bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple lineages of Streptomyces produce antimicrobials within passalid beetle galleries across eastern North America
Authors: de Cassia Pessotti Rita , Hansen Bridget L. , Reaso Jewel N. , Ceja-Navarro Javier A. , El-Hifnawi Laila , Brodie Eoin L. , Traxler Matthew F. 
Published: December 2020

ABSTRACTSome insects form symbioses in which actinomycetes provide defense against pathogens by making antimicrobials. The range of chemical strategies employed across these associations, and how these strategies relate to insect lifestyle, remains underexplored. We assessed subsocial passalid beetles of the species Odontotaenius disjunctus, and their frass (fecal material) which is an important food resource within their galleries, as a model insect/actinomycete system. Through chemical and phylogenetic analyses, we found that O. disjunctus frass collected across eastern North America harbored multiple lineages of Streptomyces and diverse antimicrobials. Metabolites detected in frass displayed synergistic and antagonistic inhibition of a fungal entomopathogen, Metarhizium anisopliae, and multiple streptomycete isolates inhibited this pathogen when co-cultivated directly in frass. These findings support a model in which the lifestyle of O. disjunctus accommodates multiple Streptomyces lineages in their frass, resulting in a rich repertoire of antimicrobials that likely insulates their galleries against pathogenic invasion.
Pluripotent stem cell derived models of neurological diseases reveal early transcriptional heterogeneity
Authors: Sorek Matan , Oweis Walaa , Nissim-Rafinia Malka , Maman Moria , Simon Shahar , Hession Cynthia C. , Adiconis Xian , Simmons Sean K. , Sanjana Neville , Shi Xi , Lu Congyi , Pan Jen Q. , Xu Xiaohong , Pouladi Mahmoud A. , Ellerby Lisa M. , Zhang Feng , Levin Joshua Z. , Meshorer Eran 
Published: December 2020

AbstractBackgroundMany neurodegenerative diseases (NDs) develop only later in life, when cells in the nervous system lose their structure or function. In genetic forms of NDs, this late onset phenomenon remains largely unexplained.ResultsAnalyzing single cell RNA sequencing (scRNA-seq) from Alzheimer’s disease (AD) patients, we find increased transcriptional heterogeneity in AD excitatory neurons. We hypothesized that transcriptional heterogeneity precedes ND pathologies. To test this idea experimentally, we used juvenile forms (72Q; 180Q) of Huntington’s disease (HD) iPSCs, differentiated them into committed neuronal progenitors, and obtained single cell expression profiles. We show a global increase in gene expression variability in HD. Autophagy genes become more stable, while energy and actin-related genes become more variable in the mutant cells. Knocking-down several differentially-variable genes resulted in increased aggregate formation, a pathology associated with HD. We further validated the increased transcriptional heterogeneity in CHD8+/-cells, a model for autism spectrum disorder.ConclusionsOverall, our results suggest that although NDs develop over time, transcriptional regulation imbalance is present already at very early developmental stages. Therefore, an intervention aimed at this early phenotype may be of high diagnostic value.
THE DYNAMIC INTERPLAY BETWEEN HOMEODOMAIN TRANSCRIPTION FACTORS AND CHROMATIN ENVIRONMENT REGULATES PRONEURAL FACTOR OUTCOMES
Authors: Ang Cheen Euong , Olmos Victor Hipolito , Zhou Bo , Lee Qian Yi , Sinha Rahul , Narayanaswamy Aadit , Mall Moritz , Chesnov Kirill , Sudhof Thomas , Wernig Marius 
Published: December 2020

SUMMARYGeneration of neurons of vast diversity involves early spatial and temporal patterning of the neuronal precursors by morphogenic gradients and combinatorial expression of transcription factors. While the proneuronal function of the basic-helix-loop-helix (bHLH) transcription factor Ngn2 is well established, its role in neuronal subtype specification remains unclear. Here, we found that coexpressing NGN2 with the forebrain homeobox factor EMX1 converts human pluripotent stem cells into a highly homogeneous glutamatergic forebrain neurons without partial cholinergic and monoaminergic gene programs observed in cells infected with NGN2 only. Our molecular characterization revealed that transcriptional output and genomic targeting of Ngn2 is altered by co-factors such as EMX1 explaining the more focused subtype specification. Ngn2 function is less modified by the chromatin environment and does not affect regionalization of pre-patterned neural progenitors. These results enable improved strategies for generating a plethora of defined neuronal subpopulations from pluripotent stem cells for therapeutic or disease-modeling purposes.HighlightsNGN2 converts human ES cells into glutamatergic neurons some of which co-express a partial cholinergic programNGN2 directly binds to and activates ISL1 in ES cells which together with PHOX2A/B induce cholinergic genesAnterior-posterior regionalization affects NGN2 binding and transcriptional output but does not focus subtype specificationForebrain homeobox factors including EMX1 and FOXG1 redirect NGN2 chromatin binding and repress posterior and cholinergic genes, resulting in homogeneous forebrain excitatory neurons
Learning interpretable latent autoencoder representations with annotations of feature sets
Authors: Rybakov Sergei , Lotfollahi Mohammad , Theis Fabian J. , Wolf F. Alexander 
Published: December 2020

