bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shaping coral traits: plasticity more than filtering
Authors: Brambilla Viviana , Barbosa Miguel , Dehnert Inga , Madin Joshua , Maggioni Davide , Peddie Clare , Dornelas Maria 
Published: August 2021

AbstractThe structure of ecosystems is usually determined by the shape of the organisms that build it, commonly known as ecosystem engineers. Understanding to what extent plasticity and environmental filtering determine variation in ecosystem engineer physical structure is necessary to predict how ecosystem structure may change. Here, we explored coral survival and the plasticity of morphological traits that are critical for habitat provision in coral reefs. We conducted a reciprocal clonal transplant experiment in which branching corals from the genus Porites and Acropora were moved to and from a deep and a shallow site within a lagoon in the Maldives. Survival and trait analyses showed that transplant destination consistently induced the strongest changes, particularly among Acropora spp. The origin of the corals only marginally affected some of the traits. We also detected variation in the way individuals from the same species and site differentiate their shape, showing that traits linked to habitat provision are phenotypically plastic. The results suggest coral phenotypic plasticity plays a stronger role than environmental filtering, in determining zonation of coral morphologies, and consequently the habitats they provide for other taxa.
Isolation, ‘omics characterization and organotypic culture of alveolar type II pulmonary epithelial cells
Authors: Li Huaibiao , Schütte Moritz , Bober Magdalena , Kroll Torsten , Frappart Lucien , About Ghina Bou , Lin Yu-Chieh , Sorg Tania , Herault Yann , Wierling Christoph , Rinner Oliver , Lange Bodo MH , Ploubidou Aspasia 
Published: August 2021

SUMMARYThe alveolar type II (AT2) epithelial cell fraction includes the stem cells of the pulmonary alveoli, functioning in lung homeostasis and post-injury repair. AT2 cells have been characterized primarily in situ, in transgenic mouse models. We report a new methodology for their isolation, their “omics” characterization and stroma-cell-free organotypic culture. Our multi-omics analysis identified high expression of genes involved in oxidative phosphorylation and of AP-1 components, as well as new phosphorylation sites in AT2 biomarkers. Furthermore, we show that supplementation with KGF, FGF10 & HGF suffices for the in vitro proliferation of AT2 cells and formation of alveolar organoids, suggesting that AT2-based organotypic development depends on ligands of the c-Met and FGFR2 receptors. The reported methodology and in-depth molecular characterization provide new tools for the in vitro and in vivo functional analysis of pulmonary cells and of mouse models of lung disease.
Identification of Potential inhibitors for Hematopoietic Prostaglandin D2 Synthase: Computational Modeling and Molecular Dynamics Simulations
Authors: Beura Satyajit , Prabhakar Chetti 
Published: August 2021

AbstractTo design a new therapeutic agent for Hematopoietic Prostaglandin D2 synthase (hPGDS), a set of 60 molecules with different molecular scaffolds were (range of pIC50 values are from 8.301 to 3.932) considered to create a pharmacophore model. Further, identification of potential hPGDS inhibitors were carried out by using virtual screening with different databases (from 15,74,182 molecules). The Molecular screening was performed using different sequential methods right from Pharmacophore based virtual screening, molecular docking, MM-GBSAstudies, ADME property analysis and molecular dynamics simulations using Maestro11.9 software. Based on the best pharmacophore model (ADRR_1), the resultant set of 18,492 molecules were screened. The preliminarily screened molecules were subjected to molecular docking (PDB_ID: 2CVD) methods. A set of 27 molecules was screened from the resultant molecular docking outcomes (360 molecules) based on binding free energy (ΔGbind) and Lipinski’s rule of five. Out of 27 molecules, 4 were selected visual data analysis and further subjected to molecular dynamics (MD) simulation study. Outcomes of the present study conclude with three new proposed molecules (SP1, SP2 and SP10) which show a good range of interaction with human hPGDS enzyme in comparison to the marketed compounds i.e., HQL-79, TFC-007, HPGDS inhibitor I and TAS-204.
Stabilising microbial communities by looped mass transfer
Authors: Li Shuang , Abdulkadir Nafi’u , Schattenberg Florian , da Rocha Ulisses Nunes , Grimm Volker , Müller Susann , Liu Zishu 
Published: August 2021

