bluuebunny/crossref_metadata_2025 huggingface dataset:
Adsorption-driven deformation and landing-footprints of the RBD proteins in SARS-CoV-2 variants onto biological and inanimate surfaces
Authors: Bosch Antonio , Guzman Horacio V. , Pérez Rubén
Published: January 2024

Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of receptor-binding domain (RBD) mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native-biological interfaces, specifically the ACE2 receptor. Notably, we identify a twofold increase in structural deformations for the protein’s receptor binding motif onto the inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of amino acids (landing-footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, with the WT RBD adsorbed more strongly than the delta or omicron RBDs. In contrast, the adsorption of delta and omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces could lead current experimental efforts in the design of virucidal surfaces.
Polydopamine Nanoparticles as Mimicking RPE Melanin for the Protection of Retinal Cells Against Blue Light-Induced Phototoxicity
Authors: Kwon Yong-Su , Zheng Min , Smirnov Alex I. , Han Zongchao
Published: January 2024

Exposure of the eyes to blue light can induce the overproduction of reactive oxygen species (ROS) in the retina and retinal pigment epithelium (RPE) cells, potentially leading to pathological damage of age-related macular degeneration (AMD). While the melanin in RPE cells absorbs blue light and prevents ROS accumulation, the loss and dysfunction of RPE melanin due to age-related changes may contribute to photooxidation toxicity. Herein, we present a novel approach utilizing a polydopamine-replenishing strategy via a single-dose intravitreal (IVT) injection to protect retinal cells against blue light-induced phototoxicity. To investigate the effects of overexposure to blue light on retinal cells, we created a blue light exposure Nrf2-deficient mouse model, which are susceptible to light-induced retinal lesions. After blue light irradiation, we observed retina degeneration and an overproduction of ROS. The Polydopamine-replenishing strategy demonstrated effectiveness in maintaining retinal structural integrity and preventing retina degeneration by reducing ROS production in retinal cells against the phototoxicity of blue light exposure. Our findings highlight the potential of polydopamine as a simple and effective replenishment for providing photoprotection against high-energy blue light exposure.

Graphical Abstract

The graphic illustration of PDA-mediated photoprotection strategies to mimic natural melanin in RPE cells against blue light-induced phototoxicity in an Nrf2-deficient mouse model via a single-dose intravitreal (IVT) administration.
Noxious stimulation induces self-protective behaviour in bumblebees
Authors: Gibbons Matilda , Pasquini Elisa , Kowalewska Amelia , Read Eva , Gibson Sam , Crump Andrew , Solvi Cwyn , Versace Elisabetta , Chittka Lars
Published: January 2024

Self-grooming directed towards a noxiously-stimulated body part is one indicator that an animal may feel pain. In insects, the lack of evidence for such behaviour has been widely argued to reflect the absence of pain experiences. Here, we tested whether bumblebees (Bombus terrestris) selectively groom one of their antennae that was touched with a noxiously-heated (65 □C) probe. In the first two minutes after being touched with the noxiously-heated probe, bees groomed their touched antenna a) more than their untouched antenna, b) more than bees that were touched on the antenna with an unheated probe, and c) more than control (untouched) bees groomed either of their antennae. Our results clearly show that bumblebees can direct grooming towards a site of noxious stimulation. Our findings thus refute arguments that claim that insects do not feel pain because of their lack of displaying this behaviour.
Single dopaminergic neuron DAN-c1 inDrosophilalarval brain mediates aversive olfactory learning through D2-like receptors
Authors: Qi Cheng , Qian Cheng , Steijvers Emma , Colvin Robert A. , Lee Daewoo
Published: January 2024

The intricate relationship between the dopaminergic system and olfactory associative learning inDrosophilahas been an intense scientific inquiry. Leveraging the formidable genetic tools, we conducted a screening of 57 dopaminergic drivers, leading to the discovery of DAN-c1 driver, uniquely targeting the single dopaminergic neuron (DAN) in each brain hemisphere. While the involvement of excitatory D1-like receptors is well-established, the role of D2-like receptors (D2Rs) remains underexplored. Our investigation reveals the expression of D2Rs in both DANs and the mushroom body (MB) of third instar larval brains. Silencing D2Rs in DAN-c1 via microRNA disrupts aversive learning, further supported by optogenetic activation of DAN-c1 during training, affirming the inhibitory role of D2R autoreceptor. Intriguingly, D2R knockdown in the MB impairs both appetitive and aversive learning. These findings elucidate the distinct contributions of D2Rs in diverse brain structures, providing novel insights into the molecular mechanisms governing associative learning inDrosophilalarvae.
Neural Dynamics and Seizure Correlations: Insights from Neural Mass Models in a Tetanus Toxin Rat Model of Epilepsy
Authors: Zarei Eskikand Parvin , Soto-Breceda Artemio , Cook Mark J. , Burkitt Anthony N. , Grayden David B.
Published: January 2024

