bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host-pathogen sympatry and differential transmissibility ofMycobacterium tuberculosis complex
Authors: Gröschel Matthias I , Pérez-Llanos Francy J. , Diel Roland , Vargas Roger , Escuyer Vincent , Musser Kimberlee , Trieu Lisa , Meissner Jeanne Sullivan , Knorr Jillian , Klinkenberg Don , Kouw Peter , Homolka Susanne , Samek Wojciech , Mathema Barun , van Soolingen Dick , Niemann Stefan , Ahuja Shama , Farhat Maha R 
Published: August 2022

SUMMARYThe obligate human pathogenMycobacteriumtuberculosis complex (Mtbc) separates genetically into nine lineages several of which demonstrate sympatry with their human host i.e. have distinct and restricted patterns of geographical distribution globally.1–3Geographically restrictedMtbclineages have been hypothesized to be adapted to infect and/or transmit among sympatric human hosts,i.e. to be niche specialists, but this is yet to be confirmed while controlling for exposure, social networks and risk of disease after exposure.1,4Here we show that strains of geographically restricted (Mtbclineages L1,L2restricted, L3,L4restricted, L5,L6 are intrinsically less transmissible than widespreadMtbclineages (L2widespread, L4widespread) across Western European and North American cosmopolitan populations. Comparing transmissibility between sympatric and allopatric contact-pathogen pairs, we find the first controlled evidence for a biological impact of sympatry betweenMtbcstrains and their human hosts; allopatric host-pathogen exposures has a 38% decrease in the odds of infection among contacts compared with sympatric exposures. We measure 10- fold lower phagocytosis and growth rates of L6 geographically restricted strains compared to L4widespreadinin vitroallopatric macrophage infections. Long-term co-existence ofMtbcstrains and humans has resulted in differential transmissibility between allopatric and sympatric hosts for strains of geographically restricted lineages. Understanding the specific genetic and immunological underpinnings of sympatry in TB may inform rational vaccine design and TB control.
Viral Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron Infection in mRNA-Vaccinated Individuals Treated and Not Treated with Nirmatrelvir-Ritonavir
Authors: Dai Eric Y. , Lee Kannon A. , Nathanson Audrey B. , Leonelli Ariana T. , Petros Brittany A. , Brock-Fisher Taylor , Dobbins Sabrina T. , MacInnis Bronwyn L. , Capone Amelia , Littlehale Nancy , Boucau Julie , Marino Caitlin , Barczak Amy K. , Sabeti Pardis C. , Springer Michael , Stephenson Kathryn E. 
Published: August 2022

ABSTRACTWe measured viral kinetics of SARS-CoV-2 Omicron infection in 36 mRNA-vaccinated individuals, 11 of whom were treated with nirmatrelvir-ritonavir (NMV-r). We found that NMV-r was associated with greater incidence of viral rebound compared to no treatment. For those that did not rebound, NMV-r significantly reduced time to PCR conversion.
Mec1-Independent Activation of the Rad53 Checkpoint Kinase Revealed by Quantitative Analysis of Protein Localization Dynamics
Authors: Ho Brandon , Sanford Ethan J. , Torres Nikko P. , Smolka Marcus B. , Brown Grant W. 
Published: August 2022

AbstractThe replication checkpoint is essential for accurate DNA replication and repair, and maintenance of genomic integrity when a cell is challenged with genotoxic stress. Several studies have defined the complement of proteins that change subcellular location in the budding yeast Saccharomyces cerevisiae following chemically-induced DNA replication stress using methyl methanesulfonate (MMS) or hydroxyurea (HU). How these protein movements are regulated remains largely unexplored. We find that the essential checkpoint kinases Mec1 and Rad53 are responsible for regulating the subcellular localization of 159 proteins during MMS-induced replication stress. Unexpectedly, Rad53 regulation of the localization of 52 proteins is independent of its known kinase activator, Mec1, and in some scenarios independent of Tel1, or mediator components, Rad9 and Mrc1. We demonstrate that Rad53 is phosphorylated and active following MMS exposure in cells lacking Mec1 and Tel1. This non-canonical mode of Rad53 activation depends partly on the retrograde signaling transcription factor Rtg3, which also facilitates proper DNA replication dynamics. We conclude that there are biologically important modes of Rad53 protein kinase activation that respond to replication stress and operate in parallel to Mec1 and Tel1.
Genome wide CRISPR screen for Pasteurella multocida toxin (PMT) binding proteins reveals LDL Receptor Related Protein1 (LRP1) as crucial cellular receptor
Authors: Schöllkopf Julian , Müller Thomas , Hippchen Lena , Müller Teresa , Großmann Sonja , Reuten Raphael , Backofen Rolf , Klugbauer Norbert , Orth Joachim , Schmidt Gudula 
Published: August 2022