AbstractExisting methods for learning latent representations for single-cell RNA-seq data are based on autoencoders and factor models. However, representations learned by autoencoders are hard to interpret and representations learned by factor models have limited flexibility. Here, we introduce a framework for learning interpretable autoencoders based on regularized linear decoders. It decomposes variation into interpretable components using prior knowledge in the form of annotated feature sets obtained from public databases. Through this, it provides an alternative to enrichment techniques and factor models for the task of explaining observed variation with biological knowledge. Benchmarking our model on two single-cell RNA-seq datasets, we demonstrate how our model outperforms an existing factor model regarding scalability while maintaining interpretability.
CXCR6 by increasing retention of memory CD8 T cells in the ovarian tumor microenvironment promotes immunosurveillance and control of ovarian cancer
Authors: Muthuswamy Ravikumar , McGray AJ Robert , Battaglia Sebastiano , He Wenjun , Miliotto Anthony , Eppolito Cheryl , Lichty Brian , Shrikant Protul , Odunsi Kunle 
Published: December 2020

AbstractPurposeResident memory CD8 T cells owing to their ability to reside and persist in peripheral tissues, impart adaptive sentinel activity and amplify local immune response, have beneficial implications for tumor surveillance and control. The current study aims to clarify the less known chemotactic mechanisms that govern the localization, retention, and residency of memory CD8 T cells in the ovarian tumor microenvironment.Experimental DesignRNA/FACS based profiling of chemokine receptor expression in CD8+resident memory T cells in human ovarian cancer and analyze their association with survival. Analyze chemokine receptor role in anti-tumor response and control by resident memory T cells using prophylactic mice models of ovarian cancer, treated with adoptive transfer of OT1 T cells and vaccination with maraba virus-OVA to target Ovalbumin expressing tumor.ResultsChemokine receptor profiling of CD8+CD103+resident memory TILs in ovarian cancer patients revealed high expression of CXCR6. Analysis of the TCGA ovarian cancer database revealed CXCR6 to be associated with CD103 and increased patient survival. Functional studies in mouse models of ovarian cancer revealed that CXCR6 is a marker of resident, but not circulatory tumor-specific memory CD8 T cells. Knockout of CXCR6 in tumor-specific CD8 T cells showed reduced retention in tumor tissues leading to diminished resident memory responses and poor control of ovarian cancerConclusionsCXCR6 by promoting increased retention in tumor tissues serves a critical role in resident memory T cell-mediated immunosurveillance and control of ovarian cancer. Future studies warrant exploiting CXCR6 to promote resident memory response in cancers.
A Novel Role for Nucleolin in Splice Site Selection
Authors: Shefer Kinneret , Boulos Ayub , Gotea Valer , Chaim Yair Ben , Sperling Joseph , Elnitski Laura , Sperling Ruth 
Published: December 2020

AbstractLatent 5’ splice sites are highly abundant in human introns, yet, are apparently not normally used. Splicing at most of these sites would incorporate in-frame stop codons generating nonsense mRNAs. Importantly, under stress and in cancer, splicing at latent sites is activated generating nonsense mRNAs from thousands of genes. Previous studies point to an unresolved RNA quality control mechanism that suppresses latent splicing independently of NMD. They further demonstrated a pivotal role for initiator-tRNA in this mechanism, through its interaction with the AUG codon, independent of its role in protein translation. To further elucidate this mechanism, here we searched for nuclear proteins directly bound to initiator-tRNA in the nucleus. We identified nucleolin (NCL), a multifunctional, abundant, and conserved protein, as a novel regulator of splice site selection. Starting with UV crosslinking, we show that NCL is directly and specifically interacting with initiator-tRNA in the nucleus, but not in the cytoplasm. In support of NCL involvement in this mechanism, we show activation of latent splicing in hundreds of transcripts upon NCL knockdown, disrupting gene transcripts involved in several important cellular pathways and cell metabolism functions (e.g. transcription factors, oncogenes, kinases, splicing factors, translation factors, and genes affecting cell motility, proliferation, and cellular trafficking). We thus propose NCL, a component of the endogenous spliceosome, through its direct interaction with initiator-tRNA and its effect on latent splicing as the first documented protein of a nuclear quality control mechanism that regulates splice site selection to protect cells from latent splicing that would generate defective mRNAs.
Triggering closure of a sialic acid TRAP transporter substrate binding protein through binding of natural or artificial substrates
Authors: Peter Martin F. , Gebhardt Christian , Glaenzer Janin , Schneberger Niels , de Boer Marijn , Thomas Gavin H. , Cordes Thorben , Hagelueken Gregor 
Published: December 2020

