bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains
Authors: Meller Artur , Lotthammer Jeffrey M. , Smith Louis G. , Novak Borna , Lee Lindsey A. , Kuhn Catherine C. , Greenberg Lina , Leinwand Leslie A. , Greenberg Michael J. , Bowman Gregory R. 
Published: September 2022

AbstractThe design of compounds that can discriminate between closely related target proteins remains a central challenge in drug discovery. Specific therapeutics targeting the highly conserved myosin motor family are urgently needed as mutations in at least 6 of its members cause numerous diseases. Allosteric modulators, like the myosin-II inhibitor blebbistatin, are a promising means to achieve specificity. However, it remains unclear why blebbistatin inhibits myosin-II motors with different potencies given that it binds at a highly conserved pocket that is always closed in blebbistatin-free experimental structures. We hypothesized that the probability of pocket opening is an important determinant of the potency of compounds like blebbistatin. To test this hypothesis, we used Markov state models (MSMs) built from over 2 milliseconds of aggregate molecular dynamics simulations with explicit solvent. We find that blebbistatin’s binding pocket readily opens in simulations of blebbistatin-sensitive myosin isoforms. Comparing these conformational ensembles reveals that the probability of pocket opening correctly identifies which isoforms are most sensitive to blebbistatin inhibition and that docking against MSMs quantitatively predicts blebbistatin binding affinities (R2=0.82). To test our ability to make blind predictions, we predicted blebbistatin’s binding affinity for an isoform (Myh7b) whose blebbistatin sensitivity was unknown. Encouragingly, we find good agreement between the predicted and measured IC50 (0.67 µM vs. 0.36 µM). Therefore, we expect this framework to be useful for the development of novel specific drugs across numerous protein targets.SignificanceDrug development requires the discovery of compounds which specifically target one member of a protein family without triggering side effects that arise from interactions with other related proteins. Myosins are a family of motor proteins that are drug targets for heart diseases, cancer, and parasitic infections. Here, we investigate why the compound blebbistatin specifically inhibits some myosins more potently than others, even though its binding site is closed in all known experimental structures. We find that the blebbistatin binding pocket opens in molecular dynamics simulations of certain myosin motors, and that the probability of opening predicts how potently blebbistatin inhibits a particular motor. Our work suggests that differences in cryptic pocket formation can be exploited to develop specific therapeutics.
4.1N and SAP97 regulate different phases of AMPA receptor intracellular transport
Authors: Bonnet Caroline , Charpentier Justine , Retailleau Natacha , Choquet Daniel , Coussen Françoise 
Published: September 2022

AbstractChanges in the number of synaptic AMPA subtypes of glutamate receptors (AMPAR) underlie many forms of synaptic plasticity. These variations are controlled by a complex interplay between their intracellular transport (IT), export to the plasma membrane, stabilization at synaptic sites, and recycling. The differential molecular mechanisms involved in these various trafficking pathways and their regulation remains partly unknown. We have recently reported the visualization of AMPAR IT in cultured hippocampal neurons and demonstrated its regulation during synaptic plasticity inducing protocols (Hangen, Cordelieres et al., 2018), opening the path to the differential analysis of the mechanisms controlling AMPAR transport and exocytosis.The cytosolic C-terminal (C-ter.) domain of AMPAR GluA1 subunit is specifically associated with cytoplasmic proteins that could be implicated in the regulation of their IT such as 4.1N and SAP97. Here we analyze how interactions between GluA1 and 4.1N or SAP97 regulate IT and exocytosis at the plasma membrane in basal condition and after cLTP induction. We use sh-RNA against 4.1N and SAP97 and specific mutations and deletions of GluA1 C-ter. domain to characterize how these interactions are involved in coupling AMPAR to the transport machinery.The down-regulation of both 4.1N or SAP97 by shRNAs decrease GluA1 containing vesicle number, modify their transport properties and decrease GluA1 export to the PM, indicating their role in GluA1 IT. The total deletion of the C-ter. domain of GluA1 fully suppresses its IT. Disruption of GluA1 binding to 4.1N decreases the number of GluA1 containing transport vesicles, inhibits GluA1 externalization but does not affect the transport properties of the remaining GluA1 containing vesicles. This indicates a role of the 4.1N-GluA1 interaction during exocytosis of the receptor in basal transmission. In contrast, disrupting the binding between SAP97 and GluA1 modifies the basal transport properties of GluA1 containing vesicles and decreases GluA1 export to the plasma membrane. Importantly, disrupting GluA1 interaction with either 4.1N or SAP97 prevents both the cLTP induced increase in the number of GluA1 containing vesicles observed in control and GluA1 externalization. Our results demonstrate that specific interactions between 4.1N or SAP97 with GluA1 have different roles in GluA1 IT and exocytosis. During basal transmission, the binding of 4.1N to GluA1 allows the fusion/fission membrane exocytosis whereas the interaction with SAP97 is essential for GluA1 IT. During cLTP the interaction of 4.1N with GluA1 allows both IT and exocytosis of the receptor in hippocampal cultured neurons. Altogether, our results identify the differential roles of 4.1N and SAP97 in the control of various phases of GluA1 IT.
Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers
Authors: Davy Tom , Ju Dan , Mathieson Iain , Skoglund Pontus 
Published: September 2022

