bluuebunny/crossref_metadata_2025 huggingface dataset:
Interoceptive Awareness of the Breath Preserves Dorsal Attention Network Activity amidst Widespread Cortical Deactivation: A Within-Participant Neuroimaging Study
Authors: Farb Norman A. S. , Zuo Zoey , Price Cynthia J.
Published: May 2022

Interoception, the representation of the body’s internal state, serves as a foundation for emotion, motivation, and wellbeing. Yet despite its centrality in human experience, the neural mechanisms of interoception are poorly understood. The Interoceptive/Exteroceptive Attention Task (IEAT) is a novel neuroimaging paradigm that compares behavioral tracking of the respiratory cycle (Active Interoception) to tracking of a visual stimulus (Active Exteroception). Twenty-two healthy participants completed the IEAT during two separate scanning sessions (N = 44) as part of a randomized control trial of Mindful Awareness in Body-oriented Therapy (MABT). Compared to Exteroception, Interoception deactivated somatomotor and prefrontal regions. Greater interoceptive sensibility (MAIA scale) predicted sparing from deactivation along the anterior cingulate cortex (ACC) and left-lateralized language regions. The right insula—typically described as a primary interoceptive cortex—was only implicated by its further deactivation during an exogenously paced respiration condition (Active Matching). Psychophysiological interaction analysis characterized Active Interoception as promoting greater ACC connectivity with lateral frontal and parietal regions commonly referred to as the Dorsal Attention Network. Interoception of the breath may therefore involve reduced corticalactivitybut greaterconnectivity, with greater sensibility sparing cortical inhibition within well-characterized attentional networks. In contrast to a literature that relates detection of liminal signals such as the heartbeat to anterior insula activity, attention towards accessible body sensations such as the breath may lead to a low activity, high connectivity state in which sensory signals from the body may be better discerned.

Significance Statement

Interoception, the representation of the body’s internal state, is poorly understood compared to the external senses, with existing neuroimaging studies failing to match task difficulty between interoceptive and exteroceptive tasks. The present study used a novel fMRI task to compare interoceptive and exteroceptive attention, and how this distinction was moderated by self-reported interoceptive awareness. The results implicate three novel interoceptive mechanisms: interoception reduces corticalactivitywhile increasingconnectivity, wherein awareness is linked to preserved activation of the brain’s salience network and left-lateralized language regions. These findings characterize interoception as a lower activity state in which awareness depends upon the ability to notice and report on body signals typically obscured by the processing of exteroceptive information and other forms of cognition.
Impaired hepatic autophagy exacerbates xenobiotics induced liver injury
Authors: Byrnes Katherine , Bailey Niani Tiaye , Mercer Arissa , Joshi Spandan , Liu Gang , Yin Xiao-Ming , Khambu Bilon
Published: May 2022

Xenobiotics can activate the hepatic survival pathway, but it is not clear how impaired hepatic survival pathways may affect xenobiotic-induced liver injury. We investigated the role of hepatic autophagy, a cellular survival pathway, in cholestatic liver injury driven by a xenobiotic. Here we demonstrate that DDC diet impaired autophagic flux, resulting in the accumulation of p62-Ub-intrahyaline bodies (IHBs) but not the Mallory Denk-Bodies (MDBs). Impaired autophagic flux was linked to a deregulated hepatic protein-chaperonin system and a significant decline in Rab family proteins. In addition, we demonstrate that heterozygous deletion of Atg7, a key autophagy gene, aggravated the p62-Ub-IHB accumulation and cholestatic liver injury. Moreover, we showed that p62-Ub-IHB accumulation did not activate the proteostasis-related ER stress signaling pathway, but rather activated the NRF2 pathway and suppressed the FXR nuclear receptor, resulting in cholestatic liver injury. Conclusion: Impaired autophagy exacerbates xenobiotic-induced cholestatic liver injury. Promotion of autophagy may represent a new therapeutic approach for xenobiotic-induced liver injury.
Huntingtin S421 phosphorylation increases kinesin and dynein engagement on early endosomes and lysosomes
Authors: Prowse Emily N. P. , Chaudhary Abdullah R. , Sharon David , Hendricks Adam G.
Published: May 2022

Huntingtin (HTT) is a scaffolding protein that recruits motor proteins to vesicular cargoes, enabling it to regulate kinesin-1, dynein, and myosin-VI-dependent transport. To maintain the native stoichiometry of huntingtin with its interacting partners, we used CRISPR/Cas9 to induce a phosphomimetic mutation of the endogenous HTT at S421 (HTT-S421D). Using single particle tracking, optical tweezers, and immunofluorescence, we examined the effects of this mutation on the motility of early endosomes and lysosomes. In HTT-S421D cells, lysosomes exhibit longer displacements and higher processive fractions compared to wild-type (HTT-WT) cells. Kinesins and dyneins exert greater forces on early endosomes and lysosomes in cells expressing HTT-S421D. Additionally, endosomes bind to microtubules faster and are more resistant to detachment under load. The recruitment of kinesins and dyneins to microtubules is enhanced in HTT-S421D cells. In contrast, overexpression of HTT had variable effects on the processivity, displacement, and directional bias of both early endosomes and lysosomes. These data indicate that phosphorylation of the endogenous huntingtin causes early endosomes and lysosomes to move longer distances and more processively by recruiting and activating both kinesin-1 and dynein.