This study focuses on the use of a neural mass model to investigate potential relationships between functional connectivity and seizure frequency in epilepsy. We fitted a three-layer neural mass model of a cortical column to intracranial EEG (iEEG) data from a Tetanus Toxin rat model of epilepsy, which also included responses to periodic electrical stimulation. Our results show that some of the connectivity weights between different neural populations correlate significantly with the number of seizures each day, offering valuable insights into the dynamics of neural circuits during epileptogenesis. We also simulated single-pulse electrical stimulation of the neuronal populations to observe their responses after the connectivity weights were optimized to fit background (non-seizure) EEG data. The recovery time, defined as the time from stimulation until the membrane potential returns to baseline, was measured as a representation of the critical slowing down phenomenon observed in nonlinear systems operating near a bifurcation boundary. The results revealed that recovery times in the responses of the computational model fitted to the EEG data were longer during 5 min periods preceding seizures compared to 1 hr before seizures in four out of six rats. Analysis of the iEEG recorded in response to electrical stimulation revealed results similar to the computational model in four out of six rats. This study supports the potential use of this computational model as a model-based biomarker for seizure prediction when direct electrical stimulation to the brain is not feasible.
FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism
Authors: Tumenbayar Bat-Ider , Tutino Vincent M. , Brazzo Joseph A. , Yao Peng , Bae Yongho
Published: January 2024

Cellular metabolism is influenced by the stiffness of the extracellular matrix. Focal adhesion kinase (FAK) and its binding partner, p130Cas, transmit biomechanical signals about substrate stiffness to the cell to regulate a variety of cellular responses, but their roles in early transcriptional and metabolic responses remain largely unexplored. We cultured mouse embryonic fibroblasts with or without siRNA-mediated FAK or p130Cas knockdown and assessed the early transcriptional responses of these cells to placement on soft and stiff substrates by RNA sequencing and bioinformatics analyses. Exposure to the stiff ECM altered the expression of genes important for metabolic and biosynthetic processes, and these responses were influenced by knockdown of FAK and p130Cas. Our findings reveal that FAK-p130Cas signaling mechanotransduces ECM stiffness to early transcriptional changes that alter cellular metabolism and biosynthesis.
Adaptive thermogenesis is mediated by GDF15 via the GFRAL neuronal axis in mice
Authors: Kim Ji Eun , Ju Sang-Hyeon , Lee Min Hee , Hong Hyun Jung , Yaseen Uzma , Kim Jung Tae , Zhang Benyuan , Yi Hyon-Seung , Lee Seong Eun , Kang Yea Eun , Yi Yoon-Sun , Jun Sangmi , Park Minsung , Kim Jinkuk , Auwerx Johan , Sohn Jong-Woo , Lee Ju Hee , Shong Minho
Published: January 2024

Adaptive thermogenesis is a key homeostatic mechanism that primarily occurs in brown adipocytes and enables the maintenance of body temperature. Although this process involves coordinated responses in multiple tissues, including the browning of white adipocytes, the precise inter-organ crosstalk underlying adaptive thermogenesis is unclear. Here, we investigate the pivotal role of the GDNF family receptor alpha-like (GFRAL) neuronal axis in modulating compensatory thermogenic responses in brown and white adipose depots under stress conditions, specifically the mitochondrial unfolded protein response resulting from genetic modification and cold exposure. We employed a mouse model with targeted deletion ofCrif1in the mitoribosomes of brown adipocytes, and cold-exposed mice and immortalized adipocytes, to uncover the mechanism by which mitochondrial stress-induced growth differentiation factor 15 (GDF15) expression affects metabolism and facilitates adaptive thermogenesis. We found thatCrif1deletion resulted in browning of inguinal white adipose depots, increased energy expenditure, reduced food intake, and resistance to weight gain. Retrograde neuronal tracing established that GFRAL-positive neurons in the hindbrain and sympathetic preganglionic neurons in the spinal cord mediated the GDF15-associated browning of inguinal white adipose tissue. Intervention studies using antisense oligonucleotides to inhibitGfralexpression blunted the effect ofCrif1deletion on energy expenditure and food intake, further confirming the essential role the GFRAL axis plays in GDF15-driven thermogenic adaptation in white adipose tissue. Our findings suggest that the GFRAL neuronal axis is key in coordinating the adaptive thermogenic response across multiple tissues and adipose depots, thereby ensuring metabolic homeostasis during mitochondrial stress.
Proliferative History Is a Novel Driver of Clinical Outcome in Splenic Marginal Zone Lymphoma
Authors: Parker Helen , Mirandari Amatta , Oquendo Carolina Jaramillo , Duran-Ferrer Martí , Stevens Benjamin , Buermann Lara , Amarasinghe Harindra E. , Thomas Jaya , Kadalayil Latha , Carr Louise , Syeda Shama , Sakthipakan Methusha , Parry Marina , Davis Zadie , McIver-Brown Neil , Xochelli Aliki , Ennis Sarah , Scarfo Lydia , Ghia Paolo , Kalpadakis Christina , Pangalis Gerassimos , Rossi Davide , Wagner Simon , Ahearne Matthew , Seifert Marc , Plass Christoph , Weichenhan Dieter , Kimby Eva , Sutton Lesley-Ann , Rosenquist Richard , Forconi Francesco , Stamatopoulos Kostas , Salido Marta , Ferrer Ana , Thieblemont Catherine , Ljungström Viktor , Amini Rose-Marie , Oscier David , Walewska Renata , Rose-Zerilli Matthew J.J. , Gibson Jane , Martín-Subero José Ignacio , Oakes Christopher , Bryant Dean , Strefford Jonathan C
Published: January 2024

