bluuebunny/crossref_metadata_2025 huggingface dataset:
Asymmetric Allostery in Estrogen Receptor-α Homodimers Drives Responses to the Ensemble of Estrogens in the Hormonal Milieu
Authors: Min Charles K. , Nwachukwu Jerome C. , Hou Yingwei , Russo Robin J. , Papa Alexandra , Min Jian , Peng Rouming , Kim Sung Hoon , Ziegler Yvonne , Rangarajan Erumbi S. , Izard Tina , Katzenellenbogen Benita S. , Katzenellenbogen John A. , Nettles Kendall W.
Published: April 2024

The estrogen receptor-α (ER) is thought to function only as a homodimer, but responds to a variety of environmental, metazoan, and therapeutic estrogens at sub-saturating doses, supporting binding mixtures of ligands as well as dimers that are only partially occupied. Here, we present a series of flexible ER ligands that bind to receptor dimers with individual ligand poses favoring distinct receptor conformations —receptor conformational heterodimers—mimicking the binding of two different ligands. Molecular dynamics simulations showed that the pairs of different ligand poses changed the correlated motion across the dimer interface to generate asymmetric communication between the dimer interface, the ligands, and the surface binding sites for epigenetic regulatory proteins. By examining binding of the same ligand in crystal structures of ER in the agonist versus antagonist conformers, we also showed that these allosteric signals are bidirectional. The receptor conformer can drive different ligand binding modes to support agonist versus antagonist activity profiles, a revision of ligand binding theory that has focused on unidirectional signaling from ligand to the coregulator binding site. We also observed differences in the allosteric signals between ligand and coregulator binding sites in the monomeric versus dimeric receptor, and when bound by two different ligands, states that are physiologically relevant. Thus, ER conformational heterodimers integrate two different ligand-regulated activity profiles, representing new modes for ligand-dependent regulation of ER activity.

Significance

The estrogen receptor-α (ER) regulates transcription in response to a hormonal milieu that includes low levels of estradiol, a variety of environmental estrogens, as well as ER antagonists such as breast cancer anti-hormonal therapies. While ER has been studied as a homodimer, the variety of ligand and receptor concentrations in different tissues means that the receptor can be occupied with two different ligands, with only one ligand in the dimer, or as a monomer. Here, we use X-ray crystallography and molecular dynamics simulations to reveal a new mode for ligand regulation of ER activity whereby sequence-identical homodimers can act as functional or conformational heterodimers having unique signaling characteristics, with ligand-selective allostery operating across the dimer interface integrating two different signaling outcomes.
β-arrestin-biased Allosteric Modulator of Neurotensin Receptor 1 Reduces Ethanol Drinking and Responses to Ethanol Administration in Rodents
Authors: Gereau Graydon B , Zhou Diana , Van Voorhies Kalynn J , Tyler Ryan E. , Campbell Jeffrey , Murray Jackson G. , Alvararez-Pamir Ali , Wykoff Luke , Companion Michel A. , Jackson Michael R. , Olson Steven H. , Barak Lawrence S. , Slosky Lauren M. , Vetreno Ryan P. , Besheer Joyce , McElligott Zoe A
Published: April 2024

Alcohol use disorders (AUDs) impose an enormous societal and financial burden, and world-wide, alcohol misuse is the 7th leading cause of premature death1. Despite this, there are currently only 3 FDA approved pharmacological treatments for the treatment of AUDs in the United States. The neurotensin (Nts) system has long been implicated in modulating behaviors associated with alcohol misuse. Recently, a novel compound, SBI-553, that biases the action of Nts receptor 1 (NTSR1) activation, has shown promise in preclinical models of psychostimulant misuse. Here we investigate the efficacy of this compound to alter ethanol-mediated behaviors in a comprehensive battery of experiments assessing ethanol consumption, behavioral responses to ethanol, sensitivity to ethanol, and ethanol metabolism. Additionally, we investigated behavior in avoidance and cognitive assays to monitor potential side effects of SBI-553. We find that SBI-553 reduces binge-like ethanol consumption in mice without altering avoidance behavior or novel object recognition. We also observe sex-dependent differences in physiological responses to sequential ethanol injections in mice. In rats, we show that SBI-553 attenuates sensitivity to the interoceptive effects of ethanol (using a Pavlovian drug discrimination task). Our data suggest that targeting NTSR1 signaling may be promising to attenuate alcohol misuse, and adds to a body of literature that suggests NTSR1 may be a common downstream target involved in the psychoactive effects of multiple reinforcing substances.
Compressed sensing based approach identifies modular neural circuitry driving learned pathogen avoidance
Authors: Hallacy Timothy , Yonar Abdullah , Ringstad Niels , Ramanathan Sharad
Published: April 2024