Statement of Significance

The ubiquitous scaffolding protein huntingtin regulates the recruitment and activity of microtubule motors. Huntingtin phosphorylation at S421 enhances the microtubule binding and force generation of kinesin and dynein on early endosomes and lysosomes. Using optical tweezers to measure the forces exerted on endosomes in CRISPR-engineered cells, we find that a phosphomimetic huntingtin mutation (S421D) enhances both kinesin- and dynein-driven forces on early endosomes and lysosomes. The ability to modulate motor activity on a range of organelles makes huntingtin unique and suggests a significant role for huntingtin in regulating intracellular transport.
The combination of feedforward and feedback processing accounts for contextual effects in visual cortex
Authors: Di Santo Serena , Dipoppa Mario , Keller Andreas , Roth Morgane , Scanziani Massimo , Miller Kenneth D.
Published: May 2022

Sensory systems must combine local features with context to infer meaning. Accordingly, context profoundly influences neural responses. We developed a unified circuit model demonstrating how feedforward and feedback inputs are integrated to produce three forms of contextual effects in mouse primary visual cortex (V1). First, reanalyzing existing data, we discovered that increasing stimulus size only weakly increases the area of V1 neural response, conflicting with previous models of surround suppression (SS). Second, through modeling, we found that, in Layer 2/3, (1) SS and its contrast dependence are largely inherited from Layer 4; (2) Inverse responses (IR) – size-tuned responses to a gray “hole” in a full-field grating – are driven by feedback connections provided they are sufficiently wide; (3) Cross-orientation surround facilitation is induced by the summation of feedback input driving IR with the feedforward-driven classical center response. The model accounts for many previous findings and makes multiple testable predictions.

Highlights

One model explains three different types of contextual modulation

The widths of spatial response patterns grow much more slowly than stimulus size.

Inverse responses depend on the geometry of feedback response fields and projections

Summation of classical and inverse response accounts for surround facilitation.
Connecting Covert Attention and Visual Perception to the Spatiotemporal Dynamics of Alpha Band Activity, Cross-Frequency Coupling (CFC), and Functional Connectivity using Multivariate Pattern Analysis (MVPA)
Authors: Sheldon Sarah S. , Fyshe Alona , Mathewson Kyle E.
Published: May 2022

Some evidence suggests that alpha activity is directly related to the baseline firing rate of sensory neurons which alters the probability of responding to a stimulus. Other evidence points to alpha indirectly modulating cortical excitability through its interactions with gamma oscillations. A third possibility is that alpha-based functional connectivity better explains attentional modulation and perceptual responses. To test this, alpha amplitude, CFC, and functional connectivity measures were extracted from EEG data recorded while participants performed a cued orientation perception task. Using pre-target data, the spatiotemporal activity of each metric was submitted to a SVM classifier to determine which activity pattern best distinguished trials with covert attention from trials without. The same metrics were submitted to SVR to find the activity that best predicted task performance. Results indicate the best metric for classifying trials with and without covert attention was alpha amplitude. This indicates that, prior to target onset, alpha amplitude alone is most sensitive to the presence of covert attention. In contrast, none of the metrics were strong predictors of task performance. Overall, our results support the idea that alpha activity is directly related to changes in the baseline firing rate of sensory neurons which changes responsiveness but not performance.
A multi-functional small molecule alleviates fracture pain and promotes bone healing
Authors: Shih Yu-Ru V. , Kingsley David , Newman Hunter , Hoque Jiaul , Gupta Ankita , Lascelles B. Duncan X. , Varghese Shyni
Published: May 2022

Skeletal injuries are a major cause of morbidities worldwide with bone fractures accounting for a substantial portion. Patients suffering from bone fractures and undergoing surgery experience different levels of pain throughout the healing process requiring pain-mitigating interventions. Furthermore, a considerable number of bone fractures suffer from delayed healing, and unresolved acute pain may transition to chronic and maladaptive pain. Current management of pain involves treatment with NSAIDs and opioids, however, these analgesics have substantial drawbacks including delaying healing, systemic side effects, and potential for addiction. Hence, a therapeutic approach that concomitantly attenuates pain locally and actively promotes healing would address a significant clinical problem and improve the overall functional outcome for patients. Herein, we tested the hypothesis that the purine molecule, adenosine, could simultaneously alleviate fracture pain and promote healing by targeting different adenosine receptor subtypes in different cell populations. Our results demonstrate that local delivery of adenosine inhibited nociceptive activity of peripheral neurons through activation of adenosine A1 receptor (ADORA1) and mitigates pain. Concurrently, localization of adenosine at the fracture site also promoted osteogenic differentiation of mesenchymal stromal cells through adenosine A2B receptor (ADORA2B) and improved bone healing. Although further work is needed to extend the findings to human patients, this study provides evidence that the unique functional properties of adenosine along with its local delivery could provide an innovative, safe, and translatable therapeutic strategy to treat bone trauma and associated pain.

