bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Insights of SARS-CoV-2 Spike Protein from Delta and Omicron Variants
Authors: Sadek Ali , Zaha David , Ahmed Mahmoud Salama 
Published: December 2021

AbstractGiven the continuing heavy toll of the COVID-19 pandemic and the emergence of the Delta (B.1.617.2) and Omicron (B.1.1.529) variants, the WHO declared both as variants of concern (VOC). There are valid concerns that the latest Omicron variant might have increased infectivity and pathogenicity. In addition, the sheer number of S protein mutations in the Omicron variant raise concerns of potential immune evasion and resistance to therapeutics such as monoclonal antibodies. However, structural insights that underpin the potential increased pathogenicity are unknown. Here we adopted an artificial intelligence (AI)-based approach to predict the structural changes induced by mutations of the Delta and Omicron variants in the spike (S) protein using Alphafold. This was followed by docking the human angiotensin-converting enzyme 2 (ACE2) with the predicted S proteins for Wuhan-Hu-1, Delta, and Omicron variants. Our in-silico structural analysis indicates that S protein for Omicron variant has a higher binding affinity to ACE-2 receptor, compared to Wuhan-Hu-1 and Delta variants. In addition, the recognition sites of the receptor binding domains for Delta and Omicron variants showed lower electronegativity compared to Wuhan-Hu-1. Importantly, further molecular insights revealed significant changes induced at fusion protein (FP) site, which may mediate enhanced viral entry. These results represent the first computational analysis of structural changes associated with Omicron variant using Alphafold, Collectively, our results highlight potential structural basis for enhanced pathogenicity of the Omicron variant, however further validation using X-ray crystallography and cryo-EM are warranted.
The Effect of Ligands and Transducers on the Neurotensin Receptor 1 (NTS1) Conformational Ensemble
Authors: Dixon Austin D. , Inoue Asuka , Robson Scott A. , Culhane Kelly J. , Trinidad Jonathan C. , Sivaramakrishnan Sivaraj , Bumbak Fabian , Ziarek Joshua J. 
Published: December 2021

ABSTRACTUsing a discrete, intracellular 19F-NMR probe on transmembrane helix 6 (TM6) of the Neurotensin receptor 1 (NTS1), we aim to understand how ligands and transducers modulate the receptor’s structural ensemble in solution. For apo NTS1, 19F-NMR spectra reveal an ensemble of at least three conformational substates (one inactive and two active-like) in equilibrium that exchange on the ms-s timescale. Dynamic NMR experiments reveal that these substates follow a linear three-site exchange process that is both thermodynamically and kinetically remodeled by orthosteric ligands. As previously observed in other GPCRs, the full agonist is insufficient to completely stabilize the active-like state. The inactive substate is abolished upon coupling to β-arrestin-1 or the C-terminal helix of Gαq, which comprises ⍰60% of the GPCR/G protein interface surface area. Whereas β-arrestin-1 exclusively selects for pre-existing active-like substates, the Gαq peptide induces a new substate. Both transducer molecules promote substantial line-broadening of active-like states suggesting contributions from additional μs-ms exchange processes. Together, our study suggests i) the NTS1 allosteric activation mechanism may be alternatively dominated by induced fit or conformational selection depending on the coupled transducer, and ii) the available static structures do not represent the entire conformational ensemble observed in solution.
Assessing the multimodal tradeoff
Authors: Booeshaghi A. Sina , Gao Fan , Pachter Lior 
Published: December 2021