An animal’s survival hinges on its ability to integrate past information to modify future behavior. The nematodeC. elegansadapts its behavior based on prior experiences with pathogen exposure, transitioning from attraction to avoidance of the pathogen. A systematic screen for the neural circuits that integrate the information of previous pathogen exposure to modify behavior has not been feasible because of the lack of tools for neuron type specific perturbations. We overcame this challenge using methods based on compressed sensing to efficiently determine the roles of individual neuron types in learned avoidance behavior. Our screen revealed that distinct sets of neurons drive exit from lawns of pathogenic bacteria and prevent lawn re-entry. Using calcium imaging of freely behaving animals and optogenetic perturbations, we determined the neural dynamics that regulate one key behavioral transition after infection: stalled re-entry into bacterial lawns. We find that key neuron types govern pathogen lawn specific stalling but allow the animal to enter nonpathogenicE. colilawns. Our study shows that learned pathogen avoidance requires coordinated transitions in discrete neural circuits and reveals the modular structure of this complex adaptive behavioral response to infection.
Population genomics ofPlasmodium ovalespecies in sub-Saharan Africa
Authors: Carey-Ewend Kelly , Popkin-Hall Zachary R. , Simkin Alfred , Muller Meredith , Hennelly Chris , He Wenqiao , Moser Kara A. , Gaither Claudia , Niaré Karamoko , Aghakanian Farhang , Feleke Sindew , Brhane Bokretsion G. , Phanzu Fernandine , Mwandagalirwa Kashamuka , Aydemir Ozkan , Sutherland Colin J. , Ishengoma Deus S. , Ali Innocent M. , Ngasala Billy , Kalonji Albert , Tshefu Antoinette , Parr Jonathan B. , Bailey Jeffrey A. , Juliano Jonathan J. , Lin Jessica T.
Published: April 2024

Plasmodium ovale curtisi(Poc)andPlasmodium ovale wallikeri(Pow) are relapsing malaria parasites endemic to Africa and Asia that were previously thought to represent a single species. Amid increasing detection of ovale malaria in sub-Saharan Africa, we performed a population genomic study of both species across the continent. We conducted whole-genome sequencing of 25 isolates from Central and East Africa and analyzed them alongside 20 previously published African genomes. Isolates were predominantly monoclonal (43/45), with their genetic similarity aligning with geography.Powshowed lower average nucleotide diversity (1.8×10−4) across the genome compared toPoc(3.0×10−4) (p < 0.0001). Signatures of selective sweeps involving the dihydrofolate reductase gene were found in both species, as were signs of balancing selection at the merozoite surface protein 1 gene. Differences in the nucleotide diversity ofPocandPowmay reflect unique demographic history, even as similar selective forces facilitate their resilience to malaria control interventions.
The dorsal fan-shaped body is a neurochemically heterogeneous sleep-regulating center inDrosophila
Authors: Jones Joseph D. , Holder Brandon L. , Montgomery Andrew C. , McAdams Chloe V. , He Emily , Burns Anna E. , Eiken Kiran R. , Vogt Alex , Velarde Adriana I. , Elder Alexandra J. , McEllin Jennifer A. , Dissel Stephane
Published: April 2024

Sleep is a behavior that is conserved throughout the animal kingdom. Yet, despite extensive studies in humans and animal models, the exact function or functions of sleep remain(s) unknown. A complicating factor in trying to elucidate the function of sleep is the complexity and multiplicity of neuronal circuits that are involved in sleep regulation. It is conceivable that distinct sleep-regulating circuits are only involved in specific aspects of sleep and may underlie different sleep functions. Thus, it would be beneficial to assess the contribution of individual circuits in sleep’s putative functions. The intricacy of the mammalian brain makes this task extremely difficult. However, the fruit flyDrosophila melanogaster,with its simpler brain organization, available connectomics, and unparalleled genetics offers the opportunity to interrogate individual sleep-regulating centers. InDrosophila, neurons projecting to the dorsal Fan-Shaped Body (dFB) have been proposed to be key regulators of sleep, particularly sleep homeostasis. We recently demonstrated that the most widely used genetic tool to manipulate dFB neurons, the 23E10-GAL4 driver, expresses in two sleep-regulating neurons (VNC-SP neurons) located in the Ventral Nerve Cord (VNC), the fly analog of the vertebrate spinal cord. Since most data supporting a role for the dFB in sleep regulation have been obtained using 23E10-GAL4, it is unclear whether the sleep phenotypes reported in these studies are caused by dFB neurons or VNC-SP cells. A recent publication replicated our finding that 23E10-GAL4 contains sleep-promoting neurons in the VNC. However, it also proposed that the dFB is not involved in sleep regulation at all, but this suggestion was made using genetic tools that are not dFB-specific and a very mild sleep deprivation protocol. In this study, using a newly created dFB-specific genetic driver line, we demonstrate that the majority of 23E10-GAL4 dFB neurons can promote sleep when activated and that these neurons are involved in sleep homeostasis. We also show that dFB neurons require stronger stimulation than VNC-SP cells to promote sleep. In addition, we demonstrate that dFB-induced sleep can consolidate Short-Term Memory (STM) into Long-Term Memory (LTM), suggesting that the benefit of sleep on memory is not circuit-specific. Finally, we show that dFB neurons are neurochemically heterogeneous and can be divided in 3 populations. Most dFB neurons express both glutamate and acetylcholine, while a minority of cells express only one of these two neurotransmitters. Importantly, dFB neurons do not express GABA, as previously suggested. Using neurotransmitter-specific dFB tools, our data also points at cholinergic dFB neurons as particularly potent at regulating sleep and sleep homeostasis.
GLMMcosinor: Flexible cosinor modeling with a generalized linear mixed modeling framework to characterize rhythmic time series
Authors: Parsons Rex , Jayasinghe Oliver , White Nicole , Chunduri Prasad , Rawashdeh Oliver
Published: April 2024

