bluuebunny/crossref_metadata_2025_split huggingface dataset:
InDeep : 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions
Authors: Mallet Vincent , Ruano Luis Checa , Franel Alexandra Moine , Nilges Michael , Druart Karen , Bouvier Guillaume , Sperandio Olivier 
Published: July 2021

AbstractMotivationProtein-protein interactions (PPIs) are key elements in numerous biological pathways and the subject of a growing number of drug discovery projects including against infectious diseases. Designing drugs on PPI targets remains a difficult task and requires extensive efforts to qualify a given interaction as an eligible target. To this end, besides the evident need to determine the role of PPIs in disease-associated pathways and their experimental characterization as therapeutics targets, prediction of their capacity to be bound by other protein partners or modulated by future drugs is of primary importance.ResultsWe presentInDeep, a tool for predicting functional binding sites within proteins that could either host protein epitopes or future drugs. Leveraging deep learning on a curated data set of PPIs, this tool can proceed to enhanced functional binding site predictions either on experimental structures or along molecular dynamics trajectories. The benchmark ofInDeepdemonstrates that our tool outperforms state of the art ligandable binding sites predictors when assessing PPI targets but also conventional targets. This offers new opportunities to assist drug design projects on PPIs by identifying pertinent binding pockets at or in the vicinity of PPI interfaces.AvailabilityThe tool is available on GitHub3along with a PyMol plugin for visualization. Predictions of InDeep can be consulted at iPPI-DB4
Calcium/Calmodulin Dependent Protein Kinase Kinase 2 Regulates the Expansion of Tumor-induced Myeloid-Derived Suppressor Cells
Authors: Huang Wei , Liu Yaping , Luz Anthony , Berrong Mark , Meyer Joel N , Zou Yujing , Swann Excel , Sundaramoorthy Pasupathi , Kang Yubin , Jauhari Shekeab , Lento William , Chao Nelson , Racioppi Luigi 
Published: July 2021

AbstractMyeloid-derived suppressor cells (MDSCs) are a heterogeneous group of cells, which can suppress the immune response, promote tumor progression and impair the efficacy of immunotherapies. Consequently, the pharmacological targeting of MDSC is emerging as a new immunotherapeutic strategy to stimulate the natural anti-tumor immune response and potentiate the efficacy of immunotherapies. Herein, we leveraged genetically modified models and a small molecule inhibitor to validate Calcium-Calmodulin Kinase Kinase 2 (CaMKK2) as a druggable target to control MDSC accumulation in tumor-bearing mice. The results indicated that deletion of CaMKK2 in the host attenuated the growth of engrafted tumor cells, and this phenomenon was associated with increased antitumor T cell response and decreased accumulation of MDSC. The adoptive transfer of MDSC was sufficient to restore the ability of the tumor to grow in Camkk2-/- mice, confirming the key role of MDSC in the mechanism of tumor rejection. In vitro studies indicated that blocking of CaMKK2 is sufficient to impair the yield of MDSC. Surprisingly, MDSC generated from Camkk2-/- bone marrow cells also showed a higher ability to terminally differentiate toward more immunogenic cell types (e.g inflammatory macrophages and dendritic cells) compared to wild type (WT). Higher intracellular levels of reactive oxygen species (ROS) accumulated in Camkk2-/- MDSC, increasing their susceptibility to apoptosis and promoting their terminal differentiation toward more mature myeloid cells. Mechanistic studies indicated that AMP-activated protein kinase (AMPK), which is a known CaMKK2 proximal target controlling the oxidative stress response, fine-tunes ROS accumulation in MDSC. Accordingly, failure to activate the CaMKK2-AMPK axis can account for the elevated ROS levels in Camkk2-/- MDSC. These results highlight CaMKK2 as an important regulator of the MDSC lifecycle, identifying this kinase as a new druggable target to restrain MDSC expansion and enhance the efficacy of anti-tumor immunotherapy.
Metallothionein 3-zinc axis suppresses caspase-11 inflammasome activation and impairs antibacterial immunity
Authors: Chowdhury Debabrata , Gardner Jason C , Satpati Abhijit , Nookala Suba , Mukundan Santhosh , Porollo Aleksey , Landero Figueroa Julio A. , Vignesh Kavitha Subramanian 
Published: July 2021