AbstractSingle-cell and single-nucleus genomics assays are becoming increasingly complex, with multiple measurements of distinct modalities performed concurrently resulting in “multimodal” readouts. While multimodal single-cell and single-nucleus genomics offers the potential to better understand how distinct cellular processes are coordinated, there can be technical and cost tradeoffs associated with increasing the number of measurement modes. To assess some of the tradeoffs inherent in multimodal assays, we have developed snATAK for preprocessing sequencing-based high-throughput assays that measure single-nucleus chromatin accessibility. Coupled with kallisto bustools for single-nucleus RNA-seq preprocessing, the snATAK workflow can be used for uniform preprocessing of 10x Genomics’ Multiome and single-nucleus ATAC-seq, SHARE-seq, ISSAAC-seq, spatial ATAC-seq and other chromatin-related assays. Using snATAK, we are able to perform cross-platform comparisons and quantify some of the tradeoffs between Multiome and unregistered single-nucleus RNA-seq/ATAC-seq experiments. We also show that snATAK can be used to assess allele concordance between paired RNAseq and ATACseq. snATAK is available athttps://github.com/pachterlab/snATAK/.
4-phenylbutyrate restored GABA uptake and reduced seizures in SLC6A1 variants-mediated disorders
Authors: Nwosu Gerald , Mermer Felicia , Flamm Carson , Poliquin Sarah , Shen Wangzhen , Rigsby Kathryn , Kang Jing-Qiong 
Published: December 2021

AbstractWe have previously studied the molecular mechanisms of solute carrier family 6 member 1 (SLC6A1) associated with a continuum of neurodevelopmental disorders, including various epilepsy syndromes, autism, and intellectual disability. Based on functional assays of variants in a large cohort with heterogenous clinical phenotypes, we conclude that partial or complete loss of GABA uptake function in the mutant GAT-1 is the primary etiology as identified in GABAA receptor mutation-mediated epilepsy and in cystic fibrosis. Importantly, we identified that there are common patterns of the mutant protein trafficking from biogenesis, oligomerization, glycosylation, and translocation to the cell membrane across variants with the conservation of this process across cell types. Conversely any approach to facilitate membrane trafficking would increase presence of the functional protein in the targeted destination in all involved cells. PBA is an FDA-approved drug for pediatric use and is orally bioavailable so it can be quickly translated to patient use. It has been demonstrated that PBA can correct protein misfolding, reduce ER stress, and attenuate unfolded protein response in neurodegenerative diseases, it has also showed promise in treatment of cystic fibrosis. The common cellular mechanisms shared by the mutant GAT-1 and the mutant cystic fibrosis transmembrane conductance regulator led us to test if PBA and other pharmaco-chaperones could be a potential treatment option for SLC6A1 mutations. We examined the impact of PBA and other small molecules in a library of variants and in cell and knockin mouse models. Because of the critical role of astrocytic GAT-1 deficit in seizures, we focused on astrocytes, and demonstrated that the existence of the mutant GAT-1 retained the wildtype GAT-1, suggesting aberrant protein oligomerization and trafficking caused by the mutant GAT-1. PBA increased GABA uptake in both mouse and human astrocytes bearing the mutations. Importantly, PBA increased GAT-1 expression and suppressed spike wave discharges (SWDS) in the heterozygous knockin mice. Although the detailed mechanisms of action for PBA are ambiguous, it is likely that PBA can facilitate the forward trafficking of the wildtype GAT-1 favoring over the mutant GAT-1, thus increasing GABA uptake. Since all patients with SLC6A1 mutations are heterozygous and carry one wildtype functional allele, this suggests a great opportunity for treatment development by leveraging the endogenous protein trafficking pathway to promote forward trafficking of the wildtype in combination with enhancing the disposal of the mutant allele as treatment mode. The study opens a novel avenue of treatment development for genetic epilepsy via drug repurposing.
Estimating Active Cases of COVID-19
Authors: Álvarez Javier , Baquero Carlos , Cabana Elisa , Champati Jaya Prakash , Anta Antonio Fernández , Frey Davide , Garcia-Agundez Augusto , Georgiou Chryssis , Goessens Mathieu , Hernández Harold , Lillo Rosa , Menezes Raquel , Moreno Raúl , Nicolaou Nicolas , Ojo Oluwasegun , Ortega Antonio , Rausell Estrella , Rufino Jesús , Stavrakis Efstathios , Jeevan Govind , Glorioso Christin 
Published: December 2021