One Sentence Summary

Adenosine as a therapeutic for fracture pain and healing
Recurrent loss of an immunity gene that protects Drosophila against a major natural parasite
Authors: Arunkumar Ramesh , Zhou Shuyu Olivia , Day Jonathan P. , Bakare Sherifat , Pitton Simone , Hsing Chi-Yun , O’Boyle Sinead , Pascual-Gil Juan , Clark Belinda , Chandler Rachael J. , Leitão Alexandre B. , Jiggins Francis M.
Published: May 2022

Polymorphisms in immunity genes can have large effects on susceptibility to infection. To understand the origins of this variation, we investigated the genetic basis of resistance to the parasitoid wasp Leptopilina boulardi in Drosophila melanogaster. A cis-regulatory polymorphism in the gene Lectin-24A abolishes expression after infection, strongly reducing survival. Other null mutations have arisen repeatedly in this gene, with additional loss-of-expression and premature stop codons segregating in nature. The frequency of these alleles varies greatly, and in some populations natural selection has driven them near to fixation. We conclude that there is a pleiotropic cost to Lectin-24A expression, and in some populations this outweighs the benefit of resistance, resulting in natural selection causing the repeated loss of this important immune defense.

Significance Statement

Genetic differences between individuals can have a large effect on susceptibility to infectious disease. We have identified a gene called Lectin-24A that is important in the immune response that protects fruit flies against one of their main natural enemies—parasitic wasps. However, in nature many flies carry mutated copies of this gene that are no longer functional. We found that the high frequency of these loss-of-function mutations can only be explained if they have a selective advantage in some populations. Therefore, we can conclude that this immune defiance is costly, and genetic variation in susceptibility is maintained because in some locations susceptible flies are fitter than resistant flies.
Plasticity in airway smooth muscle differentiation during mouse lung development
Authors: Goodwin Katharine , Lemma Bezia , Boukind Adam , Nelson Celeste M.
Published: May 2022

Smooth muscle differentiation has been proposed to sculpt airway epithelial branches in mammalian lungs. Serum response factor (SRF) acts with its cofactor myocardin to promote the expression of contractile smooth muscle markers. However, smooth muscle cells exhibit a variety of phenotypes beyond contractile that are independent of SRF/myocardin-induced transcription. To determine whether airway smooth muscle exhibits phenotypic plasticity during embryonic development, we deleted Srf from the pulmonary mesenchyme. Srf-mutant lungs branch normally, and the mesenchyme exhibits normal cytoskeletal features and patterning. scRNA-seq revealed an Srf-null smooth muscle cluster wrapping the airways of mutant lungs that lacks contractile smooth muscle markers but retains many features of control smooth muscle. Srf-null airway smooth muscle exhibits a synthetic phenotype, compared to the contractile phenotype of mature wildtype airway smooth muscle. Our findings reveal plasticity in airway smooth muscle differentiation and demonstrate that a synthetic smooth muscle layer is sufficient for airway branching morphogenesis.
MoBIE: A Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data
Authors: Pape Constantin , Meechan Kimberly , Moreva Ekaterina , Schorb Martin , Chiaruttini Nicolas , Zinchenko Valentyna , Vergara Hernando , Mizzon Giulia , Moore Josh , Arendt Detlev , Kreshuk Anna , Schwab Yannick , Tischer Christian
Published: May 2022

Facing the challenge of exploring and sharing multi-terabyte, multi-modal and multi-scale image data of heterogeneous dimensionality, we developed MoBIE, a Fiji plugin that provides rich visualization features to enable browsing data from numerous biomedical applications on a standard laptop computer. MoBIE also supports segmentations, associated measurements and annotations. Users can configure complex views of datasets, share them with collaborators, and use them for interactive figure panels. The MoBIE plugin also offers a convenient interface for converting data into compatible data formats; an additional Python library facilitates managing diverse MoBIE projects.
Dynamic genome-scale modeling ofSaccharomyces cerevisiaeunravels mechanisms for ester formation during alcoholic fermentation
Authors: Scott William T. , Henriques David , Smid Eddy J. , Notebaart Richard A. , Balsa-Canto Eva
Published: May 2022

