bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of Sugar Stereochemistry on Structural and Free Energy Landscape of Double-Stranded Nucleic Acids
Authors: Kumar Anuj , Singh Reman Kumar , Tagad Amol , Patwari G. Naresh 
Published: August 2020

ABSTRACTThe conformational landscape of 29-mer long four stereo variants of furanosal nucleic acids and their C2’ deoxy counterparts were explored using molecular dynamics and well-tempered metadynamics simulations. The ribose containing double-stranded nucleic acids exhibit helical structure, however inversion of C3’ and/or C2’ stereocentre of ribose results in structural modification. The free energy surfaces relative to the average twist angle and end-to-end distances suggests that the configuration at the C3’ position plays a pivotal role in determining the helicity. The C3’ stereocentre acts as toggle-switch for helix to non-helical structures in double-stranded nucleic acids. Thus, the ribose containing double-stranded nucleic acids result in well-organized helical structures, while those containing xylose and lyxose show a variety of structures, which include (circular) ladder configurations. Based on the present set of results, it can be inferred that ribose containing double-stranded nucleic acids form well-defined helical structures in contrast to their C2’ and C3’ epimers.
In vitro culture of aberrant basal-like cells from fibrotic lung tissue
Authors: Khan Petra , Roux Julien , Blumer Sabrina , Fang Lei , Savic Spasenija , Knudsen Lars , Jonigk Danny , Kuehnel Mark P. , Gazdhar Amiq , Geiser Thomas , Tamm Michael , Hostettler Katrin E. 
Published: August 2020

ABSTRACTRationaleIn idiopathic pulmonary fibrosis (IPF) atypical epithelial cells are present in the alveolar compartment. Their origin and contribution to IPF pathogenesis is unknown. We recently cultured a distinct population of cells, which readily grew from fibrotic lung tissue, but only rarely from non-fibrotic tissue. Here we aimed to characterize these fibrosis-enriched cells and determine transcriptomic differences between cells derived from IPF and patients with other interstitial lung diseases (ILD).MethodsCells were cultured from peripheral lung tissue of ILD patients and analysed by bulk or single cell RNA sequencing (scRNA-seq), TaqMan-PCR, immunofluorescence (IF), immunoblotting or electron microscopy (EM).ResultsscRNA-seq demonstrated an overall homogeneity and epithelial origin of the cells. The majority of cells expressed basal cell markers (Cytokeratin (KRT) 5 and 17, TP63), of which a fraction co-expressed mesenchymal cell markers (VIM, FN1, CDH2), alveolar (SLC34A2, ABCA3, LPCAT1, EMP2, HOPX) and/or secretory epithelial cell markers (SCGB1A1, MUC4). Interestingly, most of the cells showed closest transcriptomic similarity to recently described aberrant basal-like cells. Cells derived from IPF versus other ILD patients revealed significant transcriptomic differences with an up-regulation of fibrosis-associated and a down-regulation of inflammatory pathways in IPF cells.ConclusionWe here confirm the presence of aberrant basal-like cells in fibrotic lung tissue and, importantly, are the first to describe theirin vitrocharacteristics and a way of culturing these cellsin vitro. Cultured basal-like cells co-express epithelial and mesenchymal markers, suggesting a partial epithelial to mesenchymal transition (EMT). A subset of cells co-express alveolar, ciliated or secretory epithelial cell markers, possibly indicating differentiation towards these cell linages. Furthermore, cultured basal-like cells display a disease-specific transcriptome, possibly induced by their specific microenvironment. Our findings will contribute to a better understanding of the cells origin and their potential contribution to IPF pathogenesis.
LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications
Authors: Alvarez-Jarreta Jorge , Rodrigues Patricia R.S. , Fahy Eoin , O’Connor Anne , Price Anna , Gaud Caroline , Andrews Simon , Benton Paul , Siuzdak Gary , Hawksworth Jade I. , Valdivia-Garcia Maria , Allen Stuart M. , O’Donnell Valerie B. 
Published: August 2020

AbstractWe present LipidFinder 2.0, incorporating four new modules that apply artefact filters, remove lipid and contaminant stacks, in-source fragments and salt clusters, and a new isotope deletion method which is significantly more sensitive than available open-access alternatives. We also incorporate a novel false discovery rate (FDR) method, utilizing a target-decoy strategy, which allows users to assess data quality. A renewed lipid profiling method is introduced which searches three different databases from LIPID MAPS and returns bulk lipid structures only, and a lipid category scatter plot with color blind friendly pallet. An API interface with XCMS Online is made available on LipidFinder’s online version. We show using real data that LipidFinder 2.0 provides a significant improvement over non-lipid metabolite filtering and lipid profiling, compared to available tools.AvailabilityLipidFinder 2.0 is freely available athttps://github.com/ODonnell-Lipidomics/LipidFinderandhttp://lipidmaps.org/resources/tools/lipidfinder.Contactlipidfinder@cardiff.ac.ukSupplementary informationSupplementary data are available atBioinformaticsonline.
Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency
Authors: Li Yongzheng , Xue Boxin , Zhang Liwei , Su Qian Peter , Zhang Mengling , Long Haizhen , Wang Yao , Jin Yanyan , Hou Yingping , Cao Yuan , Li Guohong , Sun Yujie 
Published: August 2020

ABSTRACTMetazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Despite various genetic and epigenetic signatures are found to be related with active origins, it remains elusive how the selection of origins is determined. The classic Rosette model proposes that the origins clustered in a chromatin domain are preferentially and simultaneously fired, but direct imaging evidence has been lacking due to insufficient spatial resolution. Here, we applied dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We found that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase, in contrary to the Rosette model. Intriguingly, while both active and dormant origins are distributed homogeneously in the TAD during the G1 phase, active origins relocate to the TAD periphery before entering the S phase. We proved that such origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observed that the replication machinery protein PCNA forms immobile clusters around the TADs at the G1/S transition, which explains why origins at the TAD periphery are preferentially fired. Thus, we propose a “Chromatin Re-organization Induced Selective Initiation” (CRISI) model that the transcription-coupled chromatin structural re-organization determines the selection of replication origins, which transcends the scope of specific genetic and epigenetic signatures for origin efficiency. Ourin situsuper-resolution imaging unveiled coordination among DNA replication, transcription, and chromatin organization inside individual TADs, providing new insights into the biological functions of sub-domain chromatin structural dynamics.
The Structural Basis of Rubisco Phase Separation in the Pyrenoid
Authors: He Shan , Chou Hui-Ting , Matthies Doreen , Wunder Tobias , Meyer Moritz T. , Atkinson Nicky , Martinez-Sanchez Antonio , Jeffrey Philip D. , Port Sarah A. , Patena Weronika , He Guanhua , Chen Vivian K. , Hughson Frederick M. , McCormick Alistair J. , Mueller-Cajar Oliver , Engel Benjamin D. , Yu Zhiheng , Jonikas Martin C. 
Published: August 2020

AbstractApproximately one-third of global CO2fixation occurs in a phase separated algal organelle called the pyrenoid. Existing data suggest that the pyrenoid forms by the phase-separation of the CO2-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase-separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein EPYC1 (Essential Pyrenoid Component 1) in the model algaChlamydomonas reinhardtii. We find that EPYC1 consists of five evenly-spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of one of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation, and pyrenoid formation. Cryo-electron tomography supports a model where EPYC1 and Rubisco form a co-dependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle.
Hedgehog dysregulation contributes to tissue-specific inflammaging of resident macrophages
Authors: Babagana Mahamat , Oh Kyu-Seon , Chakraborty Sayantan , Pacholewska Alicja , Aqdas Mohammad , Sung Myong-Hee 
Published: August 2020

AbstractAge-associated low-grade sterile inflammation, commonly referred to as inflammaging, is a recognized hallmark of aging, which contributes to many age-related diseases. While tissue-resident macrophages are innate immune cells that secrete many types of inflammatory cytokines in response to various stimuli, it is not clear whether they have a role in driving inflammaging. Here we characterized the transcriptional changes associated with physiological aging in mouse resident macrophage populations across different tissues and sexes. Although the age-related transcriptomic signatures of resident macrophages were strikingly tissue-specific, the differentially expressed genes were collectively enriched for those with important innate immune functions such as antigen presentation, cytokine production, and cell adhesion. The brain-resident microglia had the most wide-ranging age-related alterations, with compromised expression of tissue-specific genes and relatively exaggerated responses to endotoxin stimulation. Despite the tissue-specific patterns of aging transcriptomes, components of the hedgehog (Hh) signaling pathway were decreased in aged macrophages across multiple tissues.In vivosuppression of Hh signaling in young animals increased the expression of pro-inflammatory cytokines, whilein vitroactivation of Hh signaling in old macrophages, in turn, suppressed the expression of these inflammatory cytokines. This suggests that hedgehog signaling could be a potential intervention axis for mitigating age-associated inflammation and related diseases. Overall, our data represent a resourceful catalog of tissue-specific and sex-specific transcriptomic changes in resident macrophages of peritoneum, liver, and brain, during physiological aging.
Multidimensional single-cell benchmarking of inducible promoters for precise dynamic control in budding yeast
Authors: Gligorovski Vojislav , Sadeghi Ahmad , Rahi Sahand Jamal 
Published: August 2020