AbstractHaving accurate and timely data on active COVID-19 cases is challenging, since it depends on the availability of an appropriate infrastructure to perform tests and aggregate their results. In this paper, we consider a case to be active if it is infectious, and we propose methods to estimate the number of active infectious cases of COVID-19 from the official data (of confirmed cases and fatalities) and from public survey data. We show that the latter is a viable option in countries with reduced testing capacity or infrastructures.
Data-driven identification of previously unrecognized communities with alarming levels of tuberculosis infection in the Democratic Republic of Congo
Authors: Faccin Mauro , Rusumba Olivier , Ushindi Alfred , Riziki Mireille , Habiragi Tresor , Boutachkourt Fairouz , André Emmanuel 
Published: December 2021

ABSTRACTWhen access to diagnosis and treatment of tuberculosis is disrupted by poverty or unequal access to health services, marginalized communities not only endorse the burden of preventable deaths, but also suffer from the dramatic consequences of a disease which impacts one’s ability to access education and minimal financial incomes. Unfortunately, these pockets are often left unrecognized in the flow of data collected National tuberculosis reports, as localized hotspots are diluted in aggregated reports focusing on notified cases. Such system is therefore profoundly inadequate for identifying these marginalized groups, which urgently require adapted interventions.We computed an estimated incidence-rate map for the South-Kivu province of the Democratic Republic of Congo, a province of 6.3 million inhabitants, leveraging available data including notified incidence, level of access to health care and exposition to identifiable risk factors. These estimations were validated in a prospective multi-centric study.We could demonstrate that combining different sources of openly-available data allows to precisely identify pockets of the population which endorses the biggest part of the burden of disease. We could precisely identify areas with a predicted annual incidence of > 1%, a value three times higher than the national estimates. While hosting only 2.5% of the total population, we estimated that these areas were responsible for 23.5% of the actual tuberculosis cases of the province. The bacteriological results obtained from systematic screenings strongly correlated with the estimated incidence (r=0.86), and much less with the incidence reported from epidemiological reports (r=0.77), highlighting the inadequacy of these reports when used alone to guide disease control programs.
A small molecule reveals role of insulin receptor-insulin like growth factor-1 receptor heterodimers
Authors: Simmons Katie J , Myers Chloe G , Viswambharan Hema , Haywood Natalie J , Bridge Katherine , Turvey Samuel , Armstrong Thomas , Lunn Lydia , Meakin Paul J , Clavane Eva , Beech David J , Cubbon Richard M , Wheatcroft Stephen B , McPhillie Martin J , Fishwick Colin WG , Kearney Mark T 
Published: December 2021

AbstractThe insulin receptor and insulin like growth factor-1 receptor are heterodimers consisting of two extracellular α-subunits and two transmembrane β-subunits. IR αβ and IGF1R αβ hemi-receptors can heterodimerize to form hybrids composed of one IR αβ and one IGF1R αβ. Widely distributed in mammalian tissues, in contrast to IR and IGF1R the physiological function of hybrids is unclear. To identify tool compounds that inhibit hybrid formation we performed a high-throughput small molecule screen based on a homology model of hybrid structure. Our studies unveil a first in class quinoline-containing heterocyclic small molecule that reduces hybrids by >50% in human umbilical vein endothelial cells with no effect on IR or IGF1R expression. Downstream of IR and IGF1R our small molecule led to reduced expression of the negative regulatory p85α subunit of phosphatidylinositol 3-kinase, an increase in phosphorylation of its downstream target Akt and enhanced insulin and shear-induced phosphorylation of Akt. We show that hybrids have a role in human endothelial cell physiology distinct from IR and IGF1R.
Lipid droplets 3D full measurement by holographic in-flow tomography
Authors: Pirone Daniele , Sirico Daniele , Miccio Lisa , Bianco Vittorio , Mugnano Martina , del Giudice Danila , Pasquinelli Gianandrea , Valente Sabrina , Lemma Silvia , Iommarini Luisa , Kurelac Ivana , Memmolo Pasquale , Ferraro Pietro 
Published: December 2021

