Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

A retrospective analysis of high sensitivity cardiac troponin-T ranges in non-myocardial infarction emergency department visits

Abstract Introduction Current evidence suggests that high sensitivity cardiac troponin-T (hs-cTnT) values differ based on sex, race, age, and kidney function. However, most studies examining the relationship of hs-cTnT and these individual factors are in healthy participants, leading to difficulty in interpreting hs-cTnT values in the Emergency Department (ED) setting. We seek to examine the relationship between hs-cTnT values and sex, race, age, and kidney function in a contemporary, urban academic setting. Methods ED visits from June 2018 through April 2019 with at least 1 hs-cTnT and no diagnosis of acute myocardial infarction (AMI) at an academic medical center in the south side of Chicago were retrospectively analyzed. Median hs-cTnT values were stratified by sex (male or female), race (African American or Caucasian), age, estimated glomerular filtration rate (eGFR), and stage of chronic kidney disease. Results 9679 encounters, representing 7989 distinct patients, were included for analysis (age 58 ± 18 years, 59% female, 85% black). Males had significantly higher median hs-cTnT values than females (16 [8–34] vs. 9 [6–22] ng/L, p < 0.001), African Americans had a significantly lower median value than Caucasians (10 [6–24] vs. 15 [6–29] ng/L, p < 0.001), and those with atrial fibrillation (27 [16–48] vs. 9 [6–19] ng/L, p < 0.001) and heart failure (28 [14–48] vs. 8 [6–15] ng/L, p < 0.001) had higher median values than those without. Median hs-cTnT values increased significantly with increased age and decreased eGFR. All relationships continued to be significant even after multivariable regression of sex, age, race, eGFR, presence of atrial fibrillation, and presence of heart failure (p < 0.01). Conclusions Analysis of hs-cTnT in non-AMI patients during ED encounters showed that males have higher values than females, African Americans have lower values than Caucasians, those with atrial fibrillation and heart failure have higher values than those without, and that older age and lower eGFR were associated with higher median values

Molecular Evolution of MDM1, a “Duplication-Resistant” Gene in Vertebrates

<div><p>Background</p><p>The mouse double minute 1 (<i>Mdm1</i>) gene was first reported and cloned in mouse tumor cell lines as an oncogene candidate. Later, it was found that mutation of <i>Mdm1</i> might cause age-related retinal degeneration 2 in mice by genetic linkage analysis. Additionally, the MDM1 protein was found to be expressed in the centrosomes, cilia, and the nucleus of multiciliated tracheal epithelial cells in mice. These observations suggest that MDM1 may have some basal functions in cell physiology. However, the evolutionary history of this gene and its expression during embryonic development remain largely unexplored.</p><p>Results</p><p>Using molecular phylogenetic analysis, we found that the <i>MDM1</i> gene encoded an evolutionarily conserved protein across all metazoans. We also found that the <i>MDM1</i> gene was in a conserved synteny in vertebrates. In almost all the species that were analyzed, there was only one <i>MDM1</i> gene based on current genome annotations. Since vertebrate genomes underwent two to three rounds of whole-genome duplications around the origin of the vertebrates, it is interesting that only one <i>MDM1</i> ohnolog was retained. This observation implies that other <i>MDM1</i> ohnologs were lost after the whole-genome duplications. Furthermore, using whole-mount <i>in situ</i> hybridization, we found that <i>mdm1</i> was expressed in the forebrain, nephric ducts, and tail buds during zebrafish early embryonic development.</p><p>Conclusion</p><p><i>MDM1</i> is an evolutionary conserved gene, and its homologous genes can be traced back to basal metazoan lineages. In vertebrates, the <i>MDM</i>1 gene is in a conserved synteny and there is only one <i>MDM1</i> ohnolog suggesting it is a “duplication-resistant” gene. Its expression patterns in early zebrafish embryos indicate that <i>mdm1</i> may play important roles in the development of the central nervous system, kidneys, and hematopoietic system.</p></div

The synteny of <i>MDM1</i> in nine representative vertebrate species.

<p>The illustration of the gene and their sizes are not proportional to the length of the bars. <i>MDM1</i> is highlighted in red, and <i>MDM2</i> is highlighted in brown. <i>MDM1</i> synteny (<i>MDM1</i>- <i>DYRK2</i>-<i>CAND1</i>-<i>GRIP1</i>) is boxed with red lines. <i>MDM2</i> synteny (<i>MDM2</i>-<i>CPM</i>-<i>CPSF61</i>) is boxed with blue lines. <i>RAP1b</i> synteny (<i>RAP1B</i>-<i>NUP107</i>-<i>SLC35E3</i>) is boxed with brown lines. <i>IL22</i> synteny (<i>IL22</i>-<i>IL26</i>-<i>IFNG</i>) is boxed with green lines.</p

The scenario of <i>MDM1</i> evolution from the syntenic analysis in vertebrates.

<p>The vertebrate phylogenetic relationships are adopted from the references [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163229#pone.0163229.ref047" target="_blank">47</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163229#pone.0163229.ref048" target="_blank">48</a>]. In tetrapod and spotted gar, the <i>MDM1</i> and <i>MDM2</i> syntenies (M1 and M2) are neighbors next to each other, while the two syntenies are located on different chromosomes in elephant shark and teleosts. The vertical red bars on the tree indicate the whole genome duplication events. There are two rounds of WGDs (1R and 2R) before the origin of the vertebrates and a third round happed before the separation of the teleosts (3R).</p

Open data from the first and second observing runs of Advanced LIGO and Advanced Virgo

Advanced LIGO and Advanced Virgo are monitoring the sky and collecting gravitational-wave strain data with sufficient sensitivity to detect signals routinely. In this paper we describe the data recorded by these instruments during their first and second observing runs. The main data products are gravitational-wave strain time series sampled at 16384 Hz. The datasets that include this strain measurement can be freely accessed through the Gravitational Wave Open Science Center at http://gw-openscience.org, together with data-quality information essential for the analysis of LIGO and Virgo data, documentation, tutorials, and supporting software