title: Dementia risk factors modify hubs but leave other connectivity measures unchanged in asymptomatic individuals: a graph theoretical analysis.

abstract:
BackgroundAlzheimers Disease (AD) is the most common form of dementia with genetic and environmental risk contributing to its development. Graph theoretical analyses of brain networks constructed from structural and functional MRI measurements have identified connectivity changes in AD and individuals with mild cognitive impairment (MCI). However, brain connectivity in asymptomatic individuals at risk of AD remains poorly understood.

MethodsWe analysed diffusion-weighted magnetic resonance imaging (dMRI) data from 160 asymptomatic individuals (38-71 years) from the Cardiff Ageing and Risk of Dementia Study (CARDS). We calculated white matter tracts and constructed whole-brain, default-mode-network and visual structural brain networks that incorporate multiple structural metrics as edge weights. We then calculated the relationship of three AD risk factors, namely Apolipoprotein-E {varepsilon}4 genotype (APOE4), family history (FH) of dementia, and central obesity, on graph theoretical measures and hubs.

ResultsWe observed no risk-related differences in clustering coefficients, characteristic path lengths, eccentricity, diameter and radius across the whole-brain, default-mode-network or visual system. However, a hub in the right paracentral lobule was present in all high-risk groups (FH, APOE4, obese) but absent in low-risk groups (no FH, APOE4-ve, healthy weight).

DiscussionWe identified no risk-related effects on graph theoretical metrics in the structural brain networks of cognitively healthy individuals. However, high-risk was associated with a hub in the right paracentral lobule, an area with motor and sensory functions related to the lower limb. If this phenotype is shown to predict symptom development in longitudinal studies, it could be used as an early biomarker of AD.

Impact StatementAlzheimers Disease is a common form of dementia which to date has no cure. Identifying early biomarkers will aid the discovery and development of treatments that may slow AD progression in the future. In this paper we report that asymptomatic individuals at heightened risk of dementia due to their family history, Apolipoprotein-E {varepsilon}4 genotype and body adiposity have a hub in the right paracentral lobule which is absent in low-risk groups. If this phenotype were to predict the development of symptoms in a longitudinal study of the same cohort, it could provide an early biomarker of disease progression.


title: Epileptic Spike Detection Using Neural Networks with Linear-Phase Convolutions

abstract: To cope with the lack of highly skilled professionals, machine learning with proper signal processing is key for establishing automated diagnostic-aid technologies with which to conduct epileptic electroencephalogram (EEG) testing. In particular, frequency filtering with the appropriate passbands is essential for enhancing the biomarkers--such as epileptic spike waves--that are noted in the EEG. This paper introduces a novel class of neural networks (NNs) that have a bank of linear-phase finite impulse response filters at the first layer as a preprocessor that can behave as bandpass filters that extract biomarkers without destroying waveforms because of a linear-phase condition. Besides, the parameters of the filters are also data-driven. The proposed NNs were trained with a large amount of clinical EEG data, including 15,833 epileptic spike waveforms recorded from 50 patients, and their labels were annotated by specialists. In the experiments, we compared three scenarios for the first layer: no preprocessing, discrete wavelet transform, and the proposed data-driven filters. The experimental results show that the trained data-driven filter bank with supervised learning behaves like multiple bandpass filters. In particular, the trained filter passed a frequency band of approximately 10-30 Hz. Moreover, the proposed method detected epileptic spikes, with the area under the receiver operating characteristic curve of 0.967 in the mean of 50 intersubject validations.

category: neuroscience


title: Genome-wide methylation data improves dissection of the effect of smoking on body mass index.

abstract: Variation in obesity-related traits has a genetic basis with heritabilities between 40 and 70%. While the global obesity pandemic is usually associated with environmental changes related to lifestyle and socioeconomic changes, most genetic studies do not include all relevant environmental covariates, so genetic contribution to variation in obesity-related traits cannot be accurately assessed. Some studies have described interactions between a few individual genes linked to obesity and environmental variables but there is no agreement on their total contribution to differences between individuals. Here we compared self-reported smoking data and a methylation-based proxy to explore the effect of smoking and genome-by-smoking interactions on obesity related traits from a genome-wide perspective to estimate the amount of variance they explain. Our results indicate that exploiting omic measures can improve models for complex traits such as obesity and can be used as a substitute for, or jointly with, environmental records to better understand causes of disease.

category: genomics


title: Antifragile therapy

abstract: Antifragility is a recently coined word used to describe the opposite of fragility. Systems or organisms can be described as antifragile if they derive a benefit from systemic variability, volatility, randomness, or disorder. Herein, we introduce a mathematical framework to quantify the fragility or antifragility of cancer cell lines in response to treatment variability. This framework enables straightforward prediction of the optimal dose treatment schedule for a range of treatment schedules with identical cumulative dose. We apply this framework to non-small-cell lung cancer cell lines with evolved resistance to ten anti-cancer drugs. We show the utility of this antifragile framework when applied to 1) treatment resistance, and 2) collateral sensitivity of sequential monotherapies.

category: cancer biology


title: Neural Network Organization for Courtship Song Feature Detection in Drosophila

abstract: Animals communicate using sounds in a wide range of contexts, and auditory systems must encode behaviorally relevant acoustic features to drive appropriate reactions. How feature detection emerges along auditory pathways has been difficult to solve due to challenges in mapping the underlying circuits and characterizing responses to behaviorally relevant features. Here, we study auditory activity in the Drosophila melanogaster brain and investigate feature selectivity for the two main modes of fly courtship song, sinusoids and pulse trains. We identify 24 new cell types of the intermediate layers of the auditory pathway, and using a new connectomic resource, FlyWire, we map all synaptic connections between these cell types, in addition to connections to known early and higher-order auditory neurons - this represents the first map of the auditory pathway. We additionally determine the sign (excitatory or inhibitory) of most synapses in this auditory connectome. We find that auditory neurons display a continuum of preferences for courtship song modes, and that neurons with different song mode preferences are highly interconnected in a network that lacks hierarchical structure. Among this network, frequency tuning is centered on the range of frequencies present in song, whereas pulse rate tuning extends to rates outside of song, suggesting that these neurons form a basis set for downstream processing. Our study provides new insights into the organization of auditory coding within the Drosophila brain.


title: Role of cell polarity dynamics and motility in pattern formation due to contact dependent signalling

abstract: A key challenge in biology is to understand how spatiotemporal patterns and structures arise during the development of an organism. An initial aggregate of spatially uniform cells develops and forms the differentiated structures of a fully developed organism. On the one hand, contact-dependent cell-cell signalling is responsible for generating a large number of complex, self-organized, spatial patterns in the distribution of the signalling molecules. On the other hand, the motility of cells coupled with their polarity can independently lead to collective motion patterns that depend on mechanical parameters influencing tissue deformation, such as cellular elasticity, cell-cell adhesion and active forces generated by actin and myosin dynamics. Although modelling efforts have, thus far, treated cell motility and cell-cell signalling separately, experiments in recent years suggest that these processes could be tightly coupled. Hence, in this paper, we study how the dynamics of cell polarity and migration influence the spatiotemporal patterning of signalling molecules. Such signalling interactions can occur only between cells that are in physical contact, either directly at the junctions of adjacent cells or through cellular protrusional contacts. We present a vertex model which accounts for contact-dependent signalling between adjacent cells and between non-adjacent neighbours through long protrusional contacts that occur along the orientation of cell polarization. We observe a rich variety of spatiotemporal patterns of signalling molecules that is influenced by polarity dynamics of the cells, relative strengths of adjacent and non-adjacent signalling interactions, range of polarized interaction, signalling activation threshold, relative time scales of signalling and polarity orientation, and cell motility. Though our results are developed in the context of Delta-Notch signalling, they are sufficiently general and can be extended to other contact dependent morpho-mechanical dynamics.

category: biophysics


title: Distinct roles of nonmuscle myosin II isoforms for establishing tension and elasticity during cell morphogenesis

abstract: Nonmuscle myosin II (NM II) is an integral part of essential cellular processes, including adhesion and migration. Mammalian cells express up to three isoforms termed NM IIA, B, and C. We used U2OS cells to create CRISPR/Cas9-based knockouts of all three isoforms and analyzed the phenotypes on homogeneous substrates, in collagen gels, and on micropatterned substrates. We find that NM IIA is essential to build up cellular tension during initial stages of force generation, while NM IIB is necessary to elastically stabilize NM IIA-generated tension. A scale-bridging mathematical model explains our observations by relating actin fiber stability to the molecular rates of the myosin crossbridge cycle. A dynamic cell stretch/release experiment confirms these predictions and in addition reveals a novel role for NM IIC, namely the ability to establish tensional homeostasis.


title: Coming together - symbiont acquisition and early development in deep-sea Bathymodiolus mussels

abstract: Symbiotic associations between animals and microorganisms are widespread and have a profound impact on the ecology, behaviour, physiology, and evolution of the host. Research on deep-sea mussels of the genus Bathymodiolus has revealed how chemosynthetic symbionts sustain their host with energy, allowing them to survive in the nutrient-poor environment of the deep ocean. However, to date, we know little about the initial symbiont colonization and how this is integrated into the early development of these mussels. Here we analysed the early developmental life stages of B. azoricus, "B". childressi and B. puteoserpentis and the changes that occur once the mussels are colonized by symbionts. We combined synchrotron-radiation based {micro}CT, correlative light and electron microscopy and fluorescence in situ hybridization to show that the symbiont colonization started when the animal settled on the sea floor and began its metamorphosis into an adult animal. Furthermore, we observed aposymbiotic life stages with a fully developed digestive system which was streamlined after symbiont acquisition. This suggests that bathymodiolin mussels change their nutritional strategy from initial filter-feeding to relying on the energy provided by their symbionts. After [~]35 years of research on bathymodiolin mussels, we are beginning to answer fundamental ecological questions concerning their life cycle and the establishment of symbiosis.

