bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracellular signal-regulated kinase mediates chromatin rewiring and lineage transformation in lung cancer
Authors: Inoue Yusuke , Nikolic Ana , Farnsworth Dylan , Liu Alvin , Ladanyi Marc , Somwar Romel , Gallo Marco , Lockwood William W. 
Published: November 2020

SummaryLineage transformation between lung cancer subtypes is a poorly understood phenomenon associated with resistance to treatment and poor patient outcomes. Here, we aimed to model this transition to define underlying biological mechanisms and identify potential avenues for therapeutic intervention. Small cell lung cancer (SCLC) is neuroendocrine in origin and, in contrast to non-SCLC (NSCLC), rarely contains mutations that drive the MAPK pathway. Likewise, NSCLCs that transform to SCLC concomitantly with development of therapy resistance downregulate MAPK signaling, suggesting an inverse relationship between pathway activation and lineage state. To test this, we activated MAPK in SCLC through conditional expression of mutant KRAS or EGFR, which revealed suppression of the neuroendocrine differentiation program via ERK. We found that ERK induces the expression of ETS factors that mediate transformation into a NSCLC-like state. ATAC-seq demonstrated ERK-driven changes in chromatin accessibility at putative regulatory regions and global chromatin rewiring at neuroendocrine and ETS transcriptional targets. Further, ERK-mediated induction of ETS factors as well as suppression of neuroendocrine differentiation were dependent on histone acetyltransferase activities of CBP/p300. Overall, we describe how the ERK-CBP/p300-ETS axis promotes a lineage shift between neuroendocrine and non-neuroendocrine lung cancer phenotypes and provide rationale for the disruption of this program during transformation-driven resistance to targeted therapy.
A Multiplexed Bacterial Two-Hybrid for Rapid Characterization of Protein-Protein Interactions and Iterative Protein Design
Authors: Boldridge W. Clifford , Ljubetič Ajasja , Kim Hwangbeom , Lubock Nathan , Szilágyi Dániel , Lee Jonathan , Brodnik Andrej , Jerala Roman , Kosuri Sriram 
Published: November 2020

AbstractMyriad biological functions require protein-protein interactions (PPIs), and engineered PPIs are crucial for applications ranging from drug design to synthetic cell circuits. Understanding and engineering specificity in PPIs is particularly challenging as subtle sequence changes can drastically alter specificity. Coiled-coils are small protein domains that have long served as a simple model for studying the sequence-determinants of specificity and have been used as modular building blocks to build large protein nanostructures and synthetic circuits. Despite their simple rules and long-time use, building large sets of well-behaved orthogonal pairs that can be used together is still challenging because predictions are often inaccurate, and, as the library size increases, it becomes difficult to test predictions at scale. To address these problems, we first developed a method called the Next-Generation Bacterial Two-Hybrid (NGB2H), which combines gene synthesis, a bacterial two-hybrid assay, and a high-throughput next-generation sequencing readout, allowing rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way. After validating the NGB2H system on previously characterized libraries, we designed, built, and tested large sets of orthogonal synthetic coiled-coils. In an iterative set of experiments, we assayed more than 8,000 PPIs, used the dataset to train a novel linear model-based coiled-coil scoring algorithm, and then characterized nearly 18,000 interactions to identify the largest set of orthogonal PPIs to date with twenty-two on-target interactions.
Nanodroplet-Benzalkonium Chloride Formulation DemonstratesIn VitroandEx-VivoBroad-Spectrum Antiviral Activity Against SARS-CoV-2 and other Enveloped Viruses
Authors: Pannu Jessie , Ciotti Susan , Ganesan Shyamala , Arida George , Costley Chad , Fattom Ali 
Published: November 2020

