bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential integration of activation and repression signals in a multi-enhancer system
Authors: Whitney Peter H. , Shrestha Bikhyat , Xiong Jiahan , Zhang Tom , Rushlow Christine A. 
Published: May 2022

ABSTRACTTranscription in the early Drosophila blastoderm is coordinated by the collective action of hundreds of enhancers. Many genes are controlled by so-called “shadow enhancers,” which provide resilience to environment or genetic insult, allowing the embryo to robustly generate a precise transcriptional pattern. Emerging evidence suggests that many shadow enhancer pairs do not drive identical expression patterns, however the biological significance of this remains unclear. In this study we characterize the shadow enhancer pair controlling the gene short gastrulation (sog). We removed either the intronic proximal enhancer or the upstream distal enhancer, and monitored sog transcriptional kinetics. Notably, each enhancer differs in sog spatial expression, timing of activation, and RNA Polymerase II loading rates. Additionally, modeling of individual enhancer activities demonstrates that these enhancers integrate activation and repression signals differently. While activation is due to the sum of the two enhancer activities, repression appears to depend on synergistic effects between enhancers. Finally, we examined the downstream signaling consequences resulting from the loss of either enhancer, and found changes in tissue patterning that are well explained by the differences in transcriptional kinetics measured.SUMMARY STATEMENTNon-intuitive shadow enhancer synergies are revealed by measuring transcriptional kinetics at the endogenous short gastrulation locus, giving rise to distinct patterning consequences in the dorsal ectoderm of Drosophila embryos.
Development and utility of a PAK1-selective degrader
Authors: Chow Hoi-Yee , Karchugina Sofiia , Groendyke Brian J. , Toenjes Sean , Hatcher John , Donovan Katherine A. , Fischer Eric S. , Abalakov Gleb , Faezov Bulat , Dunbrack Roland , Gray Nathanael S. , Chernoff Jonathan 
Published: May 2022

AbstractAmplification and/or overexpression of the PAK1 gene is common in several malignancies, and inhibition of PAK1 by small molecules has been shown to impede the growth and survival of such cells. Potent inhibitors of PAK1 and its close relatives, PAK2, and PAK3, have been described, but clinical development has been hindered by recent findings that PAK2 function is required for normal cardiovascular function in adult mice. A unique allosteric PAK1-selective inhibitor, NVS-PAK1-1, provides a potential path forward, but has relatively modest potency in cells. Here, we report the development of BJG-05-039, a PAK1-seletive degrader consisting of the allosteric PAK1 inhibitor NVS-PAK1-1 conjugated to lenalidomide, a recruiter of the E3 ubiquitin ligase substrate adaptor Cereblon (CRBN). BJG-05-039 induced degradation of PAK1, but not PAK2, and displayed enhanced anti-proliferative effects relative to its parent compound in PAK1-dependent, but not PAK2-dependent, cell lines. Notably, BJG-05-039 promoted sustained PAK1 degradation and inhibition of downstream signaling effects at ten-fold lower dosage than NVS-PAK1-1. Our findings suggest that selective PAK1 degradation may confer more potent pharmacological effects compared with catalytic inhibition and highlight the potential advantages of PAK1-targeted degradation.
No circadian clock-gene circuit in the generation of cellular bioluminescence rhythm of CaMV35S::PtRLUC in duckweed
Authors: Watanabe Emiri , Muranaka Tomoaki , Nakamura Shunji , Isoda Minako , Ito Shogo , Oyama Tokitaka 
Published: May 2022

