bluuebunny/crossref_metadata_2025_split huggingface dataset:
From Farm to Pharmacy: Strawberry-Enabled Oral Delivery of Protein Drugs
Authors: Lamson Nicholas G. , Fein Katherine C. , Gleeson John P. , Xian Sijie , Newby Alexandra , Chaudhary Namit , Melamed Jilian R. , Cochran Kyle , Ball Rebecca L. , Suri Kanika , Ahuja Vishal , Zhang Anna , Berger Adrian , Kolodieznyi Dmytro , Schmidt Brigitte F. , Silva Gloria L. , Whitehead Kathryn A. 
Published: March 2020

AbstractAlthough oral drug delivery is preferred by patients, it is not possible for proteins because the gastrointestinal tract is not sufficiently permeable. To enable the non-toxic oral uptake of protein drugs, we investigated plant-based foods as intestinal permeation enhancers, hypothesizing that compounds found in food would be well-tolerated by the gastrointestinal tract. Following a screen of over 100 fruits, vegetables, herbs, and fungi, we identified strawberry as a potent enhancer of macromolecular permeability in vitro and in mice. Natural product chemistry techniques identified pelargonidin, an anthocyanidin, as the active compound. In mice, insulin was orally administered with pelargonidin to induce sustained pharmacodynamic effects with doses as low as 1 U/kg and bioactivity of over 100% relative to the current gold standard of subcutaneous injection. Pelargonidin-induced permeability was reversible within two hours of treatment, and one month of daily dosing did not adversely affect mice as determined by weight tracking, serum concentrations of inflammatory markers, and tight junction gene expression. Results underscore the utility of plant-based foods in biomedical applications and demonstrate pelargonidin as an especially potent enhancer for the oral delivery of biologics.
How to navigate the myosin-V motor through the actin network
Authors: Spieler Peter , Oberhofer Angela , Zimmermann Dennis , Brames Edwin , Hume Alistair N. , Ökten Zeynep 
Published: March 2020

SummaryMyosin-V (MyoV) is a ubiquitous motor protein that transports an astonishingly diverse set of cargos on the actin network in eukaryotes. Phosphorylation-dependent processes often regulate MyoV-mediated cargo transport, molecular details of which remain largely unknown. We previously showed that phosphorylation regulates MyoV’s switching from microtubules onto actin filaments, not its motor activity. Regulation of switching at reconstituted microtubule-actin-crossings in fact sufficed to recapitulate the MyoVa-driven redistribution of pigment-organelles in amphibian melanophores. However, in those cells, MyoVa also encounter many actin-actin crossings. Here, we show that isolated MyoVa motors switch with equal probabilities at reconstituted actin-actin-crossings. Under the control of its adaptor-protein melanophilin (Mlph), however, the motor differentiates between the actin filaments at crossing points in a phosphorylation-regulated manner. Whereas phosphorylation of Mlph forced about ∼2/3 of MyoVa to ignore the intersections, dephosphorylation completely reversed this behavior and forced ∼2/3 to switch. We show that the filament-binding domain (FBD) of Mlph controls this switching behavior. This property evolved in amphibians, but not in the early vertebrate zebrafish. By protein engineering, we demonstrate that changes of a few residues are sufficient to impart actin-binding capability onto the zebrafish Mlph. We thus unmask the molecular beginnings of dual filament binding in Mlph that allow it to control the switching behavior of MyoVa at cytoskeletal crossings. We therefore propose a direct link between intracellular phosphorylation activity and the adaptor-protein, not to regulate MyoVa activity, but to navigate the motor through the entire cytoskeletal maze for correct positioning of cargo.Significance statementIn virtually all eukaryotic cells, numerous myosin motors have to navigate through an elaborate actin network for timely transport of intracellular cargo. Here, we unmask an unintuitive regulation of the myosin-Va motor that is involved in pigment organelle transport. We demonstrate that myosin-Va differentiates between the same actin filaments and displays regulated switching at reconstituted actin-actin crossings, an unexpected behavior that has been predicted from previous theoretical work. We trace this regulation back to the adaptor protein of the myosin-Va motor and show that this regulation was present in amphibian but had not evolved in the early vertebrate zebrafish. Notably, we demonstrate that the evolution of actin-binding capability is achieved by changing a few residues in the adaptor protein.
Morphological profiling of tubercule bacilli identifies drug pathways of action
Authors: Smith Trever C. , Pullen Krista M. , Olson Michaela C. , McNellis Morgan E. , Richardson Ian , Hu Sophia , Larkins-Ford Jonah , Wang Xin , Freundlich Joel S. , Ando D. Michael , Aldridge Bree B. 
Published: March 2020

