bluuebunny/crossref_metadata_2025 huggingface dataset:
Paternal CHH methylation potentiates stress responses against Pseudomonas syringae in Arabidopsis progenies
Authors: Li Yongping , Liu Tianjia , Leung Even Yee Man , Zhao Xusheng , Zhu Guopeng , Ng Danny W-K
Published: May 2023

Systemic acquired resistance (SAR) is an induced immune mechanism in plants, involving epigenetic regulation by chromatin remodeling and DNA methylation, which can be inherited to progeny following stress exposure. Intersexual epigenetic conflict sometimes leads to unequal expression of maternal and paternal alleles in offspring, resulting in parent-of-origin effects of inheritance. To better understand the parental contributions of epialleles in plant defense, isogenicArabidopsisparental lines were mock-treated (M) andPseudomonas syringae(Pst)-treated (P) for reciprocal crosses to produce F1 progenies (MP, PM). Together with their self-fertilized F1 descendants (MM, PP), the genome-wide inherited DNA methylation and transcriptomic changes againstPstwere analyzed. F1 descendants shared widespread DNA methylation and transcriptional changes at transposable elements (TEs) and genes. The confrontation of epigenomes triggers the reprogramming of DNA methylation in reciprocal crosses, resulting in transgressive segregation that also shows the parental effect ofPsttreatment. Compared to PM, the MP (Pst-primed paternal genome) was found to contributes to CHH hypermethylation, which is associated with processes in plant-pathogen interaction, including carbohydrate metabolism, glutathione metabolism and stronger translation process, which potentially contribute to improved disease resistance in MP in response toPstchallenge. Our data suggested a parent-of-origin effect of defense priming that contributes differently toward improved defense response in progenies.
Near-field potentials index local neural computations more accurately than population spiking
Authors: Tovar David A. , Westerberg Jacob A. , Cox Michele A. , Dougherty Kacie , Wallace Mark T. , Bastos André M. , Maier Alexander
Published: May 2023

Local field potentials (LFP) are low-frequency extracellular voltage fluctuations thought to primarily arise from synaptic activity. However, unlike highly localized neuronal spiking, LFP is spatially less specific. LFP measured at one location is not entirely generated there due to far-field contributions that are passively conducted across volumes of neural tissue. We sought to quantify how much information within the locally generated, near-field low-frequency activity (nfLFP) is masked by volume-conducted far-field signals. To do so, we measured laminar neural activity in primary visual cortex (V1) of monkeys viewing sequences of multifeatured stimuli. We compared information content of regular LFP and nfLFP that was mathematically stripped of volume-conducted far-field contributions. Information content was estimated by decoding stimulus properties from neural responses via spatiotemporal multivariate pattern analysis. Volume-conducted information differed from locally generated information in two important ways: (1) for stimulus features relevant to V1 processing (orientation and eye-of-origin), nfLFP contained more information. (2) in contrast, the volume-conducted signal was more informative regarding temporal context (relative stimulus position in a sequence), a signal likely to be coming from elsewhere. Moreover, LFP and nfLFP differed both spectrally as well as spatially, urging caution regarding the interpretations of individual frequency bands and/or laminar patterns of LFP. Most importantly, we found that population spiking of local neurons was less informative than either the LFP or nfLFP, with nfLFP containing most of the relevant information regarding local stimulus processing. These findings suggest that the optimal way to read out local computational processing from neural activity is to decode the local contributions to LFP, with significant information loss hampering both regular LFP and local spiking.

Author’s Contributions

Conceptualization, D.A.T., J.A.W, and A.M.; Data Collection, J.A.W., M.A.C., K.D.; Formal Analysis, D.A.T. and J.A.W.; Data Visualization, D.A.T. and J.A.W.; Original Draft, D.A.T., J.A.W., and A.M.; Revisions and Final Draft, D.A.T., J.A.W., M.A.C., K.D., M.T.W., A.M.B., and A.M.

Competing Interests

The authors declare no conflicts of interest.
Dysregulation of amino acid metabolism upon rapid depletion of cap-binding protein eIF4E
Authors: Diamond Paige D. , McGlincy Nicholas J. , Ingolia Nicholas T.
Published: May 2023

Protein synthesis is a crucial but metabolically costly biological process that must be tightly coordinated with cellular needs and nutrient availability. In response to environmental stress, translation initiation is modulated to control protein output while meeting new demands. The cap-binding protein eIF4E—the earliest contact between mRNAs and the translation machinery—serves as one point of control, but its contributions to mRNA-specific translation regulation remain poorly understood. To survey eIF4E-dependent translational control, we acutely depleted eIF4E and determined how this impacts protein synthesis. Despite its essentiality, eIF4E depletion had surprisingly modest effects on cell growth and protein synthesis. Analysis of transcript-level changes revealed that long-lived transcripts were downregulated, likely reflecting accelerated turnover. Paradoxically, eIF4E depletion led to simultaneous upregulation of genes involved in catabolism of aromatic amino acids, which arose as secondary effects of reduced protein biosynthesis on amino acid pools, and genes involved in the biosynthesis of amino acids. These futile cycles of amino acid synthesis and degradation were driven, in part, by translational activation ofGCN4, a transcription factor typically induced by amino acid starvation. Furthermore, we identified a novel regulatory mechanism governing translation ofPCL5,a negative regulator of Gcn4, that provides a consistent protein-to-mRNA ratio under varied translation environments. This translational control was partial dependent on a uniquely long poly-(A) tract in thePCL55’ UTR and on poly-(A) binding protein. Collectively, these results highlight how eIF4E connects translation to amino acid homeostasis and stress responses and uncovers new mechanisms underlying how cells tightly control protein synthesis during environmental challenges.
A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X
Authors: Jowhar Ziad , Xu Albert , Venkataramanan Srivats , Dossena Francesco , Hoye Mariah L , Silver Debra L , Floor Stephen N , Calviello Lorenzo
Published: May 2023