category: zoology


title: Canonical babbling during vocal turn taking and independent vocal play

abstract: There is a growing body of research emphasizing the role of social and endogenous motivations in human development. The present study evaluated canonical babbling across the second-half year of life using all-day recordings of 98 infants participating in a longitudinal study. Canonical babbling ratios were calculated from human coding along with Likert-scale ratings on vocal turn taking and vocal play in each segment. Ratios across all infants were significantly elevated during high turn taking and also during high vocal play. We conclude that both social and endogenous motivations may drive infants tendencies to produce their most advanced vocal forms.

category: developmental biology


title: Piezo2 mediates ultrasonic hearing via cochlear outer hair cells in mice

abstract:
Ultrasonic hearing is exploited for hunting and navigation as in echolocation by microbats and bottleneck dolphins, and for social communication like ultrasonic vocalization by mice and rats. However, the molecular and cellular basis for ultrasonic hearing is not known yet. Here we show that knockout of the mechanosensitive ion channel PIEZO2 in cochlea disrupts the ultrasonic hearing but not the low-frequency hearing in mice, as shown by audiometry and acoustically-associative freezing behavior. Deletion of Piezo2 in the outer hair cells specifically abolishes the associative learning of the mice upon hearing the ultrasonic frequency. Ex vivo cochlear Ca2+ imaging revealed that the ultrasonic transduction requires both PIEZO2 and the hair-cell mechanotransduction channel. Together, our study demonstrates that the outer hair cells are the effector cells with PIEZO2 as an essential molecule for ultrasonic hearing in mice.

Significance StatementSome animals have evolved an incredible ability for vocalizing and hearing ultrasonic frequencies that is inaudible for humans (> 20 kHz). For many years, it has been considered that animals hear ultrasonic frequencies with their cochlear hair cells, using the identical set of mechanotransduction molecules in the hair bundles for hearing audible frequencies. Here, we show that the mice lacking the mechanosensitive ion channel PIEZO2 hardly hear ultrasonic frequencies, while can still be sensitive to audible frequencies. Thus, animals may use a partially different mechanism for sensing physiological ultrasound.


title: Inferring Thalamocortical Monosynaptic Connectivity In-Vivo

abstract:
Abstract/SummaryAs the tools to simultaneously record electrophysiological signals from large numbers of neurons within and across brain regions become increasingly available, this opens up for the first time the possibility of establishing the details of causal relationships between monosynaptically connected neurons and the patterns of neural activation that underlie perception and behavior. Although recorded activity across synaptically connected neurons has served as the cornerstone for much of what we know about synaptic transmission and plasticity, this has largely been relegated to ex-vivo preparations that enable precise targeting under relatively well-controlled conditions. Analogous studies in-vivo, where image-guided targeting is often not yet possible, rely on indirect, data-driven measures, and as a result such studies have been sparse and the dependence upon important experimental parameters has not been well studied. Here, using in-vivo extracellular single unit recordings in the topographically aligned rodent thalamocortical pathway, we sought to establish a general experimental and computational framework for inferring synaptic connectivity. Specifically, attacking this problem within a statistical signal-detection framework utilizing experimentally recorded data in the ventral-posterior medial (VPm) region of the thalamus and the homologous region in layer 4 of primary somatosensory cortex (S1) revealed a trade-off between network activity levels needed for the data-driven inference and synchronization of nearby neurons within the population that result in masking of synaptic relationships. Taken together, we provide a framework for establishing connectivity in multi-site, multi-electrode recordings based on statistical inference, setting the stage for large-scale assessment of synaptic connectivity within and across brain structures.

New & NoteworthyDespite the fact that all brain function relies on the long-range transfer of information across different regions, the tools enabling us to measure connectivity across brain structures are lacking. Here, we provide a statistical framework for identifying and assessing potential monosynaptic connectivity across neuronal circuits from population spiking activity that generalizes to large-scale recording technologies that will help us to better understand the signaling within networks that underlies perception and behavior.


title: Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria

abstract:
The exchange of metabolites among different bacterial genotypes profoundly impacts the structure and function of microbial communities. However, the factors governing the establishment of these cross-feeding interactions remain poorly understood. While shared physiological features may facilitate interactions among more closely related individuals, a lower relatedness should reduce competition and thus increase the potential for synergistic interactions. Here we investigate how the relationship between a metabolite donor and recipient affects the propensity of strains to engage in unidirectional cross-feeding interactions. For this, we performed pairwise cocultivation experiments between four auxotrophic recipients and 25 species of potential amino acid donors. Auxotrophic recipients grew in the vast majority of pairs tested (78%), suggesting metabolic cross-feeding interactions are readily established. Strikingly, both the phylogenetic distance between donor and recipient and the dissimilarity of their metabolic networks were positively associated with the growth of auxotrophic recipients. Analysing the co-growth of species from a gut microbial community in-silico also revealed that recipient genotypes benefitted more from interacting with metabolically dissimilar partners, thus corroborating the empirical results. Together, our work identifies the metabolic dissimilarity between bacterial genotypes as key factor determining the establishment of metabolic cross-feeding interactions in microbial communities.

HighlightsO_LIThe exchange of essential metabolites is common in microbial communities
C_LIO_LIMetabolic cross-feeding interactions readily establish between auxotrophic and prototrophic bacterial strains
C_LIO_LIBoth the phylogenetic and the metabolic dissimilarity between donors and recipients determines the successful establishment of metabolic cross-feeding interactions
C_LI

category: ecology


title: Learning when effort matters: Neural dynamics underlying updating and adaptation to changes in performance efficacy

abstract: To determine how much cognitive control to invest in a task, people need to consider whether exerting control matters for obtaining rewards. In particular, they need to account for the efficacy of their performance - the degree to which rewards are determined by performance or by independent factors. Yet it remains unclear how people learn about their performance efficacy in an environment. Here we combined computational modeling with measures of task performance and EEG, to provide a mechanistic account of how people (a) learn and update efficacy expectations in a changing environment, and (b) proactively adjust control allocation based on current efficacy expectations. Across two studies subjects performed an incentivized cognitive control task while their performance efficacy (the likelihood that rewards are performance-contingent or random) varied over time. We show that people update their efficacy beliefs based on prediction errors - leveraging similar neural and computational substrates as those that underpin reward learning - and adjust how much control they allocate according to these beliefs. Using computational modeling, we show that these control adjustments reflect changes in information processing, rather than the speed-accuracy tradeoff. These findings demonstrate the neurocomputational mechanism through which people learn how worthwhile their cognitive control is.


title: Misoprostol Treatment Prevents Hypoxia-Induced Cardiac Dysfunction, Aberrant Cardiomyocyte Mitochondrial Dynamics and Permeability Transition Through Bnip3 Phosphorylation

abstract: Systemic hypoxia is a common element in most perinatal emergencies and is a known driver of Bnip3 expression in the neonatal heart. Bnip3 plays a prominent role in the evolution of necrotic cell death, disrupting ER calcium homeostasis and initiating mitochondrial permeability transition (MPT). Emerging evidence suggests a cardioprotective role for the prostaglandin E1 analogue misoprostol during periods of hypoxia, but the mechanisms for this protection are not completely understood. Using a combination of mouse and cell models, we tested if misoprostol is cardioprotective during neonatal hypoxic injury by altering Bnip3 function. Here we report that hypoxia elicits mitochondrial-fragmentation, MPT, reduced ejection fraction, and evidence of necroinflammation, which were abrogated with misoprostol treatment or Bnip3 knockout. Through molecular studies we show that misoprostol leads to PKA-dependent Bnip3 phosphorylation at threonine-181, and subsequent redistribution of Bnip3 from mitochondrial Opa1 and the ER through an interaction with 14-3-3 proteins. Taken together, our results demonstrate a role for Bnip3 phosphorylation in the regulation of cardiomyocyte contractile/metabolic dysfunction, and necroinflammation. Furthermore, we identify a potential pharmacological mechanism to prevent neonatal hypoxic injury.

category: cell biology


title: Misoprostol Treatment Prevents Hypoxia-Induced Cardiac Dysfunction Through a 14-3-3 and PKA regulatory motif on Bnip3


title: Simulations of Levy walk

abstract: We simulate stable distributions to study the ideal movement pattern for the spread of a virus using autonomous carrier. We observe Levy walks to be the most ideal way to spread and further study how the parameters in Levy distribution affects the spread.

category: animal behavior and cognition


title: Computational Model to Quantify the Growth of Antibiotic Resistant Bacteria in Wastewater

abstract:
Although wastewater and sewage systems are known to be significant reservoirs of antibiotic resistant bacterial populations and periodic outbreaks of drug resistant infection, there is little quantitative understanding of the drivers behind resistant population growth in these settings. In order to fill this gap in quantitative understanding of the development of antibiotic resistant infections in wastewater, we have developed a mathematical model synthesizing many known drivers of antibiotic resistance in these settings to help predict the growth of resistant populations in different environmental scenarios. A number of these drivers of drug resistant infection outbreak including antibiotic residue concentration, antibiotic interaction, chromosomal mutation and horizontal gene transfer, have not previously been integrated into a single computational model. We validated the outputs of the model with quantitative studies conducted on the eVOLVER continuous culture platform. Our integrated model shows that low levels of antibiotic residues present in wastewater can lead to increased development of resistant populations, and the dominant mechanism of resistance acquisition in these populations is horizontal gene transfer rather than acquisition of chromosomal mutations. Additionally, we found that synergistic antibiotic interactions lead to increased resistant population growth. These findings, consistent with recent experimental and field studies, provide new quantitative knowledge on the evolution of antibiotic resistant bacterial reservoirs, and the model developed herein can be adapted for use as a prediction tool in public health policy making, particularly in low income settings where water sanitation issues remain widespread and disease outbreaks continue to undermine public health efforts.

