bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic Analysis of KRAS-ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics
Authors: Zhao Zheng , Bohidar Niraja , Bourne Philip E. 
Published: February 2023

AbstractKRAS, a common human oncogene, has been recognized as a critical drug target in treating multiple cancers. After four decades of effort, one allosteric KRAS drug (Sotorasib) has been approved, inspiring more KRAS-targeted drug research. Here we provide the features of KRAS binding pockets and ligand-binding characteristics of KRAS complexes using a structural systems pharmacology approach. Three distinct binding sites (conserved nucleotide-binding site, shallow Switch-I/II pocket, and allosteric Switch-II/α3 pocket) are characterized. Ligand-binding features are determined based on encoded KRAS-inhibitor interaction fingerprints. Finally, the flexibility of the three distinct binding sites to accommodate different potential ligands, based on MD simulation, is discussed. Collectively, these findings are intended to facilitate rational KRAS drug design.
Neuromuscular Basis ofDrosophilaLarval Rolling Escape Behavior
Authors: Cooney Patricia C. , Huang Yuhan , Li Wenze , Perera Dulanjana M. , Hormigo Richard , Tabachnik Tanya , Godage Isuru S. , Hillman Elizabeth M.C. , Grueber Wesley B. , Zarin Aref A. 
Published: February 2023

AbstractWhen threatened by dangerous or harmful stimuli, animals engage in diverse forms of rapid escape behaviors. InDrosophilalarvae, one type of escape response involves C-shaped bending and lateral rolling followed by rapid forward crawling. The sensory circuitry that promotes larval escape has been extensively characterized; however, the motor programs underlying rolling are unknown. Here, we characterize the neuromuscular basis of rolling escape behavior. We used high-speed, volumetric, Swept Confocally-Aligned Planar Excitation (SCAPE) microscopy to image muscle activity during larval rolling. Unlike sequential peristaltic muscle contractions that progress from segment to segment during forward and backward crawling, the muscle activity progresses circumferentially during bending and rolling escape behavior. We propose that progression of muscular contraction around the larva’s circumference results in a transient misalignment between weight and the ground support forces, which generates a torque that induces stabilizing body rotation. Therefore, successive cycles of slight misalignment followed by reactive aligning rotation lead to continuous rolling motion. Supporting our biomechanical model, we found that disrupting the activity of muscle groups undergoing circumferential contraction progression lead to rolling defects. We use EM connectome data to identify premotor to motor connectivity patterns that could drive rolling behavior, and perform neural silencing approaches to demonstrate the crucial role of a group of glutamatergic premotor neurons in rolling. Our data reveal body-wide muscle activity patterns and putative premotor circuit organization for execution of the rolling escape response.Significance StatementTo escape from dangerous stimuli, animals execute escape behaviors that are fundamentally different from normal locomotion. The rolling escape behavior of Drosophila larvae consists of C-shaped bending and rolling. However, the muscle contraction patterns that lead to rolling are poorly understood. We find that following the initial body bending, muscles contract in a circumferential wave around the larva as they enter the bend, maintaining unidirectional rolling that resembles cylinder rolling on a surface. We study the structure of motor circuits for rolling, inhibit different motor neurons to determine which muscles are essential for rolling, and propose circuit and biomechanical models for roll generation. Our findings provide insights into how motor circuits produce diverse motor behaviors.
Ozanimod Attenuates Human Cerebrovascular Endothelial Derived MMP-9 Activity and Preserves Barrier Properties Following In Vitro Acute Ischemic Injury
Authors: Wendt Trevor S. , Gonzales Rayna J. 
Published: February 2023