The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology is DDX3X, an RNA binding protein that canonically regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNAs. We use interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. This result corroborates GC content-related mRNA regulation detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including aDdx3xconditional knockout mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled.
Multi-site identification and generalization of clusters of walking behaviors in individuals with chronic stroke and neurotypical controls
Authors: Sánchez Natalia , Schweighofer Nicolas , Mulroy Sara J. , Roemmich Ryan T. , Kesar Trisha M. , Torres-Oviedo Gelsy , Fisher Beth E. , Finley James M. , Winstein Carolee J.
Published: May 2023

Background

Walking patterns in stroke survivors are highly heterogeneous, which poses a challenge in systematizing treatment prescriptions for walking rehabilitation interventions.

Objective

We used bilateral spatiotemporal and force data during walking to create a multi-site research sample to: 1) identify clusters of walking behaviors in people post-stroke and neurotypical controls, and 2) determine the generalizability of these walking clusters across different research sites. We hypothesized that participants post-stroke will have different walking impairments resulting in different clusters of walking behaviors, which are also different from control participants.

Methods

We gathered data from 81 post-stroke participants across four research sites and collected data from 31 control participants. Using sparse K-means clustering, we identified walking clusters based on 17 spatiotemporal and force variables. We analyzed the biomechanical features within each cluster to characterize cluster-specific walking behaviors. We also assessed the generalizability of the clusters using a leave-one-out approach.

Results

We identified four stroke clusters: a fast and asymmetric cluster, a moderate speed and asymmetric cluster, a slow cluster with frontal plane force asymmetries, and a slow and symmetric cluster. We also identified a moderate speed and symmetric gait cluster composed of controls and participants post-stroke. The moderate speed and asymmetric stroke cluster did not generalize across sites.

Conclusions

Although post-stroke walking patterns are heterogenous, these patterns can be systematically classified into distinct clusters based on spatiotemporal and force data. Future interventions could target the key features that characterize each cluster to increase the efficacy of interventions to improve mobility in people post-stroke.
Time-resolved network control analysis links reduced control energy under DMT with the serotonin 2a receptor, signal diversity, and subjective experience
Authors: Singleton S. Parker , Timmermann Christopher , Luppi Andrea I. , Eckernäs Emma , Roseman Leor , Carhart-Harris Robin L. , Kuceyeski Amy
Published: May 2023

Psychedelics offer a profound window into the functioning of the human brain and mind through their robust acute effects on perception, subjective experience, and brain activity patterns. In recent work using a receptor-informed network control theory framework, we demonstrated that the serotonergic psychedelics lysergic acid diethylamide (LSD) and psilocybin flatten the brain’s control energy landscape in a manner that covaries with more dynamic and entropic brain activity. Contrary to LSD and psilocybin, whose effects last for hours, the serotonergic psychedelic N,N-dimethyltryptamine (DMT) rapidly induces a profoundly immersive altered state of consciousness lasting less than 20 minutes, allowing for the entirety of the drug experience to be captured during a single resting-state fMRI scan. Using network control theory, which quantifies the amount of input necessary to drive transitions between functional brain states, we integrate brain structure and function to map the energy trajectories of 14 individuals undergoing fMRI during DMT and placebo. Consistent with previous work, we find that global control energy is reduced following injection with DMT compared to placebo. We additionally show longitudinal trajectories of global control energy correlate with longitudinal trajectories of EEG signal diversity (a measure of entropy) and subjective ratings of drug intensity. We interrogate these same relationships on a regional level and find that the spatial patterns of DMT’s effects on these metrics are correlated with serotonin 2a receptor density (obtained from separately acquired PET data). Using receptor distribution and pharmacokinetic information, we were able to successfully recapitulate the effects of DMT on global control energy trajectories, demonstrating a proof-of-concept for the use of control models in predicting pharmacological intervention effects on brain dynamics.
Activity of brain stem glucagon neurons are modulated by energy state and encode sex and frequency-dependent negative valence and anxiety
Authors: Lopez CB , Duran M , Virkus SA , Yadav E , McMichen K , Singh J , Ramsey V , Stocking S , Habegger KM , Hardaway JA
Published: May 2023

