bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endothelial cell flow-mediated quiescence is temporally regulated and utilizes the cell cycle inhibitor p27
Authors: Tanke Natalie T , Liu Ziqing , Gore Michaelanthony T , Bougaran Pauline , Linares Mary B , Marvin Allison , Sharma Arya , Oatley Morgan , Yu Tianji , Quigley Kaitlyn , Vest Sarah , Cook Jeanette Gowen , Bautch Victoria L 
Published: June 2023

ABSTRACTBackgroundEndothelial cells regulate their cell cycle as blood vessels remodel and transition to quiescence downstream of blood flow-induced mechanotransduction. Laminar blood flow leads to quiescence, but how flow-mediated quiescence is established and maintained is poorly understood.MethodsPrimary human endothelial cells were exposed to laminar flow regimens and gene expression manipulations, and quiescence depth was analyzed via time to cell cycle re-entry after flow cessation. Mouse and zebrafish endothelial expression patterns were examined via scRNA seq analysis, and mutant or morphant fish lacking p27 were analyzed for endothelial cell cycle regulation andin vivocellular behaviors.ResultsArterial flow-exposed endothelial cells had a distinct transcriptome, and they first entered a deep quiescence, then transitioned to shallow quiescence under homeostatic maintenance conditions. In contrast, venous-flow exposed endothelial cells entered deep quiescence early that did not change with homeostasis. The cell cycle inhibitor p27 (CDKN1B)was required to establish endothelial flow-mediated quiescence, and expression levels positively correlated with quiescence depth. p27 lossin vivoled to endothelial cell cycle upregulation and ectopic sprouting, consistent with loss of quiescence.HES1andID3, transcriptional repressors of p27 upregulated by arterial flow, were required for quiescence depth changes and the reduced p27 levels associated with shallow quiescence.ConclusionsEndothelial cell flow-mediated quiescence has unique properties and temporal regulation of quiescence depth that depends on the flow stimulus. These findings are consistent with a model whereby flow-mediated endothelial cell quiescence depth is temporally regulated downstream of p27 transcriptional regulation by HES1 and ID3. The findings are important in understanding endothelial cell quiescence mis-regulation that leads to vascular dysfunction and disease.GRAPHICAL ABSTRACTHIGHLIGHTSDifferent quiescence stimuli lead to distinct transcriptional and functional quiescence profiles in endothelial cellsp27 is required for endothelial cell quiescence and depth is temporally regulated in a flow stimulus-dependent manner that correlates with p27 levels and flow-regulated repressorsHES1andID3p27 is expressed in endothelial cells according to flow magnitudein vivoand is functionally required for cell cycle regulation and sproutingin vivo
Protein Dynamics Govern the Oxyferrous State Lifetime of an Artificial Oxygen Transport Protein
Authors: Zhang Lei , Brown Mia C. , Mutter Andrew C. , Greenland Kelly N. , Cooley Jason W. , Koder Ronald L. 
Published: June 2023

ABSTRACTIt has long been known that the alteration of protein side chains which occlude or expose the heme cofactor to water can greatly affect the stability of the oxyferrous heme state. Here we demonstrate that the rate of dynamically-driven water penetration into the core of an artificial oxygen transport protein also correlates with oxyferrous state lifetime by reducing global dynamics, without altering the structure of the active site, via the simple linking of the two monomers in a homodimeric artificial oxygen transport protein using a glycine-rich loop. The tethering of these two helices does not significantly affect the active site structure, pentacoordinate heme binding affinity, reduction potential, or gaseous ligand affinity. It does, however, significantly reduce the hydration of the protein core as demonstrated by resonance Raman spectroscopy, backbone amide hydrogen exchange, and pKa shifts in buried histidine side chains. This further destabilizes the charge-buried entatic state and nearly triples the oxyferrous state lifetime. These data are the first direct evidence that dynamically-driven water penetration is a rate-limiting step in the oxidation of these complexes. It furthermore demonstrates that structural rigidity which limits water penetration is a critical design feature in metalloenzyme construction and provides an explanation for both the failures and successes of earlier attempts to create oxygen-binding proteins.SignificanceThis communication sheds light on one of the more controversial areas in protein folding and design: the dynamic nature of the hydrophobic core and its relationship to metalloprotein function, in particular the relationship between dynamic solvent penetration into the protein core and the stability of metalloenzyme intermediates. We demonstrate that the basic tetrameric scaffold that is the classic helical bundle model for cofactor binding and activation can be easily upgraded to a more rigid, less dynamic, single chain helical bundle by merely taking the same helical sequences and converting it to a single chain protein connected by simple, nonoptimized glycine-rich loops. Importantly, our results explain the decades-long history of failure in the design of proteins capable of stably forming an oxyferrous state – the requirement for a protein large enough to protect the heme porphyrin surface with both structural specificity and sufficient structural rigidity to restrict water penetration into the protein core. Finally, we believe this is the first use of Deep UV Resonance Raman spectroscopy to monitor dynamic water penetration in a functional protein. This method may prove useful moving forward to many research groups.
Gene family evolution in brassicaceous-feeding insects: Implications for adaptation and host plant range
Authors: Ravikanthachari Nitin , Boggs Carol L 
Published: June 2023

