bluuebunny/crossref_metadata_2025 huggingface dataset:
Spontaneous helping in pigs is mediated by helper’s social attention and distress signals of individuals in need
Authors: Moscovice Liza R. , Eggert Anja , Manteuffel Christian , Rault Jean-Loup
Published: March 2023

Helping behaviour is of special interest for prosociality because it appears to be motivated by the needs of others. We developed a novel paradigm to investigate helping in pigs (Sus scrofa domesticus) and tested 75 individuals in eight groups in their home pens. Two identical compartments were attached to the pen, equipped with a window, and a door that could be opened from the outside by lifting a handle. Pigs in all groups spontaneously opened doors during a five-day familiarization. During testing, each pig was isolated once from its group and placed in one of the two compartments, in a counter-balanced order. In 85% of cases, pigs released a trapped group member from the test compartment within 20 minutes (median latency = 2.2 minutes). Pigs were more likely and quicker to open a door to free the trapped pig than to open a door to an empty compartment. Pigs who spent more time looking at the window of the test compartment were more likely to help. Distress signals by the trapped pig increased its probability of being helped. Responses are consistent with several criteria for identifying targeted helping, but results can also be explained by selfish motivations.
DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access
Authors: Bögels Bas W.A. , Nguyen Bichlien H. , Ward David , Gascoigne Levena , Schrijver David P. , Pistikou Anna-Maria Makri , Joesaar Alex , Yang Shuo , Voets Ilja K. , Mulder Willem J.M. , Phillips Andrew , Mann Stephen , Seelig Georg , Strauss Karin , Chen Yuan-Jyue , de Greef Tom F. A.
Published: March 2023

Owing to its longevity and extremely high information density, DNA has emerged as an attractive medium for archival data storage. Scalable parallel random access of information is a desirable property of any storage system. For DNA-based storage systems, however, this yet has to be robustly established. Here we develop thermoconfined PCR, a novel method that enables multiplexed, repeated random access of compartmentalized DNA files. Our strategy is based on stable localization of biotin-functionalized oligonucleotides inside microcapsules with temperature-dependent membrane permeability. At low temperatures, microcapsules are permeable to enzymes, primers, and amplified products, while at high temperatures membrane collapse prevents molecular crosstalk during amplification. We demonstrate that our platform outperforms non-compartmentalized DNA storage with respect to repeated random access and reducing amplification bias during multiplex PCR. Using fluorescent sorting, we additionally demonstrate sample pooling and data retrieval by barcoding of microcapsules. Our thermoresponsive microcapsule technology offers a scalable, sequence-agnostic approach for repeated random access of archival DNA files.
Many Families of Lids for TonB-dependent Transporters inBacteroides
Authors: Price Morgan N. , Deutschbauer Adam M. , Arkin Adam P.
Published: March 2023

Most TonB-dependent transporters inBacteroidesbelong to the SusC family and work with an outer-membrane lipoprotein from the SusD family that functions like a lid. But the best-studied strain,B. thetaiotaomicronVPI-5482, also contains 18 TonB-dependent transporters that are not from the SusC family. We identified six families of putative lids for these transporters. The putative lids are lipoproteins that are encoded next to TonB-dependent transporters, but they are not homologous to SusD. AlphaFold-Multimer predicts that the putative lids bind the outer faces of the corresponding TonB-dependent receptors. Genetic data suggests that members of four of these families are required for the activity of the corresponding TonB-dependent receptors. Overall, of the 18 TonB-dependent receptors that do not belong to the SusC family, we identified alternate lids for nine.
Multidimensional specialization and generalization are pervasive in soil prokaryotes with generalists dominating communities and specialists more central in networks
Authors: Hernandez Damian J. , Kiesewetter Kasey N. , Almeida Brianna K. , Revillini Daniel , Afkhami Michelle E.
Published: March 2023

Habitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analyzed 236 prokaryotic communities across the United States demonstrating for the first time that 90% of >1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had a wide range of ecological and evolutionary consequences. First, multidimensional specialization and generalization are highly conserved with very few transitions between these two trajectories. Second, multidimensional generalists dominated communities because they were 73 times more abundant than specialists. Lastly, multidimensional specialists played important roles in community structure with ∼220% more connections in microbiome networks. These results indicate that multidimensional generalization and specialization are evolutionarily stable with multidimensional generalists supporting larger populations and multidimensional specialists playing important roles within communities likely stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that the vast majority of soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for evolutionary transitions, microbial dominance, and community roles.

One-Sentence Summary

Pervasive multidimensional specialization and generalization impacts evolutionary trajectories, microbial dominance, and community roles.
Mitochondrial Sodium/Calcium Exchanger (NCLX) Regulates Basal and Starvation-Induced Autophagy Through Calcium Signaling
Authors: de Miranda Ramos Vitor , Serna Julian D.C. , Vilas-Boas Eloisa A. , Cabral-Costa João Victor , da Cunha Fernanda M. , Kataura Tetsushi , Korolchuk Viktor I. , Kowaltowski Alicia J.
Published: March 2023