AbstractMorphological profiling is a method to classify target pathways of antibacterials based on how bacteria respond to treatment through changes to cellular shape and spatial organization. Here, we utilized the cell-to-cell variation in morphological features ofMycobacterium tuberculosisbacilli to develop a rapid profiling platform calledMorphologicalEvaluation andUnderstanding ofStress (MorphEUS). MorphEUS classified 94% of tested drugs correctly into broad categories according to modes of action previously identified in the literature. In the other 6%, MorphEUS pointed to key off-target or secondary bactericidal activities. We observed cell-wall damaging activity induced by bedaquiline and moxifloxacin through secondary effects downstream from their main target pathways. We implemented MorphEUS to correctly classify three compounds in a blinded study and identified an off-target effect for one compound that was not readily apparent in previous studies. We anticipate that the ability of MorphEUS to rapidly identify pathways of drug action and the proximal cause of bactericidal activity in tubercule bacilli will make it applicable to other pathogens and cell types where morphological responses are subtle and heterogeneous.Significance StatementTuberculosis is a leading cause of death in the world and requires treatment with an arduous multidrug regimen. Many new tuberculosis drugs are in development, and the drug development pipeline would benefit from more rapid methods to learn drug mechanism of action and off-target effects. Here, we describe a high throughput imaging method for rapidly classifying drugs into categories based on the primary and secondary cellular damage calledMorphologicalEvaluation andUnderstanding of drug-Stress (MorphEUS). We anticipate that MorphEUS will assist in rapidly pinpointing causes of cellular death in response to drug treatment in tuberculosis and other bacterial pathogens.
Dppa2/4CounteractDe NovoMethylation to Establish a Permissive Epigenome for Development
Authors: Gretarsson Kristjan H. , Hackett Jamie A. 
Published: March 2020

ABSTRACTEarly mammalian development entails genome-wide epigenome remodeling, including DNA methylation erasure and reacquisition, which facilitates developmental competence. To uncover the mechanisms that orchestrate DNA methylation (DNAme) dynamics, we coupled a single-cell ratiometric DNAme reporter with unbiased CRISPR screening in ESC. We identify key genes and regulatory pathways that drive global DNA hypomethylation, and characterise roles forCop1andDusp6. We also identifyDppa2andDppa4as essential safeguards of focal epigenetic states. In their absence, developmental genes and evolutionary-young LINE1 elements, which DPPA2 specifically binds, lose H3K4me3 and gain ectopicde novoDNA methylation in pluripotent cells. Consequently, lineage-associated genes (and LINE1) acquire a repressive epigenetic memory, which renders them incompetent for activation during future lineage-specification.Dppa2/4thereby sculpt the pluripotent epigenome by facilitating H3K4me3 and bivalency to counteractde novomethylation; a function co-opted by evolutionary young LINE1 to evade epigenetic decommissioning.
Complete chloroplast genomes ofAnthurium huixtlenseandPothos scandens(Pothoideae, Araceae): unique inverted repeat expansion and contraction affect rate of evolution
Authors: Abdullah  , Henriquez Claudia L. , Mehmood Furrukh , Carlsen Monica M. , Islam Madiha , Waheed Mohammad Tahir , Poczai Peter , Croat Thomas B. , Ahmed Ibrar 
Published: March 2020

AbstractThe subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae:Anthurium huixtlense(163,116 bp) andPothos scandens(164,719 bp). The chloroplast genome ofP. scandensshowed unique inverted repeats (IRs) contraction and expansion, which increases the size of the large single copy (102,956) region and decreases the size of the small single-copy (6779 bp) region. This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as opposed to IRs. We found a 2.3-fold increase of oligonucleotide repeats inP. scandenswhen compared withA. huixtlense, whereas amino acid frequency and codon usage revealed similarities. We recorded higher transition substitutions than transversion substitutions. The transition/transversion ratio was 2.26 inP. scandensand 2.12 inA. huixtlense. We also found a higher rate of transversion substitutions linked with non-synonymous substitutions than synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.
Evidence for Elton’s diversity-invasibility hypothesis from belowground
Authors: Zhang Zhijie , Liu Yanjie , Brunel Caroline , van Kleunen Mark 
Published: March 2020