Fermentation employingSaccharomyces cerevisiaehas produced alcoholic beverages and bread for millennia. More recently,S. cerevisiaehas been used to manufacture specific metabolites for the food, pharmaceutical, and cosmetic industries. Among the most important of these metabolites are compounds associated with desirable aromas and flavors, including higher alcohols and esters. Although the physiology of yeast has been well-studied, its metabolic modulation leading to aroma production in relevant industrial scenarios such as winemaking is still unclear. Here we ask what are the underlying metabolic mechanisms that explain the conserved and varying behavior of different yeasts regarding aroma formation under enological conditions? We employed dynamic flux balance analysis (dFBA) to answer this key question using the latest genome-scale metabolic model (GEM) ofS. cerevisiae. The model revealed several conserved mechanisms among wine yeasts, e.g., acetate ester formation is dependent on intracellular metabolic acetyl-CoA/CoA levels, and the formation of ethyl esters facilitates the removal of toxic fatty acids from cells using CoA. Species-specific mechanisms were also found, such as a preference for the shikimate pathway leading to more 2-phenylethanol production in the Opale strain as well as strain behavior varying notably during the carbohydrate accumulation phase and carbohydrate accumulation inducing redox restrictions during a later cell growth phase for strain Uvaferm. In conclusion, our new metabolic model of yeast under enological conditions revealed key metabolic mechanisms in wine yeasts, which will aid future research strategies to optimize their behavior in industrial settings.
Functional imaging and quantification of multi-neuronal olfactory responses in C. elegans
Authors: Lin Albert , Qin Shanshan , Casademunt Helena , Wu Min , Hung Wesley , Cain Greg , Tan Nicolas Z. , Valenzuela Raymond , Lesanpezeshki Leila , Venkatachalam Vivek , Pehlevan Cengiz , Zhen Mei , Samuel Aravinthan D.T.
Published: May 2022

Many animals perceive odorant molecules by collecting information from ensembles of olfactory neurons. Each neuron employs receptors that are tuned to recognize certain odorant molecules by chemical binding affinity. Olfactory systems are able, in principle, to detect and discriminate diverse odorants by using combinatorial coding strategies. Multineuronal imaging with high-throughput stimulus delivery allows comprehensive measurement of ensemble-level sensory representations. We have used microfluidics and multineuronal imaging to study ensemble-level olfactory representations at the sensory periphery of the nematode C. elegans. The collective activity of nematode chemosensory neurons reveals high-dimensional representations of olfactory information across a broad space of odorant molecules. We reveal diverse tuning properties and dose-response curves across chemosensory neurons and across odorants. We describe the unique contribution of each sensory neuron to an ensemble-level code for volatile odorants. We also show how natural stimuli, a set of nematode pheromones, are encoded by the sensory periphery. The integrated activity of the C. elegans chemosensory neurons contains sufficient information to robustly encode the intensity and identity of diverse chemical stimuli.
CELL-E: A Text-To-Image Transformer for Protein Localization Prediction
Authors: Khwaja Emaad , Song Yun S. , Huang Bo
Published: May 2022

Accurately predicting cellular activities of proteins based on their primary amino acid sequences would greatly improve our understanding of the proteome. In this paper, we present CELL-E, a text-to-image transformer architecture that generates a 2D probability density map of protein distribution within cells. Given a amino acid sequence and a reference image for cell or nucleus morphology, CELL-E offers a more direct representation of protein localization, as opposed to previousin silicomethods that rely on pre-defined, discrete class annotations of protein localization to subcellular compartments.
Precipitation is the main axis of tropical phylogenetic turnover across space and time
Authors: Ringelberg Jens J. , Koenen Erik J.M. , Sauter Benjamin , Aebli Anahita , Rando Juliana G. , Iganci João R. , de Queiroz Luciano P. , Murphy Daniel J. , Gaudeul Myriam , Bruneau Anne , Luckow Melissa , Lewis Gwilym P. , Miller Joseph T. , Simon Marcelo F. , Jordão Lucas S.B. , Morales Matías , Bailey C. Donovan , Nageswara-Rao Madhugiri , Loiseau Oriane , Pennington R. Toby , Dexter Kyle G. , Zimmermann Niklaus E. , Hughes Colin E.
Published: May 2022

Early natural historians – Compte de Buffon, von Humboldt and De Candolle – established ecology and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, an pantropical plant clade of 3,400 species, we show that the water availability gradient from deserts to rainforests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.
Impaired BCAA catabolism during adipocyte differentiation decreases glycolytic flux
Authors: Green Courtney R. , Wessendorf-Rodriguez Karl A. , Turner Rory , Hover Justin D. , Murphy Anne N. , Metallo Christian M. , Wallace Martina
Published: May 2022