Mitochondria shape intracellular Ca2+signaling through the concerted activity of Ca2+uptake via mitochondrial calcium uniporter, and efflux from by Na+/Ca2+exchangers (NCLX). Here, we describe a novel relationship between NCLX, intracellular Ca2+, and autophagic activity. Conditions that stimulate autophagyin vivoandin vitro,such as caloric restriction and nutrient deprivation, upregulate NCLX expression in hepatic tissue and cells. Conversely, knockdown of NCLX impairs basal and starvation-induced autophagy. Similarly, acute inhibition of NCLX activity by CGP 37157 affects bulk and endoplasmic reticulum autophagy (ER-phagy) without significant impacts on mitophagy. Mechanistically, CGP 37157 inhibited the formation of FIP200 puncta and downstream autophagosome biogenesis. Inhibition of NCLX caused decreased cytosolic Ca2+levels, and intracellular Ca2+chelation similarly suppressed autophagy. Furthermore, chelation did not exhibit an additive effect on NCLX inhibition of autophagy, demonstrating that mitochondrial Ca2+efflux regulates autophagy through the modulation of Ca2+signaling. Collectively, our results show that the mitochondrial Ca2+extrusion pathway through NCLX is an important regulatory node linking nutrient restriction and autophagy regulation.
Three-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch
Authors: Handler Annie , Zhang Qiyu , Pang Song , Nguyen Tri M. , Iskols Michael , Nolan-Tamariz Michael , Cattel Stuart , Plumb Rebecca , Sanchez Brianna , Ashjian Karyl , Shotland Aria , Brown Bartianna , Kabeer Madiha , Turecek Josef , Rankin Genelle , Xiang Wangchu , Pavarino Elisa C. , Africawala Nusrat , Santiago Celine , Lee Wei-Chung Allen , Shan Xu C. , Ginty David D.
Published: March 2023

Specialized mechanosensory end organs within mammalian skin—hair follicle-associated lanceolate complexes, Meissner corpuscles, and Pacinian corpuscles—enable our perception of light, dynamic touch1. In each of these end organs, fast-conducting mechanically sensitive neurons, called Aβ low-threshold mechanoreceptors (Aβ LTMRs), associate with resident glial cells, known as terminal Schwann cells (TSCs) or lamellar cells, to form complex axon ending structures. Lanceolate-forming and corpuscle-innervating Aβ LTMRs share a low threshold for mechanical activation, a rapidly adapting (RA) response to force indentation, and high sensitivity to dynamic stimuli1–6. How mechanical stimuli lead to activation of the requisite mechanotransduction channel Piezo27–15and Aβ RA-LTMR excitation across the morphologically dissimilar mechanosensory end organ structures is not understood. Here, we report the precise subcellular distribution of Piezo2 and high-resolution, isotropic 3D reconstructions of all three end organs formed by Aβ RA-LTMRs determined by large volume enhanced Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) imaging. We found that within each end organ, Piezo2 is enriched along the sensory axon membrane and is minimally or not expressed in TSCs and lamellar cells. We also observed a large number of small cytoplasmic protrusions enriched along the Aβ RA-LTMR axon terminals associated with hair follicles, Meissner corpuscles, and Pacinian corpuscles. These axon protrusions reside within close proximity to axonal Piezo2, occasionally contain the channel, and often form adherens junctions with nearby non-neuronal cells. Our findings support a unified model for Aβ RA-LTMR activation in which axon protrusions anchor Aβ RA-LTMR axon terminals to specialized end organ cells, enabling mechanical stimuli to stretch the axon in hundreds to thousands of sites across an individual end organ and leading to activation of proximal Piezo2 channels and excitation of the neuron.
Modular small RNA drives pathogen emergence
Authors: Balasubramanian Deepak , Almagro-Moreno Salvador
Published: March 2023

Pathogen emergence is a poorly understood complex phenomenon. To date, the molecular mechanisms that allow strains within a bacterial population to emerge as human pathogens remain mostly enigmatic. We recently uncovered that toxigenicVibrio choleraeencode preadaptations to host colonization, what we term virulence adaptive polymorphisms (VAPs), however, the molecular mechanisms driving them are not known.ompUis a VAP-encoding gene that is associated with the production of the major outer membrane porin OmpU. Here, we show that theompUORF also encodes a modular small RNA overlapping its 3’ terminus that plays a major role inV. choleraephysiology. We determined that the OmpU-encoded sRNA (OueS) strongly suppresses biofilm formation, a phenotype that is essential for host intestinal colonization, via repression of iron uptake. OueS controls over 84% of the genes regulated by ToxR, a major virulence regulator, and plays an integral role during the infection process. We demonstrate that OueS is critical for intestinal colonization and its bimodular nature dictates the virulence potential ofV. cholerae. Overall, our study reveals specific molecular mechanisms leading to the emergence of pathogenic traits in bacteria unveiling the hidden genetics associated with this process. We propose a scenario where a limited number of modular genes could explain the emergence of novel phenotypic traits in biological systems.
Understanding the neural mechanisms of emotion-cognition interaction via high resolution mapping in space, time, frequency, and information transfer
Authors: Dietrich Anya , Pinzuti Edoardo , Cabral-Calderin Yuranny , Müller-Dahlhaus Florian , Wibral Michael , Tüscher Oliver
Published: March 2023

