title: High Throughput Computational Mouse Genetic Analysis

abstract:
BackgroundGenetic factors affecting multiple biomedical traits in mice have been identified when GWAS data that measured responses in panels of inbred mouse strains was analyzed using haplotype-based computational genetic mapping (HBCGM). Although this method was previously used to analyze one dataset at a time; but now, a vast amount of mouse phenotypic data is now publicly available, which could lead to many more genetic discoveries.

ResultsHBCGM and a whole genome SNP map covering 53 inbred strains was used to analyze 8462 publicly available datasets of biomedical responses (1.52M individual datapoints) measured in panels of inbred mouse strains. As proof of concept, causative genetic factors affecting susceptibility for eye, metabolic and infectious diseases were identified when structured automated methods were used to analyze the output. One analysis identified a novel genetic effector mechanism; allelic differences within the mitochondrial targeting sequence affected the subcellular localization of a protein. We also found allelic differences within the mitochondrial targeting sequences of many murine and human proteins, and these could affect a wide range of biomedical phenotypes.

ImplicationsThese initial results indicate that genetic factors affecting biomedical responses could be identified through analysis of very large datasets, and they provide an early indication of how this type of  augmented intelligence can facilitate genetic discovery.


title: Resetting of 24-nt siRNA landscape is initiated before the first zygotic division in rice

abstract:
BackgroundThe zygote, a totipotent stem cell, constitutes a critical stage of the life cycle of sexually reproducing organisms. It is produced by the fusion of two differentiated cells -- the egg and sperm, which in plants have radically different siRNA transcriptomes from each other and from multicellular embryos. Due to technical challenges, the epigenetic changes that accompany the zygotic transition are poorly understood.

ResultsHere, we characterized the small RNA transcriptome of rice zygotes. We found widespread redistribution of 24-nt siRNAs relative to gametes, including absence of sperm signature siRNAs, reduction at egg signature siRNA loci, and upregulation at seedling signature siRNA loci. Loci with reduced siRNAs in zygote relative to egg were gene-distal and heterochromatic, while loci with increased siRNAs relative to egg had a similar genomic distribution to canonical siRNA loci. Although both egg and zygote siRNA loci had higher mCHH level in wildtype than in drm2 embryo, zygote but not egg siRNA loci were associated with hypermethylation in mature embryo. A small fraction of siRNA loci (~1%) called siren loci accounted for 60% of all siRNAs within zygote siRNA loci, that likely arose from maternal carryover as they had similarly abundant siRNAs in egg; these siren loci were not associated with embryo hypermethylation.

ConclusionsTaken together, our results indicate re-distribution of siRNAs in rice zygotes towards the canonical vegetative profile, that are consistent with the initiation of resetting of the gametic epigenome before the first embryonic division.

category: plant biology


title: Resetting of the 24-nt siRNA landscape in rice zygotes


title: Gradual development of non-adjacent dependency learning during early childhood

abstract:
In order to become proficient native speakers, children have to learn the morpho-syntactic relations between distant elements in a sentence, so-called non-adjacent dependencies (NADs). Previous research suggests that NAD learning in children comprises different developmental stages, where until 2 years of age children are able to learn NADs associatively under passive listening conditions, while starting around the age of 3 to 4 years children fail to learn NADs during passive listening. To test whether the transition between these developmental stages occurs gradually, we tested childrens NAD learning in a foreign language using event-related potentials (ERPs). We found ERP evidence of NAD learning across the ages of 1, 2 and 3 years. The amplitude of the ERP effect indexing NAD learning, however, decreased with age. These findings might indicate a gradual transition in childrens ability to learn NADs associatively. Cognitively, this transition might be driven by childrens increasing knowledge of their native language, hindering NAD learning in novel contexts. Neuroanatomically, maturation of the prefrontal cortex might play a crucial role, promoting top-down learning, affecting bottom-up, associative learning. In sum, our study suggests that NAD learning under passive listening conditions undergoes a gradual transition between different developmental stages during early childhood.

Research HighlightsO_LITransition between developmental stages of non-adjacent dependency (NAD) learning
C_LIO_LIChildren between 1 and 3 years of age showed learning of NADs in a foreign language
C_LIO_LIBrain responses revealed associative NAD learning, triggered by passive listening
C_LIO_LIGradual decrease of the strength of associative non-adjacent dependency learning
C_LI

category: neuroscience


title: Meaningful Effects in the Adolescent Brain Cognitive Development Study

abstract: The Adolescent Brain Cognitive Development (ABCD) Study is the largest single-cohort prospective longitudinal study of neurodevelopment and childrens health in the United States. A cohort of n= 11,880 children aged 9-10 years (and their parents/guardians) were recruited across 22 sites and are being followed with in-person visits on an annual basis for at least 10 years. The study approximates the US population on several key sociodemographic variables, including sex, race, ethnicity, household income, and parental education. Data collected include assessments of health, mental health, substance use, culture and environment and neurocognition, as well as geocoded exposures, structural and functional magnetic resonance imaging (MRI), and whole-genome genotyping. Here, we describe the ABCD Study aims and design, as well as issues surrounding estimation of meaningful associations using its data, including population inferences, hypothesis testing, power and precision, control of covariates, interpretation of associations, and recommended best practices for reproducible research, analytical procedures and reporting of results.


title: Ca2+ and Membrane Potential Transitions During Action Potentials are Self-Similar to Each Other and to Variability of AP Firing Intervals Across the Broad Physiologic Range of AP Intervals During Autonomic Receptor Stimulation

abstract:
Ca2+ and Vm transitions occurring throughout AP cycles in sinoatrial nodal (SAN) cells are cues that: (1) not only regulate activation states of molecules operating within criticality (Ca2+ domain) and limit-cycle (Vm domain) mechanisms of a coupled-clock system that underlies SAN cell automaticity; (2) but are also regulated by the activation states of the clock molecules they regulate. In other terms, these cues are both causes and effects of clock molecular activation (recursion). Recently, we demonstrated that Ca2+ and Vm transitions during AP cycles in single SAN cells isolated from mice, guinea pigs, rabbits and humans are self-similar (obey a power law) and are also self-similar to trans-species AP firing intervals of these cells in vitro, to heart rate in vivo, and to body mass.

Neurotransmitter stimulation of {beta} adrenergic receptor or cholinergic receptor initiated signaling in SAN cells modulates their AP firing rate and rhythm by impacting on the degree to which SAN clocks couple to each other, creating the broad physiologic range of SAN cell mean AP firing intervals and firing interval variabilities. Here we show that Ca2+ and Vm domain kinetic transitions (time to AP ignition in diastole and 90% AP recovery) occurring within given AP, the mean AP firing intervals, and AP firing interval variabilities within time-series of APs in 230 individual SAN cells are self-similar (obey power laws). In other terms, these long-range correlations inform on self-similar distributions of order among SAN cells across the entire broad physiologic range of SAN AP firing intervals, regardless of whether autonomic receptors of these cells are stimulated or not, and regardless of the type (adrenergic or cholinergic) of autonomic receptor stimulation. These long-range correlations among distributions of Ca2+ and Vm kinetic functions that regulate SAN cell clock coupling during each AP cycle in different individual, isolated SAN cells not in contact with each other. Our numerical model simulations further extended our perspectives to the molecular scale and demonstrated that many ion currents also behave self-similar across autonomic states.

Thus, to ensure rapid flexibility of AP firing rates in response to different types and degrees of autonomic input, nature "did not reinvent molecular wheels within the coupled-clock system of pacemaker cells", but differentially engaged or scaled the kinetics of gears that regulate the rate and rhythm at which the "wheels spin" in a given autonomic input context.

category: biophysics


title: Efficient Spline Regression for Neural Spiking Data

abstract: Point process generalized linear models (GLMs) provide a powerful tool for characterizing the coding properties of neural populations. Spline basis functions are often used in point process GLMs, when the relationship between the spiking and driving signals are nonlinear, but common choices for the structure of these spline bases often lead to loss of statistical power and numerical instability when the signals that influence spiking are bounded above or below. In particular, history dependent spike train models often suffer these issues at times immediately following a previous spike. This can make inferences related to refractoriness and bursting activity more challenging. Here, we propose a modified set of spline basis functions that assumes a flat derivative at the endpoints and show that this limits the uncertainty and numerical issues associated with cardinal splines. We illustrate the application of this modified basis to the problem of simultaneously estimating the place field and history dependent properties of a set of neurons from the CA1 region of rat hippocampus, and compare it with the other commonly used basis functions. We have made code available in MATLAB to implement spike train regression using these modified basis functions.


title: A Human Multi-Lineage Hepatic Organoid Model for Liver Fibrosis

abstract:
BackgroundTo characterize fibrogenic mechanisms, genome engineering and a human hepatic organoid system was used to produce an in vitro model for human liver fibrosis.

Methods and resultsHuman hepatic organoids that were engineered to express the most common causative mutation for Autosomal Recessive Polycystic Kidney Disease (ARPKD) developed the key features of ARPKD liver pathology (abnormal bile ducts and hepatic fibrosis) in only 21 days. Second harmonic generation microscopy confirmed that the ARPKD mutation increased collagen abundance and thick collagen fiber production in hepatic organoids; and we demonstrated that these changes mirrored that occurring in ARPKD liver tissue. Transcriptomic and other analyses indicated that the ARPKD mutation generates cholangiocytes with increased TGF{beta}-associated pathway activation, which are actively involved in collagen fiber generation. The abnormal cholangiocytes promote the expansion of collagen-producing myofibroblasts with markedly increased PDGFR{beta} protein expression and an activated STAT3 signaling pathway. Moreover, the transcriptome of ARPKD organoid myofibroblasts resembled that of myofibroblasts in liver tissue obtained from patients with commonly occurring acquired forms of liver fibrosis. The involvement of the PDGFRB pathway was confirmed by the anti-fibrotic effect observed when ARPKD organoids were treated with PDGFRB inhibitors.

