bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polycomb protein binding and looping mediated by Polycomb Response Elements in the ON transcriptional state
Authors: Brown J. Lesley , Zhang Liangliang , Rocha Pedro P , Kassis Judith A. , Sun Ming-an 
Published: November 2023

AbstractPolycomb group proteins (PcG) mediate epigenetic silencing of important developmental genes and other targets. In Drosophila, canonical PcG-target genes contain Polycomb Response Elements (PREs) that recruit PcG protein complexes including PRC2 that tri- methylates H3K27 forming large H3K27me3 domains. In the OFF transcriptional state, PREs loop with each other and this looping strengthens silencing. Here we address the question of what PcG proteins bind to PREs when canonical PcG target genes are expressed, and whether PREs loop when these genes are ON. Our data show that the answer to this question is PRE-specific but general conclusions can be made. First, within a PcG-target gene, some regulatory DNA can remain covered with H3K27me3 and PcG proteins remain bound to PREs in these regions. Second, when PREs are within H3K27ac domains, PcG- binding decreases, however, this depends on the protein and PRE. The DNA binding protein GAF, and the PcG protein Ph remain at PREs even when other PcG proteins are greatly depleted. In the ON state, PREs can still loop with each other, but also form loops with presumptive enhancers. These data support the model that, in addition to their role in PcG silencing, PREs can act as “promoter-tethering elements” mediating interactions between promoter proximal PREs and distant enhancers.
Hierarchical and scaffolded phosphorylation of two degrons controls PER2 stability
Authors: Francisco Joel C. , Virshup David M 
Published: November 2023

AbstractThe duration of the transcription-repression cycles that give rise to mammalian circadian rhythms is largely determined by the stability of the PERIOD protein, the rate-limiting components of the molecular clock. The degradation of PERs is tightly regulated by multisite phosphorylation by Casein Kinase 1 (CK1δ/ε). In this phosphoswitch, phosphorylation of a PER2 degron (Degron 2, D2) causes degradation, while phosphorylation of the PER2 Familial Advanced Sleep Phase (FASP) domain blocks CK1 activity on the degron, stabilizing PER2. However, this model and many other studies of PER2 degradation do not include the second degron of PER2 that is conserved in PER1, termed Degron 1, D1. We examined how these two degrons contribute to PER2 stability, affect the balance of the phosphoswitch, and how they are differentiated by CK1. Using PER2-luciferase fusions and real-time luminometry, we investigated the contribution of both D2 and of CK1-PER2 binding. We find that D1, like D2, is a substrate of CK1 but that D1 plays only a ‘backup’ role in PER2 degradation. Notably, CK1 bound to a PER1:PER2 dimer protein can phosphorylate PER1 D1 in trans. This scaffolded phosphorylation provides additional levels of control to PER stability and circadian rhythms.
The role of the AP-1 adaptor complex in outgoing and incoming membrane traffic
Authors: Robinson Margaret S. , Antrobus Robin , Sanger Anneri , Davies Alexandra K. , Gershlick David C. 
Published: November 2023

AbstractThe AP-1 adaptor complex is found in all eukaryotes, but it has been implicated in different pathways in different organisms. To look directly at AP-1 function, we generated stably transduced HeLa cells co-expressing tagged AP-1 and various tagged membrane proteins. Live cell imaging showed that AP-1 is recruited onto tubular carriers trafficking from the Golgi apparatus to the plasma membrane, as well as onto transferrin-containing early/recycling endosomes. Analysis of single AP-1 vesicles showed that they are a heterogeneous population, which start to sequester cargo by 30 minutes after exit from the ER. Vesicle capture showed that AP-1 vesicles contain transmembrane proteins found at the TGN and early/recycling endosomes, as well as lysosomal hydrolases, but very little of the anterograde adaptor GGA2. Together, our results support a model in which AP-1 retrieves proteins from post-Golgi compartments back to the TGN, analogous to COPI’s role in the early secretory pathway. We propose that this is the function of AP-1 in all eukaryotes.SummaryRobinson et al. investigate AP-1 function using complementary approaches on cells co-expressing tagged AP-1 and cargo proteins. Their results support a model in which AP-1 is recruited onto post-Golgi carriers and early/recycling endosomes, where it retrieves selected proteins back to the TGN.
HDAC inhibitors rescue MeCP2T158Mspeckles in a high content screen
Authors: Lata Rodrigo , Steegmans Liesbeth , Kellens Ranie , Nijs Marnik , Klaassen Hugo , Versele Matthias , Christ Frauke , Debyser Zeger 
Published: November 2023