Human behaviour is inextricably linked to the interaction of emotion and cognition. For decades, emotion and cognition were perceived as separable processes, yet with mutual interactions. Recently, this differen-tiation has been challenged by more integrative approaches, but without addressing the exact neurophysiological basis of their interaction. Here, we aimed to uncover neurophysiological mechanisms of emotion-cognition interaction. We used an emotional Flanker task paired with EEG/FEM beamforming in a large cohort (N=121) of healthy human participants, obtaining high temporal and fMRI-equivalent spatial resolution. Spatially, emotion and cognition processing overlapped in the right inferior frontal gyrus (rIFG), specifically inpars triangularis. Temporally, emotion and cognition processing overlapped during the transition from emotional to cognitive processing, with a stronger interaction inβ-band power leading to worse behavioral performance. Despite functionally segregated subdivisions in rIFG, frequency-specific information flowed extensively within IFG and top-down to visual areas (V2, Precuneus) – explaining the behavioral interference effect. Thus, for the first time we here show the neural mechanisms of emotion-cognition interaction in space, time, frequency and information transfer with high temporal and spatial resolution, revealing a central role forβ-band activity in rIFG. Our results support the idea that rIFG plays a broad role in both inhibitory control and emotional interference inhibition as it is a site of convergence in both processes. Furthermore, our results have potential clinical implications for understanding dysfunctional emotion-cognition interaction and emotional interference inhibition in psychiatric disor-ders, e.g. major depression and substance use disorder, in which patients have difficulties in regulating emotions and executing inhibitory control.
A sex-specific switch in a single glial cell patterns the apical extracellular matrix
Authors: Fung Wendy , Tan Taralyn M. , Kolotuev Irina , Heiman Maxwell G.
Published: March 2023

Apical extracellular matrix (aECM) constitutes the interface between every tissue and the outside world. It is patterned into diverse tissue-specific structures through unknown mechanisms. Here, we show that a male-specific genetic switch in a singleC. elegansglial cell patterns the aECM into a ∼200 nm pore, allowing a male sensory neuron to access the environment. We find that this glial sex difference is controlled by factors shared with neurons (mab-3, lep-2, lep-5) as well as previously unidentified regulators whose effects may be glia-specific (nfya-1, bed-3, jmjd-3.1). The switch results in male-specific expression of a Hedgehog-related protein, GRL-18, that we discover localizes to transient nanoscale rings at sites of aECM pore formation. Blocking male-specific gene expression in glia prevents pore formation, whereas forcing male-specific expression induces an ectopic pore. Thus, a switch in gene expression in a single cell is necessary and sufficient to pattern aECM into a specific structure.
The skate spiracular organ develops from a unique neurogenic placode, distinct from lateral line placodes
Authors: Gillis J. Andrew , Criswell Katharine E. , Baker Clare V. H.
Published: March 2023

The spiracular organ is an epithelial pouch or tube lined with mechanosensory hair cells, found embedded in the wall of the spiracle/spiracular chamber (remnant of the first pharyngeal cleft) in many non-teleost jawed fishes. It is innervated via a branch of the anterior lateral line nerve and usually considered a specialised lateral line organ, although it most likely functions as a proprioceptor for jaw movement. It is homologous to the paratympanic organ: a hair cell-lined epithelial pouch embedded in the wall of the middle ear (which evolved from the spiracular chamber) of birds, alligators andSphenodon. A previous fate-mapping study showed that the chicken paratympanic organ and its afferent neurons originate from a molecularly distinct placode immediately dorsal to the geniculate (first epibranchial) placode. Here, DiI fate-mapping in a cartilaginous fish (little skate,Leucoraja erinacea) shows that the spiracular organ derives from a previously unrecognised neurogenic placode immediately dorsal to the geniculate placode and molecularly distinct from lateral line placodes. These findings further support the developmental and evolutionary independence of this unique jawed-vertebrate mechanosensory organ from the lateral line system.

Summary statement

Fate-mapping in a cartilaginous fish supports the developmental independence from the lateral line system of the mechanosensory spiracular organ, consistent with its homology with the amniote paratympanic organ.
AspFlex: molecular tools to study gene expression and regulation inAcinetobacter baumannii
Authors: Brychcy Merlin , Kokodynski Alexis , Lloyd Devin , Godoy Veronica G.
Published: March 2023

Acinetobacter baumanniiis a gram negative nosocomial opportunistic pathogen frequently found in hospital settings, causing high incidence of in-hospital infections. It belongs to the ESKAPE group of pathogens (the “A” stands forA. baumannii) that is known to easily develop antibiotic resistances. It is crucial to create a molecular toolkit to investigate its basic biology, such as gene regulation. DespiteA. baumanniibeing a threat for almost two decades, an efficient and high-throughput plasmid system that can replicate inA. baumanniihas not yet been developed. This study adapts an existing toolkit forEscherichia colito meetA. baumannii’sunique requirements and expands it by constructing a mobile CRISPR interference (CRISPRi) system that can produce gene knockdowns inA. baumannii.
Single-Soma Deep RNA Sequencing of Human Dorsal Root Ganglion Neurons Reveals Novel Molecular and Cellular Mechanisms Underlying Somatosensation
Authors: Yu Huasheng , Usoskin Dmitry , Nagi Saad S. , Hu Yizhou , Kupari Jussi , Bouchatta Otmane , Cranfill Suna Li , Gautam Mayank , Su Yijing , Lu You , Wymer James , Glanz Max , Albrecht Phillip , Song Hongjun , Ming Guo-Li , Prouty Stephen , Seykora John , Wu Hao , Ma Minghong , Rice Frank L , Olausson Håkan , Ernfors Patrik , Luo Wenqin
Published: March 2023