AbstractHerbivores have a defined range of hostplants that they can feed on, which is mediated by underlying detoxification and sensory repertoires. Insects that feed on Brassicaceae represent one of the striking examples of co-evolutionary arms race. Insects specialized on Brassicaceae have evolved specific mechanisms to detoxify mustard oils (glucosinolates), while generalist species use detoxification enzymes that act on a variety of substrates. Understanding the gene evolution of detoxification and sensory repertoire in specialist and generalist Brassicaceae feeders will shed light on the processes involved in mediating hostplant ranges in herbivores. We use a comparative phylogenomic approach in 12 lepidopterans that feed on Brassicaceae, ranging from specialist to pests in their host range to examine the gene family expansion of detoxification and sensory gene families. We found that gene family expansions and contractions were larger in generalist herbivores compared to specialist herbivores. Gene evolutionary rate of detoxification genes reflected hostplant range where generalists had a higher evolutionary rate of detoxification genes that act on wide substrates while specialists had a higher evolutionary rate in genes that conjugate toxic compounds to hydrophilic byproducts. Our analysis on the nitrile specifier gene, a key innovation for feeding on Brassicaceae, indicated pervasive purifying selection with lineage specific differences in selection. Our results add to the growing body of work addressing gene family evolution and its role in hostplant range and specialization in insects.
A Transient High-dimensional Geometry Affords Stable Conjunctive Subspaces for Efficient Action Selection
Authors: Kikumoto Atsushi , Bhandari Apoorva , Shibata Kazuhisa , Badre David 
Published: June 2023

AbstractFlexible action selection requires cognitive control mechanisms capable of mapping the same inputs to different output actions depending on the context. From a neural state-space perspective, this requires a control representation that separates similar input neural states by context. Additionally, for action selection to be robust and time-invariant, information must be stable in time, enabling efficient readout. Here, using EEG decoding methods, we investigate how the geometry and dynamics of control representations constrain flexible action selection in the human brain. Participants performed a context-dependent action selection task. A forced response procedure probed action selection different states in neural trajectories. The result shows that before successful responses, there is a transient expansion of representational dimensionality that separated conjunctive subspaces. Further, the dynamics stabilizes in the same time window, with entry into this stable, high-dimensional state predictive of individual trial performance. These results establish the neural geometry and dynamics the human brain needs for flexible control over behavior.
Temporal dynamics of honeybee learning and decision-making are revealed by a novel automated PER system
Authors: Strelevitz Heather , Tiraboschi Ettore , Haase Albrecht 
Published: June 2023

