bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypoxia-inducible factor 2 is a key determinant of manganese excess and polycythemia in SLC30A10 deficiency
Authors: Prajapati Milankumar , Zhang Jared Z. , Mercadante Courtney J. , Kowalski Heather L. , Delaney Bradley , Anderson Jessica A. , Guo Shuling , Aghajan Mariam , Bartnikas Thomas B. 
Published: February 2023

AbstractManganese is an essential yet potentially toxic metal. Initially reported in 2012, mutations in SLC30A10 are the first known inherited cause of manganese excess. SLC30A10 is an apical membrane transport protein that exports manganese from hepatocytes into bile and from enterocytes into the lumen of the gastrointestinal tract. SLC30A10 deficiency results in impaired gastrointestinal manganese excretion, leading to severe manganese excess, neurologic deficits, liver cirrhosis, polycythemia, and erythropoietin excess. Neurologic and liver disease are attributed to manganese toxicity. Polycythemia is attributed to erythropoietin excess, but the basis of erythropoietin excess in SLC30A10 deficiency has yet to be established. Here we demonstrate that erythropoietin expression is increased in liver but decreased in kidneys in Slc30a10-deficient mice. Using pharmacologic and genetic approaches, we show that liver expression of hypoxia-inducible factor 2 (Hif2), a transcription factor that mediates the cellular response to hypoxia, is essential for erythropoietin excess and polycythemia in Slc30a10-deficient mice, while hypoxia-inducible factor 1 (HIF1) plays no discernible role. RNA-seq analysis determined that Slc30a10-deficient livers exhibit aberrant expression of a large number of genes, most of which align with cell cycle and metabolic processes, while hepatic Hif2 deficiency attenuates differential expression of half of these genes in mutant mice. One such gene downregulated in Slc30a10-deficient mice in a Hif2-dependent manner is hepcidin, a hormonal inhibitor of dietary iron absorption. Our analyses indicate that hepcidin downregulation serves to increase iron absorption to meet the demands of erythropoiesis driven by erythropoietin excess. Finally, we also observed that hepatic Hif2 deficiency attenuates tissue manganese excess, although the underlying cause of this observation is not clear at this time. Overall, our results indicate that HIF2 is a key determinant of pathophysiology in SLC30A10 deficiency.Graphical abstract
Distinct neurochemical influences on fMRI response polarity in the striatum
Authors: Cerri Domenic H. , Albaugh Daniel L. , Walton Lindsay R. , Katz Brittany , Wang Tzu-Wen , Chao Tzu-Hao Harry , Zhang Weiting , Nonneman Randal J. , Jiang Jing , Lee Sung-Ho , Etkin Amit , Hall Catherine N. , Stuber Garret D. , Shih Yen-Yu Ian 
Published: February 2023

SummaryThe striatum is the primary input nucleus of the basal ganglia, widely studied for its complex roles in health and disease. Functional magnetic resonance imaging (fMRI) studies are essential for discerning striatal function, however the relationship between neuronal and hemodynamic activity, critical for interpreting fMRI signals, has not been rigorously examined in striatum. We find that optogenetic stimulation of striatal neurons or afferents evokes negative striatal fMRI responses in rats that can occur despite broad increases in local neuronal activity. Intra-striatal pharmacological manipulations suggest that opioidergic, but not dopaminergic transmission contributes to negative striatal fMRI signals (the latter instead associated with positive signals). Striatal neuronal activity peaks are also associated with negative hemodynamic signals in behaving rats. Negative fMRI responses are observed in human striatum under conditions of anticipated neuronal activity increases. Our results prompt consideration of local cellular and neurochemical environments along with neuronal activity in fMRI signal interpretation.
Discovery and characterization of a chemical probe targeting the zinc-finger ubiquitin-binding domain of HDAC6
Authors: Harding Rachel J. , Franzoni Ivan , Mann Mandeep K. , Szewczyk Magdalena M. , Mirabi Bijan , Owens Dominic D.G , Ackloo Suzanne , Scheremetjew Alexej , Juarez-Ornelas Kevin A. , Sanichar Randy , Baker Rachel J. , Dank Christian , Brown Peter J. , Barsyte-Lovejoy Dalia , Santhakumar Vijayaratnam , Schapira Matthieu , Lautens Mark , Arrowsmith Cheryl H. 
Published: February 2023

