bluuebunny/crossref_metadata_2025_split huggingface dataset:
CMOS electrochemical imaging arrays for the detection and classification of microorganisms
Authors: Arcadia Christopher E. , Hu Kangping , Epstein Slava , Wanunu Meni , Adler Aaron , Rosenstein Jacob K. 
Published: April 2021

AbstractMicroorganisms account for most of the biodiversity on earth. Yet while there are increasingly powerful tools for studying microbial genetic diversity, there are fewer tools for studying microorganisms in their natural environments. In this paper, we present recent advances in CMOS electrochemical imaging arrays for detecting and classifying microorganisms. These microscale sensing platforms can provide non-optical measurements of cell geometries, behaviors, and metabolic markers. We review integrated electronic sensors appropriate for monitoring microbial growth, and present measurements of single-celled algae using a CMOS sensor array with thousands of active pixels. Integrated electrochemical imaging can contribute to improved medical diagnostics and environmental monitoring, as well as discoveries of new microbial populations.
M&Ms: A software for building realistic Microbial Mock communities
Authors: García-García Natalia , Tamames Javier , Puente-Sánchez Fernando 
Published: April 2021

ABSTRACTMotivationAdvances in sequencing technologies have triggered the development of many bioinformatic tools aimed to analyze these data. As these tools need to be tested, it is important to simulate datasets that resemble realistic conditions. Although there is a large amount of software dedicated to produce reads from ‘in silico’ microbial communities, often the simulated data diverge widely from real situations.ResultsHere, we introduce M&Ms, a user-friendly open-source bioinformatic tool to produce realistic amplicon datasets from reference sequences, based on pragmatic ecological parameters. This tool creates sequence libraries for ‘in silico’ microbial communities with user-controlled richness, evenness, microdiversity, and source environment. M&Ms allows the user to generate simple to complex read datasets based on real parameters that can be used in developing bioinformatic software or in benchmarking current tools. M&Ms also provides additional figures and files with extensive details on how each synthetic community is composed, so that users can make informed choices when designing their benchmarking pipelines.AvailabilityThe source code of M&Ms is freely available fromhttps://github.com/ggnatalia/MMsContactngarcia@cnb.csic.es
Developmental Circadian Disruption Alters Placental Signaling in Mice
Authors: Clarkson-Townsend Danielle A. , Bales Katie L. , Hermetz Karen E. , Burt Amber A. , Pardue Machelle T. , Marsit Carmen J. 
Published: April 2021

AbstractCircadian disruption has been largely overlooked as a developmental exposure. The placenta, a conduit between the maternal and fetal environments, may relay circadian cues to the fetus. We have previously shown that developmental chronodisruption causes visual impairment and increased retinal microglial and macrophage marker expression. Here, we investigated the impacts of environmental circadian disruption on fetal and placental outcomes in a C57BL/6J mouse (Mus musculus) model. Developmental chronodisruption had no effect on embryo count, placental weight, or fetal sex ratio. When measured with RNAseq, mice exposed to developmental circadian disruption (CD) had differential placental expression of several transcripts includingSerpinf1, which encodes pigment-epithelium derived factor (PEDF). Immunofluorescence of microglia/macrophage markers, Iba1 and CD11b, also revealed significant upregulation of immune cell markers in CD-exposed placenta. Our results suggest thatin uterocircadian disruption enhances placental immune cell expression, potentially programming a pro-inflammatory tissue environment that increases the risk of chronic disease in adulthood.
A cancer-associated RNA polymerase III identity drives robust transcription and expression of SNAR-A noncoding RNA
Authors: Van Bortle Kevin , Marciano David P. , Liu Qing , Lipchik Andrew M. , Gollapudi Sanjay , Geller Benjamin S. , Monte Emma , Kamakaka Rohinton T. , Snyder Michael P. 
Published: April 2021

