bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ciliary neurotrophic factor-mediated neuroprotection involves enhanced glycolysis and anabolism in degenerating mouse retinas
Authors: Do Rhee Kun , Wang Yanjie , ten Hoeve Johanna , Stiles Linsey , Nguyen Thao Thi Thu , Zhang Xiangmei , Vergnes Laurent , Reue Karen , Shirihai Orian , Bok Dean , Yang Xian-Jie 
Published: December 2021

ABSTRACTCiliary neurotrophic factor (CNTF) acts as a potent neuroprotective cytokine in multiple models of retinal degeneration. To understand mechanisms underlying its broad neuroprotective effects, we have investigated the influence of CNTF on metabolism in a mouse model of photoreceptor degeneration. CNTF treatment improves the morphology of photoreceptor mitochondria, but also leads to reduced oxygen consumption and suppressed respiratory chain activities. Molecular analyses show elevated glycolytic pathway gene transcripts and active enzymes. Metabolomics analyses detect significantly higher levels of ATP and the energy currency phosphocreatine, elevated glycolytic pathway metabolites, increased TCA cycle metabolites, lipid biosynthetic pathway intermediates, nucleotides, and amino acids. Moreover, CNTF treatment restores the key antioxidant glutathione to the wild type level. Therefore, CNTF significantly impacts the metabolic status of degenerating retinas by promoting aerobic glycolysis and augmenting anabolic activities. These findings reveal cellular mechanisms underlying enhanced neuronal viability and suggest potential therapies for treating retinal degeneration.
Local activation of focal adhesion kinase orchestrates the positioning of presynaptic scaffold proteins and Ca2+ channel function to control glucose dependent insulin secretion
Authors: Hallahan Nicole , Deng Kylie , Jevon Dillon , Kumar Krish , Tong Jason , Gan Wan Jun , Tran Clara , Bilek Marcela , Thorn Peter 
Published: December 2021

AbstractA developing understanding suggests that spatial compartmentalisation of components the glucose stimulus-secretion pathway in pancreatic β cells are critical in controlling insulin secretion. To investigate the mechanisms, we have developed live-cell sub-cellular imaging methods using the organotypic pancreatic slice. We demonstrate that the organotypic pancreatic slice, when compared with isolated islets, preserves intact β cell structure, and enhances glucose dependent Ca2+ responses and insulin secretion. Using the slice technique, we have discovered the essential role of local activation of integrins and the downstream component, focal adhesion kinase, in regulating β cells. Integrins and focal adhesion kinase are exclusively activated at the β cell capillary interface and using in situ and in vitro models we show their activation both positions presynaptic scaffold proteins, like ELKS and liprin, and regulates glucose dependent Ca2+ responses and insulin secretion. We conclude that focal adhesion kinase orchestrates the final steps of glucose dependent insulin secretion within the restricted domain where β cells contact the islet capillaries.
Soil collected in the Great Smoky Mountains National Park yielded a novelListeriaspecies,L. swaminathanii, effectively expanding thesensu strictoclade to ten species
Authors: Carlin Catharine R. , Liao Jingqiu , Hudson Lauren K. , Peters Tracey L. , Denes Thomas G. , Orsi Renato , Guo Xiaodong , Wiedmann Martin 
Published: December 2021