AbstractThe Covid-19 pandemic has highlighted the importance of aerosolized droplets inhaled into the nose in the transmission of respiratory viral disease. Inactivating pathogenic viruses at the nasal portal of entry may reduce viral loads, thereby reducing transmission and contagion. We have developed an oil-in-water nanoemulsion (nanodroplet)formulationcontaining the potent antiseptic 0.13% Benzalkonium Chloride (NE-BZK) which demonstrates safe and broad anti-viral activity. While The Centers for Disease Control and Prevention (CDC) have reported that BZK may have less reliable activity than ethyl alcohol against certain viruses, including coronaviruses, we have demonstrated that NE-BZK exhibits broad-spectrum, long-lasting antiviral activity with >99.99%in vitrokilling of enveloped viruses including SARS-CoV-2, human coronavirus, RSV and influenza B. Furthermore,in vitrostudies demonstrated that NE-BZK continues to kill >99.99% of human coronavirus even when diluted 20-fold, while 0.13% aqueous BZK solution (AQ-BZK) did not.Ex vivostudies of NE-BZK on human cadaver skin demonstrated persistent >99.99% killing of human coronavirus for at least 8 hours after application. AQ-BZK failed to demonstrate durable antimicrobial activity on skin over time. The repeated application of NE-BZK, twice daily for 2 weeks on to rabbit nostrils indicated safety with no irritation. These findings demonstrate that formulating BZK on the surface of proprietary nanodroplets offers a safe and effective antiviral as a significant addition to strategies to combat the spread of respiratory viral infectious diseases.
Extended spectrum β-lactamase and carbapenemase genes are substantially and sequentially reduced during conveyance and treatment of urban sewage
Authors: Li Liguan , Nesme Joseph , Quintela-Baluja Marcos , Balboa Sabela , Hashsham Syed , Williams Maggie R. , Yu Zhuofeng , Sørensen Søren J. , Graham David W. , Romalde Jesús L. , Dechesne Arnaud , Smets Barth F. 
Published: November 2020

AbstractIntegrated and quantitative observations of antibiotic resistance genes (ARGs) in urban water systems (UWSs) are lacking. We sampled three UWSs for clinically important extended spectrum β-lactamase (ESBL) and carbapenemase (CP) genes, mobile genetic elements and microbial communities. Sewage – especially from hospitals – carried substantial loads of ESBL and CP genes (106– 107per person equivalent), but those loads progressively declined along the UWS, resulting in minimal emissions (101– 104copies per person equivalent). Removal was primarily during sewage conveyance (65% ± 36%) rather than within sewage treatment (34% ± 23%). The ARGs clustered in groups based on their persistence; less persistent groups were associated to putative host taxa (especiallyEnterobacteriaceaeandMoraxellaceae), while more persistent groups appear horizontally transferred as they correlated with mobile genetic elements. This first documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based ARG surveillance.
Phylodynamic analysis of an emergentMycobacterium bovisoutbreak in an area with no previously known wildlife infections
Authors: Rossi Gianluigi , Crispell Joseph , Brough Tanis , Lycett Samantha J. , White Piran C. L. , Allen Adrian , Ellis Richard J. , Gordon Stephen V. , Harwood Roland , Palkopoulou Eleftheria , Presho Eleanor L. , Skuce Robin , Smith Graham C. , Kao Rowland R. 
Published: November 2020

AbstractUnderstanding how an emergent pathogen successfully establishes itself and persists in a previously unaffected population is a crucial problem in disease ecology. In multi-host pathogen systems this problem is particularly difficult, as the importance of each host species to transmission is often poorly characterised, and the epidemiology of the disease is complex. Opportunities to observe and analyse such emergent scenarios are few.Here, we exploit a unique dataset combining densely-collected data on the epidemiological and evolutionary characteristics of an outbreak ofMycobacterium bovis(M. bovis,the causative agent of bovine tuberculosis, bTB) in a population of cattle and badgers in an area considered low-risk for bTB, that has no previous record of either persistent infection in cattle, or of any infection in wildlife.We analyse the outbreak dynamics using a combination of mathematical modelling, machine learning and Bayesian evolutionary analyses. Comparison toM. boviswhole-genome sequences from Northern Ireland confirmed this to be a single introduction of the pathogen from the latter region, with evolutionary analysis supporting an introduction directly into the local cattle population at least six years prior to its first discovery in badgers. Once introduced, the evidence supportsM. bovisepidemiological dynamics passing through two phases, the first dominated by cattle-to-cattle transmission before becoming established in the local badger population.These findings emphasise the importance of disease surveillance for early containment of outbreaks, in particular for pathogens not causing immediately evident symptoms in the infected host, and highlight the utility of combining dynamic modelling and phylogenetic analyses for understanding the often complex infection dynamics associated with emergent outbreaks.
Stable transfection in the protist Corallochytrium limacisporum allows identification of novel cellular features among unicellular relatives of animals
Authors: Kożyczkowska Aleksandra , Najle Sebastián R. , Ocaña-Pallarès Eduard , Aresté Cristina , Ruiz-Trillo Iñaki , Casacuberta Elena 
Published: November 2020

