bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prime editing for functional repair in patient-derived disease models
Authors: Schene Imre F. , Joore Indi P. , Oka Rurika , Mokry Michal , van Vugt Anke H.M. , van Boxtel Ruben , van der Doef Hubert P.J. , van der Laan Luc J.W. , Verstegen Monique M.A. , van Hasselt Peter M. , Nieuwenhuis Edward E.S. , Fuchs Sabine A. 
Published: June 2020

AbstractPrime editing is a novel genome editing technology using fusion proteins of Cas9-nickase and reverse transcriptase, that holds promise to correct the vast majority of genetic defects. We develop prime editing for primary adult stem cells grown in organoid culture models. First, we generate precise in-frame deletions in the gene encoding ß-catenin (CTNNB1) that result in proliferation independent of Wnt-stimuli, mimicking a mechanism of the development of liver cancer. Moreover, prime editing functionally recovers diseasecausing mutations in intestinal organoids from patients with DGAT1-deficiency and liver organoids from a patient with Wilson disease (ATP7B). Prime editing is as efficient in 3D grown organoids as in 2D grown cell lines and offers greater precision than Cas9-mediated homology directed repair (HDR). Base editing remains more reliable than prime editing but is restricted to a subgroup of pathogenic mutations. Whole-genome sequencing of four prime-edited clonal organoid lines reveals absence of genome-wide off-target effects underscoring therapeutic potential of this versatile and precise gene editing strategy.
p53-dependent polyploidisation after DNA damage in G2 phase
Authors: Middleton Anna , Suman Rakesh , O’Toole Peter , Akopyan Karen , Lindqvist Arne 
Published: June 2020

AbstractCell cycle progression in the presence of damaged DNA can lead to accumulation of mutations and pose a risk for tumour development. In response to DNA damage in G2 phase, human cells can be forced to exit the cell cycle in a p53-p21- and APC/CCdh1-dependent manner. Cells that exit the cell cycle in G2 phase become senescent, but it is unclear what determines this commitment and whether other cell fates occur. We find that a subset of immortalised RPE-1 cells and primary human fibroblasts spontaneously initiate DNA re-replication several days after forced cell cycle exit in G2 phase. By combining single cell tracking for more than a week with quantitative immunofluorescence, we find that the resulting polyploid cells contain increased levels of damaged DNA and frequently exit the cell cycle again in the next G2 phase. Subsequently, these cells either enter senescence or commit to another round of DNA re-replication, further increasing the ploidy. At least a subset of the polyploid cells show abnormal centrosome numbers or localisation. In conclusion, cells that are forced to exit the cell cycle in G2 phase face multiple choices that lead to various phenotypes, including propagation of cells with different ploidies. Our findings suggest a mechanism by which p53-positive cells can evade senescence that risks genome integrity.Main points-Cell cycle exit from G2 phase does not necessarily lead to senescence-Resumption of proliferation after G2 phase cell cycle exit starts with DNA replication-Successive cell cycle exits lead to propagation of cells with different ploidies-A p53-dependent mechanism allows eventual proliferation after DNA damage
Directed information exchange between cortical layers in macaque V1 and V4 and its modulation by selective attention
Authors: Ferro Demetrio , van Kempen Jochem , Boyd Michael , Panzeri Stefano , Thiele Alexander 
Published: June 2020

SummaryAchieving behavioral goals requires integration of sensory and cognitive information, across cortical laminae and cortical regions. How this computation is performed remains unknown. Using local field potential recordings and spectrally resolved conditional Granger causality (cGC) analysis, we mapped visual information flow, and its attentional modulation, between cortical layers within and between macaque areas V1 and V4. Stimulus induced inter-laminar information flow within V1 dominated upwardly, channeling information towards supragranular cortico-cortical output layers. Within V4, information flow dominated from granular to supragranular layers, but interactions between supragranular and infragranular layers dominated downwardly. Low-frequency across-area communication was stronger from V4 to V1, with little layer specificity. Gamma-band communication was stronger in the feedforward V1 to V4 direction. Attention to the receptive field of V1 decreased communication between all V1 layers, except for granular to supragranular layers interactions. Communication within V4, and from V1 to V4, increased with attention across all frequencies. While communication from V4 to V1 was stronger in lower frequency bands (4-25 Hz), attention modulated cGCs from V4 to V1 across all investigated frequencies. Our data show that top down cognitive processes result in reduced communication within cortical areas, increased feedforward communication across all frequency bands and increased gamma band feedback communication.
Connecting conformational stiffness of the protein with energy landscape by a single experiment
Authors: Chakraborty Soham , Chaudhuri Deep , Chaudhuri Dyuti , Singh Vihan , Banerjee Souradeep , Haldar Shubhasis 
Published: June 2020