AbstractNon-canonical inflammasome activation by mouse caspase-11 (or human CASPASE- 4/5) is crucial for the clearance of certain gram-negative bacterial infections, but can lead to severe inflammatory damage. Factors that promote non-canonical inflammasome activation are well recognized, but less is known about the mechanisms underlying its negative regulation. Herein, we identify that the caspase-11 inflammasome in mouse and human macrophages (Mϕ) is negatively controlled by the zinc (Zn2+) regulating protein, metallothionein 3 (MT3). Upon challenge with intracellular lipopolysaccharide (iLPS), Mϕ increased MT3 expression that curtailed the activation of caspase-11 and its downstream targets caspase-1 and interleukin (IL)-1β. Mechanistically, MT3 increased intramacrophage Zn2+ to downmodulate the TRIF-IRF3-STAT1 axis that is prerequisite for caspase-11 effector function. MT3 suppressed activation of the caspase-11 inflammasome, while caspase-11 and MT3 synergized in impairing antibacterial immunity. The present study identifies an important yin-yang relationship between the non-canonical inflammasome and MT3 in controlling inflammation and immunity to gram- negative bacteria.GRAPHICAL ABSTRACT
Single voxel autocorrelation uncovers gradients of temporal dynamics in the hippocampus and entorhinal cortex during rest and navigation
Authors: Bouffard Nichole R. , Golestani Ali , Brunec Iva K. , Bellana Buddhika , Park Jun Young , Barense Morgan D. , Moscovitch Morris 
Published: July 2021

AbstractDuring navigation, information at multiple scales needs to be integrated. Single- unit recordings in rodents suggest that gradients of temporal dynamics in the hippocampus and entorhinal cortex support this integration. In humans, gradients of representation are observed, such that granularity of information represented increases along the long axis of the hippocampus. The neural underpinnings of this gradient in humans, however, are still unknown. Current research is limited by coarse fMRI analysis techniques that obscure the activity of individual voxels, preventing investigation of how moment-to-moment changes in brain signal are organized and how they are related to behavior. Here, we measured the signal stability of single voxels over time to uncover previously unappreciated gradients of temporal dynamics in the hippocampus and entorhinal cortex. Using our novel, single voxel autocorrelation technique, we show a medial-lateral hippocampal gradient, as well as a continuous autocorrelation gradient along the anterolateral- posteromedial entorhinal extent. Importantly, we show that autocorrelation in the anterior-medial hippocampus was modulated by navigational difficulty, providing the first evidence that changes in signal stability in single voxels are relevant for behavior. This work opens the door for future research on how temporal gradients within these structures support the integration of information for goal- directed behavior.
The universal language network: A cross-linguistic investigation spanning 45 languages and 12 language families
Authors: Malik-Moraleda Saima , Ayyash Dima , Gallée Jeanne , Affourtit Josef , Hoffmann Malte , Mineroff Zachary , Jouravlev Olessia , Fedorenko Evelina 
Published: July 2021

AbstractTo understand the architecture of human language, it is critical to examine diverse languages; yet most cognitive neuroscience research has focused on a handful of primarily Indo-European languages. Here, we report an investigation of the fronto-temporo-parietal language network across 45 languages and establish the robustness to cross-linguistic variation of its topography and key functional properties, including left-lateralization, strong functional integration among its brain regions, and functional selectivity for language processing.
Selective Requirement for Polycomb Repressor Complex 2 in the Generation of Specific Hypothalamic Neuronal Sub-types
Authors: Salmani Behzad Yaghmaeian , Balderson Brad , Bauer Susanne , Ekman Helen , Starkenberg Annika , Perlmann Thomas , Piper Michael , Bodén Mikael , Thor Stefan 
Published: July 2021

