bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Structure Study on the Polyelectrolyte Properties of Actin Filaments
Authors: Manrique-Bedoya Santiago , Marucho Marcelo 
Published: January 2022

AbstractAn accurate characterization of the polyelectrolyte properties of actin filaments might provide a deeper understanding of the fundamental mechanisms governing the intracellular ionic wave packet propagation in neurons. Infinitely long cylindrical models for actin filaments and approximate electrochemical theories for the electrolyte solutions were recently used to characterize these properties in in vitro and intracellular conditions. This article uses a molecular structure model for actin filaments to investigate the impact of roughness and finite size on the mean electrical potential, ionic density distributions, currents, and conductivities. We solved the electrochemical theories numerically without further approximations. Our findings bring new insights into the electrochemical interactions between a filament’s irregular surface charge density and the surrounding medium. The irregular shape of the filament structure model generated pockets, or hot spots, where the current density reached higher or lower magnitudes than those in neighboring areas throughout the filament surface. It also revealed the formation of a well-defined asymmetric electrical double layer with a thickness larger than that commonly used for symmetric models.
An NMR fingerprint matching approach for the identification and structural re-evaluation ofPseudomonaslipopeptides
Authors: De Roo Vic , Verleysen Yentl , Kovács Benjámin , Matthias De Vleeschouwer , Girard Léa , Höfte Monica , De Mot René , Madder Annemieke , Geudens Niels , Martins José C. 
Published: January 2022

AbstractCyclic lipopeptides (CLiPs) are secondary metabolites secreted by a range of bacterial phyla. CLiPs fromPseudomonasin particular display diverse structural variations in terms of the number of amino acid residues, macrocycle size, amino acid identity and stereochemistry (e.g. D- vs. L-amino acids). Reports detailing the discovery of novel or already characterized CLiPs from new sources appear regularly in literature. Increasingly however, the lack of detailed characterization threatens to cause considerable confusion, especially if configurational heterogeneity is present for one or more amino acids. UsingPseudomonasCLiPs from the Bananamide, Orfamide and Xantholysin groups as test cases, we demonstrate and validate that1H and13C NMR chemical shifts of CLiPs are sufficiently sensitive to differentiate between possible diastereomers of a particular sequence even when they only differ in a single D/L configuration. Rapid screening, involving simple comparison of the NMR fingerprint of a newly isolated CLiP with that of a reference CLiP of known stereochemistry, can then be applied to resolve dead-ends in configurational characterization and avoid the much more cumbersome chemical characterization protocols. Even when the stereochemistry of a particular reference CLiP remains to be established, NMR fingerprinting still allows verifying whether a CLiP from a novel source is already present in the reference collection, thus contributing to dereplication. To benefit research involving CLiPs, we have made a publicly available ‘knowledge base’ athttps://www.rhizoclip.be, where we present an overview of published NMR fingerprint data of characterized CLiPs, together with literature data on the originally determined structures.Significance StatementPseudomonasCLiPs, are ubiquitous specialized metabolites, impacting the producer’s lifestyle and interactions with the (a)biotic environment. Consequently, they generate interest for agricultural and clinical applications. Establishing structure-activity relationships as premise to their development is hindered because full structural characterization including stereochemistry requires labor-intensive analyses, without guarantee for success. Moreover, increasing use of superficial comparison with previously characterized CLiPs introduces or propagates erroneous attributions, clouding further scientific progress. We provide a generally applicable characterization methodology for structural comparison of newly isolated CLiPs to reference compounds with (un)known stereochemistry based on NMR fingerprints. The reference compound database available for the wide scientific community promises to facilitate structural assessment and dereplication of newly isolated CLiPs, and to support genome mining for novel CLiPs.
Metabolic phenotyping of marine heterotrophs on refactored media reveals diverse metabolic adaptations and lifestyle strategies
Authors: Forchielli Elena , Sher Daniel , Segrè Daniel 
Published: January 2022