AbstractAncient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe, and their consequent admixture with Mesolithic hunter-gatherers. Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus contribute to agricultural adaptations. We used genome-wide DNA from 728 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals, and to test for natural selection after admixture using a new method based on testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic ancestry in the genome (|Z| = 3.45). In contrast, we find the greatest overrepresentation of Mesolithic local ancestry across the key immunity locus that is the Major Histocompatibility Complex (MHC; |Z| > 4) which also shows allele frequency deviations indicative of a selective sweep following admixture (p =1×10−29). This could reflect negative frequency dependent selection on MHC alleles common in Neolithic populations, or that Mesolithic alleles were positively selected for and facilitated adaptation by Neolithic populations to pathogens, new diets, or other environmental factors. Our results extend previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age, and demonstrate that admixture facilitated selection by contributing new genetic variation.
EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions
Authors: Ribeiro Antonio J. M. , Riziotis Ioannis G. , Tyzack Jonathan D. , Borkakoti Neera , Thornton Janet M. 
Published: September 2022

AbstractA rich literature dedicated to understanding the reaction mechanisms of hundreds of enzymes has emerged over time from the works of experimental and computational researchers. This body of information can now be the starting point for an entirely novel approach to studying enzyme mechanisms using knowledge-based prediction methods. Here, we present such a method, EzMechanism, (pronounced as “Easy Mechanism”) which is able to automatically generate mechanism proposals for a given active site. It works by searching the chemical reaction space available to the enzyme using a set of newly created biocatalytic rules based on knowledge from the literature. EzMechanism aims to complement existing methods for studying enzyme mechanisms by facilitating and improving the hypotheses generating step. We show that EzMechanism works by validating it against 56 enzymes with a known mechanism and identify the limited coverage of the current ruleset as the main target for further improvement.
Efficient repair of human homozygous genetic mutation by CRISPR/Cas9 mediated interlocus gene conversion
Authors: Yang Fei , Pang Jingtao , Liu Guolong , Yang Yang , Qin Shenguang , Zhang Ying , Lai Yongrong , Liang Dan , Wu Yuxuan 
Published: September 2022

