bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drosophila fabpis a retinoid-inducible gene required for Rhodopsin-1 homeostasis and photoreceptor survival
Authors: Huang Huai-Wei , Ryoo Hyung Don 
Published: April 2021

AbstractRetinoids act as chromophore co-factors for light-detecting rhodopsin proteins. In vertebrates, retinoids also actively regulate gene expression. Whether retinoids regulate gene expression inDrosophilafor a specific biological function remains unclear. Here, we report thatDrosophila fatty acid binding protein(fabp) is a retinoid-inducible gene required for Rhodopsin-1 (Rh1) protein homeostasis and photoreceptor survival. Specifically, we performed a photoreceptor-specific gene expression profiling study in flies bearing a misfolding-prone Rhodopsin-1 (Rh1) mutant,ninaEG69D, which serves as aDrosophilamodel for Retinitis Pigmentosa.ninaEG69Dphotoreceptors showed increased expression of genes that control Rh1 protein levels, along with a poorly characterized gene,fabp. We found that in vivofabpexpression was reduced when the retinoids were deprived through independent methods. Conversely,fabpmRNA was induced when we challenged culturedDrosophilacells with retinoic acid. In flies reared under light, loss offabpcaused an accumulation of Rh1 proteins in cytoplasmic vesicles.fabpmutants exhibited light-dependent retinal degeneration, a phenotype also found in other mutants that block light-activated Rh1 degradation. These observations indicate that a retinoid-inducible gene expression program regulatesfabpthat is required for Rh1 proteostasis and photoreceptor survival.Author SummaryRhodopsins are light-detecting proteins that use retinoids as chromophore co-factors. In vertebrates, retinoids also actively regulate gene expression. Whether retinoids regulate Rhodopsin function aside from its role as a chromophore remains unclear. Here, we report thatDrosophila fatty acid binding protein(fabp) is a retinoid-inducible gene required for Rhodopsin-1 (Rh1) protein homeostasis and photoreceptor survival. Specifically, we found thatfabpis among the genes induced by a misfolding-prone Rhodopsin-1 (Rh1) mutant,ninaEG69D, which serves as aDrosophilamodel for Retinitis Pigmentosa. We further found thatfabpinduction inninaEG69Dphotoreceptors required retinoids.fabpwas required in photoreceptors to help degrade light-activated Rh1. In the absence offabp, Rh1 accumulated in cytoplasmic vesicles in a light-dependent manner, and exhibited light-dependent retinal degeneration. These observations indicate that a retinoid-inducible gene expression program regulatesfabpthat is required for Rh1 proteostasis and photoreceptor survival.
The UBAP2L ortholog PQN-59 contributes to stress granule assembly and development inC. elegans
Authors: Abbatemarco Simona , Bondaz Alexandra , Schwager Francoise , Wang Jing , Hammell Christopher M , Gotta Monica 
Published: April 2021

AbstractWhen exposed to stressful conditions, eukaryotic cells respond by inducing the formation of cytoplasmic ribonucleoprotein complexes called stress granules. Stress granules are thought to have a protective function but their exact role is still unclear. Here we useC. elegansto study two proteins that have been shown to be important for stress granule assembly in human cells: PQN-59, the ortholog of human UBAP2L, and GTBP-1, the ortholog of the human G3BP1 and G3BP2 proteins. Both proteins fall into stress granules in the embryo and in the germline whenC. elegansis exposed to stressful conditions. None of the two proteins is essential for the assembly of stress induced granules, but the granules formed in absence of PQN-59 or GTBP-1 are less numerous and dissolve faster than the ones formed in control embryos. Despite these differences,pqn-59orgtbp-1mutant embryos do not show a higher sensitivity to stress than control embryos.pqn-59mutants display reduced progeny and a high percentage of embryonic lethality, phenotypes that are not dependent on stress exposure and that are not shared withgtbp-1mutants. Our data indicate that both GTBP-1 and PQN-59 contribute to stress granule formation but that PQN-59 is, in addition, required forC. elegansdevelopment.Author summaryThe formation of so-called stress granules is an adaptive response that cells and organisms put into action to cope with changes in internal and environmental conditions and thus to survive to stressful conditions. Although it is generally thought that stress granule formation protects cells from stress-related damage, the exact role of stress granules in cells and organisms is not well understood. Moreover, the mechanisms governing stress granule assembly, and if and how the ability to form stress granules is important forC. elegansdevelopment is still unclear.Our work focuses on two conserved proteins, known to be involved in stress granule assembly in mammalian cells, and investigates their role inC. elegansembryos. We find that these proteins are important but not essential to assemble stress-induced granules inC. elegans. We moreover did not observe a different sensitivity to stress exposure between wild-type and mutant developing embryos, suggesting that at least in these conditions these proteins do not exert a protective role.
SARS-CoV-2 proteins bind heme and hemoglobin
Authors: Lechuga Guilherme Curty , Souza-Silva Franklin , de Queiroz Sacramento Carolina , de Oliveira Trugilho Monique Ramos , Valente Richard Hemmi , Napoleão-Pêgo Paloma , da Silva Gomes Dias Suelen , Fintelman-Rodrigues Natalia , Temerozzo Jairo Ramos , Carels Nicolas , Alves Carlos Roberto , de Souza Pereira Mirian Claudia , Provance David William , Lopez Souza Thiago Moreno , De-Simone Salvatore Giovanni 
Published: April 2021