The complexity, volume, and importance of time series data across various research domains highlight the necessity for tools that can efficiently analyze, visualize, and extract insights. Cosinor modeling is a widely used methodology to estimate or compare rhythmic characteristics in time series datasets. Time series are widely used in biomedical and clinical research studies, with a large amount of research focusing on circadian rhythms in physiology and their relationship to health outcomes. However, existing software for cosinor modeling fails to effectively equip researchers to analyze their data, often due to the hierarchical structure of the data (e.g., repeated measures over time) or non-Gaussian response variables being modeled. Here, we present GLMMcosinor, an R package for fitting the cosinor model to rhythmic time series, using a Generalized Linear Mixed Modeling framework (glmmTMB). This software extends cosinor modeling to non-Gaussian and hierarchical data due to the flexibility offered by glmmTMB. It offers multiple additional features unavailable in other cosinor modeling packages that use the linearized cosinor model or circacompare (which we previously developed), which uses nonlinear regression. GLMMcosinor includes several additional features to interpret, test, and visualize the produced models and can fit models with multiple cosinor components. A detailed description of the use of GLMMcosinor is available within the package’s online documentation and vignettes. The GLMMcosinor R package is available from GitHub (https://github.com/ropensci/GLMMcosinor), CRAN, rOpenSci, and the R-universe. A shiny app is also available and can fit and visualize a model with GLMMcosinor without having to write R code (https://github.com/RWParsons/GLMMcosinor-shinyapp).

Key Points

GLMMcosinor is an R Package for flexible cosinor modeling, a method used to estimate cyclic rhythm characteristics.

It uses a generalized linear mixed modeling framework (glmmTMB) to allow the user to fit data with non-Gaussian response variables and hierarchical data structures.

GLMMcosinor is a well documented and feature rich package allowing users to easily fit, interpret and visualize cosinor models.

GLMMcosinor supports modeling of a wider range of experimental and observation datasets.
Leg choice for volitional goal-directed stepping is primarily influenced by effort rather than success: A preliminary investigation in neurotypical adults
Authors: Charalambous Charalambos C. , Espinoza-Wade Eric R. , Cesar Guilherme M. , Gerger Michaela , Lai Yi-Hsuan , Winstein Carolee J.
Published: April 2024

During reaching, arm choice depends on success and motor effort. Whether these factors influence leg choice for stepping behavior is unknown. Here, we conducted two experiments (1: proof-of-principle; 2: kinematic analysis) to explore whether limb selection for goal-directed stepping depends on success and/or effort under twoChoiceconditions:Free(choose either leg) andConstrained(no choice – only left leg). For both experiments, in which Free trials always preceded Constrained trials, we adapted the classic center-out target array in which right-leg dominant neurotypical adults stood in the middle of the array and stepped to pre-cued targets as accurately as possible. TheFreecondition reflected the preferred limb choice. We compared success, effort, and self-perceived difficulty betweenFreeandConstrainedtrials, separately for three (Experiment 1) and two (Experiment 2) regions. Overall, inFreecondition, participants uniformly selected the limb ipsilateral to lateral left and right targets and with slight leg dominance-based bias for central targets. Success (step accuracy and consistency/precision) did not depend on Choice condition, rather, performance improved over repeated trials. Effort (peak vertical foot lift and step path ratio) depended on Choice condition. Finally, independent of Choice condition, participants perceived posterior targets (particularly far targets) as the most difficult during non-dominant left steps. Present findings suggest that effort may influence leg choice to a greater degree than success for goal-directed stepping. Future work that probes these findings’ robustness in patients with unilateral paresis (intrinsic constraint) may advance our understanding of the motor decision processes for goal-directed mobility behaviors.
Controlled Noise: Evidence of Epigenetic Regulation of Single-Cell Expression Variability
Authors: Zhong Yan , Cui Siwei , Yang Yongjian , Cai James J.
Published: April 2024

Motivation

Understanding single-cell expression variability (scEV) or gene expression noise among cells of the same type and state is crucial for delineating population-level cellular function. While epigenetic mechanisms are widely implicated in gene expression regulation, a definitive link between chromatin accessibility and scEV remains elusive. Advances in single-cell techniques now enable simultaneous measurement of scATAC-seq and scRNA-seq within individual cells, presenting an unprecedented opportunity to address this gap.

