bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Versatile and Dynamic Anaerobic Metabolism for PAOs/GAOs Competition Using Agent-based Model and Verification via Single Cell Raman Micro-spectroscopy
Authors: Li Guangyu , Tooker Nicholas B. , Wang Dongqi , Srinivasan Varun , Barnard James L. , Russell Andrew , Stinson Beverley , McQuarrie Jim , Schauer Peter , Menniti Adrienne , Varga Erika , Hauduc Hélène , Takács Imre , Bott Charles , Dombrowski Paul , Onnis-Hayden Annalisa , Gu April Z. 
Published: November 2020

ABSTRACTSide-stream enhanced biological phosphorus removal process (S2EBPR) has been demonstrated to improve performance stability and offer a suite of advantages compared to conventional EBPR design. Design and optimization of S2EBPR require modification of the current EBPR models that were not able to fully reflect the metabolic functions of and competition between the polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) under extended anaerobic conditions as in the S2EBPR conditions. In this study, we proposed and validated an improved model (iEBPR) for simulating PAO and GAO competition that incorporated heterogeneity and versatility in PAO sequential polymer usage, staged maintenance-decay, and glycolysis-TCA pathway shifts. The iEBPR model was first calibrated against bulk batch testing experiment data, being proved to perform better than the previous EBPR model for predicting the soluble orthoP, ammonia, biomass glycogen, and PHA temporal profiles in a batch starvation testing under prolonged anaerobic conditions. We further validated the model with another independent set of batch anaerobic batch testing data that included high-resolution single-cell and specific population level intracellular polymer measurements enabled by the single-cell Raman micro-spectroscopy technique. The model accurately predicted the temporal changes in the intracellular polymers at cellular and population levels within PAOs and GAOs, and further confirmed the proposed mechanism of sequential polymer utilization, and polymer availability-dependent and staged maintenance-decay in PAOs. These results indicate that under extended anaerobic phases as in S2EBPR, the PAOs may gain competitive advantages over GAOs due to the possession of multiple intracellular polymers and the adaptive switching of the anaerobic metabolic pathways that consequently lead to the later and slower decay in PAOs than GAOs. The iEBPR model can be applied to facilitate and optimize the design and operations of S2EBPR for more reliable nutrient removal and recovery from wastewater.
Identification of herboxidiene features that mediate conformation-dependent SF3B1 interactions to inhibit splicing
Authors: Lopez Adriana Gamboa , Allu Srinivasa Rao , Mendez Patricia , Reddy Guddeti Chandrashekar , Maul-Newby Hannah M. , Ghosh Arun K. , Jurica Melissa S. 
Published: November 2020

ABSTRACTSmall molecules that target the spliceosome SF3B complex are potent inhibitors of cancer cell growth. The compounds affect an early stage of spliceosome assembly when U2 snRNP first engages the branch point sequence of an intron. Recent cryo-EM models of U2 snRNP before and after intron recognition suggest several large-scale rearrangements of RNA and protein interactions involving SF3B. Employing an inactive herboxidiene analog as a competitor with SF3B inhibitors, we present evidence for multiple conformations of SF3B in the U2 snRNP, only some of which are available for productive inhibitor interactions. We propose that both thermodynamics and an ATP-binding event promote the conformation conducive to SF3B inhibitor interactions. However, SF3B inhibitors do not impact an ATP-dependent rearrangement in U2 snRNP that exposes the branch binding sequence for base pairing. We also report extended structure activity relationship analysis of herboxidiene, which identified features of the tetrahydropyran ring that mediate its interactions with SF3B and its ability to interfere with splicing. In combination with structural models of SF3B interactions with inhibitors, our data leads us to extend the model for early spliceosome assembly and inhibitor mechanism. We postulate that interactions between a carboxylic acid substituent of herboxidiene and positively charged SF3B1 sidechains in the inhibitor binding channel are required to maintain inhibitor occupancy and counteract the SF3B transition to a closed state that is promoted by stable U2 snRNA interactions with the intron.
Substrate traits shape the structure of microbial community engaged in metabolic division of labor
Authors: Wang Miaoxiao , Chen Xiaoli , Tang Yue-Qin , Nie Yong , Wu Xiao-Lei 
Published: November 2020