AbstractDNA double-strand breaks (DSBs) induced by gene editing tools are primarily resolved either by non-homologous end joining (NHEJ) or homology-directed repair (HDR) using exogenous synthetic DNA templates. Repaired by error-prone NHEJ may lead to unexpected indels at the targeted site. In the case of most genetic disorders, HDR-mediated precise correction using an exogenous homologous sequence is ideal. However, the therapeutic application of HDR might be especially challenging given the requirement for the codelivery of exogenous DNA templates with toxicity into cells, and the low efficiency of HDR could also limit its clinical application. Here, we used hematopoietic stem cells (HSCs) with genetic mutations to cause β-thalassemia in HBB coding regions and discovered that many cells are actually repaired by CRISPR/Cas9-mediated gene conversion (GC) independent of exogenous synthetic DNA templates. We show that pathogenic mutations in the HBB coding regions of HSCs can be repaired efficiently through CRISPR/GC using the paralog gene HBD as the internal template. Electroporations of Cas9 for ribonucleoprotein with sgRNA into haematopoietic stem and progenitor cells (HSPCs) with a variety of pathogenic gene mutations also resulted in effective conversion of mutations to normal wild-type sequences without exogenous DNA template. Moreover, the edited HSCs can repopulate the haematopoietic system and generate erythroid cells with a greatly reduced propensity for thalassemia after transplantations. Thus, CRISPR/GC, independent of exogenous DNA templates, holds great promise for gene therapy of genetic diseases.
TransporterPAL: An integrative database Transporter Prediction ALgorithm
Authors: Dyekjær Jane Dannow , Andersen Alexander Kruhøffer Bloch , Madsen Joel August Vest , Morth Jens Preben , Jensen Lars Juhl , Borodina Irina 
Published: September 2022

AbstractMotivationNatural products are used as drugs, cosmetic ingredients, pigments, flavors, and agricultural products. The compounds are retrievable as extracts from natural sources, but the yields are often low, and the final product may contain various impurities. These challenges can be solved by expressing the biosynthetic pathway in microbial cell factories and ensuring product secretion from the cell by using an appropriate transporter. However, insufficient knowledge of transporters for specific compounds often obstructs efficient secretion of the natural product. Therefore, our goal was to develop an algorithm that predicts transporters for a given compound using available public data.ResultsThe web application TransporterPAL predicts suitable transporters for compounds by interconnecting data for biosynthetic genes and their interactions with transporters. The web application queries the STITCH, STRING, and UniProtKB databases via their respective APIs and returns a set of potential transporters based on a compound and, optionally, the organism as input. For a test set of 61 transporter systems, each containing one or more transporters, a total of 90 unique transporters with a known substrate, we could retrieve 45% of the transporters. To our knowledge, this is the first bioinformatics tool for predicting transporter candidates for a given molecule.Availabilityhttps://transporterpal.comContactirbo@biosustain.dtu.dkSupplementary informationSupplementary data are available at Bioinformatics online.
The relationship between spectral and plant diversity: disentangling the influence of metrics and habitat types
Authors: Michela Perrone , Mirko Di Febbraro , Luisa Conti , Jan Divíšek , Milan Chytrý , Petr Keil , Laura Carranza Maria , Duccio Rocchini , Michele Torresani , Vítězslav Moudrý , Petra Šímová , Dominika Prajzlerová , Jana Müllerová , Jan Wild , Marco Malavasi 
Published: September 2022

AbstractBiodiversity monitoring is crucial for ecosystem conservation, yet field data collection is limited by costs, time, and extent. Remote sensing represents a convenient approach providing frequent, near-real-time information over wide areas. According to the Spectral Variation Hypothesis (SVH), spectral diversity (SD) is an effective proxy of environmental heterogeneity, which ultimately relates to plant diversity. So far, studies testing the relationship between SD and biodiversity have reported contradictory findings, calling for a thorough investigation of the key factors (e.g., metrics applied, ecosystem type) and the conditions under which such a relationship holds true. This study investigates the applicability of the SVH for plant diversity monitoring at the landscape scale by comparing the performance of three different types of SD metrics. Species richness and functional diversity were calculated for more than 2000 cells forming a grid covering the Czech Republic. Within each cell, we quantified SD using a Landsat-8 “greenest pixel” composite by applying: i) the standard deviation of NDVI, ii) Rao’s Q entropy index, and iii) richness of “spectral communities”. Habitat type (i.e., land cover) was included in the models describing the relationship between SD and ground biodiversity. Both species richness and functional diversity show positive and significant relationships with each SD metric tested. However, SD alone accounts for a small fraction of the deviance explained by the models. Furthermore, the strength of the relationship depends significantly on habitat type and is highest in natural transitional areas. Our results underline that, despite the stability in the significance of the link between SD and plant diversity at this scale, the applicability of SD for biodiversity monitoring is context-dependent and the factors mediating such a relationship must be carefully considered to avoid drawing misleading conclusions.HighlightsPlant species richness and functional diversity show significant and positive relationships with spectral diversitySpectral diversity alone explains a small fraction of the total variability in ground biodiversitySlight differences among the performances of the spectral diversity metrics testedThe relationship between spectral and plant diversity is context-dependent
In vitro−in silico correlation of three-dimensional turbulent flows in an idealized mouth-throat model
Authors: Nof Eliram , Bhardwaj Saurabh , Koullapis Pantelis , Bessler Ron , Kassinos Stavros , Sznitman Josué 
Published: September 2022