ImportanceThe rate at which antimicrobial resistance (AMR) has developed and spread throughout the world has increased in recent years, and according to the Review on Antimicrobial Resistance in 2014 it is suggested that the current rate will lead several million people AMR-related deaths by 205025. One major reservoir of resistant bacterial populations that has been linked to outbreaks of drug resistant bacterial infections, but is not well understood, is in wastewater settings, where antibiotic pollution is often present. Using ordinary differential equations incorporating several known drivers of resistance in wastewater, we find that interactions between antibiotic residues and horizontal gene transfer significantly affect the growth of resistant bacterial reservoirs.

category: bioengineering


title: Utilizing virtual experiments to increase understanding of discrepancies involving in vitro-in vivo predictions of hepatic clearance

abstract: We explore a virtual experiment strategy to discover plausible mechanism-based explanations for frequently inaccurate predictions of hepatic drug clearance made using established in vitro-in vivo extrapolation methods. We describe a three-protocol plan that uses validated software analogs of real in vitro and in vivo systems constructed using a common set of objects, components, spaces, and methods. Both systems utilize identical quasi-autonomous hepatocyte analogs containing enzyme-like objects. We parameterize concrete mobile objects (virtual compounds) to simulate the referent drugs disposition and removal characteristics in vitro and in vivo. The goal of Protocol one (Protocol two) is that measures of virtual compound removal using the in vitro analog (in vivo analog) map directly to the measurements used to compute intrinsic clearance (in vivo hepatic clearance). Protocol three, the focus of this work, requires achieving an essential cross-system validation target. For a subset of virtual compounds, measurements of unbound compounds entering hepatocytes (and their subsequent removal) during virtual in vitro experiments will directly predict corresponding measures made during virtual in vivo experiments. We study four highly permeable virtual compounds when their unbound fraction is fixed at one of seven values (0.05-1.0). Results span the range of hepatic extraction ratios. We achieve the cross-system validation target in 15 cases. In the other 13 cases, explanations of the in vitro-in vivo differences in disposition and removal trace to differences in compound-hepatocyte access within the two analogs during execution. The hepato-mimetic structural organization of hepatocytes within the in vivo analog, which is absent within the in vitro analog, is the determining factor. The results taken together support the feasibility of using the three-protocol plan to help explain observed in vitro-in vivo extrapolation discrepancies. We conjecture that, for some cases, the model mechanism-based explanations of discrepancies described herein will have wet-lab counterparts.


title: Expanding the Galaxy's reference data

abstract:
SummaryProperly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows to easily organize, retrieve, and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. Additionally, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenies remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS repository from GalaxyProject.org, with mirrors across the United States, Canada, Europe, and Australia, enabling easy use outside of Galaxy.

Availability and implementationThe ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 20.05, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull and released using an MIT license.

category: bioinformatics


title: Synaptic counts approximate synaptic contact area in Drosophila

abstract: The pattern of synaptic connections among neurons defines the circuit structure, which constrains the computations that a circuit can perform. The strength of synaptic connections is costly to measure yet important for accurate circuit modeling. It has been shown that synaptic surface area correlates with synaptic strength, yet in the emerging field of connectomics, most studies rely instead on the counts of synaptic contacts between two neurons. Here we quantified the relationship between synaptic count and synaptic area as measured from volume electron microscopy of the larval Drosophila central nervous system. We found that the total synaptic surface area, summed across all synaptic contacts from one presynaptic neuron to a postsynaptic one, can be accurately predicted solely from the number of synaptic contacts, for a variety of neurotransmitters. Our findings support the use of synaptic counts for approximating synaptic strength when modeling neural circuits.


title: Targeting host glycolysis as a strategy for antimalarial development.

abstract: Glycolysis controls cellular energy, redox balance, and biosynthesis. Antiglycolytic therapies are under investigation for treatment of obesity, cancer, aging, autoimmunity, and microbial diseases. Interrupting glycolysis is highly valued as a therapeutic strategy, because glycolytic disruption is generally tolerated in mammals. Unfortunately, anemia is a known dose-limiting side effect of these inhibitors and presents a major caveat to development of antiglycolytic therapies. We developed specific inhibitors of enolase - a critical enzyme in glycolysis - and validated their metabolic and cellular effects on human erythrocytes. Enolase inhibition increases erythrocyte susceptibility to oxidative damage and induces rapid and premature erythrocyte senescence, rather than direct hemolysis. We apply our model of red cell toxicity to address questions regarding erythrocyte glycolytic disruption in the context of Plasmodium falciparum malaria pathogenesis. Our study provides a framework for understanding red blood cell homeostasis under normal and disease states and clarifies the importance of erythrocyte reductive capacity in malaria parasite growth.

category: pharmacology and toxicology


title: CoRa -A general approach for quantifying biological feedback control

abstract: Feedback control is a fundamental underpinning of life, underlying homeostasis of biological processes at every scale of organization, from cells to ecosystems. The ability to evaluate the contribution and limitations of feedback control mechanisms operating in cells is a critical step for understanding and ultimately designing feedback control systems with biological molecules. Here, we introduce CoRa -or Control Ratio-, a general framework that quantifies the contribution of a biological feedback control mechanism to adaptation using a mathematically controlled comparison to an identical system that does not contain the feedback. CoRa provides a simple and intuitive metric with broad applicability to biological feedback systems.

category: systems biology


title: Smaller Hippocampal Volume among Black and Latinx Youth Living in High-Stigma Contexts

abstract:
BackgroundTo determine whether being raised in a stigmatizing context influences neurodevelopment in children.

MethodsWe drew data from one of the first national, multi-site neuroimaging studies with substantial variability in sociopolitical contexts: the Adolescent Brain and Cognitive Development study (N=11,534; M=9.9 years). We measured structural stigma surrounding gender, race, and Latinx ethnicity using objective state-level indicators of social policies and prejudicial attitudes and individual-level experiences of perceived discrimination, and examined associations with two neural markers: hippocampal volume and amygdala reactivity to threat.

ResultsIn a pre-registered analysis, we find that Black (B=-57.27, p=0.025) and Latinx (B=-41.02, p=0.037) youths raised in higher-stigma environments have smaller hippocampal volume than youths raised in low-stigma contexts, controlling for demographics and family socioeconomic status. This association was marginal among girls (p=0.082). The magnitude of the observed difference in hippocampal volume between high and low structural stigma contexts was equivalent to a $20,000 difference in annual family income. Stigmatizing environments were unrelated to hippocampal volume in non-stigmatized youth, providing evidence of specificity. Perceived discrimination was unrelated to hippocampal volume among any of the stigmatized groups. No associations between individual or structural forms of stigma and amygdala reactivity to threat were observed in the stigmatized groups.

ConclusionsWe provide novel evidence that an objective measure of stigma at the contextual level (structural stigma) may have a stronger influence on neurodevelopment than subjective perceptions of stigma measured at the individual level, suggesting that contextual approaches may yield new insights into neurodevelopment.


title: Scene wheels: Measuring perception and memory of real-world scenes with a continuous stimulus space

abstract: Precisely characterizing mental representations of visual experiences requires careful control of experimental stimuli. Recent work leveraging such stimulus control has led to important insights; however, these findings are constrained to simple visual properties like colour and line orientation. There remains a critical methodological barrier to characterizing perceptual and mnemonic representations of realistic visual experiences. Here, we introduce a novel method to systematically control visual properties of natural scene stimuli. Using generative adversarial networks (GAN), a state-of-art deep learning technique for creating highly realistic synthetic images, we generated scene wheels in which continuously changing visual properties smoothly transition between meaningful realistic scenes. To validate the efficacy of scene wheels, we conducted two behavioral experiments that assess perceptual and mnemonic representations attained from the scene wheels. In the perceptual validation experiment, we tested whether the continuous transition of scene images along the wheel is reflected in human perceptual similarity judgment. The perceived similarity of the scene images correspondingly decreased as distances between the images increase on the wheel. In the memory experiment, participants reconstructed to-be-remembered scenes from the scene wheels. Reconstruction errors for these scenes resemble error distributions observed in prior studies using simple stimulus properties. Importantly, perceptual similarity judgment and memory precision varied systematically with scene wheel radius. These findings suggest our novel approach offers a window into the mental representations of naturalistic visual experiences.


title: A General Birth-Death-Sampling Model for Epidemiology and Macroevolution

abstract: Birth-death stochastic processes are the foundation of many phylogenetic models and are widely used to make inferences about epidemiological and macroevolutionary dynamics. There are a large number of birth-death model variants that have been developed; these impose different assumptions about the temporal dynamics of the parameters and about the sampling process. As each of these variants was individually derived, it has been difficult to understand the relationships between them as well as their precise biological and mathematical assumptions. Without a common mathematical foundation, deriving new models is non-trivial. Here we unify these models into a single framework, prove that many previously developed epidemiological and macroevolutionary models are all special cases of a more general model, and illustrate the connections between these variants. This framework centers around a technique for deriving likelihood functions for arbitrarily complex birth-death(-sampling) models that will allow researchers to explore a wider array of scenarios than was previously possible. We then use this frame-work to derive general model likelihoods for both the "single-type" case in which all lineages diversify according to the same process and the "multi-type" case, where there is variation in the process among lineages. By re-deriving existing single-type birth-death sampling models we clarify and synthesize the range of explicit and implicit assumptions made by these models.