AbstractPMT is a protein toxin produced by Pasteurella multocida serotypes A and D. As causative agent of atrophic rhinitis in swine, it leads to rapid degradation of the nasal turbinate bone. The toxin acts as a deamidase to modify a crucial glutamine in heterotrimeric G proteins, which results in constitutive activation of the G proteins and permanent stimulation of numerous downstream signaling pathways.Using a lentiviral based genome wide CRISPR knockout screen in combination with a lethal toxin chimera, consisting of full length inactive PMT and the catalytic domain of diphtheria toxin, we identified the LRP1 gene encoding the Low-Density Lipoprotein Receptor-related protein 1 as a critical host factor for PMT function. Loss of LRP1 reduced PMT binding and abolished the cellular response and deamidation of heterotrimeric G proteins, confirming LRP1 to be crucial for PMT uptake. Expression of LRP1 or cluster 4 of LRP1, respectively, restored intoxication of the knockout cells. In summary our data demonstrate secretory cells as entry site of PMT into airway epithelia and present LRP1 as crucial host entry factor for PMT intoxication by acting as its primary cell surface receptor.
Cellular Uptake of His-Rich Peptide Coacervates Occurs by a Macropinocytosis-Like Mechanism
Authors: Shebanova Anastasia , Perrin Quentin , Gudlur Sushanth , Sun Yue , Lim Zhi Wei , Sun Ruoxuan , Lim Sierin , Ludwig Alexander , Miserez Ali 
Published: August 2022

AbstractCoacervates are dense microdroplets formed by liquid-liquid phase separation (LLPS) of macromolecules that have gained increasing attention as drug delivery vehicles. Recently, we have reported a new intracellular delivery system based on self-coacervating histidine (His)-rich beak peptides (HBpep and HBpep-SP) inspired by beak proteins of the Humboldt squid. These peptide microdroplets combine excellent encapsulation efficiency of therapeutics with high transfection rate and low cytotoxicity. However, the mechanism by which they cross the cell membrane remains elusive. Previous inhibitor studies provided incomplete clues into the detail uptake pathway, although they suggested a cholesterol-dependent and, possibly, an energy-independent non-classical mechanism of internalization. In this study, we improved our understanding of coacervates/cell membrane interactions using model membranes, namely Giant Unilamellar Vesicles (GUVs) and Giant Plasma Membrane Vesicles (GPMVs). We also employ a combination of electron microscopy techniques to gain detailed structural insights into the cell uptake of HBpep and HBpep-SP coacervates. We demonstrate that modulating lipid charge and cholesterol level influence coacervate attachment to GUVs. However, they are not able to cross the GUV’s lumen in an energy-independent manner. We then show that the coacervates enter HeLa and HepG2 cells via a mechanism sharing morphological features of macropinocytosis and phagocytosis, in particular involving cytoskeleton rearrangement and capture by filipodia. Our study provides key insights into the interaction of HPpep and HBpep-SP coacervates with model membranes as well as their cellular uptake pathway.
A specific anti-IFITM2 antibody bars the way to SARS-CoV-2 entry into host cells
Authors: Basile Anna , Zannella Carla , De Marco Margot , Franci Gianluigi , Galdiero Massimiliano , Sanna Giuseppina , Manzin Aldo , Chetta Massimiliano , Turco Maria Caterina , Rosati Alessandra , Marzullo Liberato 
Published: August 2022

SUMMARYThe early steps of viral infection involve protein complexes and structural lipid rearrangements, which mark the characteristic strategies of each virus in entering permissive host cells. Human IFITM proteins have been described as inhibitors of a broad range of viruses. Despite their homology and functional redundancy, recently it has been surprisingly shown that SARS-CoV-2 is able to specifically hijack the IFITM2 protein. Here has been reported the characterization of a newly generated specific anti-IFITM2 mAb able to impair SARS-CoV-2 Spike protein internalization and, consequently, to reduce the SARS-CoV-2 cytopathic effects and syncytia formation. Importantly, as evidence of the more general involvement of IFITM2 in virus entry, the anti-IFITM2 mAb was able to efficiently reduce HSVs- and RSV-dependent cytopathic effects. Hence, IFITM proteins could be promising targets that can foster the development of biological antiviral molecules, or suggest additional therapeutic strategies for the treatment of viral infections.GRAPHICAL ABSTRACT
Tuning the resorption-formation balance in anin vitro3D osteoblast-osteoclast co-culture model of bone
Authors: Remmers Stefan J.A. , van der Heijden Freek C. , de Wildt Bregje W. M. , Ito Keita , Hofmann Sandra 
Published: August 2022