ConclusionsBesides providing mechanistic insight into the pathogenesis of congenital (and possibly acquired) forms of liver fibrosis, ARPKD organoids could also be used to test the anti-fibrotic efficacy of potential anti-fibrotic therapies.

category: cell biology


title: Human belief state-based exploration and exploitation in an information-selective symmetric reversal bandit task

abstract: Humans often face sequential decision-making problems, in which information about the environmental reward structure is detached from rewards for a subset of actions. In the current exploratory study, we introduce an information-selective symmetric reversal bandit task to model such situations and obtained choice data on this task from 24 participants. To arbitrate between different decision-making strategies that participants may use on this task, we developed a set of probabilistic agent-based behavioral models, including exploitative and explorative Bayesian agents, as well as heuristic control agents. Upon validating the model and parameter recovery properties of our model set and summarizing the participants choice data in a descriptive way, we used a maximum likelihood approach to evaluate the participants choice data from the perspective of our model set. In brief, we provide quantitative evidence that participants employ a belief state-based hybrid explorative-exploitative strategy on the information-selective symmetric reversal bandit task, lending further support to the finding that humans are guided by their subjective uncertainty when solving exploration-exploitation dilemmas.


title: ASO-based PKM Splice-switching Therapy Inhibits Hepatocellular Carcinoma Cell Growth

abstract:
The M2 pyruvate kinase (PKM2) isoform is upregulated in most cancers and plays a crucial role in the Warburg effect, which is characterized by the preference for aerobic glycolysis for energy metabolism. PKM2 is an alternative-splice isoform of the PKM gene and is a potential therapeutic target. Previously, we developed antisense oligonucleotides (ASOs) that switch PKM splicing from the cancer-associated PKM2 to the PKM1 isoform and induce apoptosis in cultured glioblastoma cells. Here, we explore the potential of ASO-based PKM splice-switching as a targeted therapy for liver cancer. We utilize a more potent lead cEt/DNA ASO and demonstrate that it induces PKM splice-switching and inhibits the growth of cultured hepatocellular-carcinoma (HCC) cells. This PKM isoform switch increases pyruvate-kinase activity and alters glucose metabolism. The lead ASO and a second ASO targeting a non-overlapping site inhibit tumorigenesis in an orthotopic-xenograft HCC mouse model. Finally, a surrogate mouse-specific ASO induces Pkm splice-switching and inhibits HCC growth, without observable toxicity, in a genetic HCC mouse model. These results lay the groundwork for a potential ASO therapy for HCC.

Statement of significanceAntisense oligonucleotides are used to force a change in PKM isoform usage in HCC, reversing the Warburg effect and inhibiting tumorigenesis.

category: cancer biology


title: Striatal Direct Pathway Targets Npas1+ Pallidal Neurons

abstract:
The classic basal ganglia circuit model asserts a complete segregation of the two striatal output pathways. Empirical data argue that, in addition to indirect-pathway striatal projection neurons (iSPNs), direct-pathway striatal projection neurons (dSPNs) innervate the external globus pallidus (GPe). However, the functions of the latter were not known. In this study, we interrogated the organization principles of striatopallidal projections and their roles in full-body movement in mice (both males and females). In contrast to the canonical motor-promoting response of dSPNs in the dorsomedial striatum (DMSdSPNs), optogenetic stimulation of dSPNs in the dorsolateral striatum (DLSdSPNs) suppressed locomotion. Circuit analyses revealed that dSPNs selectively target Npas1+ neurons in the GPe. In a chronic 6-hydroxydopamine lesion model of Parkinsons disease, the dSPN-Npas1+ projection was dramatically strengthened. As DLSdSPN-Npas1+ projection suppresses movement, the enhancement of this projection represents a circuit mechanism for the hypokinetic symptoms of Parkinsons disease that has not been previously considered. In sum, our results suggest that dSPN input to the GPe is a critical circuit component that is involved in the regulation of movement in both healthy and parkinsonian states.

Significance statementIn the classic basal ganglia model, the striatum is described as a divergent structure--it controls motor and adaptive functions through two segregated, opposing output streams. However, the experimental results that show the projection from direct-pathway neurons to the external pallidum have been largely ignored. Here, we showed that this striatopallidal sub-pathway targets a select subset of neurons in the external pallidum and is motor-suppressing. We found that this sub-pathway undergoes changes in a Parkinsons disease model. In particular, our results suggest that the increase in strength of this sub-pathway contributes to the slowness or reduced movements observed in Parkinsons disease.


title: Experimentally disambiguating models of sensory cue integration

abstract: Sensory cue integration is one of the primary areas in which a normative mathematical framework has been used to define the "optimal" way in which to make decisions based upon ambiguous sensory information and compare these predictions to behaviour. The conclusion from such studies is that sensory cues are integrated in a statistically optimal fashion. However, numerous alternative computational frameworks exist by which sensory cues could be integrated, many of which could be described as "optimal" based on different criteria. Existing studies rarely assess the evidence relative to different candidate models, resulting in an inability to conclude that sensory cues are integrated according to the experimenters preferred framework. The aims of the present paper are to summarise and highlight the implicit assumptions rarely acknowledged in testing models of sensory cue integration, as well as to introduce an unbiased and principled method by which to determine, for a given experimental design, the probability with which a population of observers behaving in accordance with one model of sensory integration can be distinguished from the predictions of a set of alternative models.


title: Investigating post-breeding moult locations and diets of Common Guillemots (Uria aalge) in the North Sea using stable isotope analyses

abstract: Seabird movements and diet during the non-breeding season are poorly studied, yet understanding these aspects of seabird ecology is extremely important to effectively conserve these protected species. Stable isotope analyses (SIA) provide a cost-effective solution to filling these knowledge gaps, yielding information on diet and foraging locations of animals. This study aimed to use SIA to investigate whether Common Guillemots (Uria aalge) from different age classes and locations in the UK had contrasting diets and foraging areas during the post-breeding moult (July-September). SIA of secondary feathers and a newly-developed North Sea isoscape were used to identify the likeliest foraging areas and diets of deceased guillemots recovered from beaches in eastern Scotland and mixed fisheries in Cornwall and the Celtic Sea. Overall, guillemots foraged widely in the western, eastern and southern North Sea, consuming a variety of clupeid, gadoid and invertebrate prey. There were negligible dietary differences between age classes and birds from different recovery locations. Juveniles showed a wider range in foraging areas, but both age classes foraged in similar parts of the North Sea. Guillemots recovered from Scotland may have foraged further north, only overlapping with guillemots recovered from the southwestern UK in the southern and eastern North Sea. Their winter recovery locations also implied that they exhibited different movement strategies during the non-breeding season, meriting further investigation. Conservation efforts should target foraging areas in the southern and eastern North Sea which are highly threatened by gillnet fishing, shipping traffic and oil infrastructure.

category: ecology


title: Fine-scale spatial patterns of wildlife disease are common and understudied

abstract:
O_LIAll parasites are heterogeneous in space, yet little is known about the prevalence and scale of this spatial variation, particularly in wild animal systems. To address this question, we sought to identify and examine spatial dependence of wildlife disease across a wide range of systems.
C_LIO_LIConducting a broad literature search, we collated 31 such datasets featuring 89 replicates and 71 unique host-parasite combinations, only 51% of which had previously been used to test spatial hypotheses. We analysed these datasets for spatial dependence within a standardised modelling framework using Bayesian linear models, and we then meta-analysed the results to identify generalised determinants of the scale and magnitude of spatial autocorrelation.
C_LIO_LIWe detected spatial autocorrelation in 48/89 model replicates (54%) across 21/31 datasets (68%), spread across parasites of all groups. Even some very small study areas (under 0.01km2) exhibited substantial spatial variation.
C_LIO_LIDespite the common manifestation of spatial variation, our meta-analysis was unable to identify host-, parasite-, or sampling-level determinants of this heterogeneity across systems. Parasites of all transmission modes had easily detectable spatial patterns, implying that structured contact networks and susceptibility effects are potentially as important in spatially structuring disease as are environmental drivers of transmission efficiency.
C_LIO_LIOur findings demonstrate that fine-scale spatial patterns of infection manifest frequently and across a range of wild animal systems, and many studies are able to investigate them whether or not the original aim of the study was to examine spatially varying processes. Given the widespread nature of these findings, studies should more frequently record and analyse spatial data, facilitating development and testing of spatial hypotheses in disease ecology. Ultimately, this may pave the way for an a priori predictive framework for spatial variation in novel host-parasite systems.
C_LI


title: Gains and Losses Affect Learning Differentially at Low and High Attentional Load

abstract:
Prospective gains and losses modulate cognitive processing, but it is unresolved whether gains and losses can facilitate flexible learning in changing environments. The prospect of gains might enhance flexible learning through prioritized processing of reward-predicting stimuli but is unclear how far this learning benefit extends when task demands increase. Similarly, experiencing losses might facilitate learning when they trigger attentional re-orienting away from loss-inducing stimuli, but losses may also impair learning by reducing the precise encoding of loss-inducing stimuli. To clarify these divergent views, we tested how varying magnitudes of gains and losses affect the flexible learning of object values in environments that varied attentional load by increasing the number of interfering object features during learning. With this task design we found that larger prospective gains improved learning efficacy and learning speed, but only when attentional load was low. In contrast, expecting losses generally impaired learning efficacy and this impairment was larger at higher attentional load. These findings functionally dissociate the contributions of prospective gains and losses on flexible learning, suggesting they operate via separate control mechanisms. One process is triggered by experiencing loss and seems to disrupt the encoding of specific loss-inducing features which leads to less efficient exploration during learning. The second process is triggered by experiencing gains which enhances learning through a more efficient prioritizing of reward-predicting stimulus features as long as the interference of distracting information is limited. These results demonstrate strengths and limitations of motivational regulation of learning efficacy in multidimensional environments having variable attentional loads.