category: evolutionary biology


title: Topographical biomaterials instruct bacterial surface attachment and the in vivo host-pathogen response

abstract: Bio-instructive materials that prevent bacterial biofilm formation and drive an appropriate host immune response have the potential to significantly reduce the burden of medical device-associated infections. As bacterial surface attachment is sensitive to surface topography, we experimentally surveyed 2,176 combinatorially generated shapes using an unbiased high-throughput micro topographical polystyrene polymer chip screen. This identified topographies that reduced colonization in vitro by up to 15-fold compared with a flat surface for both motile and non-motile bacterial pathogens. Equivalent reductions were achieved on polyurethane, a polymer commonly used in medical devices. Using machine learning methods, a set of design rules based on generalisable topo-descriptors was established for predicting bacteria-resistant micro topographies. In a murine foreign body infection model, anti-attachment topographies were shown to be refractory to P. aeruginosa colonization and serendipitously, the fibrotic response to the implant was reduced, offering control of foreign body response using simple topographical patterning of non-eluting implants.

category: microbiology


title: Micro topographical instruction of bacterial attachment, biofilm formation and in vivo host response


title: Innate behavior sequence progression by peptide-mediated interorgan crosstalk

abstract: Innate behaviors consist of a succession of genetically-hardwired motor and physiological subprograms that can be coupled to drastic morphogenetic changes. How these integrative responses are orchestrated is not completely understood. Here, we provide insight into these mechanisms by studying pupariation, a multi-step innate behavior of fly larvae that is critical for survival during metamorphosis. We find that the steroid-hormone ecdysone triggers parallel pupariation neuromotor and morphogenetic subprograms, which include the induction of the relaxin-peptide hormone, Dilp8, in the epidermis. Dilp8 acts on six Lgr3-positive thoracic interneurons to couple both subprograms in time and to instruct neuromotor subprogram switching during behavior. Our work reveals that interorgan feedback gates progression between subunits of an innate behavior and points to an ancestral neuromodulatory function of relaxin signaling.


title: The landscape of antibody binding in SARS-CoV-2 infection

abstract: The search for potential antibody-based diagnostics, vaccines, and therapeutics for pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has focused almost exclusively on the spike (S) and nucleocapsid (N) proteins. Coronavirus membrane (M), ORF3a, and ORF8 proteins are humoral immunogens in other coronaviruses (CoVs) but remain largely uninvestigated for SARS-CoV-2. Here we use ultradense peptide microarray mapping to show that SARS-CoV-2 infection induces robust antibody responses to epitopes throughout the SARS-CoV-2 proteome, particularly in M, in which one epitope achieved excellent diagnostic accuracy. We map 79 B cell epitopes throughout the SARS-CoV-2 proteome and demonstrate that antibodies that develop in response to SARS-CoV-2 infection bind homologous peptide sequences in the six other known human CoVs. We also confirm reactivity against four of our top-ranking epitopes by enzyme-linked immunosorbent assay (ELISA). Illness severity correlated with increased reactivity to nine SARS-CoV-2 epitopes in S, M, N, and ORF3a in our population. Our results demonstrate previously unknown, highly reactive B cell epitopes throughout the full proteome of SARS-CoV-2 and other CoV proteins.

category: immunology


title: Medial prefrontal cortex has a causal role in selectively enhanced consolidation of emotional memories after a 24-hour delay: An iTBS study

abstract:
Previous research points to an association between retrieval-related activity in the medial prefrontal cortex (mPFC) and preservation of emotional information compared to co-occurring neutral information following sleep. Although the role of the mPFC in emotional memory likely begins at encoding, little research has examined how mPFC activity during encoding interacts with consolidation processes to enhance emotional memory. This issue was addressed in the present study using transcranial magnetic stimulation in conjunction with an emotional memory paradigm. Healthy young adults encoded negative and neutral scenes while undergoing concurrent TMS with a modified short intermittent theta burst stimulation (sTBS) protocol. Participants received stimulation to either the mPFC or an active control site (motor cortex) during the encoding phase. Recognition memory for scene components (objects and backgrounds) was assessed after a short (30-minute) and a long delay (24-hour, including a night of sleep) to obtain measures of specific and gist-based memory processes. The results demonstrated that, relative to control stimulation, sTBS to the mPFC enhanced memory for negative objects on the long delay test (collapsed across specific and gist-based memory measures). mPFC stimulation had no discernable effect on memory for objects on the short delay test nor on the background images at either test. These results suggest that mPFC activity occurring during encoding interacts with consolidation processes to preferentially preserve negatively salient information.

Significance StatementUnderstanding how emotional information is remembered over time is critical to understanding memory in the real world. The present study used noninvasive brain stimulation (repetitive transcranial magnetic stimulation, rTMS) to investigate the interplay between mPFC activity that occurs during memory encoding and its subsequent interactions with consolidation processes. rTMS delivered to the mPFC during encoding enhanced memory for negatively valenced pictures on a test following a 24-hr delay, with no such effect on a test occurring shortly after the encoding phase. These results are consistent with the hypothesis that emotional aspects of memories are differentially subjected to consolidation processes, and that the mPFC might contribute to this "tag-and-capture" mechanism during the initial formation of such memories.


title: Medial prefrontal cortex has a causal role in selectively enhanced consolidation of emotional memories after a 24-hour delay: A TBS study


title: Motor resonance is modulated by an object's weight distribution

abstract:
Transcranial magnetic stimulation (TMS) studies showed that corticospinal excitability (CSE) is modulated during observation of object lifting, an effect termed  motor resonance. Specifically, motor resonance is driven by movement features indicating object weight, such as object size or observed movement kinematics. We investigated in 16 humans (8 females) whether motor resonance is also modulated by an objects weight distribution. Participants were asked to lift an inverted T-shaped manipulandum with interchangeable center of mass after first observing an actor lift the same manipulandum. Participants and actor were instructed to minimize object roll and rely on constrained digit positioning during lifting. Constrained positioning was either collinear (i.e., fingertips on the same height) or noncollinear (i.e., fingertip on the heavy side higher than the one on the light side). The center of mass changed unpredictably before the actors lifts and participants were explained that their weight distribution always matched the actors one. Last, TMS was applied during both lift observation and planning of lift actions. Our results showed that CSE was similarly modulated during lift observation and planning: when participants observed or planned lifts in which the weight distribution was asymmetrically right-sided, CSE recorded from the thumb muscles was significantly increased compared to when the weight distribution was left-sided. During both lift observation and planning, this increase seemed to be primarily driven by the weight distribution and not specifically by the (observed) digit positioning or muscle contraction. In conclusion, our results indicate that complex intrinsic object properties such as weight distributions can modulate activation of the motor system during both observation and planning of lifting actions.

Highlights* Motor resonance is observation-induced activity in the observers motor system
* We used a dyadic lifting task of objects with asymmetrical weight distribution
* We investigated which movement features modulate motor resonance
* Motor resonance is modulated by the objects weight distribution
* Motor resonance is driven by observed and planned digit positioning


title: Universal enzyme-linked immunosorbent assays (ELISA) and utility in the immunodiagnosis of Salmonellosis

abstract: The aim of this study was to confirm the feasibility of using hybrid immunoglobulin-binding reagents in ELISAs for IgG/IgY detection and detection of specific antibodies against an infectious microorganism (Salmonella spp.) in various animal species using a universal diagnostic ELISA. Hybrid immunoglobulin-binding bacterial proteins (IBP), including recombinant protein LA, recombinant protein LG, and recombinant protein AG, have been produced to improve their binding affinity to a much larger number of immunoglobulins. Thus, this hybrid bacterial protein represents a powerful tool for the binding, detection, and purification of immunoglobulins and their fragments. However, SpLA-LG-peroxidase and SpLAG-anti-IgYperoxidase were produced using the periodate method. These compounds have been shown to be effective as reagents. Their binding affinity to immunoglobulins surpasses that of previously reported hybrid IgG-binding proteins, including the most known SpAG, SpLA, and SpLG. The IgY fraction was isolated from the egg yolks of various birds, including chicken, bantam hen, guinea hen, quail, goose, duck, wild and domestic pigeons, parakeets, cattle egrets, pheasants, and ostrich. The IgY fraction was isolated using the chloroform-polyethylene glycol (PEG) method. An ELISA for anti-Salmonella spp. antibodies was employed with some modifications to determine the presence of antibodies in humans, laying hens, geese, quails, and pigeons. Salmonella is a motile, flagellated, rod-shaped zoonotic pathogen that can survive in the presence or absence of oxygen. They belong to the family Enterobacteriaceae and are implicated in typhoid fever and food-borne illnesses. This pathogen is associated with several diseases, which may become fatal and negatively impact the health of individuals and various economies globally. The poultry industry is most vulnerable to the influence of this pernicious microbe. The authors concluded that universal enzyme-linked immunosorbent assays were effective and reproducible in detecting immunoglobulins from both avian and mammalian species, but ELISA using the SpLAG-anti-IgY-HRP conjugate only reacted with the whole panel of animal antibodies. This conjugate was further used to standardize a universal ELISA for the determination of anti-Salmonella antibodies, in which human and avian species were serologically assessed.


