bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing the distinct contributions of rostral and dorsomedial prefrontal cortex to cognitive control using temporal interference brain stimulation
Authors: Ryan Johnathan S. , Botzanowski Boris , Karkare Maya , Kubert Jessica R. , Liu Shiyin , Betters Samantha A. , Williamson Adam , Fani Negar , Treadway Michael T.
Published: June 2024

The medial prefrontal cortex has been strongly implicated in a diverse array of cognitive functions in humans, including cognitive control and emotion regulation. Numerous studies have further proposed distinct functions for dorsomedial and rostromedial areas, but direct evidence from neuromodulation studies in healthy humans has been lacking due to the limitations of commonly used non-invasive neuromodulation techniques. Temporal interference (TI) stimulation is a recently developed technique for non-invasive deep brain stimulation that utilizes the frequency difference Δƒ between pairs of high frequency electric fields to stimulate brain regions at depth and with improved precision compared to traditional techniques. Despite its theoretical potential, however, TI applications in humans have remained limited. Here, we examined the effects of TI stimulation to dorsomedial prefrontal cortex (dmPFC) and rostromedial prefrontal cortex (rmPFC) on cognitive control. Healthy adult participants (n = 32) were recruited and administered 20 Hz Δƒ TI stimulation and 0 Hz Δƒ sham stimulation in interleaved blocks while completing two variants of the Stroop Task, a well-established paradigm intended to measure cognitive control: the Color-Word and Affective Number Stroop. During the Color-Word Stroop, we found that 20 Hz Δƒ TI stimulation of dmPFC and rmPFC relative to sham stimulation slowed down reaction times, with a significantly more pronounced slowing effect specific to incongruent trials for dmPFC stimulation as well as reduced accuracy. Importantly, effects of TI on dmPFC targets localized with fMRI differed markedly from dmPFC targeting based on a generic model, highlighting the importance of individualized targeting. For the Affective Stroop, we found that stimulation of dmPFC relative to sham stimulation facilitated increased reaction times in a valence specific-manner. This research provides novel evidence for distinct effects of neuromodulation in sub-regions of medial prefrontal cortex in healthy humans and sheds light on the strengths of TI as a non-invasive stimulation method for human cognitive neuroscience.
Multiple allostery in the regulation of PDGFR beta kinase activities
Authors: Zhang Yanfeng , Wang Meimei , Shao Guangcan , Shang Qingbin , Dong Mengqiu , Qin Xiaohong , Mi Li-Zhi
Published: June 2024

Platelet-derived growth factor receptor beta (PDGFRβ), a type III receptor tyrosine kinase (RTK) with a featured kinase insert, regulates important cellular functions. Dysregulation of PDGFRβ is associated with cardiovascular and fibrosis diseases. Thus, its kinase activity needs to be precisely regulated under physiological conditions. Early studies demonstrated that its kinase was autoinhibited by its juxtamembrane segment and activated by transphosphorylation. However, additional mechanisms are required for the comprehensive regulation of the receptor kinase. Herein, we provide evidences that dimerization of activated kinases, autoinhibition by the kinase insert, and dimerization of inactive kinase, all contribute to the regulation of the receptor kinase. Moreover, we find such multiple allosteric regulation is also conserved in other type III RTKs, including colony stimulating factor 1 receptor (CSF1R). Impairing the allosteric regulation of CSF1R is associated with malfunctions of microglia and demyelination of neurons in Hereditary Diffuse Leukoencephalopathy with Spheroids (HDLS).
Mechanism of an Intrinsic Oscillation in Rat Geniculate Interneurons
Authors: Griffith Erica Y. , ElSayed Mohamed , Dura-Bernal Salvador , Neymotin Samuel A. , Uhlrich Daniel J. , Lytton William W. , Zhu J. Julius
Published: June 2024

Depolarizing current injections produced a rhythmic bursting of action potentials – a bursting oscillation – in a set of local interneurons in the lateral geniculate nucleus (LGN) of rats. The current dynamics underlying this firing pattern have not been determined, though this cell type constitutes an important cellular component of thalamocortical circuitry, and contributes to both pathologic and non-pathologic brain states. We thus investigated the source of the bursting oscillation using pharmacological manipulations in LGN slicesin vitroandin silico.1. Selective blockade of calcium channel subtypes revealed that high-threshold calcium currents ILand IPcontributed strongly to the oscillation.2. Increased extracellular K+concentration (decreased K+currents) eliminated the oscillation.3. Selective blockade of K+channel subtypes demonstrated that the calcium-sensitive potassium current (IAHP) was of primary importance. A morphologically simplified, multicompartment model of the thalamic interneuron characterized the oscillation as follows:1. The low-threshold calcium current (IT) provided the strong initial burst characteristic of the oscillation.2. Alternating fluxes through high-threshold calcium channels andIAHPthen provided the continuing oscillation’s burst and interburst periods respectively. This interplay between ILand IAHPcontrasts with the current dynamics underlying oscillations in thalamocortical and reticularis neurons, which primarily involve ITand IH, or ITand IAHPrespectively. These findings thus point to a novel electrophysiological mechanism for generating intrinsic oscillations in a major thalamic cell type. Because local interneurons can sculpt the behavior of thalamocortical circuits, these results suggest new targets for the manipulation of ascending thalamocortical network activity.
Glycolytic Disruption Triggers Interorgan Signaling to Nonautonomously RestrictDrosophilaLarval Growth
Authors: Rai Madhulika , Li Hongde , Policastro Robert A. , Zentner Gabriel E. , Nemkov Travis , D’Alessandro Angelo , Tennessen Jason M.
Published: June 2024

