High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses.

Two serious public health challenges have emerged in the current COVID-19 pandemic namely, deficits in SARS-CoV-2 variant monitoring and neglect of other co-circulating respiratory viruses. Additionally, accurate assessment of the evolution, extent, and dynamics of the outbreak is required to understand the transmission of the virus. To address these challenges, we evaluated 533 samples using a high-throughput next-generation sequencing (NGS) respiratory viral panel (RVP) that includes 40 viral pathogens. The performance metrics revealed a PPA, NPA, and accuracy of 95.98%, 85.96%, and 94.4%, respectively. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF3a, and S84L in ORF8 covarying with the D614G spike protein mutation, were the most prevalent early in the pandemic in Georgia, USA. The isolates from the same county formed paraphyletic groups, indicating virus transmission between counties. The study demonstrates the clinical and public health utility of the NGS-RVP to identify novel variants that can provide actionable information to prevent or mitigate emerging viral threats and models that provide insights into viral transmission patterns and predict transmission/resurgence of regional outbreaks as well as providing critical information on co-circulating respiratory viruses that might be independent factors contributing to the global disease burden.

Effects of shading and composition on green roof media temperature and moisture.

Three of the primary functions of green roofs in urban areas are to delay rainwater runoff, moderate building temperatures, and ameliorate the urban heat island (UHI) effect. A major impediment to the survival of plants on an unirrigated extensive green roof (EGR) is the harsh rooftop environment, including high temperatures and limited water during dry periods. Factors that influence EGR thermal and hydrologic performance include the albedo (reflectivity) of the roof and the composition of the green roof substrate (growing media). In this study we used white, reflective shading structures and three different media formulations to evaluate EGR thermal and hydrologic performance in the Pacific Northwest, USA. Shading significantly reduced daytime mean and maximum EGR media temperatures and significantly increased nighttime mean and minimum temperatures, which may provide energy benefits to buildings. Mean media moisture was greater in shaded trays than in exposed (unshaded) trays but differences were not statistically significant. Warmer nighttime media temperatures and lack of dew formation in shaded trays may have partially compensated for greater daytime evaporation from exposed trays. Media composition did not significantly influence media temperature or moisture. Results of this study suggest that adding shade structures to green roofs will combine thermal, hydrologic, and ecological benefits, and help achieve temperature and light regimes that allow for greater plant diversity on EGRs.

A framework for optimizing hydrologic performance of green roof media.

One of the primary functions of green roofs in urban areas is to moderate rainwater runoff, and one of the major impediments to the survival of plants on an extensive green roof (EGR) is a lack of available water during dry periods. Runoff moderation and water storage are both influenced by the composition of the growing media. Here we present a framework for evaluating the hydrologic performance of EGR growing media and also provide hydrologic attribute data for several commonly used EGR media constituents. In this three-phase study, we: 1) measured hydrologic attributes of individual EGR media constituents, 2) predicted attributes of media mixtures using individual constituent data, and 3) tested the seven top-ranking mixtures to evaluate hydrologic performance. Hydrologic attributes included wet weight and water held at maximum retentive capacity, long-term water retention, and hydraulic conductivity. Because perlite was light in weight yet held the greatest amount of water both at its maximum retentive capacity and in the long term, media mixtures dominated by perlite were predicted to have the best overall hydrologic performance. Mixtures dominated by pumice were also predicted to perform relatively well but were heavier. Despite the slightly greater weight and slightly lower performance, pumice may be a preferred alternative to perlite because perlite is a processed constituent with greater estimated embodied energy. Results indicate that performance of mixtures can be adequately predicted using performance of individual constituents for wet weight, water held, and long-term water retention. Hydraulic conductivity was less predictable because the pore volume in mixtures can be unrelated to the pore volume of the individual constituents. The framework presented here can be used to evaluate the performance of other EGR media, and the media attribute data can be used in formulating EGR media mixtures for specific applications. In addition, the attribute data can serve as a benchmark for evaluating other EGR media. Our results underscore the need for standardization of methods for more effective comparisons of EGR substrates, and also reinforce the need to evaluate EGR components using real-world scenarios.

STABLE results: warfarin home monitoring achieves excellent INR control.