AbstractCreating structurally and functionally stable microbiomes would be greatly beneficial to biotechnology and human health but so far has proven challenging. Here, we propose a looped mass transfer design that keeps microbiomes constant over long periods of time. The effluent of five parallel reactors that began with the same inoculum, was mixed in a reactor that represented a regional pool. Part of this pool was transferred back to the five reactors. Community dynamics were monitored and visualized by quantitative microbial flow cytometry and selected taxonomic sequencing of whole communities and sorted subcommunities. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism that led to the survival of subcommunities with zero netgrowth, especially at high mass transfer rates. The looped mass transfer approach promises to overcome notorious stochastic structural fluctuations in bioreactors and has the potential to design and stabilize communities that can perform desired functions.
Sensitivity to the slope of the amplitude spectrum is dependent on the spectral slopes of recently viewed environments: A visual adaptation study in modified reality
Authors: Richard Bruno , Shafto Patrick 
Published: August 2021

AbstractScenes contain many statistical regularities that could benefit visual processing if accounted for by the visual system. One such statistic is the orientation-averaged slope (α) of the amplitude spectrum of natural scenes. Human observers show different discrimination sensitivity to α: sensitivity is highest for α values between 1.0 and 1.2 and decreases as α is steepened or shallowed. The range of α for peak discrimination sensitivity is concordant with the average α of natural scenes, which may indicate that visual mechanisms are optimized to process information at α values commonly encountered in the environment. Here we explore the association between peak discrimination sensitivity and the most viewed αs in natural environments. Specifically, we verified whether discrimination sensitivity depends on the recently viewed environments. Observers were immersed, using a Head-Mounted Display, in an environment that was either unaltered or had its average α steepened or shallowed by 0.4. Discrimination thresholds were affected by the average shift in α, but this effect was most prominent following adaptation to a shallowed environment. We modeled these data with a Bayesian observer and explored whether a change in the prior or a change in the likelihood best explained the psychophysical effects. Change in discrimination thresholds following adaptation could be explained by a shift in the central tendency of the prior concordant with the shift of the environment, in addition to a change in the likelihood. Our findings suggest that expectations on the occurrence of α that result from a lifetime of exposure remain plastic and able to accommodate for the statistical structure of recently viewed environments.
Optimized Data-Independent Acquisition Approach for Proteomic Analysis at Single-Cell Level
Authors: Wang Yuefan , Lih Tung-Shing Mamie , Chen Lijun , Xu Yuanwei , Kuczler Morgan D. , Cao Liwei , Pienta Kenneth J. , Amend Sarah R. , Zhang Hui 
Published: August 2021

ABSTRACTSingle-cell proteomic analysis provides valuable insights into cellular heterogeneity allowing the characterization of the cellular microenvironment which is difficult to accomplish in bulk proteomic analysis. Currently, single-cell proteomic studies utilize data-dependent acquisition (DDA) mass spectrometry (MS) coupled with a TMT labelled carrier channel. Due to the extremely imbalanced MS signals among the carrier channel and other TMT reporter ions, the quantification is compromised. Thus, data-independent acquisition (DIA)-MS should be considered as an alternative approach towards single-cell proteomic study since it generates reproducible quantitative data. However, there are limited reports on the optimal workflow for DIA-MS-based single-cell analysis. Herein, we report an optimized DIA workflow for single-cell proteomics using Orbitrap Lumos Tribrid instrument. We utilized a breast cancer cell line (MDA-MB-231) and induced drug resistant polyaneuploid cancer cells (PACCs) to evaluate our established workflow. We found that a short LC gradient was preferable for peptides extracted from single cell level with less than 2 ng sample amount. The total number of co-searching peptide precursors was also critical for protein and peptide identifications at nano- and sub-nano-gram levels. Post-translationally modified peptides could be identified from a nano-gram level of peptides. Using the optimized workflow, up to 1,500 protein groups were identified from a single PACC corresponding to 0.2 ng of peptides. Furthermore, about 200 peptides with phosphorylation, acetylation, and ubiquitination were identified from global DIA analysis of 100 cisplatin resistant PACCs (20 ng). Finally, we used this optimized DIA approach to compare the whole proteome of MDA-MB-231 parental cells and induced PACCs at a single-cell level. We found the single-cell level comparison could reflect real protein expression changes and identify the protein copy number. Our results demonstrate that the optimized DIA pipeline can serve as a reliable quantitative tool for single-cell as well as sub-nano-gram proteomic analysis.
A Lentiviral Envelope Signal Sequence is a Tetherin Antagonizing Protein
Authors: Morrison James H. , Poeschla Eric M. 
Published: August 2021