AbstractThe aim of the present study was to further improve anin vitro3D osteoblast (OB) – osteoclast (OC) co-culture model of bone by tuning it towards states of formation, resorption, and equilibrium for their future applications in fundamental research, drug development and personalized medicine. This was achieved by varying culture medium composition and monocyte seeding density, the two external parameters that affect cell behavior the most. Monocytes were seeded at two seeding densities onto 3D silk-fibroin constructs pre-mineralized by MSC-derived OBs and were co-cultured in one of three different media (OC stimulating, Neutral and OB stimulating medium) for three weeks. Histology showed mineralized matrix after co-culture and OC markers in the OC medium group. Scanning Electron Microscopy showed large OC-like cells in the OC medium group. Micro-computed tomography showed increased formation in the OB medium group, equilibrium in the Neutral medium group and resorption in the OC medium group. Culture supernatant samples showed high early TRAP release in the OC medium group, a later and lower release in the Neutral medium group, and almost no release in the OB medium group. Increased monocyte seeding density showed a less-than-proportional increase in TRAP release and resorption in OC medium, while it proportionally increased TRAP release in Neutral medium without affecting net resorption. The 3D OB-OC co-culture model was effectively used to show an excess of mineral deposition using OB medium, resorption using OC medium, or an equilibrium using Neutral medium. All three media applied to the model may have their own distinct applications in fundamental research, drug development, and personalized medicine.
Precision engineering of biological function with large-scale measurements and machine learning
Authors: Tack Drew S. , Tonner Peter D. , Pressman Abe , Olson Nathanael D. , Levy Sasha F. , Romantseva Eugenia F. , Alperovich Nina , Vasilyeva Olga , Ross David 
Published: August 2022

AbstractAs synthetic biology expands and accelerates into real-world applications, methods for quantitatively and precisely engineering biological function become increasingly relevant. This is particularly true for applications that require programmed sensing to dynamically regulate gene expression in response to stimuli. However, few methods have been described that can engineer biological sensing with any level of quantitative precision. Here, we present two complementary methods for precision engineering of genetic sensors:in silicoselection and machine-learning-enabled forward engineering. Both methods use a large-scale genotype-phenotype dataset to identify DNA sequences that encode sensors with quantitatively specified dose response. First, we show thatin silicoselection can be used to engineer sensors with a wide range of dose-response curves. To demonstratein silicoselection for precise, multi-objective engineering, we simultaneously tune a genetic sensor’s sensitivity (EC50) and saturating output to meet quantitative specifications. In addition, we engineer sensors with inverted dose-response and specifiedEC50. Second, we demonstrate a machine-learning-enabled approach to predictively engineer genetic sensors with mutation combinations that are not present in the large-scale dataset. We show that the interpretable machine learning results can be combined with a biophysical model to engineer sensors with improved inverted dose-response curves.
Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins
Authors: Hirose Yujiro , Poudel Saugat , Sastry Anand V. , Rychel Kevin , Szubin Richard , Zielinski Daniel , Lim Hyun Gyu , Menon Nitasha , Bergsten Helena , Uchiyama Satoshi , Hanada Tomoki , Kawabata Shigetada , Palsson Bernhard O. , Nizet Victor 
Published: August 2022