ABSTRACTHistone deacetylase 6 (HDAC6) inhibition is an attractive strategy for treating numerous cancers, and HDAC6 catalytic inhibitors are currently in clinical trials. The HDAC6 zinc-finger ubiquitin-binding domain (UBD) binds free C-terminal diglycine motifs of unanchored ubiquitin polymer chains and protein aggregates, playing an important role in autophagy and aggresome assembly. However, targeting this domain with small molecule antagonists remains an underdeveloped avenue of HDAC6-focused drug discovery. We report SGC-UBD253 (25), a chemical probe potently targeting HDAC6-UBD in vitro with selectivity over nine other UBDs, except for weak USP16 binding. In cells,25is an effective antagonist of HDAC6-UBD at 1 µM, with marked proteome-wide selectivity. We identified SGC-UBD253N (32), a methylated derivative of25which is 300-fold less active, serving as a negative control. Together,25and32could enable further exploration of the biological function of the HDAC6 UBD and investigation of the therapeutic potential of targeting this domain.
Phenotypic and genomic characterization ofPseudomonas aeruginosaisolates recovered from catheter-associated urinary tract infections in an Egyptian hospital
Authors: Eladawy Mohamed , Thomas Jonathan C. , Hoyles Lesley 
Published: February 2023

ABSTRACTCatheter-associated urinary tract infections (CAUTIs) represent one of the major healthcare-associated infections, andPseudomonas aeruginosais a common Gram-negative bacterium associated with catheter infections in Egyptian clinical settings. The present study describes the phenotypic and genotypic characteristics of 31P. aeruginosaisolates recovered from CAUTIs in an Egyptian hospital over a 3-month period. Genomes of isolates were of good quality and were confirmed to beP. aeruginosaby comparison to the type strain (average nucleotide identity, phylogenetic analysis). Clonal diversity among the isolates was determined; eight different sequence types were found (STs 244, 357, 381, 621, 773, 1430, 1667 and 3765), of which 357 and 773 are considered high-risk clones. Antimicrobial resistance (AMR) testing according to EUCAST guidelines showed the isolates were highly resistant to quinolones [ciprofloxacin (12/31, 38.7 %) and levofloxacin (9/31, 29 %) followed by tobramycin (10/31, 32.5 %)], and cephalosporins (7/31, 22.5 %). Genotypic analysis of resistance determinants predicted all isolates to encode a range of AMR genes, including those conferring resistance to aminoglycosides, β-lactamases, fluoroquinolones, fosfomycin, sulfonamides, tetracyclines and chloramphenicol. One isolate was found to carry a 422,938 bp pBT2436-like megaplasmid encoding OXA-520, the first report from Egypt of this emerging family of clinically important mobile genetic elements. All isolates were able to form biofilms, and were predicted to encode virulence genes associated with adherence, antimicrobial activity, antiphagocytosis, phospholipase enzymes, iron uptake, proteases, secretion systems, and toxins. The present study shows how phenotypic analysis alongside genomic analysis may help us understand the AMR and virulence profiles ofP. aeruginosacontributing to CAUTIs in Egypt.
Emergence of universal computations through neural manifold dynamics
Authors: Vicente Joan Gort 
Published: February 2023