Drosophilalarval growth requires efficient conversion of dietary nutrients into biomass. Lactate Dehydrogenase (Ldh) and Glycerol-3-phosphate dehydrogenase (Gpdh1) support larval biosynthetic metabolism by maintaining NAD+/NADH redox balance and promoting glycolytic flux. Consistent with the cooperative functions of Ldh and Gpdh1, the loss of both enzymes, but neither single enzyme, induces a developmental arrest. However, Ldh and Gpdh1 exhibit complex and often mutually exclusive expression patterns, suggesting that theGpdh1; Ldhdouble mutant lethal phenotype could be mediated nonautonomously. Here we find that the developmental arrest displayed by the double mutants extends beyond simple metabolic disruption and instead stems, in part, from changes in systemic growth factor signaling. Specifically, we demonstrate that this synthetic lethality is linked to the upregulation of Upd3, a cytokine involved in the Jak/Stat signaling pathway. Moreover, we demonstrate that either loss of the Upd3 or dietary administration of the steroid hormone 20-hydroxyecdysone (20E) rescue the synthetic lethal phenotype ofGpdh1; Ldhdouble mutants. Together, these findings demonstrate that metabolic disruptions within a single tissue can nonautonomously modulate interorgan signaling to ensure synchronous developmental growth.

SUMMARY STATEMENT

We used the fruit flyDrosophila melanogasterto demonstrate that disruption of glycolysis within a single larval tissue alters systemic cytokine signaling and nonautonomously inhibits development of the entire animal.
Competitor-induced plasticity modifies the interactions and predicted competitive outcomes between annual plants
Authors: Gibbs Theo L. , Levine Jonathan M. , Turcotte Martin M.
Published: June 2024

Species can modify their traits in response to changes in the environment – a process known as phenotypic plasticity. Because species traits can plastically respond to competition, the competitive effect of one individual on another involves not only reductions in performance, but also changes in morphology, behavior, phenology or physiology that affect interactions with other individuals. In this context, plasticity is often argued to favor species coexistence by increasing the niche differentiation between species, though experimental support that explicitly considers competitive outcomes is largely lacking. Here, we transiently subjected four annual plant species to early-season intraspecific or interspecific competition to explicitly induce plastic responses, and then examined the response of these individuals to other competitors. By measuring the interactions between the species with and without early-season competitors, we isolated the impact of plasticity on species interactions and coexistence. Growing with nearby competitors early in life impacted plant traits including height and morphology. These plastic responses tended to amplify the sensitivity of individuals to competition, and particularly so for interspecific competition. This increase in inter-relative to intraspecific competition caused plasticity to decrease the predicted likelihood of pairwise coexistence. By combining recent theory with a new experimental approach, we provide a pathway towards integrating phenotypic plasticity into our quantitative understanding of coexistence.
Precise Instruction and Consideration of the VerticalandHorizontal Force Component Increase Validity and Reliability of the 90:20 Isometric Posterior Chain Test
Authors: Rasp Dominic M. , Paternoster Florian K. , Kern Jan , Schwirtz Ansgar
Published: June 2024

Hamstring injuries are associated with decreased hamstring strength. Matinlauri et al.’s 90:20 Isometric Posterior Chain Test (90:20 IPCT) efficiently assesses hamstring strength, but has not been validated so far. Furthermore, their rather unprecise original instruction allows high variability in test execution. We added a new instruction and parameters and examined, whether this measure leads to increased reliability and validity.

We assessed hamstring strength of 23 sport students via the 90:20 IPCT under the original instruction, to exert vertical force, and our new instruction, to exert verticalandhorizontal force. Instead of only using bare vertical force as outcome parameter under the original (Fz_V) and our new instruction (Fz_VH), we also calculated the resultant force (Fres_VH) and the applied torque onto the force place (M_F_ortho_VH). To test for validity, we correlated the outcome parameters with peak torque of gold standard dynamometry. Furthermore, we measured muscle activities of the mm. rectus femoris, biceps femoris, semitendinosus, and gluteus maximus under our new instruction and compared them to those under the original parameter (Fz_V) via one sample t-tests. To evaluate reliability, tests were repeated on two separate days, for which we calculated intra class correlation coefficients (ICCs) and coefficients of variation (CVs).

Our new instruction and parameters (Fz_VH, Fres_VH, M_F_ortho_VH) showed better validity (mean r = 0.77, r = 0.81, and r = 0.85) and equally good or better reliability (ICCs: 0.87, 0.89, and 0.94; CVs: 4.7 %, 4.1 %, and 4.7 %) than the original instruction and parameter (Fz_V) (mean r = 0.70; ICC: 0.91; CV: 5.6 %). There were no differences in muscle activities between the parameters and instructions of the 90:20 IPCT.