AbstractMicrobial communities, through their metabolism, drive carbon cycling in marine environments. These complex communities are composed of many different microorganisms including heterotrophic bacteria, each with its own nutritional needs and metabolic capabilities. Yet, models of ecosystem processes typically treat heterotrophic bacteria as a “black box”, which does not resolve metabolic heterogeneity nor address ecologically important processes such as the successive modification of different types of organic matter. Here we directly address the heterogeneity of metabolism by characterizing the carbon source utilization preferences of 63 heterotrophic bacteria representative of several major marine clades. By systematically growing these bacteria on 10 media containing specific subsets of carbon sources found in marine biomass, we obtained a phenotypic fingerprint that we used to explore the relationship between metabolic preferences and phylogenetic or genomic features. At the class level, these bacteria display broadly conserved patterns of preference for different carbon sources. Despite these broad taxonomic trends, growth profiles correlate poorly with phylogenetic distance or genome-wide gene content. However, metabolic preferences are strongly predicted by a handful of key enzymes that preferentially belong to a few enriched metabolic pathways, such as those involved in glyoxylate metabolism and biofilm formation. We find that enriched pathways point to enzymes directly involved in the metabolism of the corresponding carbon source and suggest potential associations between metabolic preferences and other ecologically-relevant traits. The availability of systematic phenotypes across multiple synthetic media constitutes a valuable resource for future quantitative modeling efforts and systematic studies of inter-species interactions.ImportanceHalf of the Earth’s annual primary production is carried out by phytoplankton in the surface ocean. However, this metabolic activity is heavily impacted by heterotrophic bacteria, which dominate the transformation of organic matter released from phytoplankton. Here, we characterize the diversity of metabolic preferences across many representative heterotrophs by systematically growing them on different fractions of dissolved organic carbon (DOC). Our analysis suggests that different clades of bacteria have substantially distinct preferences for specific carbon sources, in a way that cannot be simply mapped onto phylogeny. These preferences are associated with the presence of specific genes and pathways, reflecting an association between metabolic capabilities and ecological lifestyles. In addition to helping understand the importance of heterotrophs under different conditions, the phenotypic fingerprint we obtained can help build higher resolution quantitative models of global microbial activity and biogeochemical cycles in the oceans.
HDX-MS performed on BtuB in E. coli outer membranes delineates the luminal domain’s allostery and unfolding upon B12 and TonB binding
Authors: Zmyslowski Adam M. , Baxa Michael C. , Gagnon Isabelle A. , Sosnick Tobin R. 
Published: January 2022

AbstractTo import large metabolites across the outer membrane of Gram-negative bacteria, TonB dependent transporters (TBDTs) undergo significant conformational change. After substrate binding in BtuB, the E. coli vitamin B12 TBDT, TonB binds and couples BtuB to the inner membrane proton motive force that powers transport (1). But, the role of TonB in rearranging the plug domain to form a putative pore remains enigmatic. Some studies focus on force-mediated unfolding (2) while others propose force-independent pore formation (3) by TonB binding leading to breakage of a salt bridge termed the “Ionic Lock”. Our hydrogen exchange/mass spectrometry measurements in E. coli outer membranes find that the region surrounding the Ionic Lock, far from the B12 site, is fully destabilized upon substrate binding. A comparison of the exchange between the B12 bound and the B12&TonB bound complexes indicates that B12 binding is sufficient to unfold the Ionic Lock region with the subsequent binding of a TonB fragment having much weaker effects. TonB binding accelerates exchange in the third substrate binding loop, but pore formation does not obviously occur in this or any region. This study provides a detailed structural and energetic description of the early stages of B12 passage that provides support both for and against current models of the transport process.Significance StatementTonB dependent transporters such as BtuB are found in the outer membranes of Gram-negative bacteria. They import scarce nutrients essential for growth, such as B12, the substrate of BtuB. Many transport steps remain enigmatic. Recent studies have emphasized force-mediated unfolding or the breakage of the “Ionic Lock”, a moiety far from the B12 binding site. A strong dependence on the membrane environment has been noted. Accordingly, we measured hydrogen exchange on BtuB still embedded in native outer membranes and found that B12 binding is sufficient to break the Ionic Lock. The amino terminus then extends into the periplasm to bind TonB. But we find no evidence of pore formation, which likely requires energy transduction from the inner membrane by TonB.
Quantification of salt stress in wheat leaves by Raman spectroscopy and machine learning
Authors: Kecoglu Ibrahim , Sirkeci Merve , Unlu Mehmet Burcin , Sen Ayse , Parlatan Ugur , Guzelcimen Feyza 
Published: January 2022