The glucagon-like peptide 1 (GLP-1) system has emerged as an important drug target for the treatment of obesity and diabetes. Preclinical and clinical studies demonstrate that the activation of GLP-1 receptors (GLP-1Rs) directly in the brain through overexpression of GLP-1 or GLP-1R agonists produces potent anorexigenic effects, yet the behavioral role and modulation of theendogenousGLP-1 producing system in the brain by energy status is unclear. In this study, we examined the anatomical, physiological, and behavioral properties of preproglucagon-expressing neurons in the nucleus of the solitary tract,GcgNTSneurons, which serve as the primary source of GLP-1 in the brain. Using transgenic laboratory mice, we observed no sex differences in the density and distribution ofGcgNTSneurons in male and female mice. Fos immunolabeling experiments show thatGcgNTSneurons are not significantly activated after intermittent access to palatable food, but the magnitude of Fos activation was linearly related to the amount of food intake in mice provided withad libitumintermittent access to palatable food. Electrophysiological examination ofGcgNTSneurons revealed that these neurons show energy-status and sex-dependent changes in neuronal firing and intrinsic excitability. Twenty-four hour food deprivation produced a significant reduction in excitability and firing in male, but not female mice. We then used optogenetics to investigate the causal behavioral role ofGcgNTSneurons. High frequency optogenetic activation ofGcgNTSneurons using the red light-gated opsin ChrimsonR produced female-specific anxiety-like behavior and real-time place aversion. For feeding, we observed that reversible optogenetic stimulation at high frequencies produced a significant reduction in homeostatic refeeding that did not differ by sex. Using operant conditioning, we found that reversible optogenetic activation ofGcgNTSneurons at 20 Hz, but not 5, also reduces appetitive behavior. These data demonstrate thatGcgNTSneurons exert control over motivation and food-seeking behavior in addition to consumption.
Top-down modulation of sensory processing and mismatch in the mouse posterior parietal cortex
Authors: Raltschev Constanze , Kasavica Sergej , Leonardon Benjamin , Nevian Thomas , Sachidhanandam Shankar
Published: May 2023

An important function of the neocortex is to compare sensory feedback stimuli with internal predictions of the outside world and evoke mismatch responses to deviations, thus allowing expectations to be updated. The mechanisms behind sensory feedback mismatch and prediction formation however remain unclear. Here we created a learned association of an auditory-tactile stimulus sequence in awake head-fixed mice, where a sound predicted an up-coming whisker stimulus, and introduced mismatches by omitting or altering the whisker stimulus intensity. We showed that layer 2/3 posterior parietal cortex (PPC) neurons could report stimulus sequence mismatches, as well as display neural correlates of expectation. Inhibition of PPC-projecting secondary motor cortex (M2) neurons suppressed these correlates, along with population mismatch responses. Hence, M2 can influence sensory processing in the PPC and potentially provide the prediction of sensory feedback from learned relationships within sequences of sensory stimuli.
The stabilized supralinear network accounts for the contrast dependence of visual cortical gamma oscillations
Authors: Holt Caleb J. , Miller Kenneth D. , Ahmadian Yashar
Published: May 2023

When stimulated, neural populations in the visual cortex exhibit fast rhythmic activity with frequencies in the gamma band (30-80 Hz). The gamma rhythm manifests as a broad resonance peak in the powerspectrum of recorded local field potentials, which exhibits various stimulus dependencies. In particular, in macaque primary visual cortex (V1), the gamma peak frequency increases with increasing stimulus contrast. Moreover, this contrast dependence is local: when contrast varies smoothly over visual space, the gamma peak frequency in each cortical column is controlled by the local contrast in that column’s receptive field. No parsimonious mechanistic explanation for these contrast dependencies of V1 gamma oscillations has been proposed. The stabilized supralinear network (SSN) is a mechanistic model of cortical circuits that has accounted for a range of visual cortical response nonlinearities and contextual modulations, as well as their contrast dependence. Here, we begin by showing that a reduced SSN model without retinotopy robustly captures the contrast dependence of gamma peak frequency, and provides a mechanistic explanation for this effect based on the observed non-saturating and supralinear input-output function of V1 neurons. Given this result, the local dependence on contrast can trivially be captured in a retinotopic SSN which however lacks horizontal synaptic connections between its cortical columns. However, long-range horizontal connections in V1 are in fact strong, and underlie contextual modulation effects such as surround suppression. We thus explored whether a retinotopically organized SSN model of V1 with strong excitatory horizontal connections can exhibit both surround suppression and the local contrast dependence of gamma peak frequency. We found that retinotopic SSNs can account for both effects, but only when the horizontal excitatory projections are composed of two components with different patterns of spatial fall-off with distance: a short-range component that only targets the source column, combined with a long-range component that targets columns neighboring the source column. We thus make a specific qualitative prediction for the spatial structure of horizontal connections in macaque V1, consistent with the columnar structure of cortex.
Reliability of resting-state EEG modulation by continuous and intermittent theta burst stimulation of the primary motor cortex: A sham-controlled study
Authors: Rodionov Andrei , Ozdemir Recep A. , Benwell Christopher S.Y. , Fried Peter J. , Boucher Pierre , Momi Davide , Ross Jessica M. , Santarnecchi Emiliano , Pascual-Leone Alvaro , Shafi Mouhsin M.
Published: May 2023

