bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre-treatment of Nile tilapia (Oreochromis niloticus) with ozone nanobubbles improve efficacy of heat-killed Streptococcus agalactiae immersion vaccine
Authors: Linh Nguyen Vu , Dien Le Thanh , Sangpo Pattiya , Senapin Saengchan , Thapinta Anat , Panphut Wattana , St-Hilaire Sophie , Rodkhum Channarong , Dong Ha Thanh 
Published: December 2021

AbstractNanobubble technology has shown appealing technical benefits and potential applications in aquaculture. We recently found that treatment with ozone nanobubbles (NB-O3) activated expression of several immune-related genes leading to effective response to subsequent exposure to fish pathogens. In this study, we investigated whether pre-treatment of Nile tilapia (Oreochromis niloticus) with NB-O3 can enhance specific immune responses and improve efficacy of immersion vaccination against Streptococcus agalactiae. Spleen and head kidney of fish in the vaccinated groups showed a substantial upregulation in expression levels of three immunoglobulin classes(IgM, IgD, and IgT) compared with the unvaccinated control groups. At day 21 post-immunization, the relative expression was greatest (approx. 3.2 to 4.1 folds). Both systemic and mucosal IgM antibodies were elicited in vaccinated groups. As the result, the cumulative survival rate of the vaccinated groups was found to be higher than that of the unvaccinated groups, with a relative percent survival (RPS) ranging from 52.9-70.5%. However, fish in the vaccinated groups that received pre-treatment with NB-O3, bacterial antigen uptakes, expression levels of IgM, IgD, and IgT, as well as the specific-IgM antibody levels and percent survival, were all slightly or significantly higher than that of the vaccinated group without pre-treatment with NB-O3. Taken together, our findings suggest that utilizing pre-treatment with NB-O3 may improve the immune response and efficacy of immersion vaccination in Nile tilapia.HighlightsImmune response and efficacy of a heat-killed Streptococcus agalactiae immersion vaccine for Nile tilapia with and without pre-treatment with NB-O3 were accessed.Bacterial antigen uptake in the NB-O3-VAC compared to the AT-VAC groups was increased 1.32 and 1.80-fold at 3 and 6 h post-vaccination, respectively.Vaccinated group that received pre-treatment with NB-O3 had slightly to significantly higher levels of IgM, IgD, and IgT mRNA expression; IgM levels; and survival rate.Pre-treatment with NB-O3 may be a novel strategy for improving efficacy of immersion vaccine in aquaculture
Unveiling effects of growth conditions on crown architecture and growth potential of Scots pine trees
Authors: Saarinen Ninni , Kankare Ville , Huuskonen Saija , Hynynen Jari , Bianchi Simone , Yrttimaa Tuomas , Luoma Ville , Junttila Samuli , Holopainen Markus , Hyyppä Juha , Vastaranta Mikko 
Published: December 2021

AbstractTrees adapt to their growing conditions by regulating the sizes of their parts and their relationships. For example, removal or death of adjacent trees increases the growing space and the amount of light received by the remaining trees enabling their crowns to expand. Knowledge about the effects of silvicultural practices on crown size and shape as well as about the quality of branches affecting the shape of a crown is, however, still limited. Thus, the aim was to study the crown structure of individual Scots pine trees in forest stands with varying stem densities due to past forest management practices. Furthermore, we wanted to understand how crown and stem attributes as well as tree growth affects stem area at the height of maximum crown diameter (SAHMC), which could be used as a proxy for tree growth potential. We used terrestrial laser scanning (TLS) to generate attributes characterizing crown size and shape. The results showed that increasing stem density decreased Scots pine crown size. TLS provided more detailed attributes for crown characterization compared to traditional field measurements. Furthermore, decreasing stem density increased SAHMC and strong relationships (Spearman correlations >0.5) were found between SAHMC and crown and stem size as well as stem growth. Thus, this study provided quantitative and more comprehensive characterization of Scots pine crowns and their growth potential.
An mRNA silencing mechanism reliant on the cooperation between REGE-1/Regnase-1 and RLE-1/Roquin-1
Authors: Sobańska Daria , Komur Alicja A , Chabowska-Kita Agnieszka , Gumna Julita , Kumari Pooja , Pachulska-Wieczorek Katarzyna , Ciosk Rafal 
Published: December 2021