AbstractSixty year ago, Elton proposed that diverse communities are more resistant to biological invasion. However, still little is known about which processes could drive this diversity-invasibility relationship. Here we examined whether plant-soil feedback on alien invaders is more negative when the soil originates from multiple native species. We trained soils with five individually grown native species, and used amplicon sequencing to analyze the resulting bacterial and fungal soil communities. We mixed the soils to create trained soils from one, two or four native species. We then grew four alien species separately on these differently trained soils. In the soil-conditioning phase, the five native species built species-specific bacterial and fungal communities in their rhizospheres. In the test phase, it did not matter whether the soil had been trained by one or two native species. However, the alien species achieved 11.7% less aboveground biomass when grown on soils trained by four native species than on soils trained by two native species. Our results showed for the first time, that plant-soil feedback could be a process that contributes to the negative relationship between diversity and invasibility.
The RSC complex remodels nucleosomes in transcribed coding sequences and promotes transcription inSaccharomyces cerevisiae
Authors: Biernat Emily , Kinney Jeena , Dunlap Kyle , Rizza Christian , Govind Chhabi K. 
Published: March 2020

AbstractRSC (Remodels theStructure ofChromatin) is a conserved ATP-dependent chromatin remodeling complex that regulates many biological processes, including transcription by RNA polymerase II (Pol II). We report that RSC contributes to generation of accessible nucleosomes in transcribed coding sequences (CDSs). RSC MNase ChIP-seq data revealed that RSC-bound nucleosome fragments were very heterogenous (~80 bp to 180 bp) compared to a sharper profile displayed by the MNase inputs (140 bp to 160 bp), supporting the idea that RSC promotes accessibility of nucleosomal DNA. Notably, RSC binding to +1 nucleosomes and CDSs, but not with −1 nucleosomes, strongly correlated with Pol II occupancies, suggesting that RSC enrichment in CDSs is linked to transcription. We also observed that Pol II associates with nucleosomes throughout transcribed CDSs, and similar to RSC, Pol II-protected fragments were highly heterogenous, consistent with the idea that Pol II interacts with remodeled nucleosome in CDSs. This idea is supported by the observation that the genes harboring high-levels of RSC in their CDSs were the most strongly affected by ablating RSC function. We also find that rapid nuclear depletion of Sth1 decreases nucleosome accessibility and results in accumulation of Pol II in highly transcribed CDSs. This is consistent with a slower clearance of elongating Pol II in cells with reduced RSC function, and is distinct from the effect of RSC depletion on PIC assembly. Altogether, our data provide evidence in support of the role of RSC in promoting Pol II elongation, in addition to its role in regulating transcription initiation.
Split-TurboID enables contact-dependent proximity labeling in cells
Authors: Cho Kelvin F. , Branon Tess C. , Rajeev Sanjana , Svinkina Tanya , Udeshi Namrata D. , Thoudam Themis , Kwak Chulhwan , Rhee Hyun-Woo , Lee In-Kyu , Carr Steven A. , Ting Alice Y. 
Published: March 2020

AbstractProximity labeling (PL) catalyzed by promiscuous enzymes such as TurboID have enabled the proteomic analysis of subcellular regions difficult or impossible to access by conventional fractionation-based approaches. Yet some cellular regions, such as organelle contact sites, remain out of reach for current PL methods. To address this limitation, we split the enzyme TurboID into two inactive fragments that recombine when driven together by a protein-protein interaction or membrane-membrane apposition. At endoplasmic reticulum (ER)-mitochondria contact sites, reconstituted TurboID catalyzed spatially-restricted biotinylation, enabling the enrichment and identification of >100 endogenous proteins, including many not previously linked to ER-mitochondria contacts. We validated eight novel candidates by biochemical fractionation and overexpression imaging. Overall, split-TurboID is a versatile tool for conditional and spatially-specific proximity labeling in cells.
Testing the reinforcement learning hypothesis of social conformity
Authors: Levorsen Marie , Ito Ayahito , Suzuki Shinsuke , Izuma Keise 
Published: March 2020