Significance statementIncreasing the prospective gains is assumed to enhance flexible learning, but there is no consensus on whether imposing losses enhances or impairs flexible learning. We show that anticipating loss of already attained assets generally reduced learning changes in the relevance of visual objects and that this learning impediment is more pronounced when learning demands higher attentional control of interference from distracting object features. Moreover, we show that increasing the prospective gains indeed facilitates learning, but only when the learning problem has intermediate or low attentional demands. These findings document that the beneficial effects of gains hit a limit when task demands increase, and that prospective losses reduce cognitive flexibility already at low task demands which is exacerbated when task demands increase. These findings provide novel insight into the strengths and limitations of gains and of losses to support flexible learning in multidimensional environments imposing variable attentional loads.

category: animal behavior and cognition


title: Feature-based encoding of face identity by single neurons in the human amygdala and hippocampus

abstract: Neurons in the human amygdala and hippocampus that are selective for the identity of specific people are classically thought to encode a persons identity invariant to visual features (e.g., skin tone, eye shape). However, it remains largely unknown how visual information from higher visual cortical areas is translated into such a semantic representation of an individual person. Here, we show that some amygdala and hippocampal neurons are selective to multiple different unrelated face identities based on shared visual features. The encoded identities form clusters in the representation of a deep neural network trained to recognize faces. Contrary to prevailing views, these neurons thus represent an individuals face with a visual feature-based code rather than one based on association with known concepts. Feature neurons encoded faces regardless of their identity, race, gender, familiarity, or pixel-level visual features; and the region of feature space to which feature neurons are tuned predicted their response to new face stimuli. Our results reveal a new class of neurons that bridge the perception-driven representation of facial features in the higher visual cortex with mnemonic semantic representations in the MTL, which may form the basis for declarative memory.


title: Spatial distribution of Arctic bacterioplankton abundance is linked to distinct water masses and summertime phytoplankton bloom dynamics (Fram Strait, 79°N)

abstract: The Arctic is impacted by climate warming faster than any other oceanic region on Earth. Assessing the baseline of microbial communities in this rapidly changing ecosystem is vital for understanding the implications of ocean warming and sea ice retreat on ecosystem functioning. Using CARD-FISH and semi-automated counting, we quantified 14 ecologically relevant taxonomic groups of bacterioplankton (Bacteria and Archaea) from surface (0-30 m) down to deep waters (2500 m) in summerly ice-covered and ice-free regions of the Fram Strait, the main gateway for Atlantic inflow into the Arctic Ocean. Cell abundances of the bacterioplankton communities in surface waters varied from 105 cells mL-1 in ice-covered regions to 106 cells mL-1 in the ice-free regions, and were overall driven by variations in phytoplankton bloom conditions across the Strait. The bacterial classes Bacteroidia and Gammaproteobacteria showed several-fold higher cell abundances under late phytoplankton bloom conditions of the ice-free regions. Other taxonomic groups, such as the Rhodobacteraceae, revealed a distinct association of cell abundances with the surface Atlantic waters. With increasing depth (>500 m), the total cell abundances of the bacterioplankton communities decreased by up to two orders of magnitude, while largely unknown taxonomic groups (e.g., SAR324 and SAR202 clades) maintained constant cell abundances throughout the entire water column (ca. 103 cells mL-1). This suggests that these enigmatic groups may occupy a specific ecological niche in the entire water column. Our results provide the first quantitative spatial variations assessment of bacterioplankton in the summerly ice-covered and ice-free Arctic water column, and suggest that further shift towards ice-free Arctic summers with longer phytoplankton blooms can lead to major changes in the associated standing stock of the bacterioplankton communities.

category: microbiology


title: Homeostatic brain network mechanisms facilitate perceptual binding of audio-visual speech

abstract: Perceptual processes unfold along spatial and temporal hierarchies in brain dynamics. In daily lives, speech perception requires binding of spatiotemporally disjoint auditory and visual cues by distributed brain areas. The network-level information processing involving these brain areas can be characterized by two complementary mechanisms, functional segregation which refers to localization of processing within few areas, and integration which pertains to the cooperation among relevant functional modules. Here, we demonstrate using fMRI recordings that subjective perceptual experience of multisensory speech stimuli--real and illusory--are represented in differential states of segregation-integration balance. We were able to parametrically control the inter-subject variability of illusory/cross-modal perception by introducing temporal lags in the incongruent auditory-visual articulations of speech sounds using the McGurk paradigm. The functional segregation-integration balance is captured using two alternative computational approaches. First, the segregation of brain areas as modules responsible for illusory speech perception is captured using standardized parametric statistical approaches. The functional integration was quantified from exploring the temporal correlation of the relevant functional modules with the dynamics of all other brain areas. We observed that the regions with higher activation during illusory perception tended to have lower levels of cooperation with the rest of the brain indicating high levels of local segregation, but reduced global integration. Second, using graph theoretic measures of local clustering, modularity, and participation coefficient, which capture the contribution of segregation and integration among functional modules, we further validated the observation of enhanced local segregation and diminished global integration during the illusory/cross-modal perception. Further, the perceptual binding network that exhibited this observation was anticorrelated with other intrinsic functional brain networks, such as dorsal attention and default mode networks, and most importantly, inter-subject variability of perceptual categorization could be explained from the altered balance of local segregation-global integration.


title: Synergistic balance of local segregation and global integration mechanisms in large-scale brain networks underlies perceptual experience


title: No evidence for entrainment: endogenous gamma oscillations and rhythmic flicker responses coexist in visual cortex

abstract:
Over the past decades, a plethora of studies have linked cortical gamma oscillations ([~]30-100 Hz) to neuro-computational mechanisms. Their functional relevance, however, is still passionately debated. Here, we asked if endogenous gamma oscillations in the human brain can be entrained by a rhythmic photic drive >50 Hz. A noninvasive modulation of endogenous brain rhythms allows conclusions about their causal involvement in neurocognition. To this end, we systematically investigated oscillatory responses to a rapid sinusoidal flicker in the absence and presence of endogenous gamma oscillations using magnetoencephalography (MEG) in combination with a high-frequency projector. The photic drive produced a robust response over visual cortex to stimulation frequencies of up to 80 Hz. Strong, endogenous gamma oscillations were induced using moving grating stimuli as repeatedly done in previous research. When superimposing the flicker and the gratings, there was no evidence for phase or frequency entrainment of the endogenous gamma oscillations by the photic drive. Unexpectedly, we did not observe an amplification of the flicker response around participants individual gamma frequencies; rather, the magnitude of the response decreased monotonically with increasing frequency. Source reconstruction suggests that the flicker response and the gamma oscillations were produced by separate, coexistent generators in visual cortex. The presented findings challenge the notion that cortical gamma oscillations can be entrained by rhythmic visual stimulation. Instead, the mechanism generating endogenous gamma oscillations seems to be resilient to external perturbation.

Significance StatementWe aimed to investigate to what extent ongoing, high-frequency oscillations in the gamma band (30-100 Hz) in the human brain can be entrained by a visual flicker. Gamma oscillations have long been suggested to coordinate neuronal firing and enable inter-regional communication. Our results demonstrate that rhythmic visual stimulation cannot hijack the dynamics of ongoing gamma oscillations; rather, the flicker response and the endogenous gamma oscillations coexist in different visual areas. Therefore, while a visual flicker evokes a strong neuronal response even at high frequencies in the gamma-band, it does not entrain endogenous gamma oscillations in visual cortex. This has important implications for interpreting studies investigating the causal and neuroprotective effects of rhythmic sensory stimulation in the gamma band.


title: Accurate spliced alignment of long RNAsequencing reads

abstract: Long-read RNA sequencing techniques are establishing themselves as the primary sequencing technique to study the transcriptome landscape. Many such analyses are dependent on read alignments. However, the error rate and sequencing length of long-read technologies create new challenges for accurately aligning these reads. We present an alignment method uLTRA based on a novel two-pass collinear chaining algorithm. Furthermore, uLTRA can be used both as a stand-alone aligner and as a wrapper around minimap2 for improved alignments in gene regions. We show that uLTRA produces higher accuracy over state-of-the-art aligners with substantially higher accuracy for small exons on simulated and synthetic data. On biological data where true read location is unknown, we show several examples where uLTRA aligns to known and novel isoforms with exon structures that are not detected with other aligners. uLTRA is available at https://github.com/ksahlin/ultra.

category: bioinformatics


title: Evolution Without Variation and Selection

abstract: Natural selection successfully explains how organisms accumulate adaptive change despite that traits acquired over a lifetime are eliminated at the end of each generation. However, in some domains that exhibit cumulative, adaptive change--e.g., cultural evolution, and earliest life--acquired traits are retained; these domains do not face the problem that Darwins theory was designed to solve. Lack of transmission of acquired traits occurs when germ cells are protected from environmental change, due to a self-assembly code used in two distinct ways: (i) actively interpreted during development to generate a soma, and (ii) passively copied without interpretation during reproduction to generate germ cells. Early life and cultural evolution appear not to involve a self-assembly code used in these two ways. We suggest that cumulative, adaptive change in these domains is due to a lower-fidelity evolutionary process, and model it using Reflexively Autocatalytic and Foodset-generated networks. We refer to this more primitive evolutionary process as Self-Other Reorganisation (SOR) because it involves internal self-organising and self-maintaining processes within entities, as well as interaction between entities. SOR encompasses learning but in general operates across groups. We discuss the relationship between SOR and Lamarckism, and illustrate a special case of SOR without variation.