ABSTRACTRegnase-1 is an evolutionarily conserved endoribonuclease, degrading diverse mRNAs important, among others, for immune homeostasis, development, and cancer. There are two competing models of Regnase-1 mediated mRNA silencing. One model postulates that Regnase-1 works together with another RNA-binding protein, Roquin-1. The other model proposes that the two proteins function separately. Studying the C. elegans Regnase-1 ortholog, REGE-1, we have uncovered a functional relationship between REGE-1 and the nematode counterpart of Roquin-1, RLE-1. While REGE-1 and RLE-1 associate with mRNA independently of each other, both proteins are essential for mRNA silencing. Intriguingly, the functional interdependence between REGE-1 and RLE-1 is reminiscent of the proposed cooperation between mammalian Regnase-1 and Roquin-1, which may underlie a prototypic silencing mechanism involving both proteins.
Water droplet-in-oil digestion method for single-cell proteomics
Authors: Masuda Takeshi , Inamori Yuma , Furukawa Arisu , Momosaki Kazuki , Chang Chih-Hsiang , Kobayashi Daiki , Ohguchi Hiroto , Kawano Yawara , Ito Shingo , Araki Norie , Ong Shao-En , Ohtsuki Sumio 
Published: December 2021

AbstractRecent advances in single-cell proteomics highlight the promise of sensitive analyses in limited cell populations. However, technical challenges remain for sample recovery, throughput, and versatility. Here, we first report a water droplet-in-oil digestion (WinO) method based on carboxyl-coated beads and phase transfer surfactants for proteomic analysis using limited sample amounts. This method was developed to minimize the contact area between the sample solution and the container to reduce the loss of proteins and peptides by adsorption. This method increased protein and peptide recovery 10-fold as well as the number of quantified transmembrane proteins compared to an in-solution digestion (ISD) method. The proteome profiles obtained from 100 cells using the WinO method highly correlated with those from 10000 cells using the ISD method. We successfully applied the WinO method to single-cell proteomics and quantified 462 proteins. Using the WinO method, samples can be easily prepared in a multi-well plate, making it a widely applicable and suitable method for single-cell proteomics.
A mutation associated with Charcot-Marie-Tooth disease enhances the formation of stable dynamin 2 complexes in cells
Authors: Hedde Per Niklas , Barylko Barbara , Chiu Chi-Li , Albanesi Joseph P. , Jameson David M. , James Nicholas G. 
Published: December 2021

AbstractMutations in dynamin 2 (DNM2) have been associated with two distinct motor disorders, Charcot-Marie-Tooth neuropathies (CMT) and centronuclear myopathy (CNM). The majority of these mutations are clustered in the pleckstrin homology domain (PHD) which engage in intramolecular interactions that suppress dynamin self-assembly and GTPase activation. CNM mutations in the PHD interferes with these intramolecular interactions, thereby blocking the formation of the auto-inhibited state. CMT mutations are located primarily on the opposite surface of the PHD, which is specialized for lipid PIP2 binding. It has been speculated that the distinct locations and interactions of residues mutated in CMT and CNM explain why each set of mutations cause either one disease or the other, despite their close proximity within the PHD sequence. We show that at least one CMT-causing mutant, lacking residues 555DEE557 (ΔDEE), displays this inability to undergo auto-inhibition as observed in CNM-linked mutants. This ΔDEE deletion mutant induces the formation of abnormally large cytoplasmic inclusions similar to those observed for CNM-linked mutant R369W. We also found substantially reduced migration from the membrane of the ΔDEE deletion mutant. These findings call into question the molecular mechanism currently believed to underlie the absence of pathogenic overlap between DNM2-dependent CMT and CNM.
Coevolution of the olfactory organ and its receptor repertoire in ray-finned fishes
Authors: Policarpo Maxime , Bemis Katherine E , Laurenti Patrick , Legendre Laurent , Sandoz Jean-Christophe , Rétaux Sylvie , Casane Didier 
Published: December 2021