The epiCMIT (epigenetically-determined Cumulative MIToses) mitotic clock traces B-cell mitotic history via DNA methylation changes in heterochromatin and H3K27me3-containing chromatin. While high scores correlated with poor outcomes in CLL and MCL, its prognostic significance in SMZL remains unknown. Derived from 142 SMZL cases using DNA methylation microarrays, epiCMIT values were correlated with genomic, transcriptomic, and clinical data. EpiCMIT as a continuous variable was significantly higher in females (p=0.02), patients with IGHV1-2*04 allele usage (p<0001), intermediate IGHV somatic hypermutation load (97-99.9% identity,p=0.04), elevated mutational burden (25 vs. 17 mut/Mb,p=0.001), driver gene mutations [KLF2(p<0.001),NOTCH2(p<0.01),TP53(p=0.01),KMT2D(p<0.001)], and del(7q) (p=0.01). Negative correlation between epiCMIT and telomere length (r=-0.29p<0.001) supported the association between cumulated proliferation and telomere attrition. While univariate analysis highlighted epiCMIT as robust predictor of shorter treatment-free survival (TFS), multivariate analysis confirmed epiCMIT as an independent marker for shorter TFS. In summary, our matched multi-omic datasets facilitate the clinico-biological characterization of SMZL and introduces epiCMIT as a strong prognostic marker, identifying high-risk patients and predicting reduced treatment-free survival, hence providing a new tool for risk-adapted patient management.
Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit inPseudomonas aeruginosa
Authors: He Susu , Taher Noor M. , Hvorecny Kelli L. , Ragusa Michael J. , Bahl Christopher D. , Hickman Alison B. , Dyda Fred , Madden Dean R.
Published: January 2024

The opportunistic pathogenPseudomonas aeruginosainfects cystic fibrosis (CF) patient airways and produces a virulence factor Cif that is associated with worse outcomes. Cif is an epoxide hydrolase that reduces cell-surface abundance of the cystic fibrosis transmembrane conductance regulator (CFTR) and sabotages pro-resolving signals. Its expression is regulated by a divergently transcribed TetR family transcriptional repressor. CifR represents the first reported epoxide-sensing bacterial transcriptional regulator, but neither its interaction with cognate operator sequences nor the mechanism of activation has been investigated. Using biochemical and structural approaches, we uncovered the molecular mechanisms controlling this complex virulence operon. We present here the first molecular structures of CifR alone and in complex with operator DNA, resolved in a single crystal lattice. Significant conformational changes between these two structures suggest how CifR regulates the expression of the virulence genecif. Interactions between the N-terminal extension of CifR with the DNA minor groove of the operator play a significant role in the operator recognition of CifR. We also determined that cysteine residue Cys107 is critical for epoxide sensing and DNA release. These results offer new insights into the stereochemical regulation of an epoxide-based virulence circuit in a critically important clinical pathogen.
Nobiletin, a Polymethoxyflavonoid, Activates the Desuccinylase Activity of SIRT5 and Prevents the Development of Heart Failure
Authors: Sunagawa Yoichi , Funamoto Masafumi , Hamabe-Horiike Toshihide , Hieda Kehima , Yabuki Seiichiro , Tomino Midori , Ikai Yoshimi , Suzuki Anna , Ogawahara Shintaro , Yabuta Asami , Sasaki Hana , Ebe Ayaka , Naito Shiomi , Takai Hidemichi , Shimizu Kana , Shimizu Satoshi , Kawase Yuto , Naruta Ryuya , Katanasaka Yasufumi , Asakawa Tomohiro , Kan Toshiyuki , Mori Kiyoshi , Murakami Akira , Ogura Masahito , Inagaki Nobuya , Hasegawa Koji , Morimoto Tatsuya
Published: January 2024

Nobiletin is a natural compound useful for the prevention and treatment of several diseases. However, the precise role of nobiletin in heart failure is unclear. Nobiletin treatment prevents pressure overload- and myocardial infarction-induced heart failure. Using affinity purification of biotinylated nobiletin from rat heart cell lysates, we identified sirtuin 5 (SIRT5) as a novel nobiletin-binding protein. Nobiletin enhanced the desuccinylase activity of SIRT5in vitro. Compared to wild-type mice, SIRT5-overexpressing transgenic mice resisted pressure overload-induced systolic dysfunction. Conversely, SIRT5 knockout disrupted the nobiletin-mediated therapeutic effects on heart failure in mice. SIRT5 desuccinylated p300 at lysine 1568 and reduced the histone acetyltransferase (HAT) activity of p300. The desuccinylated p300 mutant suppressed the phenylephrine-induced cardiomyocyte hypertrophic responses. These findings suggest that nobiletin prevents heart failure development through SIRT5-dependent inhibition of p300-HAT activity. Nobiletin, a nontoxic dietary compound, is a potential therapeutic agent for heart failure in humans.
Community successional patterns and inter-kingdom interactions during granular biofilm development
Authors: de Celis Miguel , Modin Oskar , Arregui Lucía , Persson Frank , Santos Antonio , Belda Ignacio , Wilén Britt-Marie , Liébana Raquel
Published: January 2024