ABSTRACTDysregulation of the RNA polymerase III (Pol III) transcription program, which synthesizes tRNA and other classes of small noncoding RNA critical for cell growth and proliferation, is associated with cancer and human disease. Previous studies have identified two distinct Pol III isoforms defined by the incorporation of either subunit POLR3G (RPC7α) during early development, or POLR3GL (RPC7β) in specialized tissues. Though POLR3G is re-established in cancer and immortalized cell lines, the contributions of these isoforms to transcription potential and transcription dysregulation in cancer remain poorly defined. Using an integrated Pol III genomic profiling approach in combination within vitrodifferentiation and subunit disruption experiments, we discover that loss of subunit POLR3G is accompanied by a restricted repertoire of genes transcribed by Pol III. In particular, we observe that a specific class of small noncoding RNA,SNAR-A, is exquisitely sensitive to the availability of subunit POLR3G in proliferating cells. Taken further, large-scale analysis of Pol III subunit expression and downstream chromatin features identifies concomitant loss of POLR3G andSNAR-Aactivity across a multitude of differentiated primary immune cell lineages, and conversely, coordinate re-establishment of POLR3G expression andSNAR-Afeatures in a variety of human cancers. These results altogether argue against strict redundancy models for subunits POLR3G and POLR3GL, and instead support a model in which Pol III identity itself functions as an important transcriptional regulatory mechanism. Upregulation of POLR3G, which is driven by MYC, identifies a subgroup of patients with unfavorable survival outcomes in specific cancers, further implicating the POLR3G-enhanced transcription repertoire as a potential disease factor.
Integrin-dependent migratory switches regulate the translocation ofToxoplasma-infected dendritic cells across brain endothelial monolayers
Authors: Ross Emily C. , ten Hoeve Arne L. , Barragan Antonio 
Published: April 2021

AbstractMultiple cellular processes, such as immune responses and cancer cell metastasis, crucially depend on interconvertible migration modes. However, knowledge is scarce on how infectious agents impact the processes of cell adhesion and migration at restrictive biological barriers. In extracellular matrix, dendritic cells (DCs) infected by the obligate intracellular protozoanToxoplasma gondiiundergo mesenchymal-to-amoeboid transition (MAT) for rapid integrin-independent migration. Here, in a cellular model of the blood-brain barrier, we report that parasitised DCs adhere to polarised endothelium and shift to integrin-dependent motility, accompanied by elevated transendothelial migration (TEM). Upon contact with endothelium, parasitised DCs dramatically reduced velocities and adhered under both static and shear stress conditions, thereby obliterating the infection-induced amoeboid motility displayed in collagen matrix. The motility of adherent parasitised DCs on endothelial monolayers was restored by blockade of β1 and β2 integrins or ICAM-1, which conversely reduced motility on collagen-coated surfaces. Moreover, parasitised DCs exhibited enhanced translocation across highly polarised primary murine brain endothelial cell monolayers. Blockade of β1, β2 integrins, ICAM-1 and PECAM-1 reduced TEM frequencies. Finally, gene silencing of the pan-integrin-cytoskeleton linker talin (Tln1) or of β1 integrin (Itgb1) in primary DCs resulted in increased motility on endothelium and decreased TEM. Adding to the paradigms of leukocyte diapedesis, the findings provide novel insights in how an intracellular pathogen impacts the migratory plasticity of leukocytes in response to the cellular environment, to promote infection-related dissemination.
OXSR1 inhibits inflammasome activation by limiting potassium efflux during mycobacterial infection
Authors: Hortle Elinor , Tran Lam Vi , Fontaine Angela RM , Pinello Natalia , Wong Justin J-L , Britton Warwick J , Oehlers Stefan H 
Published: April 2021

SummaryPathogenic mycobacteria inhibit inflammasome activation as part of their pathogenesis. While it is known that potassium efflux is a trigger for inflammasome activation, the interaction between mycobacterial infection, potassium efflux and inflammasome activation has not been investigated. Here we useMycobacterium marinuminfection of zebrafish embryos andMycobacterium tuberculosisof human THP-1 cells to demonstrate that pathogenic mycobacteria upregulate the host WNK signalling pathway kinases SPAK and OXSR1 which control intracellular potassium balance. We show that genetic depletion or inhibition of OXSR1 decreases bacterial burden and intracellular potassium levels. The protective effects of OXSR1 depletion are mediated by NLRP3 inflammasome activation and are dependent on caspase-mediated release of IL-1β and the downstream activation of protective TNF-α. The elucidation of this druggable pathway to potentiate inflammasome activation provides a new avenue for the development of host-directed therapies against intracellular infections.
The fall and rise of group BStreptococcusin dairy cattle: reintroduction due to human-to-cattle host jumps?
Authors: Crestani Chiara , Forde Taya L , Lycett Samantha J , Holmes Mark A , Fasth Charlotta , Persson-Waller Karin , Zadoks Ruth N 
Published: April 2021