Theta burst stimulation (TBS) is a form of repetitive transcranial magnetic stimulation designed to induce changes of cortical excitability that outlast the period of TBS application. In this study, we explored the effects of continuous TBS (cTBS) and intermittent TBS (iTBS) versus sham TBS stimulation, applied to the primary motor cortex, on modulation of resting state electroencephalography (rsEEG) power. We first conducted hypothesis-driven region-of-interest (ROI) analyses examining changes in alpha (8-12 Hz) and beta (13-21 Hz) bands over the left and right motor cortex. Additionally, we performed data-driven whole-brain analyses across a wide range of frequencies (1-50 Hz) and all electrodes. Finally, we assessed the reliability of TBS effects across two sessions approximately 1 month apart. None of the protocols produced significant group-level effects in the ROI. Whole-brain analysis revealed that cTBS significantly enhanced relative power between 19-43 Hz over multiple sites in both hemispheres. However, these results were not reliable across visits. There were no significant differences between EEG modulation by active and sham TBS protocols. Between-visit reliability of TBS-induced neuromodulatory effects was generally low-to-moderate. We discuss confounding factors and potential approaches for improving the reliability of TBS-induced rsEEG modulation.
Metabolic response of microglia to amyloid deposition during Alzheimer’s disease progression in a mouse model
Authors: Marino Kaitlyn M. , Squirrell Jayne M. , Chacko Jenu V. , Watters Jyoti W. , Eliceiri Kevin W. , Ulland Tyler K.
Published: May 2023

Alzheimer’s disease (AD) drives metabolic changes in the central nervous system (CNS). In AD microglia are activated and proliferate in response to amyloid β plaques. To further characterize the metabolic changes in microglia associated with plaque depositionin situ, we examined cortical tissue from 2, 4, and 8-month-old wild type and 5XFAD mice, a mouse model of plaque deposition. 5XFAD mice exhibited progressive microgliosis and plaque deposition as well as changes in microglial morphology and neuronal dystrophy. Multiphoton-based fluorescent lifetime imaging microscopy (FLIM) metabolic measurements showed that older mice had an increased amount of free NAD(P)H, indicative of a shift towards glycolysis. Interestingly in 5XFAD mice, we also found an abundant previously undescribed third fluorescence component that suggests an alternate NAD(P)H binding partner associated with pathology. This work demonstrates that FLIM in combination with other quantitative imaging methods, is a promising label-free tool for understanding the mechanisms of AD pathology.
A new fluorescence-based approach for direct visualization of coat formation during sporulation inBacillus cereus
Authors: Lablaine Armand , Chamot Stéphanie , Serrano Mónica , Billaudeau Cyrille , Bornard Isabelle , Carballido-Lopez Rut , Carlin Frédéric , Henriques Adriano O. , Broussolle Véronique
Published: May 2023

The pathogenic bacteriaBacillus cereus,Bacillus anthracisandBacillus thuringiensisform spores encased in a protein coat surrounded by a balloon-like exosporium. These structures mediate spore interactions with its environment, including the host immune system, control the transit of molecules that trigger germination and thus are essential for the spore life cycle. Formation of the coat and exosporium has been traditionally visualized by transmission electronic microscopy on fixed cells. Recently, we showed that assembly of the exosporium can be directly observed in liveB. cereuscells by super resolution-structured illumination microscopy (SR-SIM) using the membrane MitoTrackerGreen (MTG) dye. Here, we demonstrate that the different steps of coat formation can also be visualized by SR-SIM using MTG and SNAP-cell TMR-star dyes duringB. cereussporulation. We used these markers to characterize a subpopulation of engulfment-defectiveB. cereuscells that develops at a suboptimal sporulation temperature. Importantly, we predicted and confirmed that synthesis and accumulation of coat material, as well as synthesis of the σK-dependent protein BxpB, occur in cells arrested during engulfment. These results suggest that, unlike the well-studied model organismBacillus subtilis, the activity of σKis not strictly linked to the state of forespore development inB. cereus.
Regulation of coronavirus nsp15 cleavage specificity by RNA structure
Authors: Salukhe Indranil , Choi Ryan , Voorhis Wesley Van , Barrett Lynn , Hyde Jennifer L.
Published: May 2023

SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, has had an enduring impact on global public health. However, SARS-CoV-2 is only one of multiple pathogenic human coronaviruses (CoVs) to have emerged since the turn of the century. CoVs encode for several nonstructural proteins (NSPS) that are essential for viral replication and pathogenesis. Among them is nsp15, a uridine-specific viral endonuclease that is important in evading the host immune response and promoting viral replication. Despite the established function of nsp15 as a uridine-specific endonuclease, little is known about other determinants of its cleavage specificity. In this study we investigate the role of RNA secondary structure in SARS-CoV-2 nsp15 endonuclease activity.