AbstractRay-finned fishes (Actinopterygii) perceive their environment through a range of sensory modalities, including olfaction 1,2. Anatomical diversity of the olfactory organ suggests that olfaction is differentially important among species 1,3,4. To explore this topic, we studied the evolutionary dynamics of the four main gene families (OR, TAAR, ORA/VR1 and OlfC/VR2) 5 coding for olfactory receptors in 185 species of ray-finned fishes. The large variation in the number of functional genes, between 28 in the Ocean Sunfish Mola mola and 1317 in the Reedfish Erpetoichthys calabaricus, is the result of parallel expansions and contractions of the four main gene families. Several ancient and independent simplifications of the olfactory organ are associated with massive gene losses. In contrast, polypteriforms, which have a unique and complex olfactory organ, have almost twice as many olfactory receptor genes as any other ray-finned fish. These observations suggest a functional link between morphology of the olfactory organ and richness of the olfactory receptor repertoire. Further, our results demonstrate that the genomic underpinning of olfaction in ray-finned fishes is heterogeneous and presents a dynamic pattern of evolutionary expansions, simplifications and reacquisitions.
Endoplasmic reticulum oxidoreductin (ERO) provides resilience against reductive stress and hypoxic conditions by mediating luminal redox dynamics
Authors: Ugalde José Manuel , Aller Isabel , Kudrjasova Lika , Schmidt Romy R. , Schlößer Michelle , Homagk Maria , Fuchs Philippe , Lichtenauer Sophie , Schwarzländer Markus , Müller-Schüssele Stefanie J. , Meyer Andreas J. 
Published: December 2021

ABSTRACTOxidative protein folding in the endoplasmic reticulum (ER) depends on the coordinated action of protein disulfide isomerases and ER oxidoreductins (EROs). Strict dependence of ERO activity on molecular oxygen as the final electron acceptor implies that oxidative protein folding and other ER processes are severely compromised under hypoxia. While many key players involved in oxidative protein folding are known, our understanding of how redox homeostasis in the ER is maintained and how EROs, the Cys residues of nascent proteins, and the luminal glutathione redox buffer interact is limited. Here, we isolated viableero1 ero2double mutants largely deficient in ERO activity, which rendered the mutants highly sensitive to reductive stress and hypoxia. To elucidate the specific redox dynamics in the ER lumenin vivo, we expressed the glutathione redox potential (EGSH) sensor Grx1-roGFP2iL-HDEL with a midpoint potential of -240 mV in the ER of Arabidopsis plants. We foundEGSHvalues of -241 mV in wild-type plants, which is less oxidizing than previously estimated. In theero1 ero2mutants, luminalEGSHwas reduced further to -253 mV. Recovery to reductive ER stress, as induced by acute exposure to dithiothreitol, was delayed inero1 ero2mutants. The characteristic signature ofEGSHdynamics in the ER lumen triggered by hypoxia was affected in theero1 ero2mutant reflecting a disrupted balance of reductive and oxidizing inputs, including nascent polypeptides and glutathione entry. The ER redox dynamics can now be dissectedin vivo, revealing a central role of EROs as major redox integrators to promote luminal redox homeostasis.One sentence summaryDynamic monitoring the ER luminal glutathione redox potential highlights the role of EROs in defining redox conditions and the interplay between different redox inputs during hypoxia and reductive stress.
Salubrinal induces fetal hemoglobin expression via the stress-signaling pathway in human sickle erythroid progenitors and sickle cell disease mice
Authors: Lopez Nicole H. , Li Biaoru , Palani Chithra , Siddaramappa Umapathy , Takezaki Mayuko , Xu Hongyan , Zhi Wenbo , Pace Betty S. 
Published: December 2021

SUMMARYSickle cell disease (SCD) is an inherited blood disorder caused by a mutation in the HBB gene leading to hemoglobin S production and polymerization under hypoxia conditions leading to vaso-occlusion, chronic hemolysis, and progressive organ damage. This disease affects ∼100,000 people in the United States and millions worldwide. An effective therapy for SCD is fetal hemoglobin (HbF) induction by pharmacologic agents such as hydroxyurea, the only Food and Drug Administration-approved drug for this purpose. Therefore, the goal of our study was to determine whether salubrinal (SAL), a selective protein phosphatase 1 inhibitor, induces HbF expression through the stress-signaling pathway by activation of p-eIF2α and ATF4 trans-activation in the γ-globin gene promoter. Sickle erythroid progenitors treated with 24µM SAL increased F-cells levels 1.4-fold (p=0.021) and produced an 80% decrease in reactive oxygen species. Western blot analysis showed SAL enhanced HbF protein by 1.6-fold (p=0.0441), along with dose-dependent increases of p-eIF2α and ATF4 levels. Subsequent treatment of SCD mice by a single intraperitoneal injection of SAL (5mg/kg) produced peak plasma concentrations at 6 hours. Chronic treatments of SCD mice with SAL mediated a 2.3-fold increase in F-cells (p=0.0013) and decreased sickle erythrocytes supporting in vivo HbF induction.
Genetic evidence that uptake of the fluorescent analog 2NBDG occurs independently of known glucose transporters
Authors: D’Souza Lucas J. , Wright Stephen H. , Bhattacharya Deepta 
Published: December 2021

