Prediction of on-target and off-target activity of CRISPR-Cas13d guide RNAs using deep learning

Transcriptome engineering applications in living cells with RNA-targeting CRISPR effectors depend on accurate prediction of on-target activity and off-target avoidance. Here we design and test ~200,000 RfxCas13d guide RNAs targeting essential genes in human cells with systematically designed mismatches and insertions and deletions (indels). We find that mismatches and indels have a position- and context-dependent impact on Cas13d activity, and mismatches that result in G-U wobble pairings are better tolerated than other single-base mismatches. Using this large-scale dataset, we train a convolutional neural network that we term targeted inhibition of gene expression via gRNA design (TIGER) to predict efficacy from guide sequence and context. TIGER outperforms the existing models at predicting on-target and off-target activity on our dataset and published datasets. We show that TIGER scoring combined with specific mismatches yields the first general framework to modulate transcript expression, enabling the use of RNA-targeting CRISPRs to precisely control gene dosage.

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox

Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms are the lack of experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental design. To address these gaps, we developed and methodically tested a strategy which pairs the RNA-targeting CRISPR/Cas13d system with guide RNAs that span exon-exon junctions in the mature RNA. We performed a high-throughput essentiality screen, quantitative RT-PCR assays, and PacBio long read sequencing to affirm our ability to specifically target and robustly knockdown individual RNA isoforms. In parallel, we provide computational tools for experimental design and screen analysis. Considering all possible splice junctions annotated in GENCODE for multi-isoform genes and our gRNA efficacy predictions, we estimate that our junction-centric strategy can uniquely target up to 89% of human RNA isoforms, including 50,066 protein-coding and 11,415 lncRNA isoforms. Importantly, this specificity spans all splicing and transcriptional events, including exon skipping and inclusion, alternative 5' and 3' splice sites, and alternative starts and ends.

An Exploratory Study on the Central Nervous Correlates of Sexual Excitation and Sexual Inhibition

The Sexual Inhibition/Sexual Excitation Scales (SIS/SES) measure sexual excitation and sexual inhibition proneness. We used SIS and SES scores of 62 heterosexual teleiophilic men (M_age 34.3, SD = 9.9) to predict brain activation levels during the presentation of male and female visual sexual stimuli in a magnetic resonance imaging (MRI) scanner. Statistical analyses revealed significant correlations. SES and SIS1 scores were positively associated with brain activation in various brain regions during the presentation of both male and female stimuli. SIS2 turned out to be a weaker predictor of brain activation, still revealing one significant correlation in the right lateral orbitofrontal cortex. Significant regions for SES and SIS1 were, among others, primary and supplementary motor areas, the caudate nucleus, the dorsal anterior cingulate cortex, anterior insula, and prefrontal areas. Our study can be seen as an exploratory investigation of SIS and SES with means of functional brain imaging. The results provide a promising contribution to the assertion of neurophysiological systems of sexual inhibition and excitation proneness.

«Mein Körper gehört mir» – Kulturgeschichte und Psychologie des Piercing und Tattoo

In heutiger Zeit können Tätowierungen und Piercings nicht länger nur als von gesellschaftlich Ausgegrenzten oder Randgruppen praktizierte, destruktive Akte der Selbstverstümmelung angesehen werden. Körperliche Markierungen finden sich in nahezu allen vorindustriellen Kulturen auf der ganzen Welt, die ihre Kunstpraktiken auf die magisch-mythische Weltsicht prähistorischer Zeiten beziehen. Die Prävalenz von Tattoo und Piercing in der deutschen Gesamtbevölkerung beträgt 8,5% bzw. 6,8%. Arbeitslose junge Männer und junge Frauen, die nicht in einer festen Partnerschaft leben, zeigen besonders hohe Prävalenzen. Körpermodifikationen korrelieren relativ stark mit «Sensation Seeking», besonders bei jungen Frauen. Sie sind zumeist Ausdruck von Individualität sowie Identitätsgenerierung sowie einem veränderten Körper- und Modebewusstsein und einem veränderten Kunstverständnis. Sie können jedoch auch einen Hinweis auf Identitätssuche und vermehrtem Risikoverhalten geben.

[Relationship, resistance and insight as depicted in measures concerning form and content of speech - a textual analysis of the course of a female in-patient with eating disorder]

OBJECTIVES

This multi-methodical single case study examines how relationship, resistance and insight, the important therapeutic factors, are conveyed in a therapeutic process.

METHODS

For depicting interaction the textual parameters - direct speech, acknowledgement tokens, activity of speech and personal pronouns - of Formal Psycholinguistic Text Analysis (Overbeck et al., 1996) are applied. The activity of the unconscious theme is measured by the Interferenzindex (Argelander, 1984). The link of emotional experiences with words is depicted by the Computerized Referential Activity method (Mergenthaler and Bucci, 1999). The attainment of emotional insight in the Model of the Therapeutic Cycle is perceived via the Emotion-/Abstraction-Patterns (Mergenthaler, 1997).

RESULTS

Three phases are discriminated accordingly: Resistance, characterised by defensive intellectualization, symbolic representation on the basis of the secure relationship and emotional insight and detachment.

CONCLUSIONS

The validity of the results in this single case study is guaranteed by the multi-methodical strategy.

[Three therapeutic processes of inpatients with eating disorders compared with the Core Conflict Relationship Method (CCRT)]

In this article the results of a research with the CCRT-method on the psychotherapies of three in-patients suffering from eating disorders are presented. The CCRT describes recurrent internal and interpersonal relationship patterns in narratives. Each therapy session was recorded on tape and transcribed. The CCRT components were identified from the verbatim transcripts. All three patients clearly showed a negative self-perception and despite a more graded attitude regarding other people they felt rejected by the community throughout the entire therapy. The CCRT of each patient was different: patient 1. had conflicts between dependence and independence with increasing autonomy; patient 2. had great symbiotic desires, which at the beginning of the therapy were warded off with a performance ideal; patient 3. showed self-assertion and an increasing level of openness against the community, despite a high level of fear and self-isolation at the onset of therapy. Despite methodological deficiencies the CCRT method proved to be sensitive enough to show similarities and differences among the individual courses of treatment.