Dysregulated branched chain amino acid (BCAA) metabolism has emerged as a key metabolic feature associated with the obese insulin resistant state, and adipose BCAA catabolism is decreased in this context. BCAA catabolism is upregulated early in adipogenesis, but the impact of suppressing this pathway on the broader metabolic functions of the resultant adipocyte remain unclear. Here, we use CRISPR/Cas9 to targetBckdhaandAcad8in pre-adipocytes and induce a deficiency in BCAA or valine catabolism through differentiation. We characterise the transcriptional and metabolic phenotype of these cells using RNAseq and13C metabolic flux analysis within a network spanning glycolysis, tricarboxylic (TCA) acid metabolism, BCAA catabolism, and fatty acid synthesis. While lipid droplet accumulation is maintained inBckdha-deficient adipocytes, they display a more fibroblast-like transcriptional signature. In contrast,Acad8deficiency minimally impacts gene expression. Decreased glycolytic flux emerges as the most distinct metabolic feature ofBckdha-deficient cells, accompanied by a ∼40% decrease in lactate secretion, yet pyruvate oxidation and utilization forde novolipogenesis are increased to compensate for loss of BCAA carbon. Glutamine anaplerosis was also increased, though we observed a general decrease in levels of most non-essential amino acids consistent with an impact on nitrogen homeostasis. Overall, our data suggest that both metabolic and regulatory cross-talk exists between BCAA catabolism, glycolysis, and nitrogen metabolism in differentiated adipocytes. Suppression of BCAA catabolism associated with metabolic syndrome may result in a metabolically compromised adipocyte.
Learning perturbation-inducible cell states of novel compounds from observability analysis of transcriptome dynamics
Authors: Hasnain Aqib , Balakrishnan Shara , Joshy Dennis M. , Smith Jen , Haase Steven B. , Yeung Enoch
Published: May 2022

A major challenge in biotechnology and biomanufacturing is the identification of a set of biomarkers for perturbations and metabolites of interest. Here, we develop a data-driven, transcriptome-wide approach to rank perturbation-inducible genes from time-series RNA sequencing data for the discovery of analyte-responsive promoters. This provides a set of biomarkers that act as a proxy for the transcriptional state referred to as cell state. We construct low-dimensional models of gene expression dynamics and rank genes by their ability to capture the perturbation-specific cell state using a novel observability analysis. Using this ranking, we extract 15 analyte-responsive promoters for the organophosphate malathion in the underutilized host organismPseudomonas fluorescensSBW25. We develop synthetic genetic reporters from each analyte-responsive promoter and characterize their response to malathion. Furthermore, we enhance malathion reporting through the aggregation of the response of individual reporters with a synthetic consortium approach, and we exemplify the library’s ability to be useful outside the lab by detecting malathion in the environment. The library of living malathion sensors can be optimized for use in environmental diagnostics while the developed machine learning tool can be applied to discover perturbation-inducible gene expression systems in the compendium of host organisms.
Surrounding Traffic Matters: Increases in Traffic Volume Are Related to Changes in EEG Rhythms in Urban Cyclists
Authors: Robles Daniel , Kuziek Jonathan W. P. , Lai Jingyi , Mazumder Robin , Scanlon Joanna E. M. , Mathewson Kyle E.
Published: May 2022

In this study, we used an oddball EEG bicycle paradigm to study how changes in urban environments elicit changes in EEG markers. Participants completed an auditory oddball task while riding in three different cycling lane environments. A low traffic condition where participants rode in a fully separated bike lane alongside a quiet residential street, an intermediate traffic condition where participants rode alongside a busy residential street in a painted lane, and a heavy traffic condition where participants rode alongside fast/heavy traffic on a shared-use path. Relative to the low traffic, heavy traffic was associated with faster reaction time and a trend towards reduced accuracy, and increased N1 amplitude evoked by the standard tones. We attribute this difference in N1 amplitude to different attentional demands evoked by the different traffic conditions. In this fashion, heavy traffic requires greater auditory filtering. Furthermore, we found no differences in P3 amplitude associated with the traffic conditions. We discuss the implications of mobile paradigms to study attention in real-world settings.
Dynamic visualization of high-dimensional data
Authors: Sun Eric D. , Ma Rong , Zou James
Published: May 2022

Dimensionality reduction (DR) is commonly used to project highdimensional data into lower dimensions for visualization, which could then generate new insights and hypotheses. However, DR algorithms necessarily introduce distortions in the visualization and cannot faithfully represent all relations in the data. As such, there is a need for methods to assess the reliability of DR visualizations. Here we present DynamicViz, a framework for generating dynamic visualizations that capture the sensitivity of DR visualizations to perturbations in the data. DynamicVic can be applied to all commonly used DR methods. We show the utility of dynamic visualizations in diagnosing common interpretative pitfalls of static visualizations and extending existing single-cell analyses. We introduce the variance score to quantify the dynamic variability of observations in these visualizations. The variance score characterizes natural variability in the data and can be used to optimize DR algorithm implementations. We have made DynamicViz freely available to assist with the evaluation of DR visualizations.
Syntaxin1 Ser14 Phosphorylation is Required for Non-Vesicular Dopamine Release
Authors: Shekar A , Mabry SJ , Cheng MH , Aguilar JI , Patel S , Zanella D , Saleeby DP , Zhu Y , Romanazzi T , Ulery-Reynolds P , Bahar I , Carter AM , Matthies HJ , Galli A
Published: May 2022