AbstractPhysiological circadian rhythms are coordinated in the plant body in an orderly manner. The coordination of time information has been studied from the aspects of cell–cell local coupling and long-distance communication between tissues. These studies were based on the idea that the behavior of the clock gene circuit represents the physiological rhythms. Here we report the cellular circadian rhythm of a bioluminescence reporter which is not governed by the clock gene circuit in the expressing cells. Using a dual-color bioluminescence monitoring system in Lemna minor transfected with the AtCCA1::LUC+ and CaMV35S::PtRLUC reporters, cellular bioluminescence rhythms with different free-running periods (FRPs) were detected in the same cells. Co-transfection experiments with the two reporters and a clock gene overexpressing effector revealed that the circadian properties of the AtCCA1::LUC+ rhythm, but not those of the CaMV35S::PtRLUC rhythm, were altered in the cells with a dysfunctional clock gene circuit. This indicates that the AtCCA1::LUC+ rhythm is a direct output of the cellular circadian clock while the CaMV35S::PtRLUC rhythm is not. After plasmolysis, the CaMV35S::PtRLUC rhythm disappeared while the AtCCA1::LUC+ rhythm persisted. The plant circadian system consists of both cell-autonomous rhythms and non-cell-autonomous rhythms that are unaffected by the cellular clock.
Signal Peptide Efficiency: from High-throughput Data to Prediction and Explanation
Authors: Grasso Stefano , Dabene Valentina , Hendriks Margriet M.W.B. , Zwartjens Priscilla , Pellaux René , Held Martin , Panke Sven , van Dijl Jan Maarten , Meyer Andreas , van Rij Tjeerd 
Published: May 2022

ABSTRACTThe passage of proteins across biological membranes via the general secretory (Sec) pathway is a universally conserved process with critical functions in cell physiology and important industrial applications. Proteins are directed into the Sec pathway by a signal peptide at their N-terminus. Estimating the impact of physicochemical signal peptide features on protein secretion levels has not been achieved so far, partially due to the extreme sequence variability of signal peptides. To elucidate relevant features of the signal peptide sequence that influence secretion efficiency, an evaluation of ~12,000 different designed signal peptides was performed using a novel miniaturized high-throughput assay. The results were used to train a machine learning model, and a post-hoc explanation of the model is provided. By describing each signal peptide with a selection of 156 physicochemical features, it is now possible to both quantify feature importance and predict the protein secretion levels directed by each signal peptide. Our analyses allow the detection and explanation of the relevant signal peptide features influencing the efficiency of protein secretion, generating a versatile tool for the in silico evaluation of signal peptides.
Area of Habitat maps for the world’s terrestrial birds and mammals
Authors: Lumbierres Maria , Dahal Prabhat Raj , Soria Carmen D. , Di Marco Moreno , Butchart Stuart H. M. , Donald Paul F. , Rondinini Carlo 
Published: May 2022

AbstractArea of Habitat (AOH) is ‘the habitat available to a species, that is, habitat within its range’. It complements a geographic range map for a species by showing potential occupancy and reducing commission errors. AOH maps are produced by subtracting areas considered unsuitable for the species from their range map, using information on each species’ associations with habitat and elevation. We present AOH maps for 5,481 terrestrial mammal and 10,651 terrestrial bird species (including 1,816 migratory bird species for which we present separate maps for the resident, breeding and non-breeding areas). Our maps have a resolution of 100 m. On average, AOH covered 66±28% of the range maps for mammals and 64±27% for birds. The AOH maps were validated independently, following a novel two-step methodology: a modelling approach to identify outliers and a species-level approach based on point localities. We used AOH maps to produce global maps of the species richness of mammals, birds, globally threatened mammals and globally threatened birds.
Post-transcriptional regulatory feedback encodes JAK-STAT signal memory of interferon stimulation
Authors: Kalliara Eirini , Kardyńska Malgorzata , Bagnall James , Spiller David G. , Muller Werner , Ruckerl Dominik , Biswas Subhra K , Śmieja Jarosław , Paszek Pawel 
Published: May 2022

AbstractImmune cells fine tune their responses to infection and inflammatory cues. Here, using live-cell confocal microscopy and mathematical modelling, we investigate interferon induced JAK-STAT signalling in innate immune macrophages. We demonstrate that transient exposure to IFN-γ stimulation induces a long-term desensitisation of STAT1 signalling and gene expression responses, revealing a dose- and time-dependent regulatory feedback that controls JAK-STAT responses upon re-exposure to stimulus. We show that IFN-α/β1 elicit different level of desensitisation from IFN-γ, where cells refractory to IFN-α/β1 are sensitive to IFN-γ, but notvice versa. We experimentally demonstrate that the underlying feedback mechanism involves regulation of STAT1 phosphorylation but is independent of new mRNA synthesis and cognate receptor expression. A new feedback model of the protein tyrosine phosphatase activity recapitulates experimental data and demonstrates JAK-STAT network’s ability to decode relative changes of dose, timing, and type of temporal interferon stimulation. These findings reveal that STAT desensitisation renders cells with signalling memory of type I and II interferon stimulation, which in the future may improve administration of interferon therapy.
Assessment of 3D MINFLUX data for quantitative structural biology in cells revisited
Authors: Gwosch Klaus C. , Balzarotti Francisco , Pape Jasmin K. , Hoess Philipp , Ellenberg Jan , Ries Jonas , Matti Ulf , Schmidt Roman , Sahl Steffen J. , Hell Stefan W. 
Published: May 2022