AbstractRett syndrome (OMIM 312750) is a rare neurodevelopmental disorder caused byde novomutations in the Methyl-CpG Binding Protein 2 (MeCP2) gene located on the X-Chromosome, typically affecting girls. Currently, available therapy for Rett Syndrome is only symptomatic. Rett syndrome symptoms first appear between 6 to 18 months of age, characterized by microcephaly and lack of motor coordination being the most prevalent. The disease continues to progress until adulthood when it reaches a stationary phase. More than 800 different mutations causing Rett syndrome have been described, yet the most common is T158M (9% prevalence), located in the Methyl-Binding domain (MBD) of MeCP2. Due to its importance for DNA binding through recognition of methylated CpG, mutations in the MBD have a significant impact on the stability and function of MeCP2. MeCP2 is a nuclear protein and accumulates in liquid-liquid phase condensates visualized as speckles in NIH3T3 by microscopy. We developed a high content phenotypic assay, detecting fluorescent MeCP2 speckles in NIH3T3 cells. The assay allows to identify small molecules that stabilize MeCP2-T158M and phenotypically rescue speckle formation. To validate the assay, a collection of 3572 drugs was screened, including FDA-approved drugs, compounds in clinical trials and biologically annotated tool compounds. 18 hits were identified showing at least 25% of rescue of speckles in the mutant cell line while not affecting wild-type MeCP2 speckles. Primary hits were confirmed in a dose response assay and in a thermal shift assay with recombinant MeCP2. One class of identified hits represents histone deacetylase inhibitors (HDACis) showing 25% speckle rescue of mutant MeCP2 without toxicity. This screening strategycan be expanded to additional compound libraries and support novel drug discovery.
H3K9me regulates heterochromatin silencing through incoherent feedforward loops
Authors: Yabe Kannosuke , Kamio Asuka , Oya Satoyo , Kakutani Tetsuji , Hirayama Mami , Tanaka Yuriko , Inagaki Soichi 
Published: November 2023

AbstractHistone H3 lysine-9 methylation (H3K9me) is associated with condensed and transcriptionally inactive heterochromatin1. Although it has long been known that H3K9me silences transcription to control a wide variety of biological phenomena in many eukaryotic species2,3, how the silencing is regulated under the control of H3K9me is still largely unclear. Moreover, how cells delimit regions with H3K9me to avoid silencing essential genes remains unexplored. Here, using Arabidopsis genetic systems that induce H3K9me2 and its associated non-CG DNA methylation (mCH) in the transcribed region of genesde novo, we show that the accumulation of H3K9me2/mCH paradoxically also leads to the deposition of the euchromatic mark H3K36me3. This induction of H3K36me3 depends on a SET domain methyltransferase, ASHH3, and brings about anti-silencing by preventing the demethylation of H3K4me1 by LDL2, which mediates transcriptional silencing downstream of H3K9me2/mCH4. H3K9me2/mCH-driven antagonistic actions of ASHH3-H3K36me3 and LDL2-H3K4me1-loss also regulate thede novosilencing of reactivated transposable elements (TEs). These results demonstrate that H3K9me2 both facilitates and impedes silencing, and the incoherent feedforward loops fine-tune the fate of genes and TEs. Our results illuminate a novel elaborate mechanism for partitioning chromatin domains and provide insights into the molecular basis underlying natural epigenetic variation.
Exploring thienothiadiazine dioxides as isosteric analogues of benzo- and pyridothiadiazine dioxides in the search of new AMPA and kainate receptor positive allosteric modulators
Authors: Francotte Pierre , Bay Yasmin , Goffin Eric , Colson Thomas , Lesenfants Cindy , Dorosz Jerzy , Laulumaa Saara , Fraikin Pierre , de Tullio Pascal , Beaufour Caroline , Botez Iuliana , Pickering Darryl S. , Frydenvang Karla , Danober Laurence , Kristensen Anders Skov , Kastrup Jette Sandholm , Pirotte Bernard 
Published: November 2023