AbstractThere is growing evidence that many forms of neural computation may be implemented by low-dimensional dynamics unfolding at the population scale. However, neither the connectivity structure nor the general capabilities of these embedded dynamical processes are currently understood. In this work, the two most common formalisms of firing-rate models are evaluated using tools from analysis, topology and nonlinear dynamics in order to provide plausible explanations for these problems. It is shown that low-rank structured connectivity predicts the formation of invariant and globally attracting manifolds in both formalisms, which generalizes existing theories to different neural models. Regarding the dynamics arising in these manifolds, it is proved they are topologically equivalent across the considered formalisms.It is also stated that under the low-rank hypothesis, dynamics emerging in neural models are universal. These include input-driven systems, which broadens previous findings. It is then explored how low-dimensional orbits can bear the production of continuous sets of muscular trajectories, the implementation of central pattern generators and the storage of memory states. It is also proved these dynamics can robustly simulate any Turing machine over arbitrary bounded memory strings, virtually endowing rate models with the power of universal computation. In addition, it is shown how the low-rank hypothesis predicts the parsimonious correlation structure observed in cortical activity. Finally, it is discussed how this theory could provide a useful tool from which to study neuropsychological phenomena using mathematical methods.
Endogenous bystander killing mechanisms enhance the activity of novel FAP-specific CAR-T cells against glioblastoma
Authors: Yu Wenbo , Truong Nga TH , Polara Ruhi , Gargett Tessa , Tea Melinda N , Pitson Stuart M , Cockshell Michaelia P , Bonder Claudine S , Ebert Lisa M , Brown Michael P 
Published: February 2023

AbstractObjectivesCAR-T cells are being investigated as a novel immunotherapy for glioblastoma, but clinical success has been limited. We recently described fibroblast activation protein (FAP) as an ideal target antigen for glioblastoma immunotherapy, with expression on both tumor cells and tumor blood vessels. However, CAR-T cells targeting FAP have never been investigated as a therapy for glioblastoma.MethodsWe generated a novel FAP targeting CAR with CD3ζ and CD28 signaling domains and tested the resulting CAR-T cells for their lytic activity and cytokine secretion functionin vitro(using real-time impedance, flow cytometry, imaging, and bead-based cytokine assays), andin vivo(using a xenograft mimicking the natural heterogeneity of human glioblastoma).ResultsFAP-CAR-T cells exhibited target specificity against model cell lines and potent cytotoxicity against patient-derived glioma neural stem cells, even when only a subpopulation expressed FAP, indicating a bystander killing mechanism. Using co-culture assays, we confirmed FAP-CAR-T cells mediate bystander killing of antigen-negative tumor cells, but only after activation by FAP-positive target cells. This bystander killing was at least partially mediated by soluble factors and amplified by IL-2 which activated the non-transduced fraction of the CAR-T product. Finally, a low dose of intravenously administered FAP-CAR-T cells controlled, without overt toxicity, the growth of subcutaneous tumors created using a mixture of antigen-negative and antigen-positive glioblastoma cells.ConclusionsOur findings advance FAP as a leading candidate for clinical CAR-T therapy of glioblastoma and highlight under-recognized antigen non-specific mechanisms that may contribute meaningfully to the antitumor activity of CAR-T cells.
Tau-Tubulin Kinase 2 restrains microtubule-depolymerizer KIF2A to support primary cilia growth
Authors: Vysloužil David , Bernatík Ondřej , Renzová Tereza , Binó Lucia , Lacigová Andrea , Čajánek Lukáš 
Published: February 2023

AbstractThe initiation of assembly of primary cilia, organelles with crucial functions in development and disease, is under the control of Tau-Tubulin Kinase 2 (TTBK2). Recent work has implicated TTBK2 also in the regulation of primary cilia maintenance and function. However, the mechanisms underlying individual functions of TTBK2 in primary cilia are not fully understood.Here, to dissect the role of TTBK2 in primary cilia maintenance in human cells, we examined disease related TTBK2 truncations. We demonstrate that these truncated protein moieties show selective activity towards TTBK2 substrates. This creates a semi-permissive condition where partial TTBK2 activity suffices to support the initiation of ciliogenesis but fails to sustain primary cilia length. Subsequently, we show that the defects in primary cilia growth are linked to aberrant turnover of kinesin KIF2A at basal body. Furthermore, we demonstrate that TTBK2 regulates KIF2A by phosphorylation, which in turn restrains its levels at the ciliary base to promote primary cilia elongation and maintenance.Taken together, our data highlight the regulation of KIF2A by TTBK2 as an important mechanism governing primary cilia in human cells.
Distinguishing examples while building concepts in hippocampal and artificial networks
Authors: Kang Louis , Toyoizumi Taro 
Published: February 2023