We recommend our new instruction and the applied torque onto the force plate as it makes the 90:20 IPCT a more reliable and valid tool to assess hamstring strength.
Global Progress in Competitive Co-Evolution: a Systematic Comparison of Alternative Methods
Authors: Nolfi Stefano , Pagliuca Paolo
Published: June 2024

We investigate the use of competitive co-evolution for synthesizing progressively better solutions. Specifically, we introduce a set of methods to measure historical and global progress. We discuss the factors that facilitate genuine progress. Finally, we compare the efficacy of four qualitatively different algorithms. The selected algorithms promote genuine progress by creating an archive of opponents used to evaluate evolving individuals, generating archives that include high-performing and well-differentiated opponents, identifying and discarding variations that lead to local progress only (i.e. progress against a subset of possible opponents and retrogressing against a larger set). The results obtained in a predator-prey scenario, commonly used to study competitive evolution, demonstrate that all the considered methods lead to global progress in the long term. However, the rate of progress and the ratio of progress versus retrogressions vary significantly among algorithms.
Comparative photosynthetic capacity, respiration rates, and nutrient content of micropropagated and wild-sourcedSphagnum
Authors: Keightley Anna T. , Field Chris D. , Rowson James G. , Caporn Simon J.M.
Published: June 2024

Rapid, effective restoration of degraded peatlands is urgently needed to reduce their current high levels of carbon loss. Re-introduction ofSphagnummoss, along with re-wetting, is key to returning carbon sequestration and retention capabilities to northern degraded bogs. Micropropagated (BeadaMoss®)Sphagnumhas already been applied in large quantities, and more is planned, for restoration projects in Britain and parts of Europe. Comparison with wild-sourcedSphagnummaterial is therefore pertinent to demonstrate its safety and suitability for wide-scale application. SixSphagnumspecies of micropropagated and wild-sourced origin were studied:S. capillifolium,S. fallax,S. palustre,S. papillosum,S. medium/divinumandS. squarrosum. MicropropagatedSphagnumhad significantly higher light-saturated photosynthesis (Pmax) rates, little colour expression, an open habit (shoots separated), higher numbers of chloroplasts, and more numerous, smaller shoot apices (capitula) than wild-sourcedSphagnum. Potentially, greater numbers of chloroplasts in micropropagatedSphagnumfacilitate higher photosynthesis rates, driving rapid growth in early-stage plants, particularly in optimum moisture conditions. Pmax rates were associated with lower bulk density (mass/volume) and higher nutrient concentrations in tissues. MicropropagatedSphagnum, grown with additional nutrients, showed no sign of nutrient toxicity or limited P or K, despite a N content approaching 30 mg g-1(well above the highest literature-reported concentration threshold), indicating its nutrient-demanding early growth stage. Ranking species according to their Pmax and respiration rates (expressed on a dry matter basis) found thatS. squarrosumwas the highest andS. medium/divinumwas the lowest, in both micropropagated and wild-sourcedSphagnum. MicropropagatedSphagnumis similar in form to wild-sourced, can be propagated in large quantities, and due to high photosynthesis rates and absorption of nutrients, is likely to establish well on application to a site where re-wetting has already occurred, therefore making it highly beneficial for restoration of degraded bogs.
Exploiting protein language model sequence representations for repeat detection
Authors: Qiu Kaiyu , Dunin-Horkawicz Stanislaw , Lupas Andrei
Published: June 2024

Duplication is an essential evolutionary mechanism that operates at the scale of chromosomes, large chunks of DNA sequences, genes, protein domains, and shorter motifs. The study of duplication is central to understanding protein evolution, but the detection of repetitive sequence patterns is often challenging due to decreasing similarity between internal repeats resulting from long-term divergence. The most sensitive sequence-based repeat detection method, HHrepID, relies on the construction of multiple sequence alignments (MSAs) to enhance homology signals and thus facilitate the detection of very ancient duplications. However, such an alignment-based approach is slow and limits the ability to perform large-scale scans. Recent advances in protein representation learning have introduced sequence embeddings extracted from protein language models as a powerful and much faster alternative to MSAs. Protein sequence representations have been shown to be effective in homology detection, as exemplified by software such as our recently developed pLM-BLAST. In this study, we implement pLM-Repeat, a pipeline built upon pLM-BLAST, to identify repeats encoded in sequence embeddings. pLM-Repeat achieves comparable sensitivity to HHrepID in detecting the presence of repeats, while predicting many more repeat units and providing significantly better run times. We also trained an auxiliary neural network, DeepRepeat, to detect domains with patterns similar to well-characterized repeat folds to support rapid filtering. Using our newly developed tools, we scanned the AFDB90v4 database and identified a collection of novel and undescribed repeat domains.
Functional Imaging of Developing Brain in Mice and Non-Human Primates
Authors: Zhu Jiejun , He Dongming , Sun Mengzhu , Zheng Hanming , Chen Zihao , Yang Jin , Lin Chengqi , Yuan Qiwen , Shi Yun Stone , Sun Lei , Qiu Zhihai
Published: June 2024