ABSTRACTSignal sequences are N-terminal peptides, generally less than 30 amino acids in length, that direct translocation of proteins into the endoplasmic reticulum and secretory pathway. The envelope glycoprotein (Env) of the nonprimate lentivirus Feline immunodeficiency virus (FIV) contains the longest signal sequence of all eukaryotic, prokaryotic and viral proteins (175 amino acids). The reason is unknown. Tetherin is a dual membrane-anchored host protein that inhibits the release of enveloped viruses from cells. Primate lentiviruses have evolved three antagonists: the small accessory proteins Vpu and Nef, and in the case of HIV-2, Env. Here we identify the FIV Env signal sequence (Fess) as the FIV tetherin antagonist. A short deletion in the central portion of Fess had no effect on viral replication in the absence of tetherin but severely impaired virion budding in its presence. Fess is necessary and sufficient, acting as an autonomous accessory protein with the rest of Env dispensable. In contrast to primate lentivirus tetherin antagonists, it functions by stringently blocking the incorporation of this restriction factor into viral particles rather than by degrading it or downregulating it from the plasma membrane.
The active zone protein Clarinet regulates ATG-9 trafficking at synapses and presynaptic autophagy
Authors: Xuan Zhao , Yang Sisi , Hill Sarah E. , Clark Benjamin , Manning Laura , Colón-Ramos Daniel A. 
Published: August 2021

AbstractIn neurons, autophagy is temporally and spatially regulated to occur near presynaptic sites. How trafficking of autophagy proteins is regulated to support synaptic autophagy is not well understood. From forward genetic screens, we identify a role for the long isoform of the active zone protein Clarinet (CLA-1L) in regulating trafficking of autophagy protein ATG-9 at synapses, and presynaptic autophagy. ATG-9 is a transmembrane protein that undergoes activity-dependent exo-endocytosis at synapses, and mutations in CLA-1L result in abnormal accumulation of ATG-9 into clathrin-rich endocytic intermediates. CLA-1L extends from the active zone to the periactive zone, and genetically interacts with periactive zone proteins required for clathrin-dependent endocytosis. We find that CLA-1L is specifically required for sorting of ATG-9 at synapses, likely via endosome-mediated endocytosis, and for activity-dependent presynaptic autophagy. Our findings provide mechanistic insights into how active zone proteins regulate key steps of ATG-9 exo-endocytosis, a process that could couple the activity state of the neuron and autophagy.Highlights•The long isoform of the active zone protein Clarinet (CLA-1L) regulates ATG-9 trafficking at synapses•CLA-1L extends from the active zone to the periactive zone and cooperates with the periactive zone endocytic proteins EHS-1/EPS15 and ITSN-1/ intersectin 1 in ATG-9 trafficking during exo-endocytosis•Mutations in CLA-1L, or in clathrin-associated adaptor molecules, result in abnormal accumulation of ATG-9 into clathrin-rich endocytic intermediates•CLA-1L mutants which affect ATG-9 trafficking are also defective in activity-dependent presynaptic autophagy
Spatial and temporal expression of PORCN is highly dynamic in the developing mouse cochlea
Authors: Oliver Brianna L. , Young Caryl A. , Munnamalai Vidhya 
Published: August 2021