AbstractThere exists an ongoing need to improve the validity and accuracy of computational fluid dynamics (CFD) simulations of turbulent airflows in the extra-thoracic and upper airways. Yet, a knowledge gap remains in providing experimentally-resolved 3D flow benchmarks with sufficient data density and completeness for useful comparison with widely-employed numerical schemes. Motivated by such shortcomings, the present work details to the best of our knowledge the first attempt to deliver in vitro−in silico correlations of 3D respiratory airflows in a generalized mouth-throat model and thereby assess the performance of Large Eddy Simulations (LES) and Reynolds-Averaged Numerical Simulations (RANS). Numerical predictions are compared against 3D volumetric flow measurements using Tomographic Particle Image Velocimetry (TPIV) at three steady inhalation flowrates varying from shallow to deep inhalation conditions. We find that a RANS k-ω SST model adequately predicts velocity flow patterns for Reynolds numbers spanning 1’500 to 7’000, supporting results in close proximity to a more computationally-expensive LES model. Yet, RANS significantly underestimates turbulent kinetic energy (TKE), thus underlining the advantages of LES as a higher-order turbulence modeling scheme. In an effort to bridge future endevours across respiratory research disciplines, we provide end users with the present in vitro −in silico correlation data for improved predictive CFD models towards inhalation therapy and therapeutic or toxic dosimetry endpoints.Author SummaryThe dispersion and ensuing deposition of inhaled airborne particulate matter in the lungs are strongly influenced by the dynamics of turbulent respiratory airflows in the mouth-throat region during inhalation. To cirumvent costly in vitro experimental measurement resources, fluid dynamics (CFD) simulations are widely sought to predict deposition outcomes but often lack detailed experimental data to first validate the three-dimensional (3D) flow structures anticipated to arise in the upper respiratory tract. In an effort to reconcile such data scarcity, we deliver experimental-numerical correlations of 3D respiratory airflows in an idealized 3D printed mouth-throat model against two widely-established numerical schemes with varying computational costs, namely coarse RANS and finer LES technique. Our time-resolved 3D flow data underline the complexity of these physiological inhalation flows, and discuss advantages and drawbacks of the different numerical techniques. With an outlook on future respiratory applications geared towards broad preclinical inhaled aerosol deposition studies, our open source data are made available for future benchmark comparisons for a broad range of end users in the respiratory research community.
Reduction of the HIV-1 reservoir in T cells from persons with HIV-1 on suppressive antiretroviral therapy using expanded natural killer cellsex vivo
Authors: Checkley Mary Ann , Luttge Benjamin G. , Dobrowolski Curtis , Wald David N. , McMahon Deborah , Haidar Ghady , Sobolewski Michele D. , Enick P. Nathan , Cyktor Joshua , Mellors John W. , Karn Jonathan 
Published: September 2022