Despite significant advances in structural and genetic studies, investigations of early embryonic functions, such as brain activity, have long been constrained by technical challenges. Functional ultrasound (fUS) has emerged as a breakthrough modality, enabling real-time monitoring of brain activity with exceptional spatial and temporal resolution and offering unprecedented opportunities for studying functional embryonic development. In this study, we used fUS to monitor whole-embryo activity in mice from embryonic days E8.5 to E18.5, revealing patterns of neural activity throughout embryogenesis. This approach provides new opportunities to explore brain development dynamically as it unfolds. Moreover, we observed embryo responses to external stimuli, including sound, in both mice and cynomolgus macaques, offering insights into early sensory processing and neural maturation. In summary, our study establishes fUS as a powerful tool for studying embryonic brain functional development, with significant implications for scientific research, especially in non- human primate models, and clinical applications.
Visual Identification of Conspecifics Shapes Social Behavior in Mice
Authors: Greer Devon , Lei Tianhao , Kryshtal Anna , Jessen Zach , Schwartz Gregory William
Published: June 2024

Recognizing conspecifics in order to determine how to interact with them appropriately is a fundamental goal of animal sensory systems. It has undergone selective pressure in nearly all species. Mice have a large repertoire of social behaviors that are the subject of a rapidly growing field of study in neuroscience. Mouse social interactions likely incorporate all available sensory modalities, and the vast majority of studies have not attempted to isolate them. Specifically the role of vision in mouse social interactions remains unclear. We developed a behavioral platform that allowed us to present a subject mouse the visual information of stimulus mice in isolation from olfactory, acoustic, and tactile cues. Our results indicate that the visual identification of the sex or individual identity of other mice influences behavior. These findings highlight the underappreciated role of vision in mouse social interactions and open new avenues to study the visual circuits underlying social behavior.
Electrostatic interactions in nucleosome and higher-order structures are regulated by protonation state of histone ionizable residue
Authors: Zhang Houfang , Guo Wenhan , Xu Wang , Li Anbang , Jiang Lijun , Li Lin , Peng Yunhui
Published: June 2024

The nucleosome serves as the fundamental unit of chromatin organization, with electrostatic interactions acting as the driving forces in the folding of nucleosomes into chromatin. Perturbations in cellular pH conditions can lead to changes in the protonation states of titratable histone residues, impacting nucleosome surface electrostatic potentials and interactions. However, the effects of proton uptake or release of histone ionizable groups on nucleosome-partner protein interactions and higher-order chromatin structures remain largely unexplored. Here, we conducted comprehensive analyses of histone titratable residue pKa values in various nucleosome contexts, utilizing 96 experimentally determined structures. We revealed that pH-induced changes in histone residue protonation states modulated nucleosome surface electrostatic potentials and significantly influenced nucleosome-partner protein interactions. Furthermore, we observed that proton uptake or release often accompanied nucleosome-partner protein interactions, facilitating their binding processes. Additionally, using a dataset of 1266 recurrent histone cancer mutations, we systematically characterized their impact on nucleosome surface electrostatics, demonstrating their profound effects on electrostatic interactions between nucleosomes and partner proteins. Finally, our findings suggest that alterations in histone protonation or cancer mutations can also regulate nucleosome self-association, thereby modulating the organization and dynamics of higher-order chromatin structure.
Disruption of G3BP1 Granules Promotes Mammalian CNS and PNS Axon Regeneration
Authors: Sahoo Pabitra K. , Agrawal Manasi , Hanovice Nicholas , Ward Patricia , Desai Meghal , Smith Terika P. , SiMa HaoMin , Dulin Jennifer N. , Vaughn Lauren S. , Tuszynski Mark , Welshhans Kristy , Benowitz Larry , English Arthur , Houle John D. , Twiss Jeffery L.
Published: June 2024

Depletion or inhibition of core stress granule proteins, G3BP1 in mammals and TIAR-2 inC. elegans, increases axon regeneration in injured neurons, showing spontaneous regeneration. Inhibition of G3BP1 by expression of its acidic or ‘B-domain’ accelerates axon regeneration after nerve injury, bringing a potential therapeutic intervention to promote neural repair in the peripheral nervous system. Here, we asked if G3BP1 inhibition is a viable strategy to promote regeneration in injured mammalian central nervous system where axons do not regenerate spontaneously. G3BP1 B-domain expression was found to promote axon regeneration in the transected spinal cord provided with a permissive peripheral nerve graft (PNG) as well as in crushed optic nerve. Moreover, a cell-permeable peptide (CPP) to a subregion of B-domain (rodent G3BP1 amino acids 190-208) accelerated axon regeneration after peripheral nerve injury and promoted regrowth of reticulospinal axons into the distal transected spinal cord through a bridging PNG. G3BP1 CPP promoted axon growth from rodent and human neurons cultured on permissive substrates, and this function required alternating Glu/Asp-Pro repeats that impart a unique predicted tertiary structure. The G3BP1 CPP disassembles axonal G3BP1, G3BP2, and FMRP, but not FXR1, granules and selectively increases axonal protein synthesis in cortical neurons. These studies identify G3BP1 granules as a key regulator of axon growth in CNS neurons and demonstrate that disassembly of these granules promotes retinal axon regeneration in injured optic nerve and reticulospinal axon elongation into permissive environments after CNS injury. This work highlights G3BP1 granule disassembly as a potential therapeutic strategy for enhancing axon growth and neural repair.