AbstractMetabolic division of labor (MDOL) is widespread in nature, whereby a complex metabolic pathway is shared between different strains within a community for mutual benefit. However, little is known about how the mutual interactions in the microbial community engaged in MDOL are regulated. We hypothesized that when degradation of an organic compound is carried out via MDOL, the substrate traits (i.e., concentration and its toxicity) modulate the benefit allocation between the two microbial populations, thus affecting the structure of this community. We tested this hypothesis by combining mathematical modelling with experiments using engineered synthetic microbial consortia. Numerous modelling analyses suggested that the proportion of the population executing the first metabolic step can be simply estimated by Monod-like formulas governed by substrate traits. The model and the proposed formula quantitatively predicted the structure of our synthetic consortia composed of two strains degrading salicylate through MDOL. Individual-based modelling and colony pattern formation assays further indicated that our rule is also applicable to estimating community structure in spatially structured environments. Our results demonstrate that the structure of the microbial communities can be quantitatively predicted from simple environmental factors, such as substrate concentration and its toxicity, which provides novel perspectives on understanding the assembly of natural communities, as well as insights into how to manage artificial microbial systems.
In ovoelectroporation of chicken limb bud ectoderm
Authors: Tomizawa Reiko R. , Tabin Clifford J. , Atsuta Yuji 
Published: November 2020

AbstractDeciphering how ectodermal tissues form, and how they maintain their integrity, is crucial for understanding epidermal development and pathogenesis. However, lack of simple and rapid gene manipulation techniques limits genetic studies to elucidate mechanisms underlying these events. Here we describe have an easy method for electroporation of chick embryo limb bud ectoderm, enabling gene manipulation during ectoderm development and wound healing. Taking advantage of a small parafilm well that constrains DNA plasmids locally and the fact that the limb ectoderm arises from a defined site, we target the limb ectoderm forming region byin ovoelectroporation. This approach results in efficient transgenesis of the limb ectodermal cells. Further, using a previously describedMsx2promoter, gene manipulation can be specifically targeted to the apical ectodermal ridge (AER), a signaling center regulating limb development. Using the electroporation technique to deliver a fluorescent marker into the embryonic limb ectoderm, we show its utility in performing time-lapse imaging during wound healing. This analysis revealed previously unrecognized dynamic remodeling of the actin cytoskeleton and lamellipodia formation at the edges of the wound. We find that the lamellipodia formation requires activity of Rac1 GTPase, suggesting its necessity for wound closure. Our method is simple and cheap, and permits high throughput tests for gene function during limb ectodermal development and wound healing.
Reducing error and increasing reliability of wildlife counts from citizen science surveys: counting Weddell Seals in the Ross Sea from satellite images
Authors: Salas Leo A. , LaRue Michelle , Nur Nadav , Ainley David G. , Stammerjohn Sharon E. , Pennycook Jean , Rotella Jay , Paterson John Terrill , Siniff Don , Stamatiou Kostas , Dozier Melissa , Saints Jon , Barrington Luke 
Published: November 2020

ABSTRACTCitizen science programs can be effective at collecting information at large temporal and spatial scales. However, sampling bias is a concern in citizen science datasets and can lead to unreliable estimates. We address this issue with a novel approach in a first-of-its-kind citizen science survey of Weddell seals for the entire coast of Antarctica. Our citizen scientists inspected very high-resolution satellite images to tag any presumptive seals hauled out on the fast ice during the pupping period. To assess and reduce the error in counts in term of bias and other factors, we ranked surveyors on how well they agreed with each other in tagging a particular feature (presumptive seal), and then ranked these features based on the ranking of surveyors placing tags on them. We assumed that features with higher rankings, as determined by “the crowd wisdom,” were likely to be seals. By comparing citizen science feature ranks with an expert’s determination, we found that non-seal features were often highly ranked. Conversely, some seals were ranked low or not tagged at all. Ranking surveyors relative to their peers was not a reliable means to filter out erroneous or missed tags; therefore, we developed an effective correction factor for both sources of error by comparing surveyors’ tags to those by the expert. Furthermore, counts may underestimate true abundance due to seals not being present on the ice when the image was taken. Based on available on-the-ground haul-out location counts in Erebus Bay, the Ross Sea, we were able to correct for the proportion of seals not detected through satellite images after accounting for year, time-of-day, location (islet vs. mainland locations), and satellite sensor effects. We show that a prospective model performed well at estimating seal abundances at appropriate spatial scales, providing a suitable methodology for continent-wide Weddell Seal population estimates.
Shape and size complementarity induced formation of supramolecular protein assemblies with metal-oxo clusters
Authors: Vandebroek Laurens , Noguchi Hiroki , Kamata Kenichi , Tame Jeremy R. H. , Van Meervelt Luc , Parac-Vogt Tatjana N. , Voet Arnout R. D. 
Published: November 2020

