Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization

Considerable effort has been devoted to refining experimental protocols to reduce levels of technical variability and artifacts in single-cell RNA-sequencing data (scRNA-seq). We here present evidence that equalizing the concentration of cDNA libraries prior to pooling, a step not consistently performed in single-cell experiments, improves gene detection rates, enhances biological signals, and reduces technical artifacts in scRNA-seq data. To evaluate the effect of equalization on various protocols, we developed Scaffold, a simulation framework that models each step of an scRNA-seq experiment. Numerical experiments demonstrate that equalization reduces variation in sequencing depth and gene-specific expression variability. We then performed a set of experiments in vitro with and without the equalization step and found that equalization increases the number of genes that are detected in every cell by 17–31%, improves discovery of biologically relevant genes, and reduces nuisance signals associated with cell cycle. Further support is provided in an analysis of publicly available data.     

First Nations status and emergency department triage scores in Alberta: a retrospective cohort study

Background:Previous studies have found that race is associated with emergency department triage scores, raising concerns about potential health care inequity. As part of a project on quality of care for First Nations people in Alberta, we sought to understand the relation between First Nations status and triage scores.Methods:We conducted a population-based retrospective cohort study of health administrative data from April 2012 to March 2017 to evaluate acuity of triage scores, categorized as a binary outcome of higher or lower acuity score. We developed multivariable multilevel logistic mixed-effects regression models using the levels of emergency department visit, patient (for patients with multiple visits) and facility. We further evaluated the triage of visits related to 5 disease categories and 5 specific diagnoses to better compare triage outcomes of First Nations and non–First Nations patients.Results:First Nations status was associated with lower odds of receiving higher acuity triage scores (odds ratio [OR] 0.93, 95% confidence interval [CI] 0.92–0.94) compared with non–First Nations patients in adjusted models. First Nations patients had lower odds of acute triage for all 5 disease categories and for 3 of 5 diagnoses, including long bone fractures (OR 0.82, 95% CI 0.76–0.88), acute upper respiratory infection (OR 0.90, 95% CI 0.84–0.98) and anxiety disorder (OR 0.67, 95% CI 0.60–0.74).Interpretation:First Nations status was associated with lower odds of higher acuity triage scores across a number of conditions and diagnoses. This may reflect systemic racism, stereotyping and potentially other factors that affected triage assessments.

Health outcomes are markedly worse for First Nations than non–First Nations people. Although this is largely because of inequities in the social determinants of health,^1–4 inequities in the provision of health care also exist.^5,6 Emergency departments serve as a point of accessible health care. Status First Nations patients make up 4.8% of unique patients and 9.4% of emergency visits in Alberta,⁷ and Canadian studies describe First Nations patients’ experiences with racism when seeking emergency care.^8,9Evaluating triage contributes empirically to understanding the health care of First Nations patients insofar as triage is a quantifiable, intermediate process by which systemic racism¹⁰ may influence patient outcomes. The Canadian Triage Acuity Scale¹¹ is a 5-level scale used to classify the severity of patient symptoms. Triage nurses use a brief assessment, medical history, and presenting signs and symptoms to assign each patient a triage score that determines the priority in which the patient should be seen by a provider. Therefore, accurate triage is important for patient health outcomes.¹² In practice, triage is a social interaction where local practice, biases, stereotypes and communication barriers come into play. Studies have found that women receive less acute triage scores than men,^13,14 and that racial minority^13,15–17 and Indigenous^18–20 patients receive less acute triage scores than white or non-Indigenous patients. Indeed, Indigenous patients in Canada have described a perception “of social triaging in the [emergency department], whereby decisions about who is seen first seemed to them [to be] based less on triaged clinical priorities but on the social positioning of the patient.”²¹ Differential triage scores for minority populations raise health equity concerns.As part of a larger mixed-methods project evaluating the quality of emergency care for First Nations people in Alberta, we sought to evaluate quantitative differences in emergency visit characteristics and outcomes of First Nations and non–First Nations people in Alberta. Specifically, we aimed to estimate the relation between First Nations status and acuity of triage, and to evaluate whether predictors of acuity differ by First Nations status.     

