Saturation Mutagenesis Genome Engineering of Infective ΦX174 Bacteriophage via Unamplified Oligo Pools and Golden Gate Assembly.

Here we present a novel protocol for the construction of saturation single-site-and massive multisite-mutant libraries of a bacteriophage. We segmented the ΦX174 genome into 14 nontoxic and nonreplicative fragments compatible with Golden Gate assembly. We next used nicking mutagenesis with oligonucleotides prepared from unamplified oligo pools with individual segments as templates to prepare near-comprehensive single-site mutagenesis libraries of genes encoding the F capsid protein (421 amino acids scanned) and G spike protein (172 amino acids scanned). Libraries possessed greater than 99% of all 11 860 programmed mutations. Golden Gate cloning was then used to assemble the complete ΦX174 mutant genome and generate libraries of infective viruses. This protocol will enable reverse genetics experiments for studying viral evolution and, with some modifications, can be applied for engineering therapeutically relevant bacteriophages with larger genomes.

Impact of In Vivo Protein Folding Probability on Local Fitness Landscapes.

It is incompletely understood how biophysical properties like protein stability impact molecular evolution and epistasis. Epistasis is defined as specific when a mutation exclusively influences the phenotypic effect of another mutation, often at physically interacting residues. In contrast, nonspecific epistasis results when a mutation is influenced by a large number of nonlocal mutations. As most mutations are pleiotropic, the in vivo folding probability-governed by basal protein stability-is thought to determine activity-enhancing mutational tolerance, implying that nonspecific epistasis is dominant. However, evidence exists for both specific and nonspecific epistasis as the prevalent factor, with limited comprehensive data sets to support either claim. Here, we use deep mutational scanning to probe how in vivo enzyme folding probability impacts local fitness landscapes. We computationally designed two different variants of the amidase AmiE with statistically indistinguishable catalytic efficiencies but lower probabilities of folding in vivo compared with wild-type. Local fitness landscapes show slight alterations among variants, with essentially the same global distribution of fitness effects. However, specific epistasis was predominant for the subset of mutations exhibiting positive sign epistasis. These mutations mapped to spatially distinct locations on AmiE near the initial mutation or proximal to the active site. Intriguingly, the majority of specific epistatic mutations were codon dependent, with different synonymous codons resulting in fitness sign reversals. Together, these results offer a nuanced view of how protein folding probability impacts local fitness landscapes and suggest that transcriptional-translational effects are as important as stability in determining evolutionary outcomes.

User-defined single pot mutagenesis using unamplified oligo pools.

User-defined mutagenic libraries are fundamental for applied protein engineering workflows. Here we show that unamplified oligo pools can be used to prepare site saturation mutagenesis libraries from plasmid DNA with near-complete coverage of desired mutations and few off-target mutations. We find that oligo pools yield higher quality libraries when compared to individually synthesized degenerate oligos. We also show that multiple libraries can be multiplexed into a single oligo pool, making preparation of multiple libraries less expensive and more convenient. We provide software for automatic oligo pool design that can generate mutagenic oligos for saturating or focused libraries.

Data-driven engineering of protein therapeutics.

Protein therapeutics requires a series of properties beyond biochemical activity, including serum stability, low immunogenicity, and manufacturability. Mutations that improve one property often decrease one or more of the other essential requirements for therapeutic efficacy, making the protein engineering challenge difficult. The past decade has seen an explosion of new techniques centered around cheaply reading and writing DNA. This review highlights the recent use of such high throughput technologies for engineering protein therapeutics. Examples include the use of human antibody repertoire sequence data to pair antibody heavy and light chains, comprehensive mutational analysis for engineering antibody specificity, and the use of ancestral and inter-species sequence data to engineer simultaneous improvements in enzyme catalytic efficiency and stability. We conclude with a perspective on further ways to integrate mature protein engineering pipelines with the exponential increases in the volume of sequencing data expected in the forthcoming decade.

Deep sequencing methods for protein engineering and design.

The advent of next-generation sequencing (NGS) has revolutionized protein science, and the development of complementary methods enabling NGS-driven protein engineering have followed. In general, these experiments address the functional consequences of thousands of protein variants in a massively parallel manner using genotype-phenotype linked high-throughput functional screens followed by DNA counting via deep sequencing. We highlight the use of information rich datasets to engineer protein molecular recognition. Examples include the creation of multiple dual-affinity Fabs targeting structurally dissimilar epitopes and engineering of a broad germline-targeted anti-HIV-1 immunogen. Additionally, we highlight the generation of enzyme fitness landscapes for conducting fundamental studies of protein behavior and evolution. We conclude with discussion of technological advances.