AbstractEndothelial integrity is critical in mitigating a vicious cascade of secondary injuries following acute ischemic stroke (AIS). Matrix metalloproteinase-9 (MMP-9), a contributor to endothelial integrity loss, is elevated during stroke and is associated with worsened stroke outcome. We investigated the FDA approved selective sphingosine-1-phosphate receptor 1 (S1PR1) ligand, ozanimod, on the regulation/activity of MMP-9 as well as endothelial barrier components (PECAM-1, claudin-5, and ZO-1) in human brain microvascular endothelial cells (HBMECs) following hypoxia plus glucose deprivation (HGD). We previously reported that S1PR1 activation improves HBMEC integrity; however, specific mechanisms underlying S1PR1 involvement in barrier integrity have not been clearly elucidated. We hypothesized that ozanimod would attenuate an HGD-induced increase in MMP-9 activity which would concomitantly attenuate the loss of integral barrier components. Male HBMECs were treated with ozanimod (0.5nM) or vehicle and exposed to 3h normoxia (21% O2) or HGD (1% O2). Immunoblotting, zymography, qRT-PCR, and immunocytochemical labeling techniques assessed processes related to MMP-9 and barrier markers. We observed that HGD acutely increased MMP-9 activity and reduced claudin-5 and PECAM-1 levels, and ozanimod attenuated these responses. In situ analysis via PROSPER, suggested that attenuation of MMP-9 activity may be a primary factor in maintaining these integral barrier proteins. We also observed that HGD increased intracellular mechanisms associated with augmented MMP-9 activation, however ozanimod had no effect on these targeted factors. Thus, we conclude that ozanimod has the potential to attenuate HGD mediated decreases in HBMEC integrity in part by decreasing MMP-9 activity as well as preserving barrier properties.Graphical Abstract
Microbiome induced complement synthesized in the gut protects against enteric infections
Authors: Wu Meng , Zheng Wen , Song Xinyang , Bao Bin , Wang Yuanyou , Ramanan Deepshika , Yang Daping , Liu Rui , Macbeth John C. , Do Elyza A. , Andrade Warrison A , Yang Tiandi , Cho Hyoung-Soo , Gazzaniga Francesca S. , Ilves Marit , Coronado Daniela , Thompson Charlotte , Hang Saiyu , Chiu Isaac M. , Moffitt Jeffrey R. , Hsiao Ansel , Mekalanos John J. , Benoist Christophe , Kasper Dennis L. 
Published: February 2023

AbstractCanonically, complement is a serum-based host defense system that protects against systemic microbial invasion. Little is known about the production and function of complement components on mucosal surfaces. Here we show gut complement component 3 (C3), central to complement function, is regulated by the composition of the microbiota in healthy humans and mice, leading to host-specific gut C3 levels. Stromal cells in intestinal lymphoid follicles (LFs) are the predominant source of intestinal C3. During enteric infection withCitrobacter rodentiumor enterohemorrhagicEscherichia coli,luminal C3 levels increase significantly and are required for protection.C. rodentiumis remarkably more invasive to the gut epithelium of C3-deficient mice than of wild-type mice. In the gut, C3-mediated phagocytosis ofC. rodentiumfunctions to clear pathogens. Our study reveals that variations in gut microbiota determine individuals’ intestinal mucosal C3 levels, dominantly produced by LF stromal cells, which directly correlate with protection against enteric infection.HighlightsGut complement component 3 (C3) is induced by the microbiome in healthy humans and mice at a microbiota-specific level.Gut stromal cells located in intestinal lymphoid follicles are a major source of luminal C3During enteric infections withCitrobacter rodentiumor enterohemorrhagicEscherichia coli,gut luminal C3 levels increase and are required for protection.C. rodentiumis significantly more invasive of the gut epithelium in C3-deficient mice when compared to WT mice.In the gut, C3-mediated opsonophagocytosis ofC. rodentiumfunctions to clear pathogens.
Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening
Authors: Fiorin Giacomo , Forrest Lucy R. , Faraldo-Gómez José D. 
Published: February 2023

AbstractAll lipid membranes have inherent morphological preferences and resist deformation. Yet adaptations in membrane shape can and do occur at multiple length scales. While this plasticity is crucial for cellular physiology, the factors controlling the morphological energetics of lipid bilayers and the dominant mechanisms of membrane remodeling remain unclear. An ongoing debate regarding the universality of the stiffening effect of cholesterol underscores the challenges facing this field, both experimentally and theoretically, even for simple lipid mixtures. On the computational side, we have argued that enhanced- sampling all-atom molecular dynamics simulations are uniquely suited for quantification of membrane conformational energetics, not only because they minimize a-priori assumptions, but also because they permit analysis of bilayers in deformed states. To showcase this approach, we examine reported inconsistencies between alternative experimental measurements of bending moduli for cholesterol-enriched membranes. Specifically, we analyze lipid bilayers with different chain saturation, and compute free-energy landscapes for curvature deformations distributed over areas from ∼5 to ∼60 nm2. These enhanced simulations, totaling over 100 microseconds of sampling time, enable us to directly quantify both bending and tilt moduli, and to dissect the contributing factors and molecular mechanisms of curvature generation at each length scale. Our results show that cholesterol effects are lipid-specific, in agreement with giantvesicle measurements, and explain why experiments probing nanometer scale lipid dynamics diverge. In summary, we demonstrate that quantitative structure-mechanics relationships can now be established for heterogenous membranes, paving the way for addressing open fundamental questions in cell membrane mechanics.SignificanceElucidating the energetics and mechanisms of membrane remodeling is an essential step towards understanding cell physiology. This problem is challenging, however, because membrane bending involves both large-scale and atomic-level dynamics, which are difficult to measure simultaneously. A recent controversy regarding the stiffening effect of cholesterol, which is ubiquitous in animal cells, illustrates this challenge. We show how enhanced molecular-dynamics simulations can bridge this length-scale gap and reconcile seemingly incongruent observations. This approach facilitates a conceptual connection between lipid chemistry and membrane mechanics, thereby providing a solid basis for future research on remodeling phenomena, such as in membrane trafficking or viral infection.
Discovery of NRG1-VII: a novel myeloid-derived class of NRG1 isoforms
Authors: Berrocal-Rubio Miguel Ángel , Pawer Yair David Joseph , Dinevska Marija , De Paoli-Iseppi Ricardo , Widodo Samuel S. , Gleeson Josie , Rajab Nadia , De Nardo Will , Hallab Jeannette , Li Anran , Mantamadiotis Theo , Clark Michael B. , Wells Christine A. 
Published: February 2023