ABSTRACTThe hypothalamus displays staggering cellular diversity, chiefly established during embryogenesis by the interplay of several signalling pathways and a battery of transcription factors. However, the contribution of epigenetic cues to hypothalamus development remains unclear. We mutated the Polycomb Repressor Complex 2 gene Eed in the developing mouse hypothalamus, which resulted in the loss of H3K27me3; a fundamental epigenetic repressor mark. This triggered ectopic expression of posteriorly expressed regulators (e.g., Hox homeotic genes), upregulation of cell cycle inhibitors and reduced proliferation. Surprisingly, despite these effects, single cell transcriptomic analysis revealed that the majority of neuronal subtypes were still generated in Eed mutants. However, we observed an increase in Glutamatergic/GABAergic double-positive cells, as well as loss/reduction of dopamine, Hypocretin/Orexin and Tac2 neurons. These findings indicate that many aspects of the hypothalamic gene regulatory flow can proceed without the key H3K27me3 epigenetic repressor mark, and points to a unique sensitivity of particular neuronal sub-types to a disrupted epigenomic landscape.
Reward Enhances Connectivity between the Ventral Striatum and the Default Mode Network
Authors: Dobryakova Ekaterina , Smith David V. 
Published: July 2021

AbstractThe default mode network (DMN) has been theorized to participate in a range of social, cognitive, and affective functions. Yet, previous accounts do not consider how the DMN contributes to other brain regions depending on psychological context, thus rendering our understanding of DMN function incomplete. We addressed this gap by applying a novel network-based psychophysiological interaction (nPPI) analysis to the reward task within the Human Connectome Project. We first focused on the task-evoked responses of the DMN and other networks involving the prefrontal cortex, including the executive control network (salience network) and the left and right frontoparietal networks. Consistent with a host of prior studies, the DMN exhibited a relative decrease in activation during the task, while the other networks exhibited a relative increase during the task. Next, we used nPPI analyses to assess whether these networks exhibit task-dependent changes in connectivity with other brain regions. Strikingly, we found that the experience of reward enhances task-dependent connectivity between the DMN and the ventral striatum, an effect that was specific to the DMN. Surprisingly, the strength of DMN-VS connectivity was correlated with personality characteristics relating to openness. Taken together, these results advance models of DMN by demonstrating how it contributes to other brain systems during task performance and how those contributions relate to individual differences.
The neuropeptide Pth2 modulates social behavior and anxiety in zebrafish
Authors: Anneser Lukas , Gemmer Anja , Eilers Tim , Alcantara Ivan C. , Loos Anett-Yvonn , Ryu Soojin , Schuman Erin M. 
Published: July 2021

SummaryAnimal behavior is strongly context-dependent and behavioral performance is often modulated by internal state. In particular, different social contexts can alter anxiety levels and modulate social behavior. The vertebrate-specific neuropeptide parathyroid hormone 2 (pth2) is directly regulated by the presence or absence of conspecifics in zebrafish. As its cognate receptor, the parathyroid hormone 2 receptor (pth2r), is widely expressed across the brain, we tested fish lacking the functional Pth2 peptide in several anxiety-related and social paradigms. Rodents lacking PTH2 display increased anxiety-related behavior. Here we show that the propensity to react to sudden stimuli with an escape response is increased in pth2-/- zebrafish, consistent with elevated anxiety. While overall social preference for conspecifics is maintained in pth2-/- fish until the early juvenile stage, we found that both social preference and shoaling are altered later in development. The data presented suggest that the neuropeptide Pth2 modulates several conserved behavioral features, and may thus enable the animal to react appropriately in different social contexts.
Annexin A1 is a polarity cue that directs planar mitotic spindle orientation during mammalian epithelial morphogenesis
Authors: Fankhaenel Maria , Hashemi Farahnaz Sadat Golestan , Mourao Larissa , Lucas Emily , Hosawi Manal Mosa , Skipp Paul , Morin Xavier , Scheele Colinda L.G.J. , Elias Salah 
Published: July 2021