AbstractPrakash and Curd provide a re-analysis1 of individual datasets taken from our report2 demonstrating MINFLUX 3D imaging in cells. Their evaluation confirms the unique localization precision provided by MINFLUX2,3 featuring a standard deviation of σ = 1-3 nm. We appreciate their confirmation and also welcome the opportunity to clarify their remaining points. The hitherto almost unconceivable 3D localization precision attained by MINFLUX is likely to hold the key to an all-optical dynamical structural biology.
CvkR, a novel MerR-type transcriptional regulator, is a repressor of class 2 type V-K CRISPR-associated transposase systems
Authors: Ziemann Marcus , Reimann Viktoria , Liang Yajing , Shi Yue , Xie Yuman , Li Hui , Zhu Tao , Lu Xuefeng , Hess Wolfgang R. 
Published: May 2022

AbstractCRISPR-associated transposons (CASTs) exist in different groups of bacteria, including certain cyanobacteria, which contain type V-K CAST systems. These systems contain genes encoding Tn7-like transposase subunits and a divergent number of cargo genes. How the activity of these systems is controlled in situ has remained largely unknown but possibly regulatory genes within these elements are prime candidates. Deletion of the respective regulator gene alr3614 in the cyanobacterium Anabaena (Nostoc) sp. PCC 7120 led to the overexpression of CRISPR tracrRNA, precursor crRNAs and mRNAs encoding the Cas12k effector protein (all3613) and Tn7-like transposase subunits. Upon complementation, these same genes were repressed again. DNase I footprinting and electrophoretic mobility shift assays verified the direct interaction between Alr3614 and the promoter of cas12k and identified a widely conserved binding motif. Structural analysis of Alr3614 at 1.5 Å resolution revealed that it belongs to the MerR-type transcription factor family but with distinct dimerization and effector-binding domains. This protein assembles into a homodimer interacting with DNA through its N-terminal winged helix-turn-helix (wHTH) domain and binds an effector molecule through a C-terminal α-helical domain lacking a conserved cysteine. These results identify Alr3614 as a transcriptional repressor of the CAST system in Anabaena sp. PCC 7120. We suggest naming this family of repressors CvkR for Cas V-K repressors, which are at the core of a widely conserved regulatory mechanism that controls type V-K CAST systems.
Vitamin K-dependent γ-carboxylation regulates calcium flux and adaptation to metabolic stress in β-cells
Authors: Lacombe Julie , Guo Kevin , Bonneau Jessica , Faubert Denis , Gioanni Florian , Vivoli Alexis , Muir Sarah M. , Hezzaz Soraya , Poitout Vincent , Ferron Mathieu 
Published: May 2022

SUMMARYVitamin K is a micronutrient necessary for the γ-carboxylation of glutamic acids. This post-translational modification occurs in the endoplasmic reticulum (ER) and affects secreted proteins. Clinical studies have recently implicated vitamin K in the pathophysiology of diabetes, but the underlying molecular mechanism remains unknown. Here, we show that mouse β-cells lacking γ-carboxylation fail to adapt their insulin secretion in the context of age-related insulin resistance or diet-induced β-cell stress. In human islets, γ-carboxylase expression positively correlates with improved insulin secretion in response to glucose. We identified Endoplasmic Reticulum Gla Protein (ERGP) as a novel γ-carboxylated ER-resident calcium-binding protein expressed in β-cells. Mechanistically, γ-carboxylation of ERGP protects cells against calcium overfilling by diminishing STIM1 and Orai1 interaction and restraining store-operated calcium entry. These results reveal a critical role for vitamin K-dependent γ-carboxylation in the regulation of calcium flux in β-cells and in their capacity to adapt to metabolic stress.
Porous marine snow differentially benefits chemotactic, motile, and non-motile bacteria
Authors: Borer Benedict , Zhang Irene , Baker Amy E. , O’Toole George A. , Babbin Andrew R. 
Published: May 2022