AbstractThe coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome virus 2 (SARS-CoV-2), has led to a global crisis that included collapsing healthcare systems and shut-down communities, producing considerable economic burden. Despite the number of effective vaccines quickly implemented, the emergence of new variants is a primary concern. The scientific community undertook a rapid response to better study this new virus. However, critical questions about viral protein-protein interactions and mechanisms of its physiopathology are still unclear. Although severe COVID-19 was associated with hematological dysfunctions, scarce experimental data were produced about iron dysmetabolism and the viral proteins’ possible interaction with hemoglobin (Hb) chains. This work demonstrates the binding of SARS-CoV-2 proteins to hemin and Hb using a multimethodological approach.In silicoanalysis indicated binding motifs between a cavity in the viral nucleoprotein and hemoglobin’s porphyrin coordination region. Different hemin binding capacities of mock and SARS-CoV-2-infected culture extracts were noticed using gel electrophoresis and TMB staining. Hemin-binding proteins were isolated from SARS-CoV-2-infected cells by affinity chromatography and identified by shotgun proteomics, indicating that structural (nucleoprotein, spike, and membrane protein) and non-structural (Nsp3 and Nsp7) viral proteins interact with hemin.In vitroanalyses of virus adsorption to host cells and viral replication studies in Vero cells demonstrated inhibitory activities - at different levels - by hemin, protoporphyrin IX (PpIX) Hb. Strikingly, free Hb at 1μM suppressed viral replication (99 %), and its interaction with SARS-CoV-2 was localized to the RBD region of the Spike protein. The findings showed clear evidence of new avenues to disrupt viral replication and understand virus physiopathology that warrants further investigation.
Photon-free (s)CMOS camera characterization for artifact reduction in high- and super-resolution microscopy
Authors: Diekmann Robin , Deschamps Joran , Li Yiming , Tschanz Aline , Kahnwald Maurice , Matti Ulf , Ries Jonas 
Published: April 2021

AbstractModern implementations of widefield fluorescence microscopy often rely on sCMOS cameras, but this camera architecture inherently features pixel-to-pixel variations. Such variations lead to image artifacts and render quantitative image interpretation difficult. Although a variety of algorithmic corrections exists, they require a thorough characterization of the camera, which typically is not easy to access or perform. Here, we developed a fully automated pipeline for camera characterization based solely on thermally generated signal, and implemented it in the popular open-source software Micro-Manager and ImageJ/Fiji. Besides supplying the conventional camera maps of noise, offset and gain, our pipeline also gives access to dark current and thermal noise as functions of the exposure time. This allowed us to avoid structural bias in single-molecule localization microscopy (SMLM), which without correction is substantial even for scientific-grade, cooled cameras. In addition, our approach enables high-quality 3D super-resolution as well as live-cell time-lapse microscopy with cheap, industry-grade cameras. As our approach for camera characterization does not require any user interventions or additional hardware implementations, numerous correction algorithms demanding camera characterization become easily applicable.
Assessing the efficacy of antibiotic treatment for the creation of axenic earthworms
Authors: Omosigho Henny O. , Swart Elmer , Sizmur Tom P. , Spurgeon Dave J. , Svendsen Claus , Shaw Liz J. 
Published: April 2021