Using a series ofin vitroendonuclease assays, we observed that thermodynamically stable RNA structures were protected from nsp15 cleavage relative to RNAs lacking stable structure. We leveraged the s2m RNA from the SARS 3’UTR as a model for our structural studies as it adopts a well-defined structure with several uridines, two of which are unpaired and thus high probably targets for nsp15 cleavage. We found that SARS-CoV-2 nsp15 specifically cleaves s2m at the unpaired uridine within the GNRNA pentaloop of the RNA. Further investigation revealed that the position of uridine within the pentaloop also impacted nsp15 cleavage efficiency, suggesting that positioning within the pentaloop is necessary for optimal presentation of the scissile uridine and alignment within the nsp15 catalytic pocket. Our findings indicate that RNA secondary structure is an important determinant of nsp15 cleavage and provides insight into the molecular mechanisms of recognition of RNA by nsp15.
Early astrocytic dysfunction is associated to mistuned synapses as well as anxiety and depressive-like behavior in the AppNL-F mouse model of Alzheimers disease
Authors: Portal Benjamin , Sodergren Moa , Pares i Borrell Teo , Giraud Romain , Metzendorf Nicole , Hultqvist Greta , Nilsson Per , Lindskog Maria
Published: May 2023

Alzheimers disease is the most common neurodegenerative disease and constitute 75% of dementia cases worldwide. Unfortunately, efficient and affordable treatments are still lacking for this mental illness, it is therefore urgent to identify new pharmacological targets. Whereas the late phases of the disease are well described, recent evidence suggest synaptic impairments at a pre-amyloid β; (Aβ) plaque stage. Astrocytes are playing a crucial role in the tuning of synaptic transmission and several studies have pointed out severe astrocyte reactivity in Alzheimers disease, especially around Aβ; plaques. Reactive astrocytes show altered physiology and function, suggesting they could have a role in the early pathophysiology of Alzheimers disease. In this study we used the AppNL-F knock-in mouse model of Alzheimers disease which carries two disease-causing mutations inserted in the amyloid precursor protein (App) gene. This strain does not start to develop Aβ; plaques until nine months of age. To better understand early changes in Alzheimer's disease, we investigated synaptic function, at both neuronal and astrocytic levels, in six months old AppNL-F mice and correlate the synaptic dysfunction with emotional behavior. Electrophysiological recordings in the hippocampus revealed an overall synaptic mistuning at a pre-plaque stage of the pathology, associated to an intact social memory but a stronger depressive-like behavior. Astrocytes displayed a reactive-like morphology and a higher tonic GABA current compared to control mice. Interestingly, we here show that the synaptic impairments in hippocampal slices are partially corrected by a pre-treatment with the monoamine oxidase B (MAO-B) blocker deprenyl or the fast-acting antidepressant ketamine (5mg/kg). Thus, we propose that reactive astrocytes can induce synaptic mistuning early in Alzheimers disease, before plaques deposition, and that these changes are associated with emotional symptoms.
Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at single cell level
Authors: Voronov Danila , Paganos Periklis , Magri Marta S. , Cuomo Claudia , Maeso Ignacio , Gómez-Skarmeta Jose Luis , Arnone Maria Ina
Published: May 2023

Drafting gene regulatory networks (GRNs) requires embryological knowledge pertaining to the cell type families, information on the regulatory genes, causal data from gene knockdown experiments and validations of the identified interactions by cis-regulatory analysis. We use multi-omics involving next-generation sequencing (-seq) to obtain the necessary information drafting the sea urchin posterior gut GRN. Here we present an update to the GRN using i) a single cell RNA-seq derived cell atlas highlighting the 2 day post fertilization (dpf) sea urchin gastrula cell type families, as well as the genes expressed at single cell level, ii) a set of putative cis-regulatory modules and transcription factor (TF) binding sites obtained from chromatin accessibility ATAC-seq data, and iii) interactions directionality obtained from differential bulk RNA-seq following knockdown of the TF Sp-Pdx1, a key regulator of gut patterning in sea urchins. Combining these datasets, we draft the GRN for the hindgutSp-Pdx1positive cells in the 2 dpf gastrula embryo. Overall, our data resolves the complex connectivity of the posterior gut GRN and increases the resolution of gene regulatory cascades operating within it.
Assessing diatom-associated bacteria by a specific CARD-FISH protocol
Authors: Den Tran Quoc , Simon Meinhard
Published: May 2023

The cell surfaces of phytoplankton algae including diatoms are usually colonized by specific bacterial populations which interact with and affect growth of the host species. Catalyzed Reported Deposition Fluorescence in situ Hybridizazion (CARD-FISH) is a well-suited technique to visualize and identify algal-associated bacterial cells. Autofluorescence and the strongly structured cell surface of the algal cell make it difficult to quantify distinct populations of the colonizing bacterial communities. To overcome these limitations, we adopted a CARD-FISH method to this specific application by reducing the algal autofluorescence by an extra ethanol treatment and by stacking epifluorescence micrographs taken at different focal planes and merging them into a composite image. Cells of the diatomThalassiosira rotulawere used as host and incubated with a consortium of different bacterial strains and a natural bacterial community. Samples were concentrated either by filtration onto polycarbonate membranes or by centrifugation and analyzed with probes CF319a, GAM42a and ROS536. The results showed easily quantifiable bacterial cells and did not reveal any significant differences in the abundance of diatom-associated bacterial populations assessed by both methods. Our CARD-FISH protocol persuasively demonstrated that bacterial populations can be easily and reliably enumerated on diatom cells and presumably also on other algal cells and autotrophic biofilms.
Predictable Modality Transitions and Amodal Representations Enable Crossmodal Statistical Learning
Authors: Pérez-Bellido Alexis , Duato Daniel , Giannelli Francesco , de Diego-Balaguer Ruth
Published: May 2023