Aerobic granular sludge is a compact and efficient biofilm process used for wastewater treatment which has received much attention and is currently being implemented worldwide. The microbial associations and their ecological implications occurring during granule development, especially those involving inter-kingdom interactions, are poorly understood. In this work, we monitored the prokaryote and eukaryote community composition and structure during the granulation of activated sludge for 343 days in a sequencing batch reactor (SBR), and investigated the influence of abiotic and biotic factors on the granule development. Sludge granulation was accomplished with low-wash out dynamics at long settling times, allowing for the microbial communities to adapt to the SBR environmental conditions. The sludge granulation and associated changes in microbial community structure could be divided into three stages: floccular, intermediate, and granular. The eukaryotic and prokaryotic communities showed parallel successional dynamics, with three main sub-communities identified for each kingdom, dominating in each stage of sludge granulation. Although inter-kingdom interactions were shown to affect community succession during the whole experiment, during granule development random factors like the availability of settlement sites or drift acquired increasing importance. The prokaryotic community was more affected by deterministic factors, including reactor conditions, while the eukaryotic community was to a larger extent shaped by biotic interactions (including inter-kingdom interactions) and stochasticity.
Genome streamlining to improve performance of a fast-growing cyanobacteriumSynechococcus elongatusUTEX 2973
Authors: Sengupta Annesha , Bandyopadhyay Anindita , Sarkar Debolina , Hendry John I. , Schubert Max G. , Liu Deng , Church George M. , Maranas Costas D. , Pakrasi Himadri B.
Published: January 2024

Cyanobacteria are photosynthetic organisms that have garnered significant recognition as potential hosts for sustainable bioproduction. However, their complex regulatory networks pose significant challenges to major metabolic engineering efforts, thereby limiting their feasibility as production hosts. Genome streamlining has been demonstrated to be a successful approach for improving productivity and fitness in heterotrophs but is yet to be explored to its full potential in phototrophs. Here we present the systematic reduction of the genome of the cyanobacterium exhibiting the fastest exponential growth,Synechococcus elongatusUTEX 2973. This work, the first of its kind in a photoautotroph, involved an iterative process using state-of-the-art genome-editing technology guided by experimental analysis and computational tools. CRISPR/Cas3 enabled large, progressive deletions of predicted dispensable regions and aided in the identification of essential genes. The large deletions were combined to obtain a strain with 55 kb genome reduction. The strains with streamlined genome showed improvement in growth (up to 23%) and productivity (by 22.7%) as compared to the WT. This streamlining strategy not only has the potential to develop cyanobacterial strains with improved growth and productivity traits but can also facilitate a better understanding of their genome to phenome relationships.

Importance

Genome streamlining is an evolutionary strategy used by natural living systems to dispense unnecessary genes from their genome as a mechanism to adapt and evolve. While this strategy has been successfully borrowed to develop synthetic heterotrophic microbial systems with desired phenotype, it has not been extensively explored in photoautotrophs. Genome streamlining strategy incorporates both computational predictions to identify the dispensable regions and experimental validation using genome editing tool and in this study we have employed a modified strategy with the goal to minimize the genome size to an extent that allows optimal cellular fitness under specified conditions. Our strategy has explored a novel genome-editing tool in photoautotrophs which, unlike other existing tools, enables large, spontaneous optimal deletions from the genome. Our findings demonstrate the effectiveness of this modified strategy in obtaining strains with streamlined genome, exhibiting improved fitness and productivity.
Monocytic fibrocyte-like cell enrichment and myofibroblastic adaptation causes nucleus pulposus fibrosis and associates with disc degeneration severity
Authors: Sun Yi , Peng Yan , Su Zezhuo , So Kyle KH , Lu Qiu-ji , Lyu Mao-jiang , Zuo Jianwei , Huang Yong-can , Guan Zhi-ping , Cheung Kenneth MC , Zheng Zhao-min , Zhang Xin-tao , Leung Victor YL
Published: January 2024

Fibrotic remodeling of nucleus pulposus (NP) leads to structural and mechanical anomalies of intervertebral discs that prone to degeneration, leading to low back pain incidence and disability. Emergence of fibroblastic cells in disc degeneration has been reported, yet their nature and origin remain elusive. In this study, we performed an integrative analysis of multiple single-cell RNA sequencing datasets to interrogate the cellular heterogeneity and fibroblast-like entities in degenerative human NP specimens. We found that disc degeneration severity is associated with an enrichment of fibrocyte-like phenotype, characterized by CD45 and collagen I dual positivity, and expression of myofibroblast marker α-smooth muscle actin. Refined clustering and classification distinguished the fibrocyte-like populations as subtypes in the NP cells - and immunocytes-clusters, expressing disc degeneration markersHTRA1andANGPTL4and genes related to response to TGF-β. In injury-induced mouse disc degeneration model, fibrocyte-like cells were found recruited into the NP undergoing fibrosis and adopted a myofibroblast phenotype. Depleting the fibrocyte-like cells in CD11b-DTR mice in which monocytic lineages were ablated by diphtheria toxin could markedly attenuate fibrous modeling and myofibroblast formation in the NP of the degenerative discs, and prevent disc height loss and histomorphological abnormalities. Marker analysis supports that disc degeneration progression is dependent on a function of CD45+COL1A1+and αSMA+cells. Our findings reveal that fibrocyte-like cells play a pivotal role in NP fibrosis and may therefore be a target for modifying disc degeneration and promoting its repair.
General mechanisms of task engagement in the primate frontal cortex
Authors: Grohn Jan , Khalighinejad Nima , Jahn Caroline , Bongioanni Alessandro , Schuffelgen Urs , Sallet Jerome , Rushworth Matthew , Kolling Nils
Published: January 2024

