The rRNAt/rDNA Ratio as a Measure of Nitrite Oxidizing Activity

A bench scale nitrification reactor (BSNR) containing nitrite oxidizing bacteria (NOB) of the genus Nitrobacter (» 1 × 1010/L; 5 - 22% of bacteria) was used to assess the ribosomal RNA transcript (rRNAt) to ribosomal RNA gene (rDNA) ratio as an in-situ nitrite oxidizing activity metric. A quantitative PCR detection system was developed that amplified a 143 base pair sequence within the Nitrobacter spp. 16S - 23S intergenenic spacer region. The resulting real-time PCR (rDNA) and real-time RT-PCR (rRNAt) assays were specific, accurate, and sensitive, requiring three replicate nucleic acid extracts to reliably detect a true 2-fold concentration difference in BSNR mixed liquor samples. These assays were used to establish upper (1.8) and lower (0.69) ratio prediction intervals (a = 0.10) for the BSNR operating at high nitrification efficiency. These intervals served as benchmarks when the ratio was measured in all subsequent experiments. It was hypothesized that during NOB inhibition the ratio would decline below 0.69 and during unlimited nitrite oxidation exceed 1.8. When the Nitrobacter rRNAt/rDNA ratio was measured in a batch nitrite oxidation experiment, the metric value increased monotonically from a lower limit less than 0.10 during nitrite starvation to an upper limit greater than 3.0 eight hours after unlimited nitrite oxidation began. The ratio declined monotonically back to 0.10 within 4 hours of nitrite exhaustion. Because of the slow Nitrobacter grow rate, the rDNA concentration (» 6 ´ 109 copies/L) did not change appreciably. Thus, the metric response was mediated by rRNAt abundance that varied as the growth prospect changed from unfavorable (nitrite starvation: » 5 ´ 108 copies/L), to favorable (excess nitrite: » 3 ´ 1010 copies/L), and back to unfavorable (nitrite starvation: » 5 ´ 108 copies/L). This demonstrated that quantitative PCR is better suited to detect activity as opposed population changes in slow growing bacteria. Batch inhibition experiments supported a hypothesized negative monotonic correlation between the Nitrobacter rRNAt/rDNA ratio and the inhibitor concentration and fraction inhibition level. For all the compounds studied, the ratio was significantly reduced (\u3c 0.69) after 4.5 hours of exposure to concentrations that extensively inhibited nitrite oxidation. However, the response varied at the same inhibition level for the different inhibitors investigated. For 3,5-DCP (an uncoupler), the ratio dropped below 0.69 at concentrations that did not significantly reduce nitrite oxidation rates, suggesting that the metric is particularly sensitive to growth inhibitors. When this compound induced near complete inhibition of nitrite oxidation, the ratio dropped to » 0.06. For azide and H+, the ratio fell below 0.69 only if unlimited nitrite oxidation rates were reduced by ³ 80%. When nitrite oxidation was completely inhibited by a sudden pH change to 5.0, the ratio fell to » 0.3. A pH change to 4.5 also stopped nitrite oxidation, but the ratio did not decline. This indicated that the metric response can be disrupted if rRNAt processing is inhibited. Though widely reported as an NOB inhibitor in the literature, free ammonia did not significantly reduce nitrite oxidation rates while ammonia oxidizing bacteria were inhibited. However, nitrite oxidation was significantly inhibited at low free ammonia concentrations if the ammonia oxidizing bacteria were allowed to remain active. This was accompanied by a low (» 0.10) rRNAt/rDNA ratio. In a staged BSNR inhibition experiment, the Nitrobacter rRNAt/rDNA ratio accurately reflected nitrite oxidizing activity. The ratio dropped significantly (\u3c 0.69) 22 hours before the nitrification efficiency fell below 90%. When nitrite oxidizing activity was later recovered, the ratio increased significantly (\u3e 0.69) before this was apparent in the reactor soluble nitrogen data. In summary, a wide range of experiments suggested the rRNAt/rDNA ratio was an effective monitor of in-situ nitrite oxidation activity. The metric could possibly be used to identify, remediate, and forecast nitrification and N-removal instability during wastewater treatment

Genome sequence of the Bacteroides fragilis phage ATCC 51477-B1

The genome of a fecal pollution indicator phage, Bacteroides fragilis ATCC 51477-B1, was sequenced and consisted of 44,929 bases with a G+C content of 38.7%. Forty-six putative open reading frames were identified and genes were organized into functional clusters for host specificity, lysis, replication and regulation, and packaging and structural proteins

Genome modeling system: A knowledge management platform for genomics

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection