Biology subjects

Lee, A. J.

Publications and source records attributed to Lee, A. J..

48 records · Page 3Linked to original sources

bioRxiv2020

Intrinsic brain activity gradients dynamically coordinate functional connectivity states

A central goal of systems neuroscience is to determine the functional-anatomical basis of brain-wide activity dynamics. While brain activity patterns appear to be low-dimensional and guided by spatial gradients, the set of gradients remains provisional and their mode of interaction is unclear. Here we applied deep learning-based dimensionality reduction to task-free fMRI images to derive an intrinsic latent space of human brain activity. Each dimension represented a discrete, dynamically fluctuating spatial activity gradient. The principal dimension was a novel unipolar sensory-association gradient underlying the global signal. A small set of gradients appeared to underlie key functional connectomics phenomena. Different task activation patterns were generated by gradients adopting task-specific configurations. Dynamical systems modelling revealed that gradients interact via state-specific coupling parameters, allowing accurate forecasts and simulations of task-specific brain activity. Together, these findings indicate that a small set of dynamic, interacting gradients create the repertoire of possible brain activity states.

neuroscience↗

bioRxiv2020

Three-Dimensional Label-Free Imaging and Quantification of Migrating Cells during Wound Healing

The wound healing assay provides essential information about collective cell migration and cell-to-cell interactions. It is a simple, effective, and widely used tool for observing the effect of numerous chemical treatments on wound healing speed. To perform and analyze a wound healing assay, various imaging techniques have been utilized. However, image acquisition and analysis are often limited in two-dimensional space or require the use of exogenous labeling agents. Here, we present a method for imaging large-scale wound healing assays in a label-free and volumetric manner using optical diffraction tomography (ODT). We performed quantitative high-resolution three-dimensional (3D) analysis of cell migration over a long period without difficulties such as photobleaching or phototoxicity. ODT enables the reconstruction of the refractive index (RI) tomogram of unlabeled cells, which provides both structural and biochemical information about the individual cell at subcellular resolution. Stitching multiple RI tomograms enables long-term (24 h) and large field-of-view imaging (> 800 x 400 m2) with a lateral resolution of 110 nm. We demonstrated the thickness changes of leading cells and studied the effects of cytochalasin D. The 3D RI tomogram also revealed increased RI values in leading cells compared to lagging cells, suggesting the formation of a highly concentrated subcellular structure. STATEMENT OF SIGNIFICANCEThe wound healing assay is a simple but effective tool for studying collective cell migration (CCM) that is widely used in biophysical studies and high-throughput screening. However, conventional imaging and analysis methods only address two-dimensional properties in a wound healing assay, such as gap closure rate. This is unfortunate because biological cells are complex 3D structures, and their dynamics provide significant information about cell physiology. Here, we presented three-dimensional (3D) label-free imaging for wound healing assays and investigated the 3D dynamics of CCM. High-resolution subcellular structures as well as their collective dynamics were imaged and analyzed quantitatively. Our label-free quantitative 3D analysis method provides a unique opportunity to study the behavior of migrating cells during the wound healing process.

biophysics↗

bioRxiv2020

Correcting for experiment-specific variability in expression compendia can remove underlying signals

MotivationIn the last two decades, scientists working in different labs have assayed gene expression from millions of samples. These experiments can be combined into compendia and analyzed collectively to extract novel biological patterns. Technical variability, sometimes referred to as batch effects, may result from combining samples collected and processed at different times and in different settings. Such variability may distort our ability to interpret and extract true underlying biological patterns. As more multi-experiment, integrative analysis methods are developed and available data collections increase in size, it is crucial to determine how technical variability affect our ability to detect desired patterns when many experiments are combined ObjectiveWe sought to determine the extent to which an underlying signal was masked by technical variability by simulating compendia comprised of data aggregated across multiple experiments. MethodWe developed a generative multi-layer neural network to simulate compendia of gene expression experiments from large-scale microbial and human datasets. We compared simulated compendia before and after introducing varying numbers of sources of undesired variability. ResultsWe found that the signal from a baseline compendium was obscured when the number of added sources of variability was small. Perhaps as expected, applying statistical correction methods rescued the underlying signal in these cases. As the number of sources of variability increased, surprisingly, we observed that detecting the original signal became increasingly easier even without correction. In fact, applying statistical correction methods reduced our power to detect the underlying signal. ConclusionWhen combining a modest number of experiments, it is best to correct for experiment-specific noise. However, when many experiments are combined, statistical correction reduces ones ability to extract underlying patterns.