ABSTRACTGroup BStreptococcus(GBS;Streptococcus agalactiae) is a major neonatal and opportunistic bacterial pathogen of humans and an important cause of mastitis in dairy cattle with significant impacts on food security. Following the introduction of mastitis control programs in the 1950s, GBS was nearly eradicated from the dairy industry in northern Europe, followed by re-emergence in the 21st century. Here, we sought to explain this re-emergence based on short and long read sequencing of historical (1953-1978; n = 44) and contemporary (1997-2012; n = 76) bovine GBS isolates. Our data show that a globally distributed bovine-associated lineage of GBS was commonly detected among historical isolates but never among contemporary isolates. By contrast, tetracycline resistance, which is present in all major GBS clones adapted to humans, was commonly and uniquely detected in contemporary bovine isolates. These observations provide evidence for strain replacement and suggest a human origin of newly emerged strains. Three novel GBS plasmids were identified, including two showing >98% homology with plasmids fromStreptococcus pyogenesandStreptococcus dysgalactiaesubsp.equisimilis, which co-exist with GBS in the human oropharynx. Our findings support introduction of GBS into the dairy population due to human to-cattle jumps on multiple occasions and demonstrate that reverse zoonotic transmission can erase successes of animal disease control campaigns.IMPACT STATEMENTPathogens can jump between humans and animals. Animal domestication and intensification of livestock production systems have caused multiple human to animal spill-over events, sometimes with significant impact on animal health and food production. The most common production-limiting disease of dairy cattle is mastitis, inflammation of the mammary gland, which can be caused by group BStreptococcus,a common commensal and pathogen of humans. Using genomic data from historical and recent isolates, we show that re-emergence of this pathogen in the dairy industry in northern Europe is due to strains with genomic signatures of human host-adaptation, including antimicrobial resistance genes and plasmids. This shows how elimination of animal diseases may be hampered by humans serving as a reservoir of multi-host pathogens, and reverse zoonotic transmission.REPOSITORIESReads for all isolates sequenced in this study have been submitted to the ENA Sequence Read Archive (SRA). SRA accession numbers are included in Table S1, supplementary material, available in the online version of this article.
Dual-axis Volta phase plate cryo-electron tomography of Ebola virus-like particles reveals actin-VP40 interactions
Authors: Winter Sophie L. , Chlanda Petr 
Published: April 2021

AbstractCryo-electron tomography (cryo-ET) is a pivotal imaging technique for studying the structure of pleomorphic enveloped viruses and their interactions with the host at native conditions. Owing to the limited tilting range of samples with a slab geometry, electron tomograms suffer from so-called missing wedge information in Fourier space. In dual-axis cryo-ET, two tomograms reconstructed from orthogonally oriented tilt series are combined into a tomogram with improved resolution as the missing wedge information is reduced to a pyramid. Volta phase plate (VPP) allows to perform in-focus cryo-ET with high contrast transfer at low-resolution frequencies and thus its application may improve the quality of dual-axis tomograms. Here, we compare dual-axis cryo-ET with and without VPP on Ebola virus-like particles to visualize and segment viral and host cell proteins within the membrane-enveloped filamentous particles. Dual-axis VPP cryo-ET reduces the missing wedge information and ray artifacts arising from the weighted back-projection during tomogram reconstruction, thereby minimizing ambiguity in the analysis of crowded environments and facilitating 3D segmentation. We show that dual-axis VPP tomograms provide a comprehensive description of macromolecular organizations such as nucleocapsid assembly states, the distribution of glycoproteins on the viral envelope and asymmetric arrangements of the VP40 layer in non-filamentous regions of virus-like particles. Our data reveal actin filaments within virus-like particles in close proximity to the viral VP40 scaffold, suggesting a direct interaction between VP40 and actin filaments. Dual-axis VPP cryo-ET provides more complete 3D information at high contrast and allows for better interpretation of macromolecule interactions and pleomorphic organizations.HighlightsVolta phase plate dual-axis cryo-electron tomography provides high contrast tomography data with reduced back-projection ray artifacts and missing wedge information in Fourier spaceVolta phase plate dual-axis cryo-electron tomography facilitates interpretation of protein-membrane interactionsVolta phase plate dual-axis cryo-electron tomography reduces ambiguity in manual 3D rendering and markedly improves 3D isosurface modelingEbola virus-like particles contain actin filaments in close proximity to the VP40 layer
IL-7 is essential for accumulation of antigen-specific CD8 T cells and to generate clonotype-specific effector responses during airway influenza/A infection
Authors: Sheikh Abdalla , Jackson Jennie , Shim Hanjoo Brian , Yau Clement , Seo Jung Hee , Abraham Ninan 
Published: April 2021