Staying engaged with a task is necessary to maintain goal-directed behaviors. Although engagement varies with the specific task at hand it also exhibits continuous, intrinsic fluctuations widely. This intrinsic component of engagement is difficult to isolate behaviorally or neurally in controlled experiments with humans. By contrast, animals spontaneously move between periods of complete task engagement and disengagement, even in experimental settings. We, therefore, looked at behavior in macaques in a series of four tasks while recording fMRI signals. We identified consistent autocorrelation in task disengagement. This made it possible to build models capturing task-independent engagement and to link it to neural activity. Across all tasks, we identified common patterns of neural activity linked to impending task disengagement in mid-cingulate gyrus. By contrast, activity centered in perigenual anterior cingulate cortex (pgACC) was associated with maintenance of task performance. Importantly, we were able to carefully control for task-specific factors such as the reward history, choice value, and other motivational effects, such as response vigor, as indexed by response time, when identifying neural activity associated with task engagement. Moreover, we showed pgACC activity had a causal link to task engagement; in one of our tasks, transcranial ultrasound stimulation of pgACC, but not of control regions, changed task engagement/disengagement patterns.
Control of iron acquisition by multiple small RNAs unravels a new role for transcriptional terminator loops in gene regulation
Authors: Flores Eugenio Solchaga , Jagodnik Jonathan , Quenette Fanny , Korepanov Alexey , Guillier Maude
Published: January 2024

Small RNAs (sRNAs) controlling gene expression by imperfect base-pairing with mRNA(s) are widespread in bacteria and regulate multiple genes, including genes involved in iron homeostasis, through a wide variety of mechanisms. We previously showed that OmrA and OmrB sRNAs repress the synthesis of theEscherichia coliFepA receptor for iron-enterobactin complexes. We now report that five additional sRNAs, namely RprA, RybB, ArrS, RseX and SdsR, that respond to different environmental cues, also repressfepA,independently of one another. While RprA follows the canonical mechanism of pairing with the translation initiation region, repression by ArrS or RseX requires a secondary structure far upstream within the longfepA5’UTR. We also demonstrate a dual action of SdsR, whose 5’ end pairs with thefepAtranslation initiation region while its 3’ end behaves like ArrS or RseX. Strikingly, mutation analysis shows a key role for the loops of these sRNAs intrinsic terminators in the regulation. Regulation furthermore depends on both the Hfq chaperone and the RNase E endonuclease. Overall, our data strongly suggest that FepA levels must be tightly controlled under a variety of conditions, and highlight the diversity of mechanisms that underly the regulation of gene expression by sRNAs in bacteria.
Assessing the relationship between neural entrainment and altered states of consciousness induced by electronic music
Authors: Aparicio-Terrés Raquel , López-Mochales Samantha , Díaz-Andreu Margarita , Escera Carles
Published: January 2024

In electronic music events, the driving four-on-the-floor music appears pivotal for inducing altered states of consciousness (ASCs). While various physiological mechanisms link repetitive auditory stimuli to ASCs, entrainment—a brainwave synchronization through periodic external stimuli— has garnered primary focus. However, there are no studies systematically exploring the relationship between entrainment and ASCs. In the present study, we depart from the finding that entrainment to auditory stimuli peaks for stimulation rates around 2 Hz compared to others. Twenty participants listened to six one-minute electronic music excerpts at different tempos (1.65 Hz, 2.25 Hz, and 2.85 Hz). For each excerpt, they performed cognitive tasks and reported phenomenological experiences related to ASCs through questionnaires. Brain activity was recorded with electroencephalography to assess whether a modulation in entrainment by the beat of electronic music affected objective and subjective proxies of ASCs. Our results revealed a tempo-driven entrainment modulation, peaking at 1.65 Hz. Similarly, participants’ experience of unity during listening to the music was higher for the excerpts at 1.65 Hz, yet no relationship with entrainment was found. Critically, a correlation was found between entrainment and participants’ reaction time. Further studies are granted to explore how individual traits, such as musical training, modulate the relationship.
An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries
Authors: Petersen Brian M. , Kirby Monica B. , Chrispens Karson M. , Irvin Olivia M. , Strawn Isabell K. , Haas Cyrus M. , Walker Alexis M. , Baumer Zachary T. , Ulmer Sophia A. , Ayala Edgardo , Rhodes Emily R. , Guthmiller Jenna J. , Steiner Paul J. , Whitehead Timothy A.
Published: January 2024

Antibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable thein silicodesign of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition. In part, this is because limited experimental platforms exist for assessing quantitative and simultaneous sequence-function relationships for multiple antibodies. Here we present MAGMA-seq, an integrated technology that combinesmultipleantigens andmultipleantibodies and determines quantitative biophysical parameters using deepsequencing. We demonstrate MAGMA-seq on two pooled libraries comprising mutants of ten different human antibodies spanning light chain gene usage, CDR H3 length, and antigenic targets. We demonstrate the comprehensive mapping of potential antibody development pathways, sequence-binding relationships for multiple antibodies simultaneously, and identification of paratope sequence determinants for binding recognition for broadly neutralizing antibodies (bnAbs). MAGMA-seq enables rapid and scalable antibody engineering of multiple lead candidates because it can measure binding for mutants of many given parental antibodies in a single experiment.
Prediction error determines how memories are organized in the brain: a study of Pavlovian fear extinction in rats
Authors: Kennedy Nicholas G. W. , Lee Jessica C. , Killcross Simon , Westbrook Fred , Holmes Nathan M.
Published: January 2024