ABSTRACTThe evolutionary path from protists to multicellular animals remains a mystery. Recent work on the genomes of several unicellular relatives of animals has shaped our understanding of the genetic changes that may have occurred in this transition. However, the specific cellular modifications that took place to accommodate these changes remain unclear. Functional approaches are now needed to unravel how different cell biological features evolved. Recent work has already established genetic tools in three of the four unicellular lineages closely related to animals (choanoflagellates, filastereans, and ichthyosporeans). However, there are no genetic tools available for Corallochytrea, the lineage that seems to have the widest mix of fungal and metazoan features, as well as a complex life cycle. Here, we describe the development of stable transfection in the corallochytrean Corallochytrium limacisporum. Using a battery of cassettes to tag key cellular components, such as nucleus, plasma membrane, cytoplasm and actin filaments, we employ live imaging to discern previously unknown biological features of C. limacisporum. In particular, we identify two different paths for cell division—binary fission and coenocytic growth—that reveal a non-linear life cycle in C. limacisporum. Additionally, we found that C. limacisporum is binucleate for most of its life cycle, and that, contrary to what happens in most eukaryotes, nuclear division is decoupled from cell division. The establishment of these tools in C. limacisporum fills an important gap in the unicellular relatives of animals, opening up new avenues of research with broad taxon sampling to elucidate the specific cellular changes that occurred in the evolution of animals.
Morphology and immunohistochemical characteristics of the otic ganglion in the chinchilla (Chinchilla lanigerMolina)
Authors: Sienkiewicz Waldemar , Kuchinka Jacek , Dudek Agnieszka , Nowak Elżbieta , Kaleczyc Jerzy , Radzimirska Małgorzata , Szczurkowski Aleksander 
Published: November 2020

AbstractThe available literature provides relatively little information on the morphology of the autonomic head ganglia in rodents including their neurochemical codding. The present study was thus designed to investigate the morphology and neurochemical properties of the otic ganglion in the chinchilla. The results will contribute to our knowledge of the organization of the autonomic nerve system in mammals.Morphological investigations of the otic ganglion were performed using the modified acetylcholinesterase method. The cellular structure was investigated with histological techniques and neurochemical properties were studied with double-labelling immunofluorescence methodMacromorphological investigations allowed the otic ganglion to be identified as a compact, oval agglomeration of neurons and nerve fibers located inside the skull on the medial surface of the mandibular nerve, just above the oval foramen. Multidimensional cross-sections revealed densely arranged neuronal perikarya and two populations of nerve cells differing in size were distinguished. The large cells (40–50 μm) accounted for about 80% of the neurons in the otic ganglion cross-sections. Moreover, a small number of intraganglionic nerve fibers was observed. Immunohistochemical staining revealed that over 85% of the neuronal cell bodies in the otic ganglion contained immunoreactivity to VAChT or ChAT. VIP-immunoreactive perikarya comprised approximately 10% of the ganglionic cells. Double staining revealed the presence of VAChT and NOS-positive neurons which amounted to about 45% of the nerve cells in the otic ganglion. NOS-positive only perikarya comprised approx. 15% of all the neurons. Immunoreactivity to enkephalin, substance P, somatostatin and galanin was expressed in single nerve cell bodies and nerve fibres except numerous SP-positive intraganglionic nerve fibres. Some of them stained also for CGRP. Single neurons stained for TH.The present results, compared with previous findings, suggest the existence interspecies differences in the morphology, cellular structure and immunohistochemical properties of the head autonomic ganglia in mammals.
Mycobacteria-host interactions in human bronchiolar airway organoids
Authors: Iakobachvili Nino , Leon Icaza Stephen Adonai , Knoops Kèvin , Sachs Norman , Mazères Serge , Simeone Roxane , Peixoto Antonio , Murris-Espin Marlène , Mazières Julien , López-Iglesias Carmen , Ravelli Raimond B.G. , Neyrolles Olivier , Meunier Etienne , Lugo-Villarino Geanncarlo , Clevers Hans , Cougoule Céline , Peters Peter J. 
Published: November 2020