The versatility of somatosensation arises from heterogeneous dorsal root ganglion (DRG) neurons. However, soma transcriptomes of individual human DRG (hDRG) neurons – critical information to decipher their functions – are lacking due to technical difficulties. Here, we developed a novel approach to isolate individual hDRG neuron somas for deep RNA sequencing (RNA-seq). On average, >9,000 unique genes per neuron were detected, and 16 neuronal types were identified. Cross-species analyses revealed remarkable divergence among pain-sensing neurons and the existence of human-specific nociceptor types. Our deep RNA-seq dataset was especially powerful for providing insight into the molecular mechanisms underlying human somatosensation and identifying high potential novel drug targets. Our dataset also guided the selection of molecular markers to visualize different types of human afferents and the discovery of novel functional properties using single-cellin vivoelectrophysiological recordings. In summary, by employing a novel soma sequencing method, we generated an unprecedented hDRG neuron atlas, providing new insights into human somatosensation, establishing a critical foundation for translational work, and clarifying human species-specific properties.
Valence-partitioned learning signals drive choice behavior and phenomenal subjective experience in humans
Authors: Sands L. Paul , Jiang Angela , Jones Rachel E. , Trattner Jonathan D. , Kishida Kenneth T.
Published: March 2023

How the human brain generates conscious phenomenal experience is a fundamental problem. In particular, it is unknown how variable and dynamic changes in subjective affect are driven by interactions with objective phenomena. We hypothesize a neurocomputational mechanism that generates valence-specific learning signals associated with ‘what it is like’ to be rewarded or punished. Our hypothesized model maintains a partition between appetitive and aversive information while generating independent and parallel reward and punishment learning signals. This valence-partitioned reinforcement learning (VPRL) model and its associated learning signals are shown to predict dynamic changes in 1) human choice behavior, 2) phenomenal subjective experience, and 3) BOLD-imaging responses that implicate a network of regions that process appetitive and aversive information that converge on the ventral striatum and ventromedial prefrontal cortex during moments of introspection. Our results demonstrate the utility of valence-partitioned reinforcement learning as a neurocomputational basis for investigating mechanisms that may drive conscious experience.

Highlights

TD-Reinforcement Learning (RL) theory interprets punishments relative to rewards.

Environmentally, appetitive and aversive events are statistically independent.

Valence-partitioned RL (VPRL) processes reward and punishment independently.

We show VPRL better accounts for human choice behavior and associated BOLD activity.

VPRL signals predict dynamic changes in human subjective experience.
A biophysical framework for double-drugging kinases
Authors: Kim C. , Ludewig H. , Hadzipasic A. , Kutter S. , Nguyen V. , Kern D.
Published: March 2023

Orthosteric inhibition of kinases has been challenging due to the conserved active site architecture of kinases and emergence of resistance mutants. Simultaneous inhibition of distant orthosteric and allosteric sites, which we refer to as “double-drugging”, has recently been shown to be effective in overcoming drug resistance. However, detailed biophysical characterization of the cooperative nature between orthosteric and allosteric modulators has not been undertaken. Here, we provide a quantitative framework for double-drugging of kinases employing isothermal titration calorimetry, Förster resonance energy transfer, coupled-enzyme assays, and X-ray crystallography. We discern positive and negative cooperativity for Aurora A kinase (AurA) and Abelson kinase (Abl) with different combinations of orthosteric and allosteric modulators. We find that a conformational equilibrium shift is the main principle governing this cooperative effect. Notably, for both kinases, we find a synergistic decrease of the required orthosteric and allosteric drug dosages when used in combination to inhibit kinase activities to clinically relevant inhibition levels. X-ray crystal structures of the doubledrugged kinase complexes reveal the molecular principles underlying the cooperative nature of double-drugging AurA and Abl with orthosteric and allosteric inhibitors. Finally, we observe the first fully-closed conformation of Abl when bound to a pair of positively cooperative orthosteric and allosteric modulators, shedding light onto the puzzling abnormality of previously solved closed Abl structures. Collectively, our data provide mechanistic and structural insights into rational design and evaluation of doubledrugging strategies.
Cyclin E/CDK2 and feedback from soluble histone protein regulate the S phase burst of histone biosynthesis
Authors: Armstrong Claire , Passanisi Victor J. , Ashraf Humza M. , Spencer Sabrina L.
Published: March 2023

Faithful DNA replication requires that cells fine-tune their histone pool in coordination with cell-cycle progression. Replication-dependent histone biosynthesis is initiated at a low level upon cell-cycle commitment, followed by a burst at the G1/S transition, but it remains unclear how exactly the cell regulates this change in histone biosynthesis as DNA replication begins. Here, we use single-cell timelapse imaging to elucidate the mechanisms by which cells modulate histone production during different phases of the cell cycle. We find that CDK2-mediated phosphorylation of NPAT at the Restriction Point triggers histone transcription, which results in a burst of histone mRNA precisely at the G1/S phase boundary. Excess soluble histone protein further modulates histone abundance by promoting the degradation of histone mRNA for the duration of S phase. Thus, cells regulate their histone production in strict coordination with cell-cycle progression by two distinct mechanisms acting in concert.
T6SS-mediated competitive exclusion amongPantoea agglomeransassociated with plants
Authors: Ripcke Kai , Picazo Devani Romero , Vichare Shreya , Unterweger Daniel , Dagan Tal , Hülter Nils F.
Published: March 2023