AbstractThe proboscis extension response (PER) has been widely used for decades to evaluate honeybees’ (Apis mellifera)learning and memory abilities. This classical conditioning paradigm is traditionally administered manually, and produces a binary score for each subject depending on the presence or absence of the proboscis extension in response to a stimulus - typically an odor which has been associated with a sucrose reward - to classify whether or not the bee has learned the association. Here we present a fully automated PER system which delivers stimuli in a more controlled manner, and thus standardizes the protocol within and between labs; further, the AI-facilitated behavioral scoring reduces human error and allows us to extract a richer meaning from the outcome. The automated frame-by-frame assessment goes beyond the binary classification of “learned” or “not learned”, expanding the possibilities for many other measures. Using this method, we investigate the real-time decision-making processes of honeybees faced with difficult learning tasks. When posed with a quantitative (rather than qualitative, as in the case of different odors) PER association, honeybees show a pattern of rapid generalization to both the rewarded and non-rewarded stimuli, followed by a slowly acquired discrimination between the two. Our work lays the foundation for deeper exploration of the honeybee cognitive processes when posed with complex learning challenges.
Comparative genetic, biochemical, and biophysical analyses of the fourE. coliABCF paralogs support distinct functions related to mRNA translation
Authors: Ousalem Farès , Singh Shikha , Bailey Nevette A. , Wong Kam-Ho , Zhu Lingwei , Neky Matthew J. , Sibindi Cosmas , Fei Jingyi , Gonzalez Ruben L. , Boël Grégory , Hunt John F. 
Published: June 2023

AbstractMultiple paralogous ABCF ATPases are encoded in most genomes, but the physiological functions remain unknown for most of them. We herein compare the fourEscherichia coliK12 ABCFs – EttA, Uup, YbiT, and YheS – using assays previously employed to demonstrate EttA gates the first step of polypeptide elongation on the ribosome dependent on ATP/ADP ratio. A Δuupknockout, like ΔettA, exhibits strongly reduced fitness when growth is restarted from long-term stationary phase, but neither ΔybiTnor ΔyheSexhibits this phenotype. All four proteins nonetheless functionally interact with ribosomes based onin vitrotranslation and single-molecule fluorescence resonance energy transfer experiments employing variants harboring glutamate-to-glutamine active-site mutations (EQ2) that trap them in the ATP-bound conformation. These variants all strongly stabilize the same global conformational state of a ribosomal elongation complex harboring deacylated tRNAValin the P site. However, EQ2-Uup uniquely exchanges on/off the ribosome on a second timescale, while EQ2-YheS-bound ribosomes uniquely sample alternative global conformations. At sub-micromolar concentrations, EQ2-EttA and EQ2-YbiT fully inhibitin vitrotranslation of an mRNA encoding luciferase, while EQ2-Uup and EQ2-YheS only partially inhibit it at ~10-fold higher concentrations. Moreover, tripeptide synthesis reactions are not inhibited by EQ2-Uup or EQ2-YheS, while EQ2-YbiT inhibits synthesis of both peptide bonds and EQ2-EttA specifically traps ribosomes after synthesis of the first peptide bond. These results support the fourE. coliABCF paralogs all having different activities on translating ribosomes, and they suggest that there remains a substantial amount of functionally uncharacterized “dark matter” involved in mRNA translation.
Profiling of microglia nodules in multiple sclerosis reveals propensity for lesion formation
Authors: van den Bosch Aletta M.R. , van der Poel Marlijn , Fransen Nina L. , Vincenten Maria C.J. , Bobeldijk Anneleen M. , Jongejan Aldo , Engelenburg Hendrik J. , Moerland Perry D. , Smolders Joost , Huitinga Inge , Hamann Jörg 
Published: June 2023

AbstractClusters of ramified HLA-DR+cells, known as microglia nodules, are associated with brain pathology. Here we investigated if microglia nodules in the normal-appearing white matter (NAWM) of multiple sclerosis (MS) are different from microglia nodules in white matter (WM) in stroke and whether they may relate to the start of demyelinating MS lesions. We studied the relation between microglia nodules and pathological severity in an MS autopsy cohort (n=167), and we compared frequency, size, and gene expression of microglia nodules in MS (n=7) and stroke (n=7). MS donors with microglia nodules (64%) had a higher lesion load and a higher proportion of active lesions compared to donors without microglia nodules (36%). We found altered expression of genes in microglia nodules in MS compared to stroke, including genes previously shown to be upregulated in MS lesions. Genes associated with lipid metabolism, presence and proliferation of T and B cells, production of and response to immunoglobulins and cytokines (specifically TNF and IFN), activation of the complement cascade, and metabolic stress were upregulated. Using immunohistochemistry, we confirmed that in MS, more than in stroke, microglia nodules are associated with membrane attack complexes, have phagocytosed oxidized phospholipids, and have a tubular mitochondrial network reflecting increased metabolic activity. Furthermore, in MS, some nodules encapsulated partially demyelinated axons. Taken together, we propose that activation of some microglia nodules in MS by pro-inflammatory cytokines and immunoglobulins in combination with phagocytosis of oxidized phospholipids may lead to a volatile phenotype prone to form MS lesions.
Cyclic mechanical stretching stimuli promotes angiocrine signals duringin vitroliver bud formation from human pluripotent stem cells
Authors: Yoshimoto Koki , Maki Koichiro , Adachi Taiji , Kamei Ken-ichiro 
Published: June 2023