AbstractAirborne diseases are the leading cause of infectious disease-related deaths in the world. In particular, the influenza virus activates a network of immune cells that leads to clearance or an overzealous response that can be fatal. Tight regulation of the cytokines that enable proper activation and function of immune cells is necessary to clear infections efficiently while minimizing damage to the host. Interleukin-7 (IL-7) is a cytokine known for its importance in T cell development and survival. How IL-7 shapes CD8 T cell responses during an acute viral infection is less understood. We had previously shown that IL-7 signaling deficient mice have reduced accumulation of influenza-specific CD8 T cells following infection. We sought to determine whether IL-7 affects early CD8 T cell expansion in the mediastinal lymph node and effector function in the lungs. Using IL-7Rα signaling deficient mice, we show that IL-7 is required for a normal sized mediastinal lymph node and the early clonal expansion of antigen-specific CD8 T cells therein. Bone marrow chimeric models and adoptive transfer of transgenic TCR CD8 T cells reveal a cell-intrinsic role for IL-7 in the accumulation of NP366–374and PA224–233-specific CD8 T cells. We also found that IL-7 dictates terminal differentiation, degranulation and cytokine production in PA224–233-specific but not NP366–374-specific CD8 T cells. We further demonstrate that IL-7 is induced in the lung tissue by viral infection and we characterize multiple cellular sources that contribute to IL-7 production. Drugs that manipulate IL-7 signaling are currently under clinical trial for multiple conditions. Our findings on IL-7 and its effects on lower respiratory diseases will be important for expanding the utility of these therapeutics.Author SummaryInterleukin-7 plays an important role in development of immune cells such as lymphocytes. In recent years, its role in the immune system has been expanded beyond the development of immune cells to include revitalizing of lymphocytes during tumor and chronic viral response. We show here that IL-7 is required for accumulation and function of specialized lymphocytes in the lungs during an acute influenza infection.
Defining function of wild-type and patient specificTP53mutations in a zebrafish model of embryonal rhabdomyosarcoma
Authors: Chen Jiangfei , Baxi Kunal , Lipsitt Amanda E. , Hensch Nicole R. , Wang Long , Baudin Antoine , Robledo Daniel G. , Bandyopadhyay Abhik , Sugalski Aaron , Challa Anil K. , Gilbert Andrea R. , Tomlinson Gail E. , Houghton Peter , Chen Eleanor Y. , Libich David S. , Ignatius Myron S. 
Published: April 2021

AbstractIn embryonal rhabdomyosarcoma (ERMS) and generally in sarcomas, the role of wild-type and loss or gain of functionTP53mutations remains largely undefined. Eliminating mutant or restoring wild-type p53 is challenging; nevertheless, understandingTP53effects on tumorigenesis remains central to realizing better treatment outcomes. In ERMS, >70% of patients retain wild-typeTP53, yetTP53mutations when present in tumors are associated with poor prognosis. Employing akRASG12D-driven ERMS tumor model and newly generated tp53 null (tp53-/-) zebrafish, we define both wild-type and patient-specificTP53mutant effects on tumorigenesis. We demonstrate thattp53is a major suppressor of tumor initiation, wheretp53loss expands tumors initiation from <35% to >97% of animals. Next, characterizing three patient-specific mutants finds thatTP53C176Fpartially retains wild-type p53 apoptotic activity that can be exploited, while theTP53P153Δand TP53Y220Cmutants define two structural mutations that predispose to head musculature ERMS.
Enabling high throughput target-based drug discovery in 3D cell cultures through novel bioprinting workflow
Authors: Engel Martin , Belfiore Lisa , Aghaei Behnaz , Sutija Margareta 
Published: April 2021