AbstractProteins are versatile biopolymers whose functions are determined by their structures. Understanding the structural dynamicity, with respect to energy landscape, is essential to describe their biological functions. The ability to study the dynamical properties of a single protein molecule is thus crucial, but ensuring that multiple physical properties can be simultaneously extracted within a single experiment on the exact same protein molecule in real-time has hitherto been infeasible.Here, we present magnetic tweezers technology that surmounts this limitation, providing real-time dynamic information about changes in several molecular properties (ΔG0, conformation, and mean first passage time of unfolding and refolding) from a single experiment, byremeasuring the very same protein moleculein varying chemical condition. We illustrate the versatility of the method by studying electrolyte-dependent conformational flexibility and the energy landscape of substrate protein L under force. Changing salt concentrations reshapes the energy landscape by two specific ways: it speeds-up refolding kinetics while slowing down unfolding kinetics. From the same trajectory, we calculate the stiffness of the protein polymer, a quantity that varies with salt concentration. The data is described within the framework of a modified ‘electrolyte FJC model’ that we propose and study here. The observed correlation betweenΔG0, kinetics and polymer elasticity connect protein chain physics and the energy landscape, while the experimental methodology we describe of getting energy landscape from a single experiment could have wide-ranging applications.
Efficient detection of transposable element insertion polymorphisms between genomes using short-read sequencing data
Authors: Baduel P. , Quadrana L. , Colot V. 
Published: June 2020

AbstractTransposable elements (TEs) are powerful generators of major-effect mutations, most of which are deleterious at the species level and maintained at very low frequencies within populations. As reference genomes can only capture a minor fraction of such variants, methods were developed to detect TE insertion polymorphisms (TIPs) in non-reference genomes from short-read sequencing data, which are becoming increasingly available. We present here a bioinformatic framework combining an improved version of the SPLITREADER and TEPID pipelines to detect non-reference TE presence and reference TE absence variants, respectively. We benchmark our method on ten non-referenceArabidopsis thalianagenomes and demonstrate its high specificity and sensitivity in the detection of TIPs between genomes.
Excess histone H3 is a Chk1 inhibitor that controls embryonic cell cycle progression
Authors: Shindo Yuki , Amodeo Amanda A. 
Published: June 2020

AbstractThe early embryos of many species undergo a switch from rapid, reductive cleavage divisions to slower, cell fate-specific division patterns at the Mid-Blastula Transition (MBT). The maternally loaded histone pool is used to measure the increasing ratio of nuclei to cytoplasm (N/C ratio) to control MBT onset, but the molecular mechanism of how histones regulate the cell cycle has remained elusive. Here, we show that excess histone H3 inhibits the DNA damage checkpoint kinase Chk1 to promote cell cycle progression in theDrosophilaembryo. We find that excess H3-tail that cannot be incorporated into chromatin is sufficient to shorten the embryonic cell cycle and reduce the activity of Chk1in vitroandin vivo. Removal of the Chk1 phosphosite in H3 abolishes its ability to regulate the cell cycle. Mathematical modeling quantitatively supports a mechanism where changes in H3 nuclear concentrations over the final cell cycles leading up to the MBT regulate Chk1-dependent cell cycle slowing. We provide a novel mechanism for Chk1 regulation by H3, which is crucial for proper cell cycle remodeling during early embryogenesis.
Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing
Authors: Egeter Bastian , Veríssimo Joana , Lopes-Lima Manuel , Chaves Cátia , Pinto Joana , Riccardi Nicoletta , Beja Pedro , Fonseca Nuno A. 
Published: June 2020

AbstractTraditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and to substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. We extracted, amplified and sequenced eDNA with a turnaround of 3.5 days. The majority of processed reads were ≥ 99 % identical to reference sequences. There were no taxa detected other than those known to occur. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples. The approach can be easily adapted for other metabarcoding applications, such as biodiversity assessment, ecosystem health assessment and diet studies.
Ancient bacterial genomes reveal a formerly unknown diversity ofTreponema pallidumstrains in early modern Europe
Authors: Majander Kerttu , Pfrengle Saskia , Neukamm Judith , Kocher Arthur , du Plessis Louis , Pla-Díaz Marta , Arora Natasha , Akgül Gülfirde , Salo Kati , Schats Rachel , Inskip Sarah , Oinonen Markku , Valk Heiki , Malve Martin , Kriiska Aivar , Onkamo Päivi , González-Candelas Fernando , Kühnert Denise , Krause Johannes , Schuenemann Verena J. 
Published: June 2020

SummarySexually transmitted (venereal) syphilis marked European history with a devastating epidemic at the end of the 15thcentury, and is currently re-emerging globally. Together with non-venereal treponemal diseases, like bejel and yaws, found in subtropical and tropical regions, it poses a prevailing health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis’ potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a previously unknown diversity ofTreponema pallidumin historical Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws were already present in Northern Europe in the early modern period. We also discovered a previously unknownT. pallidumlineage recovered as a sister group to yaws and bejel. These findings imply a more complex pattern of geographical prevalence and etiology of early treponemal epidemics than previously understood.
Self-renewal of double negative 3 (DN3) early thymocytes allows for thymus autonomy but compromises the β-selection checkpoint
Authors: Paiva Rafael A. , Sousa António G. G. , Ramos Camila V. , Ávila Mariana , Lilue Jingtao , Paixão Tiago , Martins Vera C. 
Published: June 2020

ABSTRACTT lymphocyte differentiation in the thymus relies on high cellular turnover, and cell competition enforces thymocyte replenishment. If deprived of competent progenitors, the thymus can maintain thymopoiesis autonomously for several weeks but this bears a high risk of leukemia. Here we show that double negative 3 early (DN3e) thymocytes can acquire stem cell like properties, which enables them to maintain thymopoiesis. Specifically, DN3e proved to be long-lived, they proliferated and differentiatedin vivo, were necessary for autonomous thymopoiesis, and included DNA-label-retaining cells. Single cell RNAseq revealed a transcriptional program of thymopoiesis similar in autonomy and the controls. Nevertheless, a new population was identified in thymus autonomy that was enriched for an aberrant Notch target gene signature and bypassed the β−selection checkpoint. In sum, DN3e have the potential to self-renew and differentiatein vivoif cell competition is compromised but this enables the accumulation of atypical cells, probably leading to leukemia.
Epigenome-wide change and variation in DNA methylation from birth to late adolescence
Authors: Mulder Rosa H. , Neumann Alexander , Cecil Charlotte A. M. , Walton Esther , Houtepen Lotte C. , Simpkin Andrew J. , Rijlaarsdam Jolien , Heijmans Bastiaan T. , Gaunt Tom R. , Felix Janine F. , Jaddoe Vincent W. V. , Bakermans-Kranenburg Marian J. , Tiemeier Henning , Relton Caroline L. , van IJzendoorn Marinus H. , Suderman Matthew 
Published: June 2020

AbstractDNA methylation (DNAm) is known to play a pivotal role in childhood health and development, but a comprehensive characterization of genome-wide DNAm trajectories across this age period is currently lacking. We have therefore performed a series of epigenome-wide association studies in 5,019 blood samples collected at multiple time-points from birth to late adolescence from 2,348 participants of two large independent cohorts. DNAm profiles of autosomal CpG sites (CpGs) were generated using the Illumina Infinium HumanMethylation450 BeadChip. Change over time was widespread, observed at over one-half (53%) of CpGs. In most cases DNAm was decreasing (36% of CpGs). Inter-individual variation in linear trajectories was similarly widespread (27% of CpGs). Evidence for nonlinear change and inter-individual variation in nonlinear trajectories was somewhat less common (11% and 8% of CpGs, respectively). Very little inter-individual variation in change was explained by sex differences (0.4% of CpGs) even though sex-specific DNAm was observed at 5% of CpGs. DNAm trajectories were distributed non-randomly across the genome. For example, CpGs with decreasing DNAm were enriched in gene bodies and enhancers and were annotated to genes enriched in immune-developmental functions. By contrast, CpGs with increasing DNAm were enriched in promoter regions and annotated to genes enriched in neurodevelopmental functions. These findings depict a methylome undergoing widespread and often nonlinear change throughout childhood. They support a developmental role for DNA methylation that extends beyond birth into late adolescence and has implications for understanding life-long health and disease. DNAm trajectories can be visualized athttp://epidelta.mrcieu.ac.uk.
NMDA receptors require multiple pre-opening gating steps for efficient synaptic activity
Authors: Amin Johansen , Gochman Aaron , He Miaomiao , Certain Noele , Wollmuth Lonnie P. 
Published: June 2020