AbstractParticulate organic carbon settling through the marine water column is a key process that regulates global climate by sequestering atmospheric carbon. The initial colonization of marine particles by heterotrophic bacteria represents the first step in recycling this carbon back to inorganic constituents – setting the magnitude of vertical carbon transport to the abyss. Here, we demonstrate experimentally that bacterial motility is required for particle colonization and chemotaxis specifically benefits at higher settling velocities. We further explore the role of particle microstructure on the colonization efficiency of bacteria with different motility traits. We highlight that non-motile cells benefit disproportionally from the porous microstructure and are relatively enriched in the particle wake due to the efficient particle colonization of chemotactic and motile cells. Our results imply that although the chemotactic and motile bacteria benefit from the high nutrient availability when colonizing the particles, scavenging of these cells benefits the often oligotrophic, non-motile cells common among the planktonic community.Significance statementBacteria in the ocean rely on ephemeral nutrient patches from sinking marine particles, but attaching to these structures is challenging as particle settling rates often exceed bacterial swimming velocities and the numerically dominant marine bacteria are non-motile – posing an interesting paradox about the prominence of particle foraging. Here, we quantify the importance of chemotaxis and motility for the efficient colonization of marine particles and find that although chemotaxis provides a clear advantage, motility is the basic requirement for particle colonization. We expand this analysis to consider highly heterogeneous particle structures and find a disproportionate benefit for non-motile cells by facilitating a direct encounter with the particle surface and enriching non-motile microbes in the nutrient-rich particle plume.
Aberrant association of chromatin with nuclear periphery induced by Rif1 leads to mitotic defect and cell death
Authors: Kanoh Yutaka , Matsumoto Seiji , Ueno Masaru , Hayano Motoshi , Kudo Satomi , Masai Hisao 
Published: May 2022

AbstractChromatin is compartmentalized in nuclei and its architecture and nuclear location may have impacts on chromatin events. Rif1, identified as a potent suppressor of hsk1-null mutation (defective in initiation of DNA replication) in fission yeast, recognizes G-quadruplex structures and inhibits origin firing in their 50∼100-kb vicinity, leading us to postulate that Rif1 may generate chromatin higher-order structures inhibitory for initiation. However, effects of Rif1 on chromatin localization in nuclei have not been known. We show here that overexpression of Rif1 causes growth inhibition and eventually cell death in fission yeast. Chromatin binding activities of Rif1, but not recruitment of phosphatase PP1, are required for growth inhibitory effect. Overexpression of a PP1 binding site mutant of Rif1 does not delay S-phase, but still causes cell death, indicating that cell death is caused not by S-phase problems but by issues in other phases of cell cycle, most likely M-phase. Indeed, Rif1 overexpression generates cells with unequally segregated chromosomes. Rif1 overexpression relocates chromatin near nuclear periphery in a manner dependent on its chromatin-binding ability, and this correlates with growth inhibition and cell death induction. Thus, regulated Rif1-mediated chromatin association with nuclear periphery is important for coordinated progression of S- and M-phases.
Status epilepticus induces chronic silencing of burster and dominance of regular firing neurons during sharp wave-ripples in the mouse subiculum
Authors: Lippmann Kristina , Klaft Zin-Juan , Salar Seda , Hollnagel Jan-Oliver , Maslarova Anna 
Published: May 2022

