bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full site-specific addressability in DNA origami-templated silica nanostructures
Authors: Wassermann Lea M. , Scheckenbach Michael , Baptist Anna V. , Glembockyte Viktorija , Heuer-Jungemann Amelie 
Published: December 2022

AbstractDNA nanotechnology allows for the fabrication of nano-meter-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here we show that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. We used the conjugation of fluorescently labelled oligonucleotides to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. We also demonstrate that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally we demonstrate the power of this approach by forming 3D DNA origami crystals from silicified monomers. Our results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.
FAZ assembly in bloodstream formTrypanosoma bruceirequires kinesin KIN-E
Authors: Albisetti Anna C. , Douglas Robert L. , Welch Matthew D. 
Published: December 2022

AbstractTrypanosoma brucei, the causative agent of African sleeping sickness, uses its flagellum for movement, cell division, and signaling. The flagellum is anchored to the cell body membraneviathe flagellar attachment zone (FAZ), a complex of proteins, filaments, and microtubules that spans two membranes with elements on both flagellum and cell body sides. How FAZ components are carried into place to form this complex is poorly understood. Here, we show that the trypanosome-specific kinesin KIN-E is required for building the FAZ in bloodstream-form parasites. KIN-E is localized along the flagellum with a concentration at its distal tip. Depletion of KIN-E by RNAi rapidly inhibits flagellum attachment and leads to cell death. A detailed analysis reveals that KIN-E depletion phenotypes include failure in cytokinesis completion, kinetoplast DNA mis-segregation, and transport vesicle accumulation. Together with previously published results in procyclic form parasites, these data suggest KIN-E plays a critical role in FAZ assembly inT. brucei.
Strong non-ideality effects at low protein concentrations: considerations for elongated proteins
Authors: Yarawsky Alexander E. , Dinu Vlad , Harding Stephen E. , Herr Andrew B. 
Published: December 2022

AbstractA recent investigation was aimed at obtaining structural information on a highly extended protein via SEC-MALS-SAXS. Significantly broadened elution peaks were observed, reminiscent of a phenomenon known as viscous fingering. This phenomenon is usually observed above 50 mg/mL for proteins like bovine serum albumin (BSA). Interestingly, the highly extended protein (Brpt5.5) showed viscous fingering at concentrations lower than 5 mg/mL. The current study explores this and other non-ideal behavior, emphasizing the presence of these effects at relatively lower concentrations for extended proteins. BSA, Brpt5.5, and a truncated form of Brpt5.5 referred to as Brpt1.5 are studied systematically using size-exclusion chromatography (SEC), sedimentation velocity analytical ultracentrifugation (AUC), and viscosity. The viscous fingering effect is quantified using two approaches and is found to correlate well with the intrinsic viscosity of the proteins – Brpt5.5 exhibits the most severe effect and is the most extended protein tested in the study. By AUC, the hydrodynamic non-ideality was measured for each protein via global analysis of a concentration series. Compared to BSA, both Brpt1.5 and Brpt5.5 showed significant non-ideality that could be easily visualized at concentrations at or below 5 mg/mL and 1 mg/mL, respectively. A variety of relationships were examined for their ability to differentiate the proteins by shape using information from AUC and/or viscosity. Furthermore, these relationships were also tested in the context of hydrodynamic modeling. The importance of considering non-ideality when investigating the structure of extended macromolecules is discussed.
A central helical fulcrum in eIF2B coordinates allosteric regulation of Integrated Stress Response signaling
Authors: Lawrence Rosalie E , Shoemaker Sophie , Deal Aniliese , Sangwan Smriti , Anand Aditya , Wang Lan , Marqusee Susan , Walter Peter 
Published: December 2022