AbstractThe controlled formation of protein supramolecular assemblies is challenging but it could provide an important route for the development of hybrid biomaterials. In this work, we demonstrate formation of well-defined complexes formed between the 8-fold symmetrical designer protein Tako8 and soluble metal-oxo clusters from the family of Anderson-Evans, Keggin and ZrIV- substituted Wells-Dawson polyoxometalates. A combination of x-ray crystallography and solution studies showed that metal-oxo clusters are able to serve as linker nodes for the bottom-up creation of protein based supramolecular assemblies. Our findings indicate that clusters with larger size and negative charge are capable of modulating the crystal packing of the protein, highlighting the need for a size and shape complementarity with the protein node for optimal alteration of the crystalline self-assembly.
Subtractive CRISPR screen identifies factors involved in non-canonical LC3 lipidation
Authors: Ulferts Rachel , Marcassa Elena , Timimi Lewis , Lee Liam C , Daley Andrew , Montaner Beatriz , Turner Suzanne D. , Florey Oliver , Baillie J. Kenneth , Beale Rupert 
Published: November 2020

AbstractAlthough commonly associated with autophagosomes, LC3 can also be recruited to membranes in a variety of non-canonical contexts. These include responses to ionophores such as the M2 proton channel of influenza A virus. LC3 is attached to membranes by covalent lipidation that depends on recruitment of the ATG5-12-16L1 complex. Non-canonical LC3 lipidation requires the C-terminal WD40 domain of ATG16L1 that is dispensable for canonical autophagy. We devised a subtractive CRISPR knock-out screening strategy to investigate the requirements for non-canonical LC3-lipidation. This correctly identified the enzyme complexes directly responsible for LC3-lipidation. We additionally identified the RALGAP complex as important for M2-induced, but not ionophore drug induced LC3 lipidation. In contrast, we identified ATG4D as responsible for LC3 recycling in M2-induced and basal LC3-lipidation. Identification of a vacuolar ATPase subunit in the screen suggested a common mechanism for non-canonical LC3 recruitment. Influenza-induced and ionophore drug induced LC3-lipidation leads to association of the vacuolar ATPase and ATG16L1 and can be antagonised by Salmonella SopF. LC3 recruitment to erroneously neutral compartments may therefore represent a response to damage caused by diverse invasive pathogens.
Long-chain polyphosphates impair SARS-CoV-2 infection and replication: a route for therapy in man
Authors: Ferrucci Veronica , Kong Dae-Young , Asadzadeh Fatemeh , Marrone Laura , Siciliano Roberto , Cerino Pellegrino , Criscuolo Giuseppina , Pisano Ida , Quarantelli Fabrizio , Izzo Barbara , Fusco Giovanna , Comegna Marika , Boccia Angelo , Viscardi Maurizio , Borriello Giorgia , Brandi Sergio , Pierri Bianca Maria , Tiberio Claudia , Atripaldi Luigi , Paolella Giovanni , Castaldo Giuseppe , Pascarella Stefano , Bianchi Martina , Monica Rosa Della , Chiariotti Lorenzo , Yun Kyong-Seop , Cheong Jae-Ho , Kim Hong-Yeoul , Zollo Massimo 
Published: November 2020

AbstractAnti-viral activities of long-chain inorganic polyphosphates (PolyPs) against severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection were investigated. In molecular docking analyses, PolyPs interacted with several conserved angiotensin-converting enzyme (ACE)2 and RNA-dependent RNA polymerase (RdRp) amino acids. We thus tested PolyPs for functional interactionsin vitroin SARS-CoV-2–infected Vero E6, Caco2 and human primary nasal epithelial cells. Immunofluorescence, qPCR, direct RNA sequencing, FISH and Immunoblotting were used to determine virus loads and transcription levels of genomic(g)RNAs and sub-genomic(sg)RNAs. We show that PolyP120 binds to ACE2 and enhances its proteasomal degradation. PolyP120 shows steric hindrance of the genomic Sars-CoV-2-RNA/RdRP complex, to impair synthesis of positive-sense gRNAs, viral subgenomic transcripts and structural proteins needed for viral replication. Thus, PolyP120 impairs infection and replication of Korean and European (containing non-synonymous variants) SARS-CoV-2 strains. As PolyPs have no toxic activities, we envision their use as a nebulised formula for oropharyngeal delivery to prevent infections of SARS-CoV-2 and during early phases of antiviral therapy.
Bivariate confidence probability plots as a method to test the accuracy and variability of microbiological measures
Authors: Monleon-Getino Antonio ,   AC Marca Home Care
Published: November 2020