AbstractThe fluorescent derivative of glucose, 2-Deoxy-2-[(7-nitro-2,1,3-benzoxadiazol-4-yl)-amino]-D-glucose (2NBDG), is a widely used surrogate reagent to visualize glucose uptake in live cells at single cell resolution. Using a model of CRISPR-Cas9 gene editing in 5TGM1 myeloma cells, we demonstrate that ablation of the glucose transporter gene Slc2a1 abrogates radioactive glucose uptake but has no effect on the magnitude or kinetics of 2NBDG import. Extracellular 2NBDG, but not NBD-fructose was transported by plasma cells into the cytoplasm suggesting specific activity that is unlinked to glucose import and that of chemically similar compounds. RNA-Seq analysis of primary plasma cells and the 5TGM1 myeloma cell line revealed expression of other candidate glucose transporters. Yet, deletion of these transporters individually or in combination with one another also had no impact on 2NBDG uptake. Ablation of the genes in the Slc29 and Slc35 families of nucleoside and nucleoside sugar transporters as well as the ATP-binding cassette (ABC) transporter family also failed to impact 2NBDG import. Thus, cellular uptake of 2NBDG is promoted by an unknown mechanism and is not a faithful indicator of glucose transport.
Inactivation of SARS-CoV-2 and influenza A virus by spraying hypochlorous acid solution and hydrogen peroxide solution in the form of Dry Fog
Authors: Urushidani Masahiro , Kawayoshi Akira , Kotaki Tomohiro , Saeki Keiichi , Mori Yasuko , Kameoka Masanori 
Published: December 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is transmitted by droplet and contact infection. SARS-CoV-2 that adheres to environmental surfaces remains infectious for several days. We herein attempted to inactivate SARS-CoV-2 and influenza A virus adhering to an environmental surface by spraying aerosolized hypochlorous acid solution and hydrogen peroxide solution in the form of Dry Fog (fog that does not wet objects even if touched). SARS-CoV-2 and influenza virus were dried on plastic plates and placed into a test chamber for inactivation by the Dry Fog spraying of disinfectants. The results obtained showed that Dry Fog spraying inactivated SARS-CoV-2 and influenza A virus in time- and exposed disinfectant amount-dependent manners. SARS-CoV-2 was more resistant to the virucidal effects of aerosolized hypochlorous acid solution and hydrogen peroxide solution than influenza A virus; therefore, higher concentrations of spray solutions were required to inactivate SARS-CoV-2 than influenza A virus. The present results provide important information for the development of a strategy that inactivates SARS-CoV-2 and influenza A virus on environmental surfaces by spatial spraying.
Absolute Scaling of Single-Cell Transcriptomes Reveals Pervasive Hypertranscription in Adult Stem and Progenitor Cells
Authors: Kim Yun-Kyo , Ramalho-Santos Miguel 
Published: December 2021

ABSTRACTHypertranscription facilitates biosynthetically demanding cellular state transitions through global upregulation of the nascent transcriptome. Despite its potential widespread relevance, documented examples of hypertranscription remain few and limited predominantly to early development. This limitation is in large part due to the fact that modern sequencing approaches, including single-cell RNA sequencing (scRNA-seq), generally assume similar levels of transcriptional output per cell. Here, we use molecule counting and spike-in normalization to develop absolute scaling of single-cell RNA sequencing data. Absolute scaling enables an estimation of total transcript abundances per cell, which we validate in embryonic stem cell (ESC) and germline data and apply to adult mouse organs at steady-state or during regeneration. The results reveal a remarkable dynamic range in transcriptional output among adult cell types. We find that many different multipotent stem and progenitor cell populations are in a state of hypertranscription, including in the hematopoietic system, intestine and skin. Hypertranscription marks cells with multilineage potential in adult organs, is redeployed in conditions of tissue injury, and can precede by 1-2 days bursts of proliferation during regeneration. In addition to the association between hypertranscription and the stem/progenitor cell state, we dissect the relationship between transcriptional output and cell cycle, ploidy and secretory behavior. Our analyses reveal a common set of molecular pathways associated with hypertranscription across adult organs, including chromatin remodeling, DNA repair, ribosome biogenesis and translation. Our findings introduce an approach towards maximizing single-cell RNA-seq profiling. By applying this methodology across a diverse collection of cell states and contexts, we put forth hypertranscription as a general and dynamic cellular program that is pervasively employed during development, organ maintenance and regeneration.SUMMARY STATEMENTAbsolute scaling of single-cell transcriptomic data reveals highly dynamic global levels of transcription across adult cell lineages
Rapid generation of ventral spinal cord-like astrocytes from human iPSCs for modeling non-cell autonomous mechanisms of lower motor neuron disease
Authors: Soubannier Vincent , Chaineau Mathilde , Gursu Lale , Haghi Ghazal , Franco Flores Anna Kristyna , Rouleau Guy , Durcan Thomas M , Stifani Stefano 
Published: December 2021