AbstractThe hippocampal subfield CA3 is thought to function as an autoassociative network that stores experiences as memories. Information from these experiences arrives via the entorhinal cortex (EC), which projects to CA3 directly as well as indirectly through the dentate gyrus (DG). DG sparsifies and decorrelates the information before also projecting to CA3. The computational purpose for receiving two encodings of the same sensory information has not been firmly established. We model CA3 as a Hopfield-like network that stores both correlated and decorrelated encodings and retrieves them at low and high inhibitory tone, respectively. As more memories are stored, the dense, correlated encodings merge along shared features while the sparse, decorrelated encodings remain distinct. In this way, the model learns to transition between concept and example representations by controlling inhibitory tone. To experimentally test for the presence of these complementary encodings, we analyze the theta-modulated tuning of place cells in rat CA3. In accordance with our model’s prediction, these neurons exhibit more precise spatial tuning and encode more detailed task features during theta phases with sparser activity. Finally, we generalize the model beyond hippocampal architecture and find that feedforward neural networks trained in multitask learning benefit from a novel loss term that promotes hybrid encoding using correlated and decorrelated representations. Thus, the complementary encodings that we have found in CA3 can provide broad computational advantages for solving complex tasks.
Modulation of WNT, Activin/Nodal and MAPK Signaling Pathways Increases Arterial Hemogenic Endothelium and Hematopoietic Stem/Progenitor Cell Formation During Human iPSC Differentiation
Authors: Li Yongqin , Ding Jianyi , Araki Daisuke , Zou Jizhong , Larochelle Andre 
Published: February 2023

AbstractSeveral differentiation protocols enable the emergence of hematopoietic stem and progenitor cells (HSPCs) from human induced pluripotent stem cells (iPSCs), yet optimized schemes to promote the development of HSPCs with self-renewal, multilineage differentiation and engraftment potential are lacking. To improve human iPSC differentiation methods, we modulated WNT, Activin/Nodal and MAPK signaling pathways by stage-specific addition of small molecule regulators CHIR99021, SB431542 and LY294002, respectively, and measured the impact on hematoendothelial formation in culture. Manipulation of these pathways provided a synergy sufficient to enhance formation of arterial hemogenic endothelium (HE) relative to control culture conditions. Importantly, this approach significantly increased production of human HSPCs with self-renewal and multilineage differentiation properties, as well as phenotypic and molecular evidence of progressive maturation in culture. Together, these findings provide a stepwise improvement in human iPSC differentiation protocols and offer a framework for manipulating intrinsic cellular cues to enablede novogeneration of human HSPCs with functionalityin vivo.Significance StatementThe ability to produce functional HSPCs by differentiation of human iPSCsex vivoholds enormous potential for cellular therapy of human blood disorders. However, obstacles still thwart translation of this approach to the clinic. In keeping with the prevailing arterial-specification model, we demonstrate that concurrent modulation of WNT, Activin/Nodal and MAPK signaling pathways by stage-specific addition of small molecules during human iPSC differentiation provides a synergy sufficient to promote arterialization of HE and production of HSPCs with features of definitive hematopoiesis. This simple differentiation scheme provides a unique tool for disease modeling, in vitro drug screening and eventual cell therapies.
Self-organization of Long-lasting Human Endothelial Capillary Networks guided by DLP Bioprinting
Authors: Mazari-Arrighi Elsa , Lépine Matthieu , Ayollo Dmitry , Faivre Lionel , Larghero Jérôme , Chatelain François , Fuchs Alexandra 
Published: February 2023