Metallic CoS2 nanowire electrodes for high cycling performance supercapacitors.

We report metallic cobalt pyrite (CoS2) nanowires (NWs) prepared directly on current collecting electrodes, e.g., carbon cloth or graphite disc, for high-performance supercapacitors. These CoS2 NWs have a variety of advantages for supercapacitor applications. Because the metallic CoS2 NWs are synthesized directly on the current collector, the good electrical connection enables efficient charge transfer between the active CoS2 materials and the current collector. In addition, the open spaces between the sea urchin structure NWs lead to a large accessible surface area and afford rapid mass transport. Moreover, the robust CoS2 NW structure results in high stability of the active materials during long-term operation. Electrochemical characterization reveals that the CoS2 NWs enable large specific capacitance (828.2 F g(-1) at a scan rate of 0.01 V s(-1)) and excellent long term cycling stability (0-2.5% capacity loss after 4250 cycles at 5 A g(-1)) for pseudocapacitors. This example of metallic CoS2 NWs for supercapacitor applications expands the opportunities for transition metal sulfide-based nanostructures in emerging energy storage applications.

Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing.

Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day.

Earth-Abundant Metal Pyrites (FeS2, CoS2, NiS2, and Their Alloys) for Highly Efficient Hydrogen Evolution and Polysulfide Reduction Electrocatalysis.

Many materials have been explored as potential hydrogen evolution reaction (HER) electrocatalysts to generate clean hydrogen fuel via water electrolysis, but none so far compete with the highly efficient and stable (but cost prohibitive) noble metals. Similarly, noble metals often excel as electrocatalytic counter electrode materials in regenerative liquid-junction photoelectrochemical solar cells, such as quantum dot-sensitized solar cells (QDSSCs) that employ the sulfide/polysulfide redox electrolyte as the hole mediator. Here, we systematically investigate thin films of the earth-abundant pyrite-phase transition metal disulfides (FeS2, CoS2, NiS2, and their alloys) as promising alternative electrocatalysts for both the HER and polysulfide reduction. Their electrocatalytic activity toward the HER is correlated to their composition and morphology. The emergent trends in their performance suggest that cobalt plays an important role in facilitating the HER, with CoS2 exhibiting highest overall performance. Additionally, we demonstrate the high activity of the transition metal pyrites toward polysulfide reduction and highlight the particularly high intrinsic activity of NiS2, which could enable improved QDSSC performance. Furthermore, structural disorder introduced by alloying different transition metal pyrites could increase their areal density of active sites for catalysis, leading to enhanced performance.

High-performance electrocatalysis using metallic cobalt pyrite (CoS2) micro- and nanostructures.

The development of efficient and robust earth-abundant electrocatalysts for the hydrogen evolution reaction (HER) is an ongoing challenge. We report metallic cobalt pyrite (cobalt disulfide, CoS2) as one such high-activity candidate material and demonstrate that its specific morphology--film, microwire, or nanowire, made available through controlled synthesis--plays a crucial role in determining its overall catalytic efficacy. The increase in effective electrode surface area that accompanies CoS2 micro- and nanostructuring substantially boosts its HER catalytic performance, with CoS2 nanowire electrodes achieving geometric current densities of -10 mA cm(-2) at overpotentials as low as -145 mV vs the reversible hydrogen electrode. Moreover, micro- and nanostructuring of the CoS2 material has the synergistic effect of increasing its operational stability, cyclability, and maximum achievable rate of hydrogen generation by promoting the release of evolved gas bubbles from the electrode surface. The benefits of catalyst micro- and nanostructuring are further demonstrated by the increased electrocatalytic activity of CoS2 nanowire electrodes over planar film electrodes toward polysulfide and triiodide reduction, which suggests a straightforward way to improve the performance of quantum dot- and dye-sensitized solar cells, respectively. Extension of this micro- and nanostructuring strategy to other earth-abundant materials could similarly enable inexpensive electrocatalysts that lack the high intrinsic activity of the noble metals.

Changes in the daily rhythm of lipid metabolism in the diabetic retina.