How is new information organized in memory? According to latent state theories, this is determined by the level of surprise, or prediction error, generated by the new information: small prediction error leads to updating of existing memory, large prediction error leads to encoding of a new memory. We tested this idea using a protocol in which rats were first conditioned to fear a stimulus paired with shock. The stimulus was then gradually extinguished by progressively reducing the shock intensity until the stimulus was presented alone. Consistent with latent state theories, this gradual extinction protocol (small prediction errors) was better than standard extinction (large prediction errors) in producing long-term suppression of fear responses; and the benefit of gradual extinction was due to updating of the conditioning memory with information about extinction. Thus, prediction error determines how new information is organized in memory, and latent state theories adequately describe the ways in which this occurs.
Macrophage-induced reduction of bacteriophage density limits the efficacy ofin vivopulmonary phage therapy
Authors: Zborowsky Sophia , Seurat Jérémy , Balacheff Quentin , Ecomard Solène , Minh Chau Nguyen Ngoc , Titécat Marie , Evrard Emma , Rodriguez-Gonzalez Rogelio A. , Marchi Jacopo , Weitz Joshua S. , Debarbieux Laurent
Published: January 2024

The rise of antimicrobial resistance has led to renewed interest in evaluating phage therapy. In murine models highly effective treatment of acute pneumonia caused byPseudomonas aeruginosarelies on the synergistic antibacterial activity of bacteriophages with neutrophils. Here, we show that depletion of alveolar macrophages (AM) shortens the survival of mice without boosting theP. aeruginosaload in the lungs. Unexpectedly, upon bacteriophage treatment, pulmonary levels ofP. aeruginosawere significantly lower in AM-depleted than in immunocompetent mice. To explore potential mechanisms underlying the benefit of AM-depletion in treated mice, we developed a mathematical model of phage, bacteria, and innate immune system dynamics. Simulations from the model fitted to data suggest that AM reduce bacteriophage density in the lungs. We experimentally confirmed that thein vivodecay of bacteriophage is faster in immunocompetent compared to AM-depleted animals. These findings demonstrate the involvement of feedback between bacteriophage, bacteria, and the immune system in shaping the outcomes of phage therapy in clinical settings.
Scaling and merging macromolecular diffuse scattering withmdx2
Authors: Meisburgera Steve P. , Andob Nozomi
Published: January 2024

Diffuse scattering is a promising method to gain additional insight into protein dynamics from macro-molecular crystallography (MX) experiments. Bragg intensities yield the average electron density, while the diffuse scattering can be processed to obtain a three-dimensional reciprocal space map, that is further analyzed to determine correlated motion. To make diffuse scattering techniques more accessible, we have created software for data processing calledmdx2that is both convenient to use and simple to extend and modify.Mdx2is written in Python, and it interfaces withDIALSto implement self-contained data reduction workflows. Data are stored in NeXusformat for software interchange and convenient visualization.Mdx2can be run on the command line or imported as a package, for instance to encapsulate a complete workflow in a Jupyter notebook for reproducible computing and education. Here, we describemdx2version 1.0, a new release incorporating state-of-the-art techniques for data reduction. We describe the implementation of a complete multi-crystal scaling and merging workflow, and test the methods using a high-redundancy dataset from cubic insulin. We show that redundancy can be leveraged during scaling to correct systematic errors, and obtain accurate and reproducible measurements of weak diffuse signals.

Synopsis

Mdx2is a Python toolkit for processing diffuse scattering data from macromolecular crystals. We describe multi-crystal scaling and merging procedures implemented in the latest version ofmdx2. A high-redundancy dataset from cubic insulin is processed to reveal weak scattering features.
Forced mouth opening induces post-traumatic hyperalgesia and associated peripheral sensitization after temporomandibular joints injury in mice
Authors: Alshanqiti Ishraq , Son Hyeonwi , Shannonhouse John , Hu Jiaxin , Kumari Sinu , Parastooei Ghazaal , Wang Sheng , Ro Jin Y. , Kim Yu Shin , Chung Man-Kyo
Published: January 2024

Temporomandibular disorder (TMD) is the most prevalent painful condition in the craniofacial area. The pathophysiology of TMD is not fully understood, and it is necessary to understand pathophysiology underlying painful TMD conditions to develop more effective treatment methods. Recent studies suggested that external or intrinsic trauma to TMJ is associated with chronic TMD in patients. Here, we investigated the effects of the TMJ trauma through forced-mouth opening (FMO) in mice to determine pain behaviors and peripheral sensitization of trigeminal nociceptors. FMO increased mechanical hyperalgesia assessed by von Frey test, spontaneous pain-like behaviors assessed by mouse grimace scale, and anxiety-like behaviors assessed by open-field test. In vivo GCaMP Ca2+imaging of intact trigeminal ganglia (TG) showed increased spontaneous Ca2+activity and mechanical hypersensitivity of TG neurons in the FMO compared to the sham group. Ca2+responses evoked by cold, heat, and capsaicin stimuli were also increased. FMO-induced hyperalgesia and neuronal hyperactivities were not sex dependent. TG neurons sensitized following FMO were primarily small to medium-sized nociceptive afferents. Consistently, most TMJ afferents in the TG were small-sized peptidergic neurons expressing calcitonin gene-related peptides, whereas nonpeptidergic TMJ afferents were relatively low. FMO-induced intraneural inflammation in the surrounding tissues of the TMJ indicates potentially novel mechanisms of peripheral sensitization following TMJ injury. These results suggest that the TMJ injury leads to persistent post-traumatic hyperalgesia associated with peripheral sensitization of trigeminal nociceptors.
Mitochondria-containing extracellular vesicles from mousevs. human brain endothelial cells for ischemic stroke therapy
Authors: Dave Kandarp M. , Venna Venugopal R. , Rao Krithika S. , Stolz Donna B. , Brady Bodhi , Quaicoe Victoria A. , Maniskas Michael E. , Hildebrand Ella E. , Green Dawson , Chen Mingxi , Milosevic Jadranka , Zheng Si-yang , Shiva Sruti S. , McCullough Louise D. , Manickam Devika S
Published: January 2024