AbstractLiver organoids derived from human pluripotent stem cells (hPSCs) allow elucidation of liver development and have great potential for drug discovery. However, current methods for generating liver organoids using biochemical substances do not realize the vascular network of the liver lobule, due to the lack of knowledge of the role ofin vivomechanical environments during liver development. Here, we investigate the role of cyclic mechanical stretch (cMS) to angiocrine signals of hepatoblasts (HBs) and endothelial progenitor cells (EPCs) using an organ-on-a-chip platform to emulatein vivo-like mechanical environments and hPSCs to recapitulate hepatic differentiation. RNA sequencing revealed that the expression of angiocrine signal genes, such asHGFand matrix metallopeptidase 9 (MMP9), was increased by cMS in co-cultured HBs and EPCs. The secretion of HGF and MMP9 increased by 3.23-folds and 3.72-folds with cMS in the co-cultured HBs and EPCs but was not increased by cMS in the mono-cultured HBs and EPCs. Immunofluorescence micrographs with anti-KRT19, HGF, and MMP9 antibodies also revealed that cMS increased HGF and MMP9 expression when HBs and EPCs were co-cultured. cMS increased HGF and MMP9 expression and secretion when HBs and EPCs were co-cultured. Our findings provide new insights into the mechanical factors involved in the vascular network of human liver bud formation and liver organoid generation.
Hepatic lipid-associated macrophages mediate the beneficial effects of bariatric surgery against MASH
Authors: Fredrickson Gavin , Florczak Kira , Barrow Fanta , Dietsche Katrina , Wang Haiguang , Parthiban Preethy , Almutlaq Rawan , Adeyi Oyedele , Herman Adam , Bartolomucci Alessandro , Staley Christopher , Jahansouz Cyrus , Williams Jesse , Mashek Douglas G. , Ikramuddin Sayeed , Revelo Xavier S. 
Published: June 2023

ABSTRACTFor patients with obesity and metabolic syndrome, bariatric procedures such as vertical sleeve gastrectomy (VSG) have a clear benefit in ameliorating metabolic dysfunction-associated steatohepatitis (MASH). While the effects of bariatric surgeries have been mainly attributed to nutrient restriction and malabsorption, whether immuno-modulatory mechanisms are involved remains unclear. Here we report that VSG ameliorates MASH progression in a weight loss- independent manner. Single-cell RNA sequencing revealed that hepatic lipid-associated macrophages (LAMs) expressing the triggering receptor expressed on myeloid cells 2 (TREM2) increase their lysosomal activity and repress inflammation in response to VSG. Remarkably, TREM2 deficiency in mice ablates the reparative effects of VSG, suggesting that TREM2 is required for MASH resolution. Mechanistically, TREM2 prevents the inflammatory activation of macrophages and is required for their efferocytotic function. Overall, our findings indicate that bariatric surgery improves MASH through a reparative process driven by hepatic LAMs, providing insights into the mechanisms of disease reversal that may result in new therapies and improved surgical interventions.
Diversity of hydrodynamic radii of intrinsically disordered proteins
Authors: Białobrzewski Michał K. , Klepka Barbara P. , Michaś Agnieszka , Cieplak-Rotowska Maja K. , Staszałek Zuzanna , Niedźwiecka Anna 
Published: June 2023