AbstractSharp wave-ripples (SWRs) are hippocampal oscillations associated with memory consolidation. The subiculum, as the hippocampal output structure, ensures that hippocampal memory representations are transferred correctly to the consolidating neocortical regions. Because patients with temporal lobe epilepsy often develop memory deficits, we hypothesized that epileptic networks may disrupt subicular SWRs. We therefore investigated the impact of experimentally induced status epilepticus (SE) on subicular SWRs and contributing pyramidal neurons using electrophysiological recordings in mouse hippocampal slices. Subicular SWRs expressed hyperexcitable features post-SE, including increased ripple and unit activity. While regular firing neurons normally remain silent during SWRs, selective disinhibition recruited more regular firing neurons for action potential generation during SWRs post-SE. By contrast, burster neurons generated fewer action potential bursts during SWRs post-SE. Furthermore, altered timing of postsynaptic and action potentials suggested distorted neuronal recruitment during SWRs. Distorted subicular SWRs may therefore impair information processing and memory consolidation in epilepsy.
Three-doses of BNT162b2 COVID-19 mRNA vaccine establishes long-lasting CD8+ T cell immunity in CLL and MDS patients
Authors: Amaya Hernandez Susana Patricia , Hersby Ditte Stampe , Munk Kamilla Kjærgaard , Tamhane Tripti , Trubach Darya , Tagliamonte Maria , Buonaguro Luigi , Gang Anne Ortved , Hadrup Sine Reker , Saini Sunil Kumar 
Published: May 2022

AbstractPatients with hematological malignancies are prioritized for COVID-19 vaccine due to their high risk for severe SARS-CoV-2 infection related disease and mortality. To understand T cell immunity, its long-term persistence, and correlation with antibody response, we evaluated the BNT162b2 COVID-19 mRNA vaccine-specific immune response in chronic lymphocytic leukemia (CLL) and myeloid dysplastic syndrome (MDS) patients. Longitudinal analysis of CD8+ T cells using DNA-barcoded peptide-MHC multimers covering the full SARS-CoV-2 Spike-protein (415 peptides) showed vaccine-specific T cell activation and persistence of memory T cells up to six months post-vaccination. Surprisingly, a higher frequency of vaccine-induced antigen-specific CD8+ T cell was observed in the patient group compared to a healthy donor group. Furthermore, and importantly, immunization with the second booster dose significantly increased the frequency of antigen-specific CD8+ T cells as well as the total number of T cell specificities. Altogether 59 BNT162b2 vaccine-derived immunogenic epitopes were identified, of which 23 established long-term CD8+ T cell memory response with a strong immunodominance for NYNYLYRLF (HLA-A24:02) and YLQPRTFLL (HLA-A02:01) epitopes. In summary, we mapped the vaccine-induced antigen-specific CD8+ T cells and showed a booster-specific activation and enrichment of memory T cells that could be important for long-term disease protection in this patient group.Key PointsCOVID-19 mRNA vaccine induced an early and persistent activation of antigen-specific CD8+ T cells in this patient group.Vaccination with a booster dose is required to maintain vaccine-specific CD8+ T cells.
Reversal of splicing infidelity is a pre-activation step in B cell differentiation
Authors: O’Grady Tina M. , Baddoo Melody , Flemington Samuel A. , Ungerleider Nate A. , Flemington Erik K. 
Published: May 2022

AbstractB cell activation and differentiation is central to the adaptive immune response. Changes in exon usage can have major impacts on cellular signaling and differentiation but have not been systematically explored in differentiating B cells. We analyzed exon usage and intron retention in RNA-Seq data from subsets of human B cells at various stages of differentiation, and in anin vitrolaboratory model of B cell activation and differentiation (Epstein Barr virus infection). Blood naïve B cells were found to have an unusual splicing profile, with unannotated splicing events in over 30% of expressed genes. Splicing changed substantially upon naïve B cell entry into secondary lymphoid tissue and before activation, involving significant increases in exon commitment and reductions in intron retention. These changes preferentially involved short introns with weak splice sites and were likely mediated by an overall increase in splicing efficiency induced by the lymphoid environment. The majority of transcripts affected by splicing changes showed restoration of encoded conserved protein domains and/or reduced targeting to the nonsense-mediated decay pathway. Affected genes were enriched in functionally important immune cell activation pathways such as antigen-mediated signaling, cell cycle control and mRNA processing and splicing. Functional observations from donor B cell subsets in progressive states of differentiation and from timecourse experiments using thein vitromodel suggest that these widespread changes in mRNA splicing play a role in preparing naïve B cells for the decisive step of antigen-mediated activation and differentiation.