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Biology subjects

Davis, E. E.

Publications and source records attributed to Davis, E. E..

7 recordsLinked to original sources

Not all memory declines with age: Neural correlates of implicit associative memory in younger and older adults.

While explicit associative memory declines with age, implicit associative memory remains preserved. Few studies have examined the neural basis of implicit associative memory in aging, and it remains unclear whether the hippocampus is required as it is more often associated with explicit associative memory. While undergoing functional magnetic resonance imaging, young and old adults completed a speeded object categorization task in which they viewed pictured objects with superimposed words. Implicit memory was tested by presenting intact (original pairs) and rearranged pairs (items previously presented, but not together) from encoding while participants did the same categorization task. Associative priming was defined as faster reaction times (behavioural associative priming) and less activation for intact than rearranged pairs at retrieval (neural associative priming). Whole-brain analyses revealed neural associative priming in occipitotemporal and frontal regions that did not differ by age. A region of interest analysis (using subject-specific masks of medial temporal lobe regions) showed that only older adults had greater posterior hippocampal activation to intact than rearranged items at test, though activation in the hippocampus did not relate to behavioural associative priming. In contrast, greater behavioural associative priming was related to greater neural associative priming in the perirhinal cortex in both age groups. Together, these findings suggest that implicit associative priming remains intact with age, possibly because it relies on additional processes outside the hippocampus such as perirhinal-dependent unitization.

neuroscience↗

Three-dimensional flow assessment of microvascular beds with interstitial space

The health and function of microvascular beds are dramatically impacted by the mechanical forces that they experience due to fluid flow. These fluid flow-generated forces are challenging to measure directly and are typically calculated from experimental flow data. However, current computational fluid dynamics (CFD) models either employ truncated 2D models or overlook the presence of extraluminal flows within the interstitial space between vessels that result from the permeability of the endothelium lining the vessels, which are crucial components affecting flow dynamics. To address this, we present a bottom-up modeling approach that assesses fluid flow in 3D-engineered vessel networks featuring an endothelial lining and interstitial space. Using image processing algorithms to segment 3D confocal image stacks from engineered capillary networks, we reconstructed a 3D computational model of the networks. We incorporated vascular permeability and matrix porosity values to model the contributions of the endothelial lining and interstitial spaces to the flow dynamics in the networks. Simulations suggest that including the endothelial monolayer and the interstitium significantly affects the predicted flow magnitude in the vessels and flow profiles in the interstitium. To demonstrate the importance of these factors, we showed experimentally and computationally that while cytokine (IL-1{beta}) treatment did not affect the network architecture, it significantly increased vessel permeability and resulted in a dramatic decrease in wall shear stresses and flow velocities intraluminally within the networks. In conclusion, this framework offers a robust methodology for studying flow dynamics in 3D in vitro vessel networks, enhancing our understanding of vascular physiology and pathology. TRANSLATIONAL IMPACT STATEMENTThis study introduces a new approach to modeling and flow assessment in 3D microvascular beds and surrounding interstitial spaces. Modeling interstitial space and endothelial monolayer thickness is essential for capturing fluid leakage from the microvascular network into the interstitial space and vice versa when the endothelial monolayer permeability is significantly affected in pathological conditions. Our approach to modeling 3D vascular networks can be used in vivo and in clinical settings to understand flow in tissue microvasculature and its surroundings under disease and healthy conditions.

bioengineering↗

Leveraging biobank-scale rare and common variant analyses to identify ASPHD1 as the main driver of reproductive traits in the 16p11.2 locus

Whereas genome-wide association studies (GWAS) allowed identifying thousands of associations between variants and traits, their success rate in pinpointing causal genes has been disproportionately low. Here, we integrate biobank-scale phenotype data from carriers of a rare copy-number variant (CNV), Mendelian randomization and animal modeling to identify causative genes in a GWAS locus for age at menarche (AaM). We show that the dosage of the 16p11.2 BP4-BP5 interval is correlated positively with AaM in the UK and Estonian biobanks and 16p11.2 clinical cohorts, with a directionally consistent trend for pubertal onset in males. These correlations parallel an increase in reproductive tract disorders in both sexes. In support of these observations, 16p11.2 mouse models display perturbed pubertal onset and structurally altered reproductive organs that track with CNV dose. Further, we report a negative correlation between the 16p11.2 dosage and relative hypothalamic volume in both humans and mice, intimating a perturbation in the gonadotropin-releasing hormone (GnRH) axis. Two independent lines of evidence identified candidate causal genes for AaM; Mendelian randomization and agnostic dosage modulation of each 16p11.2 gene in zebrafish gnrh3:egfp models. ASPHD1, expressed predominantly in brain and pituitary gland, emerged as a major phenotype driver; and it is subject to modulation by KCTD13 to exacerbate GnRH neuron phenotype. Together, our data highlight the power of an interdisciplinary approach to elucidate disease etiologies underlying complex traits.

