bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trans-segmental imaging in the spinal cord of behaving mice
Authors: Shekhtmeyster Pavel , Duarte Daniela , Carey Erin M. , Ngo Alexander , Gao Grace , Olmstead Jack A. , Nelson Nicholas A. , Nimmerjahn Axel 
Published: December 2021

AbstractSpinal cord circuits play crucial roles in transmitting and gating cutaneous somatosensory modalities, such as pain, but the underlying activity patterns within and across spinal segments in behaving mice have remained elusive. To enable such measurements, we developed a wearable widefield macroscope with a 7.9 mm2 field of view, subcellular lateral resolution, 2.7 mm working distance, and <10 g overall weight. We show that highly localized painful mechanical stimuli evoke widespread, coordinated astrocyte excitation across multiple spinal segments.
Fusion protein strategies for cryo-EM study of G protein-coupled receptors
Authors: Zhang Kaihua , Wu Hao , Hoppe Nicholas , Manglik Aashish , Cheng Yifan 
Published: December 2021

AbstractSingle particle cryogenic-electron microscopy (cryo-EM) is used extensively to determine structures of activated G protein-coupled receptors (GPCRs) in complex with G proteins or arrestins. However, applying it to GPCRs without signaling proteins remains challenging because most receptors lack structural features in their soluble domains to facilitate image alignment. In GPCR crystallography, inserting a fusion protein between transmembrane helices 5 and 6 is a highly successful strategy for crystallization. Although the similar strategy has the potential to broadly facilitate cryo-EM structure determination of GPCRs alone without signaling protein, the critical determinants that make this approach successful are not yet clear. Here, we address this shortcoming by exploring different fusion protein designs, which led to structures of antagonist bound A2A adenosine receptor at 3.4Å resolution and unliganded Smoothened at 3.7Å resolution. The fusion strategies explored here are likely applicable to cryo-EM interrogation of other GPCRs and small integral membrane proteins.
Astroglial CD38 regulates social memory and synapse formation through SPARCL1 in the medial prefrontal cortex
Authors: Hattori Tsuyoshi , Cherepanov Stanislav M , Sakaga Ryo , Roboon Jureepon , Nguyen Dinh Thi , Ishii Hiroshi , Takarada-Iemata Mika , Nishiuchi Takumi , Kannon Takayuki , Hosomichi Kazuyoshi , Tajima Atsushi , Yamamoto Yasuhiko , Okamoto Hiroshi , Sugawara Akira , Higashida Haruhiro , Hori Osamu 
Published: December 2021

AbstractSocial behavior is essential for the health, survival and reproduction of animals, yet the role of astrocytes in social behavior is largely unknown. CD38 is critical for social behaviors by regulating oxytocin release from hypothalamic neurons. On the other hand, CD38 is most abundantly expressed in astrocytes especially in the postnatal cortex, and is important for astroglial development. Here, we demonstrate that astroglial CD38 plays a pivotal role in the social behavior. Selective deletion of CD38 in postnatal astrocytes, but not in adult astrocytes, specifically impaired social memory without any other behavioral abnormalities. Morphological analysis revealed reductions in spine numbers, mature spines and excitatory synapse numbers in the pyramidal neurons of the medial prefrontal cortex (mPFC) due to deletion of astroglial CD38 in the postnatal brain. Astrocyte-conditioned medium (ACM) of CD38 KO astrocytes reduced synaptogenesis of cortical neurons by reducing extracellular SPARCL1, a synaptogenic protein. Finally, the release of SPARCL1 from astrocytes is regulated by CD38/cADPR/calcium signaling. Our data indicate that astroglial CD38 developmentally regulates social memory and neural circuit formation in the developing brain by promoting synaptogenesis through SPARCL1.
Reciprocal interactions between the gut microbiome and mammary tissue mast cells promote metastatic dissemination of HR+ breast tumors
Authors: Feng Tzu-Yu , Azar Francesca N. , Rosean Claire Buchta , McGinty Mitchell T. , Putelo Audrey M. , Koli Sree , Marino Natascia , German Rana , Podicheti Ram , Dreger Sally A. , Fowler Wesley J. , Greenfield Stephanie , Robinson Stephen D. , Rutkowski Melanie R. 
Published: December 2021