Assessing detectability for monitoring of rare species: a case study of the cobblestone tiger beetle (Cicindela marginipennis Dejean)

Interpreting data on distribution or population trends may be difficult unless detection probability is accounted for. We wished to determine the detectability of the rare and patchily distributed cobblestone tiger beetle (Cicindela marginipennis) along the upper Genesee River in western New York for development of a monitoring strategy. We used occupancy surveys and distance sampling to examine two types of detectability. The first type was site-level detectability: the probability of detecting a single cobblestone tiger beetle on an occupied cobble bar, calculated using program PRESENCE. The second type was individual-level detectability: the probability of detecting an individual cobblestone tiger beetle in a population on a single cobble bar, calculated using program DISTANCE. Our occupancy surveys consisted of collecting presence and absence data on cobble bars along the Genesee River; these showed a relatively narrow range of site-level detection probabilities (0.60?C0.68) for cobblestone tiger beetles in 2008 and 2009. Three visits were necessary to detect cobblestone tiger beetles on 90% of occupied cobble bars. Individual cobblestone tiger beetles were detectable one-half of the time (0.50) in our surveys. It is important for ecologists to distinguish between the two kinds of detectability, as monitoring implications could differ substantially depending on which is calculated. Our monitoring recommendations include (1) continuing occupancy surveys with at least three visits to each cobble bar; (2) conducting occupancy surveys between 10:00 and 17:00 on warm sunny days in mid-July and mid-August; and (3) conducting surveys at three- to five-year intervals depending on the study objective.     

Saccharum spontaneum L. ‘SES 208’ genetic linkage map combining RFLP- and PCR-based markers

A 527 marker linkage map ofSaccharum spontaneum L. SES 208 (2n = 64) was established by analyzing 208 single-dose (SD) arbitrarily primed PCR polymorphisms, 234 SD RFLPs, 41 double-dose (DD) and one triple-dose (TD) polymorphisms. A map hypothesis constructed using these markers (minimum LOD = 4.00, = 0.25 M) had 64 linkage groups with 13 SD, nine DD, and one TD markers unlinked. Eight chromosome homology groups were identified by using DD fragments as well as SD RFLPs that identified more than one linkage group. Linkages in repulsion phase were absent from the map, as found in two previous genetic studies of this species. Together, these data demonstrate that SES 208 displayed polysomic segregation, a genetic behavior typical of autopolyploid species. As with previous studies, it was concluded that SES 208 behaved like an auto-octoploid, which was also in agreement with the number of homology groups observed. A ² was used to test whether the 527 markers were randomly distributed throughout the genome: both arbitrarily primed PCR markers and RFLPs had a distribution that was statistically indistinguishable from random. The integrated arbitrarily primed PCR-RFLP map had a predicted genomic coverage of 93% (considering only 442 SD polymorphisms) and an average interval between markers of 6 cM. SD markers were used to estimate the genome size of SES 208 at ca. 33 00 cM.     

Expression, Purification, and Characterization of Recombinant Human Factor X

A system is described for producing recombinant factor X with properties very similar to human plasma factor X. Optimization of the expression system for factor X resulted in the finding that human kidney cells (293 cells) are superior to the widely utilized baby hamster kidney cells (BHK cells) for the expression of functional factor X. It was also determined that production of factor X by 293 cells requires the substitution of the −2 residue (Thr → Arg) which affords the removal of the factor X propeptide. Purification of recombinant and plasma factor X is accomplished using a calcium-dependent monoclonal antibody directed against the gla domain. The proteins are comparable by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The rate and extent of activation by the factor X coagulant protein from Russell's viper venom and by factors IXa and VIIIa are similar; activation of the recombinant protein by VIIa and tissue factor is mildly faster. The activated enzymes have the same activity toward a chromogenic substrate and the biologic substrate, prothrombin. Both enzymes have the same apparent affinity for the activated platelet surface as judged by their ability to activate prothrombin. Finally, inhibition by antithrombin, with or without heparin, and inhibition by the tissue factor pathway inhibitor are equivalent. Recombinant factor X produced by this method is therefore well suited for probing structure–function relationships by mutational analysis.     