SIGNIFICANCE STATEMENT

The central nervous system (CNS) axon does not have the capacity for spontaneous axon regeneration, as seen in the peripheral nervous system (PNS). We previously showed that stress granule-like aggregates of G3BP1 are present in uninjured PNS axons, and these slow nerve regeneration. We now report that CNS axons contain G3BP1 granules, and G3BP1 granule disassembling strategies promote axon regeneration in the injured sciatic nerve, transected spinal cord with a peripheral nerve graft, and injured optic nerve. Thus, G3BP1 granules are a barrier to axon regeneration and can be targeted for stimulating neural repair following traumatic injury, including in the regeneration refractory CNS.
The “don’t eat me” signal CD47 contributes to microglial phagocytosis defects and autism-like behaviors in 16p11.2 deletion mice
Authors: Ju Jun , Pan Yifan , Yang Xinyi , Li Xuanyi , Chen Jinghong , Wu Shiyu , Hou Sheng-Tao
Published: June 2024

Various pathological characteristics of autism spectrum disorder (ASD) stem from abnormalities in brain resident immune cells, specifically microglia, to prune unnecessary synapses or neural connections during early development. Animal models of ASD exhibit an abundance of synapses in different brain regions, which is strongly linked to the appearance of ASD behaviors. Overexpression of CD47 on neurons acts as a “don’t eat me” signal, safeguarding synapses from inappropriate pruning by microglia. Indeed, CD47 overexpression occurs in 16p11.2 deletion carriers, causing decreased synaptic phagocytosis and the manifestation of ASD characteristics. However, the role of CD47 in synaptic pruning impairment leading to ASD phenotypes in the 16p11.2 deletion mouse model is unclear. Moreover, whether blocking CD47 can alleviate ASD mice’s behavioral deficits remains unknown. Here, we demonstrate a strong link between increased CD47 expression, decreased microglia phagocytosis capacity, and increased impairment in social novelty preference in the 16p11.2 deletion mice. The reduction in microglia phagocytosis caused a rise in excitatory synapses and transmission in the prefrontal cortex of 16p11.2 deletion mice. Importantly, blocking CD47 using a specific CD47 antibody or reducing CD47 expression using a specific shRNA enhanced the microglia phagocytosis and reduced excitatory transmission. Reduction in CD47 expression improved social novelty preference deficits in 16p11.2 mice. These findings demonstrate that CD47 contributes to the ASD phenotypes in the 16p11.2 deletion mice and could be a promising target for the development of treatment for ASD.

Significance Statement

Autism spectrum disorder (ASD) is a neurological developmental condition characterized by stereotyped behaviors and cognitive deficits. However, therapeutic options for ASD remain limited. Activation of the classical complement system, an innate immune signaling pathway component, supports microglia-mediated synaptic pruning during development and disease. In particular, CD47, a “don’t eat me” signal, protects synapses from inappropriate clearance. Here, we investigated the role of CD47 in microglial phagocytosis using the 16p11.2 deletion mouse model, demonstrating that reducing CD47 signaling enhances microglial phagocytose synapses in the prefrontal cortex. This enhancement leads to improved synaptic function and reduced social behavioral deficits. These findings provide mechanistic insights into the role of CD47, laying the groundwork for developing more effective treatments for ASD.
SpyDen: Automating molecular and structural analysis across spines and dendrites
Authors: Eggl Maximilian F. , Wagle Surbhit , Filling Jean P. , Chater Thomas E. , Goda Yukiko , Tchumatchenko Tatjana
Published: June 2024

Investigating the molecular composition across neural compartments such as axons, dendrites, or synapses is critical for our understanding of learning and memory. State-of-the-art microscopy techniques can now resolve individual molecules and pinpoint their position with micrometre or even nanometre resolution across tens or hundreds of micrometres, allowing the labelling of multiple structures of interest simultaneously. Algorithmically, tracking individual molecules across hundreds of micrometres and determining whether they are inside any cellular compartment of interest can be challenging. Historically, microscopy images are annotated manually, often using multiple software packages to detect fluorescence puncta (e.g. labelled mRNAs) and then trace and quantify cellular compartments of interest. Advanced ANN-based automated tools, while powerful, are often able to help only with selected parts of the data analysis pipeline, may be optimised for specific spatial resolutions or cell preparations or may not be fully open source and open access to be sufficiently customisable. To address these challenges, we developed SpyDen. SpyDen is a Python package based upon three principles:i)ease of use for multi-task scenarios,ii)open-source accessibility and data export to a common, open data format,iii)the ability to edit any software-generated annotation and generalise across spatial resolutions. Equipped with a graphical user interface and accompanied by video tutorials, SpyDen provides a collection of powerful algorithms that can be used for neurite and synapse detection as well as fluorescent puncta and intensity analysis. We validated SpyDen using expert annotation across numerous use cases to prove a powerful, integrated platform for efficient and reproducible molecular imaging analysis.
Crystal structure of a MarR family transcriptional regulator protein
Authors: Goswami Arpita , Ravindranath Kannika Byadarahalli , Shankar Madan Kumar
Published: June 2024