AbstractTuberculosis, one of the oldest human pathogens remains a major global health threat. Recent advances in organoid technology offer a unique opportunity to grow different human “organs”in vitro, including the human airway, that faithfully recapitulate tissue architecture and function. We have explored the potential of human airway organoids (AOs) as a novel system in which to model tuberculosis infection. To this end, we adapted biosafety containment level 3–approved procedures to allow successful microinjection ofMycobacterium tuberculosis, the causative agent of tuberculosis, into AOs. We reveal that mycobacteria infected epithelial cells with low efficiency, and that the organoid microenvironment was able to control, but not eliminate the pathogen. We demonstrate that AOs responded to infection by inducing cytokine and antimicrobial peptide production, and inhibiting mucins. Given the importance of myeloid cells in tuberculosis infection, we co-cultured mycobacteria-infected organoids with human monocyte-derived macrophages, and found that these cells were recruited to the organoid epithelium. We conclude that adult stem cell–derived airway organoids can be used to model early events of tuberculosis infection and offer new avenues for fundamental and therapeutic research.
Transcriptome Analysis of NPFR Neurons Reveals a Connection Between proteome Diversity and Social Behavior
Authors: Ryvkin Julia , Bentzur Assa , Shmueli Anat , Tannenbaum Miriam , Shallom Omri , Dokarker Shiran , Levi Mali , Shohat-Ophir Galit 
Published: November 2020

AbstractComplex social behaviors are mediated by the activity of highly intricate neuronal networks, the function of which is shaped by their transcriptomic and proteomic content. Contemporary advances in neurogenetics, genomics, and tools for automated behavior analysis make it possible to functionally connect the transcriptome profile of candidate neurons to their role in regulating behavior. In this study we usedDrosophila melanogasterto explore the molecular signature of neurons expressing receptor for neuropeptide F (NPF), the fly homologue of neuropeptide Y (NPY). By comparing the transcription profile of NPFR neurons to those of nine other populations of neurons, we discovered that NPFR neurons exhibit a unique transcriptome, enriched with receptors for various neuropeptides and neuromodulators, as well as with genes known to regulate behavioral processes, such as learning and memory. By manipulating RNA editing and protein ubiquitination programs specifically in NPFR neurons, we demonstrate that their delicate transcriptome and proteome repertoires are required to suppress male courtship and certain features of social group interaction. Our results highlight the importance of transcriptome and proteome diversity in the regulation of complex behaviors and pave the path for future dissection of the spatiotemporal regulation of genes within highly complex tissues, such as the brain.
DeletingMecp2from the entire cerebellum rather than its neuronal subtypes causes a delay in motor learning in mice
Authors: Achilly Nathan P. , He Lingjie , Kim Olivia A. , Ohmae Shogo , Wojaczynski Gregory J. , Lin Tao , Sillitoe Roy V. , Medina Javier F. , Zoghbi Huda Y. 
Published: November 2020

ABSTRACTRett syndrome is a devastating childhood neurological disorder caused by mutations inMECP2. Of the many symptoms, motor deterioration is a significant problem for patients. In mice, deletingMecp2from the cortex or basal ganglia causes motor dysfunction, hypoactivity, and tremor, which are abnormalities observed in patients. However, little is known about the consequences of deletingMecp2from the cerebellum, a brain region critical for motor function. Here we show that deletingMecp2from the entire cerebellum, but not from individual cerebellar cell types, causes a delay in motor learning that is overcome by additional training. We also observed irregular firing rates of Purkinje cells and transcriptional misregulation within the cerebellum of knockout mice. These findings demonstrate that the motor deficits present in Rett syndrome arise, in part, from cerebellar dysfunction. For Rett syndrome as well as other neurodevelopmental disorders, our results highlight the importance of understanding which brain regions contribute to disease phenotypes.
CERI, CEFX, and CPI: largely improved positive controls for testing antigen-specific T cell function in PBMC compared to CEF
Authors: Lehmann Alexander A. , Reche Pedro A. , Zhang Ting , Suwansaard Maneewan , Lehmann Paul. V. 
Published: November 2020

AbstractMonitoring antigen-specific T cell immunity relies on functional tests that require T cells and antigen presenting cells to be uncompromised. Drawing of blood, its storage and shipment from the clinical site to the test laboratory, and the subsequent isolation, cryopreservation and thawing of peripheral blood mononuclear cells (PBMC) before the actual test is performed can introduce numerous variables that may jeopardize the results. Therefore, no T cell test is valid without assessing the functional fitness of the PBMC being utilized. This can only be accomplished through inclusion of positive controls that actually evaluate the performance of the antigen-specific T cell and antigen presenting cell (APC) compartments. CEF peptides have been commonly used to this extent. Here we show that CEF peptides fail as a positive control in nearly half of test subjects. Moreover, CEF peptides only measure CD8+ T cell functionality. More reliable alternatives for the assessment of CD8+ T cells are introduced here, as well as positive controls for the CD4+ T cell and APC compartments. In sum, we offer new tools and strategies for the assessment of PBMC functional fitness required for reliable T cell immune monitoring.
A practical PPE decontamination method using warm air and ambient humidity
Authors: Kwiek Jesse J. , Pickett Christopher R. , Flanigan Chloe A. , Lee Marcia V. , Saif Linda J. , Jahnes Jeff , Blonder Greg 
Published: November 2020