genomics↗

Analysis of single nucleotide variants in CRISPR-Cas9 edited zebrafish embryos shows no evidence of off-target inflation

Therapeutic applications of CRISPR-Cas9 gene editing have spurred innovation in Cas9 enzyme engineering and single guide RNA (sgRNA) design algorithms to minimize potential off-target events. While recent work in rodents outlines favorable conditions for specific editing and uses a trio design to control for the contribution of natural genome variation, the potential for CRISPR-Cas9 to induce de novo mutations in vivo remains a topic of interest. In zebrafish, we performed whole exome sequencing (WES) on two generations of offspring derived from the same founding pair: 54 exomes from control and CRISPR-Cas9 edited embryos in the first generation (F0), and 16 exomes from the progeny of inbred F0 pairs in the second generation (F1). We did not observe an increase in the number of transmissible variants in edited individuals in F1, nor in F0 edited mosaic individuals, arguing that in vivo editing does not precipitate an inflation of deleterious point mutations.

developmental biology↗

Oligogenic effects of 16p11.2 copy number variation on craniofacial development

A copy number variant (CNV) of 16p11.2, which encompasses 30 genes, is associated with developmental and psychiatric disorders, head size and body mass. The genetic mechanisms that underlie these associations are not understood. To elucidate the effects of genes on development, we exploited the quantitative effects of CNV on craniofacial structure in humans and model organisms. We show that reciprocal deletion and duplication of 16p11.2 have characteristic "mirror" effects on craniofacial features that are conserved in human, rat and mouse. By testing gene dosage effects on the shape of the mandible in zebrafish, we show that the distribution of effects for all individual genes is consistent with that of the CNV, and some combinations have non-additive effects. Our results suggest that, at minimum, one third of genes within the 16p11.2 region influence craniofacial development, and the facial gestalt of each CNV represents a product of 30 dosage effects. HighlightsO_LIReciprocal CNVs of 16p11.2 have mirror effects on craniofacial structure. Copy number is associated with a positive effect on nasal and mandibular regions and a negative effect on frontal regions of the face. C_LIO_LIEffects of CNV on craniofacial development in human are well conserved in rat and mouse models of 16p11.2 deletion and duplication. C_LIO_LI7/30 genes each independently have significant effects on the shape of the mandible in zebrafish; these include SPN, C16orf54, SEZ6L2, ASPHD1, TAOK2, INO80E and FAM57B. Others (MAPK3, MVP, KCTD13) have detectable effects only in combination. C_LIO_LIOverexpression of 30 genes individually showed a distribution of effects that was skewed in the same direction as that of the full duplication, suggesting that specific facial features represent the net of all individual effects combined. C_LI

genetics↗

Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy

The influence of genetic background on driver mutations is well established; however, the mechanisms by which the background interacts with Mendelian loci remains unclear. We performed a systematic secondary-variant burden analysis of two independent Bardet-Biedl syndrome (BBS) cohorts with known recessive biallelic pathogenic mutations in one of 17 BBS genes for each individual. We observed a significant enrichment of trans-acting rare nonsynonymous secondary variants compared to either population controls or to a cohort of individuals with a non-BBS diagnosis and recessive variants in the same gene set. Strikingly, we found a significant over-representation of secondary alleles in chaperonin-encoding genes, a finding corroborated by the observation of epistatic interactions involving this complex in vivo. These data indicate a complex genetic architecture for BBS that informs the biological properties of disease modules and presents a model paradigm for secondary-variant burden analysis in recessive disorders.

genetics↗

Actin Impacts The Late Stages Of Prion Formation And Prion Propagation

In yeast, the [PSI+] and [PIN+] prions are aggregated forms of the Sup35 and Rnq1 proteins, respectively. The cellular mechanisms that underlie the formation and propagation of these prion states are not clearly understood. Our previous work suggested that actin networks play a role in early and late steps of the formation of [PSI+]. To further explore how actin impacts yeast prions, we turned to a set of actin point mutants. We found that the disruption of actin cables, either by an actin destabilizing drug or the act1-101 mutant, can enhance prion formation during the later stages of prion formation. Our data suggest that under normal conditions, actin cables play a role in limiting the inheritance of newly made prion particles to daughter cells. We also found actin can impact prion propagation. The act1-122 mutant, which contains a substitution in the fimbrin binding region, destabilized the [PIN+] prion over time. This is the first evidence that actin has a role in [PIN+] propagation. Taken together, our findings reveal novel roles for actin in the formation and propagation of prions.

cell biology↗