AbstractAdvanced three-dimensional cell culture techniques have been adopted in many laboratories to better modelin vivotissue by recapitulating multi-cellular architecture and the presence of extracellular matrix features. We describe here a 3D cell culture platform in a small molecule screening workflow that uses traditional biomarker and intracellular kinase end point assay readouts. By combining the high throughput bioprinter Rastrum with the high throughput screening assay AlphaLISA, we demonstrate the utility of the workflow in 3D synthetic hydrogel cultures with breast cancer (MDA-MB-231 and MCF-7) and fibroblast cells. To establish and validate the workflow, we treated the breast cancer cultures with doxorubicin, while fibroblast cultures were stimulated with the pro-inflammatory lipopolysaccharide. 3D and 2D MDA-MB-231 cultures were equally susceptible to doxorubicin treatment, while showing opposite ERK phosphorylation changes. Doxorubicin readily entered embedded MCF-7 spheroids and markedly reduced intracellular GSK3β phosphorylation. Furthermore, quantifying extracellular interleukin 6 levels showed a very similar activation profile for fibroblasts in 2D and 3D cultures, with 3D fibroblast networks being more resistant against the immune challenge. Through these validation experiments we demonstrate the full compatibility of the bioprinted 3D cell cultures with several widely-used 2D culture assays. The efficiency of the workflow, minimal culture handling, and applicability of traditional screening assays, demonstrates that advanced encapsulated 3D cell cultures can be used in 2D cell culture screening workflows, while providing a more holistic view on cell biology to increase the predictability toin vivodrug response.
AGO104 is an RdDM effector of paramutation at the maizeb1locus
Authors: Aubert Juliette , Bellegarde Fanny , Oltehua-Lopez Omar , Leblanc Olivier , Arteaga-Vazquez Mario A. , Martienssen Robert A. , Grimanelli Daniel 
Published: April 2021

AbstractParamutation is an exception among eukaryotes, in which epigenetic information is conserved through mitosis and meiosis. It has been studied for over 70 years in maize, but the mechanisms involved are largely unknown. Previously described actors of paramutation encode components of the RNA-dependent DNA-methylation (RdDM) pathway all involved in the biogenesis of 24-nt small RNAs. However, no actor of paramutation have been identified in the effector complex of RdDM. Here, through a combination of reverse genetics, immunolocalization and immunoprecipitation (siRNA-IP) we found that ARGONAUTE104 (AGO104), AGO105 and AGO119 are members of the RdDM effector complex in maize and bind siRNAs produced from the tandem repeats required for paramutation at theb1locus. We also showed that AGO104 is an effector of theb1paramutation in maize.Author summaryReprogramming of epigenetic information has been described in both plants and mammals. Here, we show that maizeARGONAUTE (AGO) AGO104andAGO105/AGO119, respectively the close homologs ofA. thaliana AGO9andAGO4, are required to enable paramutation at theb1locus in maize. Paramutation is an epigenetic phenomenon that is stable over many generations (both mitotically and meiotically). A classic example is thebooster1(b1) gene in maize, where the weakly expressedBooster’(B’) allele stably decreases the expression of theBooster-Intense(B-I) allele, and changes it into a newB’allele. This newB’allele will in turn changeB-Iinto newB’in subsequent crosses. Previous research demonstrated that paramutation requires several proteins involved in the biosynthesis of small interfering RNAs (siRNAs) all related to the RNA-dependent DNA-methylation (RdDM) pathway. Yet, few members of the RdDM were functionally identified in maize. Here, we identify two new members of the maize RdDM pathway, and provide evidence that they are also involved in paramutation at theb1locus.