The multiple antibiotic resistance regulator (MarR) family of transcription factor proteins form a large group of multitasking bio-molecules in pathogenicEscherichia coli(E. coli). HosA is one of these MarR transcription factors reported in dozens of pathogenicE. coliwith highly conserved sequence profiles. The HosA from the enteropathogenicE. coliO127:H6 (strain E2348/69), a predominantly monomeric protein, was overexpressed inE. coliand purified. The HosA protein crystals were obtained in microbatch under oil method at 4° C. The X-rays of the diffracted spots were extended to 2.21 Å resolution. The crystal belongs to the space groupP4322, with unit-cell parametersa= 67.16 Å,b= 67.16 Å,c= 95.66 Å and α = β = γ = 90°. In the asymmetric unit, monomeric HosA protein was crystallized and confirmed with the Matthew coefficient analysis (3.48 Å3Da-1). The monomeric structure is compared with previously solved structures of other homologous transcription factors. This confirmed the winged loop at the DNA binding region of the HosA protein.
HCNetlas: Human cell network atlas enabling cell type-resolved disease genetics
Authors: Yu Jiwon , Cha Junha , Koh Geon , Lee Insuk
Published: June 2024

Cell type-specific actions of disease genes add a significant layer of complexity to the genetic architecture underlying diseases, obscuring our understanding of disease mechanisms. Single-cell omics have revealed the functional roles of genes at the cellular level, identifying cell types critical for disease progression. Often, a gene impact on disease through its altered network within specific cell types, rather than mere changes in expression levels. To explore the cell type-specific roles of disease genes, we developed HCNetlas (human cell network atlas), a resource cataloging cell type-specific gene networks (CGNs) for various healthy tissue cells. We also devised three network analysis methods to investigate cell type-specific functions of disease genes. These methods involve comparing HCNetlas CGNs with those derived from disease-affected tissue samples. These methods find that systemic lupus erythematosus genes predominantly function in myeloid cells, and Alzheimer’s disease genes mainly play roles in inhibitory and excitatory neurons. Moreover, they show many lung cancer genes exert their roles in immune cells. These findings suggest that HCNetlas has the potential to link disease-associated genes to cell types of action, facilitating development of cell type-resolved diagnostics and therapeutic strategies for complex human diseases.
Genomic Insights and Biocontrol Potential of Ten Bacterial Strains from the Tomato Core Microbiome
Authors: Nicotra Daniele , Ghadamgahi Farideh , Ghosh Samrat , Anzalone Alice , Dimaria Giulio , Mosca Alexandros , Massimino Maria Elena , Vetukuri Ramesh Raju , Catara Vittoria
Published: June 2024

Despite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health. We therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. These taxa included some that are commonly used as biofertilizers and biocontrol agents (PseudomonasandBacillus) as well as the less studied generaLeclercia, Chryseobacterium, Glutamicibacter,andPaenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits. This yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth. The gathered genomic information will be instrumental in planning the use of these bacteria individually or in consortia to enhance plant growth by coupling strains with different traits, effects, and mechanisms of action.
DNA methylation contributes to plant acclimation to naturally fluctuating light
Authors: Emmerson Robyn A , Bechtold Ulrike , Zabet Nicolae Radu , Lawson Tracy
Published: June 2024

Plants in the natural environment experience continuous dynamic changes in light intensity. We have limited understanding on how plants adapt to such variable conditions. Here, we exposedArabidopsis thalianaplants to naturally fluctuating light regimes alongside traditional square light regimes such as those often found in control environment growth chambers. The physiological response was highly consistent across experiments, indicating the involvement of an epigenetic mechanism, leading us to investigated differences in DNA methylation. Our results identified a large number of alterations in DNA methylation patterns between fluctuating light acclimated plants, and square light acclimated plants, demonstrating natural fluctuations in light impacts the plant epigenetic mechanisms. Most importantly, there are more differences in DNA methylation patterns between different light pattern regimes than between different light intensities. These differences in DNA methylation were accompanied by significant changes in gene expression, some of which correlated with altered DNA methylation. Interestingly, several transposable elements which displayed differential methylation were found to be differentially expressed between light regimes. Our data suggests DNA methylation plays a role in acclimation to natural light which may directly regulate gene expression and impact transposable element activation.
Should I stay or should I go? Spatio-temporal dynamics of bacterial biofilms in confined flows
Authors: Benbelkacem Massinissa , Ramos Gabriel , El Garah Fatima , Abidine Yara , Roques Christine , Davit Yohan
Published: June 2024