AbstractThe growth factor Neuregulin-1 (NRG1) has pleiotropic roles in proliferation and differentiation of the stem cell niche in different tissues. It has been implicated in gut, brain and muscle development and repair. Six isoform classes of NRG1 and over 28 protein isoforms have been previously described. Here we report a new class of NRG1, designated NRG1-VII to denote that these NRG1 isoforms arise from a myeloid-specific transcriptional start site (TSS) previously uncharacterized. Long-read sequencing was used to identify eight high-confidence NRG1-VII transcripts. These transcripts presented major structural differences from one another, through the use of cassette exons and alternative stop codons. Expression of NRG1-VII was confirmed in primary human monocytes and tissue resident macrophages and iPSC-derived macrophages. Isoform switching via cassette exon usage and alternate polyadenylation was apparent during monocyte maturation and macrophage differentiation. NRG1-VII is the major class expressed by the myeloid lineage, including tissue-resident macrophages. Analysis of public gene expression data indicates that monocytes and macrophages are a primary source of NRG1, suggesting that NRG1-VII is the most common class of NRG1 in most adult human tissues, except brain. The size and structure of type VII isoforms suggests that they may be more diffusible through tissues than other NRG1 classes. However, the specific roles of type VII variants in tissue homeostasis and repair have not yet been determined.
An Innovative Non-Hormonal Strategy Targeting Redox Active Metals to Down-Regulate Estrogen-, Progesterone-, Androgen- and Prolactin-Receptors in Breast Cancer
Authors: Shehadeh-Tout Faten , Milioli Heloisa H. , Roslan Suraya , Jansson Patric J. , Dharmasivam Mahendiran , Graham Dinny , Anderson Robin , Wijesinghe Tharushi , Azad Mahan Gholam , Richardson Des R. , Kovacevic Zaklina 
Published: February 2023

AbstractEstrogen receptor-α (ER-α) is a key driver of breast cancer (BC) targeted by tamoxifen. However, tamoxifen resistance is a major problem. An important mechanism of resistance is the activation of EGFR/HER2/HER3 signaling and other hormone receptors (androgen receptor (AR), progesterone receptor (PR), prolactin receptor (PRL-R)) that intrinsically activate ER-α. Hence, therapeutics targeting multiple receptors, rather than ER-α alone, would be extremely useful and may overcome tamoxifen resistance. This study examined the activity of redox-active di-2-pyridylketone-4,4-dimethyl-3-thiosemicarbazone (Dp44mT) and di-2-pyridylketone-4-cyclohexyl-4-methyl-3-thiosemicarbazone (DpC), on the expression and activation of crucial hormone receptors, their co-factors, and key resistance pathways in ER-α-positive BC. Strikingly, DpC differentially regulated 106 estrogen-response genes with Sankey diagram analysis demonstrating this was linked to decreased mRNA levels of 4 central hormone receptors involved in BC pathogenesis, namelyER,PR,AR, andPRL-R. Mechanistic dissection demonstrated that due to DpC and Dp44mT binding metal ions, these agents caused a pronounced decrease in ER-α, AR, PR, and PRL-R protein expression. Ablation of the metal-binding site in the thiosemicarbazone totally prevented its suppressive activity, demonstrating a unique non-hormonal mechanism. DpC and Dp44mT also inhibited EGFR, HER2, and HER3 activation, their downstream signaling, and the expression of co-factors that promote ER-α transcriptional activity, including SRC3, NF-κB p65, and SP1.In vivo,DpC was highly tolerable and effectively inhibited ER-α-positive BC growth. In conclusion, through a bespoke non-hormonal mechanism targeting redox active metals, Dp44mT and DpC disrupt multiple key inter-receptor interactions between PR, AR, PRL-R, and tyrosine kinases that act with ER-α to promote BC, constituting an innovative therapeutic approach.
Oral administration of 4-methylumbelliferone reduces glial scar and promotes anatomical plasticity
Authors: Štepánková Kateřina , Chudíčková Milada , Šimková Zuzana , Martinez-Varea Noelia , Kubinová Šárka , Urdzíková Lucia Machová , Jendelová Pavla , Kwok Jessica C F 
Published: February 2023