AbstractThe salinity level of the growing medium has diverse effects on the development of plants, including both physical and biochemical changes. To determine the salt stress level of a plant endures, one can measure these structural and chemical changes. Raman spectroscopy and biochemical analysis are some of the most common techniques in the literature. Here, we present a combination of machine learning and Raman spectroscopy with which we can both find out the biochemical change that occurs while the medium salt concentration changes and predict the level of salt stress a wheat sample experiences accurately using our trained regression models. In addition, by applying different machine learning algorithms, we compare the level of success for different algorithms and determine the best method to use in this application. Production units can take actions based on the quantitative information they get from the trained machine learning models related to salt stress, which can potentially increase efficiency and avoid the loss of crops.
A single amino acid substitution in PB1 of pandemic H1N1 with A/Ann Arbor/6/60 master donor virus mutations as a novel live-attenuated influenza virus vaccine
Authors: Nogales Aitor , Steel John , Liu Wen-Chun , Lowen Anice C. , Rodriguez Laura , Chiem Kevin , Cox Andrew , García-Sastre Adolfo , Albrecht Randy A. , Dewhurst Stephen , Martínez-Sobrido Luis 
Published: January 2022

ABSTRACTInfluenza A viruses (IAV) remain emerging threats to human public health. Live-attenuated influenza vaccines (LAIV) are one of the most effective prophylactic options to prevent disease caused by influenza infections. However, licensed LAIV remain restricted for use in 2- to 49-year old healthy and non-pregnant people. Therefore, development of LAIV with increased safety, immunogenicity, and protective efficacy is highly desired. The United States (U.S.) licensed LAIV is based on the master donor virus (MDV) A/Ann Arbor/6/60 H2N2 backbone, which was generated by adaptation of the virus to growth at low temperatures. Introducing the genetic signature of the U.S. MDV into the backbone of other IAV strains resulted in varying levels of attenuation. While the U.S. MDV mutations conferred an attenuated phenotype to other IAV strains, the same amino acid changes did not significantly attenuate the pandemic A/California/04/09 H1N1 (pH1N1) strain. To attenuate pH1N1, we replaced the conserved leucine at position 319 with glutamine (L319Q) in PB1 and analyzed the in vitro and in vivo properties of pH1N1 viruses containing either PB1 L319Q alone or in combination with the U.S. MDV mutations using two animal models of influenza infection and transmission, ferrets and guinea pigs. Our results demonstrated that L319Q substitution in the pH1N1 PB1 alone or in combination with the mutations of the U.S. MDV resulted in reduced pathogenicity (ferrets) and transmission (guinea pigs), and an enhanced temperature sensitive phenotype. These results demonstrate the feasibility of generating an attenuated MDV based on the backbone of a contemporary pH1N1 IAV strain.IMPORTANCEVaccination represents the most effective strategy to reduce the impact of seasonal IAV infections. Although LAIV are superior in inducing protection and sterilizing immunity, they are not recommended for many individuals who are at high risk for severe disease. Thus, development of safer and more effective LAIV are needed. A concern with the current MDV used to generate the U.S. licensed LAIV is that it is based on a virus isolated in 1960. Moreover, mutations that confer the temperature sensitive, cold-adapted, and attenuated phenotype of the U.S. MDV resulted in low level of attenuation in the contemporary pandemic A/California/04/09 H1N1 (pH1N1). Here, we show that introduction of PB1 L319Q substitution, alone or in combination with the U.S. MDV mutations, resulted in pH1N1 attenuation. These findings support the development of a novel LAIV MDV based on a contemporary pH1N1 strain as a medical countermeasure against currently circulating H1N1 IAV.
Anterior Cingulate Metabolite Levels, Memory, and Inhibitory Control in Abstinent Men and Women with Alcohol Use Disorder
Authors: Oot Emily N. , Sawyer Kayle S. , Oscar-Berman Marlene , Luhar Riya B. , Jensen J.E. , Silveri Marisa M. 
Published: January 2022