AbstractThe mammalian organ of Corti is a highly specialized sensory organ of the cochlea with a fine-grained pattern that is essential for auditory function. The sensory epithelium, the organ of Corti consists of a single row of inner hair cells and three rows of outer hair cells that are intercalated by support cells in a mosaic pattern. Previous studies show that the Wnt pathway regulates proliferation, promotes medial compartment formation in the cochlea, differentiation of the mechanosensory hair cells and axon guidance of Type II afferent neurons. WNT ligand expressions are highly dynamic throughout development but are insufficient to explain the roles of the Wnt pathway. We address a potential way for how WNTs specify the medial compartment by characterizing the expression of Porcupine (PORCN), an O-acyltransferase that is required for WNT secretion. We show PORCN expression across embryonic ages (E)12.5 - E14.5, E16.5, and postnatal day (P)1. Our results showed enriched PORCN in the medial domains during early stages of development, indicating that WNTs have a stronger influence on patterning of the medial compartment. PORCN was rapidly downregulated after E14.5, following the onset of sensory cell differentiation; residual expression remained in some hair cells and supporting cells. On E14.5 and E16.5, we also examined the spatial expression of Gsk3β, an inhibitor of canonical Wnt signaling to determine its potential role in radial patterning of the cochlea. Gsk3β was broadly expressed across the radial axis of the epithelium; therefore, unlikely to control WNT-mediated medial specification. In conclusion, the spatial expression of PORCN enriches WNT secretion from the medial domains of the cochlea to influence the specification of cell fates in the medial sensory domain.HighlightsWnt ligands are broadly expressed during cochlear development.PORCN expression is highly dynamic during early cochlear developmentPORCN becomes restricted to the medial domains along the longitudinal axis.Wnt medial specification is regulated at the level of WNT ligand secretion.
Extracellular Vesicles Facilitate Large-Scale, Homogenizing Dynamic Exchange of Proteins and RNA Among Cultured Chinese Hamster Ovary (CHO) and Human Cells
Authors: Belliveau Jessica , Papoutsakis Eleftherios T. 
Published: August 2021

AbstractCells in culture are viewed as unique individuals in a large population communicating through extracellular molecules and, more recently extracellular vesicles (EVs). Our data here paints a different picture: the homogenizing effect of large-scale exchange of cellular material through EVs. We show that Chinese Hamster Ovary (CHO) cells dynamically produce and uptake EVs, to exchange proteins and RNAs at large-scale. To visualize the dynamic production and cellular uptake of EVs, we used correlative confocal microscopy and scanning electron microscopy, as well as flow cytometry to interrogate labeled cells. We employed cells expressing fluorescent proteins (GFP, miRFP703) and tagged cells with protein and RNA dyes. Flow cytometry was used to quantify the exchange of cellular RNA between cells through EVs. This EV-mediated dynamic exchange observed in CHO cultures was also observed in cultures of the human CHRF-288-11 cell line and of primary human hematopoietic stem and progenitor cells. This study demonstrates an underappreciated native cell communication and protein/RNA exchange mechanism mediated by EVs spanning cell type and lines, suggesting the proximity of cells in normal and tumor tissues may also result in prolific cellular exchange. This exchange would be expected to homogenize the cell-population cytoplasm and dynamically regulate cell proliferation and cellular state.
Organ protection by caloric restriction depends on activation of the de novo NAD+ synthesis pathway
Authors: Späth Martin Richard , Hoyer-Allo Karla Johanna Ruth , Johnsen Marc , Höhne Martin , Lucas Christina , Brodesser Susanne , Lackmann Jan-Wilm , Kiefer Katharina , Koehler Felix Carlo , Schiller Petra , Kubacki Torsten , Grundmann Franziska , Benzing Thomas , Schermer Bernhard , Burst Volker , Müller Roman-Ulrich 
Published: August 2021

AbstractTherapeutic strategies to treat acute kidney injury (AKI) are lacking in clinical practice. Interestingly, preconditioning by hypoxia (HP) and caloric restriction (CR) is highly protective in rodent AKI models. However, the underlying molecular mechanisms of this process are unknown. A comparative transcriptome analysis of murine kidneys after HP and CR identified Kynureninase (KYNU) as a common downstream target. Using a newly generated KYNU-deficient mouse line, we show that KYNU strongly contributes to the protective effect of preconditioning. Metabolome, transcriptome and proteome analyses reveal the KYNU-dependent de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis pathway as necessary for CR-associated maintenance of NAD+ levels. Importantly, the impact of CR on the de novo NAD+ biosynthesis pathway can be recapitulated in humans. These findings provide a valuable insight into the molecular mechanisms mediating protection upon preconditioning and point towards the de novo branch of NAD+ biosynthesis as a conserved target in nephroprotection.
Acoustic light-sheet microscopy
Authors: Wunderl S. , Ishijima A. , Susaki E. A. , Xu Z. , Song H. , Zha H. , Azuma T. , Sakuma I. , Fukuoka H. , Okada E. , Ueda H. R. , Takagi S. , Nakagawa K. 
Published: August 2021