category: evolutionary biology


title: An Evolutionary Process Without Variation and Selection


title: The Effect of Population Structure on Murine Genome-Wide Association Studies

abstract: Population structure (PS) has been shown to cause false positive signals in genome-wide association studies (GWAS). Since PS correction is routinely used in human GWAS, it was assumed that it also should be utilized for murine GWAS using inbred strains. Nevertheless, there are fundamental differences between murine and human GWAS, and the impact of PS on murine GWAS results has not been thoroughly investigated. To assess the impact of PS on murine GWAS, we examined 8223 datasets that characterized biomedical responses in panels of inbred mouse strains. Surprisingly, we found that the PS had a minimal impact on datasets characterizing responses in [≤]20 strains; and relatively little impact on the majority of datasets characterizing >20 strains. Moreover, there were examples where association signals within known causative genes could be rejected if PS correction methods were utilized. PS assessment should be carefully used and should be considered in conjunction with other criteria when assessing the candidate genes identified in GWAS using inbred mouse strains.

category: genetics


title: Contribution of enhancer-driven and master-regulator genes to autoimmune disease revealed using functionally informed SNP-to-gene linking strategies

abstract: Gene regulation is known to play a fundamental role in human disease, but mechanisms of regulation vary greatly across genes. Here, we explore the contributions to disease of two types of genes: genes whose regulation is driven by enhancer regions as opposed to promoter regions (Enhancer-driven) and genes that regulate many other genes in trans (Master-regulator). We link these genes to SNPs using a comprehensive set of SNP-to-gene (S2G) strategies and apply stratified LD score regression to the resulting SNP annotations to draw three main conclusions about 11 autoimmune diseases and blood cell traits (average Ncase=13K across 6 autoimmune diseases, average N =443K across 5 blood cell traits). First, several characterizations of Enhancer-driven genes defined in blood using functional genomics data (e.g. ATAC-seq, RNA-seq, PC-HiC) are conditionally informative for autoimmune disease heritability, after conditioning on a broad set of regulatory annotations from the baseline-LD model. Second, Master-regulator genes defined using trans-eQTL in blood are also conditionally informative for autoimmune disease heritability. Third, integrating Enhancer-driven and Master-regulator gene sets with protein-protein interaction (PPI) network information magnified their disease signal. The resulting PPI-enhancer gene score produced >2x stronger conditional signal (maximum standardized SNP annotation effect size ({tau}*) = 2.0 (s.e. 0.3) vs. 0.91 (s.e. 0.21)), and >2x stronger gene-level enrichment for approved autoimmune disease drug targets (5.3x vs. 2.1x), as compared to the recently proposed Enhancer Domain Score (EDS). In each case, using functionally informed S2G strategies to link genes to SNPs that may regulate them produced much stronger disease signals (4.1x-13x larger{tau} * values) than conventional window-based S2G strategies. We conclude that our characterizations of Enhancer-driven and Master-regulator genes identify gene sets that are important for autoimmune disease, and that combining those gene sets with functionally informed S2G strategies enables us to identify SNP annotations in which disease heritability is concentrated.


title: Synthetic mammalian signaling circuits for robust cell population control

abstract: In multicellular organisms, cells actively sense and control their own population density. Synthetic mammalian quorum sensing circuits could provide insight into principles of population control and extend cell therapies. However, a key challenge is reducing their inherent sensitivity to "cheater" mutations that evade control. Here, we repurposed the plant hormone auxin to enable orthogonal mammalian cell-cell communication and quorum sensing. We designed a paradoxical population control circuit, termed Paradaux, in which auxin stimulates and inhibits net cell growth at different concentrations. This circuit limited population size over extended timescales, of up to 42 days of continuous culture. By contrast, when operating in a non-paradoxical regime, the same cells limited population growth, but were more susceptible to mutational escape. These results establish auxin as a versatile "private" communication system, and demonstrate that paradoxical circuit architectures can provide robust population control.

category: synthetic biology


title: Temporal variabilities provide additional category-related information in object category decoding: a systematic comparison of informative EEG features

abstract: How does the human brain encode visual object categories? Our understanding of this has advanced substantially with the development of multivariate decoding analyses. However, conventional electroencephalography (EEG) decoding predominantly use the "mean" neural activation within the analysis window to extract category information. Such temporal averaging overlooks the within-trial neural variability which is suggested to provide an additional channel for the encoding of information about the complexity and uncertainty of the sensory input. The richness of temporal variabilities, however, has not been systematically compared with the conventional "mean" activity. Here we compare the information content of 31 variability-sensitive features against the "mean" of activity, using three independent highly-varied datasets. In whole-trial decoding, the classical event-related potential (ERP) components of "P2a" and "P2b" provided information comparable to those provided by "Original Magnitude Data (OMD)" and "Wavelet Coefficients (WC)", the two most informative variability-sensitive features. In time-resolved decoding, the "OMD" and "WC" outperformed all the other features (including "mean"), which were sensitive to limited and specific aspects of temporal variabilities, such as their phase or frequency. The information was more pronounced in Theta frequency band, previously suggested to support feed-forward visual processing. We concluded that the brain might encode the information in multiple aspects of neural variabilities simultaneously e.g. phase, amplitude and frequency rather than "mean" per se. In our active categorization dataset, we found that more effective decoding of the neural codes corresponds to better prediction of behavioral performance. Therefore, the incorporation of temporal variabilities in time-resolved decoding can provide additional category information and improved prediction of behavior.


title: Rapid acting antidepressant (2R,6R)-hydroxynorketamine (HNK) targets glucocorticoid receptor signaling: a longitudinal cerebrospinal fluid proteome study

abstract: Delayed onset of antidepressant action is a shortcoming in depression treatment. Ketamine and its metabolite (2R,6R)-hydroxynorketamine (HNK) have emerged as promising rapidacting antidepressants. However, their mechanism of action remains unknown. In this study, we first described the anxious and depression-prone inbred mouse strain, DBA/2J, as a animal model to assess the antidepressant-like effects of ketamine and HNK in vivo. To decode the molecular mechanisms mediating HNKs rapid antidepressant effects, a longitudinal cerebrospinal fluid (CSF) proteome profiling of its acute and sustained effects was conducted using an unbiased, hypothesis-free mass spectrometry-based proteomics approach. A total of 387 proteins were identified, with a major implication of significantly differentially expressed proteins in the glucocorticoid receptor (GR) signaling pathway, providing evidence for a link between HNK and regulation of the stress hormone system. Mechanistically, we identified HNK to repress GR-mediated transcription and reduce hormonal sensitivity of GR in vitro. In addition, mammalian target of rapamycin (mTOR) and brain-derived neurotrophic factor (BDNF) were predicted to be important upstream regulators of HNK treatment. Our results contribute to precise understanding of the temporal dynamics and molecular targets underlying HNKs rapid antidepressant-like effects, which can be used as a benchmark for improved treatment strategies for depression in future.


title: Re-examining Kozlov et al.: Estimation of biases in museum specimen data requires robust sampling

abstract: Kozlov and colleagues1 call into question the application of herbarium specimens to quantify historical patterns of herbivory2-5. It is already widely appreciated that collectors of herbarium specimens may tend to avoid insect damage, thus making herbivory estimates from herbarium specimens potentially down-biased2. However, Kozlov et al. additionally suggest that variation in sampling selectivity among collectors and curators may lead herbarium specimens to misrepresent patterns of herbivory in nature. The authors sought to quantify these biases by collecting and contrasting insect herbivory data across 17 plant species from herbarium versus standard field ecological sampling procedures, and then assessed the selection of these specimens by curators. They concluded that herbivory estimates from herbarium specimens are highly variable, rendering them an inaccurate representation of herbivory in nature. Our re-analysis of Kozlov et al.s data suggests that, in contrast with their results, herbarium specimens indeed provide a useful record of herbivory as long as sample sizes are appropriate. In addition, we assert that by arguing that herbarium specimens are "distorting mirrors", Kozlov et al.s conclusions fundamentally overstep their data, which narrowly assesses biases across species. Kozlov et al. argue that herbarium specimens are inaccurate data sources, but fail to characterize the specific circumstances under which assumed biases would apply. Thus, Kozlov et al.s data do not support their main premise, and the authors extrapolate beyond the specific biases investigated in their study; we believe their contribution does a disservice to researchers interested in exploring the potential value of herbarium specimens for studying herbivory through time.


title: Cellular aging in vitro recapitulates multi-tissue epigenetic aging in vivo

abstract: ii.Aging is known to elicit dramatic changes to DNA methylation (DNAm), although the causes and consequences of such alterations are not clear and require further exploration. Our ability to experimentally uncover mechanisms of epigenetic aging will be greatly enhanced by our ability to study and manipulate these changes using in vitro models. However, it remains unclear whether the changes elicited by cells in culture can serve as a model of what is observed in aging tissues in vivo. To test this, we serially passaged mouse embryonic fibroblasts (MEFs) and assessed changes in DNAm at each time-point via RRBS. By developing a measure that tracked cellular aging in vitro, we tested whether it tracked physiological aging in various mouse tissues and whether anti-aging interventions modulate this measure. Our measure, termed DNAmCULTURE, was shown to strongly increase with age when examined in multiple tissues (liver, lung, kidney, blood, and adipose). As a control, we confirmed that the measure was not a marker of cellular senescence, suggesting that it reflects a distinct yet progressive cellular aging phenomena that can be induced in vitro. Furthermore, we demonstrated slower epigenetic aging in animals undergoing caloric restriction and a resetting of our measure in lung and kidney fibroblasts when re-programmed to iPSCs. Enrichment and clustering analysis implicated SUZ12, EED and Polycomb group (PcG) factors as potentially important chromatin regulators in translational culture aging phenotypes. Overall, this study supports the concept that physiologically relevant aging changes can be induced in vitro and moving forward, used to uncover mechanistic insights into epigenetic aging.

category: pathology


title: Evolution and regulation of microbial secondary metabolism

abstract:
Microbes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large groups and cooperatively secrete massive amounts of secondary metabolites that impact their environment. Yet, the conditions enabling secondary metabolism without compromising primary needs remain unclear. Here we investigated the biosynthesis of rhamnolipids, a secondary metabolite that Pseudomonas aeruginosa makes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that biosynthesis of rhamnolipids from glycerol varies inconsistently across the phylogenetic tree; instead, non-producer lineages are also those worse at reducing the oxidative stress of primary glycerol metabolism. The link to oxidative stress explains the inconsistent distribution across the P. aeruginosa tree, adding a new layer to the regulation of rhamnolipids--a microbial secondary metabolite important for fitness in natural and clinical settings.