Ischemic stroke-induced mitochondrial dysfunction in the blood-brain barrier-forming brain endothelial cells (BECs) results in long-term neurological dysfunction post-stroke. We previously data from a pilot study whereintravenousadministration of human BEC (hBEC)-derived mitochondria-containing extracellular vesicles (EVs) showed a potential efficacy signal in a mouse middle cerebral artery occlusion (MCAo) model of stroke. Wehypothesizedthat EVs harvested from donor species homologous to the recipient species (e.g.,mouse) may improve therapeutic efficacy, and therefore, use of mouse BEC (mBEC)-derived EVs may improve post-stroke outcomes in MCAo mice.

We investigated potential differences in the mitochondria transfer of EVs derived from the same species as the recipient cell (mBEC-EVs and recipient mBECs or hBECs-EVs and recipient hBECs)vs. cross-species EVs and recipient cells (mBEC-EVs and recipient hBECs orvice versa). Our results showed that while both hBEC- and mBEC-EVs transferred EV mitochondria, mBEC-EVs outperformed hBEC-EVs in increasing ATP levels and improved recipient mBEC mitochondrial function via increasing oxygen consumption rates. mBEC-EVs significantly reduced brain infarct volume and neurological deficit scores compared to vehicle-injected MCAo mice. The superior therapeutic efficacy of mBEC-EVs in a mouse MCAo stroke support the continued use of mBEC-EVs to optimize the therapeutic potential of mitochondria-containing EVs in preclinical mouse models.

Graphical Abstract
Structural basis of respiratory complexes adaptation to cold temperatures
Authors: Shin Young-Cheul , Latorre-Muro Pedro , Djurabekova Amina , Zdorevskyi Oleksii , Bennett Christopher F. , Burger Nils , Song Kangkang , Xu Chen , Sharma Vivek , Liao Maofu , Puigserver Pere
Published: January 2024

In response to cold, mammals activate brown fat for respiratory-dependent thermogenesis reliant on the electron transport chain (1, 2). Yet, the structural basis of respiratory complex adaptation to cold remains elusive. Herein we combined thermoregulatory physiology and cryo-EM to study endogenous respiratory supercomplexes exposed to different temperatures. A cold-induced conformation of CI:III2(termed type 2) was identified with a ∼25° rotation of CIII2around its inter-dimer axis, shortening inter-complex Q exchange space, and exhibiting different catalytic states which favor electron transfer. Large-scale supercomplex simulations in lipid membrane reveal how unique lipid-protein arrangements stabilize type 2 complexes to enhance catalytic activity. Together, our cryo-EM studies, multiscale simulations and biochemical analyses unveil the mechanisms and dynamics of respiratory adaptation at the structural and energetic level.
Elucidation of neuronal activity in mouse models of TMJ injury byin vivoGCaMP Ca2+imaging of intact trigeminal ganglion neurons
Authors: Son Hyeonwi , Shannonhouse John , Zhang Yan , Gomez Ruben , Chung Man-Kyo , Kim Yu Shin
Published: January 2024

Patients with temporomandibular disorders (TMD) typically experience facial pain and discomfort or tenderness in the temporomandibular joint (TMJ), causing disability in daily life. Unfortunately, existing treatments for TMD are not always effective, creating a need for more advanced, mechanism-based therapies. In this study, we usedin vivoGCaMP3 Ca2+imaging of intact trigeminal ganglia (TG) to characterize functional activity of the TG neuronsin vivo, specifically in TMJ animal models. This system allows us to observe neuronal activity in intact anatomical, physiological, and clinical conditions and to assess neuronal function and response to various stimuli. We observed a significant increase in spontaneously and transiently activated neurons responding to mechanical, thermal, and chemical stimuli in the TG of forced mouth open (FMO) mice. An inhibitor of the CGRP receptor significantly attenuated FMO-induced facial hypersensitivity. In addition, we confirmed the attenuating effect of CGRP antagonist on FMO-induced sensitization byin vivoGCaMP3 Ca2+imaging of intact TG. Our results contribute to unraveling the role and activity of TG neurons in the TMJ pain animal models of TMD, bringing us closer understanding the pathophysiological processes underlying TMD. Our study also illustrates the utility ofin vivoGCaMP3 Ca2+imaging of intact TG for studies aimed at developing more targeted and effective treatments for TMD.
Testosterone-Induced Metabolic Changes in Seminal Vesicle Epithelial cells Alter Plasma Components to Enhance Sperm Motility
Authors: Yamanaka Takahiro , Xiao Zimo , Tsujita Natsumi , Awad Mahmoud , Umehara Takashi , Shimada Masayuki
Published: January 2024

