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Biology subjects

McGrath, P.

Publications and source records attributed to McGrath, P..

5 recordsLinked to original sources

Do Topographic Deep ANN Models of the Primate Ventral Stream Predict the Perceptual Effects of Direct IT Cortical Interventions?

Ever-advancing artificial neural network (ANN) models of the ventral visual stream capture core object recognition behavior and the neural mechanisms underlying it with increasing precision. These models take images as input, propagate through simulated neural representations that resemble biological neural representations at all stages of the primate ventral stream, and produce simulated behavioral choices that resemble primate behavioral choices. We here extend this modeling approach to make and test predictions of neural intervention experiments. Specifically, we enable a new prediction regime for topographic deep ANN (TDANN) models of primate visual processing through the development of perturbation modules that translate micro-stimulation, optogenetic suppression, and muscimol suppression into changes in model neural activity. This unlocks the ability to predict the behavioral effects from particular neural perturbations. We compare these predictions with the key results from the primate IT perturbation experimental literature via a suite of nine corresponding benchmarks. Without any fitting to the benchmarks, we find that TDANN models generated via co-training with both a spatial correlation loss and a standard categorization task qualitatively predict all nine behavioral results. In contrast, TDANN models generated via random topography or via topographic unit arrangement after classification training predict less than half of those results. However, the models quantitative predictions are consistently misaligned with experimental data, over-predicting the magnitude of some behavioral effects and under-predicting others. None of the TDANN models were built with separate model hemispheres and thus, unsurprisingly, all fail to predict hemispheric-dependent effects. Taken together, these findings indicate that current topographic deep ANN models paired with perturbation modules are reasonable guides to predict the qualitative results of direct causal experiments in IT, but that improved TDANN models will be needed for precise quantitative predictions.

neuroscience↗

A scalable, GMP-compatible, autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa

BackgroundGene editing in induced pluripotent stem (iPS) cells has been hailed to enable new cell therapies for various monogenetic diseases including dystrophic epidermolysis bullosa (DEB). However, manufacturing, efficacy and safety roadblocks have limited the development of genetically corrected, autologous iPS cell-based therapies. MethodsWe developed Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a new generation GMP-compatible (cGMP), reproducible, and scalable platform to produce autologous clinical-grade iPS cell-derived organotypic induced skin composite (iSC) grafts to treat incurable wounds of patients lacking type VII collagen (C7). DEBCT uses a combined high-efficiency reprogramming and CRISPR-based genetic correction single step to generate genome scar- free, COL7A1 corrected clonal iPS cells from primary patient fibroblasts. Validated iPS cells are converted into epidermal, dermal and melanocyte progenitors with a novel 2D organoid differentiation protocol, followed by CD49f enrichment and expansion to minimize maturation heterogeneity. iSC product characterization by single cell transcriptomics was followed by mouse xenografting for disease correcting activity at 1 month and toxicology analysis at 1-6 months. Culture-acquired mutations, potential CRISPR-off targets, and cancer-driver variants were evaluated by targeted and whole genome sequencing. FindingsiPS cell-derived iSC grafts were reproducibly generated from four recessive DEB patients with different pathogenic mutations. Organotypic iSC grafts onto immune-compromised mice developed into stable stratified skin with functional C7 restoration. Single cell transcriptomic characterization of iSCs revealed prominent holoclone stem cell signatures in keratinocytes and the recently described Gibbin-dependent signature in dermal fibroblasts. The latter correlated with enhanced graftability. Multiple orthogonal sequencing and subsequent computational approaches identified random and non-oncogenic mutations introduced by the manufacturing process. Toxicology revealed no detectable tumors after 3-6 months in DEBCT- treated mice. InterpretationDEBCT successfully overcomes previous roadblocks and represents a robust, scalable, and safe cGMP manufacturing platform for production of a CRISPR-corrected autologous organotypic skin graft to heal DEB patient wounds.

bioengineering↗

A beneficial genomic rearrangement creates multiple versions of calcipressin in C. elegans

Gene duplication is a major source of genetic novelty and evolutionary adaptation, providing a molecular substrate that can generate biological complexity and diversity (Ohno 1967, Taylor and Raes 2004). Despite an abundance of genomic evidence from extant organisms suggesting the importance of gene duplication, consensus about how they arise and functionally diversify is lacking (Innan and Kondrashov 2010). In the process of studying the adaptation of laboratory strains of C. elegans to new food sources, we identified a recombinant inbred line (RIL) with higher relative fitness and hyperactive exploration behavior compared to either parental strain. Using bulk-segregant analysis and short-read resequencing, we identified a de novo beneficial, complex rearrangement of the rcan-1 gene, which we resolved into five new unique tandem inversion/duplications using Oxford Nanopore long-read sequencing. rcan-1 encodes an ortholog to human RCAN1/DSCR1, which has been implicated as a causal gene for Down syndrome (Fuentes, Genesca et al. 2000). The genomic rearrangement in rcan-1 causes two complete and two truncated versions of the rcan-1 coding region, with a variety of modified promoter and 3 regions, which ultimately reduce whole-body gene expression. This rearrangement does not phenocopy a loss-of-function allele, which indicates that the rearrangement was necessary for the observed fitness gains. Our results demonstrate that adaptation can occur through unexpectedly complex genetic changes that can simultaneously duplicate and diversify a gene, providing the molecular substrate for future evolutionary change.