Results

This paper introduces an innovative testing pipeline to investigate the association between chromatin accessibility and scEV. The pipeline hinges on comparing the prediction performance of scATAC-seq data on gene expression levels between highly variable genes (HVGs) and non-highly variable genes (non-HVGs). Applying this pipeline to paired scATAC-seq and scRNA-seq data from human hematopoietic stem and progenitor cells, we observed a significantly superior prediction performance of scATAC-seq data for HVGs compared to non-HVGs. Notably, there was substantial overlap between well-predicted genes and HVGs. The gene pathways enriched from well-predicted genes are highly pertinent to cell type-specific functions. Our findings support the notion that scEV largely stems from cell-to-cell variability in chromatin accessibility, providing compelling evidence for the epigenetic regulation of scEV and offering promising avenues for investigating gene regulation mechanisms at the single-cell level.

Availability and implementation

The source code and data used in this paper can be found athttps://github.com/SiweiCui/EpigeneticControlOfSingle-CellExpressionVariability.
Optimising crown-of-thorns starfish control effort on the Great Barrier Reef
Authors: Agarwal Kanupriya , Bode Michael , Helmstedt Kate J.
Published: April 2024

Outbreaks of crown-of-thorns starfishAcanthaster planci(COTS), a disruptive coral-eating predator, are responsible for almost half of total coral cover loss on Australia’s Great Barrier Reef. As the pressures of climate change continue to intensify the frequency and severity of disturbance events such as cyclones and coral bleaching, efficiently managing COTS outbreaks is essential for reef protection. We aim to understand how the spatial distribution and intensity of crown-of-thorns starfish control – specifically manual culling of COTS by human divers – can impact coral cover on the GBR. We construct a metapopulation model based on a predator-prey model with larval dispersal and removal of crown-of-thorns starfish to simulate and compare spatial control strategies. When outbreaks begin on reefs between Cairns and Cooktown, we found the best strategy is to target those reefs at the source of the COTS outbreak. Increasing the spatial spread of control results in a larger spatial area protected across the GBR, but a lower total coral cover on the GBR. Our findings suggest that carefully targeting future control by considering larval connectivity patterns and spatial control strategies could lead to more efficient crown-of-thorns management. With the increasing pressures of climate change, any efficiency gains in reef management will prove beneficial for the Great Barrier Reef.
A fast fish swimming protocol that provides similar insights as critical sustained swimming speed
Authors: Bamford Stephanie M. , Seebacher Frank
Published: April 2024

Performance measures are an important tool to assess the impact of environmental change on animals. In fish, performance is often measured as critical sustained swimming speed (Ucrit), which reflects individual physiological capacities. A drawback of Ucritis that trials are relatively long (∼30-75 min). Ucritis therefore not suitable for repeated measurements because of the potential for training effects, long recovery periods, and low throughput. Here we test a shorter (∼4-5 min) protocol, “Ucritfast” (UCfast) in zebrafish (Danio rerio). We show that UCfastand Ucrithave similar, significant repeatabilities within individuals. Unlike Ucrit, repeated UCfasttrials do not elicit a training effect. Both UCfastand Ucritprovide the same insights into thermal acclimation, and both provide similar estimates of individual acclimation capacity in doubly acclimated fish. We propose that UCfastis a valid substitute for Ucritparticularly when higher throughput and repeated measures are necessary.
Drp1-JNKknockdown mitigates Scribble loss induced cell proliferation, metastasis and lethality phenotypes inDrosophila
Authors: Singh Jyotsna , Srikrishna Saripella
Published: April 2024

Mitochondrial dynamics are emerging as master regulators for targeting several types of cancers, including breast cancer, cervical cancer, and hepatocellular carcinoma, for therapeutic intervention. Mitochondrial morphology, size, position and activity within cells is regulated by dynamic fission and fusion events. Dynamin-related protein 1 (Drp1) promotes mitochondrial fission and maintains mitochondrial homeostasis. Loss ofScribis implicated in several human cancers wherein mitochondrial dysfunction leads to excessive cell proliferation and metastasis. However, the exact molecular mechanisms behind theScribloss induced dysregulation of mitochondrial dynamics in cancer progression remains obscure. Although the role of mitochondrial dynamics are being investigated in several types of cancers, but the role ofDrp1- mediated fission event in regulating the maintenance of polarity of cells upon loss ofScribfunction is elusive. In this study, for the first time, we blocked the function ofDrp1activity inScribknockdown induced metastasis cancer model by two ways, firstly, through genetic ablation ofDrp1,and secondly by using mdivi-1, aDrp1specific inhibitor. Genetic depletion ofDrp1expression (Drp1RNAi) inScribknockdown cells inhibits MetalloproteinaseMMP1, reduces ROS production, restores apico-basal (A/B) cell polarity and enhances ATP production. Further to confirm role of Drp1 in regulation of cell polarity, we employed mdivi, a Drp1 specific inhibitor which has dose dependent effect in cell polarity regulation. This study also reveals thatJNKinhibition (JNKRNAi) inScribabrogated cells mitigates theDrp1expression and controls cell proliferation leading to restoration of mitochondrial morphology and epithelial cellpolarity. Our results highlightDrp1as a key regulator in maintaining the apico-basal polarity of cells which gets affected upon loss ofScribbutDrp1-JNKdownregulation effectively mitigatesScribRNAiassociated cell proliferation, metastasis and pupal lethality phenotypes.
Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq
Authors: Su Dingwen , Peters Moritz , Soltys Volker , Chan Yingguang Frank
Published: April 2024