AbstractStreptococcus pyogenes can cause a wide variety of acute infections throughout the body of its human host. The underlying transcriptional regulatory network (TRN) is responsible for altering the physiological state of the bacterium to adapt to each host environment. Consequently, an in-depth understanding the comprehensive dynamics of its TRN could inform new therapeutic strategies. Here, we compiled 116 existing high-quality RNA-seq data sets of S. pyogenes serotype M1, and estimated the TRN structure in a top-down fashion by performing independent component analysis (ICA). The algorithm computed 42 independently modulated sets of genes (iModulons). Four iModulons contained nga-ifs-slo virulence-related operon, which allowed us to identify carbon sources that control its expression. In particular, dextrin utilization upregulated nga-ifs-slo operon by activation of two-component regulatory system CovRS-related iModulons, and changed bacterial hemolytic activity compared to glucose or maltose utilization. Finally, we show that the iModulon-based TRN structure can be used to simplify interpretation of noisy bacterial transcriptome at the infection site.
Phosphosite Scanning reveals a complex phosphorylation code underlying CDK-dependent activation of Hcm1
Authors: Conti Michelle M. , Li Rui , Narváez Ramos Michelle A. , Zhu Lihua Julie , Fazzio Thomas G. , Benanti Jennifer A. 
Published: August 2022

AbstractOrdered cell cycle progression is coordinated by cyclin dependent kinases (CDKs). CDKs often phosphorylate substrates at multiple sites clustered within disordered regions. However, for most substrates, it is not known which phosphosites are functionally important. We developed a high-throughput approach, Phosphosite Scanning, that tests the importance of each phosphosite within a multisite phosphorylated domain. We show that Phosphosite Scanning identifies multiple combinations of phosphosites that can regulate protein function and reveals specific phosphorylations that are required for phosphorylation at additional sites within a domain. We applied this approach to the yeast transcription factor Hcm1, a conserved regulator of mitotic genes that is critical for accurate chromosome segregation. Phosphosite Scanning revealed a complex CDK-regulatory circuit that mediates processive phosphorylation of key activating sites in vivo. These results illuminate the mechanism of Hcm1 activation by CDK and establish Phosphosite Scanning as a powerful tool for decoding multisite phosphorylated domains.
Vibrio cholerae alkalizes its environment via citrate metabolism to inhibit enteric growth
Authors: Kostiuk Benjamin , Becker Mark E. , Churaman Candice N. , Black Joshua J. , Payne Shelley M. , Pukatzki Stefan , Koestler Benjamin J. 
Published: August 2022

AbstractVibrio cholerae is a Gram-negative pathogen, living in constant competition with other bacteria in both marine environments and during human infection. One competitive advantage of V. cholerae is the ability to metabolize diverse carbon sources such as chitin and citrate. We observed that when V. cholerae strains were grown on a medium with citrate, the medium’s chemical composition turned into a hostile alkaline environment for Gram-negative bacteria such as Escherichia coli and Shigella flexneri. We found that although the ability to exclude competing bacteria was not contingent on exogenous citrate, V. cholerae citrate metabolism mutants ΔoadA-1, ΔcitE, and ΔcitF mutants were not able to inhibit S. flexneri or E. coli growth. Lastly, we demonstrated that while the V. cholerae mediated increased medium pH was necessary for the enteric exclusion phenotype, secondary metabolites such as bicarbonate (protonated to carbonate in the raised pH) from the metabolism of citrate enhanced the ability to inhibit the growth of E. coli. These data provide a novel example of how V. cholerae outcompetes other Gram-negative bacteria.
The Alphaherpesvirus Latency Associated Promoter 2 (LAP2) Drives Strong Transgene Expression in Peripheral Tissue Depending on Administration Route and AAV Serotype
Authors: Maturana Carola J. , Chan Angela , Verpeut Jessica L. , Engel Esteban A. 
Published: August 2022

AbstractAdeno-associated virus (AAV) has shown great translational potential in treating a variety of diseases often requiring strong and ubiquitous transgene expression. However, the genetic payload of AAV vectors is limited to <4.9 kb and some commonly used gene promoters are large in sizeable and susceptible to transcriptional silencing. We validated a short (404 bp), strong and persistent promoter obtained from the genome of pseudorabies virus (PRV) called alphaherpesvirus latency-associated promoter 2 (LAP2). We evaluated the biodistribution and potency of transgene expression in mouse peripheral tissue and organs when using AAV8-LAP2 and AAV9-LAP2, both of which achieved transgene expression like that of the ubiquitous promoter, EF1α. LAP2 drives potent transgene expression in liver and kidney after systemic retro-orbital administration and in skeletal muscle after intramuscular delivery. Additionally, we observed broad transduction throughout the lung albeit at lower levels than other tissues. Notably, in skeletal muscle LAP2 resulted in preferential transduction of myofiber types 2. A direct side-by-side comparison between LAP2 and EF1α, demonstrates that regardless of the AAV serotype and route of administration, LAP2 is as powerful and persistent as EF1α promoter despite being 66% smaller in size, thus allowing for larger therapeutic payloads.
Depletion of Plasma Membrane PI4P by ORP5 Requires Hydrolysis by SAC1 in Acceptor Membranes
Authors: Doyle Colleen P. , Timple Liz , Hammond Gerald R. V. 
Published: August 2022