Establishment of symbiotic interactions with a host habitat depends on colonization success of the microbiome members. One route to success is increasing competitiveness against genotypes having similar adaptations. Many bacteria deploy the type VI secretion system (T6SS) to deliver toxic effector proteins into the cytoplasm of competing cells, whereas the attacking cells are protected from self-intoxication by immunity proteins. While the evolution of antagonistic interactions between species competing for similar niches is expected, the interactions between closely related strains having a similar core genetic makeup, remains understudied. Here we show that the strength of T6SS-mediated competition between closely relatedP. agglomeransstrains is not associated with phylogenetic relatedness and rather depends on their effector and immunity genes repertoire. Annotating the T6SS components in elevenP. agglomeransisolates from wheat seeds, we observed a heterogeneous composition of effector and immunity determinants. Competition experiments further showed profound differences in the strain survival following reciprocal T6SS-mediated interactions. Reconstructing the evolution of T6SS loci across plant-associatedP. agglomeransisolates indicates intra-chromosomal recombination as the main driver of effector and immunity gene diversification. Our results provide empirical data on intraspecific interactions during microbiota assembly likely to be at play during colonization of germinating plant seeds.
AttenuatedMycobacterium tuberculosisVaccine Protection in a Low Dose Murine Challenge Model
Authors: Vidal Samuel J. , Sellers Daniel , Yu Jingyou , Wakabayashi Shoko , Sixsmith Jaimie , Aid Malika , Barrett Julia , Stevens Sage F. , Liu Xiaowen , Li Wenjun , Plumlee Courtney R. , Urdahl Kevin B. , Martinot Amanda J. , Barouch Dan H.
Published: March 2023

Bacillus Calmette–Guérin (BCG) remains the only clinically approved tuberculosis (TB) vaccine despite limited efficacy. Preclinical studies of next generation TB vaccines have typically used a murine aerosol challenge model that employs a high supraphysiologic challenge dose. Here we show that the protective efficacy of a live attenuatedMycobacterium tuberculosis(Mtb) vaccine candidate ΔLprG markedly exceeds that of BCG in a low dose murine aerosol challenge model. BCG vaccination reduced bacterial loads but failed to prevent establishment or dissemination of infection in this model. In contrast, ΔLprG prevented detectable infection in 61% of mice and resulted in striking anatomic containment of 100% breakthrough infections to a single lung. Protection was partially abrogated in a repeated low dose challenge model, which revealed serum IL-17A, IL-6, CXCL2, CCL2, IFN-γ, and CXCL1 as correlates of protection. These data demonstrate that ΔLprG provides strikingly increased protection compared to BCG, including reduced detectable infection and anatomic containment, in a low dose murine challenge model.
CRISPR-ChIP delineates a Menin-dependent oncogenic DOT1L complex in MLL- leukaemia
Authors: Gilan Omer , Bell Charles C. , Talarmain Laure , Neville Daniel , Knezevic Kathy , Ferguson Daniel , Boudes Marion , Chan Yih-Chih , Davidovich Chen , Lam Enid Y.N. , Dawson Mark A.
Published: March 2023

The regulation of all chromatin-templated processes involves the selective recruitment of chromatin factors to facilitate DNA repair, replication, and transcription. Chromatin immunoprecipitation (ChIP) is a critical experimental method used to provide spatiotemporal evidence for the coordination of these chromatin-based events including the dynamic regulation of chromatin modifications at cis-regulatory elements. However, obtaining a global appreciation of all the factors that influence a specific chromatin event has remained challenging. Here, as a proof of concept we demonstrate the utility of coupling unbiased functional genomics with ChIP to identify the factors associated with active transcription. Specifically, we use this method to identify the major chromatin factors associated with the catalysis of two evolutionarily conserved histone modifications; H3K4me3 present at the transcriptional start site and H3K79me2 present through the gene body of actively transcribed genes. With CRISPR-ChIP, we identify all the non-redundant COMPASS complex members required for H3K4me3 and demonstrate that RNA polymerase II is dispensable for the maintenance of H3K4me3. As H3K79me2 has a putative oncogenic function in leukaemia cells driven by MLL-translocations, using CRISPR-ChIP we reveal a functional partitioning of H3K79 methylation into two distinct regulatory units. An oncogenic DOT1L complex, where the malignant driver directs the catalytic activity of DOT1L at MLL-Fusion target genes and a separate endogenous DOT1L complex, where catalytic activity is directed by MLLT10. This functional demarcation provides an explanation for the observed synergy with Menin and DOT1L inhibitors and why Menin inhibition surprisingly controls methylation of H3K79 at a critical subset of genes that sustain MLL-fusion leukaemia. Overall, CRISPR-ChIP provides a powerful tool for the unbiased interrogation of the mechanisms underpinning chromatin regulation.
Tandem mobilization of anti-phage defenses alongside SCCmeccassettes
Authors: Hossain Motaher , Aslan Barbaros , Hatoum-Aslan Asma
Published: March 2023