ABSTRACTSoil samples collected in the Great Smoky Mountains National Park yielded aListeriaisolate that could not be classified to the species level. Whole-genome sequence-based average nucleotide identity BLAST andin silicoDNA-DNA Hybridization analyses confirmed this isolate to be a novelListeria sensu strictospecies with the highest similarity toL. marthii(ANI=93.9%, isDDH=55.9%). Additional whole-genome-based analysis using the Genome Taxonomy Database Toolkit, an automated program for classifying bacterial genomes, further supported delineation as a novelListeria sensu strictospecies, as this tool failed to assign a species identification but identifiedL. marthiias the closest match. Phenotypic and genotypic characterization results indicate that this species is nonpathogenic. Specifically, the novelListeriaspecies described here is phenotypically (i) non-hemolytic and (ii) negative for phosphatidylinositol-specific phospholipase C activity; the draft genome lacks all virulence genes found in theListeriapathogenicity island 1 (LIPI-1), as well as the internalin genesinlAandinlB. While the type strain for the new species is phenotypically catalase-negative (an unusual characteristic forListeria sensu strictospecies), its genome contained an apparently intact catalase gene (kat); hence assessment of this phenotype with future isolates will be important. Rapid species identification systems (ListeriaAPI, VITEK 2, VITEK MS) misidentified this novel species as eitherL. monocytogenes, L. innocua, orL. marthii. We propose the nameL. swaminathanii, and the type strain is FSL L7-0020T(=ATCC TSD-239T).IMPORTANCEL. swaminathaniiis a novelsensu strictospecies that originated from a US National Park, and its place of origin is ultimately preventing this species from achieving valid status. The US National Park Service restricts strain accessibility and open access is currently a prerequisite for species validation. Essentially the only criteria that was not met forL. swaminathaniivalidation is accessibility of the type strain, therefore nomenclature status should not negate the significance of this discovery. As a novelsensu strictospecies,L. swaminathaniiexpands the group of species whose presence is associated with an increased risk of anL. monocytogenescontamination, and therefore could play an important role in public health. While developers ofListeriaspp. detection methods historically only included validly publish species in their validation studies,L. swaminathaniiis unequivocally asensu strictospecies and should be included as well.
Novel regimens of bedaquiline-pyrazinamide combined with moxifloxacin, rifabutin, delamanid and/or OPC-167832 in murine tuberculosis models
Authors: Tasneen Rokeya , Garcia Andrew , Converse Paul J. , Zimmerman Matthew D. , Dartois Veronique , Kurbatova Ekaterina , Vernon Andrew A. , Carr Wendy , Stout Jason E. , Dooley Kelly E. , Nuermberger Eric L. 
Published: December 2021

ABSTRACTA recent landmark trial showed a 4-month regimen of rifapentine, pyrazinamide, moxifloxacin and isoniazid (PZMH) to be non-inferior to the 6-month standard of care. Here, two murine models of tuberculosis were used to test whether novel regimens replacing rifapentine and isoniazid with bedaquiline and another drug would maintain or increase the sterilizing activity of the regimen. In BALB/c mice, replacing rifapentine in the PZM backbone with bedaquiline (i.e., BZM) significantly reduced both lung CFU counts after 1 month and the proportion of mice relapsing within 3 months after completing 1.5 months of treatment. Addition of rifabutin to BZM (BZMRb) further increased the sterilizing activity. In the C3HeB/FeJ mouse model characterized by caseating lung lesions, treatment with BZMRb resulted in significantly fewer relapses than PZMH after 2 months of treatment. A regimen combining the new DprE1 inhibitor OPC-167832 and delamanid (BZOD) also had superior bactericidal and sterilizing activity compared to PZM in BALB/c mice and was similar in efficacy to PZMH in C3HeB/FeJ mice. Thus, BZM represents a promising backbone for treatment-shortening regimens. Given the prohibitive drug-drug interactions between bedaquiline and rifampin or rifapentine, the BZMRb regimen represents the best opportunity to combine, in one regimen, the treatment-shortening potential of the rifamycin class with that of BZM and deserves high priority for evaluation in clinical trials. Other 4-drug BZM-based regimens and BZOD represent promising opportunities for extending the spectrum of treatment-shortening regimens to rifamycin- and fluoroquinolone-resistant tuberculosis.
NK cells acquire CCR5 and CXCR4 by trogocytosis in people living with HIV-1
Authors: Vo Dang-Nghiem , Leventoux Nicolas , Campos-Mora Mauricio , Gimenez Sandrine , Corbeau Pierre , Villalba Martin 
Published: December 2021