AbstractLight-sheet imaging of 3D objects with high spatial resolution remains an open challenge because of the trade-off between field-of-view (FOV) and axial resolution originating from the diffraction of light. We developed acoustic light-sheet microscopy (acoustic LSM), which actively manipulates the light propagation inside a large sample to obtain wide-field microscopic images deep inside a target. By accurately coupling a light-sheet illumination pulse into a planar acoustic pulse, the light-sheet can be continuously guided over large distances. We imaged a fluorescence-labeled transparent mouse brain for the FOVs of 19.3 × 12.4 mm2 and 9.7 × 5.9 mm2 with resolved microstructures and single cells deep inside the brain. Acoustic LSM creates new opportunities for the application of light-sheet in the field of industry to basic science.One Sentence SummaryAn acoustic-optical method overcomes a trade-off between field-of-view and axial resolution in light-sheet microscopy.
Screening of surface exposed lipoproteins of Leptospira involved in modulation of host innate immune response
Authors: Kumar Ajay , Varma Vivek P. , Faisal Syed M. 
Published: August 2021

AbstractLeptospira, a zoonotic pathogen is capable of causing both chronic and acute infection in susceptible host. Surface exposed lipoproteins play major role in modulating the host immune response by activating the innate cells like macrophages and DCs or evading complement attack and killing by phagocytes like neutrophils to favour pathogenesis and establish infection. In this study we screened some of surface exposed lipoproteins which are known to be involved in pathogenesis for their possible role in immune modulation (innate immune activation or evasion). Surface proteins of Len family (LenB, LenD, LenE), Lsa30, Loa22 and Lipl21 were purified in recombinant form and then tested for their ability to activate macrophages of different host (mouse, human and bovine). These proteins were tested for binding with complement regulators (FH, C4BP), host protease (plasminogen, PLG) and as nucleases to access their possible role in innate immune evasion. Our results show that of various proteins tested Loa22 induced strong innate activation and Lsa30 was least stimulatory as evident from production of pro-inflammatory cytokines (IL-6, TNF-a) and expression of surface markers (CD80, CD86, MHCII). All the tested proteins were able to bind to FH, C4BP and PLG, however Loa22 showed strong binding to PLG correlating to plasmin activity. All the proteins except Loa22 showed nuclease activity albeit with requirement of different metal ions. The nuclease activity of these proteins correlated to in vitro degradation of Neutrophil extracellular trap (NET). These results indicate that these surface proteins are involved in innate immune modulation and may play critical role in assisting the bacteria to invade and colonize the host tissue for persistent infection.
A nitrite-oxidizing bacterium constitutively consumes atmospheric hydrogen
Authors: Leung Pok Man , Daebeler Anne , Chiri Eleonora , Cordero Paul R. F. , Hanchapola Iresha , Gillett David L. , Schittenhelm Ralf B. , Daims Holger , Greening Chris 
Published: August 2021

AbstractChemolithoautotrophic nitrite-oxidizing bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidizer Nitrospira moscoviensis oxidizes hydrogen (H2) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [Km(app) = 32 nM]. Atmospheric H2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Respirometry analysis indicates the hydrogenase and nitrite oxidoreductase are bona fide components of the aerobic respiratory chain of N. moscoviensis, though they transfer electrons to distinct electron carriers in accord with the contrasting redox potentials of their substrates. Collectively, this study suggests atmospheric H2 oxidation enhances the growth and survival of NOB in amid variability of nitrite supply. These findings also extend the phenomenon of atmospheric H2 oxidation to a seventh phylum (Nitrospirota) and reveal unexpected new links between the global hydrogen and nitrogen cycles.