Statistical learning involves extracting statistical regularities from the environment. Despite the ubiquitous crossmodal relations in our environment, previous research has failed in showing crossmodal learning suggesting that statistical learning is modality-specific, occurring within but not between sensory modalities. The present study investigates under which circumstances statistical learning can occur between modalities. In the first experiment, participants viewed a stream of meaningless visual fractals and synthetic auditory stimuli. Importantly, the sequence of stimuli could be grouped into unimodal or crossmodal pairs based on their internal transitional probabilities. Using implicit and explicit measures of learning, we found that participants only learned the unimodal pairs. In the second experiment, pairs were presented in separate unimodal and crossmodal blocks. The crossmodal blocks alternated visual and auditory modalities allowing participants to anticipate the upcoming modality. This manipulation allowed significant statistical learning for the crossmodal pairs, reflected only by implicit measures. This suggests that modality transitions predictability aids correct attention deployment across sensory modalities, crucial for learning crossmodal statistical contingencies. In the third experiment, where audiovisual stimuli with semantic content were used leaving access to an amodal shared representation, participants could explicitly recognize statistical regularities between crossmodal pairs even when the upcoming modality was unpredictable. This finding suggests statistical learning between crossmodal pairs can occur when sensory-level limitations are bypassed, and when learning unfolds at an amodal level of representation. These findings challenge the view that statistical learning is strictly modality-specific, instead indicating that crossmodal statistical learning depends on attentional mechanisms and representational level.

Public significance statement

Previous research has established that low-level statistical learning occurs within individual sensory modalities. However, evidence for statistical learning across modalities remains limited. This has led to the hypothesis that statistical learning operates as a modality-specific system, constrained by the perceptual properties and content of each sensory system. In this study, we demonstrate that modality transitions’ predictability enables crossmodal statistical learning, even in the absence of semantic information. Notably, this constraint does not apply to meaningful stimuli, which can be processed at an amodal level. Our findings broaden the classical neurobiological model of statistical learning by highlighting the roles of attentional mechanisms and representational levels in supporting crossmodal statistical learning.
Hypoxia delays steroid-induced developmental maturation inDrosophilaby suppressing EGF signaling
Authors: Turingan Michael J , Li Tan , Wright Jenna , Grewal Savraj S
Published: May 2023

Animals often grow and develop in unpredictable environments where factors like food availability, temperature, and oxygen levels can fluctuate dramatically. To ensure proper sexual maturation into adulthood, juvenile animals need to adapt their growth and developmental rates to these fluctuating environmental conditions. Failure to do so can result in impaired maturation and incorrect body size. Here we describe a mechanism by whichDrosophilalarvae adapt their development in low oxygen (hypoxia). During normal development, larvae grow and increase in mass until they reach critical weight (CW), after which point a neuroendocrine circuit triggers the production of the steroid hormone ecdysone from the prothoracic gland (PG), which promotes maturation to the pupal stage. However, when raised in hypoxia (5% oxygen), larvae slow their growth and delay their maturation to the pupal stage. We find that, although hypoxia delays the attainment of CW, the maturation delay occurs mainly because of hypoxia acting late in development to suppress ecdysone production. This suppression operates through a distinct mechanism from nutrient deprivation, occurs independently of HIF-1 alpha and does not involve modulation of PTTH, the main neuropeptide that initiates ecdysone production in the PG. Instead, we find that hypoxia lowers the expression of the EGF ligand, spitz, and that the delay in maturation occurs due to reduced EGFR/ERK signaling in the PG. Our study sheds light on how animals can adjust their development rate in response to changing oxygen levels in their environment. Given that hypoxia is a feature of both normal physiology and many diseases, our findings have important implications for understanding how low oxygen levels may impact animal development in both normal and pathological situations.
Anionic phospholipids stimulate the proton pumping activity of the plant plasma membrane P-type H+-ATPase
Authors: Paweletz Laura C. , Holtbrügge Simon L. , Löb Malina , De Vecchis Dario , Schäfer Lars V. , Pomorski Thomas Günther , Justesen Bo Højen
Published: May 2023