AbstractNK cells play a major role in the antiviral immune response, including against HIV-1. HIV patients have impaired NK cell activity with decrease in CD56dim NK cells and increase in CD56−CD16+ subset and recently it has been proposed that a population of CD56+NKG2C+KIR+CD57+ cells represents antiviral memory NK cells. Antiretroviral therapy (ART) partly restores the functional activity of this lymphocyte lineage. NK cells when interacting with their targets can gain antigens from them by the process of trogocytosis. Here we show that NK cells can obtain CCR5 and CXCR4, but barely CD4, from T cell lines by trogocytosis in vitro. By UMAP (Uniform Manifold Approximation and Projection), we show that aviremic HIV patients have unique NK cell clusters that encompass for cells expressing CCR5, NKG2C and KIRs, but lack CD57 expression. Viremic patients have a larger proportion of CXCR4+ and CCR5+ NK cells than healthy donors (HD) and this is largely increased in CD107+ cells, suggesting a link between degranulation and trogocytosis. In agreement, UMAP identified a specific NK cell cluster in viremic HIV patients, which contains most of the CD107a+, CCR5+ and CXCR4+ cells. However, this cluster lacks NKG2C expression. Therefore, NK cells can gain CCR5 and CXCR4 by trogocytosis, which depends on degranulation.Author SummaryNK cells play a major role in the antiviral immune response, including against HIV-1. HIV-1 infection largely impacts NK cell lineage. However, identification of the NK cells fighting the virus and eliminating infected cells has remained elusive. By using FACs analysis and analyzing T cell markers, we identify specific NK cell subsets that have gained T cell antigen markers by trogocytosis. We show a strong association of degranulation and trogocytosis ex vivo suggesting that NK cells are eliminating or trying to eliminate HIV-1 infected cells.Moreover, we show that NK cells can obtain the HIV-1 coreceptors CCR5 and CXCR4, but barely CD4, from T cells. Therefore, by uncovering that NK cells gain CCR5 and CXCR4 by trogocytosis we show that NK cells are actively fighting against HIV-1 infection in viremic and aviremic patients. This should help to identify why certain patients better control the virus, to develop new anti-HIV-1, NK cell-based, immunotherapies and to understand if NK cells can be a new HIV-1 reservoir.
Phenotyping Polarization Dynamics Of Immune Cells Using A Lipid Droplet - Cell Pairing Microfluidic Platform
Authors: Pinon Léa , Ruyssen Nicolas , Pineau Judith , Mesdjian Olivier , Cuvelier Damien , Chipont Anna , Allena Rachele , Guerin Coralie L. , Asnacios Sophie , Asnacios Atef , Pierobon Paolo , Fattaccioli Jacques 
Published: December 2021

AbstractThe immune synapse is the tight contact zone between a lymphocyte and a cell presenting its cognate antigen. This structure serves as a signaling platform and entails a polarization of intra-cellular components, necessary to the immunological function of the cell. While the surface properties of the presenting cell are known to control the formation of the synapse, their impact on polarization has not yet been studied.Using functional lipid droplets as tunable artificial presenting cells combined with a microfluidic pairing device, we simultaneously observe synchronized synapses and dynamically quantify polarization patterns of individual B cells. By assessing how ligand concentration, surface fluidity and substrate rigidity impact lysosome polarization, we show that its onset and kinetics depend on the local antigen concentration at the synapse and on substrate rigidity. Our experimental system enables a fine phenotyping of monoclonal cell populations based on their synaptic readout.
A guide to trajectory inference and RNA velocity
Authors: Weiler Philipp , Van den Berge Koen , Street Kelly , Tiberi Simone 
Published: December 2021

AbstractTechnological developments have led to an explosion of high-throughput single cell data, which are revealing unprecedented perspectives on cell identity. Recently, significant attention has focused on investigating, from single-cell RNA-sequencing (scRNA-seq) data, cellular dynamic processes, such as cell differentiation, cell cycle and cell (de)activation. Trajectory inference methods estimate a trajectory, a collection of differentiation paths of a dynamic system, by ordering cells along the paths of such a dynamic process. While trajectory inference tools typically work with gene expression levels, common scRNA-seq protocols allow the identification and quantification of unspliced pre-mRNAs and mature spliced mRNAs, for each gene. By exploiting the abundance of unspliced and spliced mRNA, one can infer the RNA velocity of individual cells, i.e., the time derivative of the gene expression state of cells. Whereas traditional trajectory inference methods reconstruct cellular dynamics given a population of cells of varying maturity, RNA velocity relies on a dynamical model describing splicing dynamics. Here, we initially discuss conceptual and theoretical aspects of both approaches, then illustrate how they can be combined together, and finally present an example use-case on real data.
The dual role of the RETINOBLASTOMA-RELATED protein in the DNA damage response is spatio-temporally coordinated by the interaction with LXCXE-containing proteins
Authors: Zaragoza Jorge Zamora , Klap Katinka , Heidstra Renze , Zhou Wenkun , Scheres Ben 
Published: December 2021