AbstractFor quantitative systems biology, simultaneous readout of multiple cellular processes as well as precise, independent control over different genes’ activities are essential. In contrast to readout systems such as fluorescent proteins, control systems such as inducible transcription-factor-promoter systems have only been characterized in anad hocfashion, impeding precise system-level manipulations of biological systems and reliable modeling.We designed and performed systematic benchmarks involving easy-to-communicate units to characterize and compare inducible transcriptional systems. We built a comprehensive single-copy library of inducible systems controlling standardized fluorescent protein expression in budding yeast, includingGAL1pr,GALL,MET3pr,CUP1pr,PHO5pr,tetOpr,terminator-tetOpr, Z3EV system, the blue-light optogenetic systems El222-LIP, El222-GLIPand the red-light inducible PhyB-PIF3 system. To analyze these systems’ dynamic properties, we performed high-throughput time-lapse microscopy. The analysis of >100 000 cell images was made possible by the recently developed convolutional neural network YeaZ. We report key kinetic parameters, scaling of noise levels, impacts on growth, and, crucially, the fundamental leakiness of each system. Our multidimensional benchmarking additionally uncovers unexpected disadvantages of widely used tools, e.g., nonmonotonic activity of theMET3andGALLpromoters, slow off kinetics of the doxycycline and estradiol-inducible systemstetOprand Z3EV, and high variability ofPHO5prand red-light activated PhyB-PIF3 system. We introduce two new tools for controlling gene expression: strongLOV, a more light-sensitive El222 mutant, andARG3prthat functions as an OR gate induced by the lack of arginine or presence of methionine. To demonstrate the ability to finely control genetic circuits, we experimentally tuned the time between cell cycle Start and mitotic entry in budding yeast, artificially simulating near-wild-type timing.The characterizations presented here define the compromises that need to be made for quantitative experiments in systems and synthetic biology. To calibrate perturbations across laboratories and to allow new inducible systems to be benchmarked, we deposited single-copy reporter yeast strains, plasmids, and computer analysis code in public repositories. Furthermore, this resource can be accessed and expanded through the websitehttps://promoter-benchmark.epfl.ch/.
Quantitative PCR assays to detect humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge) in marine water samples
Authors: Andruszkiewicz Elizabeth A. , Yamahara Kevan M. , Closek Collin J. , Boehm Alexandria B. 
Published: August 2020

AbstractMonitoring aquatic species by identification of environmental DNA (eDNA) is becoming more common. In order to obtain quantitative datasets for individual species, species-specific quantitative PCR (qPCR) assays are required. Here, we present detailed methodology of qPCR assay design and testing, includingin silico, in vitro, andin vivotesting, and comment on the challenges associated with assay design and performance. We use the presented methodology to design assays for three important marine organisms common in the California Current Ecosystem (CCE): humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge). All three assays have excellent sensitivity and high efficiencies ranging from 92% to 99%. However, specificities of the assays varied from species-specific in the case of common murre to the genus-specific shortbelly rockfish assay, to the humpback whale assay which cross-amplified with other two other whale species, including one in a different family. All assays detected their associated targets in complex environmental water samples.
Learning Patterns of the Ageing Brain in MRI using Deep Convolutional Networks
Authors: Dinsdale Nicola K. , Bluemke Emma , Smith Stephen M , Arya Zobair , Vidaurre Diego , Jenkinson Mark , Namburete Ana I. L. 
Published: August 2020

AbstractBoth normal ageing and neurodegenerative diseases cause morphological changes to the brain. Age-related brain changes are subtle, nonlinear, and spatially and temporally heterogenous, both within a subject and across a population. Machine learning models are particularly suited to capture these patterns and can produce a model that is sensitive to changes of interest, despite the large variety in healthy brain appearance. In this paper, the power of convolutional neural networks (CNNs) and the rich UK Biobank dataset, the largest database currently available, are harnessed to address the problem of predicting brain age. We developed a 3D CNN architecture to predict chronological age, using a training dataset of 12, 802 T1-weighted MRI images and a further 6, 885 images for testing. The proposed method shows competitive performance on age prediction, but, most importantly, the CNN prediction errors ΔBrainAge=AgePredicted−AgeTruecorrelated significantly with many clinical measurements from the UK Biobank in the female and male groups. In addition, having used images from only one imaging modality in this experiment, we examined the relationship between ΔBrainAgeand the image-derived phenotypes (IDPs) from all other imaging modalities in the UK Biobank, showing correlations consistent with known patterns of ageing. Furthermore, we show that the use of nonlinearly registered images to train CNNs can lead to the network being driven by artefacts of the registration process and missing subtle indicators of ageing, limiting the clinical relevance. Due to the longitudinal aspect of the UK Biobank study, in the future it will be possible to explore whether the ΔBrainAgefrom models such as this network were predictive of any health outcomes.HighlightsBrain age is estimated using a 3D CNN from 12,802 full T1-weighted images.Regions used to drive predictions are different for linearly and nonlinearly registered data.Linear registrations utilise a greater diversity of biologically meaningful areas.Correlations with IDPs and non-imaging variables are consistent with other publications.Excluding subjects with various health conditions had minimal impact on main correlations.
Post-weaning shifts in microbiome composition and metabolism revealed by over 25,000 pig gut metagenome assembled genomes
Authors: Gaio Daniela , DeMaere Matthew Z. , Anantanawat Kay , Chapman Toni A. , Djordjevic Steven P. , Darling Aaron E. 
Published: August 2020