OBJECTIVES: Point-of-care, home international normalized ratio (INR) monitoring (patient self-testing, or PST) provides an opportunity to optimize warfarin therapy as demonstrated in randomized trials. This study sought to determine the quality of warfarin therapy as determined by time in therapeutic INR range (TTR) in patients who perform home monitoring outside of a clinical trial setting. STUDY DESIGN: Retrospective analysis. METHODS: The data base of an independent diagnostic testing facility was retrospectively queried over a 2.5-year period (January 2008-June 2011) and patient TTR was analyzed based on frequency of testing, age, gender, indication for therapy, duration of therapy, and critical value occurrence. RESULTS: A total of 29,457 patients with multiple indications for warfarin therapy comprised the database. The mean TTR for the entire group was 69.7%, with weekly testers achieving a TTR of 74% versus 68.9% for variable testers (testing every 2-4 weeks)(P <.0001). In all categories analyzed (age, indication for anticoagulation, and referral site volume), weekly testers performed significantly better than variable testers. Older individuals had a higher TTR than younger patients. Weekly testers experienced significantly fewer critical values (INR <1.5 or >5.0) than did variable testers. CONCLUSIONS: Point-of-care patient self-testing at home achieves high-quality warfarin therapy outside of clinical trials and compares favorably with the results achieved in randomized trials or in anticoagulation clinic settings.

Optimizing blood collection, transport and storage conditions for cell free DNA increases access to prenatal testing.

OBJECTIVES: Fetal mutations and fetal chromosomal abnormalities can be detected by molecular analysis of circulating cell free fetal DNA (ccffDNA) from maternal plasma. This comprehensive study was aimed to investigate and verify blood collection and blood shipping conditions that enable Noninvasive Prenatal Testing. Specifically, the impact of shipping and storage on the stability and concentration of circulating cell-free DNA (ccfDNA) in Streck® Cell-Free DNA™ Blood Collection Tubes (Streck BCTs, Streck, Omaha NE). These BCTs were designed to minimize cellular degradation, and thus effectively prevent dilution of fetal ccf DNA by maternal genomic DNA, was evaluated. DESIGN AND METHODS: Peripheral venous maternal blood was collected into Streck BCTs to investigate four aspects of handling and processing conditions: (1) time from blood draw to plasma processing; (2) storage temperature; (3) mechanical stress; and (4) lot-to-lot tube variations. RESULTS: Maternal blood stored in Streck BCTs for up to 7 days at ambient temperature provides stable concentrations of ccffDNA. The amount of fetal DNA did not change over a broad range of storage temperatures (4°C, 23°C, 37°C, 40°C), but the amount of total (largely maternal) DNA increased in samples stored at 23°C and above, indicating maternal cell degradation and genomic DNA release at elevated temperatures. Shipping maternal blood in Streck BCTs, did not affect sample quality. CONCLUSIONS: Maternal plasma DNA stabilized for 0 to 7 days in Streck BCTs can be used for non-invasive prenatal molecular applications, when temperatures are maintained within the broad parameters assessed in this study.

Engineering hyperthermostability into a GH11 xylanase is mediated by subtle changes to protein structure.

Understanding the structural basis for protein thermostability is of considerable biological and biotechnological importance as exemplified by the industrial use of xylanases at elevated temperatures in the paper pulp and animal feed sectors. Here we have used directed protein evolution to generate hyperthermostable variants of a thermophilic GH11 xylanase, EvXyn11. The Gene Site Saturation Mutagenesis (GSSM) methodology employed assesses the influence on thermostability of all possible amino acid substitutions at each position in the primary structure of the target protein. The 15 most thermostable mutants, which generally clustered in the N-terminal region of the enzyme, had melting temperatures (Tm) 1-8 degrees C higher than the parent protein. Screening of a combinatorial library of the single mutants identified a hyperthermostable variant, EvXyn11TS, containing seven mutations. EvXyn11TS had a Tm approximately 25 degrees C higher than the parent enzyme while displaying catalytic properties that were similar to EvXyn11. The crystal structures of EvXyn11 and EvXyn11TS revealed an absence of substantial changes to identifiable intramolecular interactions. The only explicable mutations are T13F, which increases hydrophobic interactions, and S9P that apparently locks the conformation of a surface loop. This report shows that the molecular basis for the increased thermostability is extraordinarily subtle and points to the requirement for new tools to interrogate protein folding at non-ambient temperatures.

Exploring nitrilase sequence space for enantioselective catalysis.