AbstractIntrinsically disordered proteins (IDPs) form an important class of biomolecules regulating biological processes in higher organisms. The lack of a fixed spatial structure facilitates them to perform their regulatory functions. Due to the possibility of large conformational changes of IDPs, the cellular milieu can also control productivity of biochemical reactions. From the biophysical point of view, IDPs are biopolymers with a broad configuration state space. The conformation of such a biopolymer depends on non-covalent interactions of its amino acid side chain groups at given temperature and chemical conditions. Thus, the hydrodynamic radius (Rh) of an IDP of a given polymer length (N) is a sequence- and environment-dependent variable. We have reviewed the literature values of hydrodynamic radii of IDPs determined experimentally by SEC, AUC, PFG NMR, DLS, and FCS, and complement them with our FCS results obtained for a series of protein fragments involved in regulation of human gene expression. The data collected herein show that the values of hydrodynamic radii of intrinsically disordered proteins can span the full space between the folded globular and denatured proteins in the Rh(N) diagram.
Immuno-Engineered Mitochondria for Efficient Therapy of Acute Organ Injuries via Modulation of Inflammation and Cell Repair
Authors: Zhang Qing , Shen Yan , Zhang Hanyi , Li Xuemei , Yang Shengqian , Dai Chen , Yu Xiuyan , Lou Jie , Zhang Chengyuan , Feng Jinwei , Hu Chenglu , Lin Zhihua , Li Xiaohui , Zhou Xing 
Published: June 2023

AbstractAcute organ injuries represent a major public health concern, and despite recent advances in organ support therapy, managing patients with organ failure stemming from such injuries remains a formidable challenge. The pathogenesis of acute organ injuries is driven by a cascade of inflammatory reactions and mitochondrial dysfunction-mediated cell damage, two interrelated events that fuel a vicious cycle of disease progression. In this study, we engineered neutrophil membrane-fused mitochondria (nMITO) that inherit the injury-targeting and broad-spectrum anti-inflammatory activities from neutrophil membrane proteins while retaining the cell-repairing activity of mitochondria. We demonstrated that nMITO can effectively block the inflammatory cascade and replenish mitochondrial function to simultaneously modulate these two key mechanisms in diverse acute organ injuries. Furthermore, by virtue of the β-integrin inherited from neutrophils, nMITO exhibit selective homing to injured endothelial cells and can be efficiently delivered to damaged tissue cells via tunneling nanotubes, amplifying their regulatory effects on local inflammation and cell injury. In mouse models of acute myocardial injury, acute liver injury, and acute pancreatitis, nMITO effectively ameliorated immune dysfunction and repaired damaged tissues. Our findings suggest that nMITO represents a promising therapeutic strategy for managing acute organ injuries.
Characterization and super-resolution imaging of small tau aggregates in human samples
Authors: Böken Dorothea , Cox Dezerae , Burke Melanie , Lam Jeff Y. L. , Katsinelos Taxiarchis , Danial John S. H. , McEwan William A. , Rowe James B. , Klenerman David 
Published: June 2023

AbstractHyperphosphorylation and aggregation of the microtubule binding protein tau plays a key role in the development of Alzheimer’s disease. While the structure of the filamentous aggregates formed in humans has recently been determined to atomic resolution, there is far less information available about the smaller aggregate precursors, thought to be the most neurotoxic. To address this gap, we have developed a single molecule pull-down (SiMPull) able to detect tau aggregates in clinically relevant human samples. This method enables the detection and characterisation of individual tau aggregates, as opposed to averaged features obtained from traditional bulk techniques. We report the number, size and shape of individual aggregates measured via super-resolution microscopy, revealing disease-specific differences in tau aggregate morphology. By adapting the assay to simultaneously detect multiple phosphorylation sites in individual aggregates, we were also able to derive compositional profiles for pathological modifications present in individual aggregates. We demonstrate that tau aggregates in Alzheimer’s disease are significantly more likely to contain both the AT8 and T181 pathological phosphorylation markers, rather than only one. Together, tau SiMPull identified distinct subpopulations of large, modified tau aggregates that were invisible to traditional methodologies. These morphological and compositional differences distinguish samples taken from disease cohorts, offering to illuminate underlying disease mechanisms, and providing a foundation for novel diagnostic strategies.