ABSTRACTUsing a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50,000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5% of which were classified as >70% complete with a <10% contamination rate, and 24.4% were nearly complete genomes. Here we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental program in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic “signatures” that characterize the microbiome development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut, identifying 294 carbohydrate active enzymes. We tracked the shifts in abundance of these enzymes across time, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs, raising the possibility of modifying the piglet microbiome through the tailored provision of carbohydrate substrates.
Room-temperature performance of 3 mm-thick cadmium–zinc–telluride pixel detectors with sub-millimetre pixelization
Authors: Buttacavoli Antonino , Principato Fabio , Gerardi Gaetano , Bettelli Manuele , Sarzi Amadè Nicola , Zappettini Andrea , Seller Paul , Veale Matthew C. , Fox Oliver , Sawhney Kawal , Abbene Leonardo 
Published: August 2020

Cadmium–zinc–telluride (CZT) pixel detectors represent a consolidated choice for the development of room-temperature spectroscopic X-ray imagers, finding important applications in medical imaging, often as detection modules of a variety of new SPECT and CT systems. Detectors with 3–5 mm thicknesses are able to efficiently detect X-rays up to 140 keV giving reasonable room-temperature energy resolution. In this work, the room-temperature performance of 3 mm-thick CZT pixel detectors, recently developed at IMEM/CNR of Parma (Italy), is presented. Sub-millimetre detector arrays with pixel pitch less than 500 µm were fabricated. The detectors are characterized by good room-temperature performance even at high bias voltage operation (6000 V cm−1), with energy resolutions (FWHM) of 3% (1.8 keV) and 1.6% (2 keV) at 59.5 keV and 122.1 keV, respectively. Charge-sharing investigations were performed with both uncollimated and collimated synchrotron X-ray beams with particular attention to recovering the charge losses at the inter-pixel gap region. High rate measurements demonstrated the absence of high-flux radiation-induced polarization phenomena up to 25 × 106 photons mm−2 s−1.
Recognition of an α-helical hairpin in P22 large terminase by a synthetic antibody fragment
Authors: Lokareddy Ravi K. , Ko Ying-Hui , Hong Nathaniel , Doll Steven G. , Paduch Marcin , Niederweis Michael , Kossiakoff Anthony A. , Cingolani Gino 
Published: August 2020

The genome-packaging motor of tailed bacteriophages and herpesviruses is a multisubunit protein complex formed by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal protein vertex of an empty precursor capsid to power the energy-dependent packaging of viral DNA. Both the ATPase and nuclease activities associated with genome packaging reside in TerL. Structural studies of TerL from bacteriophage P22 have been hindered by the conformational flexibility of this enzyme and its susceptibility to proteolysis. Here, an unbiased, synthetic phage-display Fab library was screened and a panel of high-affinity Fabs against P22 TerL were identified. This led to the discovery of a recombinant antibody fragment, Fab4, that binds a 33-amino-acid α-helical hairpin at the N-terminus of TerL with an equilibrium dissociation constant K
d of 71.5 nM. A 1.51 Å resolution crystal structure of Fab4 bound to the TerL epitope (TLE) together with a 1.15 Å resolution crystal structure of the unliganded Fab4, which is the highest resolution ever achieved for a Fab, elucidate the principles governing the recognition of this novel helical epitope. TLE adopts two different conformations in the asymmetric unit and buries as much as 1250 Å2 of solvent-accessible surface in Fab4. TLE recognition is primarily mediated by conformational changes in the third complementarity-determining region of the Fab4 heavy chain (CDR H3) that take place upon epitope binding. It is demonstrated that TLE can be introduced genetically at the N-terminus of a target protein, where it retains high-affinity binding to Fab4.