ABSTRACTFollowing a spinal cord injury (SCI), chondroitin sulfate proteoglycans (CSPGs) are up-regulated at the glial scar inhibiting neuroregeneration. Under normal physiological condition, CSPGs interact with hyaluronan (HA) and other extracellular matrix on neuronal surface forming a macromolecular structure called perineuronal nets (PNNs) which regulate neuroplasticity. 4-methylumbelliferone (4-MU) has been used previously to down-regulate HA synthesis but not been tested in SCI. In this study, we have evaluated the effect of 4-MU, an inhibitor of HA, in a chronic contusion model of SCI in rats. At a dose of 1.2 g/kg/day of 4-MU, we observed not only the reduction of HA in the uninjured spinal cords after 60 days of 4-MU administration, but also a down-regulation of CS glycosaminoglycans (CS-GAGs). In order to assess the effect of 4-MU in chronic SCI, rats with T8 spinal contusion injury were fed with 4-MU or placebo for 8 weeks in combination with daily treadmill rehabilitation for 16 weeks to promote neuroplasticity. 4-MU treatment promoted significant sprouting of 5-hydroxytryptamine (5-HT) positive fibres into ventral horns and reduced the HA synthesis by astrocytes around the lesion site. While 4-MU reduced astrogliosis in chronic stage of SCI, the current dose was not sufficient to down-regulate the increased production of CS-GAGs or behavioural performance. Together, these data suggest that oral treatment with 4-MU is able to induce anatomical plasticity but further adjustment on the dosage will be required to benefit functional recovery after SCI.
Conformational plasticity and allosteric communication networks govern Shelterin protein TPP1 binding to human telomerase
Authors: Aureli Simone , Raniolo Stefano , Limongelli Vittorio 
Published: February 2023

AbstractThe molecular binding interaction between the Shelterin complex protein TPP1 and human telomerase enzyme (TERT) triggers the telomerase maintenance mechanism that marks cell lifespan. The TPP1’s structural element deputed to bind TERT is the OB-domain, which is able to interact with TERT’s hTEN (TPP1 binding telomerase domain) through the TEL-patch, a group of amino acids whose mutations provoke harsh pathologies. Indeed, aberrations in the formation of TPP1-TERT het-erodimer can lead to severe diseases like Hoyeraal-Hreidarsson syndrome (HHS), whose patients are affected by short telomeres and extremely poor life expectancy. In the present study, we provide a thorough characterization of the structural properties of the TPP1’s OB-domain by combining data coming from microsecond-long molecular dynamics calculations, time-series analyses, and graph-based networks. Our results show that the conformational plasticity of the TPP1’s TEL-patch region is influenced by a network of long-range amino acid communications, needed for the proper TPP1-hTEN binding. Furthermore, we reveal that in the Glu169Δand Lys170ΔTPP1 variants, responsible for HHS, the plasticity of the TEL-patch region is reduced, affecting the correct binding to hTEN and in turn the telomere processivity, which eventually leads to accelerated ageing of affected cells. Our study provides an unprecedented structural basis for the design of TPP1-targeting ligands with therapeutic potential against cancer and telomerase deficiency diseases.
PermaNet® Dual, a new deltamethrin-chlorfenapyr mixture net, shows improved efficacy against pyrethroid-resistantAnopheles gambiae sensu latoin southern Benin
Authors: Syme Thomas , N’dombidjé Boris , Gbegbo Martial , Todjinou Damien , Ariori Victoria , De Vos Patricia , Pigeon Olivier , Ngufor Corine 
Published: February 2023