AbstractLiving organisms face threats to genome integrity caused by environmental challenges or metabolic errors in proliferating cells. To avoid the spread of mutations, cell division is temporarily arrested while repair mechanisms deal with DNA lesions. Afterwards, cells either resume division or respond to unsuccessful repair by withdrawing from the cell cycle and undergoing cell differentiation or cell death. How the success rate of DNA repair connects to the execution of cell death remains incompletely known, particularly in plants. Here we provide evidence that the Arabidopsis thaliana RETINOBLASTOMA-RELATED1 (RBR) protein, shown to play structural and transcriptional functions in the DNA damage response (DDR), coordinates these processes in time by successive interactions through its B-pocket sub-domain. Upon DNA damage induction, RBR forms nuclear foci; but the N849F substitution in the B-pocket, which specifically disrupts binding to LXCXE motif-containing proteins, abolishes RBR focus formation and leads to growth arrest. After RBR focus formation, the stress-responsive gene NAC044 arrests cell division. As RBR is released from nuclear foci, it can be bound by the conserved LXCXE motif in NAC044. RBR-mediated cell survival is inhibited by the interaction with NAC044. Disruption of NAC044-RBR interaction impairs the cell death response but is less important for NAC044 mediated growth arrest. Noteworthy, unlike many RBR interactors, NAC044 binds to RBR independent of RBR phosphorylation. Our findings indicate that the availability of the RBR B-pocket to interact with LXCXE-containing proteins couples RBR DNA repair functions and RBR transcriptional functions of in the cell death program.
Chronic Alcohol Dysregulates Glutamatergic Function in the Basolateral Amygdala in a Projection- and Sex-Specific Manner
Authors: Price Michaela E. , McCool Brian A. 
Published: December 2021

AbstractChronic intermittent ethanol (CIE) produces alcohol dependence, facilitates anxiety-like behavior, and increases post-CIE alcohol intake. The basolateral amygdala (BLA) is one of several brain regions that regulates anxiety-like behavior and alcohol intake through downstream projections. The BLA receives information from two distinct input pathways. Afferents from medial structures like the thalamus and prefrontal cortex enter the BLA through thestria terminaliswhereas lateral cortical structures like the anterior insula cortex enter the BLA through the external capsule. CIE induces input- and sex-specific adaptations to glutamatergic function in the BLA. Previous studies sampled neurons throughout the BLA, but did not distinguish between projection-specific populations. The current study investigated BLA neurons that project to the NAC (BLA-NAC neurons) or the BNST (BLA-BNST neurons) as representative ‘reward’ and ‘aversion’ BLA neurons, and showed that CIE alters glutamatergic function and excitability in a projection- and sex-specific manner. CIE increases glutamate release fromstria terminalisinputs only onto BLA-BNST neurons. At external capsule synapses, CIE increases postsynaptic glutamatergic function in male BLA-NAC neurons and female BLA-BNST neurons. Subsequent experiments demonstrated that CIE enhanced the excitability of male BLA-NAC neurons and BLA-BNST neurons in both sexes when glutamatergic but not GABAergic function was intact. Thus, CIE-mediated increased glutamatergic function facilitates hyperexcitability in male BLA-NAC neurons and BLA-BNST neurons of both sexes.
Function-guided protein design by deep manifold sampling
Authors: Gligorijević Vladimir , Berenberg Daniel , Ra Stephen , Watkins Andrew , Kelow Simon , Cho Kyunghyun , Bonneau Richard 
Published: December 2021

AbstractProtein design is challenging because it requires searching through a vast combinatorial space that is only sparsely functional. Self-supervised learning approaches offer the potential to navigate through this space more effectively and thereby accelerate protein engineering. We introduce a sequence denoising autoencoder (DAE) that learns the manifold of protein sequences from a large amount of potentially unlabelled proteins. This DAE is combined with a function predictor that guides sampling towards sequences with higher levels of desired functions. We train the sequence DAE on more than 20M unlabeled protein sequences spanning many evolutionarily diverse protein families and train the function predictor on approximately 0.5M sequences with known function labels. At test time, we sample from the model by iteratively denoising a sequence while exploiting the gradients from the function predictor. We present a few preliminary case studies of protein design that demonstrate the effectiveness of this proposed approach, which we refer to as “deep manifold sampling”, including metal binding site addition, function-preserving diversification, and global fold change.
Therapeutic advantages of combined gene/cell therapy strategies in a murine model of GM2 gangliosidosis
Authors: Sala Davide , Ornaghi Francesca , Morena Francesco , Argentati Chiara , Valsecchi Manuela , Alberizzi Valeria , Di Guardo Roberta , Bolino Alessandra , Aureli Massimo , Martino Sabata , Gritti Angela 
Published: December 2021