AbstractOriented cell divisions are critical for the formation and maintenance of structured epithelia. Proper mitotic spindle orientation relies on polarised anchoring of force generators to the cell cortex by the evolutionarily conserved Gαi-LGN-NuMA complex. However, the polarity cues that control cortical patterning of this ternary complex remain largely unknown in mammalian epithelia. Here we identify the membrane-associated protein Annexin A1 (ANXA1) as a novel interactor of LGN in mammary epithelial cells. ANXA1 acts independently of Gαito instruct the accumulation of LGN and NuMA at the lateral cortex to ensure cortical anchoring of Dynein-Dynactin and astral microtubules and thereby planar alignment of the mitotic spindle. Loss of ANXA1 randomises mitotic spindle orientation, which in turn disrupts epithelial architecture and luminogenesis in three-dimensional cultures of primary mammary epithelial cells. Our findings establish ANXA1 as an upstream cortical cue that regulates LGN to direct planar cell divisions during mammalian epithelial morphogenesis.
Patient-specific Boolean models of signaling networks guide personalized treatments
Authors: Montagud Arnau , Béal Jonas , Tobalina Luis , Traynard Pauline , Subramanian Vigneshwari , Szalai Bence , Alföldi Róbert , Puskás László , Valencia Alfonso , Barillot Emmanuel , Saez-Rodriguez Julio , Calzone Laurence 
Published: July 2021

AbstractProstate cancer is the second most occurring cancer in men worldwide. To better understand the mechanisms of tumorigenesis and possible treatment responses, we developed a mathematical model of prostate cancer which considers the major signalling pathways known to be deregulated.We personalised this Boolean model to molecular data to reflect the heterogeneity and specific response to perturbations of cancer patients. 488 prostate samples were used to build patient-specific models and compared to available clinical data. Additionally, eight prostate cell-line-specific models were built to validate our approach with dose-response data of several drugs.The effects of single and combined drugs were tested in these models under different growth conditions. We identified 15 actionable points of interventions in one cell-line-specific model whose inactivation hinders tumorigenesis. To validate these results, we tested nine small molecule inhibitors of five of those putative targets and found a dose-dependent effect on four of them, notably those targeting HSP90 and PI3K. These results highlight the predictive power of our personalized Boolean models and illustrate how they can be used for precision oncology.
A repurposed, non-canonical cytochrome c, chaperones calcium binding by PilY1 for type IVa pili formation
Authors: Herfurth Marco , Treuner-Lange Anke , Glatter Timo , Wittmaack Nadine , Hoiczyk Egbert , Pierik Antonio J. , Søgaard-Andersen Lotte 
Published: July 2021

AbstractType IVa pili (T4aP) are versatile bacterial cell surface structures that undergo extension/adhesion/retraction cycles powered by the cell envelope-spanning T4aP machine. In this machine, a complex composed of four minor pilins and PilY1 primes T4aP extension and is also present at the pilus tip mediating adhesion. Similar to many other bacteria, Myxococcus xanthus contains multiple minor pilins/PilY1 sets that are incompletely understood. Here, we report that minor pilins and PilY1 (PilY1.1) of cluster_1 form priming and tip complexes contingent on a non-canonical cytochrome c (TfcP) with an unusual His/Cys heme ligation and calcium. We provide evidence that TfcP is unlikely to participate in electron transport and has been repurposed to promote calcium binding by PilY1.1 at low calcium concentrations, thereby stabilising PilY1.1 and enabling T4aP function in a broader range of calcium concentrations. These results identify a novel function of cytochromes c and illustrate how incorporating an accessory factor expands the environmental range under which the T4aP system functions.
Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor
Authors: Mukhi N , Brown H , Gorenkin D , Ding P , Bentham AR , Jones JDG , Banfield MJ 
Published: July 2021