AbstractPyrethroid-chlorfenapyr nets have demonstrated improved entomological and epidemiological impact in trials across Africa. This is driving increased demand for this novel net class in malaria endemic countries. PermaNet® Dual is a new deltamethrin-chlorfenapyr net developed by Vestergaard Sàrl to provide more options to malaria control programmes. We performed an experimental hut trial to evaluate the efficacy of PermaNet® Dual against wild, free-flying pyrethroid-resistantAnopheles gambiae sensu latoin Covè, Benin. PermaNet® Dual induced superior levels of mosquito mortality compared to a pyrethroid-only net and a pyrethroid-piperonyl butoxide net both when unwashed (77% with PermaNet® Dual vs. 23% with PermaNet® 2.0 and 56% with PermaNet® 3.0, p<0.001) and after 20 standardised washes (75% with PermaNet® Dual vs. 14% with PermaNet® 2.0 and 30% with PermaNet® 3.0, p<0.001). Using a provisional non-inferiority margin defined by the World Health Organisation, PermaNet® Dual was also non-inferior to a pyrethroid-chlorfenapyr net that has demonstrated improved public health value (Interceptor® G2), for vector mortality (79% vs. 76%, OR=0.854, 95% CIs: 0.703–1.038) but not for blood-feeding protection (35% vs. 26%, OR=1.445, 95% CIs: 1.203–1.735). PermaNet® Dual presents an additional option of this highly effective net class for improved control of malaria transmitted by pyrethroid-resistant mosquitoes.
Social affective behaviors among female rats involve the basolateral amygdala and insular cortex
Authors: Djerdjaj Anthony , Rieger Nathaniel S. , Brady Bridget H. , Carey Bridget N. , Ng. Alexandra J. , Christianson John P. 
Published: February 2023

AbstractThe ability to detect, appraise, and respond to another’s emotional state is essential to social affective behavior. This is mediated by a network of brain regions responsible for integrating external cues with internal states to orchestrate situationally appropriate behavioral responses. The basolateral amygdala (BLA) and the insular cortex are reciprocally connected regions involved in social cognition and prior work in male rats revealed their contributions to social affective behavior. We investigated the functional role of these regions in female rats in a social affective preference (SAP) test in which experimental rats approach stressed juvenile but avoid stressed adult conspecifics. In separate experiments, the BLA or the insula were inhibited by local infusion of muscimol (100ng/side in 0.5μL saline) or vehicle prior to SAP tests. In both regions, muscimol interfered with preference for the stressed juvenile and naive adult, indicating that these regions are necessary for appropriate social affective behavior. In male rats, SAP behavior requires insular oxytocin but there are noteworthy sex differences in the oxytocin receptor distribution in rats. Oxytocin (500nM) administered to the insula did not alter social behavior but oxytocin infusions to the BLA increased social interaction. In sum, female rats appear to use the same BLA and insula regions for social affective behavior but sex differences exist in contribution of oxytocin in the insula.
An unbiased, automated platform for scoring dopaminergic neurodegeneration inC. elegans
Authors: Clark Andrew S. , Kalmanson Zachary , Morton Katherine , Hartman Jessica , Meyer Joel , San-Miguel Adriana 
Published: February 2023

AbstractCaenorhabditis elegans(C. elegans) has served as a simple model organism to study dopaminergic neurodegeneration, as it enables quantitative analysis of cellular and sub-cellular morphologies in live animals. These isogenic nematodes have a rapid life cycle and transparent body, making high-throughput imaging and evaluation of fluorescently tagged neurons possible. However, the current state-of-the-art method for quantifying dopaminergic degeneration requires researchers to manually examine images and score dendrites into groups of varying levels of neurodegeneration severity, which is time consuming, subject to bias, and limited in data sensitivity. We aim to overcome the pitfalls of manual neuron scoring by developing an automated, unbiased image processing algorithm to quantify dopaminergic neurodegeneration inC. elegans. The algorithm can be used on images acquired with different microscopy setups and only requires two inputs: a maximum projection image of the four cephalic neurons in theC. eleganshead and the pixel size of the user’s camera. We validate the platform by detecting and quantifying neurodegeneration in nematodes exposed to rotenone, cold shock, and 6-hydroxydopamine using 63x epifluorescence, 63x confocal, and 40x epifluorescence microscopy, respectively. Analysis of tubby mutant worms with altered fat storage showed that, contrary to our hypothesis, increased adiposity did not sensitize to stressor-induced neurodegeneration. We further verify the accuracy of the algorithm by comparing code-generated, categorical degeneration results with manually scored dendrites of the same experiments. The platform, which detects 19 different metrics of neurodegeneration, can provide comparative insight into how each exposure affects dopaminergic neurodegeneration patterns.