Amphetamine (AMPH), a psychostimulant commonly prescribed for the treatment of neuropsychiatric and neurological disorders, has a high liability for abuse. The abuse and psychomotor stimulant properties of AMPH are primarily associated with its ability to increase dopamine (DA) neurotransmission. This increase is mediated, in large part, by non-vesicular DA release (DA efflux). DA efflux is the result of reversal of the DA transporter (DAT) promoted by AMPH. Syntaxin 1 (Stx1) is a SNARE protein that plays a pivotal role in vesicular release. Previously, we have shown that Stx1 also interacts with the distal DAT N-terminus, an event promoted by AMPH. Stx1 is phosphorylated at Ser14 by casein kinase II (CK2). Using Drosophila Melanogaster as an animal model, we show that this phosphorylation event is critical for non-vesicular DA release and regulates the expression of AMPH preference as well as the ability of AMPH to promote mating drive. We also show that reverse transport of DA mediated by DAT underlies these complex behaviors promoted by AMPH. Our molecular dynamics (MD) simulations of the phosphorylated DAT/Stx1 complex demonstrate that the phosphorylation state of these proteins plays a key role in allowing DAT to dwell in an efflux-willing state. This state also supports constitutive DA efflux (CDE), an event that occurs in the absence of AMPH. The DAT-Stx1 phosphorylated complex is characterized by the breakdown of two key salt bridges in DAT, K66-D345 and E428-R445, which are critical for the formation of the intracellular (IC) gate and for transport function. The breaking of these salt bridges leads to an opening and hydration of the DAT intracellular vestibule, allowing DA to bind from the cytosol, a mechanism that we hypothesize leads to CDE. We further determine the importance of Stx1 phosphorylation in CDE by pharmacologically inhibiting CK2 with CX-4945, a molecule currently in phase II clinical trials for cancer treatment. CX-4945 treatment prevented the expression of CDE in isolated Drosophila Melanogaster brains as well as behaviors associated with CDE. Thus, our results suggest that Stx1 phosphorylation is a possible pharmacological target for the treatment of AMPH abuse.
Modeling the effects of genetic and diet induced obesity on melanoma progression in zebrafish
Authors: Montal Emily , Lumaquin Dianne , Ma Yilun , Suresh Shruthy , White Richard M.
Published: May 2022

Obesity is a rising concern and associated with an increase in numerous cancers often in a sex-specific manner. Preclinical models are needed to deconvolute the intersection between obesity, sex, and cancer. We have generated a zebrafish system that can be used as a platform for studying these factors. We studied how germline overexpression of AgRP along with a high-fat diet (HFD) affects melanomas dependent on BRAFV600E. This revealed an increase in tumor incidence and area in male obese fish, but not females, consistent with the clinical literature. This is dependent on the somatic mutations, as male tumors generated with an RB1 mutation are sensitive to obesity, but this is not observed with PTEN. These data indicate that both germline and somatic mutations contribute to obesity related effects in melanoma. Given the rapid genetic tools available in the zebrafish, this provides a high-throughput system to dissect the interactions of genetics, diet, sex, and host factors in obesity-related cancers.

Summary Statement

Due to the rising incidence of obesity, there is a corresponding increased occurrence of obesity related cancers, which is often described to be dependent on sex. Here we developed a model to investigate the intersection between obesity, sex, and cancer.
Transmembrane protein 184B (TMEM184B) promotes expression of synaptic gene networks in the mouse hippocampus
Authors: Wright Elizabeth B. , Larsen Erik G. , Coloma-Roessle Cecilia M. , Hart Hannah R. , Bhattacharya Martha R.C.
Published: May 2022

In Alzheimer’s Disease (AD) and other dementias, hippocampal synaptic dysfunction and loss contribute to the progression of memory impairment. Recent analysis of human AD transcriptomes has provided a list of gene candidates that may serve as drivers of disease. One such candidate is the membrane protein TMEM184B. To evaluate whether TMEM184B contributes to neurological impairment, we asked whether loss of TMEM184B in mice causes gene expression or behavior alterations, focusing on the hippocampus. Because one major risk factor for AD is age, we compared young adult (5-month-old) and aged (15-month-old) wild type andTmem184b-mutant mice to assess the dual contributions of age and genotype. TMEM184B loss altered expression of pre- and post-synaptic transcripts by 5 months and continued through 15 months, specifically affecting genes involved in synapse assembly and neural development. Wnt-activated enhancer elements were enriched among differentially expressed genes, suggesting an intersection with this pathway. Few differences existed between young adult and aged mutants, suggesting that transcriptional effects of TMEM184B loss are relatively constant. To understand how TMEM184B disruption may impact behaviors, we evaluated memory using the novel object recognition test and anxiety using the elevated plus maze. Young adultTmem184b-mutant mice show normal object discrimination, suggesting a lack of memory impairment at this age. However, mutant mice showed decreased anxiety, a phenotype seen in some neurodevelopmental disorders. Taken together, our data suggest that TMEM184B is required for proper synaptic gene expression and anxiety-related behavior and is more likely to be linked to neurodevelopmental disorders than to dementia.
Improving Protein-Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge
Authors: Giri Nabin , Cheng Jianlin
Published: May 2022