Bacterial viruses (phages) and the immune systems targeted against them significantly impact bacterial survival, evolution, and the emergence of pathogenic strains. While recent research has made spectacular strides towards discovering and validating new defenses in a few model organisms1-3, the inventory of immune systems in clinically-relevant bacteria remains under-explored, and little is known about the mechanisms by which these systems horizontally spread. Such pathways not only impact the evolutionary trajectory of bacterial pathogens, but also threaten to undermine the effectiveness of phage-based therapeutics. Here, we investigate the battery of defenses in staphylococci, opportunistic pathogens that constitute leading causes of antibiotic-resistant infections. We show that these organisms harbor a variety of anti-phage defenses encoded within/near the infamous SCC (staphylococcal cassette chromosome)meccassettes, mobile genomic islands that confer methicillin resistance. Importantly, we demonstrate that SCCmec-encoded recombinases mobilize not only SCCmec, but also tandem cassettes enriched with diverse defenses. Further, we show that phage infection potentiates cassette mobilization. Taken together, our findings reveal that beyond spreading antibiotic resistance, SCCmeccassettes play a central role in disseminating anti-phage defenses. This work underscores the urgent need for developing adjunctive treatments that target this pathway to save the burgeoning phage therapeutics from suffering the same fate as conventional antibiotics.
Ozone mediates tumor-selective cell death caused by air plasma-activated medium independently of NOx
Authors: Suzuki-Karasaki Manami , Ochiai Yushi , Innami Shizuka , Okajima Hiroshi , Suzuki-Karasaki Miki , Nakayama Hideki , Suzuki-Karasaki Yoshihiro
Published: March 2023

Cold atmospheric plasma and plasma-treated liquids (PTLs) are emerging promising tools for tumor-targeted cancer treatment, as they preferentially injure tumor cells more than non-malignant cells. Oxidative stress is critical to the antitumor effect, but the oxidant mediating the effect is debatable. Previously, we reported that air plasma-activated medium (APAM) has tumor-selective cytotoxicity in vitro and in vivo. Moreover, an unusual mitochondrial positioning named monopolar perinuclear mitochondrial clustering (MPMC) and nuclear damage proceeds to cell death. We noticed that air plasma generation was accompanied by ozone (O3) formation, leading to suppose the possible role of O3in the effect of APAM. In this study, we produced an O3-dissolved medium (ODM) and comparatively analyzed its biological effect with APAM. Both agents had comparable amounts of dissolved O3(dO3), while APAM, but not ODM, contained nitrite and nitrate. Like APAM, ODM could induce apoptosis, nonapoptotic cell death, tubulin remodeling, MPMC, and nuclear shrinkage. Catalase mitigated all these events. The increases in various intracellular and mitochondrial reactive oxygen species (ROS) and lipid peroxides proceeded to cell death, and catalase also prevented them. Conversely, suppressing cellular H2O2removal systems augmented mitochondrial ROS production and cell death. In contrast, like APAM, ODM minimally increased ROS production and MPMC in non-malignant cells. These results indicate that dO3is a critical mediator of the actions of APAM, including tumor-selective induction of MPMC and cell death. Our findings suggest ODM could be a more chemically-defined alternative to PTLs in cancer treatment.
The streptococcal phase-variable Type I Restriction-Modification system SsuCC20p dictates the methylome ofStreptococcus suisand impacts virulence
Authors: Roodsant Thomas J. , van der Putten Boas , Brizuela Jaime , Coolen Jordy P.M. , Baltussen Tim J.H. , Schipper Kim , Pannekoek Yvonne , Van der Ark Kees C.H. , Schultsz Constance
Published: March 2023

Phase-variable Type I Restriction Modification (RM) systems are epigenetic regulatory systems that have been identified in numerous human bacterial pathogens. We previously showed that an emerging zoonotic lineage ofStreptococcus suisacquired a phase-variable Type I RM system named SsuCC20p. The SsuCC20p locus was present in the genome of disease-associated isolates from multiple streptococcal species. This indicates that it is not restricted toS. suisand can be acquired through horizontal gene transfer. We demonstrate that SsuCC20p phase-variability relies on a recombinase present within the locus.In vitro, only SsuCC20p is responsible for the genome methylation profiles that were detected in the representative zoonoticS. suisisolate 861160. In addition, we show that, contrary to previous observations,hsdSgenes located downstream of thehsdMgene and the recombinase gene, can contribute to the SsuCC20p genome methylation profile. SsuCC20p locked mutants expressing a singlehsdSeach showed unique genome methylation profiles. The differential genome methylation of the distinct locked mutants caused phase dependent differences in global gene expression in a growth condition dependent manner. We observed significant differences in virulence betweenhsdSlocked mutants in a zebrafish larvae infection model. These data indicate that the streptococcal phase-variable Type I RM system SsuCC20p can impact bacterial virulence via epigenetic regulation of gene expression and potentially contributes to the zoonotic potential ofS. suis.