AbstractDespite a year-and-a-half of Sars-CoV-2 pandemic experience, personal protective equipment (PPE) remains in short supply1. Current decontamination methods are complex, slow, expensive and particularly ill-suited for low to middle income nations where the need is greatest. We propose a low temperature, ambient humidity decontamination method (WASP-D) based on the thirty minute or less half-life of Sars-CoV-2 (and other common pathogens) at temperatures above 45°C, combined with the observation that most PPE are designed to be safely transported and stored at temperatures below 50°C. Decontamination at 12 hours, 46°C (115°F) and ambient humidity should consistently reduce SARS-CoV-2 viral load by a factor of 106, without negatively affecting PPE materials or performance.
ORF3a mediated-incomplete autophagy facilitates SARS-CoV-2 replication
Authors: Qu Yafei , Wang Xin , Zhu Yunkai , Wang Yuyan , Yang Xing , Hu Gaowei , Liu Chengrong , Li Jingjiao , Ren Shanhui , Xiao Zixuan , Liu Zhenshan , Wang Weili , Li Ping , Zhang Rong , Liang Qiming 
Published: November 2020

ABSTRACTSARS-CoV-2 is the causative agent for the COVID-19 pandemic and there is an urgent need to understand the cellular response to SARS-CoV-2 infection. Beclin-1 is an essential scaffold autophagy protein that forms two distinct subcomplexes with modulators Atg14 and UVRAG, responsible for autophagosome formation and maturation, respectively. In the present study, we found that SARS-CoV-2 infection triggers an incomplete autophagy response, elevated autophagosome formation but impaired autophagosome maturation, and declined autophagy by genetic knockout of essential autophagic genes reduces SARS-CoV-2 replication efficiency. By screening 28 viral proteins of SARS-CoV-2, we demonstrated that expression of ORF3a alone is sufficient to induce incomplete autophagy. Mechanistically, SARS-CoV-2 ORF3a interacts with autophagy regulator UVRAG to facilitate Beclin-1-Vps34-Atg14 complex but selectively inhibit Beclin-1-Vps34-UVRAG complex. Interestingly, although SARS-CoV ORF3a shares 72.7% amino acid identity with the SARS-CoV-2 ORF3a, the former had no effect on cellular autophagy response. Thus, our findings provide the mechanistic evidence of possible takeover of host autophagy machinery by ORF3a to facilitate SARS-CoV-2 replication and raises the possibility of targeting the autophagic pathway for the treatment of COVID-19.
Polycomb Repressive Complex 2-controlled Essrg regulates intestinal Microfold cell differentiation
Authors: George Joel Johnson , Oittinen Mikko , Martin-Diaz Laura , Zapilko Veronika , Iqbal Sharif , Rintakangas Terhi , Martins Fábio Tadeu Arrojo , Niskanen Henri , Katajisto Pekka , Kaikkonen Minna , Viiri Keijo 
Published: November 2020

AbstractMicrofold cells (M cells) are immunosurveillance epithelial cells located in the Peyer’s patches in the intestine responsible for monitoring and transcytosis of antigens, microorganisms and pathogens. Many transcription factors, e.g., Spi-B and Sox8, necessary to M cell differentiation have been described but the exhaustive set of factors sufficient for differentiation and development of a mature M cell remains elusive. Moreover, the role of polycomb repressive complex 2 (PRC2) as an epigenetic regulator of M cell development has not yet been interrogated. Here, we show that PRC2 regulates a significant set of genes during the M cell differentiation including many transcription factors. Estrogen related receptor gamma (Esrrg) is a novel M cell specific transcription factor acting on a RankL-Rank induced NF-kB pathway, upstream of Sox8 and necessary but not sufficient for a mature M cell marker Gp2 expression. To conclude, with the aid of PRC2 target survey we identified the list of developmental genes specifically implicated in M cell development and Essrg as a necessary factor for Sox8-mediated M cell differentiation.