AbstractEstablishing commensal dysbiosis, defined as an inflammatory gut microbiome with low biodiversity, prior to breast tumor initiation, enhances early dissemination of hormone-receptor positive (HR+) mammary tumor cells. Here, we sought to define mammary tissue mediators of dysbiosis-induced tumor dissemination. We found that commensal dysbiosis increased both the frequency and profibrogenicity of mast cells in the mammary tissue, a phenotypic change that persisted after tumor implantation. Fibroblast activation and tissue remodeling associate with enhanced breast tumor metastasis. We employed pharmacological and adoptive transfer approaches to demonstrate that mammary tissue mast cells from dysbiotic animals enhances dissemination of HR+ tumor cells. Collagen levels in mammary tissues from HR+ breast cancer patients correlated with mast cell abundance, suggesting clinical relevance of mast cell-mediated fibroblast activation. Together, these data demonstrate that a gut-mast cell axis exists that induces fibroblast activation and orchestrates early dissemination of HR+ breast tumors.SignificanceOur study defines the mechanism by which an inflammatory gut microbiome facilitates HR+ breast tumor cell dissemination. We establish that gut commensal dysbiosis triggers mammary tissue mast cells to facilitate early metastatic dissemination. These findings highlight a novel gut microbiome-innate immune cell axis involved in negative breast cancer outcomes.
Time-resolved analysis of transcription kinetics in single live mammalian cells
Authors: Choi Hongyoung , Lee Byung Hun , Park Hye Yoon 
Published: December 2021

AbstractIn eukaryotic cells, RNA polymerase II synthesizes mRNA in three stages, initiation, elongation, and termination, and numerous factors determine how quickly a gene is transcribed to produce mRNA molecules through these steps. However, there are few techniques available to measure the rate of each step in living cells, which prevents a better understanding of transcriptional regulation. Here, we present a quantitative analysis method to extract kinetic rates of transcription from time-lapse imaging data of fluorescently labeled mRNA in live cells. Using embryonic fibroblasts cultured from two knock-in mouse models, we monitored transcription of β-actin and Arc mRNA labeled with MS2 and PP7 stem–loop systems, respectively. After inhibiting transcription initiation, we measured the elongation rate and the termination time by fitting the time trace of transcription intensity with a mathematical model function. We validated our results by comparing them with steady-state fluctuation analysis and stochastic simulations. This live-cell transcription analysis method will be useful for studying the regulation of elongation and termination steps and may provide insight into the diverse mechanisms of transcriptional processes.
Neural stemness unifies cell tumorigenicity and pluripotent differentiation potential
Authors: Zhang Min , Liu Yang , Shi Lihua , Fang Lei , Xu Liyang , Cao Ying 
Published: December 2021

AbstractTumorigenicity and pluripotent differentiation potential are kernel cell properties for tumorgenesis and embryogenesis. A growing number of studies have demonstrated that neural stemness is the source of the two cell properties, because neural stem cells and cancer cells share cell features and regulatory networks and neural stemness has an evolutionary advantage. However, it needs to validate whether neural stemness is a cell property that would unify tumorigenicity and pluripotent differentiation potential. SETDB1/Setdb1 is an epigenetic factor that is upregulated in cancer cells and promotes cancers, and correspondingly, is enriched in embryonic neural cells during vertebrate embryogenesis. We show that knockdown of SETDB1/Setdb1 led to neuronal differentiation in neural stem and cancer cells, concomitant with reduced tumorigenicity and pluripotent differentiation potential in these cells; whereas overexpression caused an opposite effect. On one hand, SETDB1 maintains a regulatory network comprised of proteins involved in developmental programs and basic cellular functional machineries, including epigenetic modifications (EZH2), ribosome biogenesis (RPS3), translation initiation (EIF4G), spliceosome assembly (SF3B1), etc., all of which play active roles in cancers. On the other, it represses transcription of genes promoting differentiation and cell cycle and growth arrest. Moreover, neural stemness, tumorigenicity and pluripotent differentiation potential were simultaneously enhanced during serial transplantation of cancer cells. Expression of proteins involved in developmental programs and basic cellular functional machineries, including SETDB1 and other proteins above, was gradually increased. In agreement with increased expression of spliceosome proteins, alternative splicing events also increased in tumor cells derived from later transplantations, suggesting that different machineries should work concertedly to match the status of high proliferation and pluripotent differentiation potential. The study presents the evidence that neural stemness unifies tumorigenicity and differentiation potential. Tumorigenesis represents a process of gradual loss of original cell identity and gain of neural stemness in somatic cells, which might be a distorted replay of neural induction during normal embryogenesis.
The Kishony Mega-Plate Experiment, a Markov Process
Authors: Kleinman Alan 
Published: December 2021