SignificanceThe bacterium Pseudomonas aeruginosa is a major source of hospital-acquired infections. This pathogens knack for virulence relies on its ability to multiply and secrete massive amounts of substances that overwhelm microbial competitors and weaken host defenses. It remains unclear how the bacteria conciliate their need to grow and multiply--a need at the individual-level-- with their ability to secrete products--a need of the population. Here we combined genomics, metabolomics and mathematical modeling to study the biosynthesis of rhamnolipids, a surfactant that P. aeruginosa makes to reduce the surface tension of surrounding liquids. Our study reveals a new link between oxidative stress and rhamnolipid synthesis, which helps explain how this important bacterial product has evolved and how it persists in many lineages of pathogens.

category: systems biology


title: Sunday driver mediates multi-compartment Golgi outposts defects induced by amyloid precursor protein

abstract: Golgi defects including Golgi fragmentation are pathological features of Alzheimer disease (AD). As a pathogenic factor of AD, amyloid precursor protein (APP) induces Golgi fragmentation in soma. However, how APP regulates Golgi outposts (GOs) in dendrites remains unclear. Given that APP resided and affected GOs movements, especially reversed the distribution of multi-compartment GOs (mcGOs), we investigated the regulatory mechanism of mcGOs movements in Drosophila larvae. Knockdown experiments showed the bidirectional mcGOs movements were cooperatively controlled by dynein heavy chain (Dhc) and kinesin heavy chain subunits. Notably, only Dhc mediated APPs regulation on mcGOs movements. Further, by loss-of-function screening, the adaptor protein Sunday driver (Syd) was identified to mediate APP-induced alteration of the direction of mcGOs movements, and dendritic defects. Collectively, by elucidating a model of bidirectional mcGOs movements, we revealed the mechanism of APPs regulation on the direction of mcGOs movements. It provides new insights into AD pathogenesis.


title: MetaFunc: Taxonomic and Functional Analyses of High Throughput Sequencing for Microbiomes

abstract:
BackgroundThe identification of functional processes taking place in microbiome communities augment traditional microbiome taxonomic studies, giving a more complete picture of interactions taking place within the community. While there are applications that perform functional annotation on metagenomes or metatranscriptomes, very few of these are able to link taxonomic identity to function and are limited by their input types or databases used.

ResultsHere we present MetaFunc, a workflow which takes input reads, and from these 1) identifies species present in the microbiome sample and 2) provides gene ontology (GO) annotations associated with the species identified. MetaFunc can also provide a differential abundance analysis step comparing species between sample conditions. In addition, MetaFunc allows mapping of reads to a host genome, and separates these reads, before proceeding with the microbiome analyses. From the host reads, MetaFunc is able to identify host genes, perform differential abundance analysis, and gene-set enrichment analysis. A final correlation analysis between microbial species and host genes can also be performed. Finally, MetaFunc builds an R shiny application that allows users to view and interact with the microbiome results. In this paper we showed how MetaFunc can be applied to metatranscriptomic datasets of colorectal cancer.

ConclusionMetaFunc is a one-stop shop microbiome analysis pipeline that can identify taxonomies and their respective functional contributions in a microbiome sample through GO annotations. It can also analyse host reads in a microbiome sample, providing information on host gene expression, and allowing for correlations between the microbiome and host genes. MetaFunc comes with a user-friendly R shiny application that allows for easier visualisation and exploration of its results. MetaFunc is freely available through https://gitlab.com/schmeierlab/workflows/metafunc.git.


title: Graph Convolutional Network-based Method for ClusteringSingle-cell RNA-seq Data

abstract: Single-cell RNA sequencing (scRNA-seq) technologies promise to characterize the transcriptome of genes at cellular resolution, which shed light on unfolding cell heterogeneity and diversity. Fast-growing scRNA-seq profiles require efficient clustering algorithms to identify the same type of cells. Although many methods have been developed for cell clustering, existing clustering methods are limited to extract the representations from expression data of individual cells, while ignoring the high-order structural relations between cells. Here, we proposed GraphSCC, a robust graph artificial intelligence model to cluster single cells by accounting for structural relations between cells. The representation learned from the graph convolutional network, together with another representation output from a denoising autoencoder network, are optimized by a dual self-supervised module for better cell clustering. The experimental results indicate that GraphSCC model outperforms state-of-the-art methods in terms of various evaluation metrics on both simulated and real datasets. Further visualizations show that GraphSCC provides representations for better intra-cluster compactness and inter-cluster separability.


title: Simulating the outcome of amyloid treatments in Alzheimer's Disease from multi-modal imaging and clinical data

abstract: In this study we investigate a novel quantitative instrument for the development of intervention strategies for disease modifying drugs in Alzheimers disease. Our framework is based on the modeling of the spatio-temporal dynamics governing the joint evolution of imaging and clinical biomarkers along the history of the disease, and allows the simulation of the effect of intervention time and drug dosage on the biomarkers progression. When applied to multi-modal imaging and clinical data from the Alzheimers Disease Neuroimaging Initiative our method enables to generate hypothetical scenarios of amyloid lowering interventions. The results quantify the crucial role of intervention time, and provide a theoretical justification for testing amyloid modifying drugs in the pre-clinical stage. Our experimental simulations are compatible with the outcomes observed in past clinical trials, and suggest that anti-amyloid treatments should be administered at least 7 years earlier than what is currently being done in order to obtain statistically powered improvement of clinical endpoints.


title: A mesh microelectrode array for non-invasive electrophysiology within neural organoids

abstract: Organoids are emerging in vitro models of human physiology. Neural models require the evaluation of functional activity of single cells and networks, which is best measured by microelectrode arrays. The characteristics of organoids clash with existing in vitro or in vivo microelectrode arrays. With inspiration from implantable mesh electronics and growth of organoids on polymer scaffolds, we fabricated suspended hammock-like mesh microelectrode arrays for neural organoids. We have demonstrated the growth of organoids enveloping these meshes and the culture of organoids on meshes for up to one year. Furthermore, we present proof-of-principle recordings of spontaneous electrical activity across the volume of an organoid. Our concept enables a new class of microelectrode arrays for in vitro models of three-dimensional electrically active tissue.


title: Migration without interbreeding: evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes

abstract: Wild plant populations show extensive genetic subdivision and are far from the ideal of panmixia which permeates population genetic theory. Understanding the spatial and temporal scale of population structure is therefore fundamental for empirical population genetics - and of interest in itself, as it yields insights into the history and biology of a species. In this study we extend the genomic resources for the wild Mediterranean grass Brachypodium distachyon to investigate the scale of population structure and its underlying history at whole-genome resolution. 86 accessions were sampled at local and regional scales in Italy and France, which closes a conspicuous gap in the collection for this model organism. The analysis of 196 accessions, spanning the Mediterranean from Spain to Iraq, suggests that the interplay of high selfing and seed dispersal rates has shaped genetic structure in B. distachyon. At the continental scale, the evolution in B. distachyon is characterized by the independent expansion of three lineages during the Upper Pleistocene. Today, these lineages may occur on the same meadow yet do not interbreed. At the regional scale, dispersal and selfing interact and maintain high genotypic diversity, thus challenging the textbook notion that selfing in finite populations implies reduced diversity. Our study extends the population genomic resources for B. distachyon and suggests that an important use of this wild plant model is to investigate how selfing and dispersal, two processes typically studied separately, interact in colonizing plant species.


title: The need for high-quality oocyte mitochondria at extreme ploidy dictates germline development

abstract: Selection against deleterious mitochondrial mutations is facilitated by germline processes, lowering the risk of genetic diseases. How selection works is disputed: experimental data are conflicting and previous modelling work has not clarified the issues. Here we develop computational and evolutionary models that compare the outcome of selection at the level of individuals, cells and mitochondria. Using realistic de novo mutation rates and germline development parameters, the evolutionary model predicts the observed prevalence of mitochondrial mutations and diseases in human populations. We show the importance of organelle-level selection, seen in the selective pooling of mitochondria into the Balbiani body, in achieving high-quality mitochondria at extreme ploidy in mature oocytes. Alternative mechanisms debated in the literature, bottlenecks and follicular atresia, are unlikely to account for the clinical data, because neither process effectively eliminates mitochondrial mutations under realistic conditions. Our findings explain the major features of female germline architecture, notably the longstanding paradox of over-proliferation of primordial germ cells followed by massive loss. The near-universality of these processes across animal taxa makes sense in light of the need to maintain mitochondrial quality at extreme ploidy in mature oocytes, in the absence of sex and recombination.


title: mTOR inhibition represses transcription of cholesterol biosynthesis genes and alters cholesterol levels in primary neurons and in the developing brain

abstract:
Dysregulated mammalian target of rapamycin (mTOR) activity is associated with various neurodevelopmental disorders ranging from idiopathic autism spectrum disorders to syndromes caused by single gene defects. This suggests that maintaining mTOR activity levels in a physiological range is essential for brain development and functioning. Upon activation, mTOR regulates a variety of cellular processes such as cell growth, autophagy and metabolism. On a molecular level, however, the consequences of mTOR activation in the brain are not well understood.