AbstractEarthworms are an integral part of soil ecosystems, especially for their role in soil functions such as organic matter (OM) decomposition and nutrient cycling. Earthworms and microorganisms are interdependent, and a considerable portion of the contribution earthworms make to influencing OM fate is through interactions with microorganisms. However, the importance of the earthworm-associated microbiome is not fully understood, because it is difficult to separate the direct influence of the earthworms from the indirect influence of their microbiome. Here, we evaluated an antibiotic-based procedure for producing axenic ecologically-contrasting earthworm species (E. fetida, L. terrestris, A. chlorotica) as the first step towards soil studies aimed at understanding the importance of the earthworm microbiome for host health and function. Individual earthworms were exposed to antibiotics: cycloheximide (150 μg ml−1), ampicillin (100 μg ml−1), ciprofloxacin (50 μg ml−1), nalidixic acid (50 μg ml−1), and gentamicin (50 μg ml−1) either singly or in a cocktail via culture (96 h) in a semi-solid agar carrier. Compared to the non-antibiotic treated control, the cocktail (for all three species) and ciprofloxacin (forE. fetidaandA. chlorotica) treatments significantly reduced (P<0.05) culturable microbial abundance on nutrient agar and potato dextrose agar. The microbial counts were reduced to below detection (<50 CFU individual−1) forE. fetidaandA. chloroticareceiving the cocktail. Illumina 16S rDNA amplicon sequence analysis of culturableL. terrestris-associated bacteria showed that antibiotic treatment influenced community composition revealing putative sensitive (Comomonas, KosakoniaandSphingobacterium) and insensitive (Aeromonas, Pseudochrobactrum) taxa. Overall, we report a rapid, with minimal earthworm-handling, process of creating ‘axenic’E. fetidaandA. chloroticaindividuals orL. terrestriswith a suppressed microbiome as a tool to be used in future ecological studies of earthworm microbial interactions affecting host health and function.
Neuroprotection in early stages of Alzheimer’s Disease is promoted by Transthyretin angiogenic properties
Authors: Gião Tiago , Saavedra Joana , Vieira José Ricardo , Pinto Marta Teixeira , Arsequell Gemma , Cardoso Isabel 
Published: April 2021

AbstractWhile still controversial, it has been demonstrated that vascular defects can precede the onset of the other AD hallmarks features, making it an important therapeutic target. Given that the protein transthyretin (TTR) has been established as neuroprotective in AD, here we investigated the influence of TTR in the vasculature. AD transgenic mice with TTR genetic reduction, AD/TTR+/−, exhibited a thicker BM in brain microvessels and decreased vessel length than animals with normal TTR levels, AD/TTR+/+. Furtherin vivoinvestigation, using the chick chorioallantoic membrane (CAM) assay, revealed that TTR is a pro-angiogenic molecule. Also, TTR increased the expression of key angiogenic molecules, by endothelial cells under tube formation conditions. We showed that TTR reduction leads to a thicker BM in AD mice than in NT animals, strengthening the idea that TTR is a neuroprotective protein. We also studied the effect of TTR tetrameric stabilization on BM thickness, showing that AD mice treated with iododiflunisal (IDIF) displayed a significant reduction of BM thickness and increased vessel length when compared to non-treated littermates. Ourin vivoresults show the involvement of TTR in angiogenesis, particularly as a modulator of vascular alterations occurring in AD. Since TTR is decreased early in AD, its tetrameric stabilization can represent a therapeutic avenue for the early treatment of AD through the maintenance of the vascular structure.
Cholesterol promotes both head group visibility and clustering of PI(4,5)P2driving unconventional secretion of Fibroblast Growth Factor 2
Authors: Lolicato Fabio , Saleppico Roberto , Griffo Alessandra , Pokrandt Bianca , Müller Hans-Michael , Ewers Helge , Hähl Hendrik , Fleury Jean-Baptiste , Seemann Ralf , Brügger Britta , Jacobs Karin , Vattulainen Ilpo , Nickel Walter 
Published: April 2021