evolutionary biology↗

Evolution of sperm competition: Natural variation and genetic determinants of Caenorhabditis elegans sperm size

Sperm morphology is critical for sperm competition and thus for reproductive fitness. In the male-hermaphrodite nematode Caenorhabditis elegans, sperm size is a key feature of sperm competitive ability. Yet despite extensive research, the molecular mechanisms regulating C. elegans sperm size and the genetic basis underlying its natural variation remain unknown. Examining 97 genetically distinct C. elegans strains, we observe significant heritable variation in male sperm size but genome-wide association mapping did not yield any QTL (Quantitative Trait Loci). While we confirm larger male sperm to consistently outcompete smaller hermaphrodite sperm, we find natural variation in male sperm size to poorly predict male fertility and competitive ability. In addition, although hermaphrodite sperm size also shows significant natural variation, male and hermaphrodite sperm size do not correlate, implying a sex-specific genetic regulation of sperm size. To elucidate the molecular basis of intraspecific sperm size variation, we focused on recently diverged laboratory strains, which evolved extreme sperm size differences. Using mutants and quantitative complementation tests, we demonstrate that variation in the gene nurf-1 - previously shown to underlie the evolution of improved hermaphrodite reproduction - also explains the evolution of reduced male sperm size. This result illustrates how adaptive changes in C. elegans hermaphrodite function can cause the deterioration of a male-specific fitness trait due to a sexually antagonistic variant, representing an example of intralocus sexual conflict with resolution at the molecular level. Our results further provide first insights into the genetic determinants of C. elegans sperm size, pointing at an involvement of the NURF chromatin remodelling complex.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC=\"FIGDIR/small/501486v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (166K):\norg.highwire.dtl.DTLVardef@1ff917org.highwire.dtl.DTLVardef@11a5e4corg.highwire.dtl.DTLVardef@250996org.highwire.dtl.DTLVardef@1989580_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

Modeling of a negative feedback mechanism explains age-dependent genetic architecture in reproduction in domesticated C. elegans strains

Most biological traits and common diseases have a strong but complex genetic basis, controlled by large numbers of genetic variants with small contributions to a trait or disease risk. The effect-size of most genetic variants is not absolute, but can depend on a number of factors including the age and genetic background of an organism. In order to understand the mechanisms that cause these changes, we are studying heritable trait differences between two domesticated strains of C. elegans. We previously identified a major effect locus, caused by a mutation in a component of the NURF chromatin remodeling complex, that regulated reproductive output in an age-dependent manner. The effect-size of this locus changes from positive to negative over the course of an animals reproductive lifespan. Using a previously published macroscale model of egg-laying rate in C. elegans, we show how time-dependent effect-size can be explained by an unequal use of sperm combined with negative feedback between sperm and ovulation rate. We validate a number of key predictions of this model using controlled mating experiments and quantification of oogenesis and sperm use. By incorporating this model into QTL mapping, we identify and partition new QTLs into specific aspects of the egg-laying process. Finally, we show how epistasis between two genetic variants is predicted by this modeling as a consequence of unequal use of sperm. This work demonstrates how modeling of multicellular communication systems can improve our ability to predict and understand the role of genetic variation on a complex phenotype. Negative autoregulatory feedback loops, common in transcriptional regulation, could play an important role in modifying genetic architecture in other traits.\n\nAUTHOR SUMMARYComplex traits are influenced not only by the individual effects of genetic variants, but also how these variants interact with the environment, age, and each other. While complex genetic architectures seem to be ubiquitous in natural traits, little is known about the mechanisms that cause them. Here we identify an example of age-dependent genetic architecture controlling the rate and timing of reproduction in the hermaphroditic nematode C. elegans. Using computational modeling, we demonstrate how this age-dependent genetic architecture can arise as a consequence of two factors: hormonal feedback on oocytes mediated by major sperm protein (MSP) released by sperm stored in the spermatheca and life history differences in sperm use caused by genetic variants. Our work also suggests how age-dependent epistasis can emerge from multicellular feedback systems.

genetics↗