A common objective across ATAC-seq and ChIP-seq analyses is to identify differential signals across contrasted conditions. However, in differential analyses, the impact of copy number variation is often overlooked. Here, we demonstrated copy number differences among samples could drive, if not dominate, differential signals. To address this, we propose a pipeline featuring copy number normalization. By comparing the averaged signal per gene copy, it effectively segregates differential signals driven by copy number differences from other factors. Further applying it to Down syndrome, we unveiled distinct dosage-dependent and -independent changes on chromosome 21. Thus, we recommend normalization as a general approach.
An intestinal Sir2-HSF1-ATGL1 pathway regulates lipolysis inC. elegans
Authors: Somogyvári Milán , Khatatneh Saba , Hajdú Gábor , Sotil Bar , Murányi József , Sőti Csaba
Published: April 2024

Proteostasis maintenance and lipid metabolism are critical for survival and promote longevity, however, their coordination is largely unclear. Here we show that the heat shock factor HSF-1 and the proteostasis state regulates lipolysis inC. elegans. We find that in response to starvation, the sirtuin 1 ortholog SIR-2.1 activates lipolysis by upregulation of the adipose triglyceride lipase ATGL-1. In feeding worms, intestinal HSF-1 represses ATGL-1 expression and lipolysis via the microRNA system. In starving worms, SIR-2.1 suspends amiR-53-mediated suppression of lipolysis by inhibiting its HSF-1-dependent expression. The apparent antagonism of SIR-2.1 and HSF-1, distinct from their synergism at heat shock promoters suggests a context-specific regulation of HSF-1 by SIR-2.1. We demonstrate that the SIR-2.1 and protein kinase A pathways are both indispensable, and independently converge on ATGL- 1 for lipolysis. HSF-1 activation by proteostasis disturbances inhibits starvation-induced lipid mobilization, whereas its age-related decline limits fat deposition throughatgl-1. Our findings reveal a crosstalk between proteostasis and lipid/energy metabolism, which may modulate stress resilience and aging.
Longevity hinders evolutionary rescue through slower growth but not necessarily slower adaptation
Authors: Nordstrom Scott W. , Melbourne Brett A.
Published: April 2024

“Evolutionary rescue” is the process by which a population experiencing severe environmental change avoids extinction through adaptation. Theory and empirical work typically focus on short life histories with non-overlapping generations, leaving longevity’s effects on rescue relatively understudied. Recent models demonstrate that longevity can inhibit rescue through slower phenotypic evolution but have assumptions that may not generalize across life histories. We built a model integrating evolutionary rescue with concepts from life-history theory, particularly the fast-slow pace-of-life continuum. Longevity is modeled by the balance of survival and reproduction with selection acting on survival, allowing for multiple selection episodes throughout the lifespan. We used this model to simulate three life-history strategies along the fast-slow continuum responding to sudden environmental change. Under nearly all simulated conditions, higher longevities (slower pace of life) resulted in more time at low density and increased extinctions. With perfect trait heritability, rates of adaptation were nearly identical across longevities. But at lower heritabilities, longevity allowed for repeated selection and decoupling of mean genotypes and phenotypes, producing a transient phase of rapid phenotypic change. Our results demonstrate that prior findings that longevity slows adaptation do not hold in all cases and are relevant to long-lived conservation targets.
Current genomic deep learning architectures generalize across grass species but not alleles
Authors: Wrightsman Travis , Ferebee Taylor H. , Romay M. Cinta , Seetharam Arun S. , AuBuchon-Elder Taylor , Phillips Alyssa R. , Syring Michael , Hufford Matthew B. , Kellogg Elizabeth A. , Buckler Edward S.
Published: April 2024

Non-coding regions of the genome are just as important as coding regions for understanding the mapping from genotype to phenotype. Interpreting deep learning models trained on RNA-seq is an emerging method to highlight functional sites within non-coding regions. Most of the work on RNA abundance models has been done within humans and mice, with little attention paid to plants. Here, we benchmark four genomic deep learning model architectures with genomes and RNA-seq data from 18 species closely related to maize and sorghum within the Andropogoneae. The Andropogoneae are a tribe of C4 grasses that have adapted to a wide range of environments worldwide since diverging 18 million years ago. Hundreds of millions of years of evolution across these species has produced a large, diverse pool of training alleles across species sharing a common physiology. As model input, we extracted 1,026 base pairs upstream of each gene’s translation start site. We held out maize as our test set and two closely related species as our validation set, training each architecture on the remaining Andropogoneae genomes. Within a panel of 26 maize lines, all architectures predict expression across genes moderately well but poorly across alleles. DanQ consistently ranked highest or second highest among all architectures yet performance was generally very similar across architectures despite orders of magnitude differences in size. This suggests that state-of-the-art supervised genomic deep learning models are able to generalize moderately well across related species but not sensitively separate alleles within species, the latter of which agrees with recent work within humans. We are releasing the preprocessed data and code for this work as a community benchmark to evaluate new architectures on our across-species and across-allele tasks.
Infanticide is driven by unfamiliarity with offspring location and associated with androgenic shifts in mimic poison frogs
Authors: Lewis Amaris R. , Goolsby Billie C. , Juarez Bryan H. , Lacey Madison P. , O’Connell Lauren A.
Published: April 2024