title: A parental transcriptional response to microsporidia infection induces inherited immunity in offspring

abstract: Inherited immunity is an emerging field and describes how the transfer of immunity from parents to offspring can promote progeny survival in the face of infection. The mechanisms of how inherited immunity is induced are mostly unknown. The intracellular parasite Nematocida parisii is a natural microsporidian pathogen of Caenorhabditis elegans. Here, we show that N. parisii-infected worms produce primed offspring that are resistant to microsporidia infection. We find that immunity is induced in a dose dependent manner and lasts for a single generation. Intergenerational immunity prevents host cell invasion by N. parisii and also enhances survival to the bacterial pathogen Pseudomonas aeruginosa. Further, we show that inherited immunity is triggered by the host transcriptional response to infection, which can also be induced through maternal somatic depletion of negative regulators PALS-22 and the retinoblastoma protein ortholog LIN-35. We show that other biotic and abiotic stresses, such as viral infection and cadmium exposure, that induce a similar transcriptional response to microsporidia can also induce immunity in progeny. Our results demonstrate that distinct stimuli can induce inherited immunity to provide resistance against multiple classes of pathogens. These results show that activation of an innate immune response can provide protection against pathogens not only within a generation, but also in the next generation.


title: Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay

abstract: The positive-sense, single-stranded RNA alphaviruses pose a potential epidemic threat. Understanding the complex interactions between the viral and the host cell proteins is crucial for elucidating the mechanisms underlying successful virus replication strategies and for developing specific antiviral interventions. Here we present the first comprehensive protein-protein interaction map between the proteins of Semliki Forest Virus (SFV), a mosquito-borne member of the alphaviruses, and host cell proteins. Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. In addition to observing a general inhibition of NMD about 4 hours post infection, we also demonstrate that transient expression of the SFV capsid protein is sufficient to inhibit NMD in cells, suggesting that the massive production of capsid protein during the SFV reproduction cycle is responsible for NMD inhibition.

category: molecular biology


title: Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

abstract:
Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA.

Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species.

eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with distance between sites. The distance decay of similarity derived from eDNA was similar, and even more pronounced, than that obtained with capture-based methods (gil-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species.

Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provide a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture based methods, which describes fish fauna over a few hundred metres.


title: Developing Human Pluripotent Stem Cell-Based Cerebral Organoids with a Controllable Microglia Ratio for Modeling Brain Development and Pathology

abstract: Microglia, as brain-resident macrophages, play critical roles in brain development, homeostasis, and disease. Microglia in animal models cannot accurately model the properties of human microglia due to notable transcriptomic and functional differences between human and other animal microglia. Efficient generation of microglia from human pluripotent stem cells (hPSCs) provides unprecedented opportunities to study the function and behavior of human microglia. Particularly, incorporating hPSCs-derived microglia into brain organoids facilitates their development in a 3-dimensional context, mimicking the brain environment. However, an optimized method that integrates an appropriate amount of microglia into brain organoids at a proper time point, resembling in vivo brain development, is still lacking. Here, we report the development of a new brain region-specific, microglia-containing organoid model by co-culturing hPSCs-derived primitive neural progenitor cells (pNPCs) and primitive macrophage progenitors (PMPs). In these organoids, hPSCs-derived pNPCs and PMPs interact with each other and develop into functional neurons, astroglia, and microglia, respectively. Importantly, the numbers of human microglia in the organoids can be controlled, resulting in a cell type ratio similar to that seen in the human brain. Using super-resolution microscopy, we demonstrate that these human microglia are able to phagocytize neural progenitor cells (NPCs) and apoptotic cells, as well as to prune synapses at different developmental stages of the organoids. Furthermore, these human microglia respond to Zika virus infection of the organoids, as indicated by amoeboid-like morphology, increased expression of gene transcripts encoding inflammatory cytokines, and excessive pruning of synaptic materials. Together, our findings establish a new microglia-containing brain organoid model that will serve to study human microglial function in a variety of neurological disorders.

category: neuroscience


title: Stable isotope fractionation reveals similar atomic level controls during aerobic and anaerobic microbial Hg transformation pathways

abstract:
Mercury (Hg) is a global pollutant and potent neurotoxin that bioaccumulates in food webs as monomethylmercury (MeHg). The production of MeHg is driven by anaerobic and Hg redox cycling pathways such as Hg reduction, which control the availability of Hg to methylators. Anaerobes play an important role in Hg reduction in methylation hotspots, yet their contributions remain underappreciated due to how challenging these pathways are to study in the absence of dedicated genetic targets and low levels of Hg0 in anoxic environments. In this study we used Hg stable isotope fractionation to explore Hg reduction during anoxygenic photosynthesis and fermentation in the model anaerobe Heliobacterium modesticaldum Ice1. We show that cells preferentially reduce lighter Hg isotopes in both metabolisms leading to mass-dependent fractionation, but mass-independent fractionation commonly induced by UV-visible light is absent. We show that isotope fractionation is affected by the interplay between pathways controlling Hg recruitment, accessibility, and availability alongside metabolic redox reactions. The combined contributions of these processes lead to isotopic enrichment during anoxygenic photosynthesis that is in between the values reported for anaerobic respiratory microbial Hg reduction and abiotic photoreduction. Isotope enrichment during fermentation is closer to what has been observed in aerobic bacteria that reduce Hg through dedicated detoxification pathways. These results demonstrate that common controls exist at the atomic level for Hg reduction during photosynthesis and fermentation in H. modesticaldum. Our work suggests that similar controls likely underpin diverse microbe-mediated Hg transformations that affect Hgs fate in oxic and anoxic habitats.

IMPORTANCEAnaerobic and photosynthetic bacteria that reduce mercury affect mercury delivery to microbes in methylation sites that drive bioaccumulation in food webs. Anaerobic mercury reduction pathways remain underappreciated in the current view of the global mercury cycle because they are challenging to study, bearing no dedicated genetic targets to establish physiological mechanisms. In this study we used stable isotopes to show that common physiological processes control mercury reduction during photosynthesis and fermentation in the model anaerobe Heliobacterium modesticaldum Ice1. The sensitivity of isotope analyses highlighted the subtle contribution of mercury uptake towards the isotope signature associated with anaerobic mercury reduction. When considered alongside the isotope signatures associated with microbial pathways for which genetic determinants have been identified, our findings underscore the narrow range of isotope enrichment that is characteristic of microbial mercury transformations. This suggests that there exist common atomic-level controls for biological mercury transformations across a broad range of geochemical conditions.


title: Common physiological processes control mercury reduction during photosynthesis and fermentation


title: Delta- and theta-band cortical tracking and phase-amplitude coupling to sung speech by infants

abstract:
The amplitude envelope of speech carries crucial low-frequency acoustic information that assists linguistic decoding at multiple time scales. Neurophysiological signals are known to track the amplitude envelope of adult-directed speech (ADS), particularly in the theta-band. Acoustic analysis of infant-directed speech (IDS) has revealed significantly greater modulation energy than ADS in an amplitude-modulation (AM) band centered on [~]2 Hz. Accordingly, cortical tracking of IDS by delta-band neural signals may be key to language acquisition. Speech also contains acoustic information within its higher-frequency bands (beta, gamma). Adult EEG and MEG studies reveal an oscillatory hierarchy, whereby low-frequency (delta, theta) neural phase dynamics temporally organize the amplitude of high-frequency signals (phase amplitude coupling, PAC). Whilst consensus is growing around the role of PAC in the matured adult brain, its role in the development of speech processing is unexplored.

Here, we examined the presence and maturation of low-frequency (<12 Hz) cortical speech tracking in infants by recording EEG longitudinally from 60 participants when aged 4-, 7- and 11-months as they listened to nursery rhymes. After establishing stimulus-related neural signals in delta and theta, cortical tracking at each age was assessed in the delta, theta and alpha [control] bands using a multivariate temporal response function (mTRF) method. Delta-beta, delta-gamma, theta-beta and theta-gamma phase-amplitude coupling (PAC) was also assessed. Significant delta and theta but not alpha tracking was found. Significant PAC was present at all ages, with both delta and theta -driven coupling observed.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/329326v4_ufig1.gif" ALT="Figure 1">
View larger version (25K):
org.highwire.dtl.DTLVardef@c7c7feorg.highwire.dtl.DTLVardef@1afa39org.highwire.dtl.DTLVardef@121d616org.highwire.dtl.DTLVardef@6e7c7b_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LILongitudinal EEG study in which 4, 7- & 11-month infants listened to nursery rhymes
C_LIO_LIWe demonstrate cortical speech tracking via delta & theta neural signals (mTRF)
C_LIO_LIPeriodogram (PSD) analysis revealed stimulus related delta & theta PSD peaks
C_LIO_LIDelta and theta driven phase amplitude coupling (PAC) was found at all ages
C_LIO_LIGamma frequency amplitudes displayed stronger PAC to low frequency phases than beta
C_LI


title: Codon usage pattern reveals SARS-CoV-2 as a monomorphic pathogen of hybrid origin with role of silent mutations in rapid evolutionary success

abstract: Viruses are dependent on the host tRNA pool, and an optimum codon usage pattern (CUP) is the driving force in its evolution. Systematic analysis of CUP of the coding sequences (CDS) of representative major pangolin lineages A and B of SARS-CoV-2 indicate a single transmission event of a codon-optimized virus from its source into humans. Here, no direct congruence could be detected in CUP of all CDS of SARS-CoV-2 with the non-human natural SARS viruses further reiterating its novelty. Several CDS show similar CUP with bat or pangolin, while others have distinct CUP pointing towards a possible hybrid nature of the virus. At the same time, phylogenetic diversity suggests the role of even silent mutations in its success by adapting to host tRNA pool. However, genomes of SARS-CoV-2 from primary infections are required to investigate the origins amongst the competing natural or lab leak theories.