AbstractPlants use intracellular immune receptors (NLRs) to detect pathogen-derived effector proteins. The Arabidopsis NLR pair RRS1-R/RPS4 confers disease resistance to different bacterial pathogens by perceiving structurally distinct effectors AvrRps4 from Pseudomonas syringae pv. pisi and PopP2 from Ralstonia solanacearum via an integrated WRKY domain in RRS1-R. How the WRKY domain of RRS1 (RRS1WRKY) perceives distinct classes of effector to initiate an immune response is unknown. We report here the crystal structure of the in planta processed C-terminal domain of AvrRps4 (AvrRps4C) in complex with RRS1WRKY. Perception of AvrRps4C by RRS1WRKY is mediated by the β2-β3 segment of RRS1WRKY that binds an electronegative patch on the surface of AvrRps4C. Structure-based mutations that disrupt AvrRps4C/RRS1WRKY interactions in vitro compromise RRS1/RPS4-dependent immune responses. We also show that AvrRps4C can associate with the WRKY domain of the related but distinct RRS1B/RPS4B NLR pair, and the DNA binding domain of AtWRKY41, with similar binding affinities. This work demonstrates how integrated domains in plant NLRs can directly bind structurally distinct effectors to initiate immunity.SignificanceThis study reveals a mechanism of effector recognition by a plant NLR immune receptor that carries an integrated domain (ID) which mimics an authentic pathogen effector target. An Arabidopsis immune receptor carrying RRS1 and RPS4 NLR proteins detects the Pseudomonas syringae pv. pisi secreted effector AvrRps4 via a WRKY ID in RRS1. We used structural biology to reveal the mechanisms of AvrRps4/WRKY interaction and demonstrated that this binding is essential for effector recognition in planta. Our analysis revealed distinctive features of the WRKY ID that mediate the recognition of structurally distinct effectors from different bacterial pathogens. These insights could enable engineering NLRs with novel recognition specificities, and enhances our understanding of how effectors interact with host proteins.
Chromatin Patterns Distinguish Breast Tumor Subtypes and Disease Progression in Association withANP32Elevels
Authors: Ruff Garrett L. , Murphy Kristin E. , Vertino Paula M. , Murphy Patrick J. 
Published: July 2021

ABSTRACTDespite highly advanced diagnosis and treatment strategies, breast cancer patient outcomes vary extensively, even among individuals with the same diagnosis. Thus, a better understanding of the unique molecular characteristics that underlie tumor trajectories and responses to therapy remains a central goal. We report that chromatin patterns represent an important characteristic, capable of stratifying tumor identity and progression. We find that patterns of chromatin accessibility can be classified into 3 major groups, representing Basal-like tumors, hormone receptor (HR)-expressing tumors, and invasive lobular Luminal-A tumors. Major chromatin differences occur throughout the genome at motifs for the transcription factor FOXA1 in HR-positive tumors, and motifs for SOX9 in Basal-like tumors. A large portion of lobular Luminal-A tumors display a chromatin signature defined by accessibility at FOXA1 binding motifs, distinguishing them from others within this subtype. Expression of the histone chaperoneANP32Eis inversely correlated with tumor progression and chromatin accessibility at FOXA1 binding sites. Tumors with high levels of ANP32E exhibit an immune response and proliferative gene expression signature, whereas tumors with low ANP32E levels appear programmed for differentiation. Our results indicate that ANP32E may function through chromatin state regulation to control breast cancer differentiation and tumor plasticity.
In situ cryo-electron tomography reveals local cellular machineries for axon branch development
Authors: Nedozralova Hana , Basnet Nirakar , Ibiricu Iosune , Bodakuntla Satish , Biertümpfel Christian , Mizuno Naoko 
Published: July 2021

AbstractNeurons are highly polarized cells forming an intricate network of dendrites and axons. They are shaped by the dynamic reorganization of cytoskeleton components and cellular organelles. Axon branching allows to form new paths and increases circuit complexity. However, our understanding of branch formation is sparse due to technical limitations. Using in situ cellular cryo-electron tomography on primary mouse neurons, we directly visualized the remodeling of organelles and cytoskeleton structures at axon branches. Strikingly, branched areas functioned as hotspots concentrating organelles to support dynamic activities. Unaligned actin filaments assembled at the base of premature branches and remained while filopodia diminished. Microtubules and ER co-migrated into preformed branches to support outgrowth together with accumulating compact ~500 nm mitochondria and locally clustered ribosomes. We obtained a roadmap of events and present the first direct evidence of local protein synthesis selectively taking place at axon branches, allowing to serve as unique control hubs for axon development and downstream neural network formation.