AbstractThe most recent discoveries in the biochemical field are highlighting the increasingly important role of lipid droplets (LDs) in several regulatory mechanisms in living cells. LDs are dynamic organelles and therefore their complete characterization in terms of number, size, spatial positioning and relative distribution in the cell volume can shed light on the roles played by LDs. Until now, fluorescence microscopy and transmission electron microscopy are assessed as the gold standard methods for identifying LDs due to their high sensitivity and specificity. However, such methods generally only provide 2D assays and partial measurements. Furthermore, both can be destructive and with low productivity, thus limiting analysis of large cell numbers in a sample. Here we demonstrate for the first time the capability of 3D visualization and the full LD characterization in high-throughput with a tomographic phase-contrast flow-cytometer, by using ovarian cancer cells and monocyte cell lines as models. A strategy for retrieving significant parameters on spatial correlations and LD 3D positioning inside each cell volume is reported. The information gathered by this new method could allow more in depth understanding and lead to new discoveries on how LDs are correlated to cellular functions.
Shared mechanisms of auditory and non-auditory vocal learning in the songbird brain
Authors: McGregor James N. , Grassler Abigail , Jaffe Paul , Jacob Amanda , Brainard Michael S. , Sober Samuel J. 
Published: December 2021

AbstractSongbirds and humans share the ability to adaptively modify their vocalizations based on sensory feedback. Prior studies have focused primarily on the role that auditory feedback plays in shaping vocal output throughout life. In contrast, it is unclear whether and how non-auditory information drives vocal plasticity. Here, we first used a reinforcement learning paradigm to establish that non-auditory feedback can drive vocal learning in adult songbirds. We then assessed the role of a songbird basal ganglia-thalamocortical pathway critical to auditory vocal learning in this novel form of vocal plasticity. We found that both this circuit and its dopaminergic inputs are necessary for non-auditory vocal learning, demonstrating that this pathway is not specialized exclusively for auditory-driven vocal learning. The ability of this circuit to use both auditory and non-auditory information to guide vocal learning may reflect a general principle for the neural systems that support vocal plasticity across species.
Exploring the Connection between Autophagy and Heat-Stress Tolerance in Drosophila melanogaster
Authors: Willot Quentin , du Toit Andre , de Wet Sholto , Huisamen Elizabeth J. , Loos Ben , Terblanche John S. 
Published: December 2021

AbstractMechanisms aimed at recovering from heat-induced damage are closely associated with the ability of ectotherms to survive exposition to stressful temperatures. Among these mechanisms the respective contribution of autophagy, a ubiquitous stress-responsive catabolic process, has more recently come to light. By increasing the turnover of cellular structures as well as the clearance of long-lived protein and protein aggregates, the induction of autophagy has been linked to increased tolerance to range of abiotic stressors in diverse ectothermic organisms. Since our understanding of the relationship between autophagy and heat-tolerance currently remains limited in insect models, we hypothesized that (1) heat-stress would cause an increase of autophagy inDrosophila melanogastertissues and (2) rapamycin exposure would trigger a detectable autophagic response in flies and increase their heat-tolerance. In line with our hypothesis, we report that flies exposed to heat-stress present signs of protein aggregation and appears to trigger an autophagy-related homoeostatic response as a result. We further show that rapamycin feeding causes the systemic effect associated with TOR inhibition, induces autophagy at least locally in the fly gut, and increase the heat-stress tolerance of individuals. This points toward a likely substantial contribution of this autophagy to cope with stressful temperatures in insects.
Multiplexed mRNA analysis of brain-derived extracellular vesicles upon experimental stroke in mice reveals increased mRNA content related to inflammation and recovery processes
Authors: Bub Annika , Brenna Santra , Alawi Malik , Kügler Paul , Gui Yuqi , Kretz Oliver , Altmeppen Hermann , Magnus Tim , Puig Berta 
Published: December 2021