AbstractThe Integrated Stress Response (ISR) enables cells to survive a variety of acute stresses, but chronic activation of the ISR underlies age-related diseases. ISR signaling down-regulates translation and activates expression of stress-responsive factors that promote return to homeostasis, and is initiated by inhibition of the decameric guanine nucleotide exchange factor eIF2B. Conformational and assembly transitions regulate eIF2B activity, but the allosteric mechanisms controlling these dynamic transitions are unknown. Using hydrogen deuterium exchange-mass spectrometry and cryo-EM, we identified a single alpha-helix whose orientation allosterically controls eIF2B conformation and assembly. Biochemical and signaling assays show that this “Switch-Helix” controls eIF2B activity and signaling in cells. In sum, the Switch-Helix acts as a fulcrum of eIF2B conformational regulation and is a highly conserved actuator of ISR signal transduction. This work uncovers a novel allosteric mechanism and unlocks new therapeutic possibilities for ISR-linked diseases.
Best: A Tool for Characterizing Sequencing Errors
Authors: Liu Daniel , Belyaeva Anastasiya , Shafin Kishwar , Chang Pi-Chuan , Carroll Andrew , Cook Daniel E. 
Published: December 2022

AbstractSummaryPlatform-dependent sequencing errors must be understood to develop accurate sequencing technologies. We propose a new tool,best(Bam Error Stats Tool), for efficiently quantifying and summarizing error types in sequenced reads.bestingests reads aligned to a high-quality reference assembly and produces per-read metrics, summary statistics, and stratified metrics across genomic intervals. We show thatbestis 16 times faster than a prior method. In addition to being useful to support development that improves the accuracy of sequencing platforms, best can also be applied to evaluate and improve other experimental factors such as library preparation and error correction methods.Availability and implementationbestis an open-source command-line utility available on Github (github.com/google/best) under an MIT license.Contactdanielecook@google.com
Lipid Nanoparticle Composition Drives mRNA Delivery to the Placenta
Authors: Young Rachel E. , Nelson Katherine M. , Hofbauer Samuel I. , Vijayakumar Tara , Alameh Mohamad-Gabriel , Weissman Drew , Papachristou Charalampos , Gleghorn Jason P. , Riley Rachel S. 
Published: December 2022

ABSTRACTIonizable lipid nanoparticles (LNPs) have gained attention as mRNA delivery platforms for vaccination against COVID-19 and for protein replacement therapies. LNPs enhance mRNA stability, circulation time, cellular uptake, and preferential delivery to specific tissues compared to mRNA with no carrier platform. However, LNPs have yet to be developed for safe and effective mRNA delivery to the placenta as a method to treat placental dysfunction. Here, we develop LNPs that enable high levels of mRNA delivery to trophoblastsin vitroand to the placentain vivowith no toxicity. We conducted a Design of Experiments to explore how LNP composition, including the type and molar ratio of each lipid component, drives trophoblast and placental delivery. Our data revealed that a specific combination of ionizable lipid and phospholipid in the LNP design yields high transfection efficiencyin vitro. Further, we present one LNP platform that exhibits highest delivery of placental growth factor mRNA to the placenta in pregnant mice, which demonstrates induced protein synthesis and secretion of a therapeutic protein. Lastly, our high-performing LNPs have no toxicity to both the pregnant mice and fetuses. Our results demonstrate the feasibility of LNPs as a platform for mRNA delivery to the placenta. Our top LNPs may provide a therapeutic platform to treat diseases that originate from placental dysfunction during pregnancy.
Structural Basis of Prostaglandin Efflux by MRP4
Authors: Pourmal Sergei , Green Evan , Bajaj Ruchika , Chemmama Ilan E. , Knudsen Giselle M. , Gupta Meghna , Sali Andrej , Cheng Yifan , Craik Charles S. , Kroetz Deanna L. , Stroud Robert M. 
Published: December 2022