The activity of membrane proteins depends strongly on the surrounding lipid environment. Here, we characterize the lipid stimulation of the plant plasma membrane H+-ATPase AHA2 upon purification and reconstitution into liposomes of defined lipid compositions. We show that the proton pumping activity of AHA2 is stimulated by anionic phospholipids, especially by phosphatidylserine. Molecular dynamics simulations revealed several preferential contact sites for anionic phospholipids in the transmembrane domain of AHA2. These contact sites are partly conserved across functionally different P-type ATPases from several organisms, suggesting a general regulation mechanism by the membrane lipid environment. Our findings highlight the fact that anionic lipids play an important role in the control of H+-ATPase activity.
A sensory-motor decoder that transforms neural responses in extrastriate area MT into smooth pursuit eye movements
Authors: Behling Stuart , Lisberger Stephen G.
Published: May 2023

Visual motion drives smooth pursuit eye movements through a sensory-motor decoder that uses multiple parallel components and neural pathways to transform the population response in extrastriate area MT into movement. We evaluated the decoder by challenging pursuit in monkeys with reduced motion reliability created by reducing coherence of motion in patches of dots. Reduced dot coherence caused deficits in both the initiation of pursuit and steady-state tracking, revealing the paradox of steady-state eye speeds that fail to accelerate to target speed in spite of persistent image motion. We recorded neural responses to reduced dot coherence in MT and found a decoder that transforms MT population responses into eye movements. During pursuit initiation, decreased dot coherence reduces MT population response amplitude without changing the preferred speed at the peak of the population response. The successful decoder reproduces the measured eye movements by multiplication of (i) the estimate of target speed from the peak of the population response with (ii) visual-motor gain based on the amplitude of the population response. During steady-state tracking, the decoder that worked for pursuit initiation failed. It predicted eye acceleration to target speed even when monkeys’ eye speeds were steady at a level well below target speed. We can account for the effect of dot coherence on steady-state eye speed if sensorymotor gain also modulates the eye velocity positive feedback that normally sustains perfect steadystate tracking. Then, poor steady-state tracking persists because of balance between deceleration caused by low positive feedback gain and acceleration driven by MT.
Mutual inclusivity improves decision-making by smoothing out choice’s competitive edge
Authors: Leng Xiamin , Frömer Romy , Summe Thomas , Shenhav Amitai
Published: May 2023

Decisions form a central bottleneck to most tasks, one that people often experience as costly. Past work proposes mitigating those costs by lowering one’s threshold for deciding. Here, we test an alternative solution, one that targets the basis for most choice costs: that choosing one option sacrifices others (mutual exclusivity). Across 5 studies (N = 462), we test whether this tension can be relieved by framing choices as inclusive (allowing selection of more than one option, as in buffets). We find that inclusivity makes choices more efficient, by selectively reducing competition between potential responses as participants accumulate information for each of their options. Inclusivity also made participants feel less conflicted, especially when they couldn’t decide which good option to keep or which bad option to get rid of. These inclusivity benefits were also distinguishable from the effects of manipulating decision threshold (increased urgency), which improved choices but not experiences thereof.
Transposable elements impact the population divergence of rice blast fungusMagnaporthe oryzae
Authors: Lin Lianyu , Sun Ting , Guo Jiayuan , Lin Lili , Chen Meilian , Wang Zhe , Bao Jiandong , Norvienyeku Justice , Zhang Dongmei , Han Yijuan , Lu Guodong , Rensing Christopher , Zheng Huakun , Zhong Zhenhui , Wang Zonghua
Published: May 2023

Dynamic transposition of transposable elements (TEs) in fungal pathogens have significant impact on genome stability, gene expression, and virulence to the host. InMagnaporthe oryzae, genome plasticity resulting from TE insertion is a major driving force leading to the rapid evolution and diversification of this fungus. Despite their importance inM. oryzaepopulation evolution and divergence, our understanding of TEs in this context remains limited. Here we conducted a genome-wide analysis of TE transposition dynamics in the 11 most abundant TE families inM. oryzaepopulations. Our results show that these TEs have specifically expanded in recently isolatedM. oryzaerice populations, with the presence/absence polymorphism of TE insertions highly concordant with population divergence on Geng/Japonicaand Xian/Indicarice cultivars. Notably, the genes targeted by clade-specific TEs showed clade-specific expression patterns and are involved in the pathogenic process, suggesting a transcriptional regulation of TEs on targeted genes. Our study provides a comprehensive analysis of TEs inM. oryzaepopulations and demonstrates a crucial role of recent TE bursts in adaptive evolution and diversification of theM. oryzaerice-infecting lineage.

IMPORTANCE

M. oryzaeis the causal agent of the destructive blast disease, which caused massive loss of yield annually worldwide. The fungus diverged into distinct clades during adaptation toward two rice subspecies, Xian/indica and Geng/japonica. Although the role of TEs in the adaptive evolution was well established, mechanisms underlying how TEs promote the population divergence ofM. oryzaeremains largely unknown. In this study, we reported that TEs shape the population divergence ofM. oryzaeby differentially regulating gene expression between Xian/Indica-infecting and Geng/Japonica-infecting populations. Our results revealed a TE insertion mediated gene expression adaption that led to the divergence ofM. oryzaepopulation infecting different rice subspecies.
The gut microbiome mediates adaptation to scarce food in Coleoptera
Authors: Moldovan Oana Teodora , Carrell Alyssa A. , Bulzu Paul Adrian , Levei Erika , Bucur Ruxandra , Sitar Cristian , Faur Luchiana , Mirea Ionu□ Cornel , □enilă Marin , Cadar Oana , Podar Mircea
Published: May 2023

Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles’ microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibulae adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineagesSpiroplasmaorWolbachia. All beetles had relatively high levels of fermentativeCarnobacteriumandVagococcusinvolved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.
Stable expression ofHelicobacter pylori cagAoncoprotein in brinjal
Authors: Mehran Mohammad Javad , Barzigar Rambod , Sathish Kumar Basaralu Yadurappa , Haraprasad Nanjundappa , Fakrudin Bashasab , Paul Sayan , Ramasamy Rajesh Kumar , Malla Sudhakar
Published: May 2023

Helicobacter pyloriis closely connected to upper gastrointestinal tract diseases including gastric cancer. Transgenic plants are found to be successful in expressing the bacterial antigens, which could elicit an immune response when consumed. The Cytotoxicity-associated immunodominant antigen protein (cagA) ofH. pyloriis kindred with pathogenicity and cancer risk. We expressed thecagAtransgenically in the brinjal. We amplified thecagAgene fromH. pyloristrain 26695 chromosomal DNA and transformed it into brinjal callus derived from leaf explants using the pBI121 expression vector. The stable expression and accumulation of the recombinantcagAgene were confirmed by using quantitative real-time PCR, western blot analysis and ELISA. The RT-PCR, western blot and ELISA showed stable expression ofcagAgene in the transgenic lines B3, B5, B11, B17 and B21. Among them, B11 and B17 samples showed higher expression of thecagAcompared to the other samples. Besides, the immunohistochemistry assay showed the abundant expression ofcagAprotein in the parenchymal regions of the transgenic plants. Out of the 52 plants, a set five plants were found to be positive forcagAexpression. Our experimental outcomes can be used further to design the vaccines againstH. pylorifrom the transgenic brinjal plants.
Factors influencing the detergent-free membrane protein isolation using synthetic nanodisc-forming polymers
Authors: Krishnarjuna Bankala , Sharma Gaurav , Ravula Thirupathi , Ramamoorthy Ayyalusamy
Published: May 2023

The detergent-free isolation of membrane proteins using synthetic polymers is becoming the desired approach for functional and structural studies of membrane proteins. Since the expression levels for many membrane proteins are low and a high yield of functionalized reconstituted membrane proteins is essential forin vitrostudies, it is crucial to optimize the experimental conditions for a given polymer to effectively solubilize target membranes/proteins. The factors that affect membrane solubilization and subsequently the isolation of a target membrane protein include polymer concentration, polymer charge, temperature, pH, and concentration of divalent metal ions. Therefore, it is important to have knowledge about the efficacy of different types of polymers in solubilizing cell membranes. In this study, we evaluate the efficacy of inulin-based non-ionic polymers in solubilizingE. colimembranes enriched with rat flavin mononucleotide binding-domain (FBD) of cytochrome-P450-reductase (CPR) and rabbit cytochrome-b5 (Cyt-b5) under various solubilization conditions. Our results show that a 1:1 (w/w) membrane:polymer ratio, low temperature, high pH and sub-millimolar concentration of metal ions favor the solubilization ofE. colimembrane enriched with FBD or Cyt-b5. Conversely, the presence of excess divalent metal ions affected the final protein levels in the polymer-solubilized samples. We believe that the results from this study provides knowledge to assess and plan the use of non-ionic polymers in membrane protein studies.
Pathogenic bacteria experience pervasive RNA polymerase backtracking during infection
Authors: Browning Kaitlyn R. , Merrikh Houra
Published: May 2023

Pathogenic bacteria and their eukaryotic hosts are in a constant arms race. Hosts have numerous defense mechanisms at their disposal that not only challenge the bacterial invaders, but have the potential to disrupt molecular transactions along the bacterial chromosome. However, it is unclear how the host impacts association of proteins with the bacterial chromosome at the molecular level during infection. This is partially due to the lack of a method that could detect these events in pathogens while they are within host cells. We developed and optimized a system capable of mapping and measuring levels of bacterial proteins associated with the chromosome while they are actively infecting the host (referred to as PIC-seq). Here, we focused on the dynamics of RNA polymerase (RNAP) movement and association with the chromosome in the pathogenic bacteriumSalmonella entericaas a model system during infection. Using PIC-seq, we found that RNAP association patterns with the chromosome change during infection genome-wide, including at regions that encode for key virulence genes. Importantly, we found that infection of a host significantly increases RNAP backtracking on the bacterial chromosome. RNAP backtracking is the most common form of disruption to RNAP progress on the chromosome. Interestingly, we found that the resolution of backtracked RNAPs via the anti-backtracking factors GreA and GreB is critical for pathogenesis, revealing a new class of virulence genes. Altogether, our results strongly suggest that infection of a host significantly impacts transcription by disrupting RNAP movement on the chromosome within the bacterial pathogen. The increased backtracking events have important implications not only for efficient transcription, but also for mutation rates as stalled RNAPs increase the levels of mutagenesis.