SCEPTRE improves calibration and sensitivity in single-cell CRISPR screen analysis

Single-cell CRISPR screens are a promising biotechnology for mapping regulatory elements to target genes at genome-wide scale. However, technical factors like sequencing depth impact not only expression measurement but also perturbation detection, creating a confounding effect. We demonstrate on two single-cell CRISPR screens how these challenges cause calibration issues. We propose SCEPTRE: analysis of single-cell perturbation screens via conditional resampling, which infers associations between perturbations and expression by resampling the former according to a working model for perturbation detection probability in each cell. SCEPTRE demonstrates very good calibration and sensitivity on CRISPR screen data, yielding hundreds of new regulatory relationships supported by orthogonal biological evidence.

Internal oligo(dT) priming in bulk and single cell RNA sequencing

Significant advances in RNA sequencing have been recently made possible by the use of oligo(dT) primers for simultaneous mRNA enrichment and reverse transcription priming. The associated increase in efficiency has enabled more economical bulk RNA sequencing methods as well as the advent of high throughput single cell RNA sequencing, now already one of the most widely adopted new methods in the study of transcriptomics. However, the effects of off-target oligo(dT) priming on gene expression quantification have not been fully appreciated. In the present study, we describe the extent, the possible causes, and the consequences of internal oligo(dT) priming across multiple publicly available datasets obtained from a variety of bulk and single cell RNA sequencing platforms. In order to explore and address this issue, we developed a computational algorithm for identification of sequencing read alignments that likely resulted from internal oligo(dT) priming and their subsequent removal from the data. Directly comparing filtered datasets to those obtained by an alternative method reveals significant improvements in gene expression measurement. Finally, we infer a list of genes whose expression quantification is most likely to be affected by internal oligo(dT) priming.

Arg-Vasotocin Directly Activates Isotocin Receptors and Induces COX2 Expression in Ovoviviparous Guppies

Oxytocin (OT) is a crucial regulator of reproductive behaviors, including parturition in mammals. Arg-vasopressin (AVP) is a nonapeptide homologous to Arg-vasotocin (AVT) in teleosts that has comparable affinity for the OT receptor. In the present study, ovoviviparous guppies (Poecilia reticulata) were used to study the effect of AVT on delivery mediated by the activation of prostaglandin (PG) biosynthesis via isotocin (IT) receptors (ITRs). One copy each of it and avt and two copies of itrs were identified in guppies. The results of the affinity assay showed that various concentrations of AVT and IT (10−6, 10−7, and 10−8 mol/L) significantly activated itr1 (P < 0.05). In vitro experiments revealed significant upregulation (P < 0.05) of cyclooxygenase 2 (cox2), which is the rate-limiting enzyme involved in PG biosynthesis, and itr1 by AVT and IT. Furthermore, dual in situ hybridization detected positive signals for itr1 and cox2 at the same site, implying that ITR1 may regulate cox2 gene expression. Measurement of prostaglandin F2a (PGF2a) concentrations showed that AVT induced PGF2a synthesis (P < 0.05) and that the effect of IT was not significant. Finally, intraperitoneal administration of PGF2a significantly induced premature parturition of guppies. This study is the first to identify and characterize AVT and ITRs in guppies. The findings suggest that AVT promotes PG biosynthesis via ITR and that PGF2a induces delivery behavior in ovoviviparous guppies.

Measuring Farm Animal Emotions—Sensor-Based Approaches

Understanding animal emotions is a key to unlocking methods for improving animal welfare. Currently there are no ‘benchmarks’ or any scientific assessments available for measuring and quantifying the emotional responses of farm animals. Using sensors to collect biometric data as a means of measuring animal emotions is a topic of growing interest in agricultural technology. Here we reviewed several aspects of the use of sensor-based approaches in monitoring animal emotions, beginning with an introduction on animal emotions. Then we reviewed some of the available technological systems for analyzing animal emotions. These systems include a variety of sensors, the algorithms used to process biometric data taken from these sensors, facial expression, and sound analysis. We conclude that a single emotional expression measurement based on either the facial feature of animals or the physiological functions cannot show accurately the farm animal’s emotional changes, and hence compound expression recognition measurement is required. We propose some novel ways to combine sensor technologies through sensor fusion into efficient systems for monitoring and measuring the animals’ compound expression of emotions. Finally, we explore future perspectives in the field, including challenges and opportunities.

Influence of immunomodulation on intracellular cytokine expression by spleen T-helpers of mice immunized by Yersinia pestis EV NIIEG

Aim. To characterize the intracellular expression of cytokines by spleen T-helpers and the spontaneous production of cytokines in the blood of BALB/c mice immunized with Yersinia pestis EV NIIEG against the background of immunomodulation.Materials and methods. Intracellular expression of CD4+IFN-γ+, CD4+IL-4+, CD4+IL-17+ was determined in mice spleen cell suspensions by flow cytometry, IFN-γ and IL-10 were measured in ELISA in blood supernatants on day 3 and day 21 after the immunization with Y. pestis EV against the background of immunomodulation. On day 21 after the immunization animals were infected by Y. pestis 231 at a dose of 400 LD50.Results. Differences in cytokine response to studied drugs, correlated with CD4+IFN-γ+ levels in animals, were identified. On day 3, a significant decrease in CD4+IFN-γ+ was observed in response to Y. pestis EV and to recombinant gamma interferon (Ingaron). A significant increase in CD4+IFN-γ+ was detected in response to vaccine strain administered with azoximer bromide (Polyoxidonium). Intracellular expression of IFN-γ, IL-4 and IL-17 increased on day 21by an average of 2,3 times when immunomodulators were used in the immunization schedule. In addition, on day 21 a significant (p ˂ 0.05) increase in the proportion of T-helpers expressing IFN-γ, as well as in level of spontaneous IFN-γ production in blood supernatants was observed only in animals immunized by schedules that included immunomodulators. After the challenge with Y. pestis 231 of animals previously immunized by schedules that included Polyoxidonium, the correlation analysis confirmed the association (r = 0,94; p = 0,0004) of mice survival with intensity of CD4+IFN-γ+ expression.Conclusion. The data obtained confirm the effectiveness of Polyoxidonium application in experimental animal Y. pestis EV immunization schedule and the usefulness of intracellular cytokine expression measurement for assessment of the level of protection following the immunization.

Conditional resampling improves calibration and sensitivity in single-cell CRISPR screen analysis

Single-cell CRISPR screens are an emerging biotechnology promising unprecedented insights into gene regulation. However, the analysis of these screens presents significant statistical challenges. For example, technical factors like sequencing depth impact not only expression measurement but also perturbation detection, creating a confounding effect. We demonstrate on two recent large-scale single-cell CRISPR screens how these challenges cause calibration issues among existing analysis methods. To address these challenges, we propose SCEPTRE: analysis of single-cell perturbation screens via conditional resampling. This methodology, designed to avoid calibration issues due to technical confounders and expression model misspecification, infers associations between perturbations and expression by resampling the former according to a working model for perturbation detection probability in each cell. SCETPRE demonstrates excellent calibration and sensitivity on the CRISPR screen data and yields 200 new regulatory relationships, many of which are supported by existing functional data.