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van Leeuwen, J.

Publications and source records attributed to van Leeuwen, J..

3 recordsLinked to original sources

Working memory implements distinct maintenance mechanisms depending on task goals

Working memory is the function by which we temporarily maintain information to achieve current task goals. Models of working memory typically debate where this information is stored, rather than how it is stored. Here we ask instead what neural mechanisms are involved in storage, and how these mechanisms change as a function of task goals. Participants either had to reproduce the orientation of a memorized bar (continuous recall task), or identify the memorized bar in a search array (visual search task). The sensory input and retention interval were identical in both tasks. Next, we used decoding and forward modeling on multivariate electroencephalogram (EEG) and time-frequency decomposed EEG to investigate which neural signals carry more informational content during the retention interval. In the continuous recall task, working memory content was preferentially carried by induced oscillatory alpha-band power, while in the visual search task it was more strongly carried by the distribution of evoked (consistently elevated and non-oscillatory) EEG activity. To show the independence of these two signals, we were able to remove informational content from one signal without affecting informational content in the other. Finally, we show that the tuning characteristics of both signals change in opposite directions depending on the current task goal. We propose that these signals reflect oscillatory and elevated firing-rate mechanisms that respectively support location-based and object-based maintenance. Together, these data challenge current models of working memory that place storage in particular regions, but rather emphasize the importance of different distributed maintenance signals depending on task goals.\n\nSignificance statement (120 words)Without realizing, we are constantly moving things in and out of our minds eye, an ability also referred to as working memory. Where did I put my screwdriver? Do we still have milk in the fridge? A central question in working memory research is how the brain maintains this information temporarily. Here we show that different neural mechanisms are involved in working memory depending on what the memory is used for. For example, remembering what a bottle of milk looks like invokes a different neural mechanism from remembering how much milk it contains: the first one primarily involved in being able to find the object, and the other one involving spatial position, such as the milk level in the bottle.

neuroscience

Evaluation and Design of Genome-wide CRISPR/Cas9 Knockout Screens

The adaptation of CRISPR/Cas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs), targeting human protein-coding genes and encoded in viral vectors, have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we re-analyze 17 genome-scale knockout screens in human cell lines from three research groups using three different genome-scale gRNA libraries, using the Bayesian Analysis of Gene Essentiality (BAGEL) algorithm to identify essential genes, to refine and expand our previously defined set of human core essential genes, from 360 to 684 genes. We use this expanded set of reference Core Essential Genes (CEG2), plus empirical data from six CRISPR knockout screens, to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines.

systems biology

Functional Annotation of Chemical Libraries across Diverse Biological Processes

Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells to a compound, revealing chemical-genetic interactions that can elucidate a compounds mode of action. We developed a highly parallel and unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized, diagnostic mutant collection that is predictive all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode sequencing protocol, enabling assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened 7 different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.

systems biology