The vast majority of bacteria live in sessile biofilms that colonize the channels, pores and crevices of confined structures. Flow in these structures carries the nutrients necessary for growth, but also generates stresses and detachment from surfaces. Conversely, bacteria tend to occupy a large part of the available space and, in so doing, increase resistance to flow and modify transport properties. Although the importance of advective transport and hydrodynamic forces on bacteria is well known, the complex feedback effects that control development in confined geome-tries are much less understood. Here, we study how couplings between flow and bacterial development control the spatio-temporal dynamics ofPseudomonas aeruginosain microchannel flows. We demonstrate that nutrient limitation drives the longitudinal distribution of biomass, while a competition between growth and flow-induced detachment controls the maximum clogging and the temporal dynamics. We find that successive cycles of sloughing and growth cause persistent fluctuations of the hydraulic resistance and prevent the system from ever reaching a true steady-state. Our results indicate that these self-sustained fluctuations are a signature effect of biofilm development in confined flows and could thus be a key component of the spreading of biofilms in infections, environmental processes and engineering applications. Consistent with the description of other bursting events, such as earthquakes or avalanches, we further show that the dynamics of sloughing can be described as a jump stochastic process with a gamma distribution of interevent times. This stochastic modeling approach opens the way towards a new quantitative approach to the characterization of the apparent randomness and irreproducibility of biofilm experiments in such systems.
Date palm acclimates to aridity by diverting organic osmolytes for root osmotic adjustment in parallel with leaf membrane remodeling and ROS scavenging
Authors: Franzisky Bastian L. , Mueller Heike M. , Du Baoguo , Lux Thomas , White Philip J. , Carpentier Sebastien Christian , Winkler Jana Barbro , Schnitzler Joerg-Peter , Kudla Jörg , Kangasjärvi Jaakko , Reichelt Michael , Mithöfer Axel , Mayer Klaus F.X. , Rennenberg Heinz , Ache Peter , Hedrich Rainer , Messerer Maxim , Geilfus Christoph-Martin
Published: June 2024

Highlight statement

Osmotic strength of date palm roots increases with soil desiccation, for which the accumulation of organic osmolytes, such as sugars, is essential in complement to energetically cheap mineral osmotics.

Date palm (Phoenix dactyliferaL.) is an important crop in arid regions that is well-adapted to desert ecosystems. To understand the remarkable ability to grow and yield in water-limited environments, experiments were conducted in a simulated desert environment with water-withholding for up to four weeks. In response to drought, root, rather than leaf, osmotic strength increased, with sugars contributing more to the osmolyte increase than minerals. Consistently, carbon and amino acid metabolism was acclimated toward biosynthesis at both the transcriptional and translational levels. In leaves, a remodeling of membrane systems was observed, suggesting changes in thylakoid lipid composition, which together with the restructuring of the photosynthetic apparatus, indicated an acclimation preventing oxidative damage. Thus, xerophilic date palm avoids oxidative damage under drought by combined prevention and rapid detoxification of oxygen radicals. Although minerals were expected to serve as cheap key osmotics, date palm also relies on organic osmolytes for osmotic adjustment of the roots during desiccation. The diversion of these resources away from growth is consistent with date palm’s strategy of generally slow growth in harsh environments and clearly indicates a trade-off between growth and stress-related physiological responses.
Association of GLOD4 with Alzheimer’s Disease in Humans and Mice
Authors: Utyro Olga , Włoczkowska-Łapińska Olga , Jakubowski Hieronim
Published: June 2024

Background

Glyoxalase domain containing protein 4 (GLOD4), a protein of an unknown function, is associated with Alzheimer’s disease (AD). Three GLOD4 isoforms are known. The mechanism underlying GLOD4’s association with AD was unknown.

Objective

To assess GLOD4’s role in the central nervous system by studying GLOD4 isoforms expression in human frontal cerebral cortical tissues from AD patients and in brains ofBlmh−/−5xFAD mouse AD model of AD.

Methods

GLOD4 protein and mRNA were quantified in human and mouse brains by western blotting and RT-qPCR, respectively. Mouse brain amyloid β (Aβ) was quantified by western blotting. Behavioral assessments of mice were performed by cognitive/neuromotor testing.Glod4gene in mouse neuroblastoma N2a-APPswe cells was silenced by RNA interference and Glod4 protein/mRNA, Aβ precursor protein (Aβpp)/mRNA,Atg5,p62, andLc3mRNAs were quantified.

Results

GLOD4mRNA and protein isoforms were downregulated in cortical tissues from AD patients compared to non-AD controls.Glod4mRNA was downregulated in brains ofBlmh−/−5xFAD mice compared toBlmh+/+5xFAD sibling controls, but not inBlmh−/−mice without the 5xFAD transgene compared toBlmh+/+sibling controls. The 5xFAD transgene downregulated Glod4 mRNA inBlmh−/−mice of both sexes and inBlmh+/+males but not females. Attenuated Glod4 was associated with elevated Aβ and worsened memory/sensorimotor performance inBlmh−/−5xFAD mice. Glod4 depletion in N2a-APPswe cells upregulated AβPP and downregulated autophagy-relatedAtg5,p62, andLc3genes.

Conclusions

These findings suggest that GLOD4 interacts with AβPP and the autophagy pathway, and that disruption of these interactions leads to Aβ accumulation and cognitive/neurosensory deficits.
High-resolution, high-throughput analysis ofDrosophilageotactic behavior
Authors: Canic Tijana , Lopez Juan , Ortiz-Vega Natalie , Zhai R. Grace , Syed Sheyum
Published: June 2024