AbstractMRP4 is unique among the C family of ATP-binding cassette transporters for its role in translocating prostanoids, an important group of signaling molecules derived from unsaturated fatty acids. Using a reconstituted system, we report that a pair of prostaglandins (PGs) and the sulfonated-sterol DHEA-S preferentially enhance the ATPase activity of MRP4 over other previously proposed physiological substrates such as cyclic nucleotides or leukotrienes. We determined the cryo-EM structures of nanodisc embedded bovine MRP4 in (i) a nucleotide- and substrate-free state, (ii) in complex with PGE1, (iii) PGE2, and (iv) DHEA-S, and (v) a catalytically dead mutant E1202Q bound to ATP-Mg2+. The substrate-bound structures suggest unique features of the MRP4 binding site that distinguish its specificity for prostanoids from that of the related leukotriene transporter MRP1. The ATP-bound structure is in an outward-occluded conformation, revealing a novel state in the proposed alternate-access mechanism of MRP transport. Our study provides insights into the endogenous function of this versatile efflux transporter.
Behavioral assessment of Zwicker tone percepts in rodents
Authors: Schilling Achim , Tziridis Konstantin , Schulze Holger , Krauss Patrick 
Published: December 2022

AbstractThe Zwicker tone illusion can serve as an interesting model for acute tinnitus, an auditory phantom percept still not fully understood. Recent mechanistic models suggest that the underlying neural mechanisms of both percepts are similar. However, to date it is not clear if animals do perceive the Zwicker tone at all, as up to now no behavioral paradigms are available to objectively assess the presence of this phantom percept.Here we introduce, for the first time, a modified version of the gap pre-pulse inhibition of the acoustic startle reflex (GPIAS) paradigm - usually used to assess the presence of a tinnitus percept in animals - to test if it is possible to induce a Zwicker tone percept in our rodent model, the Mongolian gerbil. Furthermore, we developed a new aversive conditioning shuttle box learning paradigm and compare the two approaches.We found a significant increase in the GPIAS effect when presenting a notched noise compared to flat white noise gap pre-pulse inhibition, indicating that the animals actually perceived a Zwicker tone. However, in the aversive conditioning learning paradigm, no clear effect could be observed in the discrimination performance of the tested animals. When investigating the CR+ responses, an effect of a possible Zwicker tone percept can be seen, i.e. animals show identical behavior as if a pure tone was presented, but the paradigm needs to be further improved.
Common dandelion (Taraxacum officinale) leaf extract efficiently inhibits SARS-CoV-2 Omicron infectionin vitro
Authors: Tran Hoai Thi Thu , Gigl Michael , Dawid Corinna , Lamy Evelyn 
Published: December 2022

AbstractAs the COVID-19 pandemic continues to pose a health risk concern to humans, despite a significant increase in vaccination rates, an effective prevention and treatment of SARS-CoV-2 infection is being sought worldwide. Herbal medicines have been used for years and played a tremendous role in several epidemics of respiratory viral infections. Thus, they are considered as a promising platform to combat SARS-CoV-2. Previously, we reported that common dandelion (Taraxacum officinale) leaf extract and its high molecular weight compounds strongly suppressedin vitrolung cell infection by SARS-CoV-2 Spike D614 and Delta variant pseudotyped lentivirus. We now here demonstrate thatT. officinaleextract protects against the most prominent Omicron variant using hACE2-TMPRSS2 overexpressing A549 cells asin vitromodel system. Notably, compared to the original D614, and the Delta variant, we could confirm a higher efficacy. Short-term interval treatment of only 30 min was then sufficient to block the infection by 80% at 10 mg/mL extract. Further subfractionation of the extract identified compounds larger than 50 kDa as effective ACE2-Spike binding inhibitors. In summary, the evolution of SARS-CoV-2 virus to the highly transmissible Omicron variant did not lead to resistance, but rather increased sensitivity to the preventive effect of the extract.
Global analysis of the yeast knock-out phenome
Authors: Turco Gina , Chang Christie , Wang Rebecca Y. , Kim Griffin , Stoops Emily , Richardson Brianna , Sochat Vanessa , Rust Jennifer , Oughtred Rose , Thayer Nathaniel , Kang Fan , Livstone Michael S. , Heinicke Sven , Schroeder Mark , Dolinski Kara J. , Botstein David , Baryshnikova Anastasia 
Published: December 2022