AbstractOxysterol binding protein (OSBP)-related proteins (ORPs) 5 and 8 have been shown to deplete the lipid phosphatidylinositol 4-phosphate (PI4P) at sites of membrane contact between the endoplasmic reticulum (ER) and plasma membrane (PM). This is believed to be caused by transport of PI4P from the PM to the ER, where PI4P is degraded by an ER-localized SAC1 phosphatase. This is proposed to power the anti-port of phosphatidylserine (PS) lipids from ER to PM, up their concentration gradient. Alternatively, ORPs have been proposed to sequester PI4P, dependent on the concentration of their alternative lipid ligand. Here, we aimed to distinguish these possibilities in living cells by orthogonal targeting of ORP5 to PM-mitochondrial contact sites. We demonstrate that ORP5 is unable to deplete PM PI4P or accumulate the lipid in mitochondrial outer membranes when acting alone, ruling out both lipid transport and sequestration models. However, when combined with orthogonal targeting of SAC1 to the mitochondrial outer membrane, ORP5 facilitates depletion of PM PI4P when targeted to PM-mitochondria contact sites. We conclude that PI4P depletion from the PM by ORP5 requires transport of PI4P to the tethered organelle membrane, which must be closely coupled to PI4P hydrolysis by SAC1. The data are most compatible with a lipid transfer reaction by ORP family members.
A two-decade microbial time series from a freshwater lake, introducing the limony and TYMEFLIES datasets
Authors: Rohwer Robin R. , McMahon Katherine D. 
Published: August 2022

AbstractHow microbial communities change over time is key to understanding how ecosystems will respond to global change, and to answering fundamental questions about how microbial ecology and evolution unfold. However, our understanding of microbial change is limited by a lack of long-term observations. Using archived filters from freshwater Lake Mendota (WI, USA), we created a 20-year microbial time series that begins in year 2000, a decade before Illumina DNA sequencing hit the market. We characterized 1,023 samples and controls with 16S rRNA gene amplicon sequencing in the “limony” dataset, and 471 samples and controls with shotgun metagenome sequencing in the “TYMEFLIES” dataset. In addition to the raw sequencing data, we point users to associated data products: paired environmental data collected by the North Temperate Lakes Long-Term Ecological Research program (NTL-LTER), our R package to work with curated limony data, and metagenomic assemblies and metagenome-assembled genomes (MAGs) created from the TYMEFLIES dataset. The limony and TYMEFLIES datasets, along with their paired environmental data and reference genomes, are a unique and ready-to-use resource for diverse scientists including limnologists, ecologists, evolutionary biologists, bioinformaticians, modellers, and educators.
Production of brain-derived neurotrophic factor gates plasticity in developing visual cortex
Authors: Kaneko Megumi , Stryker Michael P. 
Published: August 2022

AbstractWe have previously shown that recovery of visual responses to a deprived eye during the critical period in mouse primary visual cortex (V1) requires both export of mRNA encoding brain derived neurotrophic factor (BDNF) to the dendrites of cortical cells (Kaneko et al., 2012) and phosphorylation of the TrkB receptor for BDNF (Kaneko et al., 2008a). TrkB phosphorylation is not required for the loss of response during monocular deprivation (MD). Studies in vitro show that formation of new connections requires BDNF (Meyer-Franke et al., 1995, 1998; Gottmann et al., 2009). We have now studied the temporal relationship between the production of mature BDNF and the recovery of visual responses. Visual cortical responses to an eye whose vision has been occluded for several days during the critical period and is then re-opened recovers rapidly during binocular vision or more slowly following reverse occlusion, when the previously intact fellow eye is occluded in a model of “patch therapy” for amblyopia. The time to recovery of visual responses differed by 18 hours between these two procedures, but in each the production of mature BDNF preceded the recovery by 6 hours. These findings suggest that a spurt of BDNF secretion stimulates the growth of connections serving the deprived eye to restore visual responses.Significance StatementBy demonstrating that BDNF production precedes rather than merely accompanies the increase in cortical responses, we provide further evidence that BDNF production plays a causal role, thereby gating the plasticity that underlies the recovery of visual cortex from monocular deprivation.