Disruption of circadian regulation was recently shown to cause diabetes and metabolic disease. We have previously demonstrated that retinal lipid metabolism contributed to the development of diabetic retinopathy. The goal of this study was to determine the effect of diabetes on circadian regulation of clock genes and lipid metabolism genes in the retina and retinal endothelial cells (REC). Diabetes had a pronounced inhibitory effect on the negative clock arm with lower amplitude of the period (per) 1 in the retina; lower amplitude and a phase shift of per2 in the liver; and a loss of cryptochrome (cry) 2 rhythmic pattern in suprachiasmatic nucleus (SCN). The positive clock arm was increased by diabetes with higher amplitude of circadian locomotor output cycles kaput (CLOCK) and brain and muscle aryl-hydrocarbon receptor nuclear translocator-like 1 (bmal1) and phase shift in bmal1 rhythmic oscillations in the retina; and higher bmal1 amplitude in the SCN. Peroxisome proliferator-activated receptor (PPAR) α exhibited rhythmic oscillation in retina and liver; PPARγ had lower amplitude in diabetic liver; sterol regulatory element-binding protein (srebp) 1c had higher amplitude in the retina but lower in the liver in STZ- induced diabetic animals. Both of Elongase (Elovl) 2 and Elovl4 had a rhythmic oscillation pattern in the control retina. Diabetic retinas lost Elovl4 rhythmic oscillation and had lower amplitude of Elovl2 oscillations. In line with the in vivo data, circadian expression levels of CLOCK, bmal1 and srebp1c had higher amplitude in rat REC (rREC) isolated from diabetic rats compared with control rats, while PPARγ and Elovl2 had lower amplitude in diabetic rREC. In conclusion, diabetes causes dysregulation of circadian expression of clock genes and the genes controlling lipid metabolism in the retina with potential implications for the development of diabetic retinopathy.

N-3 polyunsaturated Fatty acids prevent diabetic retinopathy by inhibition of retinal vascular damage and enhanced endothelial progenitor cell reparative function.

OBJECTIVE: The vasodegenerative phase of diabetic retinopathy is characterized by not only retinal vascular degeneration but also inadequate vascular repair due to compromised bone marrow derived endothelial progenitor cells (EPCs). We propose that n-3 polyunsaturated fatty acid (PUFA) deficiency in diabetes results in activation of the central enzyme of sphingolipid metabolism, acid sphingomyelinase (ASM) and that ASM represents a molecular metabolic link connecting the initial damage in the retina and the dysfunction of EPCs. RESEARCH DESIGN AND METHODS: Type 2 diabetic rats on control or docosahexaenoic acid (DHA)-rich diet were studied. The number of acellular capillaries in the retinas was assessed by trypsin digest. mRNA levels of interleukin (IL)-1ß, IL-6, intracellular adhesion molecule (ICAM)-1 in the retinas from diabetic animals were compared to controls and ASM protein was assessed by western analysis. EPCs were isolated from blood and bone marrow and their numbers and ability to form colonies in vitro, ASM activity and lipid profiles were determined. RESULTS: DHA-rich diet prevented diabetes-induced increase in the number of retinal acellular capillaries and significantly enhanced the life span of type 2 diabetic animals. DHA-rich diet blocked upregulation of ASM and other inflammatory markers in diabetic retina and prevented the increase in ASM activity in EPCs, normalized the numbers of circulating EPCs and improved EPC colony formation. CONCLUSIONS: In a type 2 diabetes animal model, DHA-rich diet fully prevented retinal vascular pathology through inhibition of ASM in both retina and EPCs, leading to a concomitant suppression of retinal inflammation and correction of EPC number and function.

Quantum dot nanoscale heterostructures for solar energy conversion.

Quantum dot nanoscale semiconductor heterostructures (QDHs) are a class of materials potentially useful for integration into solar energy conversion devices. However, realizing the potential of these heterostructured systems requires the ability to identify and synthesize heterostructures with suitably designed materials, controlled size and morphology of each component, and structural control over their shared interface. In this review, we will present the case for the utility and advantages of chemically synthesized QDHs for solar energy conversion, beginning with an overview of various methods of heterostructured material synthesis and a survey of heretofore reported materials systems. The fundamental charge transfer properties of the resulting materials combinations and their basic design principles will be outlined. Finally, we will discuss representative solar photovoltaic and photoelectrochemical devices employing QDHs (including quantum dot sensitized solar cells, or QDSSCs) and examine how QDH synthesis and design impacts their performance.

Earth-Abundant Cobalt Pyrite (CoS2) Thin Film on Glass as a Robust, High-Performance Counter Electrode for Quantum Dot-Sensitized Solar Cells.

