl, and pentachlorophenyl groups, four of which are novel species, have been studied as the acidic component of frustrated Lewis pairs for the heterolytic cleavage of H2. Under mild conditions eight of these will cleave H2; the rate of cleavage depending on both the electrophilicity of the borane and the steric bulk around the boron atom. Electrochemical studies allow comparisons of the electrophilicity with spectroscopic measurements of Lewis acidity for different series of boranes.

Facile Protocol for Water-Tolerant "Frustrated Lewis Pair"-Catalyzed Hydrogenation.

Despite rapid advances in the field of metal-free, "frustrated Lewis pair" (FLP)-catalyzed hydrogenation, the need for strictly anhydrous reaction conditions has hampered wide-scale uptake of this methodology. Herein, we report that, despite the generally perceived moisture sensitivity of FLPs, 1,4-dioxane solutions of B(CF) actually show appreciable moisture tolerance and can catalyze hydrogenation of a range of weakly basic substrates without the need for rigorously inert conditions. In particular, reactions can be performed directly in commercially available nonanhydrous solvents without subsequent drying or use of internal desiccants.

Spectroscopic Characterization of the Bridging Amine in the Active Site of [FeFe] Hydrogenase Using Isotopologues of the H-Cluster.

The active site of [FeFe] hydrogenase contains a catalytic binuclear iron subsite coordinated by CN(-) and CO ligands as well as a unique azadithiolate (adt(2-)) bridging ligand. It has been established that this binuclear cofactor is synthesized and assembled by three maturation proteins HydE, -F, and -G. By means of in vitro maturation in the presence of (15)N- and (13)C-labeled tyrosine it has been shown that the CN(-) and CO ligands originate from tyrosine.

Artificially maturated [FeFe] hydrogenase from Chlamydomonas reinhardtii: a HYSCORE and ENDOR study of a non-natural H-cluster.

Hydrogenases are enzymes that catalyze the oxidation of H2 as well as the reduction of protons to form H2. The active site of [FeFe] hydrogenase is referred to as the "H-cluster" and consists of a "classical" [4Fe-4S] cluster connected via a bridging cysteine thiol group to a unique [2Fe]H sub-cluster, containing CN(-) and CO ligands as well as a bidentate azadithiolate ligand. It has been recently shown that the biomimetic [Fe2(adt)(CO)4(CN)2](2-) (adt(2-) = azadithiolate) complex resembling the diiron sub-cluster can be inserted in vitro into the apo-protein of [FeFe] hydrogenase, which contains only the [4Fe-4S] part of the H-cluster, resulting in a fully active enzyme.

Electronic control of the protonation rates of Fe-Fe bonds.

Protonation at metal-metal bonds is of fundamental interest in the context of the function of the active sites of hydrogenases and nitrogenases. In diiron dithiolate complexes bearing carbonyl and electron-donating ligands, the metal-metal bond is the highest occupied molecular orbital (HOMO) with a "bent" geometry. Here we show that the experimentally measured rates of protonation (kH) of this bond and the energy of the HOMO as measured by the oxidation potential of the complexes (E1/2(ox)) correlate in a linear free energy relationship: ln kH = ((F(c - βE1/2(ox)))/(RT)), where c is a constant and β is the dimensionless Brønsted coefficient.

Spontaneous activation of [FeFe]-hydrogenases by an inorganic [2Fe] active site mimic.

Hydrogenases catalyze the formation of hydrogen. The cofactor ('H-cluster') of [FeFe]-hydrogenases consists of a [4Fe-4S] cluster bridged to a unique [2Fe] subcluster whose biosynthesis in vivo requires hydrogenase-specific maturases. Here we show that a chemical mimic of the [2Fe] subcluster can reconstitute apo-hydrogenase to full activity, independent of helper proteins.

Functionalization of nitrogen-doped carbon nanotubes with gallium to form Ga-CN(x)-multi-wall carbon nanotube hybrid materials.

In an effort to combine group III-V semiconductors with carbon nanotubes, a simple solution-based technique for gallium functionalization of nitrogen-doped multi-wall carbon nanotubes has been developed. With an aqueous solution of a gallium salt (GaI(3)), it was possible to form covalent bonds between the Ga(3+) ion and the nitrogen atoms of the doped carbon nanotubes to form a gallium nitride-carbon nanotube hybrid at room temperature. This functionalization was evaluated by x-ray photoelectron spectroscopy, energy dispersive x-ray spectroscopy, Raman spectroscopy, scanning electron microscopy and transmission electron microscopy.

High-sensitivity bolometers from self-oriented single-walled carbon nanotube composites.

In this work, films of horizontally aligned single-walled carbon nanotubes were thermally and electrically characterized in order to determine the bolometric performance. An average thermal time constant of τ = 420 μs along with a temperature coefficient of resistance of TCR = -2.94% K(-1) were obtained.