bioinformatics↗

bioRxiv2019

Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin

Pseudomonas aeruginosa strains with loss-of-function mutations in the transcription factor are frequently encountered in the clinic and the environment. Among the characteristics common to LasR-defective (LasR-) strains is increased activity of the transcription factor Anr, relative to their LasR+ counterparts, in low oxygen conditions. One of the Anr-regulated genes that was highly induced in the LasR-strains encoded a putative oxygen-binding hemerythrin encoded by PA14_42860 (PA1673) which we named mhr for microoxic hemerythrin. Purified P. aeruginosa Mhr protein contained the predicted di-iron center and binds oxygen with a Kd of 1 {micro}M. Both Anr and Mhr were necessary for fitness in lasR+ and lasR mutant strains in colony biofilms grown in microoxic conditions, and the effects were more striking in the lasR mutant. Among genes in the Anr regulon, mhr was most closely co-regulated with the Anr-controlled high affinity cytochrome c oxidase genes and in the absence of high affinity cytochrome c oxidase activity, deletion of mhr no longer caused a fitness disadvantage suggesting that Mhr works in concert with microoxic respiration. We demonstrate that Anr and Mhr contribute to LasR-strain fitness even in the normoxic biofilm conditions, and metabolomics data indicate that in a lasR mutant, expression of Anr-regulated mhr leads to differences in metabolism in cells grown on LB and artificial sputum medium. Together these data indicate that increased Anr activity in microoxically-grown lasR mutants confers an advantage in part for its regulation of the O2 binding protein Mhr.\n\nSignificancePseudomonas aeruginosa, a versatile bacterium that both lives in environmental habitats and causes life-threatening opportunistic infections, uses quorum sensing to coordinate gene expression with cell density. The lasR gene, which encodes a quorum sensing regulator, is often deleteriously mutated in clinical isolates. Interestingly, LasR-strains have high activity of the oxygen-sensitive transcription factor Anr in microoxic conditions. This report identifies and characterizes an Anr-regulated microoxic hemerythrin that reversibly binds oxygen. We showed both anr and mhr are critical to fitness in microoxia, and these genes uniquely benefit LasR-strains in normoxia. Our findings enrich our understanding of the success of P. aeruginosa as a pulmonary resident through its propensity to lose LasR functionality in the context of low-oxygen infection environments.

microbiology↗

bioRxiv2019

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Here we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility (P. aureginosa only). We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. We conclude that, while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. We finally report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bioontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

bioinformatics↗

bioRxiv2018

A new class of constitutively active super-enhancers is associated with fast recovery of 3D chromatin loops

Super-enhancers or stretch enhancers are clusters of active enhancers that often coordinate cell-type specific gene regulation. However, little is known about the function of super-enhancers beyond gene regulation. In this study, through a comprehensive analysis of super-enhancers in 30 human cell/tissue types, we identified a new class of super-enhancers which are constitutively active across most cell/tissue types. These common super-enhancers are associated with universally highly expressed genes in contrast to the canonical definition of super-enhancers that assert cell-type specific gene regulation. In addition, the genome sequence of these super-enhancers is highly conserved by evolution and among humans, advocating their universal function in genome regulation. Integrative analysis of 3D chromatin loops demonstrates that, in comparison to the cell-type specific super-enhancers, the cell-type common super-enhancers present a striking association with rapidly recovering loops. We propose that a new class of super-enhancers may play an important role in the early establishment of 3D chromatin structure.\n\nBackgroundSuper-enhancers or stretch enhancers are defined by a strong enrichment of mediators and transcription-regulating proteins, appearing to play a deterministic role in cellular identity by controlling the expression of cell-type specific genes[1, 2]. Previous studies have revealed the critical function of super-enhancers during development and differentiation[3]. The enrichment of disease-associated single nucleotide polymorphism (SNP) in super-enhancers compared to that of typical enhancers proposed a substantial link between super-enhancers and many complex human diseases[2]. In addition, a set of recent studies have proposed potential functions of super-enhancers in the extremely long-range chromatin communications and the establishment of 3D chromatin loops[4]. These results suggest a more universal role of super-enhancers in genome regulation apart from cell-type specific gene regulation, but little is known about the mechanisms underlying these various functions. To extend the current knowledge of super-enhancers and their biological roles, we conducted a comprehensive analysis of super-enhancer activities across 30 human cell/tissue types. Our analysis suggests that a substantial number of super-enhancers exhibits prevalent activities across cell-types in terms of H3K27ac signals, and that these non-canonical super-enhancers are involved in the formation of fast recovering chromatin loops.\n\nNoteA genome browser session has been set up for visualization of the super-enhancer domains described in the current study- https://genome.ucsc.edu/cgi-bin/hgTracks?hgS-doOtherUser=submit&hgS-otherUserName=abundantiavosliberabit&hgS-otherUserSessionName=SuperEnhancerDomain