AbstractThe pathogensVibrio choleraeandHaemophilus influenzaeuse tripartite ATP-independent periplasmic transporters (TRAPs) to scavenge sialic acid from host tissues. They use it as a nutrient or to evade the innate immune system by sialylating surface lipopolysaccharides. An essential component of TRAP transporters is a periplasmic substrate binding protein (SBP). Without substrate, the SBP has been proposed to rest in an open-state, which is not recognised by the transporter. Substrate binding induces a conformational change of the SBP and it is thought that this closed state is recognised by the transporter, triggering substrate translocation. Here we use real time single molecule FRET experiments and crystallography to investigate the open- to closed-state transition of VcSiaP, the SBP of the sialic acid TRAP transporter fromV. cholerae. We show that the conformational switching of VcSiaP is strictly substrate induced, confirming an important aspect of the proposed transport mechanism. Two new crystal structures of VcSiaP provide insights into the closing mechanism. While the first structure contains the natural ligand, sialic acid, the second structure contains an artificial peptide in the sialic acid binding site. Together, the two structures suggest that the ligand itself stabilises the closed state and that SBP closure is triggered by physically bridging the gap between the two lobes of the SBP. Finally, we demonstrate that the affinity for the artificial peptide substrate can be substantially increased by varying its amino acid sequence and by this, serve as a starting point for the development of peptide-based inhibitors of TRAP transporters.
Non-invasive Differentiation of M1 and M2 Activation in Macrophages using Hyperpolarized13C MRS of Pyruvate and DHA at 1.47 Tesla
Authors: Qiao Kai , Le Page Lydia M. , Chaumeil Myriam M. 
Published: December 2020

AbstractMacrophage activation, first generalized to the M1/M2 dichotomy, is a complex and central process of the innate immune response. Simply, M1 describes the classical pro-inflammatory activation, leading to tissue damage, and M2 the alternative activation promoting tissue repair. Given the central role of macrophages in multiple diseases, the ability to non-invasively differentiate between M1 and M2 activation states would be highly valuable for monitoring disease progression and therapeutic responses. Since M1/M2 activation patterns are associated with differential metabolic reprogramming, we hypothesized that hyperpolarized13C magnetic resonance spectroscopy (HP13C MRS), an innovative metabolic imaging approach, could distinguish between macrophage activation states noninvasively. The metabolic conversions of HP [1-13C]pyruvate to HP [1-13C]lactate and HP [1-13C]dehydroascorbic acid to HP [1-13C]ascorbic acid were monitored in live M1 and M2 activated J774a.1 macrophages non-invasively by HP13C MRS on a 1.47 Tesla NMR system. Our results show that both metabolic conversions were significantly increased in M1 macrophages compared to M2 and non-activated cells. Biochemical assays and high resolution1H MRS were also performed to investigate the underlying changes in enzymatic activities and metabolite levels linked to M1/M2 activation. Altogether, our results demonstrate the potential of HP13C MRS for monitoring macrophage activation states non-invasively.
The indoor environment - a potential source for intact human-associated anaerobes
Authors: Pausan Manuela-Raluca , Blohs Marcus , Mahnert Alexander , Moissl-Eichinger Christine 
Published: December 2020

AbstractBackgroundPeople in westernised countries spend most of their time indoors. A healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. For this reason, the built environment might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes, such as obligate or facultative anaerobes.MethodsWe sampled ten households and used propidium monoazide to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses.ResultsQuantitative and qualitative analysis revealed that most of the microbial taxa are of human origin. Less than 25% of the prokaryotic signatures found in built environment (BE) samples originate from intact – and thus potentially living – cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. Although the dominant microbial fraction identified on the bathroom floors is composed of aerobes, we confirmed the presence of strictly anaerobic taxa, including methanogenic archaea, in PMA-treated samples. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that these taxa have a limited but substantial ability to survive in the BE. We determined that human-associated methanogens can survive oxic conditions for at least 6 h.ConclusionsThis study enabled us to collect strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.
In vitroanalysis of colistin and ciprofloxacin antagonism ofPseudomonas aeruginosaphage PEV2 infection activities
Authors: Danis-Wlodarczyk Katarzyna , Cai Alice , Chen Anna , Gittrich Marissa , Sullivan Matthew B. , Wozniak Daniel J. , Abedon Stephen T. 
Published: December 2020