AbstractAstrocytes play important roles in the function and survival of neuronal cells. Dysfunctions of astrocytes are associated with numerous disorders and diseases of the nervous system, including motor neuron diseases such as amyotrophic lateral sclerosis (ALS). Human induced pluripotent stem cell (iPSC)-based approaches are becoming increasingly important for the study of the mechanisms underlying the involvement of astrocytes in non-cell autonomous processes of motor neuron degeneration in ALS. These studies must account for the molecular and functional diversity among astrocytes in different regions of the brain and spinal cord. It is essential that the most pathologically-relevant astrocyte preparations are used when investigating non-cell autonomous mechanisms of either upper or lower motor neuron degeneration in ALS. In this context, the main aim of this study was to establish conditions enabling rapid and robust generation of physiologically-relevant ventral spinal cord-like astrocytes that would provide an enhanced experimental model for the study of lower motor neuron degeneration in ALS. Neural progenitor cells with validated caudal and ventral features were derived from human iPSCs and differentiated into astrocytes, which were then characterized by examining morphology, markers of ventral spinal cord astrocytes, spontaneous and induced calcium transients, and astrogliosis markers. Efficient and streamlined generation of human iPSC-derived astrocytes with molecular and biological properties similar to physiological astrocytes in the ventral spinal cord was achieved. These induced astrocytes express markers of mature ventral spinal cord astrocytes, exhibit spontaneous and ATP-induced calcium transients, and lack signs of overt activation. Human iPSC- derived astrocytes with ventral spinal features offer advantages over more generic astrocyte preparations for the study of both ventral spinal cord astrocyte biology and the involvement of astrocytes in mechanisms of lower motor neuron degeneration in ALS.
Transcription Factor RFX3 Stabilizes Mammary Basal Cell Identity
Authors: Tross Erica M. , de Caestecker Christian R. , Lau Ken S. , Macara Ian G. 
Published: December 2021

ABSTRACTThe myoepithelial cell compartment of the murine postnatal mammary gland is generated from basal cap cells in the terminal end bud and maintained by self-renewal. Transdifferentiation to the luminal lineage does not normally occur but can be induced by DNA damage, luminal cell death or transplantation into a recipient mammary fat pad. Myoepithelial cells cultivated in vitro can also transdifferentiate towards the luminal lineage. Little is known about the molecular mechanisms and gene regulatory networks underlying this plasticity. Using a transgenic mouse (Tg11.5kb-GFP) that marks cap cells with GFP, we discovered that mature myoepithelial cells placed in culture begin to express GFP within ∼24 hrs and later express the Keratin 8 (K8) luminal marker. Cell tracking showed that most K8+ cells arose from GFP+ cells, suggesting that myoepithelial cells de-differentiate towards a progenitor state before changing lineage. Differential gene expression analysis, comparing pure GFP+ cap cells with mature myoepithelial cells, identified multiple transcription factors that iRegulon predicted might regulate the myoepithelial to cap cell transition. Knockout of one of these genes, Regulatory Factor 3 (Rfx3), significantly reduced the population of GFP+ cells and increased differentiation to the K8+ luminal lineage. Rfx3 knockout also reduced mammosphere growth and mammary gland regeneration efficiency in a transplantation assay, but had no effect on proliferation in vitro. Together, these data support a key role for Rfx3 in the stabilization of the mammary basal cell lineages.