Biology subjects

van Leeuwen, J.

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

9 recordsLinked to original sources

bioRxiv2025

Microbial and organic matter composition jointly drive phosphorus cycling genes and phosphorus availability in Amazonian soils

Soil phosphorus (P) is a limiting factor for vegetation growth in the Amazon rainforest, where plants depend on microorganisms for organic matter cycling and nutrient uptake. However, forest-to-agriculture conversion changes plant-microbe-soil interactions, affecting P cycling, which may additionally changed by land-use intensity. This study examined the 30-year effects of converting a primary forest into two contrasting systems: a low-intensity agroforest and a high-intensity citrus plantation. We investigated how microbial and water-extractable organic matter (WEOM) composition interacted with soil physicochemical attributes and P fractions (labile, moderately labile, non-labile, and residual). Agroforest soils retained physicochemical and enzymatic attributes similar to the primary forest, while soils of the citrus plantation showed increased P in all fractions due to fertilization and reduced soil organic matter content, mainly in deeper layers. Microbial and WEOM composition patterns reflected land-use, with agroforest representing an intermediate state between primary forest and citrus plantation. Proteobacteria and nutrient-rich WEOM were more abundant in the agroforest, whereas Ascomycota and nutrient-poor WEOM predominated the citrus plantation. Genes related to "P acquisition" were more abundant in agroforest soils, while genes related to "P-compound synthesis" were more abundant in citrus plantation. Labile P was negatively correlated with genes related to microbial metabolism, suggesting that reduced P availability may induce a boost in microbial activity for internal P-cycling. These findings demonstrate that forest-to-agriculture conversion strongly affects microbial functions, with responses aligning with land-use intensity and WEOM resource availability. Nonetheless, microbes adapt by shifting strategies: prioritizing mineralization and solubilization or favoring biosynthesis depending on P availability.

microbiology↗

bioRxiv2025

A global genetic interaction map of a human cell reveals conserved principles of genetic networks

We generated a genome-scale, genetic interaction network from the analysis of more than 4 million double mutants in the haploid human cell line, HAP1. The network maps [~]90,000 genetic interactions, including thousands of extreme synthetic lethal and genetic suppression interactions. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes, pathways, biological processes, and cellular compartments. Comparative analyses showed that general principles of genetic networks are conserved from yeast to human cells. A genetic interaction network mapped in a single genetic background complements the DepMap gene co-essentiality network, recapitulating many of the same biological connections and also capturing unique functional information to reveal roles of uncharacterized genes and molecular determinants of specific cancer cell line genetic dependencies.

systems biology↗

bioRxiv2025

Quantitative analysis of genetic interactions in human cells from genome-wide CRISPR-Cas9 screens

Genetic interaction (GI) networks in model organisms have revealed how combinations of genome variants can impact phenotypes. To advance efforts toward a reference human GI network, we developed the quantitative Genetic Interaction (qGI) score, a method for precise GI measurement from genome-wide CRISPR-Cas9 screens in different query mutants constructed in a single human cell line. We found surprising prevalent systematic variation unrelated to GIs in CRISPR screen data, including both genomically linked effects and functionally coherent covariation. Leveraging [~]40 control screens in wild-type cells and half a billion differential fitness effect measurements, we developed a pipeline for CRISPR screen data processing and normalization to correct these artifacts and measure accurate, quantitative GIs. We also comprehensively characterized GI reproducibility by characterizing 4 - 5 biological replicates for [~]125,000 unique gene pairs. The qGI framework enables systematic identification of human GIs and provides broadly applicable strategies for analyzing context-specific CRISPR screen data.

bioinformatics↗

bioRxiv2024

Genetic suppression interactions are highly conserved across genetic backgrounds

Genetic suppression occurs when the phenotypic defects caused by a deleterious mutation are rescued by another mutation. Suppression interactions are of particular interest for genetic diseases, as they identify ways to reduce disease severity, thereby potentially highlighting avenues for therapeutic intervention. To what extent suppression interactions are influenced by the genetic background in which they operate remains largely unknown. However, a high degree of suppression conservation would be crucial for developing therapeutic strategies that target suppressors. To gain an understanding of the effect of the genetic context on suppression, we isolated spontaneous suppressor mutations of temperature sensitive alleles of SEC17, TAO3, and GLN1 in three genetically diverse natural isolates of the budding yeast Saccharomyces cerevisiae. After identifying and validating the genomic variants responsible for suppression, we introduced the suppressors in all three genetic backgrounds, as well as in a laboratory strain, to assess their specificity. Ten out of eleven tested suppression interactions were conserved in the four yeast strains, although the extent to which a suppressor could rescue the temperature sensitive mutant varied across genetic backgrounds. These results suggest that suppression mechanisms are highly conserved across genetic contexts, a finding that is potentially reassuring for the development of therapeutics that mimic genetic suppressors.

genetics↗

bioRxiv2022

Global analysis of suppressor mutations that rescue human genetic defects

Genetic suppression occurs when the deleterious effects of a primary "query" mutation, such as a disease-causing mutation, are rescued by a suppressor mutation elsewhere in the genome. To capture existing knowledge on suppression relationships between human genes, we examined 2,400 published papers for potential interactions identified through either genetic modification of cultured human cells or through association studies in patients. The resulting network encompassed 476 unique suppression interactions that frequently linked genes that function in the same biological process. Suppressors were strongly enriched for genes with a role in stress response or signaling, suggesting that deleterious mutations can often be buffered by modulating signaling cascades or immune responses. Suppressor mutations tended to be deleterious when they occurred in absence of the query mutation, in apparent contrast with their protective role in the presence of the query. We formulated and quantified mechanisms of genetic suppression that could explain 71% of interactions and provided mechanistic insight into disease pathology. Finally, we used these observations to accurately predict suppressor genes in the human genome. The emerging frequency of suppression interactions and range of underlying mechanisms suggest that compensatory mutations may exist for the majority of genetic diseases.

genomics↗

bioRxiv2020

Diverse natural variants suppress mutations in hundreds of essential genes

The consequence of a mutation can be influenced by the context in which it operates. For example, loss of gene function may be tolerated in one genetic background, but lead to lethality in another. The extent to which mutant phenotypes are malleable, the complexity of the architecture of modifiers, and the identities of causal genes and pathways remain largely unknown. Here, we measure the fitness effects of ~1,500 temperature sensitive alleles of yeast essential genes in the context of variation from ten different natural genetic backgrounds, and map the modifiers for 19 combinations. Altogether, fitness defects for 183 of the 530 tested genes (35%) could be suppressed by standing genetic variation in at least one wild strain. Suppression was generally driven by gain-of-function of a single, strong modifier gene. The validated causes included both variants in protein interaction partners or pathway members suppressing specific genes, as well as general modifiers altering the effect of many temperature sensitive alleles. The emerging frequency of suppression and range of possible suppression mechanisms suggest that a substantial fraction of monogenic diseases could be repressed by modulating other gene products.

genetics↗

bioRxiv2017

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↗

bioRxiv2017

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↗

bioRxiv2017

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↗