Low levels of cholesterol are associated with a wide variety of neurodevelopmental disorders. We here describe numerous genes of the sterol/cholesterol biosynthesis pathway to be transcriptionally regulated by mTOR complex 1 (mTORC1) signaling in vitro in primary neurons and in vivo in the developing cerebral cortex of the mouse. We find that these genes are shared targets of the transcription factors SREBP, SP1 and NF-Y. Prenatal as well as postnatal mTORC1 inhibition downregulated expression of these genes which directly translated into reduced cholesterol levels pointing towards a substantial metabolic function of the mTORC1 signaling cascade. Altogether, our results indicate that mTORC1 is an essential transcriptional regulator of the expression of sterol/cholesterol biosynthesis genes in the developing brain. Altered expression of these genes may be an important factor contributing to the pathogenesis of neurodevelopmental disorders associated with dysregulated mTOR signaling.


title: mTOR driven gene transcription is required for cholesterol production in neurons of the developing cerebral cortex


title: Epithelial and neutrophil interactions and innate immune response to Shigella in a human intestinal enteroid-neutrophil co-culture

abstract:
Polymorphonuclear neutrophils (PMN) are recruited to the gastrointestinal mucosa in response to inflammation, injury, and infection. Herein, we report the development and the characterization of an ex vivo tissue co-culture model consisting of human primary intestinal enteroid monolayers and PMN, and a mechanistic interrogation of PMN-epithelial cell interaction and response to Shigella, a primary cause of childhood dysentery. Cellular adaptation and tissue integration, barrier function, PMN phenotypic and functional attributes, and innate immune responses were examined. PMN within the enteroid monolayers acquired a distinct activated/migratory phenotype that was influenced by direct epithelial cell contact as well as by molecular signals. Seeded on the basal side of the intestinal monolayer, PMN intercalated within the epithelial cells and moved paracellularly toward the apical side. Co-cultured PMN also increased basal secretion of IL-8. Shigella added to the apical surface of the monolayers evoked additional PMN phenotypic adaptations, including increased expression of cell surface markers associated with chemotaxis and cell degranulation (CD47, CD66b, and CD88). Apical Shigella infection triggered rapid transmigration of PMN to the luminal side, NET formation as well as bacterial phagocytosis and killing. Shigella infection modulated cytokine production in the co-culture; apical MCP-1, TNF-, and basolateral IL-8 production were downregulated, while basolateral IL-6 secretion was increased. We demonstrated, for the first time, PMN phenotypic adaptation, mobilization, and coordinated epithelial cell-PMN innate response upon Shigella infection in the human intestinal environment. The enteroid monolayer-PMN co-culture represents a technical innovation for mechanistic interrogation of gastrointestinal physiology, host-microbe interaction, innate immunity, and evaluation of preventive/therapeutic tools.

ImportanceStudies of mucosal immunity and microbial host cell interaction have traditionally relied on animal models and in vitro tissue culture using immortalized cancer cell lines, which render non-physiological and often unreliable results. Herein we report the development and characterization of an ex vivo enteroid-PMN co-culture consisting of normal human intestinal epithelium and a mechanistic interrogation of PMN and epithelial cell interaction and function in the context of Shigella infection. We demonstrated tissue-driven phenotypic and functional adaptation of PMN and a coordinated epithelial cell and PMN response to Shigella, a primary cause of dysentery in young children in the developing world.

category: immunology


title: Epithelial and neutrophil interactions and coordinated response to Shigella in a human intestinal enteroid-neutrophil co-culture model


title: The dirty north: Evidence for multiple colonisations and Wolbachia infections shaping the genetic structure of the widespread butterfly Polyommatus icarus in the British Isles

abstract: The paradigm of differentiation in southern refugia during glacial periods followed by expansions during interglacials, producing limited genetic diversity and population sub-division in northern areas, dominates European phylogeography. However, the existence of complex structured populations in formerly glaciated areas, and on islands connected to mainland areas during glacial maxima, call for alternative explanations. Here, we reconstruct the mtDNA phylogeography of the widespread Polyommatus icarus butterfly over its native range, with an emphasis on the formerly glaciated and connected British Isles. We found distinct geographical structuring of CO1 mitotypes, with an ancient lineage restricted to the marginal European areas, including Northern Scotland and Outer Hebrides. We detected perfect mtDNA-Wolbachia associations in Northern Britain that support the possibility of at least two post-glacial Wolbachia-mediated sweeps, suggesting a series of sequential replacement of mtDNA in the British Isles and potentially in Europe. Population genomic analysis, using ddRADSeq genomic markers, also reveal unexpected genetic structuring within Britain. However, weak mito-nuclear concordance suggests the potential for independent histories of nuclear versus mitochondrial genomes. We found clustering of genomic SNPs of French samples, with respect to those in the British Isles, is not consistent with a scenario of a single recolonisation. Taken together our mtDNA and ddRADseq observations are consistent with a history of at least two distinct colonisations, a phylogeographic scenario previously put forth to explain diversity and structuring in other British flora and fauna. Additionally, we also present preliminary evidence that Wolbachia-induced feminization may be occurring in the isolated population in the Outer Hebrides.


title: preciseTAD: A transfer learning framework for 3D domain boundary prediction at base-pair resolution

abstract: Chromosome conformation capture technologies (Hi-C) revealed extensive DNA folding into discrete 3D domains, such as Topologically Associating Domains and chromatin loops. The correct binding of CTCF and cohesin at domain boundaries is integral in maintaining the proper structure and function of these 3D domains. 3D domains have been mapped at the resolutions of 1 kilobase and above. However, it has not been possible to define their boundaries at the resolution of boundary-forming proteins. To predict domain boundaries at base-pair resolution, we developed preciseTAD, an optimized transfer learning framework trained on high-resolution genome annotation data. In contrast to current TAD/loop callers, preciseTAD-predicted boundaries are strongly supported by experimental evidence. Importantly, this approach can accurately delineate boundaries in cells without Hi-C data. preciseTAD provides a powerful framework to improve our understanding of how genomic regulators are shaping the 3D structure of the genome at base-pair resolution.


title: SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells

abstract: The SARS-CoV-2 virus is the causative agent of the global COVID-19 infectious disease outbreak, which can lead to acute respiratory distress syndrome (ARDS). However, it is still unclear how the virus interferes with immune cell and metabolic functions in the human body. In this study, we investigated the immune response in acute or convalescent COVID19 patients. We characterized the peripheral blood mononuclear cells (PBMCs) using flow cytometry and found that CD8+ T cells were significantly subsided in moderate COVID-19 and convalescent patients. Furthermore, characterization of CD8+ T cells suggested that patients with a mild and moderate course of the COVID-19 disease and convalescent patients have significantly diminished expression of both perforin and granzyme A in CD8+ T cells. Using 1H-NMR spectroscopy, we characterized the metabolic status of their autologous PBMCs. We found that fructose, lactate and taurine levels were elevated in infected (mild and moderate) patients compared with control and convalescent patients. Glucose, glutamate, formate and acetate levels were attenuated in COVID-19 (mild and moderate) patients. In summary, our report suggests that SARS-CoV-2 infection leads to disrupted CD8+ T cytotoxic functions and changes the overall metabolic functions of immune cells.


title: Preliminary report of preclinical efficacy and safety analysis of gamma-irradiated inactivated SARS-CoV-2 vaccine candidates, SK-01 version 1 and OZG-3861 version 1

abstract: COVID-19 outbreak caused by SARS-CoV-2 created an unprecedented health crisis since there is no vaccine for this novel virus. Therefore, SARS-CoV-2 vaccines have become crucial for reducing morbidity and mortality. In this study, in vitro and in vivo safety and efficacy analyzes of lyophilized vaccine candidates inactivated by gamma-irradiation were performed. The candidate vaccines in this study were OZG-3861 version 1 (V1), an inactivated SARS-CoV-2 virus vaccine, and SK-01 version 1 (V1), a GM-CSF adjuvant added vaccine. The candidate vaccines were applied intradermally to BALB/c mice to assess toxicity and immunogenicity. Preliminary results in vaccinated mice are reported in this study. Especially, the vaccine models containing GM-CSF caused significant antibody production with neutralization capacity in absence of the antibody-dependent enhancement feature, when considered in terms of T and B cell responses. Another important finding was that the presence of adjuvant was more important in T cell in comparison with B cell response. Vaccinated mice showed T cell response upon restimulation with whole inactivated SARS-CoV-2 or peptide pool. This study shows that the vaccines are effective and leads us to start the challenge test to investigate the gamma-irradiated inactivated vaccine candidates for infective SARS-CoV-2 virus in humanized ACE2+ mice.


title: Inter-specific Variability in Demographic Processes Affects Abundance-Occupancy Relationships

abstract: Species with large local abundances tend to occupy more sites. One of the mechanisms proposed to explain this widely reported inter-specific relationship is a cross-scale hypothesis based on dynamics at the population level. Called the vital rates mechanism, it uses within-population demographic processes of population growth and density dependence to predict when inter-specific abundance-occupancy relationships can arise and when these relationships can weaken and even turn negative. Even though the vital rates mechanism is mathematically simple, its predictions has never been tested directly because of the difficulty estimating the demographic parameters involved. Here, using a recently introduced mark-recapture analysis method, we show that there is a weakly positive relationship between abundance and occupancy among 17 bird species. Our results are consistent with the predictions of the vital rate mechanism regarding the demographic processes that are expected to weaken this relationship. Specifically, we find that intrinsic growth rate and local abundance are weakly correlated; and density dependence strength shows considerable variation across species. Variability in density dependence strength is related to variability in species-level local average abundance and intrinsic growth rate; species with lower growth rate have higher abundance and are strongly regulated by density dependent processes, especially acting on survival rates. Species with higher growth rate, on average, have lower abundance and are more weakly regulated by density dependent processes especially acting on fecundity. More generally, our findings support a cross scale mechanism of macroecological abundance-occupancy relationship emerging from density-dependent dynamics at the population level.