title: Mathematical formulation and application of kernel tensor decomposition based unsupervised feature extraction

abstract: In this work, we extended the recently developed tensor decomposition (TD) based unsupervised feature extraction (FE) to a kernel-based method through a mathematical formulation. Subsequently, the kernel TD (KTD) based unsupervised FE was applied to two synthetic examples as well as real data sets, and the findings were compared with those obtained previously using the TD-based unsupervised FE approaches. The KTD-based unsupervised FE outperformed or performed comparably with the TD-based unsupervised FE in large p small n situations, which are situations involving a limited number of samples with many variables (observations). Nevertheless, the KTD-based unsupervised FE outperformed the TD-based unsupervised FE in non large p small n situations. In general, although the use of the kernel trick can help the TD-based unsupervised FE gain more variations, a wider range of problems may also be encountered. Considering the outperformance or comparable performance of the KTD-based unsupervised FE compared to the TD-based unsupervised FE when applied to large p small n problems, it is expected that the KTD-based unsupervised FE can be applied in the genomic science domain, which involves many large p small n problems, and, in which, the TD-based unsupervised FE approach has been effectively applied.


title: Jurassic NLR: conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1

abstract: In plants, NLR immune receptors generally exhibit hallmarks of rapid evolution even at the intraspecific level. We used iterative sequence similarity searches coupled with phylogenetic analyses to reconstruct the evolutionary history of ZAR1, an atypically conserved NLR that traces its origin to early flowering plant lineages [~]220 to 150 million years ago (Jurassic period). We discovered 120 ZAR1 orthologs in 88 species, including the monocot Colacasia esculenta, the magnoliid Cinnamomum micranthum and the majority of eudicots, notably the early diverging eudicot species Aquilegia coerulea. Ortholog sequence analyses revealed highly conserved features of ZAR1, including regions for pathogen effector recognition, intramolecular interactions and cell death activation. We functionally reconstructed the cell death activity of ZAR1 and its partner receptor-like cytoplasmic kinase (RLCK) from distantly related plant species, experimentally validating the hypothesis that ZAR1 has evolved to be a partner with RLCKs early in its evolution. In addition, ZAR1 acquired novel features, such as a C-terminal integration of a thioredoxin-like domain. ZAR1 duplicated into two paralog families, which underwent distinct evolutionary paths. We conclude that ZAR1 stands out among angiosperm NLRs for having experienced relatively limited gene duplication and expansion throughout its deep evolutionary history. Nonetheless, ZAR1 did also give rise to non-canonical NLR proteins with integrated domains and degenerated molecular features.

category: plant biology


title: Between-subject correlation of heart rate variability predicts movie preferences

abstract: We introduce a novel and simple method for assessing audiences emotional responses to audiovisuals (e.g. films). Viewers (N=21) watched movies and TV commercials from different genres while wearing photoplethysmography (PPG) optic sensors on their wrists. Heart rate variability (HRV) synchrony was observed among the audience. Based on this between-subject synchrony measure, we identified emotionally arousing segments from the materials. New participants (N=24; N=16) were then invited to watch these identified segments along with some randomly selected segments as control; they reported that the former was more engaging (effect size w=.67; w=.5). This finding was confirmed in an online study with a larger cohort (N=300). While some specific effects varied depending on movie genre or gender, HRV-based editing generally performed better than the control. These findings suggest that HRV synchrony can be used as a new tool for audience psychology, and potentially also for automatically creating short trailers out of movies in a principled manner while taking into account the human perspective.


title: A high-throughput amplicon sequencing approach for population-wide species diversity and composition survey

abstract: Management of agricultural pests requires an understanding of pest species diversity, their interactions with beneficial insects and spatial-temporal patterns of pest abundance. Invasive and agriculturally important insect pests can build up very high populations, especially in cropping landscapes. Traditionally, sampling effort for species identification involves small sample sizes and is labour intensive. Here, we describe a multi-primer high throughput sequencing (HTS) metabarcoding method and associated analytical workflow for a rapid, intensive, high-volume survey of pest species compositions. We demonstrate our method using the taxonomically challenging Bemisia pest cryptic species complex as examples. The whiteflies Bemisia including the  tabaci species are agriculturally important capable of vectoring diverse plant viruses that cause diseases and crop losses. Our multi-primer metabarcoding HTS amplicon approach simultaneously process high volumes of whitefly individuals, with efficiency to detect rare (i.e., 1%) test-species, while our improved whitefly primers for metabarcoding also detected beneficial hymenopteran parasitoid species from whitefly nymphs. Field-testing our redesigned Bemisia metabarcoding primer sets across the Tanzania, Uganda and Malawi cassava cultivation landscapes, we identified the sub-Saharan Africa 1 Bemisia putative species as the dominant pest species, with other cryptic Bemisia species being detected at various abundances. We also provide evidence that Bemisia species compositions can be affected by host crops and sampling techniques that target either nymphs or adults. Our multi-primer HTS metabarcoding method incorporated two over-lapping amplicons of 472bp and 518bp that spanned the entire 657bp 3 barcoding region for Bemisia, and is particularly suitable to molecular diagnostic surveys of this highly cryptic insect pest species complex that also typically exhibited high population densities in heavy crop infestation episodes. Our approach can be adopted to understand species biodiversity across landscapes, with broad implications for improving trans-boundary biosecurity preparedness, thus contributing to molecular ecological knowledge and the development of control strategies for high-density, cryptic, pest-species complexes.


title: Mathematical modeling of N-803 treatment in SIV-infected non-human primates

abstract:
Immunomodulatory drugs could contribute to a functional cure for Human Immunodeficiency Virus (HIV). Interleukin-15 (IL-15) promotes expansion and activation of CD8+ T cell and natural killer (NK) cell populations. In one study, an IL-15 superagonist, N-803, suppressed Simian Immunodeficiency Virus (SIV) in non-human primates (NHPs) who had received prior SIV vaccination. However, viral suppression attenuated with continued N-803 treatment, partially returning after long treatment interruption. While there is evidence of concurrent drug tolerance, immune regulation, and viral escape, the relative contributions of these mechanisms to the observed viral dynamics have not been quantified. Here, we utilize mathematical models of N-803 treatment in SIV-infected macaques to estimate contributions of these three key mechanisms to treatment outcomes: 1) drug tolerance, 2) immune regulation, and 3) viral escape. We calibrated our model to viral and lymphocyte responses from the above-mentioned NHP study. Our models track CD8+ T cell and NK cell populations with N-803-dependent proliferation and activation, as well as viral dynamics in response to these immune cell populations. We compared mathematical models with different combinations of the three key mechanisms based on Akaike Information Criterion and important qualitative features of the NHP data. Two minimal models were capable of reproducing the observed SIV response to N-803. In both models, immune regulation strongly reduced cytotoxic cell activation to enable viral rebound. Either long-term drug tolerance or viral escape (or some combination thereof) could account for changes to viral dynamics across long breaks in N-803 treatment. Theoretical explorations with the models showed that less-frequent N-803 dosing and concurrent immune regulation blockade (e.g. PD-L1 inhibition) may improve N-803 efficacy. However, N-803 may need to be combined with other immune therapies to countermand viral escape from the CD8+ T cell response. Our mechanistic model will inform such therapy design and guide future studies.

Author summaryImmune therapy may be a critical component in the functional cure for Human Immunodeficiency Virus (HIV). N-803 is an immunotherapeutic drug that activates antigen-specific CD8+ T cells of the immune system. These CD8+ T cells eliminate HIV-infected cells in order to limit the spread of infection in the body. In one study, N-803 reduced plasma viremia in macaques that were infected with Simian Immunodeficiency Virus, an analog of HIV. Here, we used mathematical models to analyze the data from this study to better understand the effects of N-803 therapy on the immune system. Our models indicated that inhibitory signals may be reversing the stimulatory effect of N-803. Results also suggested the possibilities that tolerance to N-803 could build up within the CD8+ T cells themselves and that the treatment may be selecting for virus strains that are not targeted by CD8+ T cells. Our models predict that N-803 therapy may be made more effective if the time between doses is increased or if inhibitory signals are blocked by an additional drug. Also, N-803 may need to be combined with other immune therapies to target virus that would otherwise evade CD8+ T cells.


title: Leptospira surface protein LigA plays a multifaceted role in modulating the host innate immune response

abstract: Leptospira, a zoonotic pathogen, is known to infect various hosts and can establish persistent infection. This remarkable ability of bacteria is attributed to its potential to modulate the host immune response by exploiting its surface proteins. We have identified and characterized the domain of the variable region of Leptospira immunoglobulin-like protein A (LAV) involved in immune modulation. The 11th domain (A11) of the variable region of LigA (LAV) induces a strong TLR4 dependent innate response leading to subsequent induction of humoral and cellular immune responses in mice. A11 is also involved in acquiring complement regulator FH and binds to host protease Plasminogen (PLG), there by mediating functional activity to escape from complement-mediated killing. The deletion of A11 domain significantly impaired TLR4 signaling and subsequent reduction in the innate and adaptive immune response. It also inhibited the binding of FH and PLG thereby mediating killing of bacteria. Our study discovered an unprecedented role of LAV as a nuclease capable of degrading Neutrophil Extracellular Traps (NETs). This nuclease activity was primarily mediated by A11. These results highlighted the moonlighting function of LigA and demonstrated that a single domain of a surface protein is involved in evading a myriad of host innate immune defenses, which might allow the persistence of Leptospira in different hosts for a long term without clearance.


title: A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within Vibrio cholerae infected patients

abstract:
Vibrio cholerae can cause a range of symptoms, ranging from severe diarrhea to asymptomatic infection. Previous studies using whole genome sequencing (WGS) of multiple bacterial isolates per patient showed that V. cholerae can evolve modest genetic diversity during symptomatic infection. To further explore the extent of V. cholerae within-host diversity, we applied culture-based WGS and metagenomics to a cohort of both symptomatic and asymptomatic cholera patients from Bangladesh. While metagenomics allowed us to detect more mutations in symptomatic patients, WGS of cultured isolates was necessary to detect V. cholerae diversity in asymptomatic carriers, likely due to their low V. cholerae load. Using both metagenomics and isolate WGS, we report three lines of evidence that V. cholerae hypermutators evolve within patients. First, we identified nonsynonymous in V. cholerae DNA repair genes in five out of 11 patient metagenomes sequenced with sufficient coverage of the V. cholerae genome, and in one of three patients with isolate genomes sequenced. Second, mutations in DNA repair genes tended to be accompanied by an excess of intrahost single nucleotide variants (iSNVs). Third, these iSNVs were enriched in transversion mutations, a known hallmark of hypermutator phenotypes. While hypermutators appeared to generate mostly selectively neutral mutations, non-mutators showed signs of convergent mutation across multiple patients, suggesting V. cholerae adaptation within hosts. Our results highlight the power and limitations of metagenomics combined with isolate sequencing to characterize within-patient diversity in acute V. cholerae infections, while providing evidence for hypermutator phenotypes within cholera patients.