AbstractOur preferences are influenced by the opinions of others. The past human neuroimaging studies on social conformity have identified a network of brain regions related to social conformity that includes the posterior medial frontal cortex (pMFC), anterior insula, and striatum. It was hypothesized that since these brain regions are also known to play important roles in reinforcement learning (i.e., processing prediction error), social conformity and reinforcement learning have a common neural mechanism. However, these two processes have previously never been directly compared; therefore, the extent to which they shared a common neural mechanism had remained unclear. This study aimed to formally test the hypothesis. The same group of participants (n = 25) performed social conformity and reinforcement learning tasks inside a functional magnetic resonance imaging (fMRI) scanner. Univariate fMRI data analyses revealed activation overlaps in the pMFC and bilateral insula between social conflict and unsigned prediction error and in the striatum between social conflict and signed prediction error. We further conducted multi-voxel pattern analysis (MVPA) for more direct evidence of a shared neural mechanism. MVPA did not reveal any evidence to support the hypothesis in any of these regions but found that activation patterns between social conflict and prediction error in these regions were largely distinct. Taken together, the present study provides no clear evidence of a common neural mechanism between social conformity and reinforcement learning.
Complex interactions between DksA and stress-responsive alternative sigma factors control inorganic polyphosphate accumulation inEscherichia coli
Authors: Gray Michael J. 
Published: March 2020

ABSTRACTBacteria synthesize inorganic polyphosphate (polyP) in response to a variety of different stress conditions. PolyP protects bacteria by acting as a protein-stabilizing chaperone, metal chelator, or regulator of protein function, among other mechanisms. However, little is known about how stress signals are transmitted in the cell to lead to increased polyP accumulation. Previous work in the model enterobacteriumEscherichia colihas indicated that the RNA polymerase-binding regulatory protein DksA is required for polyP synthesis in response to nutrient limitation stress. In this work, I set out to characterize the role of DksA in polyP regulation in more detail. I found that overexpression of DksA increases cellular polyP content (explaining the long-mysterious phenotype ofdksAoverexpression rescuing growth of adnaKmutant at high temperature) and characterized the roles of known functional residues of DksA in this process, finding that binding to RNA polymerase is required, but none of the other functions of DksA appear to be necessary. Transcriptomics revealed genome-wide transcriptional changes upon nutrient limitation, many of which were affected by DksA, and follow-up experiments identified complex interactions between DksA and the stress-sensing alternative sigma factors FliA, RpoN, and RpoE that impact polyP production, indicating that regulation of polyP synthesis is deeply entwined in the multifactorial stress response network ofE. coli.IMPORTANCEInorganic polyphosphate (polyP) is an evolutionarily ancient, widely conserved biopolymer required for stress resistance and pathogenesis in diverse bacteria, but we do not understand how its synthesis is regulated. In this work, I gained new insights into this process by characterizing the role of the transcriptional regulator DksA in polyP regulation inEscherichia coliand identifying previously unknown links between polyP synthesis and the stress-responsive alternative sigma factors FliA, RpoN, and RpoE.
A Combined Evidence Approach to Prioritize Nipah Virus Inhibitors
Authors: Kumari Nishi , Upadhyay Ayush , Kalia Kishan , Kumar Rakesh , Tuteja Kanika , Paul Priyanka Rani , Covernton Eugenia , Sharma Tina , Scaria Vinod , Bhardwaj Anshu 
Published: March 2020