SummaryFibroblast Growth Factor 2 (FGF2) is a cell survival factor involved in tumor-induced angiogenesis. FGF2 is secreted through an unconventional secretory pathway based upon direct protein translocation across the plasma membrane. Here we demonstrate that both PI(4,5)P2-dependent FGF2 recruitment at the inner plasma membrane leaflet and FGF2 membrane translocation into the extracellular space are positively modulated by cholesterol in living cells. We further reveal cholesterol to enhance FGF2 binding to PI(4,5)P2-containing lipid bilayers in a fully reconstituted system. Based on extensive atomistic molecular dynamics simulations and membrane tension experiments, we propose cholesterol to modulate FGF2 binding to PI(4,5)P2by (i) increasing head group visibility of PI(4,5)P2on the membrane surface, (ii) increasing avidity by cholesterol-induced clustering of PI(4,5)P2molecules triggering FGF2 oligomerization and (iii) increasing membrane tension facilitating the formation of lipidic membrane pores. Our findings have general implications for phosphoinositide-dependent protein recruitment to membranes and explain the highly selective targeting of FGF2 towards the plasma membrane, the subcellular site of FGF2 membrane translocation during unconventional secretion of FGF2.
Bioelectricity generation from live marine photosynthetic macroalgae
Authors: Shlosberg Yaniv , Krupnik Nimrod , Tóth Tünde N. , Eichenbaum Ben , Meirovich Matan , Meiri David , Yehezkeli Omer , Schuster Gadi , Israel Álvaro , Adir Noam 
Published: April 2021

AbstractConversion of solar energy into electrical current by photosynthetic organisms has the potential to produce clean energy. Previously reported bio-photoelectrochemical cells (BPECs) have utilized unicellular photosynthetic microorganisms. In this study, we describe for the first time BPECs that utilize intact live marine macroalgae (seaweeds) in natural seawater or saline buffer or natural seawater. The BPECs produce electrical currents from of >50mA/cm2, from both light-dependent (photosynthesis) and light independent processes. These values are significantly greater than the current densities that have been reported for single-cell microorganisms. The photocurrent is inhibited by the Photosystem II inhibitor DCMU, indicating that the source of light-driven electrons is from water oxidation via NADPH and other reduced molecules. We show here that intact seaweed cultures can be used in a large-scale BPEC containing seawater that produces bias-free photocurrent. The ability to produce bioelectricity from intact seaweeds may pave the way to future development of a low-cost energy technology using BPECs.
Subgroup-specific gene expression profiles and mixed epistasis in chronic lymphocytic leukemia
Authors: Lütge Almut , Lu Junyan , Hüllein Jennifer , Walther Tatjana , Sellner Leopold , Wu Bian , Rosenquist Richard , Oakes Christopher C. , Dietrich Sascha , Huber Wolfgang , Zenz Thorsten 
Published: April 2021

AbstractDespite the extensive catalogue of recurrent mutations in chronic lymphocytic leukaemia (CLL), the diverse molecular driving events and the resulting range of disease phenotypes remain incompletely understood. To study the molecular heterogeneity of CLL, we performed RNA-sequencing on 184 CLL patient samples. Unsupervised analysis revealed two major independent axes of gene expression variation: the first one aligned with the mutational status of the immunoglobulin heavy variable (IGHV) genes, and concomitantly, with the three-group stratification of CLL by global DNA methylation pattern, and affected biological functions including B- and T-cell receptor signaling. The second one aligned with trisomy 12 status and affected chemokine signaling. Furthermore, we searched for differentially expressed genes associated with gene mutations and copy-number aberrations and detected strong signatures forTP53, BRAFandSF3B1, as well as for del(11)(q22.3), del(17)(p13) and del(13)(q14) beyond the dosage effect. We discovered strong non-additive effects (i.e., genetic interactions, or epistasis) of IGHV mutation status and trisomy 12 on multiple phenotypes, including the expression of 893 genes. Multiple types of epistasis were observed, including synergy, buffering, suppression and inversion. Our study reveals previously underappreciated gene expression signatures for (epi)genomic variants in CLL and the presence of epistasis between them. The findings will serve as a reference for a functional resolution of CLL molecular heterogeneity.
Major effect loci for plant size before onset of nitrogen fixation allow accurate prediction of yield in white clover
Authors: Moeskjær Sara , Skovbjerg Cathrine Kiel , Tausen Marni , Wind Rune , Roulund Niels , Janss Luc , Andersen Stig U. 
Published: April 2021