AbstractPhage therapy is a century-old technique employing viruses (phages) to treat bacterial infections. In the clinic, phage therapy often is used in combination with antibiotics. Antibiotics, however, interfere with critical bacterial activities, such as DNA and protein synthesis, which also are required for phage infection processes. Resulting antagonistic impacts of antibiotics on phages nevertheless are not commonly determined in association with phage therapy studies using standard, planktonic approaches. Here we assess the antagonistic impact of two antibiotics, colistin and ciprofloxacin, on the bactericidal, bacteriolytic, and new virion production activities ofPseudomonas aeruginosapodovirus PEV2, using a broth culture, optical density-based ‘lysis profile’ assay. Though phage-antibiotic combinations were more potent in reducing cell viability than phages or antibiotics alone, colistin substantially interfered with phage PEV2 bacteriolytic and virion-production activities at minimum inhibitory concentration (MIC). Ciprofloxacin, by contrast, had no such impact at 1x MIC or 3x MIC. At higher but still clinically relevant concentrations (9× MIC) burst sizes were still significant (~30 phages/infected bacterium). We corroborated these lysis profile results by more traditional measurements (colony forming units, plaque forming units, one-step growth experiments) and two otherP. aeruginosaphages. To our knowledge this is the first study in which detailed antibiotic impact onP. aeruginosaphage infection activities has been determined under conditions similar to those used to determine antibiotic MICs and could point especially to ciprofloxacin as a minimally antagonistic phage therapy co-treatment ofP. aeruginosainfections.
Allosteric activation of T-cell antigen receptor signalling by quaternary structure relaxation
Authors: Lanz Anna-Lisa , Masi Giulia , Porciello Nicla , Cohnen André , Cipria Deborah , Prakaash Dheeraj , Bálint Štefan , Raggiaschi Roberto , Galgano Donatella , Cole David K. , Lepore Marco , Dushek Omer , Dustin Michael L. , Sansom Mark S. P. , Kalli Antreas C. , Acuto Oreste 
Published: December 2020

AbstractThe mechanism of T cell antigen receptor (TCR-CD3) signalling remains elusive. Here, we identified mutations in the transmembrane region of TCRβ or CD3ζ that augmented pMHC-induced signalling, not explicable by enhanced ligand binding, lateral diffusion, clustering or co-receptor function. Using a novel biochemical assay and molecular dynamics simulation, we demonstrated that the gain-of-function mutations loosened interaction between TCRαβ and CD3ζ. We found that, similar to the activating mutations, pMHC binding reduced TCRαβ cohesion with CD3ζ. This event occurred prior to CD3ζ phosphorylation and at 0°C. Moreover, we demonstrated that soluble monovalent pMHC alone induced signalling and reduced TCRαβ cohesion with CD3ζ in membrane-bound or solubilised TCR-CD3. Our data provide compelling evidence that pMHC binding suffices to activate allosteric changes propagating from TCRαβ to the CD3 subunits, reconfiguring interchain transmembrane region interactions. These dynamic modifications could change the arrangement of TCR-CD3 boundary lipids to licence CD3ζ phosphorylation and initiate signal propagation.
Light spectra modify nitrogen assimilation and nitrogen content inQuercus variabilisBlume seedling components: A bioassay with15N pulses
Authors: Gao Jun , Zhang Jinsong , He Chunxia , Wang Qirui 
Published: December 2020

AbstractThe light spectra that reach plants change across different shading conditions, may alter the pattern of nitrogen (N) uptake and assimilation by understory regenerations that are also exposed to N deposition. We conducted a bioassay on Chinese cork oak (Quercus variabilisBlume) seedlings subjected to five-month N pulsing with15NH4Cl (10.39 atom %) at 120 mg15N plant-1under the blue (48.5% blue, 33.7% green, and 17.8% red), red (14.6% blue, 71.7% red, 13.7% green), and green (17.4% blue, 26.2% red, 56.4% green) spectra provided by light-emitting diodes (LEDs). Half of the seedlings were fed twice a week using a 250 ppm N solution with added phosphorus, potassium, and micro-nutrients, while the other half received only distilled water. Neither treatment affected growth of height, diameter, or leaf area. Compared to the red light spectrum, the blue light treatment increased chlorophyll and soluble protein contents and glutamine synthetase (GS) activity, root N concentration, and N derived from the pulses. The green light spectrum induced more biomass to allocate to the roots and a higher percentage of N derived from internal reserves compared to the other two spectra. The15N pulses demonstrated no interaction with spectra but weakened the reliance on N remobilization from acorns, strengthened biomass allocation to shoots, and induced higher chlorophyll content, GS activity, and N concentration. In conclusion, the red light spectrum should be avoided forQ. variabilisregenerations whose biomass allocation to underground organs are weakened under this condition.