AbstractNipah Virus (NiV) came into limelight due to an outbreak in Kerala, India. NiV causes severe disease and death in people with over 75% case fatality rate. It is a public health concern and has the potential to become a global pandemic. Lack of treatment has forced the containment methods to be restricted to isolation and surveillance. WHO’s ‘R&D Blueprint list of priority diseases’ (2018) indicates that there is an urgent need for accelerated research & development for addressing NiV. In the quest for druglike NiV inhibitors (NVIs) a thorough literature search followed by systematic data curation was conducted. Rigorous data analysis was done with curated NVIs for prioritizing druglike compounds. For the same, more than 1800 descriptors of NVIs were computed and comparative analysis was performed with the FDA approved small molecules and antivirals. These compounds were further evaluated through PAINS filter to study their toxicity profile. Simultaneously, compounds were also prioritized based on the robustness of the assays through which they were identified. Our efforts lead to the creation of a well-curated structured knowledgebase of 182 NVIs with 98 small molecule inhibitors. The reported IC50/EC50 values for some of these inhibitors are in the nanomolar range – as low as 0.47 nM. In order to prioritize these inhibitors, we performed several tests and applied filters to identify drug-like non-toxic compounds. Of 98, a few compounds passed DruLito & PAINS filters exhibiting drug-like properties and were also prioritized in an independent screen based only the assay robustness. The NVIs have diverse structural features and offer a wide spectrum of ways in which they can be developed further as druglike molecules. We report a knowledgebase for furthering the development of NVIs. The platform has a diverse set of 98 NVIs of which a few have been prioritized based on a combined evidence strategy. The platform has the provision to submit new inhibitors as and when reported by the community for further enhancement of NiV inhibitor landscape.
Feeding-dependent tentacle development in the sea anemoneNematostella vectensis
Authors: Ikmi Aissam , Steenbergen Petrus J. , Anzo Marie , McMullen Mason R. , Stokkermans Anniek , Ellington Lacey R. , Gibson Matthew C. 
Published: March 2020

SummaryIn cnidarians, axial patterning is not restricted to embryonic development but continues throughout a prolonged life history filled with unpredictable environmental changes. How this developmental capacity copes with fluctuations of food availability and whether it recapitulates embryonic mechanisms remain poorly understood. To address these questions, we utilize the tentacles of the sea anemoneNematostella vectensisas a novel paradigm for developmental patterning across distinct life history stages. As a result of embryonic development,Nematostellapolyps feature four primary tentacles, while adults have 16 or more. By analyzing over 1000 growing polyps, we find that tentacle progression is remarkably stereotyped and occurs in a feeding-dependent manner. Mechanistically, we show that discreteFibroblast growth factor receptor b(Fgfrb)-positive ring muscles prefigure the sites of new tentacles in unfed polyps. In response to feeding, a Target of Rapamycin (TOR)-dependent mechanism controls the expansion ofFgfrbexpression in oral tissues which defines tentacle primordia. Using a combination of genetic, cellular and molecular approaches, we demonstrate that FGFRb regionally enhances TOR signaling activity and promotes polarized growth, a spatial pattern that is restricted to polyp but not to embryonic tentacle primordia. These findings reveal an unexpected plasticity of tentacle development, and show that the crosstalk between TOR-mediated nutrient signaling and FGFRb pathway couples post-embryonic body patterning with food availability.
A single domain shark antibody targeting the transferrin receptor 1 delivers a TrkB agonist antibody across the blood brain barrier to provide full neuroprotection in a mouse model of Parkinson’s Disease
Authors: Clarke Emily , Sinclair Liz , Fletcher Edward J R , Krawczun-Rygmaczewska Alicja , Duty Susan , Stocki Pawel , Rutowski J Lynn , Doherty Patrick , Walsh Frank S 
Published: March 2020

AbstractSingle domain shark antibodies that bind to the transferrin receptor 1 (TfR1) on brain endothelial cells can be used to shuttle antibodies and other cargos across the blood brain barrier (BBB). We have fused one of these (TXB4) to differing regions of TrkB and TrkC neurotrophin receptor agonist antibodies (AAb) and determined the effect on agonist activity, brain accumulation and engagement with neurons in the mouse brain following systemic administration. The TXB4-TrkB and TXB4-TrkC fusion proteins retain agonist activity at their respective neurotrophin receptors and in contrast to their parental AAb they rapidly accumulate in the brain reaching nM levels following a single IV injection. Following SC administration, the most active TrkB fusion protein, TXB4-TrkB1, associates with and activates ERK1/2 signalling in TrkB positive cells in the cortex and tyrosine hydroxylase (TH) positive dopaminergic neurons in the substantia nigra pars compacta (SNc). When tested in the 6-hydroxydopamine (6-OHDA) mouse model of Parkinson’s disease (PD) TXB4-TrkB1, but not the parental TrkB AAb or a TXB4-TrkC1fusion protein, completely prevented the 6-OHDA induced death of TH positive neurons in the SNc. In conclusion, the fusion of the TXB4 TfR1 binding module allows a TrkB AAb to reach neuroprotective concentrations in the brain parenchyma following systemic administration.