Nitrilases are important in the biosphere as participants in synthesis and degradation pathways for naturally occurring, as well as xenobiotically derived, nitriles. Because of their inherent enantioselectivity, nitrilases are also attractive as mild, selective catalysts for setting chiral centers in fine chemical synthesis. Unfortunately, <20 nitrilases have been reported in the scientific and patent literature, and because of stability or specificity shortcomings, their utility has been largely unrealized. In this study, 137 unique nitrilases, discovered from screening of >600 biotope-specific environmental DNA (eDNA) libraries, were characterized. Using culture-independent means, phylogenetically diverse genomes were captured from entire biotopes, and their genes were expressed heterologously in a common cloning host. Nitrilase genes were targeted in a selection-based expression assay of clonal populations numbering 10(6) to 10(10) members per eDNA library. A phylogenetic analysis of the novel sequences discovered revealed the presence of at least five major sequence clades within the nitrilase subfamily. Using three nitrile substrates targeted for their potential in chiral pharmaceutical synthesis, the enzymes were characterized for substrate specificity and stereospecificity. A number of important correlations were found between sequence clades and the selective properties of these nitrilases. These enzymes, discovered using a high-throughput, culture-independent method, provide a catalytic toolbox for enantiospecific synthesis of a variety of carboxylic acid derivatives, as well as an intriguing library for evolutionary and structural analyses.

Creation of a productive, highly enantioselective nitrilase through gene site saturation mutagenesis (GSSM).

Gene site saturation mutagenesis (GSSM) technology is applied for the directed evolution of a nitrilase. The nitrilase effectively catalyzes the desymmetrization of the prochiral substrate 3-hydroxyglutaronitrile to afford (R)-4-cyano-3-hydroxybutyric acid, a precursor to the valuable cholesterol-lowering drug Lipitor. The discovered wild-type enzyme effectively performs the reaction at the industrially relevant 3 M substrate concentration but affords a product enantiomeric excess of only 87.6% ee. Through GSSM, a mutagenesis technique that effects the combinatorial saturation of each amino acid in the protein to each of the other 19 amino acids, combined with a novel high-throughput mass spectroscopy assay, a number of improved variants were identified, the best of which is the Ala190His mutant that yields product enantiomeric excess of 98.5% at 3 M substrate loading and a volumetric productivity of 619 g L-1 d-1.

Structure-based mutagenesis approaches toward expanding the substrate specificity of D-2-deoxyribose-5-phosphate aldolase.

2-Deoxyribose-5-phosphate aldolase (DERA, EC 4.1.2.4) catalyzes the reversible aldol reaction between acetaldehyde and D-glyceraldehyde-3-phosphate to generate D-2-deoxyribose-5-phosphate. It is unique among the aldolases as it catalyzes the reversible asymmetric aldol addition reaction of two aldehydes. In order to expand the substrate scope and stereoselectivity of DERA, structure-based substrate design as well as site-specific mutation has been investigated. Using the 1.05 A crystal structure of DERA in complex with its natural substrate as a guide, five site-directed mutants were designed in order to improve its activity with the unnatural nonphosphorylated substrate, D-2-deoxyribose. Of these, the S238D variant exhibited a 2.5-fold improvement over the wild-type enzyme in the retroaldol reaction of 2-deoxyribose. Interestingly, this S238D mutant enzyme was shown to accept 3-azidopropinaldehyde as a substrate in a sequential asymmetric aldol reaction to form a deoxy-azidoethyl pyranose, which is a precursor to the corresponding lactone and the cholesterol-lowering agent Lipitor. This azidoaldehyde is not a substrate for the wild-type enzyme. Another structure-based design of new nonphosphorylated substrates was focused on the aldol reaction with inversion in enantioselectivity using the wild type or the S238D variant as the catalyst and 2-methyl-substituted aldehydes as substrates. An example was demonstrated in the asymmetric synthesis of a deoxypyranose as a new effective synthon for the total synthesis of epothilones. In addition, to facilitate the discovery of new enzymatic reactions, the engineered E. coli strain SELECT (Deltaace, adhC, DE3) was developed to be used in the future for selection of DERA variants with novel nonphosphorylated acceptor specificity.

An enzyme library approach to biocatalysis: development of nitrilases for enantioselective production of carboxylic acid derivatives.

The discovery, from Nature, of a large and diverse set of nitrilases is reported. The utility of this nitrilase library for identifying enzymes that catalyze efficient production of valuable hydroxy carboxylic acid derivatives is demonstrated. Unprecedented enantioselectivity and substrate scope are highlighted for three newly discovered and distinct nitrilases. For example, a wide array of (R)-mandelic acid derivatives and analogues were produced with high rates, yields, and enantiomeric excesses (95-99% ee). We also have found nitrilases that provide direct access to (S)-phenyllactic acid and other aryllactic acid derivatives, again with high yields and enantioselectivities. Finally, different nitrilases have been discovered that catalyze enantiotopic hydrolysis of 3-hydroxyglutaronitrile to afford either enantiomer of 4-cyano-3-hydroxybutyric acid with high enantiomeric excesses (>95% ee). The first enzymes are reported that effect this transformation to furnish the (R)-4-cyano-3-hydroxybutyric acid which is a precursor to the blockbuster drug Lipitor.