ABSTRACTThe GM2 gangliosidoses Tay-Sachs disease and Sandhoff disease (SD) are respectively caused by mutations in the HEXA and HEXB genes encoding the α and β subunits of β-N-acetylhexosaminidase (Hex). The consequential accumulation of ganglioside in the brain leads to severe and progressive neurological impairment. There are currently no approved therapies to counteract or reverse the effects of GM2 gangliosidosis. Adeno-associated vector (AAV)-based investigational gene therapy (GT) products have raised expectations but come with safety and efficacy issues that need to be addressed. Thus, there is an urgent need to develop novel therapies targeting the CNS and other affected tissues that are appropriately timed to ensure pervasive metabolic correction and counteract disease progression. In this report, we show that the sequential administration of lentiviral vector (LV)-mediated intracerebral (IC) GT and bone marrow transplantation (BMT) in pre-symptomatic SD mice provide a timely and long-lasting source of the Hex enzyme in the central and peripheral nervous systems and peripheral tissues, leading to global rescue of the disease phenotype. Combined therapy showed a clear therapeutic advantage compared to individual treatments in terms of lifespan extension and normalization of the neuroinflammatory and neurodegenerative phenotypes of the SD mice. These benefits correlated with a time-dependent increase in Hex activity and a remarkable reduction in GM2 storage in the brain tissues that single treatments failed to achieve. Our results highlight the complementary and synergic mode of action of LV-mediated IC GT and BMT, clarify the relative contribution of treatments to the therapeutic outcome, and inform on the realistic threshold of enzymatic activity that is required to achieve a significant therapeutic benefit, with important implications for the monitoring and interpretation of ongoing experimental therapies, and for the design of more effective treatment strategies for GM2 gangliosidosis.
ATP:Mg2+shapes condensate properties of rRNA-NPM1in vitronucleolus model and its partitioning of ribosomes
Authors: Yewdall N. Amy , André Alain A. M. , van Haren Merlijn H. I. , Nelissen Frank H.T. , Jonker Aafke , Spruijt Evan 
Published: December 2021

AbstractNucleoli have viscoelastic gel-like condensate dynamics that are not well representedin vitro. Nucleoli models, such as those formed by nucleophosmin 1 (NPM1) and ribosomal RNA (rRNA), exhibit condensate dynamics orders of magnitude faster thanin vivonucleoli. Here we show that an interplay between magnesium ions (Mg2+) and ATP governs rRNA dynamics, and this ultimately shapes the physical state of these condensates. Using quantitative fluorescence microscopy, we demonstrate that increased RNA compaction occurs in the condensates at high Mg2+concentrations, contributing to the slowed RNA dynamics. At Mg2+concentrations above 7 mM, rRNA is fully arrested and the condensates are gels. Below the critical gel point, NPM1-rRNA droplets age in a temperature-dependent manner, suggesting that condensates are viscoelastic materials, undergoing maturation driven by weak multivalent interactions. ATP addition reverses the dynamic arrest of rRNA, resulting in liquefaction of these gel-like structures. Surprisingly, ATP and Mg2+both act to increase partitioning of NPM1-proteins as well as rRNA, which influences the partitioning of small client molecules. By contrast, larger ribosomes form a halo around NPM1-rRNA coacervates when Mg2+concentrations are higher than ATP concentrations. Within cells, ATP levels fluctuate due to biomolecular reactions, and we demonstrate that a dissipative enzymatic reaction can control the biophysical properties ofin vitrocondensates through depletion of ATP. This enzymatic ATP depletion also reverses the formation of the ribosome halos. Our results illustrate how cells, by changing local ATP concentrations, may regulate the state and client partitioning of RNA-containing condensates such as the nucleolus.Significance StatementThere is a significant discrepancy between the dynamics ofin vitronucleolus models andin vivonucleoli – with the latter more gel-like.The interplay between Mg2+ions, ATP and the nucleolus components – specifically RNA – governs the dynamics, and ultimately the physical state, of nucleolus-like condensates.We show that the nucleolus are dynamically adapting condensates, responding to local ATP concentrations through Mg2+-induced compaction of the RNA, and reversible relaxation when ATP binds Mg2+again. Other condensates containing RNA probably respond in similar ways to Mg2+and ATP.