ABSTRACTExtracellular vesicles (EVs) are lipid bilayer enclosed structures that not only represent a newly discovered means for cell-to-cell communication but may also serve as promising disease biomarkers and therapeutic tools. Apart from proteins, lipids, and metabolites, EVs can deliver genetic information such as mRNA eliciting a response in the recipient cells. In the present study, we have analyzed the mRNA content of brain-derived EVs (BDEVs) isolated 72 hours after experimental stroke in mice and compared them to controls (shams) using the nCounter® Nanostring panels, with or without prior RNA isolation from BDEVs. We found that both panels show similar results when comparing upregulated mRNA in stroke. Notably, the higher upregulated mRNAs were related to processes of stress and immune system responses, but also to anatomical structure development, cell differentiation, and extracellular matrix organization, indicating that regenerative mechanisms are already taking place at this time-point. The five top overexpressed mRNAs in stroke mice compared to shams were confirmed by RT-qPCR and, interestingly, were found to be present as full-length open-reading frame in BDEVs. We could reveal that the majority of the mRNA cargo in BDEVs was of microglial origin and probably predominantly present in small BDEVs (≤ 200 nm in diameter). However, the EV population with the highest increase in the total BDEVs pool at 72 h after stroke was of oligodendrocytic origin. Our study shows that nCounter® panels are a good tool to study mRNA content in tissue-derived EVs as they can be carried out even without previous mRNA isolation and that the mRNA cargo of BDEVs indicates their participation in inflammatory but also recovery processes after stroke.
Manganese is a Physiologically Relevant TORC1 Activator in Yeast and Mammals
Authors: Nicastro Raffaele , Gaillard Hélène , Zarzuela Laura , Péli-Gulli Marie-Pierre , Fernández-García Elisabet , Tomé Mercedes , García-Rodríguez Néstor , Dúran Raúl V. , De Virgilio Claudio , Wellinger Ralf Erik 
Published: December 2021

AbstractThe essential biometal manganese (Mn) serves as a cofactor for several enzymes that are crucial for the prevention of human diseases. Whether intracellular Mn levels may be sensed and modulate intracellular signaling events has so far remained largely unexplored. The highly conserved target of rapamycin complex 1 (TORC1, mTORC1 in mammals) protein kinase requires divalent metal cofactors such as magnesium (Mg2+) to phosphorylate effectors as part of a homeostatic process that coordinates cell growth and metabolism with nutrient and/or growth factor availability. Here, our genetic approaches reveal that TORC1 activity is stimulated in vivo by elevated cytoplasmic Mn levels, which can be induced by loss of the Golgi-resident Mn2+ transporter Pmr1 and which depends on the natural resistance-associated macrophage protein (NRAMP) metal ion transporters Smf1 and Smf2. Accordingly, genetic interventions that increase cytoplasmic Mn2+ levels antagonize the effects of rapamycin in triggering autophagy, mitophagy, and Rtg1-Rtg3-dependent mitochondrion-to-nucleus retrograde signaling. Surprisingly, our in vitro protein kinase assays uncovered that Mn2+ activates TORC1 substantially better than Mg2+, which is primarily due to its ability to lower the Km for ATP, thereby allowing more efficient ATP coordination in the catalytic cleft of TORC1. These findings, therefore, provide both a mechanism to explain our genetic observations in yeast and a rationale for how fluctuations in trace amounts of Mn can become physiologically relevant. Supporting this notion, TORC1 is also wired to feedback control mechanisms that impinge on Smf1 and Smf2. Finally, we also show that Mn2+-mediated control of TORC1 is evolutionarily conserved in mammals, which may prove relevant for our understanding of the role of Mn in human diseases.Significance StatementThe target of rapamycin complex 1 (TORC1, mTORC1 in mammals) is a central, highly conserved controller of cell growth and aging in eukaryotes. Our study shows that the essential biometal manganese (Mn) acts as a primordial activator of TORC1 and that NRAMP metal ion transporters control TORC1 activity by regulating cytoplasmic Mn2+ levels. Moreover, TORC1 activity regulates Mn2+ levels through feedback circuits impinging on NRAMP transporters. Altogether, our results indicate that Mn homeostasis is highly regulated and modulates key cellular processes such as autophagy, mitophagy, and Rtg1-3 complex-dependent retrograde response. These findings open new perspectives for the understanding of neurodegenerative disorders and aging-related processes