Infanticide is widespread across the animal kingdom, but the physiological drivers of infanticide versus care or neglect are relatively unexplored. Here, we identified salient environmental and physiological antecedents of infanticide in the mimic poison frog (Ranitomeya imitator), a biparental amphibian in which female parents feed their tadpoles unfertilized eggs. Specifically, we explored potential environmental cues influencing infant- directed behavior by evaluating changes in the frequency of food provisioning and tadpole mortality after either cross-fostering tadpoles between family units or displacing tadpoles within the terraria of their parents. We found that changes in offspring location reduce care and increase infanticide. Specifically, parents fed their displaced offspring less and, in some instances, tadpole mortality increased. We also investigated whether care and infanticide were related to changes in steroid hormone concentrations in an unfamiliar setting. Infanticide of fertilized eggs and hatchlings in the new territory included cannibalism and was associated with lower testosterone concentrations, but not with changes in corticosterone. Overall, our results support earlier findings that familiarity with offspring location drives parental investment in poison frogs, while indicating an association between low androgen levels and infanticidal behavior in an amphibian.

Highlights

Offspring location drives parental decisions of care vs. infanticide.

In novel territories, adults cannibalize conspecific, unrelated young.

Lower circulating testosterone in novel territory is associated with infanticide.
Interstitial telomeric sequences promote gross chromosomal rearrangement via multiple mechanisms
Authors: Rosas Bringas Fernando R. , Yin Ziqing , Yao Yue , Boudeman Jonathan , Ollivaud Sandra , Chang Michael
Published: April 2024

Telomeric DNA sequences are difficult to replicate. Replication forks frequently pause or stall at telomeres, which can lead to telomere truncation and dysfunction. In addition to being at chromosome ends, telomere repeats are also present at internal locations within chromosomes, known as interstitial telomeric sequences (ITSs). These sequences are unstable and prone to triggering gross chromosomal rearrangements (GCRs). In this study, we quantitatively examined the effect of ITSs on GCR rate inSaccharomyces cerevisiaeusing a genetic assay. We find that GCR rate increases exponentially with ITS length. This increase can be attributed to the telomere repeat binding protein Rap1 impeding DNA replication and a bias of repairing DNA breaks at or distal to the ITS via de novo telomere addition. Additionally, we performed a genome-wide screen for genes that modulate the rate of ITS-induced GCRs. We find that mutation of core components of the DNA replication machinery leads to an increase in GCRs, but many mutants known to increase GCR rate in the absence of an ITS do not significantly affect GCR rate when an ITS is present. We also identified genes that promote the formation of ITS-induced GCRs, including genes with roles in telomere maintenance, nucleotide excision repair, and transcription. Our work thus uncovers multiple mechanisms by which an ITS promotes GCR.

Significance statement

Telomeric DNA repeats are found at the ends of linear chromosomes where they, together with specialized proteins that bind to them, protect chromosome ends from degradation and unwanted DNA repair activities. Telomeric repeats can also be found at internal locations in the genome, where they are called interstitial telomeric sequences (ITSs). ITSs are prone to breakage and are associated with human diseases. In this study, using baker’s yeast as a model organism, we show that instability at ITSs is driven by multiple factors, and identify genes that either promote or suppress gross chromosomal rearrangements induced by the presence of an ITS.
Revisiting the role of the spindle assembly checkpoint in the formation of gross chromosomal rearrangements inSaccharomyces cerevisiae
Authors: Yao Yue , Yin Ziqing , Rosas Bringas Fernando R. , Boudeman Jonathan , Novarina Daniele , Chang Michael
Published: April 2024

Multiple pathways are known to suppress the formation of gross chromosomal rearrangements (GCRs), which can cause human diseases including cancer. In contrast, much less is known about pathways that promote their formation. The spindle assembly checkpoint (SAC), which ensures the proper separation of chromosomes during mitosis, has been reported to promote GCR, possibly by delaying mitosis to allow GCR-inducing DNA repair to occur. Here we show that this conclusion is the result of an experimental artifact arising from the synthetic lethality caused by disruption of the SAC and loss of theCIN8gene, which is often lost in the genetic assay used to select for GCRs. After correcting for this artifact, we find no role of the SAC in promoting GCR.