ABSTRACTAimsAlcohol use disorder (AUD), has been shown to have harmful cognitive and physiological effects, including altered brain chemistry. Further, although men and women may differ in vulnerability to the neurobiological effects of AUD, results of existing studies have been conflicting. Brain metabolite levels and cognitive functions were examined in a cross section of men with AUD (AUDm) and women with AUD (AUDw) to determine degree of abnormalities after extended periods of abstinence (mean, six years), and to evaluate gender differences in cognitive and metabolite measures.MethodsParticipants were 40 abstinent individuals with AUD (22 AUDw, 18 AUDm) and 50 age-equivalent non-AUD comparison participants (26 NCw, 24 NCm). Proton magnetic resonance spectroscopy (MRS) was employed at 3 Tesla to acquire metabolite spectra from the dorsal anterior cingulate cortex (dACC). Brain metabolites N-acetylaspartate (NAA), choline (Cho), myo-Inositol (mI), and glutamate & glutamine (Glx) were examined relative to measures of memory and inhibitory control.ResultsMetabolite levels in the AUD group showed no significant differences from the NC group. Memory and inhibitory-control impairments were observed in the AUD group. There also were significant group-specific associations between metabolite ratios and measures of inhibitory control. There were no Group-by-Gender interactions for the four metabolite ratios.ConclusionsThese findings demonstrate that brain metabolite levels in men and women with AUD, following long-term abstinence, do not differ from individuals without AUD. The data also provide evidence of associations between metabolite levels and measures of inhibitory control, a functional domain important for curtailing harmful drinking.
Radiofrequency ablation remodels the tumor microenvironment and promotes systemic immunomodulation in pancreatic cancer
Authors: Faraoni Erika Y. , Thosani Nirav C. , O’Brien Baylee , Strickland Lincoln N. , Mota Victoria , Chaney Jarod , Cen Putao , Rowe Julie , Cardenas Jessica , Poulsen Kyle L. , Wray Curtis J. , Bailey-Lundberg Jennifer 
Published: January 2022

ABSTRACTBackground and AimsPancreatic ductal adenocarcinoma (PDAC) is characterized by resistance to therapy. A major contributing factor to therapeutic failure is profound desmoplasia and a well-documented hypoxic tumor microenvironment (TME). In PDAC, several therapeutic approaches, including chemotherapy and radiation alone or combined with immune checkpoint inhibitors, have shown minimal therapeutic success, placing an imperative need for the discovery and application of innovative treatments. Endoscopic ultrasound guided radiofrequency ablation (EUS-RFA) is a promising immunomodulator therapy for PDAC. In this work, we hypothesized RFA promotes local and systemic stromal and immunomodulating effects that can be identified for new combination therapeutic strategies.MethodsTo test our hypothesis, a syngeneic PDAC mouse model was performed by symmetrically injecting 100k murine KPC cells in bilateral flanks of C57BL/6 female mice. RFA treatment initiated when tumors reached 200-500 mm3 and was performed only in the right flank. The left flank tumor (non-RFA contralateral side) was used as a paired control for further analysis.ResultsRFA promoted a significant reduction in tumor growth rate 4 days after treatment in RFA treated and non-RFA side contralateral tumors from treated mice when compared to controls. Histological analysis revealed a significant increase in expression of cleaved Caspase3 in RFA treated tumors. In addition, collagen deposition and CD31+ cells were significantly elevated in RFA side and non-RFA contralateral tumors from RFA treated mice. Proteome profiling showed changes in C5a and IL-23 in RFA responsive tumors, indicating a role of RFA in modulating intratumoral inflammatory responses.ConclusionsThese data indicate RFA promotes local and systemic anti-tumor responses in a syngeneic mouse model of PDAC implicating RFA treatment for local tumors as well as metastatic disease.Graphical Abstract
Liquid-liquid phase separation of the chromosomal passenger complex drives parallel bundling of midzone microtubules
Authors: Niedzialkowska Ewa , Truong Tan M. , Eldredge Luke A. , Redemann Stefanie , Chretien Denis , Stukenberg P. Todd 
Published: January 2022