title: Proteome dynamics during antibiotic persistence and resuscitation

abstract: During antibiotic persistence, bacterial cells become transiently tolerant to antibiotics by restraining their growth and metabolic activity. Detailed molecular characterization of antibiotic persistence is hindered by low count of persisting cells and the need for their isolation. Here we used sustained addition of stable isotope-labeled lysine to selectively label the proteome during hipA-induced persistence and hipB-induced resuscitation of E. coli cells in minimal medium after antibiotic treatment. Time-resolved, 24-hour measurement of label incorporation allowed detection of over 500 newly synthesized proteins in viable cells, demonstrating low but widespread protein synthesis during persistance. Many essential proteins were newly synthesized and several ribosome-associated proteins, such as RaiA and Sra showed high synthesis levels, pointing to their roles in maintenance of persistence. At the onset of resuscitation, cells synthesized the ribosome-splitting GTPase HflX and various ABC transporters, restored translation machinery and resumed metabolism by inducing glycolysis and biosynthesis of amino acids.


title: Unsupervised clustering analysis reveals global population structure of SARS-CoV-2

abstract: Identifying the population structure of the newly emerged coronavirus SARS-CoV-2 has significant potential to inform public health management and diagnosis. As SARS-CoV-2 sequencing data accrued, grouping them into clusters is important for organizing the landscape of the population structure of the virus. Due to the limited prior information on the newly emerged coronavirus, we utilized four different clustering algorithms to group 16,873 SARS-CoV-2 strains, which automatically enables the identification of spatial structure for SARS-CoV-2. A total of six distinct genomic clusters were identified using mutation profiles as input features. Comparison of the clustering results reveals that the four algorithms produced highly consistent results, but the state-of-the-art unsupervised deep learning clustering algorithm performed best and produced the smallest intra-cluster pairwise genetic distances. The varied proportions of the six clusters within different continents revealed specific geographical distributions. In particular, our analysis found that Oceania was the only continent on which the strains were dispersively distributed into six clusters. In summary, this study provides a concrete framework for the use of clustering methods to study the global population structure of SARS-CoV-2. In addition, clustering methods can be used for future studies of variant population structures in specific regions of these fast-growing viruses.


title: Unsupervised clustering analysis of SARS-Cov-2population structure reveals six major subtypes atearly stage across the world


title: Transcription factors from multiple families ensure enhancer selectivity and robust neuron terminal differentiation

abstract:
To systematically investigate the complexity of neuron-specification regulatory networks we performed an RNA interference (RNAi) screen against all 875 transcription factors (TFs) encoded in Caenorhabditis elegans genome and searched for defects in nine different neuron types of the monoaminergic (MA) superclass and two cholinergic motoneurons.

We identified 91 TF candidates to be required for correct generation of these neuron types of which 28 were confirmed by mutant analysis. We found that correct reporter expression in each individual neuron type requires at least nine different TFs. Individual neuron types do not usually share TFs involved in their specification but share a common pattern of TFs belonging to the five most common TF families: Homeodomain (HD), basic Helix Loop Helix (bHLH), Zinc Finger (ZF), Basic Leucine Zipper Domain (bZIP) and Nuclear Hormone Receptors (NHR). HD TF members are over-represented, supporting a key role for this family in the establishment of neuronal identities. These five TF families area also prevalent when considering mutant alleles with previously reported neuronal phenotypes in C. elegans, Drosophila or mouse. In addition, we studied terminal differentiation complexity focusing on the dopaminergic terminal regulatory program. We found two HD TFs (UNC-62 and VAB-3) that work together with known dopaminergic terminal selectors (AST-1, CEH-43, CEH-20). Combined TF binding sites for these five TFs constitute a cis-regulatory signature enriched in the regulatory regions of dopaminergic effector genes. Our results provide new insights on neuron-type regulatory programs in C. elegans that could help better understand neuron specification and evolution of neuron types.


title: Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity


title: REACTION-DIFFUSION MODEL FOR THE ARREST OF OSCILLATIONS IN THE SOMITOGENESIS SEGMENTATION CLOCK

abstract:
AO_SCPLOWBSTRACTC_SCPLOWThe clock and wavefront paradigm is arguably the most widely accepted model for explaining the embryonic process of somitogenesis. According to this model, somitogenesis is based upon the interaction between a genetic oscillator, known as segmentation clock, and a differentiation wavefront, which provides the positional information indicating where each pair of somites is formed. Shortly after the clock and wavefront paradigm was introduced, Meinhardt presented a conceptually different mathematical model for morphogenesis in general, and somitogenesis in particular. Recently, Cotterell et al. rediscovered an equivalent model by systematically enumerating and studying small networks performing segmentation. Cotterell et al. called it a progressive oscillatory reaction-diffusion (PORD) model. In the Meinhardt-PORD model, somitogenesis is driven by short-range interactions and the posterior movement of the front is a local, emergent phenomenon, which is not controlled by global positional information. With this model, it is possible to explain some experimental observations that are incompatible with the clock and wavefront model. However the Meinhardt-PORD model has some important disadvantages of its own. Namely, it is quite sensitive to fluctuations and depends on very specific initial conditions (which are not biologically realistic). In this work, we propose an equivalent Meinhardt-PORD model, and then amend it to couple it with a wavefront consisting of a receding morphogen gradient. By doing so, we get a hybrid model between the Meinhardt-PORD and the clock-and-wavefront ones, which overcomes most of the deficiencies of the two originating models.

Somitogenesis, the process by which somites are formed, is an essential developmental stage in many vertebrates. This process occurs with a strikingly regular periodicity, that is preserved among embryos of a single species. The clock and wavefront paradigm is arguably the most widely accepted model for explaining somitogenesis. However, it is incapable of explaining some experimental facts, like the appearance of somites in the absence of an external wavefront (i.e. a receding morphogen gradient). Shortly after the clock and wavefront paradigm was introduced, Meinhardt presented a conceptually different mathematical model for morphogenesis in general, and somitogenesis in particular. Recently, Cotterell et al. rediscovered an equivalent model by systematically enumerating and studying small networks performing segmentation, and called it a progressive oscillatory reaction-diffusion (PORD) model. The Meinhardt-PORD model tackles some of the deficiencies of the clock and wave-front models, but it has some serious issues of its own. In the present work, we introduce an equivalent Meinhardt-PORD model, and then amend it to couple it with a receding morphogen gradient. By doing so, we get a hybrid model that incorporates characteristics of the Meinhardt-PORD and clock-and-wavefront models. We show that this hybrid model under-goes a bifurcation, from a stable to an unstable limit cycle, as the value of the parameter accounting for a background regulatory input (associated to the receding morphogen gradient) decreases. This bifurcation allows the model to explain why somites can form in the absence of an external wavefront, reassesses the role of the receding morphogen gradient as a conductor for somitogenesis, and makes the model behavior robust to random fluctuations, as well as independent from specific initial conditions (the latter, are two of the weak points of the Meinhardt-PORD model). We argue that this findings provide convincing evidence that reaction-diffusion and positional information (receding morphogen gradient) mechanisms could work together in somitogenesis.

category: developmental biology


title: HYBRID REACTION-DIFFUSION AND CLOCK-AND-WAVEFRONT MODEL FOR THE ARREST OF OSCILLATIONS IN THE SOMITOGENESIS SEGMENTATION CLOCK


title: Large Mammals Have More Powerful Antibacterial Defenses Than Expected from Their Metabolic Rates

abstract: Terrestrial mammals span 7 orders of magnitude in body size, ranging from the < 2 g pygmy shrew (Suncus etruscus) to the > 3900 kg African elephant (Loxodonta africana). Although body size has profound effects on the behavior, physiology, ecology, and evolution of animals, how investment in immune defenses changes with body size is unknown. Here, we develop a novel 12-point dilution-curve approach to describe and compare antibacterial capacity against 3 bacterial species among >160 terrestrial species of mammals. We show that antibacterial activity in serum across mammals exhibits isometry, but the serum of large mammals is less hospitable to bacteria than would be predicted by their metabolic rates. Specifically, hypometric metabolic rates would predict that a large species should have disproportionately lower antibacterial capacity than small species, but body size is unrelated to killing capacity across species. Scaling of antibacterial immune defenses provides novel perspectives on the ecology of host-pathogen interactions, and on their co-evolutionary dynamics. These results have direct implications for effectively modeling the evolution of immune defenses and identifying potential reservoir hosts of zoonotic pathogens.


title: Genome Methylation Predicts Age and Longevity of Bats

abstract: Exceptionally long-lived species, including many bats, rarely show overt signs of aging, making it difficult to determine why species differ in lifespan. Here, we use DNA methylation (DNAm) profiles from 712 known-age bats, representing 26 species, to identify epigenetic changes associated with age and longevity. We demonstrate that DNAm accurately predicts chronological age. Across species, longevity is negatively associated with the rate of DNAm change at age-associated sites. Furthermore, analysis of several bat genomes reveals that hypermethylated age- and longevity-associated sites are disproportionately located in promoter regions of key transcription factors (TF) and enriched for histone and chromatin features associated with transcriptional regulation. Predicted TF binding site motifs and enrichment analyses indicate that age-related methylation change is influenced by developmental processes, while longevity-related DNAm change is associated with innate immunity or tumorigenesis genes, suggesting that bat longevity results from augmented immune response and cancer suppression.

category: genomics


title: Resolving the spatial and cellular architecture of lung adenocarcinoma by multi-region single-cell sequencing

abstract:
Little is known of the geospatial architecture of individual cell populations in lung adenocarcinoma (LUAD) evolution. Here, we perform single-cell RNA sequencing of 186,916 cells from 5 early-stage LUADs and 14 multi-region normal lung tissues of defined spatial proximities from the tumors. We show that cellular lineages, states, and transcriptomic features geospatially evolve across normal regions to LUADs. LUADs also exhibit pronounced intratumor cell heterogeneity within single sites and transcriptional lineage-plasticity programs. T regulatory cell phenotypes are increased in normal tissues with proximity to LUAD, in contrast to diminished signatures and fractions of cytotoxic CD8+ T cells, antigen-presenting macrophages and inflammatory dendritic cells. We further find that the LUAD ligand-receptor interactome harbors increased expression of epithelial CD24 which mediates pro-tumor phenotypes. These data provide a spatial atlas of LUAD evolution, and a resource for identification of targets for its treatment.