genomics↗

bioRxiv2018

Facial masculinity is only weakly correlated with handgrip strength in young adult women

ObjectivesAncestrally, strength is likely to have played a critical role in determining the ability to obtain and retain resources and the allocation of social status among humans. Responses to facial cues of strength are therefore thought to play an important role in human social interaction. Although many researchers have proposed that sexually dimorphic facial morphology is reliably correlated with physical strength, evidence for this hypothesis is somewhat mixed. Moreover, to date, only one study has investigated the putative relationship between facial masculinity and physical strength in women. Consequently, we tested for correlations between handgrip strength and objective measures of face-shape masculinity.\n\nMethods531 women took part in the study. We measured each participants handgrip strength (dominant hand). Sexual dimorphism of face shape was objectively measured from each face photograph using two methods: discriminant analysis and vector analysis. These methods use shape components derived from principal component analyses of facial landmarks to measure the probability of the face being classified as male (discriminant analysis method) or to locate the face on a female-male continuum (vector analysis method).\n\nResultsOur analyses revealed that handgrip strength is, at best, only weakly correlated with facial masculinity in women. There was a weak significant association between handgrip strength and one measure of womens facial masculinity. The relationship between handgrip strength and our other measure of womens facial masculinity was not significant.\n\nDiscussionTogether, these results do not support the hypothesis that face-shape masculinity is an important cue of physical strength, at least in women.

animal behavior and cognition↗

bioRxiv2018

Dissecting bacterial resistance and resilience in antibiotic responses

An essential property of microbial communities is the ability to survive a disturbance. Survival can be achieved through resistance, the ability to absorb effects of a disturbance without a significant change, or resilience, the ability to recover after being perturbed by a disturbance. These concepts have long been applied to the analysis of ecological systems, though their interpretations are often subject to debate. Here we show that this framework readily lends itself to the dissection of the bacterial response to antibiotic treatment, where both terms can be unambiguously defined. The ability to tolerate the antibiotic treatment in the short term corresponds to resistance, which primarily depends on traits associated with individual cells. In contrast, the ability to recover after being perturbed by an antibiotic corresponds to resilience, which primarily depends on traits associated with the population. This framework effectively reveals the phenotypic signatures of bacterial pathogens expressing extended spectrum {beta}-lactamases (ESBLs), when treated by a {beta}-lactam antibiotic. Our analysis has implications for optimizing treatment of these pathogens using a combination of a {beta}-lactam and a {beta}-lactamase (Bla) inhibitor. In particular, our results underscore the need to dynamically optimize combination treatments based on the quantitative features of the bacterial response to the antibiotic or the Bla inhibitor.

cell biology↗

bioRxiv2017

Hormonal regulation of women’s prosocial, but not sexual, responses to kinship cues