ABSTRACTGenome-wide phenotypic screens in the budding yeastSaccharomyces cerevisiaehave produced the largest, richest and most systematic phenotypic description of any organism. Such an achievement was enabled by the development of highly scalable phenotypic assays and construction of the yeast knock-out (YKO) collection, comprising ~5,000 isogenic strains each deleted for exactly one open reading frame. Systematic screening of the YKO collection led to ~500 publications describing ~14,500 phenotypes capturing nearly every aspect of yeast biology. Yet, integrative analyses of this rich data source have been virtually impossible due to the lack of a central repository and consistent meta-data annotations. Here, we describe the aggregation, harmonization and analysis of all published phenotypic screens of the YKO collection, which we refer to as the Yeast Phenome (www.yeastphenome.org). To demonstrate the power of data integration and illustrate how much it facilitates the generation of testable hypotheses, we present three discoveries uniquely enabled by Yeast Phenome. First, we use the variation in the number of phenotypes per gene to identify tryptophan homeostasis as a central point of vulnerability to a wide range of chemical compounds, including FDA-approved drugs. Second, using phenotypic profiles as a tool for predicting gene function, we identify and validate the role ofYHR045Was a novel regulator of ergosterol biosynthesis and DNA damage response, andYGL117Was a new member of the aromatic amino acid biosynthesis pathway. Finally, we describe a surprising exponential relationship between phenotypic similarity and intergenic distance in both yeast and human genomes. This relationship, which stretches as far as 380 kb in yeast and 100 Mb in humans, suggests that gene positions are optimized for function to a much greater extent than appreciated previously. Overall, we show that Yeast Phenome enables systematic enquiries into the nature of gene-gene and gene-phenotype relationships and is an important new resource for systems biology.
Speciation on a complex landscape; phylogeny and demography of Mexican Goodeid fish
Authors: Yusuf Leeban H. , Lemus Yolitzi Saldívar , Thorpe Peter , Garcia Constantino Macías , Ritchie Michael G. 
Published: December 2022

AbstractUnderstanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. Vicariance has clearly played a major role in diversification across diverse groups of organisms, but how this interacts with intrinsic biological features such as changes in reproductive system or sexual selection is less well understood. TheGoodeinaeare a Mexican endemic group of live-bearing fish. Here, we develop genomic resources for species within theGoodeinaeand use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four newGoodeinaegenomes, includingA. toweri, the only matrotrophic live-bearing fish without a trophotaenia in the group. We produced a phylogeny of theGoodeinaeand estimate timings of species divergence. We determined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We also analyse patterns in the changes of effective population size for the species and examine the time course of expansion and decline. We used branch-site models to detect genome-wide positive selection acrossGoodeinae, and we specifically ask if this differs inA. toweri, where reversal of placental viviparity has recently occurred. We find that Goodeinae diverged rapidly, with reductions in effective population size after each split. Contrary to expectations, we find evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, potentially as a result of river piracy. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae.
Air-Liquid-Interface Reorganizes Membrane Lipid and Enhance Recruitment of Slc26a3 to Lipid-Rich Domains in Human Colon
Authors: Tse Ming , Rong Yan , Zhang Zixin , Lin Ruxian , Sarker Rafiq , Donowitz Mark , Singh Varsha 
Published: December 2022