Isolation, Mapping, and Functional Expression of the Mouse X Chromosome Glycerol Kinase Gene

Glycerol kinase (Gyk) participates in the metabolism of endogenously derived and dietary glycerol. Deficiency of the human enzyme activity is an X-linked recessive disorder with a clinical picture varying from childhood metabolic crisis to asymptomatic adults incidentally identified by hyperlipidemia screening (pseudohypertriglyceridemia). Gyk is a member of a small group of kinases termed ambiquitous enzymes that are found in the cytosol or as membrane-bound enzymes associated with the voltage-dependent anion channel of the mitochondrial outer membrane. It was recently reported that in humans there are X-linked and autosomal copies of Gyk sequences, both apparently functional genes and processed pseudogenes. To understand the role of Gyk in normal metabolism and the variable clinical features seen with Gyk deficiency, we have characterized the mouse Gyk gene. We present the sequence of a full-length mouse Gyk cDNA that is alternatively spliced in brain. The Gyk gene was mapped to the mouse X chromosome by both fluorescencein situhybridization and an interspecies backcross panel, demonstrating conservation of synteny withdmd.To confirm the functional identity of the cDNA, transient transfection of the cDNA into COS7 cells was shown to cause a marked elevation in glycerol kinase activity.     

Pathways of glycosphingolipid biosynthesis in SW13 cells in the presence and absence of vimentin intermediate filaments

We reported previously that the incorporation of sugars intoglycosphingolipids (GSL) is diminished in SW13 cells that lacka vimentin intermediate filament (IF) network (vim–) comparedto vim+ cells. To further analyze the nature of this abnormality,we double-labeled cells with ³H-serine and ^l4C-sugars. Therewas no difference between vim+ and vim– cells in the incorporationof serine into GSL, although the usual difference in sugar incorporationwas observed. This indicated that the defect in vim– cellswas not in the incorporation of sugars into ceramide synthesizedde novo by acylation of sphinganine (pathway 1). Sugars canalso be incorporated into ceramide synthesized from sphingosinethat is derived from catabolism of sphin-golipids (pathway 2),and into GSL that recycle through the Golgi apparatus from endosomes(pathway 3). The amount of galactose and glucosamine incorporatedinto GSL in these three pathways was analyzed by the use oftwo inhibitors of sphingolipid biosynthesis. ß-Chloroala-nineinhibits the de novo synthesis of sphinganine (pathway 1), andfumonisin Bl inhibits the acylation of sphinganine and sphingosine(pathways 1 and 2). We were surprised to observe that in bothvim+ and vim– cells only 20–40% of sugar incorporationinto GSL took place in pathway 1, and 60–80% of sugarincorporation took place in the recycling pathways. Moreover,in contrast to larger GSL, GlcCer was not synthesized in pathway3. Our observations indicate that vimentin IF facilitate therecycling of GSL and sphingosine, and that the differences betweenvim+ and vim– cells are predominantly in pathways 2 and3. Furthermore, although it is generally believed that virtuallyall GSL are synthesized in the de novo pathway, these data indicatethat the recyling pathways predominate in the incorporationof sugars into GSL in SW13 cells. glycosphingolipid biosynthesis intermediate filaments SW13 cells sphingolipid recycling vimentin     

Novel plasma biomarker of atenolol-induced hyperglycemia identified through a metabolomics-genomics integrative approach

Introduction

While atenolol is an effective antihypertensive agent, its use is also associated with adverse events including hyperglycemia and incident diabetes that may offset the benefits of blood pressure lowering. By combining metabolomic and genomic data acquired from hypertensive individuals treated with atenolol, it may be possible to better understand the pathways that most impact the development of an adverse glycemic state.

Objective

To identify biomarkers that can help predict susceptibility to blood glucose excursions during exposure to atenolol.

Methods

Plasma samples acquired from 234 Caucasian participants treated with atenolol in the Pharmacogenomic Evaluation of Antihypertensive Responses trial were analyzed by gas chromatography Time-Of-Flight Mass Spectroscopy. Metabolomics and genomics data were integrated by first correlating participant’s metabolomic profiles to change in glucose after treatment with atenolol, and then incorporating genotype information from genes involved in metabolite pathways associated with glucose response.

Results

Our findings indicate that the baseline level of β-alanine was associated with glucose change after treatment with atenolol (Q = 0.007, β = 2.97 mg/dL). Analysis of genomic data revealed that carriers of the G allele for SNP rs2669429 in gene DPYS, which codes for dihydropyrimidinase, an enzyme involved in β-alanine formation, had significantly higher glucose levels after treatment with atenolol when compared with non-carriers (Q = 0.05, β = 2.76 mg/dL). This finding was replicated in participants who received atenolol as an add-on therapy (P = 0.04, β = 1.86 mg/dL).

Conclusion

These results suggest that β-alanine and rs2669429 may be predictors of atenolol-induced hyperglycemia in Caucasian individuals and further investigation is warranted.