IMPORTANCEPathogen evolution within patients can impact phenotypes such as drug resistance and virulence, potentially affecting clinical outcomes. V. cholerae infection can result in life-threatening diarrheal disease, or asymptomatic infection. Here we describe whole-genome sequencing of V. cholerae isolates and culture-free metagenomic sequencing from stool of symptomatic cholera patients and asymptomatic carriers. Despite the typically short duration of cholera, we found evidence for adaptive mutations in the V. cholerae genome that occur independently and repeatedly within multiple symptomatic patients. We also identified V. cholerae hypermutator phenotypes within several patients, which appear to generate mainly neutral or deleterious mutations. Our work sets the stage for future studies of the role of hypermutators and within-patient evolution in explaining the variation from asymptomatic carriage to symptomatic cholera.


title: Sequences in the cytoplasmic tail of SARS-CoV-2 Spike facilitate expression at the cell surface and syncytia formation

abstract: The Spike (S) protein of SARS-CoV-2 binds ACE2 to direct fusion with host cells. S comprises a large external domain, a transmembrane domain (TMD) and a short cytoplasmic tail. Understanding the intracellular trafficking of S is relevant to SARS-CoV-2 infection, and to vaccines expressing full-length S from mRNA or adenovirus vectors. We have applied proteomics to identify cellular factors that interact with the cytoplasmic tail of S. We confirmed interactions with the COPI and COPII vesicle coats, ERM family actin regulators, and the WIPI3 autophagy component. The COPII binding-site promotes exit from the endoplasmic reticulum (ER), and although COPI-binding should retain S in the early Golgi where viral budding occurs, there is a suboptimal histidine residue in the recognition motif. As a result, S leaks to the surface where it accumulates and can direct the formation of multinucleate syncytia. Thus, the trafficking signals in the tail of S indicate that syncytia play a role in the SARS-CoV-2 lifecycle.


title: Single cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree

abstract:
Lineage tracing using genetically engineered mouse models is an essential tool for investigating cell-fate decisions of progenitor cells and biology of mature cell types, with relevance to physiology and disease progression. To study disease development, an inventory of an organs cell types and understanding of physiologic function is paramount. Here, we performed single-cell RNA sequencing to examine heterogeneity of murine pancreatic duct cells, pancreatobiliary cells, and intrapancreatic bile duct cells. We describe an epithelial-mesenchymal transitory axis in our three pancreatic duct subpopulations and identify SPP1 as a regulator of this fate decision as well as human duct cell de-differentiation. Our results further identify functional heterogeneity within pancreatic duct subpopulations by elucidating a role for Geminin in accumulation of DNA damage in the setting of chronic pancreatitis. Our findings implicate diverse functional roles for subpopulations of pancreatic duct cells in maintenance of duct cell identity and disease progression and establish a comprehensive road map of murine pancreatic duct cell, pancreatobiliary cell, and intrapancreatic bile duct cell homeostasis.

SIGNIFICANCEMurine models are extensively used for pancreatic lineage tracing experiments and investigation of pancreatic disease progression. Here, we describe the transcriptome of murine pancreatic duct cells, intrapancreatic bile duct cells, and pancreatobiliary cells at single cell resolution. Our analysis defines novel heterogeneity within the pancreatic ductal tree and supports the paradigm that more than one population of pancreatic duct cells harbors progenitor capacity. We identify and validate unique functional properties of subpopulations of pancreatic duct cells including an epithelial-mesenchymal transcriptomic axis and roles in chronic pancreatic inflammation.


title: Homeostatic depression shows heightened sensitivity to synaptic calcium

abstract:
Synapses and circuits rely on homeostatic forms of regulation in order to transmit meaningful information. The Drosophila melanogaster neuromuscular junction (NMJ) is a well-studied synapse that shows robust homeostatic control of function. Most prior studies of homeostatic plasticity at the NMJ have centered on presynaptic homeostatic potentiation (PHP). PHP happens when postsynaptic muscle neurotransmitter receptors are impaired, triggering retrograde signaling that causes an increase in presynaptic neurotransmitter release. As a result, normal levels of evoked excitation are maintained. The counterpart to PHP at the NMJ is presynaptic homeostatic depression (PHD). Overexpression of the Drosophila vesicular glutamate transporter (VGlut) causes an increase in the amplitude of spontaneous events. PHD happens when the synapse responds to the challenge by decreasing quantal content during evoked neurotransmission - again, resulting in normal levels of postsynaptic excitation.

We hypothesized that there may exist a class of molecules that affects both PHP and PHD. Impairment of any such molecule could hurt a synapses ability to respond to any significant homeostatic challenge. We conducted an electrophysiology-based screen for blocks of PHD. We did not observe a block of PHD in the genetic conditions screened, but we did find loss-of-function conditions that led to a substantial deficit in evoked amplitude when combined with VGlut overexpression. The conditions causing this phenotype included a double heterozygous loss-of-function condition for genes encoding the inositol trisphosphate receptor (IP3R - itpr) and ryanodine receptor (RyR). IP3Rs and RyRs gate calcium release from intracellular stores. Pharmacological agents targeting IP3R and RyR recapitulated the genetic losses of these factors, as did lowering calcium levels from other sources. Our data are consistent with the idea that the homeostatic signaling process underlying PHD is especially sensitive to levels of calcium at the presynapse.


title: Quantifying year-round nocturnal bird migration with a fluid dynamics model

abstract:
The movements of migratory birds constitute huge biomass flows that influence ecosystems and human economy, agriculture and health through the transport of energy, nutrients, seeds, and parasites. To better understand the influence on ecosystems and the corresponding services and disservices, we need to characterize and quantify the migratory movements at various spatial and temporal scales.

Representing the flow of birds in the air as a fluid, we applied a flow model to interpolated maps of bird density and velocity retrieved from the European weather radar network, covering almost a full year. Using this model, we quantified how many birds take-off, fly, and land across Western Europe, (1) to track waves of bird migration between nights, (2) cumulate the number of bird on the ground and (3) quantify the seasonal flow into and out of the study area through several regional transects.

Our results show that up to 188 million (M) birds take-off over a single night. Exemplarily, we tracked a migration wave in spring, in which birds crossed the study area in 4 days with nocturnal flights of approximately 300 km. Over the course of a season, we estimated that 494 million (M) birds entered through the southern transects and, at the same time, 251 M left in the northern transects, creating a surplus of 243 M birds within the study area. Similarly, in autumn, 544 M more birds departed than arrived: 314 M birds entered through the northern transects while 858 M left through the southern transects.

Our study show-cases the potential of combining interdisciplinary data and methods to elucidate the dynamics of avian migration from nightly to seasonal and yearly time-scales and from regional to continental spatial scales.


title: Evolution of Honey Resistance in Experimental Populations of Bacteria Depends on the Type of Honey, and Has no Major Side Effects for Antibiotic Susceptibility

abstract: With rising antibiotic resistance, alternative treatments for communicable diseases are increasingly relevant. One possible alternative for some types of infections is honey, used in wound care since before 2000 BCE and more recently in licensed, medical-grade products. However, it is unclear whether medical application of honey results in the evolution of bacterial honey resistance, and whether this has collateral effects on other bacterial traits such as antibiotic resistance. Here, we used single-step screening assays and serial transfer at increasing concentrations to isolate honey-resistant mutants of Escherichia coli. We only detected bacteria with consistently increased resistance to the honey they evolved in with two of the four tested honey products, and the observed increases were small (maximum two-fold increase in IC90). Genomic sequencing and experiments with single-gene knockouts showed a key mechanism by which bacteria increased their honey resistance was by mutating genes involved in detoxifying methylglyoxal, which contributes to the antibacterial activity of Leptospermum honeys. Crucially, we found no evidence that honey adaptation conferred cross-resistance or collateral sensitivity against nine antibiotics from six different classes. These results reveal constraints on bacterial adaptation to different types of honey, improving our ability to predict downstream consequences of wider honey application in medicine.