AbstractA correct understanding of the DNA evolution of drug resistance is critical in developing strategies for suppressing and preventing this process. The Kishony Mega-Plate Experiment demonstrates this important phenomenon that occurs in the practice of medicine, that of the evolution of drug-resistance. The evolutionary process which the bacteria in this experiment are doing is called a Markov Process or Markov Chain. Understanding this process enables clinicians and researchers to predict the evolution of drug-resistance and develop strategies to prevent this process. This paper will show how to apply the Markov Chain model of DNA evolution to the Kishony Mega-Plate Experiment and why the experiment behaves the way it does by contrasting the Jukes-Cantor model of DNA evolution (a stationary model) with a modification of the Jukes-Cantor model that makes it a non-stationary, non-equilibrium Markov Chain. The numerical behaviors of the stationary and non-stationary models are compared. What this analysis shows is that DNA evolution is a non-stationary, non-equilibrium process and that by using the correct non-stationary, non-equilibrium model that one can simulate and predict the behavior of real evolutionary examples and that these analytical tools can give the clinician guidance on how to use antimicrobial selection pressures for treating infectious diseases. This in turn can help reduce the numbers and costs of hospitalization for sepsis, pneumonia and other infectious diseases.
PERIOD phosphoclusters control temperature compensation of the Drosophila circadian clock
Authors: Joshi Radhika , Cai Yao D. , Xia Yongliang , Chiu Joanna C. , Emery Patrick 
Published: December 2021

AbstractTemperature compensation is a critical feature of circadian rhythms, but how it is achieved remains elusive. Here, we uncovered the important role played by the Drosophila PERIOD (PER) phosphodegron in temperature compensation. Using CRISPR-Cas9, we introduced a series of mutations that altered three Serines (S44, 45 and 47) belonging to the PER phosphodegron, the functional homolog of mammalian PER2’s S487 phosphodegron, which impacts temperature compensation. While all three Serine to Alanine substitutions lengthened period at all temperatures tested, temperature compensation was differentially affected. S44A and S45A substitutions caused decreased temperature compensation, while S47A resulted in overcompensation. These results thus reveal unexpected functional heterogeneity of phosphodegron residues in thermal compensation. Furthermore, mutations impairing phosphorylation of the pers phosphocluster decreased thermal compensation, consistent with its inhibitory role on S47 phosphorylation. Interestingly, the S47A substitution caused increased accumulation of hyper-phosphorylated PER at warmer temperatures. This finding was corroborated by cell culture assays in which S47A resulted in excessive temperature compensation of phosphorylation-dependent PER degradation. Thus, we show a novel role of the PER phosphodegron in temperature compensation through temperature-dependent modulation of the abundance of hyper-phosphorylated PER. Our work also reveals interesting mechanistic convergences and differences between mammalian and Drosophila temperature compensation of the circadian clock.Author summaryCircadian rhythms are critical adaptive mechanisms that enable most organisms to adjust their physiology and behavior to the changes that occur in their environment every day. Ambient temperature varies constantly, but interestingly molecular circadian pacemakers do not accelerate with increasing temperature, while most biochemical reactions are sensitive to temperature. This phenomenon of circadian temperature compensation is poorly understood. Using genome editing and transgenic approaches, we found that two phosphorylated motifs in the Drosophila PERIOD protein, which regulate stability, impact temperature compensation. Moreover, we observed that mutation of a key Serine residue controlling PER degradation, S47, affects the accumulation of phosphorylated PER in a temperature-dependent manner, and causes PER degradation kinetics to become overly protected from increased temperature. As a result, the circadian clock of S47 mutant flies is excessively temperature-compensated. Our work thus reveals an interesting mechanism that controls temperature compensation in Drosophila. Moreover, comparison with mammals reveal interesting similarities, but also important differences in how temperature compensation of the circadian clock is achieved.
Novel allosteric mechanism of dual p53/MDM2 and p53/MDM4 inhibition by a small molecule
Authors: Grinkevich Vera V. , Aparna Vema , Fawkner Karin , Issaeva Natalia , Andreotti Virginia , Dickinson Eleanor R. , Hedström Elisabeth , Spinnler Clemens , Inga Alberto , Larsson Lars-Gunnar , Karlén Anders , Wilhelm Margareta , Barran Perdita E. , Okorokov Andrei L. , Selivanova Galina , Zawacka-Pankau Joanna E. 
Published: December 2021