AbstractIntroductionIn an interlaboratory calibration analysis to validate a methodology that will be proposed as a European standard for domestic laundry disinfection, tests were carried out to detect if there are different behaviors in the measurements regarding accuracies and variabilities. Interlaboratory tests using different doses of disinfectant and microorganisms were carried out. ISO 5725-2 and ISO 13528 form the basis of validations of quantitative methods, providing validation specifications for interlaboratory studies. However, a need for a simple graphical method to detect interlaboratory differences in accuracy and variability was observed.ObjectivesThe general goal of this work is to present a new exploratory methodology, graphical and easy to interpret, that can determine the accuracy and variability (precision) of a variable, and compare it to the methodology applied in ISO 5725-2 and ISO 13528.MethodsWe used confidence probability plots of the multivariate Student’s t-distribution to observe the accuracy and variability of microbiological measures carried out by different laboratories during a ring trial exercise. A function in R was built for this purpose: Miriam.analysis.ellipse(Y, factor_a, eel.plot = “ t-Student”). The different observations of accuracy and variability are represented in the ellipses. If any of the points are outside the ellipse with 95% confidence, we can assume a deviation in accuracy and / or variability.ResultsTwo examples are provided with real microbiological data (logarithmic unit reductions (LR) forPseudomonas aeruginosa, Escherichia coli, Staphilococcus aureus, Enterococcus hirae, Candida albicansand microbial counts in water (WW)). The proposed new method allowed us to detect possible deviations in the WWMEA variable and we believe it has future application for the rapid control of microbiological measures.
Cell-to-cell heterogeneity in Sox2 and Brachyury expression ratios guides progenitor destiny by controlling their motility.
Authors: Romanos Michèle , Allio Guillaume , Combres Léa , Médevielle Francois , Escalas Nathalie , Soula Cathy , Steventon Ben , Trescases Ariane , Bénazéraf Bertrand 
Published: November 2020

AbstractAlthough cell-to-cell heterogeneity in gene and protein expression within cell populations has been widely documented, we know little about its potential biological functions. We addressed this issue by studying progenitors that populate the posterior region of the vertebrate embryos, a cell population known for its capacity to self-renew or to contribute to the formation of the neural tube and paraxial mesoderm tissues. Posterior progenitors are characterized by the co-expression of Sox2 and Brachyury (Bra), two transcription factors related to neural and mesodermal lineages, respectively. In this study, we show that the respective levels of Sox2 and Bra proteins display a high degree of variability among posterior progenitors of the quail embryo. By developing forced expression and downregulation approaches, we further provide evidence that the value of the Sox2-to-Bra ratio in a given progenitor directs its choice of staying in place or exit the progenitor zone to generate neural or mesodermal cells. Time-lapse imaging together with mathematical modeling then reveal that variations of the Sox2-to-Bra ratio confer these cells heterogeneous motile behaviors. While high Bra levels display high motile properties that push cells to join the mesoderm, high levels of Sox2 tend to inhibit cell movement making cells get integrated into the neural tube. Our work thus provides evidence that the spatial heterogeneity of posterior progenitors, with regards to their relative contents of Sox2 and Bra and thus to their motile properties, is fundamental to maintain a pool of resident progenitors while others segregate to contribute to tissue formation. More broadly, our work reveals that heterogeneity among a population of progenitor cells is critical to ensure robust multi-tissue morphogenesis.
Formulation of a composite nasal spray enabling enhanced surface coverage and prophylaxis of SARS-COV-2
Authors: Moakes R. J. A. , Davies S. P. , Stamataki Z. , Grover L. M. 
Published: November 2020