We report a cobalt pyrite (cobalt disulfide, CoS2) thin film on glass as a robust, high-performance, low-cost, earth-abundant counter electrode for liquid-junction quantum dot-sensitized solar cells (QDSSCs) that employ the aqueous sulfide/polysulfide (S(2-)/Sn(2-)) redox electrolyte as the hole-transporting medium. The metallic CoS2 thin film electrode is prepared via thermal sulfidation of a cobalt film deposited on glass and has been characterized by powder X-ray diffraction and electron microscopy. Using the CoS2 counter electrode, CdS/CdSe-sensitized QDSSCs display improved short-circuit photocurrent density and fill factor, achieving solar light-to-electricity conversion efficiencies as high as 4.16%, with an average efficiency improvement of 54 (±14)% over equivalent devices assembled with a traditional platinum counter electrode. Electrochemical measurements verify that CoS2 shows high electrocatalytic activity toward polysulfide reduction, rationalizing the improved QDSSC performance. CoS2 is also less susceptible to poisoning by the sulfide/polysulfide electrolyte, a problem that plagues platinum electrodes in this application; furthermore, CoS2 exhibits excellent stability in sulfide/polysulfide electrolyte, resulting in highly reproducible performance.

Evaluation of sex-specific gene expression in archived dried blood spots (DBS).

Screening newborns for treatable serious conditions is mandated in all US states and many other countries. After screening, Guthrie cards with residual blood (whole spots or portions of spots) are typically stored at ambient temperature in many facilities. The potential of archived dried blood spots (DBS) for at-birth molecular studies in epidemiological and clinical research is substantial. However, it is also challenging as analytes from DBS may be degraded due to preparation and storage conditions. We previously reported an improved assay for obtaining global RNA gene expression from blood spots. Here, we evaluated sex-specific gene expression and its preservation in DBS using oligonucleotide microarray technology. We found X inactivation-specific transcript (XIST), lysine-specific demethylase 5D (KDM5D) (also known as selected cDNA on Y, homolog of mouse (SMCY)), uncharacterized LOC729444 (LOC729444), and testis-specific transcript, Y-linked 21 (TTTY21) to be differentially-expressed by sex of the newborn. Our finding that trait-specific RNA gene expression is preserved in unfrozen DBS, demonstrates the technical feasibility of performing molecular genetic profiling using such samples. With millions of DBS potentially available for research, we see new opportunities in using newborn molecular gene expression to better understand molecular pathogenesis of perinatal diseases.

Synthesis and properties of semiconducting iron pyrite (FeS2) nanowires.

We report the growth and structural, electrical, and optical characterization of vertically oriented single-crystalline iron pyrite (FeS(2)) nanowires synthesized via thermal sulfidation of steel foil for the first time. The pyrite nanowires have diameters of 4-10 nm and lengths greater than 2 µm. Their crystal phase was identified as cubic iron pyrite using high-resolution transmission electron microscopy, Raman spectroscopy, and powder X-ray diffraction. Electrical transport measurements showed the pyrite nanowires to be highly p-doped, with an average resistivity of 0.18 ± 0.09 Ω cm and carrier concentrations on the order of 10(21) cm(-3). These pyrite nanowires could provide a platform to further study and improve the physical properties of pyrite nanostructures toward solar energy conversion.

Spontaneous growth and phase transformation of highly conductive nickel germanide nanowires.

We report the synthesis, phase transformation, and electrical property measurement of single-crystal NiGe and ε-Ni(5)Ge(3) nanowires (NWs). NiGe NWs were spontaneously synthesized by chemical vapor deposition of GeH(4) onto a porous Ni substrate without the use of intentional catalysts. The as-grown NWs of the orthorhombic NiGe phase were transformed to the hexagonal ε-Ni(5)Ge(3) phase by thermal annealing induced Ni enrichment. This controllable conversion of germanide phases is desirable for phase-dependent property study and applications, and the observation of novel metastable ε-Ni(5)Ge(3) phase suggests the importance of kinetic factors in such nanophase transformations. Electrical studies reveal that NiGe NWs are highly conductive, with an average resistivity of 35 ± 15 µΩ·cm, while the resistivity of ε-Ni(5)Ge(3) NWs is more than 4 times that of the NiGe phase. NWs of nickel germanides, particularly NiGe, would be useful building blocks for germanium-based nanoelectronic devices.