AbstractRestoration of the p53 tumor suppressor for personalised cancer therapy is a promising strategy. However, high-affinity MDM2 inhibitors have shown substantial side effects in clinical trials. Thus, elucidation of the molecular mechanisms of action of p53 reactivating molecules with alternative functional principle is of the utmost importance.Here, we report a discovery of a novel allosteric mechanism of p53 reactivation through targeting the p53 N-terminus which blocks both p53/MDM2 and p53/MDM4 interactions. Using biochemical assays and molecular docking, we identified the binding site of two p53 reactivating molecules, RITA and protoporphyrin IX (PpIX). Ion-mobility mass spectrometry revealed that the binding of RITA to serine 33 and serine 37 is responsible for inducing the allosteric shift in p53, which shields the MDM2 binding residues of p53 and prevents its interactions with MDM2 and MDM4. Our results point to an alternative mechanism of blocking p53 interaction with MDM2 and MDM4 and may pave the way for the development of novel allosteric inhibitors of p53/MDM2 and p53/MDM4 interactions.Contribution to the fieldGiven the immense importance of the p53 tumor suppressor for cancer, efforts have been made to identify p53 activators, which sterically inhibit MDM2. Because high-affinity MDM2 inhibitors are facing problems with considerable side effects, other approaches are needed to reactivate p53 for improved cancer therapy. The allosteric mechanism of action of p53 activator RITA, which we discovered, and its dependence on the oncogenic switch, is an unexpected turn in the p53 story. Our findings provide a basis for the development of p53 activators with a similar mode of functioning, either through the classical drug discovery route or through the drug repurposing approach. Allosteric modulators might have great potential as single agents, or in combination with the standard of care. Further, p53 modulators could serve as invaluable tools to better understand its biology.
SpaceX: Gene Co-expression Network Estimation for Spatial Transcriptomics
Authors: Acharyya Satwik , Zhou Xiang , Baladandayuthapani Veerabhadran 
Published: December 2021

AbstractMotivationThe analysis of spatially-resolved transcriptome enables the understanding of the spatial interactions between the cellular environment and transcriptional regulation. In particular, the characterization of the gene-gene co-expression at distinct spatial locations or cell types in the tissue enables delineation of spatial co-regulatory patterns as opposed to standard differential single gene analyses. To enhance the ability and potential of spatial transcriptomics technologies to drive biological discovery, we develop a statistical framework to detect gene co-expression patterns in a spatially structured tissue consisting of different clusters in the form of cell classes or tissue domains.ResultsWe develop SpaceX (spatially dependent gene co-expression network), a Bayesian methodology to identify both shared and cluster-specific co-expression network across genes. SpaceX uses an over-dispersed spatial Poisson model coupled with a high-dimensional factor model which is based on a dimension reduction technique for computational efficiency. We show via simulations, accuracy gains in co-expression network estimation and structure by accounting for (increasing) spatial correlation and appropriate noise distributions. In-depth analysis of two spatial transcriptomics datasets in mouse hypothalamus and human breast cancer using SpaceX, detected multiple hub genes which are related to cognitive abilities for the hypothalamus data and multiple cancer genes (e.g. collagen family) from the tumor region for the breast cancer data.Availability and implementationThe SpaceX R-package is available at github.com/bayesrx/SpaceX.Contactxzhousph@umich.edu, veerab@umich.eduSupplementary informationSupplementary data are available at bookdown.org/satwik91/SpaceX_supplementary/.
Anticancer immunotherapies transition postcapillary venules into high-endothelial venules that generate TCF1+ T lymphocyte niches through a feed-forward loop
Authors: Hua Yichao , Vella Gerlanda , Rambow Florian , Allen Elizabeth , Martinez Asier Antoranz , Duhamel Marie , Junius Steffie , Smeets Ann , Nittner David , Laoui Damya , Dimmeler Stefanie , Hehlgans Thomas , Liston Adrian , Floris Guiseppe , Lambrechts Diether , Merchiers Pascal , Bosisio Francesca Maria , Marine Jean-Christophe , Schlenner Susan , Bergers Gabriele 
Published: December 2021