Elucidating protein-ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein-ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein-ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein-ligand interactions from cryo-EM density maps of proteins and ligands.DeepProLigandfirst uses a deep learning method to predict the structure of proteins from cryo-EM maps, which is averaged with a reference (template) structure of the proteins to produce a combined structure to add ligands. The ligands are then identified and added into the structure to generate a protein-ligand complex structure, which is further refined. The method based on the deep learning prediction and template-based modeling was blindly tested in the 2021 EMDataResource Ligand Challenge and was ranked first in fitting ligands to cryo-EM density maps.This results demonstrate that the deep learning bioinformatics approach is a promising direction to model protein-ligand interaction on cryo-EM data using prior structural information. The source code, data, and instruction to reproduce the results are available on GitHub repository :https://github.com/jianlin-cheng/DeepProLigand
Large-scale whole-genome sequencing of migratory Bogong moths Agrotis infusa reveals genetic variants associated with migratory direction in a panmictic population
Authors: Wallace Jesse RA , Maleszka Ryszard , Warrant Eric J
Published: May 2022

One of the most interesting macroscopic phenomena in the animal world is seasonal migration. A central goal of research into animal migration is to better understand the mechanisms that evolved to solve the complex challenges which a migratory life history presents. Each year, and with a high degree of species-level site fidelity, the Australian Bogong moth makes a return migration of up to and over 1000 km between widely distributed breeding grounds and a specific set of aestivation sites in the Australian Alps. It does this without any opportunity to learn the migratory route or the location of the aestivation sites from either older generations or repeated migrations, meaning that the information required by the moth to navigate during its migration must be inherited. The migratory direction, and therefore the inherited navigational information in Bogong moths, varies with breeding site, providing us with an opportunity to search for the source of that heritability by comparing the genomes of moths collected from different breeding areas. We successfully sequenced whole nuclear genomes of 77 Bogong moths collected from across their breeding grounds and summer range, and found that the Bogong moth population contains a large amount of (mostly rare) variation. We found no evidence of population structure, indicating that Bogong moths are panmictic. A genome-wide scan for signals of selection indicate that the Bogong population has recently recovered from a past bottleneck, however genomic regions which have likely undergone balancing selection were also detected. Despite panmixia, four genetic variants in breeding-ground-caught Bogong moths were found to be significantly associated with geographic location, and therefore migratory direction, indicating promising future avenues of research into the molecular basis of long-distance navigation.
Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genusSebastes)
Authors: Muto Nozomu , Kawasaki Takuma , Kakioka Ryo , Nagano Atsushi J. , Shimizu Yuta , Inose Shu , Shimizu Yohei , Takahashi Hiroshi
Published: May 2022

Postmating isolation is thought to be an important driver of the late stages of speciation. However, relatively little is empirically known about the process compared to other isolating mechanisms that drive the early stages of speciation, especially in non-model organisms. We characterized the genetic architecture of postmating isolation between two rockfishes,Sebastes schlegeliiandS. trivittatus, whose reproductive isolation is complete. We examined transmission ratio distortion (TRD) patterns of genetic markers in two reciprocal backcross populations. Markers showing either of the two types of TRD was widespread across the genome, with some of the distorted markers forming extensive clusters around the recombination coldspots. These suggest that the postmating isolation effectively prevents gene flow across the genome and the recombination landscape contributes to the genetic architecture. Comparisons between two backcross families and two developmental stages showed little similarity in the distorted markers, suggesting asymmetry and stage-specificity of the isolation. This may be due to hybrid incompatibility involving maternal factors or extrinsic selection. The lack of sex-ratio distortion in the mapping families suggested that Haldane’s rule in terms of hybrid inviability does not hold. Additionally, QTL mapping detected significant QTLs for sex and the morphological traits relevant to speciation and convergence of rockfishes, including body coloration. Genes in the melanocortin system, includingagouti-signaling protein 1(asip1) andmelanocortin 1 receptor(mc1r), might underlie the horizontal and vertical color patterns on the body, respectively. These findings constitute an essential step towards a comprehensive understanding of speciation and morphological diversification of rockfishes.
The outer surface protease, SepM, is required for blp locus activation in three of the four most common pherotypes of Streptococcus pneumoniae
Authors: Ratner Samantha , Bollinger Kevin , Richardson John , Dawid Suzanne
Published: May 2022

Streptococcus pneumoniae (pneumococcus) is an important human pathogen that primarily resides in the nasopharynx. To persist in this polymicrobial environment, pneumococcus must compete with other members of the bacterial community. Competition is mediated in part by the action of the blp locus which encodes a variable array of bacteriocins and their associated immunity proteins. The locus is controlled by a two-component regulatory system that senses the extracellular concentration of the peptide pheromone, BlpC. There are four major pherotypes of BlpC that can be found in most pneumococcal genomes. Here, we show that the protease, SepM, is required for activation of three of the four major pherotypes. The only SepM independent BlpC type is 9AA shorter than the SepM-dependent peptides, consistent with a cleavage event at the C-terminal end. The processing event occurs following secretion and removal of the C terminal region is required for binding to the histidine kinase receptor. Synthetic truncated peptides or full-length peptides pre-incubated with SepM-expressing bacteria can upregulate the blp locus independent of SepM. We show that SepM-independent peptides accumulate in the supernatant of secreting cells at low levels suggesting a role for the tail in peptide secretion, stability or solubility and demonstrating a significant tradeoff for SepM-independence.