ABSTRACTTissue engineering holds great promise for regenerative medicine, drug discovery and as an alternative to animal models. However, as soon as the dimensions of engineered tissue exceed the diffusion limit of oxygen and nutriments, a necrotic core forms leading to irreversible damage. To overcome this constraint, the establishment of a functional perfusion network is essential and is a major challenge to be met. In this work, we explore a promising Digital Light Processing (DLP) bioprinting approach to encapsulate endothelial progenitor cells (EPCs) in 3D photopolymerized hydrogel scaffolds to guide them towards vascular network formation. We observed that EPCs encapsulated in the appropriate photopolymerized hydrogel can proliferate and self-organize within a few days into branched tubular structures with predefined geometry, forming capillary-like vascular tubes or trees of various diameters (in the range of 10 to 100 μm). Presenting a monolayer wall of endothelial cells strongly connected by tight junctions around a central lumen, these structures can be microinjected with fluorescent dye and are stable for several weeksin vitro. Interestingly, our technology has proven to be versatile in promoting the formation of vascular structures using a variety of vascular cell lines, including EPCs, human vascular endothelial cells (HUVECs) and human dermal lymphatic endothelial cells (HDLECs). We have also demonstrated that these vascular structures can be recovered and manipulated in an alginate patch without altering their shape or viability. This opens new opportunities for future applications, such as stacking these endothelial vascular structures with other cell sheets or multicellular constructs to yield bioengineered tissue with higher complexity and functionality.
Regional Gene Expression in the Retina, Optic Nerve Head, and Optic Nerve of Mice with Experimental Glaucoma and Optic Nerve Crush
Authors: Keuthan Casey J. , Schaub Julie , Wei Meihan , Fang Weixiang , Quillen Sarah , Kimball Elizabeth , Johnson Thomas V. , Ji Hongkai , Zack Donald J. , Quigley Harry A. 
Published: February 2023

AbstractA major risk factor for glaucomatous optic neuropathy is the level of intraocular pressure (IOP), which can lead to retinal ganglion cell axon injury and cell death. The optic nerve has a rostral unmyelinated portion at the optic nerve head followed by a caudal myelinated region. The unmyelinated region is differentially susceptible to IOP-induced damage in rodent models and in human glaucoma. While several studies have analyzed gene expression changes in the mouse optic nerve following optic nerve injury, few were designed to consider the regional gene expression differences that exist between these distinct areas. We performed bulk RNA-sequencing on the retina and on separately micro-dissected unmyelinated and myelinated optic nerve regions from naïve C57BL/6 mice, mice after optic nerve crush, and mice with microbead-induced experimental glaucoma (total = 36). Gene expression patterns in the naïve unmyelinated optic nerve showed significant enrichment of the Wnt, Hippo, PI3K-Akt, and transforming growth factor β pathways, as well as extracellular matrix–receptor and cell membrane signaling pathways, compared to the myelinated optic nerve and retina. Gene expression changes induced by both injuries were more extensive in the myelinated optic nerve than the unmyelinated region, and greater after nerve crush than glaucoma. Changes three and fourteen days after injury largely subsided by six weeks. Gene markers of reactive astrocytes did not consistently differ between injury states. Overall, the transcriptomic phenotype of the mouse unmyelinated optic nerve was significantly different from immediately adjacent tissues, likely dominated by expression in astrocytes, whose junctional complexes are inherently important in responding to IOP elevation.
choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
Authors: Mok Amanda , Tunney Robert , Benegas Gonzalo , Wallace Edward W. J. , Lareau Liana F. 
Published: February 2023

AbstractRibosome profiling quantifies translation genome-wide by sequencing ribosome-protected fragments, or footprints. Its single-codon resolution allows identification of translation regulation, such as ribosome stalls or pauses, on individual genes. However, enzyme preferences during library preparation lead to pervasive sequence artifacts that obscure translation dynamics. Widespread over- and under-representation of ribosome footprints can dominate local footprint densities and skew estimates of elongation rates by up to five fold. To address these biases and uncover true patterns of translation, we presentchoros, a computational method that models ribosome footprint distributions to provide bias-corrected footprint counts.chorosuses negative binomial regression to accurately estimate two sets of parameters: (i) biological contributions from codon-specific translation elongation rates; and (ii) technical contributions from nuclease digestion and ligation efficiencies. We use these parameter estimates to generate bias correction factors that eliminate sequence artifacts. Applyingchorosto multiple ribosome profiling datasets, we are able to accurately quantify and attenuate ligation biases to provide more faithful measurements of ribosome distribution. We show that a pattern interpreted as pervasive ribosome pausing near the beginning of coding regions is likely to arise from technical biases. Incorporatingchorosinto standard analysis pipelines will improve biological discovery from measurements of translation.