AbstractTreatment with latency-reversing agents (LRAs) alone has been ineffective in reducing HIV-1 reservoirs in persons with HIV-1 (PWH) on antiretroviral therapy (ART), due to inefficiencies in reservoir reactivation and adaptive immune responses. However, NK cells that are activated with cytokines may be able to target HIV-1 reservoirs more efficiently. To study the therapeutic potential of NK cells, we expanded blood NK cells from multiple donorsex vivointo CD56brightCD16+“eNK” cells using artificial antigen presenting cells (aAPCs) expressing membrane-bound IL21. eNK cells express multiple activating receptors and are highly cytotoxic against specific target cells. eNK cells can also kill HIV-infected CD4 T cells via antibody dependent cell-mediated cytotoxicity (ADCC) using broadly neutralizing antibodies against HIV-1 Env gp120/gp41. Importantly, eNK cells from PWH on ART efficiently killed autologous HIV-1+T cells reactivated by a combination of vorinostat (SAHA) and IL-15 or an IL-15 superagonist (N-803), as detected by declines in proviral load, inducible HIV-1 mRNA, and virus release. Adoptive immunotherapy with eNK cells is therefore a promising approach to reduce the latent HIV-1 reservoir in PWH when combined with LRA treatment.Author SummarySuccessful antiretroviral therapy (ART) eliminates progression to AIDS by reducing HIV to nearly indetectable levels by routine clinical measurements of blood samples. However, more sensitive DNA and RNA measurements show that most persons on ART retain a reservoir of long lived latently infected cells, which remain undetected by the immune system while no HIV is being produced. In nearly all cases, ART interruption results in a rebound of HIV production and spread, requiring an immediate return to ART. Currently the goal of HIV eradication is to achieve a “functional cure”, where HIV reservoirs are reduced to the point where ART can be interrupted indefinitely, and low levels of infected cells remaining can be controlled by the immune system. Our eradication strategy combines HIV latency-reversing agents (LRAs), ex vivo expansion of natural killer (NK) cells, and enhancement of specificity and killing of infected cells with broadly neutralizing antibodies against HIV. In this study, we have demonstrated that NK cells from person living with HIV can be isolated and expanded ex vivo into “eNK” cells that kill HIV-infected cells without killing uninfected cells, especially when broadly neutralizing antibodies are present, and can significantly reduce HIV reservoirs after LRA treatment.
Oocyte and cumulus cell cooperativity and metabolic plasticity under the direction of oocyte paracrine factors
Authors: Richani Dulama , Poljak Anne , Wang Baily , Mahbub Saabah B. , Biazik Joanna , Campbell Jared M. , Habibalahi Abbas , Stocker William A. , Marinova Maria B. , Nixon Brett , Bustamante Sonia , Skerrett-Byrne David , Harrison Craig A. , Goldys Ewa , Gilchrist Robert B. 
Published: September 2022

ABSTRACTMammalian oocytes develop and mature in a mutually dependent relationship with surrounding cumulus cells. The oocyte actively regulates cumulus cell differentiation and function by secreting soluble paracrine oocyte-secreted factors (OSFs). We characterized the molecular mechanisms by which two model OSFs, cumulin and BMP15, regulate oocyte maturation and cumulus-oocyte cooperativity. Exposure to these OSFs during maturation altered the proteomic and multispectral autofluorescence profiles of both the oocyte and cumulus cells. In oocytes, cumulin significantly upregulated proteins involved in nuclear function. In cumulus cells, both OSFs elicited marked upregulation of a variety of metabolic processes (mostly anabolic), including lipid, nucleotide, and carbohydrate metabolism, while mitochondrial metabolic processes were downregulated. The mitochondrial changes were validated by functional assays confirming altered mitochondrial morphology, respiration, and content, whilst maintaining ATP homeostasis. Collectively, these data demonstrate that OSFs remodel cumulus cell metabolism during oocyte maturation in preparation for ensuing fertilization and embryonic development.HIGHLIGHTSDuring oocyte maturation, oocyte-secreted factors promote cell cooperativity between the oocyte and cumulus cells by altering the molecular composition of both cell types.Oocyte-secreted factors downregulate protein catabolic processes, and upregulate DNA binding, translation, and ribosome assembly in oocytes.Oocyte-secreted factors alter mitochondrial number, morphology, and function in cumulus cells.Oocyte-secreted factors further enhance metabolic plasticity in cumulus cells by upregulating anabolic pathways for macromolecules and small molecule organics.The oocyte, via oocyte-secreted factors, instructs cumulus cells to increase metabolic workload on its behalf, thereby subduing oocyte metabolism.