Significance statement

A gross chromosomal rearrangement (GCR) is an abnormal structural change of a native chromosome. Examples of GCRs include deletions, duplications, inversions, and translocations. GCRs can lead to genetic diseases such as cancer. A previous study implicated the spindle assembly checkpoint (SAC), which ensures the proper separation of chromosomes during cell division, in facilitating the formation of GCRs. In this study, we show that this is not the case; the SAC does not promote GCR.
Quantitative tests of albendazole resistance in beta-tubulin mutants
Authors: Collins J.B. , Stone Skyler A. , Koury Emily J. , Paredes Anna G. , Shao Fiona , Lovato Crystal , Chen Michael , Shi Richelle , Li Anwyn Y. , Candal Isa , Moutaa Khadija Al , Moya Nicolas , Andersen Erik C.
Published: April 2024

Benzimidazole (BZ) anthelmintics are among the most important treatments for parasitic nematode infections in the developing world. Widespread BZ resistance in veterinary parasites and emerging resistance in human parasites raise major concerns for the continued use of BZs. Knowledge of the mechanisms of resistance is necessary to make informed treatment decisions and circumvent resistance. Benzimidazole resistance has traditionally been associated with mutations and natural variants in theC. elegansbeta-tubulin geneben-1and orthologs in parasitic species. However, variants inben-1alone do not explain the differences in BZ responses across parasite populations. Here, we examine the roles of fiveC. elegansbeta-tubulin genes (tbb-1,mec-7,tbb-4,ben-1, andtbb-6) to identify the role each gene plays in BZ response. We generatedC. elegansstrains with a loss of each beta-tubulin gene, as well as strains with a loss oftbb-1,mec-7,tbb-4, ortbb-6in a genetic background that also lacksben-1to test beta-tubulin redundancy in BZ response. We found that only the individual loss ofben-1conferred a substantial level of BZ resistance, although the loss oftbb-1was found to confer a small benefit in the presence of albendazole (ABZ). The loss ofben-1was found to confer an almost complete rescue of animal development in the presence of 30 µM ABZ, likely explaining why no additive effects caused by the loss of a second beta-tubulin were observed. We demonstrate thatben-1is the only beta-tubulin gene inC. eleganswhere loss confers substantial BZ resistance.

Highlights

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Loss ofben-1provides almost complete rescue of development in albendazole (ABZ)

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Loss of different beta-tubulin genes does not confer ABZ resistance

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Loss ofben-1and a second beta-tubulin does not enhance theben-1level of ABZ resistance
Lipid-Based Transfection of Zebrafish Embryos: A Robust Protocol for Nucleic Acid Delivery in Zebrafish
Authors: Terzi Aslihan , Lao Tiger , Jacobo Adrian
Published: April 2024

Zebrafish, a widely used model organism in developmental and biomedical research, offers several advantages such as external fertilization, embryonic transparency, and genetic similarity to humans. However, traditional methods for introducing exogenous genetic material into zebrafish embryos, particularly microinjection, pose significant technical challenges and limit throughput. To address this, we developed a novel approach utilizing Lipofectamine LTX for the efficient delivery of nucleic acids into zebrafish embryos by lipid-based transfection. Our protocol bypasses the need for microinjection, offering a cost-effective, high-throughput, and user-friendly alternative. This protocol out-lines new strategies for gene delivery in zebrafish to enhance the efficiency and scope of genetic studies in this model system.
Human cytomegalovirus infection coopts chromatin organization to diminish TEAD1 transcription factor activity
Authors: Sayeed Khund , Parameswaran Sreeja , Beucler Matthew J. , Edsall Lee E. , VonHandorf Andrew , Crowther Audrey , Donmez Omer , Hass Matthew , Richards Scott , Forney Carmy , Wright Jay , Leong Merrin Man Long , Murray-Nerger Laura A. , Gewurz Ben E. , Kaufman Kenneth M. , Harley John B. , Zhao Bo , Miller William E. , Kottyan Leah C. , Weirauch Matthew T.
Published: April 2024

Human cytomegalovirus (HCMV) infects up to 80% of the world’s population. Here, we show that HCMV infection leads to widespread changes in human chromatin accessibility and chromatin looping, with hundreds of thousands of genomic regions affected 48 hours after infection. Integrative analyses reveal HCMV-induced perturbation of Hippo signaling through drastic reduction of TEAD1 transcription factor activity. We confirm extensive concordant loss of TEAD1 binding, active H3K27ac histone marks, and chromatin looping interactions upon infection. Our data position TEAD1 at the top of a hierarchy involving multiple altered important developmental pathways. HCMV infection reduces TEAD1 activity through four distinct mechanisms: closing of TEAD1-bound chromatin, reduction of YAP1 and phosphorylated YAP1 levels, reduction of TEAD1 transcript and protein levels, and alteration ofTEAD1exon-6 usage. Altered TEAD1-based mechanisms are highly enriched at genetic risk loci associated with eye and ear development, providing mechanistic insight into HCMV’s established roles in these processes.
Missing Wedge Completion via Unsupervised Learning with Coordinate Networks
Authors: Van Veen Dave , Galaz-Montoya Jesús G. , Shen Liyue , Baldwin Philip , Chaudhari Akshay S. , Lyumkis Dmitry , Schmid Michael F. , Chiu Wah , Pauly John
Published: April 2024

Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3 − 20× compared to supervised methods. Ourin silicoresults show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.
Inferring residue level hydrogen deuterium exchange with ReX
Authors: Crook Oliver M. , Gittens Nathan , Chung Chun-wa , Deane Charlotte M.
Published: April 2024

Hydrogen-Deuterium Exchange Mass-Spectrometry (HDX-MS) has emerged as a powerful technique to explore the conformational dynamics of proteins and protein complexes in solution. The bottom-up approach to MS uses peptides to represent an average of residues, leading to reduced resolution of deuterium exchange and complicates the interpretation of the data. Here, we introduce ReX, a method to infer residue-level uptake patterns leveraging the overlap in peptides, the temporal component of the data and the correlation along the sequence dimension. This approach infers statistical significance for individual residues by treating HDX-MS as a multiple change-point problem. By fitting our model in a Bayesian non-parametric framework, we perform parameter number inference, differential HDX confidence assessments, and uncertainty estimation for temporal kinetics. Benchmarking against existing methods using a three-way proteolytic digestion experiment shows our method’s superior performance at predicting unseen HDX data. Moreover, it aligns HDX-MS with the reporting standards of other structural methods by providing global and local resolution metrics. Using ReX, we analyze the differential flexibility of BRD4’s two Bromodomains in the presence of I-BET151 and quantify the conformational variations induced by a panel of seventeen small molecules on LXRα. Our analysis reveals distinct residue-level HDX signatures for ligands with varied functional outcomes, highlighting the potential of this characterisation to inform mode of action analysis.
Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence
Authors: Went Sam C , Picton David M , Morgan Richard D , Nelson Andrew , Dryden David TF , Smith Darren L , Wenner Nicolas , Hinton Jay C. D. , Blower Tim R
Published: April 2024

Bacteria have evolved a broad range of systems that provide defence against their viral predators, bacteriophages. Bacteriophage Exclusion (BREX) systems recognize and methylate 6 bp non-palindromic motifs within the host genome, and prevent replication of non-methylated phage DNA that encodes these same motifs. How BREX recognizes cognate motifs has not been fully understood. We have characterised BREX from pathogenic Salmonella and generated the first X-ray crystallographic structures of the conserved BREX protein, PglX. The PglX N-terminal domain encodes the methyltransferase, whereas the C-terminal domain is for motif recognition. We also present the structure of PglX bound to the phage-derived DNA mimic, Ocr, an inhibitor of BREX activity. Our analyses propose modes for DNA-binding by PglX and indicate that larger BREX complexes are required for methyltransferase activity and defence. Through rational engineering of PglX, we broadened both the range of phages targeted, and the host motif sequences that are methylated by BREX. Our data demonstrate that PglX is the sole specificity factor for BREX activity, providing motif recognition for both phage defence and host methylation.
Early-life stress alters postnatal chromatin development in the nucleus accumbens
Authors: Rashford Rebekah L. , DeBerardine Michael , Kim Hye Ji J. , Arzouni Nibal , Hirschfield Laura W. , Oke Oluwamayowa M. , Bennett Shannon N. , Peña Catherine Jensen
Published: April 2024

Early-life stress sensitizes individuals to subsequent stressors to increase lifetime risk for psychiatric disorders. Within the nucleus accumbens (NAc) — a key limbic brain region — early-life stress sensitizes both cellular and transcriptional response to later stress. However, the molecular mechanisms linking initial activation of neurons by early-life stress with continued stress sensitivity across the lifespan are poorly understood. Using a combination of activity-dependent cellular tagging and ATAC-sequencing across postnatal development, we find that early-life stress initially opens chromatin in stress-activated cells and that chromatin opening predicts gene expression response to adult stress, suggesting epigenetic priming as a mechanism of stress sensitization. Moreover, early-life stress accelerates both chromatin development within these activated cells, and H3K4me1 deposition broadly in NAc — a post-translational histone modification associated with open chromatin and epigenetic priming. By adulthood, we observe chromatin remodeling throughout the NAc, indicating that the effects of stress are long-lasting and propagate across development into the broader cell population. Lastly, through viral-mediated epigenome editing and behavioral quantification, we find that deposition of H3K4me1 in NAc during early postnatal development is sufficient to mimic early-life stress and prime hypersensitivity to subsequent stress. Together, our results show that a molecular memory of early-life stress is encoded at an epigenetic level through changes in chromatin architecture. This constitutes a novel biological mechanism by which early-life stress programs lifelong stress sensitivity.
A framework for quality control in quantitative proteomics
Authors: Tsantilas Kristine A. , Merrihew Gennifer E. , Robbins Julia E. , Johnson Richard S. , Park Jea , Plubell Deanna L. , Canterbury Jesse D. , Huang Eric , Riffle Michael , Sharma Vagisha , MacLean Brendan X. , Eckels Josh , Wu Christine C. , Bereman Michael S. , Spencer Sandra E. , Hoofnagle Andrew N. , MacCoss Michael J.
Published: April 2024

A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible. Data are available on Panorama Public and on ProteomeXchange under the identifierPXD051318.