Importance

Phase-variation contributes to the virulence of bacterial pathogens as it allows a single strain to produce phenotypic diverse subpopulations. Phase-variable Restriction Modification (RM) systems are systems that allow for such phase-variation via epigenetic regulation of gene expression levels. The phase-variable RM system SsuCC20p was found in multiple streptococcal species and was acquired by an emerging zoonotic lineage ofStreptococcus suis. We show that the phase-variability of SsuCC20p is dependent on a recombinase encoded within the SsuCC20p locus. We characterized the genome methylation profiles of the different phases of SsuCC20p and showed that the differential genome methylation within the phases causes differences in gene expression levels and virulence. Altogether, we show that the acquisition of a phase-variable RM system impacts virulence and can potentially contribute to the zoonotic potential ofS. suis. Bacterial pathogens can increase their virulence through acquisition of mobile elements containing epigenetic regulatory systems such as RM systems.
The ELEMI healthcare professional Study
Authors: Delanerolle Gayathri , Li Yunshan , Cavalini Heitor , Barnard-Kelly Katharine , Elliot Katheryn , Raymont Vanessa , Pluchino Nicola , Flores Idaliz , Elneil Sohier , Majumder Kingshuk , Welsh Amy Boyd , Sillem Martin , Hull M. Louise , O’Hara Rebecca , Rathod Shanaya , Shetty Ashish , Shi Jian Qing , Hapangama Dharani K , Phiri Peter
Published: March 2023

Introduction

Endometriosis impacts 1 in 10 women and can be a debilitating disease. Late diagnosis is a major challenge with Endometriosis, contributing further to the exacerbation of symptoms and suboptimal clinical management. Regardless of the commonality of the condition, public awareness and research around endometriosis is severely lacking.

Methods

To explore the knowledge base about Endometriosis we developed a digital cross-sectional study. We used the Qualtrics XM platform and developed a questionnaire. The primary objective of the study was to report the understanding of Endometriosis among healthcare professionals in a mental healthcare setting in the UK.

Results

We gathered the responses of 144 healthcare professionals, although only 68 participants responded to all questions. Approximately 96% of participants agreed that there is a need for a comprehensive clinical strategy where mental health care services could assist women very early in the pathway. Around 63.1% confirmed awareness of endometriosis although the χ2(p-value=0.158) test showed that the perceived clinical knowledge was not necessarily associated with their profession. Over 92% of participants confirmed that it would be useful to conduct mental health-based research among endometriosis patients.

Discussion

It is clear than patients with endometriosis would greatly benefit from a streamlined clinical pathway. It would also have financial benefits to the NHS, including less visits to A&E. The absence of comprehensive knowledge and understanding amongst healthcare professional on endometriosis leads to delayed diagnosis and treatment, exacerbating their psychological and physiological symptoms.

Conclusions

Our study shows the importance of funding mental health research to further add to the body of knowledge in order to develop evidence based clinical practices that are equally acceptable to women with endometriosis. This will have benefits for both the patients, healthcare professional, and also the NHS. It will enable for better treatment pathways and symptom management, aiding the development for improved healthcare policies.
The mitophagy receptor BNIP3L/Nix coordinates nuclear calcium signaling to modulate the muscle phenotype
Authors: Field Jared T. , Chapman Donald , Hai Yan , Ghavami Saeid , West Adrian R. , Ozerklig Berkay , Saleem Ayesha , Kline Julia , Mendelson Asher A. , Kindrachuk Jason , Triggs-Raine Barbara , Gordon Joseph W.
Published: March 2023

Mitochondrial quality control is critical in muscle to ensure both contractile and metabolic function. Nix is a BCL-2 family member, mitophagy receptor, and has been implicated in muscle atrophy. Human GWAS suggests altered Nix expression could predispose to manifestations of mitochondrial disease. To interrogate Nix function, we generated a muscle-specific knockout model. Nix knockout mice displayed a ragged-red fibre phenotype, along with accumulation of mitochondria and endo/sarcoplasmic reticulum with altered morphology. Intriguingly, Nix knockout mice were more insulin sensitive with a corresponding increase in glycogen-rich muscle fibres. Kinome- and gene expression analyses revealed that Nix knockout impairs NFAT and canonical myostatin signaling, with alterations in muscle fibre-type composition and evidence of regeneration. Mechanistic experiments demonstrated that Nix modulates mitophagy, along with ER-phagy leading to altered nuclear calcium signaling. Collectively, these observations identify novel roles for Nix coordinating selective autophagy, oxidative gene expression, and signaling pathways that maintain the muscle phenotype.
Variational Log-Gaussian Point-Process Methods for Grid Cells
Authors: Rule Michael Everett , Chaudhuri-Vayalambrone Prannoy , Krstulovic Marino , Bauza Marius , Krupic Julija , O’Leary Timothy
Published: March 2023

We present practical solutions to applying Gaussian-process methods to calculate spatial statistics for grid cells in large environments. Gaussian processes are a data efficient approach to inferring neural tuning as a function of time, space, and other variables. We discuss how to design appropriate kernels for grid cells, and show that a variational Bayesian approach to log-Gaussian Poisson models can be calculated quickly. This class of models has closed-form expressions for the evidence lower-bound, and can be estimated rapidly for certain parameterizations of the posterior covariance. We provide an implementation that operates in a low-rank spatial frequency subspace for further acceleration, and demonstrate these methods on experimental data.
Long-term tracking of social structure in groups of rats
Authors: Nagy Máté , Davidson Jacob D. , Vásárhelyi Gábor , Ábel Dániel , Kubinyi Enikő , El Hady Ahmed , Vicsek Tamás
Published: March 2023