AbstractThe synthesis and biological evaluation on AMPA and kainate receptors of new examples of 3,4-dihydro-2H-1,2,4-thieno[3,2-e]-1,2,4-thiadiazine 1,1-dioxides is described.The introduction of a cyclopropyl chain instead of an ethyl chain at the 4-position of the thiadiazine ring was found to dramatically improve the potentiator activity on AMPA receptors, with compound32(BPAM395) expressingin vitroactivity on AMPARs (EC2x = 0.24 µM) close to that of the reference 4-cyclopropyl-substituted benzothiadiazine dioxide10(BPAM344).Interestingly, the 4-allyl-substituted thienothiadiazine dioxide27(BPAM307) emerged as the most promising compound on kainate receptors being a more effective potentiator than the 4-cyclopropyl-substituted thienothiadiazine dioxide32and supporting the view that the 4-allyl substitution of the thiadiazine ring could be more favorable than the 4-cyclopropyl substitution to induce marked activity on kainate receptors versus AMPA receptors.The thieno-analogue36(BPAM279) of the clinically tested S18986 (11) was selected forin vivoevaluation in mice as a cognitive enhancer due to a safer profile than32after massiveper osdrug administration. Compound36was found to increase the cognition performance in mice at low doses (1 mg/kg)per ossuggesting that the compound was well absorbed after oral administration and able to reach the central nervous system.Finally, compound32was selected for co-crystallization with the GluA2-LBD (L504Y,N775S) and glutamate to examine the binding mode of thienothiadiazine dioxides within the allosteric binding site of the AMPA receptor. At the allosteric site, this compound established similar interactions as the previously reported BTD-type AMPA receptor modulators.HighlightsThe study explored AMPA/kainate receptor PAMs belonging to thienothiadiazine dioxidesThe 4-cyclopropyl-substituted compound32was the most potent AMPA receptor modulator4-Allyl substitution improved activity and selectivity for kainate receptorsThe tricyclic compound36expressed cognitive improvementin vivoin miceCompound32was co-crystallized with GluA2-LBD to examine receptor binding modeGraphical abstract
Predictive Uncertainty in State-Estimation Drives Active Sensing
Authors: Karagoz Osman Kaan , Kilic Aysegul , Aydin Emin Yusuf , Ankarali Mustafa Mert , Uyanik Ismail 
Published: November 2023

ABSTRACTAnimals use active sensing movements to shape the spatiotemporal characteristics of sensory signals to better perceive their environment under varying conditions. However, the underlying mechanisms governing the generation of active sensing movements are not known. To address this, we investigated the role of active sensing movements in the refuge tracking behavior ofEigenmannia virescens, a species of weakly electric fish. These fish track the longitudinal movements of a refuge in which they hide by swimming back and forth in a single linear dimension. During refuge tracking,Eigenmanniaexhibits stereotyped whole-body oscillations when the quality of the sensory signals degrades. We developed a feedback control model to examine the role of these ancillary movements on the task performance. Here, we show that the proposed model generates fish trajectories that are statistically indistinguishable from the actual fish, implying that active sensing movements are regulated to minimize the predictive uncertainty in state estimation.
Lac-Phe mediates the anti-obesity effect of metformin
Authors: Xiao Shuke , Li Veronica L. , Lyu Xuchao , Chen Xudong , Wei Wei , Abbasi Fahim , Knowles Joshua W. , Deng Shuliang , Tiwari Gaurav , Shi Xu , Zheng Shuning , Farrell Laurie , Chen Zsu-Zsu , Taylor Kent D. , Guo Xiuqing , Goodarzi Mark O. , Wood Alexis C. , Chen Yii-Der Ida , Lange Leslie A. , Rich Stephen S. , Rotter Jerome I. , Clish Clary B. , Tahir Usman A. , Gerszten Robert E. , Benson Mark D. , Long Jonathan Z. 
Published: November 2023