Drosophilainnate response to gravity, geotaxis, has been previously used to assess the impact of aging and disease on motor performance. Despite its rich history, fly geotaxis continues to be largely measured manually and assessed through simplistic metrics. The manual nature of this assay introduces substantial experimental variability while simplistic metrics provide limited analytic insights into the behavior. To address these shortcomings, we have constructed a fully automated, programable apparatus, and developed a multi-object tracking software capable of following sub-second movements of individual flies, thus allowing reproducible, detailed, and quantitative analysis of geotactic behavior. The apparatus triggers and monitors geotaxis of 10 fly cohorts simultaneously, with each cohort consisting of up to 7 flies. The tracking program isolates cohorts and records individual fly coordinate outputs allowing for simultaneous multi-group, multifly tracks per experiment, greatly improving throughput and resolution. The algorithm tracks individual flies during the entire run with ∼97% accuracy, yielding detailed climbing curve, speed, and movement direction with 1/30 second resolution. Our tracking also allows the construction of multi-variable metrics and the detection of transitory movement phenotypes, such as slips and falls, which have thus far been neglected in geotaxis studies due to limited spatio-temporal resolution. Through a combination of automation and robust tracking, the platform is therefore poised to advanceDrosophilageotaxis assay into a comprehensive assessment of locomotor behavior.
TLR4 deficiency does not alter glaucomatous progression in a mouse model of chronic glaucoma
Authors: Zhang Chi , Simón Marina , Harder Jeffrey M. , Lim Haeyn , Montgomery Christa , Wang Qing , John Simon W.M.
Published: June 2024

Glaucoma is a leading cause of irreversible blindness worldwide. Toll-like receptor 4 (TLR4) is a pattern-recognition transmembrane receptor that induces neuroinflammatory processes in response to injury.Tlr4is highly expressed in ocular tissues and is known to modulate inflammatory processes in both anterior and posterior segment tissues. TLR4 activation can lead to mitochondrial dysfunction and metabolic deficits in inflammatory disorders. Due to its effects on inflammation and metabolism, TLR4 is a candidate to participate in glaucoma pathogenesis. It has been suggested as a therapeutic target based on studies using acute models, such as experimentally raising IOP to ischemia-inducing levels. Nevertheless, its role in chronic glaucoma needs further evaluation. In the current study, we investigated the role of TLR4 in an inherited mouse model of chronic glaucoma, DBA/2J. To do this, we analyzed the effect ofTlr4knockout (Tlr4−/−) on glaucoma-associated phenotypes in DBA/2J mice. Our studies found no significant differences in intraocular pressure, iris disease, or glaucomatous progression inTlr4−/−compared toTlr4+/+DBA/2J mice. These data do not identify a role for TLR4 in this chronic glaucoma, but further research is warranted to understand its role in other glaucoma models and different genetic contexts.
The ventral CA2 region of the hippocampus and its differential contributions to social memory and social aggression
Authors: Boyle Lara M. , Sheng Wanhui , Leroy Felix , Sahai Rhea , Irfan Sarah , Lee Heon-Jin , Villegas Andres , Young W.Scott , Siegelbaum Steven A.
Published: June 2024

Although it is well-known that the hippocampus mediates declarative memory (the repository of information of people, places, things and events) and influences behavior, the differential contributions of the dorsal and ventral hippocampus to specific forms of memory and behavior remain largely unknown. Studies to date show that the dorsal hippocampal CA1 region is important for cognitive and spatial tasks whereas the ventral CA1 region is associated with affective or emotional processing. Whether other regions and forms of hippocampal-dependent memory and behavior show a similar distinction remains unclear. Here we examine how social memory and related social behaviors are encoded across the dorso-ventral axis of the hippocampus. Although recent studies show that the dorsal hippocampal CA2 region is required for social memory and acts to promote social aggression, the behavioral role of ventral CA2 remains unknown. Indeed, whether a defined CA2 region extends throughout ventral hippocampus is controversial. Here, we report that a molecularly, anatomically and electrophysiologically defined CA2 region extends to the extreme ventral pole of hippocampus, with both similarities and important differences in its projection patterns and synaptic impact compared to dorsal CA2. Of particular importance, we find that ventral CA2 is not required for social memory but is critical for promoting social aggression. These results support the view that the ventral region of hippocampus is more generally tuned for emotionally-related behaviors compared to the cognitively-tuned dorsal hippocampus.
Functional coupling between MC4R and Kir7.1 contributes to clozapine-induced hyperphagia
Authors: Li Li , Hernandez Ciria C. , Gimenez Luis E. , Xu Baijie , Dahir Naima S. , Swati  , Birnbaum Shari G. , Cone Roger D. , Liu Chen
Published: June 2024

Most antipsychotic drugs (APDs) induce hyperphagia and weight gain. However, the neural mechanisms are poorly understood, partly due to challenges replicating their metabolic effects in rodents. Here, we report a new mouse model that recapitulates overeating induced by clozapine, a widely prescribed APD. Our study shows that clozapine boosts food intake by inhibiting melanocortin 4 receptor (MC4R) expressing neurons in the paraventricular nucleus of the hypothalamus. Interestingly, neither clozapine nor risperidone, another commonly used APD, affects receptor-ligand binding or the canonical Gαs signaling of MC4R. Instead, they inhibit neuronal activity by enhancing the coupling between MC4R and Kir7.1, leading to the open state of the inwardly rectifying potassium channel. Deletion ofKir7.1inMc4r-Creneurons prevents clozapine-induced weight gain, while treatment with a selective Kir7.1 blocker mitigates overeating in clozapine-fed mice. Our findings unveil a molecular pathway underlying the effect of APDs on feeding behavior and suggest its potential as a therapeutic target.