Rodents serve as an important model for examining both individual and collective behavior. Dominance within rodent social structures can determine access to critical resources, such as food and mating opportunities. Yet, many aspects of the intricate interplay between individual behaviors and the resulting group social hierarchy, especially its evolution over time, remain unexplored. In this study, we utilized an automated tracking system that continuously monitored groups of male rats for over 250 days to enable an in-depth analysis of individual behavior and the overarching group dynamic. We describe the evolution of social structures within a group and additionally investigate how past behaviors influence the emergence of new social hierarchies when group composition and experimental area changes. Notably, we find that conventional individual and pairwise tests exhibit a weak correlation with group behavior, highlighting their limited accuracy in predicting behavioral outcomes in a collective context. These results emphasize the context-dependence of social behavior as an emergent property of interactions within a group and highlight the need to measure and quantify social behavior in more naturalistic environments.
Neuron cilia constrain glial regulators to microdomains around distal neurons
Authors: Ray Sneha , Gurung Pralaksha , Manning R. Sean , Kravchuk Alexandra , Singhvi Aakanksha
Published: March 2023

Each glia interacts with multiple neurons, but the fundamental logic of whether it interacts with all equally remains unclear. We find that a single sense-organ glia modulates different contacting neurons distinctly. To do so, it partitions regulatory cues into molecular microdomains at specific neuron contact-sites, at its delimited apical membrane. For one glial cue, K/Cl transporter KCC-3, microdomain-localization occurs through a two-step, neuron-dependent process. First, KCC-3 shuttles to glial apical membranes. Second, some contacting neuron cilia repel it, rendering it microdomain-localized around one distal neuron-ending. KCC-3 localization tracks animal aging, and while apical localization is sufficient for contacting neuron function, microdomain-restriction is required for distal neuron properties. Finally, we find the glia regulates its microdomains largely independently. Together, this uncovers that glia modulate cross-modal sensor processing by compartmentalizing regulatory cues into microdomains. Glia across species contact multiple neurons and localize disease-relevant cues like KCC-3. Thus, analogous compartmentalization may broadly drive how glia regulate information processing across neural circuits.
Speed-independent modulation of locomotor gait preference by sensory feedback in mice
Authors: Mitrevica Zane , Murray Andrew J
Published: March 2023

Locomotion is one of the most ubiquitous motor actions in the animal kingdom, essential for behaviours as diverse as foraging, migration, and escape. Successful execution of all these tasks relies on continual adjustment of locomotor gait in line with the behavioural demand for speed as well as the terrain. Failure in this process would disrupt locomotor smoothness, raise its energetic cost, and increase the risk of injury due to skeletal stress [1, 2]. Animals avoid these scenarios, in part, by transitioning from left-right alternating (walk, trot) to synchronous (gallop, bound) gaits as they increase the speed [3, 4]. However, this relationship is not deterministic [5, 6] and its connection to biomechanical factors, like the loading of limbs [7, 8], is unclear. To address this, we developed a head-fixed locomotor paradigm that decouples the speed- and leg loading-related influences on gait by combining optogenetic stimulation of an established speed-control pathway [9, 10] with head height or surface incline modulation. We found a pronounced speed-independent shift in homolateral limb coordination from strict alternation to a gallop-like pattern at upward oriented body postures and upsloping terrains. Both conditions are associated with greater relative loading of the hindlimbs and have a consistent effect on gait preference during head-fixed and head-free locomotion. These results suggest that mice use proprioceptive feedback from the limbs to coordinate their gait across speeds and environments, and implicate ipsilateral control mechanisms in this process. More broadly, our work serves as a principled entry point to a behaviour-driven study of gait circuits.
Predicting an Individual’s Cerebellar Activity from Functional Connectivity Fingerprints
Authors: Tripathi Vaibhav , Somers David C
Published: March 2023

The cerebellum is gaining scientific attention as a key neural substrate of cognitive function; however, individual differences in the cerebellar organization have not yet been well studied. Individual differences in functional brain organization can be closely tied to individual differences in brain connectivity. ‘Connectome Fingerprinting’ is a modeling approach that predicts an individual’s brain activity from their connectome. Here, we extend ‘Connectome Fingerprinting’ (CF) to the cerebellum. We examined functional MRI data from 160 subjects (98 females) of the Human Connectome Project young adult dataset. For each of seven cognitive task paradigms, we constructed CF models from task activation maps and resting-state cortico-cerebellar functional connectomes, using a set of training subjects. For each model, we then predicted task activation in novel individual subjects, using their resting-state functional connectomes. In each cognitive paradigm, the CF models predicted individual subject cerebellar activity patterns with significantly greater precision than did predictions from the group average task activation. Examination of the CF models revealed that the cortico-cerebellar connections that carried the most information were those made with the non-motor portions of the cerebral cortex. These results demonstrate that the fine-scale functional connectivity between the cerebral cortex and cerebellum carries important information about individual differences in cerebellar functional organization. Additionally, CF modeling may be useful in the examination of patients with cerebellar dysfunction, since model predictions require only resting-state fMRI data which is more easily obtained than task fMRI.