Statement of significanceThe geospatial ecosystem of the peripheral lung and early-stage LUAD is not known. Our multi-region single-cell sequencing analyses unravel cell populations, states, and phenotypes in the spatial and ecological evolution of LUAD from the lung that comprise high-potential targets for early interception.


title: Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance

abstract: A major disease affecting sugarcane, a leading sugar and energy crop, is sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV). Despite damages caused by SCYLV, the genetic basis of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic basis of SCYLV resistance using dominant and codominant markers and genotypes of interest for breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them, demonstrating their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.

category: plant biology


title: An Inducible Model for Unraveling the Effects of Advanced Glycation End-Products in Aging Connective Tissues

abstract:
PurposeIn connective tissues there is a clear link between increasing age and degeneration. Advanced glycation end-products (AGEs) are believed to play a central role. AGEs are sugar-induced non-enzymatic crosslinks which accumulate in collagen with age and diabetes, altering tissue mechanics and cellular function. Despite ample correlative evidence linking collagen glycation to tissue degeneration, little is known how AGEs impact cell-matrix interactions, limiting therapeutic options. One reason for this limited understanding is AGEs are typically induced using high concentrations of ribose which decrease cell viability, making it impossible to investigate cell-matrix interactions. The objective of this study was to develop a system to trigger AGE accumulation while maintaining cell viability.

Materials and MethodsUsing cell-seeded high density collagen gels, we investigated the effect of two systems for AGE induction, ribose at low concentrations (30, 100, and 200 mM) over 15 days of culture and riboflavin (0.25 mM and 0.75mM) induced with blue light for 40 seconds (riboflavin-465 nm).

ResultsWe found ribose and riboflavin-465 nm treatment produces fluorescent AGE quantities which match and/or exceed human fluorescent AGE levels for various tissues, ages, and diseases, without affecting cell viability or metabolism. Interestingly, a 40 second treatment of riboflavin-465 nm produced similar levels of fluorescent AGEs as 3 days of 100 mM ribose treatment.

ConclusionsRiboflavin-465 nm is a promising method to trigger AGE crosslinks on demand in vivo or in vitro without impacting cell viability and offers potential for unraveling the mechanism of AGEs in age and diabetes related tissue damage.

category: bioengineering


title: Evolution is in the details: Regulatory differences in modern human and Neanderthal

abstract:
Transcription factor (TF) proteins play a critical role in the regulation of eukaryote gene expression by sequence-specific binding to genomic locations known as transcription factor binding sites.

Here we present the TFBSFootprinter tool which has been created to combine transcription-relevant data from six large empirical datasets: Ensembl, JASPAR, FANTOM5, ENCODE, GTEX, and GTRD to more accurately predict functional sites. A complete analysis integrating all experimental datasets can be performed on genes in the human genome, and a limited analysis can be done on a total of 125 vertebrate species.

As a use-case, we have used TFBSFootprinter to study sites of genomic variation between modern humans and Neanderthal promoters. We found significant differences in binding affinity for 86 transcription factors, groups of which are both highly expressed, and show correlation of expression, in immune cells and adult and developing neural tissues.


title: Stable 3D Head Direction Signals in the Primary Visual Cortex

abstract: Visual signals influence the brains computation of spatial position and orientation. Accordingly, the primary visual cortex (V1) is extensively interconnected with areas involved in computing head direction (HD) information. Predictive coding theories posit that higher cortical areas send sensory or motor predictions to lower areas, but whether this includes cognitive variables like the HD signal--and whether HD information is present in V1--is unknown. Here we show that V1 encodes the yaw, roll, and pitch of the head in freely behaving rats, either in the presence or absence of visual cues. HD tuning was modulated by lighting and movement state, but was stable on a population level for over a week. These results demonstrate the presence of a critical spatial orientation signal in a primary cortical sensory area and support predictive coding theories of brain function.

category: neuroscience


title: Neuroendocrine and behavioral measures of stress-reactivity in male goal-tracker and sign-tracker rats

abstract:
Environmental cues attain the ability to guide behavior via learned associations. As predictors, cues can elicit adaptive behavior and lead to valuable resources (e.g., food). For some individuals, however, cues are transformed into incentive stimuli and elicit motivational states that can be maladaptive. The goal-tracker/sign-tracker animal model captures individual differences in cue-motivated behaviors, with reward-associated cues serving as predictors of reward for both phenotypes but becoming incentive stimuli to a greater degree for sign-trackers. While these distinct phenotypes are characterized based on Pavlovian conditioned approach behavior, they exhibit differences on a number of behaviors relevant to psychopathology. To further characterize the neurobehavioral endophenotype associated with individual differences in cue-reward learning, neuroendocrine and behavioral profiles associated with stress and anxiety were investigated in male goal-tracker, sign-tracker, and intermediate responder rats. It was revealed that baseline corticosterone increases with Pavlovian learning, but to the same degree, regardless of phenotype. No significant differences in behavior were observed between goaltrackers and sign-trackers during an elevated plus maze or open field test, nor were there differences in corticosterone response to the open field test or physiological restraint. Upon examination of central markers associated with stress-reactivity, we found that sign-trackers have greater glucocorticoid receptor mRNA expression in the ventral hippocampus, with no phenotypic differences in the dorsal hippocampus or prelimbic cortex. These findings demonstrate that goal-trackers and sign-trackers do not differ on stress- and anxiety-related behaviors, and suggest that differences in neuroendocrine measures between these phenotypes can be attributed to distinct cue-reward learning styles.

Significance StatementWhile the goal-tracker/ sign-tracker animal model derives from individual differences in Pavlovian conditioned approach behavior, other traits, including some of relevance to addiction and post-traumatic stress disorder, have been shown to co-exist with the propensity to sign-track. The extent to which this model encompasses differences in aversive arousal and associated neuroendocrine measures, however, remains largely unexplored. Here we show that behavioral and corticosterone response to stress-related paradigms do not differ between goal-trackers and sign-trackers. However, glucocorticoid receptor expression in the ventral hippocampus does differ between phenotypes, suggesting that this central marker that is typically associated with stress-responsivity, may, in fact, play an important role in appetitive motivation.


title: High-content analysis and Kinetic Image Cytometry identify toxic and epigenotoxic effects of HIV antiretrovirals on human iPSC-neurons and primary neural precursor cells

abstract: Despite viral suppression due to combination antiretroviral therapy (cART), HIV-associated neurocognitive disorders (HAND) continue to affect half of people with HIV, suggesting that certain antiretrovirals (ARVs) may contribute to HAND. We examined the effects of nucleoside/nucleotide reverse transcriptase inhibitors tenofovir disproxil fumarate (TDF) and emtricitabine (FTC) and the integrase inhibitors dolutegravir (DTG) and elvitegravir (EVG) on viability, structure, and function of glutamatergic neurons (a subtype of CNS neuron involved in cognition) derived from human induced pluripotent stem cells (hiPSC-neurons), and primary human neural precursor cells (hNPCs), which are responsible for neurogenesis. Using automated digital microscopy and image analysis (high content analysis, HCA), we found that DTG, EVG, and TDF decreased hiPSC-neuron viability, neurites, and synapses after seven days of treatment. Analysis of hiPSC-neuron calcium activity using Kinetic Image Cytometry (KIC) demonstrated that DTG and EVG also decreased the frequency and magnitude of intracellular calcium transients. Longer ARV exposures and simultaneous exposure to multiple ARVs increased the magnitude of these neurotoxic effects. Using the Microscopic Imaging of Epigenetic Landscapes (MIEL) assay, we found that TDF decreased hNPC viability and changed the distribution of histone modifications that regulate chromatin packing, suggesting that TDF may reduce neuroprogenitor pools important for CNS development and maintenance of cognition in adults. This study establishes human preclinical assays that can screen potential ARVs for CNS toxicity to develop safer cART regimens and HAND therapeutics.


title: Reduction of a stochastic model of gene expression: Lagrangian dynamics gives acces to basins of attraction as cell types and metastability

abstract: Differentiation is the process whereby a cell acquires a specific phenotype, by differential gene expression as a function of time. This is thought to result from the dynamical functioning of an underlying Gene Regulatory Network (GRN). The precise path from the stochastic GRN behavior to the resulting cell state is still an open question. In this work we propose to reduce a stochastic model of gene expression, where a cell is represented by a vector in a continuous space of gene expression, to a discrete coarse-grained model on a limited number of cell types. We develop analytical results and numerical tools to perform this reduction for a specific model characterizing the evolution of a cell by a system of piecewise deterministic Markov processes (PDMP). Solving a spectral problem, we find the explicit variational form of the rate function associated to a large deviations principle, for any number of genes. The resulting Lagrangian dynamics allows us to define a deterministic limit of which the basins of attraction can be identified to cellular types. In this context the quasipotential, describing the transitions between these basins in the weak noise limit, can be defined as the unique solution of an Hamilton-Jacobi equation under a particular constraint. We develop a numerical method for approximating the coarse-grained model parameters, and show its accuracy for a symmetric toggle-switch network. We deduce from the reduced model an approximation of the stationary distribution of the PDMP system, which appears as a Beta mixture. Altogether those results establish a rigorous frame for connecting GRN behavior to the resulting cellular behavior, including the calculation of the probability of jumps between cell types.