Mate preferences and mating-related behaviors are hypothesized to change over the menstrual cycle in ways that function to increase reproductive fitness. Results of recent large-scale studies suggest that many of these hormone-linked behavioral changes are less robust than was previously thought. One hypothesis that has not yet been subject to a large-scale test is the proposal that womens preference for associating with male kin is down-regulated during the ovulatory (high-fertility) phase of the menstrual cycle. Consequently, we used a longitudinal design to investigate the relationship between changes in womens steroid hormone levels and their perceptions of faces experimentally manipulated to possess kinship cues. Analyses suggested that women viewed mens faces displaying kinship cues more positively (i.e., more attractive and trustworthy) when estradiol-to-progesterone ratio was high. Since estradiol-to-progesterone ratio is positively associated with conception risk during the menstrual cycle, these results directly contradict the hypothesis that womens preference for associating with male kin is down-regulated during the ovulatory (high-fertility) phase of the menstrual cycle. Data and code are publicly available at https://osf.io/wnhma/.

animal behavior and cognition↗

bioRxiv2017

DAFi: A Directed Recursive Filtering and Clustering Approach to Data-Driven Identification of Cell Populations from Polychromatic Flow Cytometry Data

Computational methods for identification of cell populations from high-dimensional flow cytometry data are changing the paradigm of cytometry bioinformatics. Data clustering is the most common computational approach to unsupervised identification of cell populations from multidimensional cytometry data. We found that combining recursive filtering and clustering with constraints converted from the user manual gating strategy can effectively identify overlapping and rare cell populations from smeared data that would have been difficult to resolve by either a single run of data clustering or manual segregation. We named this new method DAFi: Directed Automated Filtering and Identification of cell populations. Design of DAFi preserves the data-driven characteristics of unsupervised clustering for identifying novel cell-based biomarkers, but also makes the results interpretable to experimental scientists as in supervised classification through mapping and merging the high-dimensional data clusters into the user-defined 2D gating hierarchy. By recursive data filtering before clustering, DAFi can uncover small local clusters which are otherwise difficult to identify due to the statistical interference of the irrelevant major clusters. Quantitative assessment of cell type specific characteristics demonstrates that the population proportions calculated by DAFi, while being highly consistent with those by expert centralized manual gating, have smaller technical variance than those from individual manual gating analysis. Visual examination of the dot plots showed that the boundaries of the DAFi-identified cell populations followed the natural shapes of the data distributions. To further exemplify the utility of DAFi, we show that DAFi can incorporate the FLOCK clustering method to identify novel cell-based biomarkers. Implementation of DAFi supports options including clustering, bisecting, slope-based gating, and reversed filtering to meet various auto-gating needs from different scientific use cases.

bioinformatics↗

bioRxiv2017

Women’s preferences for facial masculinity are not related to their hormonal status

Although widely cited as strong evidence that sexual selection has shaped human facial attractiveness judgments, evidence that preferences for masculine characteristics in mens faces are related to womens hormonal status is equivocal and controversial. Consequently, we conducted the largest ever longitudinal study of the hormonal correlates of womens preferences for facial masculinity (N=584). Analyses showed no compelling evidence that preferences for facial masculinity were related to changes in womens salivary steroid hormone levels. Furthermore, both within-subject and between-subject comparisons showed no evidence that oral contraceptive use decreased masculinity preferences. However, women generally preferred masculinized over feminized versions of mens faces, particularly when assessing mens attractiveness for short-term, rather than long-term, relationships. Our results do not support the hypothesized link between womens preferences for facial masculinity and their hormonal status.

animal behavior and cognition↗

bioRxiv2017

Within-Woman Hormone-Attractiveness Correlations Are Not Simply Byproducts Of Between-Women Hormone-Attractiveness Correlations

Putative associations between sex hormones and attractive physical characteristics in women are central to many theories of human physical attractiveness and mate choice. Although such theories have become very influential, evidence that physically attractive and unattractive women have different hormonal profiles is equivocal. Consequently, we investigated hypothesized relationships between salivary estradiol and progesterone and two aspects of womens physical attractiveness that are commonly assumed to be correlated with levels of these hormones: facial attractiveness (N=249) and waist-to-hip ratio (N=247). Our analyses revealed no evidence that women with more attractive faces or lower (i.e., more attractive) waist-to-hip ratios had higher levels of estradiol or progesterone. These results do not support the influential hypothesis that between-woman differences in physical attractiveness are related to estradiol and/or progesterone.

animal behavior and cognition↗