AbstractAirborne pathogens pose high risks in terms of both contraction and transmission within the respiratory pathways, in particular the nasal region. Although knowledge of airborne transmission has long been known, there is little in the way of adequate intervention that can protect the individual, or even prevent further spread. This study focuses on a nasal applicant with the capacity to combat such issues, by focussing on the SARS-CoV-2 virus. Formulation of a spray containing polysaccharides known for their mucoadhesive properties was undertaken and characterised for their mechanical, spray patterns and antiviral properties. The ability to engineer key behaviours such as yielding have been shown, through systematic understanding of a composite mixture containing two polymers: gellan and λcarrageenan. Furthermore, spray systems demonstrated highly potent antiviral capacities, resulting in complete inhibition of the virus when studied for both prophylaxis and prevention of spread. Finally, a mechanism has been proposed to explain such findings. Therefore, demonstrating the first fully preventative device, targeted to protect the lining of the upper respiratory pathways.
The centriolar satellite protein Cfap53/Ccdc11 facilitates the formation of the first zygotic microtubule organizing center in the zebrafish embryo
Authors: Willekers Sven , Tessadori Federico , van der Vaart Babet , Henning Heiko , Stucchi Riccardo , Altelaar Maarten , Roelen Bernard A.J. , Akhmanova Anna , Bakkers Jeroen 
Published: November 2020

AbstractIn embryos from most animal species a zygotic centrosome is assembled by the centriole derived from the sperm cell and pericentriolar proteins present in the oocyte. This zygotic centrosome acts as a microtubule organizing center (MTOC) to assemble the mitotic spindle in the first and all subsequent cell divisions. As MTOC formation has been studied mainly in adult cells, very little is known about the formation of the first zygotic MTOC. Here we find that zebrafish (Danio rerio) embryos lacking maternal or paternal Cfap53, a centriolar satellite protein, arrest during the first cell cycle due to a failure in proper formation of the mitotic spindle. During the first cell cycle Cfap53 co-localizes with γ-tubulin and other centrosomal and centriolar satellite proteins to the very large MTOC. Furthermore, we find that γ-tubulin localization to the MTOC is impaired in the absence of Cfap53 or when the microtubule network is disrupted. Based on these results we propose a model in which maternal and paternal Cfap53 participates in the organization of the first zygotic MTOC of the embryo. Once the zygotic MTOC is formed, Cfap53 is dispensable for MTOC formation and integrity in subsequent cell divisions.
Universally available herbal teas based on sage and perilla elicit potent antiviral activity against SARS-CoV-2 variants of concern by HMOX-1 upregulation in human cells
Authors: Le-Trilling Vu Thuy Khanh , Mennerich Denise , Schuler Corinna , Sakson Roman , Lill Julia K. , Kopczynski Dominik , Loroch Stefan , Flores-Martinez Yulia , Katschinski Benjamin , Wohlgemuth Kerstin , Gunzer Matthias , Meyer Folker , Dittmer Ulf , Sickmann Albert , Trilling Mirko 
Published: November 2020

AbstractThe current SARS-CoV-2/COVID-19 pandemic wreaks medical and socioeconomic havoc. Despite the availability of vaccines, cost-effective acute treatment options preventing morbidity and mortality are urgently needed. To identify affordable, ubiquitously available, and effective treatments, we tested herbs consumed worldwide as herbal teas regarding their antiviral activity against SARS-CoV-2. Aqueous infusions prepared by boiling leaves of theLamiaceaeperilla and sage elicit potent and sustained antiviral activity against SARS-CoV-2 in therapeutic as well as prophylactic regimens. The herbal infusions exerted antiviral effects comparable to interferon-β and remdesivir but outperformed convalescent sera and interferon-α2 upon short-term treatment early after infection. Based on protein fractionation analyses, we identified caffeic acid, perilla aldehyde, and perillyl alcohol as antiviral compounds. Global mass spectrometry (MS) analyses performed comparatively in two different cell culture infection models revealed changes of the proteome upon treatment with herbal infusions and provided insights into the mode of action. As inferred by the MS data, induction of heme oxygenase 1 (HMOX-1) was confirmed as effector mechanism by the antiviral activity of the HMOX-1-inducing compounds sulforaphane and fraxetin. In conclusion, herbal teas based on perilla and sage exhibit antiviral activity against SARS-CoV-2 including variants of concern such as Alpha, Beta, Delta, and Omicron.