SummaryThe lack of T-cell infiltrates is a major obstacle to effective immunotherapy in cancer. Conversely, the formation of tumor-associated tertiary-lymphoid-like structures (TA-TLS), which are the local site of humoral and cellular immune responses against cancers, are associated with good prognosis and have recently been detected in Immune Checkpoint Blockade (ICB)-responding patients. However, how these lymphoid aggregates develop remains poorly understood. By employing scRNA sequencing, endothelial fate mapping, and functional multiplex immune profiling, we demonstrate that antiangiogenic immune-modulating therapies evoke the transition of postcapillary venules into inflamed high endothelial venules (HEVs), which generate permissive TA-TLS-like lymphocyte niches with PD1negand PD1+TCF1+CD8 T cell progenitors that differentiate into GrzB+TCF1negTIM3+PD1+CD8 T effector cells. Tumor-HEVs require continuous CD8 and NK cell-derived lymphotoxin signals revealing that tumor-HEV maintenance is actively sculpted by the adaptive immune system through a feed-forward loop.In BriefHua & Vella et al. reveal that effective antiangiogenic immunotherapy transitions postcapillary venules into inflamed high-endothelial venules (HEV), sustained by CD8 T and NK cell-derived signals through a feed-forward loop. Thereby, tumoral HEVs establish perivascular niches in which TCF1+PD1+ lymphocytes expand and produce cytolytic PD1+ TIM3+ CD8 T cells that facilitate anti-tumoral immunity.HighlightsHigh endothelial venule induction by anticancer immunotherapies generates perivascular immune niches permissive for TCF1+PD1+CD8 progenitor T cell expansion and production of TCF1negPD1+TIM3+CD8 effector T cellsTumoral high-endothelial venules exhibit characteristics of inflamed lymph node HEVs and postcapillary venulesPostcapillary venules dynamically transdifferentiate into high-endothelial venules in tumors, which requires continuous signals from surrounding immune cellsCD8 and NK cells drive tumoral high-endothelial venule formation during antiangiogenic immunotherapies in a feed-forward loop via lymphotoxin beta receptor signaling
MEMO: Mass Spectrometry-based Sample Vectorization to Explore Chemodiverse Datasets
Authors: Gaudry Arnaud , Huber Florian , Nothias Louis-Félix , Cretton Sylvian , Kaiser Marcel , Wolfender Jean-Luc , Allard Pierre-Marie 
Published: December 2021

AbstractIn natural products research, chemodiverse extracts coming from multiple organisms are explored for novel bioactive molecules, sometimes over extended periods. Samples are usually analyzed by liquid chromatography coupled with fragmentation mass spectrometry to acquire informative mass spectral ensembles. Such data is then exploited to establish relationships among analytes or samples (e.g. via molecular networking) and annotate metabolites. However, the comparison of samples profiled in different batches is challenging with current metabolomics methods. Indeed, the experimental variation - changes in chromatographical or mass spectrometric conditions - often hinders the direct comparison of the profiled samples. Here we introduce MEMO - MS2 BasEd SaMple VectOrization - a method allowing to cluster large amounts of chemodiverse samples based on their LC-MS/MS profiles in a retention time agnostic manner. This method is particularly suited for heterogeneous and chemodiverse sample sets. MEMO demonstrated similar clustering performance as state-of-the-art metrics taking into account fragmentation spectra. More importantly, such performance was achieved without the requirement of a prior feature alignment step and in a significantly shorter computational time. MEMO thus allows the comparison of vast ensembles of samples, even when analyzed over long periods of time, and on different chromatographic or mass spectrometry platforms. This new addition to the computational metabolomics toolbox should drastically expand the scope of large-scale comparative analysis.Abstract Figure