AbstractWhite clover is an agriculturally important forage legume grown throughout temperate regions as a mixed clover-grass crop. It is typically cultivated with low nitrogen input, making yield dependent on nitrogen fixation by rhizobia in root nodules. Here, we investigate the effects of clover and rhizobium genetic variation by monitoring plant growth and quantifying dry matter yield of 704 combinations of 145 clover and 169 rhizobium genotypes. We find no significant effect of rhizobium variation. In contrast, we can predict yield based on a few white clover markers strongly associated with plant size prior to nitrogen fixation, and the prediction accuracy for polycross offspring yield is remarkably high. Several of the markers are located near a homolog ofArabidopsis thaliana GIGANTUS 1, which regulates growth rate and biomass accumulation. Our work provides fundamental insight into the genetics of white clover yield and identifies specific candidate genes as breeding targets.
Controlling gene expression in mammalian cells using multiplexed conditional guide RNAs for Cas12a
Authors: Oesinghaus Lukas , Simmel Friedrich C. 
Published: April 2021

AbstractSpatiotemporal control of the activity of Cas proteins is of considerable interest for both basic research and therapeutics. Only few mechanisms have been demonstrated for regulating the activity of guide RNAs (gRNAs) for Cas12a in mammalian cells, however, and combining and compactly integrating multiple control instances on single transcripts has not been possible so far. Here, we show that conditional processing of the 3’ tail is a viable general approach towards switchable Pol II-transcribed Cas12a gRNAs that can activate gene expression in mammalian cells in an input-dependent manner. Processing of the 3’ tail can be achieved using microRNA and short hairpin RNA as inputs, via a guanine-responsive ribozyme, and also using an RNA strand displacement mechanism. We further show that Cas12a along with several independently switchable gRNAs can be integrated on a single transcript using stabilizing RNA triplexes, providing a route towards compact Cas12a-based gene regulation constructs with multi-input switching capabilities.
Chronic toxicity of three neonicotinoid insecticides and their mixture on two daphniid species:Daphnia magnaandCeriodaphnia dubia
Authors: Duchet Claire , Mitchell Chelsea J. , McIntyre Jenifer K. , Stark John D. 
Published: April 2021

AbstractNeonicotinoid insecticides represent nearly a quarter of the global market and are widely used in agriculture but also for lawn, garden care, and pest control. They are highly water-soluble, persistent in soil, and may enter the aquatic compartment via spray drift, runoff, or leaching, and contribute to downstream aquatic toxicity. Although insects appear to be the most sensitive group to neonicotinoids, other groups, such as crustaceans and birds, may also be affected. Furthermore, most studies focus on single-insecticide exposure and very little is known concerning the impact of neonicotinoid mixtures on aquatic invertebrates. The present study was designed to test potential toxicological effects of an environmentally relevant mixture of imidacloprid, clothianidin, and thiamethoxam on populations ofCeriodaphnia dubiaandDaphnia magnaunder controlled conditions. Chronic toxicity tests were conducted in the laboratory, and survival and reproduction were measured for both species under exposure to nominal concentrations of imidacloprid (0.256 µg/L), clothianidin (3.11 µg/L), thiamethoxam (1.49 µg/L), and a mixture of the three compounds at the same concentrations of the individual compounds. The neonicotinoids did not affect the survival ofC. dubiaandD. magnafounders. Reproduction ofC. dubiawas affected only by the mixture. All three individual insecticides as well as the mixture caused a significant reduction in the reproduction ofD. magna. Our results highlight the complexity of pesticide toxicity and show that traditional toxicological approaches such as acute mortality studies, especially tests with single compounds, can underestimate negative impacts that occur in the environment.HighlightsNeonicotinoids are currently the most frequently used insecticides worldwide.An environmentally relevant mixture of three neonicotinoids was evaluated on two daphniid species.The mixture negatively affected the reproduction ofC. dubiaandDaphnia magna.Traditional toxicological approaches with single compounds may underestimate the effects occurring in the environment at low concentrations.