AbstractBackground and AimsCholesterol-rich membrane domains, also called lipid rafts (LR), are specialized membrane domains that provide a platform for intracellular signal transduction. Membrane proteins often cluster in LR that further aggregate into larger platform-like structures that are enriched in ceramide and are called ceramide-rich platforms (CRPs). The role of CRPs in the regulation of intestinal epithelial functions remains unknown. Down Regulated in Adenoma (DRA) is an intestinal Cl-/HCO3-antiporter which is enriched in LR. However, little is known regarding the mechanisms involved in the regulation of DRA activity.MethodsAir liquid interface (ALI) was created by removing apical media for a specified number of days from 12-14 days post confluency Caco-2/BBe cells or confluent colonoid monolayer grown as submerged cultures. Confocal imaging was used to examine the dimensions of membrane microdomains that contain DRA.ResultsDRA expression and activity were enhanced by culturing Caco-2/BBe cells and human colonoids using an ALI culture method. ALI causes an increase in acid sphingomyelinase (ASMase) activity, an enzyme responsible for enhancing ceramide content in the plasma membrane. ALI cultures expressed a larger number of DRA-containing platforms with dimensions >2 μm compared to cells grown as submerged cultures. ASMase inhibitor, desipramine disrupted CRPs and reduced the ALI-induced increase in DRA expression in the apical membrane. Exposing normal human colonoid monolayers to ALI increased the ASMase activity and enhanced differentiation of colonoids along with enhancing basal and forskolin-stimulated DRA activity.ConclusionsALI increases DRA activity and expression by increasing ASMase activity and platform formation in Caco-2/BBe cells and by enhancing the differentiation of normal human colonoids.SynopsisAir-liquid interface (ALI) enhances total and brush border DRA expression and activity in Caco-2/BBe cells and human colonoids by causing differentiation of enterocytes and acid sphingomyelinase-dependent enhanced retention of DRA in ceramide-rich platform-like structures at the plasma membrane.
Glyco-engineered pentameric SARS-CoV-2 IgMs show superior activities compared to IgG1 orthologues
Authors: Kallolimath Somanath , Palt Roman , Föderl-Höbenreich Esther , Sun Lin , Chen Qiang , Pruckner Florian , Eidenberger Lukas , Strasser Richard , Zatloukal Kurt , Steinkellner Herta 
Published: December 2022

AbstractImmunoglobulin M (IgM) is the largest antibody isotype with unique features like extensive glycosylation and oligomerization. Major hurdles in characterizing its properties are difficulties in the production of well-defined multimers. Here we report the expression of two SARS-CoV-2 neutralizing monoclonal antibodies in glycoengineered plants. Isotype switch from IgG1 to IgM resulted in the production of pentameric IgMs, comprising of correctly assembled 21 human protein subunits. All four recombinant monoclonal antibodies carried a highly reproducible human-type N-glycosylation profile, with a single dominant N-glycan species at each glycosite. Both pentameric IgMs exhibited increased antigen binding and virus neutralization potency, up to 390-fold, compared to the parental IgG1. Collectively, the results may impact on the future design of vaccines, diagnostics and antibody-based therapies and emphasize the versatile use of plants for the expression of highly complex human proteins with targeted posttranslational modifications.
Robotically-induced auditory-verbal hallucinations: combining self-monitoring and strong perceptual priors
Authors: Orepic Pavo , Bernasconi Fosco , Faggella Melissa , Faivre Nathan , Blanke Olaf 
Published: December 2022

AbstractInducing hallucinations under controlled experimental conditions in non-hallucinating individuals represents a novel research avenue oriented towards understanding complex hallucinatory phenomena, avoiding confounds observed in patients. Auditory-verbal hallucinations (AVH) are one of the most common and distressing psychotic symptoms, whose etiology remains largely unknown. Two prominent accounts portray AVH either as a deficit in auditory-verbal self-monitoring, or as a result of overly strong perceptual priors. In order to test both theoretical models and evaluate their potential integration, we developed a robotic procedure able to induce self-monitoring perturbations (consisting of sensorimotor conflicts between poking movements and corresponding tactile feedback) and a perceptual prior associated with otherness sensations (i.e., feeling the presence of a non-existing another person). Here, in two independent studies, we show that this robotic procedure led to AVH-like phenomena in healthy individuals, which was further associated with delusional ideation. Specifically, a condition with stronger sensorimotor conflicts induced more AVH-like sensations (self-monitoring), while, in the otherness-related experimental condition, there were more AVH-like sensations when participants were detecting other-voice stimuli, compared to detecting self-voice stimuli (strong-priors). By demonstrating an experimental procedure able to induce AVH-like sensations in non-hallucinating individuals, we shed new light on AVH phenomenology, thereby integrating self-monitoring and strong-priors accounts.