AbstractMetformin is a widely prescribed anti-diabetic medicine that also reduces body weight. The mechanisms that mediate metformin’s effects on energy balance remain incompletely defined. Here we show that metformin is a powerful pharmacological inducer of the anorexigenic metabolite Lac-Phe in mice as well as in two independent human cohorts. In cell culture, metformin drives Lac-Phe biosynthesis via inhibition of complex I, increased glycolytic flux, and intracellular lactate mass action. Other biguanides and structurally distinct inhibitors of oxidative phosphorylation also increase Lac-Phe levelsin vitro. Genetic ablation of CNDP2, the principal biosynthetic enzyme for Lac-Phe, in mice renders animals resistant to metformin’s anorexigenic and anti-obesity effects. Mediation analyses also support a role for Lac-Phe in metformin’s effect on body mass index in humans. These data establish the CNDP2/Lac-Phe pathway as a critical mediator of the effects of metformin on energy balance.
Female cichlids attack and avoid—but will still mate with—androgen receptor mutant males that lack male-typical body coloration
Authors: Howard Megan R. , Ramsaroop Maxximus G. , Hoadley Andrew P. , Jackson Lillian R. , Lopez Mariana S. , Saenz Lauren A. , Alward Beau 
Published: November 2023

AbstractA key challenge in animal behavior is disentangling the social stimuli that drive conspecific behaviors. For behaviors like birdsong, insights can be made through the experimental isolation of relevant cues that affect behavior. However, for some species like teleost fish, putative sexual signaling cues are inextricably linked to others, making it difficult to parse the precise roles distinct signals play in driving conspecific behaviors. In the African cichlidAstatotilapia burtoni, males are dominant or subordinate, wherein bright coloration and territorial and courtship behavior inextricably correlate positively with rank. Here, we leveraged androgen receptor (AR) mutant maleA. burtonithat lack dominance-typical coloration but not behavior to isolate the role of male coloration in driving female mating behaviors in this species. We found in independent behavioral assays that females behave aggressively towards AR mutant but not WT males but still mated with both types of males. Females showed enhanced activation ofesr2b+cells in the hypothalamus when housed with either mutant or WT males and this activation scaled with spawning activities. Therefore, there is not a simple relationship between male coloration and female mating behaviors inA. burtoni, suggesting independent sensory mechanisms converge on hypothalamicesr2b+cells to coordinate behavioral output.
Genome-scale annotation of protein binding sites via language model and geometric deep learning
Authors: Yuan Qianmu , Tian Chong , Yang Yuedong 
Published: November 2023

AbstractRevealing protein binding sites with other molecules, such as nucleic acids, peptides, or small ligands, sheds light on disease mechanism elucidation and novel drug design. With the explosive growth of proteins in sequence databases, how to accurately and efficiently identify these binding sites from sequences becomes essential. However, current methods mostly rely on expensive multiple sequence alignments or experimental protein structures, limiting their genome-scale applications. Besides, these methods haven’t fully explored the geometry of the protein structures. Here, we propose GPSite, a multi-task network for simultaneously predicting binding residues of DNA, RNA, peptide, protein, ATP, HEM, and metal ions on proteins. GPSite was trained on informative sequence embeddings and predicted structures from protein language models, while comprehensively extracting residual and relational geometric contexts in an end-to-end manner. Experiments demonstrate that GPSite substantially surpasses state-of-the-art sequence-based and structure-based approaches on various benchmark datasets, even when the structures are not well-predicted. The low computational cost of GPSite enables rapid genome-scale binding residue annotations for over 568,000 sequences, providing opportunities to unveil unexplored associations of binding sites with molecular functions, biological processes, and genetic variants. The GPSite webserver and annotation database can be freely accessed athttps://bio-web1.nscc-gz.cn/app/GPSite.
Feeding Behavior Modifies the Circadian Variation in RR and QT intervals by Distinct Mechanisms in Mice
Authors: Ono Makoto , Burgess Don E. , Johnson Sidney R. , Elayi Claude S. , Esser Karyn A. , Seward Tanya S. , Boychuk Carie R. , Carreño Andrés P. , Stalcup Rebecca A. , Prabhat Abhilash , Schroder Elizabeth A. , Delisle Brian P. 
Published: November 2023