AbstractThe spindle midzone is a dynamic structure that forms during anaphase, mediates chromosome segregation, and provides a signaling platform to position the cleavage furrow. The spindle midzone comprises two antiparallel bundles of microtubules (MTs) but the process of their formation is poorly understood. Here, we show that the Chromosomal Passenger Complex (CPC) undergoes liquid-liquid phase separation (LLPS) to generate parallel MT bundles in vitro when incubated with free tubulin and GTP. MT bundles emerge from CPC droplets with protruding minus-ends that then grow into long, tapered MT structures. During this growth, the CPC in condensates apparently reorganize to coat and bundle the resulting MT structures. CPC mutants attenuated for LLPS or MT binding prevented the generation of parallel MT bundles in vitro and reduced the number of MTs present at spindle midzones in HeLa cells. Our data uncovers a kinase-independent function of the CPC and provides models for how cells generate parallel-bundled MT structures that are important for the assembly of the mitotic spindle.
Enhanced competitive protein exchange at the nano-bio interface enables ultra-deep coverage of the human plasma proteome
Authors: Hornburg Daniel , Ferdosi Shadi , Hasan Moaraj , Tangeysh Behzad , Brown Tristan R. , Wang Tianyu , Elgierari Eltaher M. , Zhao Xiaoyan , Alavi Amir , Chu Jessica , Figa Mike , Tao Wei , Wang Jian , Goldberg Martin , Xia Hongwei , Stolarczyk Craig , Batzoglou Serafim , Siddiqui Asim , Farokhzad Omid C. 
Published: January 2022

AbstractWe have developed a scalable system that leverages protein-nano interactions to overcome current limitations of deep plasma proteomics in large cohorts. Introducing proprietary engineered nanoparticles (NPs) into a biofluid such as blood plasma leads to the formation of a selective and reproducible protein corona at the particle-protein interface, driven by the relationship between protein-NP affinity and protein abundance. Here we demonstrate the importance of tuning the protein to NP-surface ratio (P/NP), which determines the competition between proteins for binding. We demonstrate how optimized P/NP ratio affects protein corona composition, ultimately enhancing performance of a fully automated NP-based deep proteomic workflow (Proteograph). By limiting the available binding surface of NPs and increasing the binding competition, we identify 1.2 – 1.7x more proteins with only 1% false discovery rate on the surface of each NP, and up to 3x compared to a standard neat plasma proteomics workflow. Moreover, increased competition means proteins are more consistently identified and quantified across replicates, yielding precise quantification and improved coverage of the plasma proteome when using multiple physicochemically distinct NPs. In summary, by optimizing NPs and assay conditions, we capture a larger and more diverse set of proteins, enabling deep proteomic studies at scale.
A visual atlas of genes’ tissue-specific pathological roles
Authors: Rai Priyadarshini , Jain Atishay , Jha Neha , Sharma Divya , Kumar Shivani , Raj Abhijit , Gupta Apoorva , Poonia Sarita , Chawla Smriti , Majumdar Angshul , Chakraborty Tanmoy , Ahuja Gaurav , Sengupta Debarka 
Published: January 2022

AbstractDysregulation of a gene’s function, either due to mutations or impairments in regulatory networks, often triggers pathological states in the affected tissue. Comprehensive mapping of these apparent gene-pathology relationships is an ever daunting task, primarily due to genetic pleiotropy and lack of suitable computational approaches. With the advent of high throughput genomics platforms and community scale initiatives such as the Human Cell Landscape (HCL) project [1], researchers have been able to create gene expression portraits of healthy tissues resolved at the level of single cells. However, a similar wealth of knowledge is currently not at our finger-tip when it comes to diseases. This is because the genetic manifestation of a disease is often quite heterogeneous and is confounded by several clinical and demographic covariates. To circumvent this, we mined ~18 million PubMed abstracts published till May 2019 and selected ~6.1 million of them that describe the pathological role of genes in different diseases. Further, we employed a word embedding technique from the domain of Natural Language Processing (NLP) to learn vector representation of entities such as genes, diseases, tissues, etc., in a way such that their relationship is preserved in a vector space. Notably, Pathomap, by the virtue of its underpinning theory, also learns transitive relationships. Pathomap provided a vector representation of words indicating a possible association between DNMT3A/BCOR with CYLD cutaneous syndrome (CCS). The first manuscript reporting this finding was not part of our training data.Key pointsWe mined ~18 million PubMed abstracts to extract latent knowledge pertaining to tissue specific pathological roles of genes.We found well-defined gene modules implicated in disease pathogenesis in anatomically proximal tissues.We demonstrated an ahead of time discovery of the association between DNMT3A/BCOR with CYLD cutaneous syndrome (CCS), as a knowledge synthesis use-case.