title: Genetic variation in heat tolerance of the coral Platygyra daedalea indicates the potential for adaptation to ocean warming

abstract: Climate change induced increases in global ocean temperature represent the greatest threat to the persistence of reef ecosystems and most coral populations are projected to experience temperatures above their current bleaching thresholds annually by 2050. Adaptation to higher temperatures is necessary if corals are to persist in a warming future. While many aspects of heat stress have been well studied, few data are available for predicting the capacity for adaptive cross-generational responses in corals. Consistent sets of heat tolerant genomic markers that reliably predict thermal tolerance have yet to be identified. To address this knowledge gap, we quantified the heritability and genetic variation associated with heat tolerance in Platygyra daedalea from the Great Barrier Reef. We tracked the survival of quantitative genetic crosses of larvae in a heat tolerance selection experiment. We also identified allelic shifts in heat-selected survivors compared with paired, non-selected controls. The narrow-sense heritability of survival under heat stress was 0.66 and a total of 1,069 single nucleotide polymorphisms (SNPs) were associated with different survival probabilities. While 148 SNPs were shared between several experimental crosses, no common SNPs were identified for all crosses suggesting that specific combinations of many markers are responsible for heat tolerance. However, we found two regions that overlap with previously identified loci associated with heat tolerance in Persian Gulf populations of P. daedalea reinforcing the importance of these markers for heat tolerance. These results illustrate the importance of high heritability and the complexity of the genomic architecture underpinning host heat tolerance. These findings suggest that this P. daedalea population has the genetic prerequisites for adaptation to increasing temperatures. This study also provides knowledge for the development of high throughput genomic tools to screen for variation within and across populations to enhance adaptation through assisted gene flow and assisted migration.


title: Dimensionality-Reduction in the Drosophila Wing as Revealed by Landmark-Free Measurements of Phenotype

abstract: Organismal development is a complex process, involving a vast number of molecular constituents interacting on multiple spatio-temporal scales in the formation of intricate body structures. Despite this complexity, development is remarkably reproducible and displays tolerance to both genetic and environmental perturbations. This robust-ness implies the existence of hidden simplicities in developmental programs. Here, using the Drosophila wing as a model system, we develop a new quantitative strategy that enables a robust description of biologically salient phenotypic variation. Analyzing natural phenotypic variation across a highly outbred population, and variation generated by weak perturbations in genetic and environmental conditions, we observe a highly constrained set of wing phenotypes. Remarkably, the phenotypic variants can be described by a single integrated mode that corresponds to a non-intuitive combination of structural variations across the wing. This work demonstrates the presence of constraints that funnel environmental inputs and genetic variation into phenotypes stretched along a single axis in morphological space. Our results provide quantitative insights into the nature of robustness in complex forms while yet accommodating the potential for evolutionary variations. Methodologically, we introduce a general strategy for finding such invariances in other developmental contexts.


title: Global Constraints within the Developmental Program of the Drosophila Wing


title: Massive genome decay and expansion of insertion sequences drive the evolution of a novel host-restricted bacterial pathogen

abstract:
BackgroundThe emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as those associated with a switch in host or disease tropism are often accompanied by genetic adaptation. Staphylococcus aureus is a multi-host bacterial species comprising strains with distinct tropisms for human and livestock species. A microaerophilic subspecies, Staphylococcus aureus subsp. anaerobius, is responsible for outbreaks of Morels disease, a lymphadenitis in small ruminants. However, the evolutionary history of S. aureus subsp. anaerobius and its relatedness to S. aureus are unknown.

ResultsEvolutionary genomic analyses of clinical S. aureus subsp. anaerobius isolates revealed a highly conserved clone that descended from a S. aureus progenitor about 1000 years ago before differentiating into distinct lineages representing African and European isolates. S. aureus subsp. anaerobius has undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower than S. aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, several large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes resulting in a highly fastidious metabolism. Importantly, expansion of [~]87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, representing a novel concept of the IS regulon.

ConclusionsOur findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of the S. aureus genome through an array of parallel mechanisms.


title: Sequential infection with influenza A virus followed by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leads to more severe disease and encephalitis in a mouse model of COVID-19.

abstract: COVID-19 is a spectrum of clinical symptoms in humans caused by infection with SARS-CoV-2, a recently emerged coronavirus that has rapidly caused a pandemic. Coalescence of a second wave of this virus with seasonal respiratory viruses, particularly influenza virus is a possible global health concern. To investigate this, transgenic mice expressing the human ACE2 receptor driven by the epithelial cell cytokeratin-18 gene promoter (K18-hACE2) were first infected with IAV followed by SARS-CoV-2. The host response and effect on virus biology was compared to K18-hACE2 mice infected with IAV or SARS-CoV-2 only. Infection of mice with each individual virus resulted in a disease phenotype compared to control mice. Although SARS-CoV-2 RNA synthesis appeared significantly reduced in the sequentially infected mice, these mice had a more rapid weight loss, more severe lung damage and a prolongation of the innate response compared to singly infected or control mice. The sequential infection also exacerbated the extrapulmonary manifestations associated with SARS-CoV-2. This included a more severe encephalitis. Taken together, the data suggest that the concept of  twinfection is deleterious and mitigation steps should be instituted as part of a comprehensive public health response to the COVID-19 pandemic.


title: Defects in plant immunity modulate the rates and patterns of RNA virus evolution

abstract: It is assumed that host genetic variability for susceptibility to infection necessarily conditions virus evolution. Differences in host susceptibility can either drive the virus to diversify into strains that track different defense alleles (e.g., antigenic diversity) or to infect only the most susceptible genotypes. To clarify these processes and their effect on virulence, we have studied how variability in host defense responses determine the evolutionary fate of viruses. To accomplish this, we performed evolution experiments with Turnip mosaic potyvirus in Arabidopsis thaliana mutants. Mutant plants had disruptions in infection-response signaling pathways or in genes whose products are essential for potyvirus infection. Genotypes were classified into five phenogroups according to their response to infection. In order to disentangle how host susceptibility affects virus adaptation, independent viral lineages were evolved in selected plant genotypes. Evaluating disease-related traits of the evolved lineages, we found that evolution proceeded faster in the most resistant hosts than in the most permissive ones, as expected for adaptation to a harsh environment. By sequencing the genomes of the evolved viral lineages, we found that the multifunctional protein VPg turned out to be the target of selection in most host genotypes. When all evolved viral lineages were tested for fitness in all plant genotypes used in the experiments, we found compelling evidences that generalist viruses were selected by the most restrictive plant genotypes, while permissive genotypes selected for specialist viruses. Overall, this work illustrates how different host defense signaling pathways constrain not only disease-related traits but virus evolution.


title: In Situ Optical Quantification of Extracellular Electron Transfer using Plasmonic Metal Oxide Nanocrystals

abstract: Extracellular electron transfer (EET) is a critical form of microbial metabolism that enables respiration on a variety of inorganic substrates, including metal oxides. However, quantifying current generated by electroactive bacteria has been predominately limited to biofilms formed on electrodes. To address this, we developed a platform for quantifying EET flux from cell suspensions using aqueous dispersions of infrared plasmonic tin-doped indium oxide nanocrystals. Tracking the change in optical extinction during electron transfer enabled quantification of current generated by planktonic Shewanella oneidensis cultures. Using this method, we differentiated between starved and actively respiring cells, between cells of varying genotype, and between cells engineered to differentially express a key EET gene using an inducible genetic circuit. Overall, our results validate the utility of colloidally stable plasmonic metal oxide nanocrystals as quantitative biosensors in native biological environments and contribute to a fundamental understanding of planktonic S. oneidensis electrophysiology using simple in situ spectroscopy.


title: Myofibrillar Structural Variability Underlies Contractile Function in Stem Cell-Derived Cardiomyocytes

abstract: Disease modeling and pharmaceutical testing using cardiomyocytes derived from induced pluripotent stem cell (iPSC-CMs) requires accurate assessment of contractile function. Micropatterning iPSC-CMs on elastic substrates controls cell shape and alignment to enable contractile studies, but determinants of intrinsic variability in this system have been incompletely characterized. The objective of this study was to determine the impact of myofibrillar structure on contractile function in iPSC-CMs. Automated analysis of micropatterned iPSC-CMs labeled with a cell permeant F-actin dye revealed that myofibrillar abundance is widely variable among iPSC-CMs and strongly correlates with contractile function. This variability is not reduced by subcloning from single iPSCs and is independent of iPSC-CM purification method. Controlling for myofibrillar structure reduces false positive findings related to batch effect and improves sensitivity for pharmacologic testing and disease modeling. This analysis provides compelling evidence that myofibrillar structure should be assessed concurrently in studies investigating contractile function in iPSC-CMs.


title: Nonameric structures of the cytoplasmic domain of FlhA and SctV in the context of the full-length protein

abstract: Type three secretion is the mechanism of protein secretion found in bacterial flagella and injectisomes. At its centre is the export apparatus (EA), a complex of five membrane proteins through which secretion substrates pass the inner membrane. While the complex formed by four of the EA proteins has been well characterised structurally, little is known about the structure of the membrane domain of the largest subunit, FlhA in flagella, SctV in injectisomes. Furthermore, the biologically relevant nonameric assembly of FlhA/SctV has been infrequently observed and differences in conformation of the cytoplasmic portion of FlhA/SctV between open and closed states have been suggested to reflect secretion system specific differences. FlhA has been shown to bind to chaperone-substrate complexes in an open state, but in previous assembled ring structures, SctV is in a closed state. Here, we identify FlhA and SctV homologues that can be recombinantly produced in the oligomeric state and study them using cryo-electron microscopy. The structures of the cytoplasmic domains from both FlhA and SctV are in the open state and we observe a conserved interaction between a short stretch of residues at the N-terminus of the cytoplasmic domain, known as FlhAL/SctVL, with a groove on the adjacent protomers cytoplasmic domain, which stabilises the nonameric ring assembly.