Importance

Streptococcus pneumoniae is an important cause of disease in humans that occurs when the bacteria in the nasopharynx bypasses host defenses to invade deeper tissues. Colonization fitness thus represents an important initial step in pathogenesis. S. pneumoniae produces antimicrobial peptides called bacteriocins which provide a competitive advantage over neighboring bacteria in the nasopharynx. The blp locus encodes a variable array of bacteriocins that participate in competition. Here, we demonstrate that activation of the blp locus requires a surface protease that activates the blp signal peptide. There are naturally occurring signal peptides that do not require cleavage, but these are characterized by poor secretion. We describe an additional, previously unappreciated activation step in the control of bacteriocin production in S. pneumoniae.
Multiple viral protein genome-linked proteins compensate viral translation in a +ssRNA virus infection
Authors: Warsaba Reid , Stoynov Nikolay , Moon Kyung-Mee , Flibotte Stephane , Foster Leonard , Jan Eric
Published: May 2022

Viral protein genome-linked (VPg) protein plays an essential role in protein-primed replication of plus stranded RNA viruses. VPg is covalently linked to the 5’ end of the viral RNA genome via a phosphodiester bond typically at a conserved amino acid. Whereas most viruses have a single VPg, some viruses encode multiple VPgs that are proposed to have redundant yet undefined roles in viral replication. Here, we use the dicistrovirus, cricket paralysis virus (CrPV), which encodes four non-identical copies of VPg, as a model to characterize the role of VPg copies in infection. Dicistroviruses encode two main open reading frames (ORFs) that are driven by distinct IRESs. We systematically generated single and combinatorial deletions and mutations of VPg1-4 within the CrPV infectious clone and monitored viral yield in Drosophila S2 cells. Deletion of one to three VPg copies progressively decreased viral yield and delayed viral replication, suggesting a threshold number of VPgs for productive infection. Mass spectrometry analysis of CrPV VPg-linked RNAs revealed viral RNA linkage to either a serine or threonine in VPg, from which mutations in all VPgs attenuated infection. Mutating serine 4 in a single VPg abolished viral infection, indicating a dominant-negative effect. Using viral minigenome reporters that monitor dicistrovirus 5’ untranslated (UTR) and intergenic internal ribosome entry site (IRES) translation revealed a relationship between VPg copy number and the ratio of distinct IRES translation. We uncover a novel viral strategy whereby VPg copies in dicistrovirus genomes compensate for the relative IRES translation efficiencies to promote infection.

Importance

Genetic duplication is exceedingly rare in small RNA viral genomes as there is selective pressure to prevent RNA genomes from expanding. However, some small RNA viruses encode multiple copies of a viral protein, most notably an unusual viral protein that is linked to the viral RNA genome. Here, we investigate a family of viruses that contains multiple viral protein genome-linked proteins and reveal a novel viral strategy whereby viral protein copy number counterbalances differences in viral protein synthesis mechanisms.
A robust, highly multiplexed mass spectrometry assay to identify SARS-CoV-2 variants
Authors: Hernandez Matthew M. , Banu Radhika , Shrestha Paras , Gonzalez-Reiche Ana S. , van de Guchte Adriana , Farrugia Keith , Sebra Robert ,   Mount Sinai PSP Study Group, Gitman Melissa R. , Nowak Michael D. , Cordon-Cardo Carlos , Simon Viviana , van Bakel Harm , Sordillo Emilia Mia , Luna Nicolas , Ramirez Angie , Castañeda Sergio Andres , Patiño Luz Helena , Ballesteros Nathalia , Muñoz Marina , Ramírez Juan David , Paniz-Mondolfi Alberto E.
Published: May 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole viral genome sequencing (WGS) is the “gold standard” for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY® SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA as well as in Bogotá, Colombia (September 2, 2020 – March 2, 2022). We demonstrate almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlight distinct target patterns that can be utilized to identify variants not yet defined on the panel including the Omicron BA.2 and other sublineages. These findings exemplify the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones.

Importance

The continued circulation of SARS-CoV-2 amidst limited surveillance efforts and inconsistent vaccination of populations has resulted in emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to inform diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlight the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated at over September 2, 2020 – March 2, 2022 among patients seeking care at our health systems. This assay demonstrates variant-specific signatures of nucleotide/amino acid polymorphisms and underscores its utility for detection of contemporary and emerging SARS-CoV-2 variants of concern.