AbstractRhythmic feeding behavior is critical for regulating the phase and amplitude in the ≍24-hour variation of the heart rate (RR intervals), ventricular repolarization (QT intervals), and core body temperature in mice. We hypothesized the changes in cardiac electrophysiology associated with feeding behavior were secondary to changes in core body temperature. Telemetry was used to record electrocardiograms and core body temperature in mice during ad libitum-fed conditions and after inverting normal feeding behavior by restricting food access to the light cycle. Light cycle-restricted feeding quickly modified the phase and amplitude of the 24-hour rhythms in RR intervals, QT intervals, and core body temperature to realign with the new feeding time. Heart rate variability analysis and inhibiting β-adrenergic and muscarinic receptors suggested that the changes in the phase and amplitude of the 24-hour rhythms in RR intervals were secondary to changes in autonomic signaling. In contrast, the changes in the QT intervals closely mirrored changes in core body temperature. Studies at thermoneutrality confirmed the daily variation in the QT interval, but not the RR interval, and reflected daily changes in core body temperature (even in ad libitum-fed conditions). Correcting the QT interval for differences in core body temperature helped to unmask QT interval prolongation after starting light cycle-restricted feeding and in a mouse model of long QT syndrome. We conclude feeding behavior alters autonomic signaling and core body temperature to regulate the phase and amplitude in RR and QT intervals, respectively.
The Effects of Flow Speeds on Smooth Pursuit Tracking and Active Sensing Movements of Weakly Electric Fish
Authors: Aydin Emin Yusuf , Unlutabak Burcu , Uyanik Ismail 
Published: November 2023

ABSTRACTWeakly electric fish employ refuge-tracking behavior to survive, seeking and utilizing hiding places to shield themselves from predators and unfavorable environmental conditions. This adaptive mechanism enables them to minimize the risk of predation, maintain optimal electrocommunication, and adapt to changing surroundings. While studies have explored smooth pursuit tracking and active sensing movements of these fish in stationary environments, limited emphasis has been given to how varying flow speeds in their natural habitats may impact these behaviors. This study addresses this gap by investigating the effects of different flow speeds on smooth pursuit tracking and active sensing movements in weakly electric fish. Active sensing provides sensory data and multisensory integration processes and combines this data to create a holistic perception of the environment. The synergy between these processes is fundamental for enhancing an organism’s sensory capabilities and enabling it to adapt and interact effectively with its surroundings. For this study, a specialized experimental setup was designed and built to facilitate refuge-tracking behavior under controlled flow conditions. The experiments involvedApteronotus albifronsfish exposed to visual and complex electrosensory stimuli, which consisted of a sum of sine signals. Data was recorded for different sensory conditions, including variations in flow speeds, illumination levels, and refuge structures. The analysis revealed that increased flow speeds correlated with reduced tracking gain and phase lag in the fish. Additionally, it was observed that active sensing movements were more pronounced in dark conditions. These findings highlight the significant impact of flow speeds on smooth pursuit tracking and active sensing movements and emphasize the importance of studying these behaviors within the context of water flow. Understanding the biological motivations underlying these effects is vital for their potential application in engineering fields.
‘Optical Von-Frey’ method to determine nociceptive thresholds: a novel paradigm for preclinical pain assessment and analgesic screening
Authors: Iredale Jacqueline A , Pearl Amy J , Callister Robert J , Dayas Christopher V , Manning Elizabeth E , Graham Brett A 
Published: November 2023

ABSTRACTThe goal of this study was to characterize a model that specifically activates peripheral nociceptors, allowing pure nociceptive thresholds to be monitored over a range of conditions including pathology or in screening analgesic compounds. Transgenic mice expressing channelrhodopsin-2 (ChR2) in cell populations positive for the transient receptor potential cation channel subfamily V member 1 (TRPV1) gene were bred to enable peripheral nociceptor photostimulation. Preliminary experiments confirmed the expected localisation pattern of ChR2 positive profiles in the dorsal root ganglion and superficial dorsal horn, mirroring TPRV1 expression. Brief hindpaw photostimulation with 470nm light caused hindpaw withdrawal and nocifensive behaviours in ChR2 positive animals but not control ChR2 negative animals. Using a simplified up/down approach, ‘optical’ nociceptive thresholds were assessed with a 5-intensity hindpaw photostimulation paradigm, establishing the minimum intensity required to produce a withdrawal response (optical threshold). All testing was also video recorded and analysed post-hoc to assess additional photostimulation evoked behaviours. Repeated testing over several days showed optical nociceptive thresholds and response duration were similar, supporting the stability of these variables across a timeframe relevant to onset of pathology or drug administration. Optical nociceptive thresholds were also assessed following morphine administration (30 mg/kg), which significantly raised thresholds, highlighting analgesic screening utility of this model. Together, these findings demonstrate the peripheral photostimulation with optical thresholding is a useful addition to the preclinical nociception assessment toolkit, with the key advantage of inducing a purely nociceptive response to a non-invasive, non-tissue damaging stimulus.