Male factors account for almost half of the causes of infertility. In rodents and humans, most of the components of semen are supplied by the seminal vesicles, and they support male reproductive ability, but there are many unknown details. In this study, the metabolic changes in the seminal vesicle epithelial cells were focused on, and the mechanisms by which testosterone affected the seminal plasma composition were investigated. A factor improving the linear motility of sperm was secreted from the seminal vesicles, and it was produced in an androgen-dependent manner. Bioassays, gene expression, and flux analysis studies demonstrated that testosterone promotes glucose uptake in seminal vesicle epithelial cells via GLUT4, resulting in fatty acid synthesis. ACLY was a critical factor in this metabolic change, which produced fatty acid, especially oleic acid. In conclusion, the critical role of testosterone-induced metabolic changes in the seminal vesicles is to ensure the synthesis of fatty acid. These findings provide new understanding the male fertility mechanisms and may perspective for the development of potential biomarkers of male fertility and advance in the treatment of male infertility.
Stimulation of NCAM1-14.3.3.ζδ-derived Peptide Interaction Fuels Angiogenesis and Osteogenesis in Ageing
Authors: Yesin Taha Kadir , Liu Hanyu , Ding Zhangfan , Singh Amit , Tian Qi , Zhang Yuheng , Borah Biswajyoti , Chen Junyu , Kusumbe Anjali P.
Published: January 2024

The skeletal structure and bone marrow endothelium collectively form a critical functional unit essential for bone development, health, and aging. At the core of osteogenesis and bone formation lies the dynamic process of angiogenesis. In this study, we reveal a potent new endogenous anabolic NCAM1-14.3.3.ζδ-derived-Peptide interaction, which stimulates bone angiogenesis and osteogenesis during homeostasis, aging, and age-related bone diseases. Employing high-resolution imaging and inducible cell-specific mouse genetics, our results elucidate the pivotal role of the NCAM1-14.3.3.ζδ-derived-Peptide interaction in driving the expansion of Clec14a+ angiogenic endothelial cells. Notably, Clec14a+ endothelial cells express key osteogenic factors. The NCAM1-14.3.3.ζδ-derived-Peptide interaction in osteoblasts drives osteoblast differentiation, ultimately contributing to the genesis of new bone. Moreover, the NCAM1-14.3.3.ζδ-derived-Peptide interaction leads to a reduction in bone resorption. In age-associated vascular and bone loss diseases, stimulating the NCAM1-14.3.3.ζδ-derived-Peptide interaction not only promotes angiogenesis but also reverses bone loss. Consequently, harnessing the endogenous anabolic potential of the NCAM1-14.3.3.ζδ-derived-Peptide interaction emerges as a promising therapeutic modality for managing age-related bone diseases.
SAM-DNMT3A, a strategy for induction of genome-wide DNA methylation, identifies DNA methylation as a vulnerability in ER-positive breast cancers
Authors: Hosseinpour Mahnaz , Malaver-Ortega Luis , Perlaza-Jimenez Laura , Joo Jihoon E. , Liu Ling , Caldon Elizabeth C. , Dugué Pierre-Antoine , Dowty James G. , Southey Melissa C. , Rosenbluh Joseph
Published: January 2024

DNA methylation is an epigenetic mark that plays a critical role in regulation of gene expression. DNA methylase (DNMT) inhibitors, inhibit global DNA methylation, and have been a key tool in studies of DNA methylation in healthy or disease conditions. A major bottleneck is the lack of tools to induce global DNA methylation. Here, we engineered a CRISPR based approach, that was initially designed, to enable site specific DNA methylation. Using the synergistic activation mediator (SAM) system, we unexpectedly found that regardless of the targeted sequence any sgRNA induced global genome-wide DNA methylation. We termed this new method SAM-DNMT3A and show that induction of global DNA methylation is a unique vulnerability in ER-positive breast cancer suggesting a therapeutic approach. Our findings highlight the need of caution when using CRISPR based approaches for inducing DNA methylation and demonstrate a new method for global induction of DNA methylation.
WITHDRAWN: Development and external validation of a practical diagnostic support tool, ‘ABC 2-Screener’, to predict sarcopenia among patients on maintenance haemodialysis: A multicentre cross-sectional study
Authors: Matsunami Masatoshi , Aita Tetsuro , Kamitani Tsukasa , Munakata Yu , Kawaji Atsuro , Kuji Hiroshi , Suzuki Tomo , Kurita Noriaki
Published: January 2024

Withdrawal Statement

The authors have withdrawn their manuscript owing to uncorrectable data errors which were discovered after posting. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Key role of vimentin in the organization of the primary cilium
Authors: Lalioti Vasiliki , Moneo-Corcuera Diego , Pérez-Sala Dolores
Published: January 2024

We previously reported the presence of the intermediate filament vimentin at the primary cilium of lung cancer epithelial cells. In this study we further demonstrate that vimentin is intimately intertwined with acetylated tubulin at this structure. Interestingly, although vimentin can be detected along the whole length of the primary cilium, phospho-serine 56 vimentin is found particularly enriched at its basal region in A549 lung cancer cells. Vimentin appears to play a pivotal role in ciliogenesis, since its depletion in MEF or in A549 cells results in a lower proportion of cells displaying primary cilia and recognizable basal bodies. Furthermore, the detectable cilia in vimentin depleted cells are shorter. In addition, the centriolar structure appears disrupted in vimentin deficient cells, as indicated by an abnormal distribution of γ- and acetylated tubulin. Moreover, these cells display a defective organization of the pericentriolar material, characterized by a marked decrease in the levels of pericentrin and a diffuse distribution of Rab11. Taken together, our results show that vimentin is present at the primary cilium and suggest that it plays an important role in cilium structure and biogenesis, since its depletion leads to marked morphological defects and altered organization of key elements of this structure.