ABSTRACTNMDA receptors (NMDAR) are glutamate-gated ion channels that mediate the majority of fast excitatory synaptic transmission in the nervous system. A central feature of NMDAR physiology is the opening of the ion channel driven by presynaptically-released glutamate. Using glutamate applications to outside-out patches containing a single NMDAR in the continuous presence of the co-agonist glycine, we find that agonist-bound receptors transition to the open state via two conformations, an ‘unconstrained pre-active’ state that can rapidly transition to the open state and contributes to synaptic events, and a ‘constrained pre-active’ state that requires more energy and hence time to open and does not contribute to fast signaling. To define how agonist binding might drive these conformations, we decoupled the ligand-binding domains from specific transmembrane segments for the GluN1 and GluN2A subunits. Displacements of the central pore-forming M3 segments define the energy of fast channel opening. However, to enter the unconstrained conformation and contribute to fast signaling, a peripheral helix, the GluN2 pre-M1, must be displaced before the M3 segments move. This pre-M1 displacement is facilitated by the flexibility of another nearby peripheral element, the GluN1 and GluN2A S2-M4. We conclude that peripheral structural elements – pre-M1 and S2-M4 – work in concert to remove constraints and prime the channel for rapid opening, thus facilitating fast synaptic transmission.
Extensive transfer of genes for edible seaweed digestion from marine to human gut bacteria
Authors: Pudlo Nicholas A. , Pereira Gabriel Vasconcelos , Parnami Jaagni , Cid Melissa , Markert Stephanie , Tingley Jeffrey P. , Unfried Frank , Ali Ahmed , Campbell Austin , Urs Karthik , Xiao Yao , Adams Ryan , Martin Duña , Bolam David N. , Becher Dörte , Schmidt Thomas M. , Abbott D. Wade , Schweder Thomas , Hehemann Jan Hendrik , Martens Eric C. 
Published: June 2020

SummaryHumans harbor numerous species of colonic bacteria that digest the fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible macroalgae seaweeds containing unique polysaccharides. It remains unclear how extensively gut bacteria have adapted to digest these nutrients and use these abilities to colonize microbiomes around the world, especially outside Asia. Here, we show that the ability of gut bacteria to digest seaweed polysaccharides is more pervasive than previously appreciated. Using culture-based approaches, we show that knownBacteroidesgenes involved in seaweed degradation have mobilized into many members of this genus. We also identify several previously unknown examples of marine bacteria-derived genes, and their corresponding mobile DNA elements, that are involved in degrading seaweed polysaccharides. Some of these genes reside in gut-resident, Gram-positive Firmicutes, for which phylogenetic analysis suggests an origin in theEpulopisciumgut symbionts of marine fishes. Our results are important for understanding the metabolic plasticity of the human gut microbiome, the global exchange of genes in the context of dietary selective pressures and identifying new functions that can be introduced or engineered to design and fill orthogonal niches for a future generation of engineered probiotics.
Mechanisms Coordinating Ribosomal Protein Gene Transcription in Response to Stress
Authors: Zencir Sevil , Dilg Daniel , Rueda Maria Paula , Shore David , Albert Benjamin 
Published: June 2020

AbstractWhile expression of ribosomal protein genes (RPGs) in the budding yeastSaccharomyces cerevisiaehas been extensively studied, a longstanding enigma persists regarding their co-regulation under fluctuating nutrient and stress conditions. Most (<90%) of RPG promoters display one of two distinct arrangements of a core set of transcription factors (TFs; Rap1, Fhl1 and Ifh1) and are further differentiated by the presence or absence of the HMGB box protein Hmo1. However, a third group of promoters appears not to bind any of these proteins, raising the question of how the whole suite of genes is co-regulated. We demonstrate that all RPGs are regulated by two distinct, but complementary mechanisms driven by the TFs Ifh1 and Sfp1, both of which are required for maximal expression in optimal conditions and coordinated down-regulation upon stress. At the majority of RPG promoters Ifh1-dependent regulation predominates, whereas Sfp1 plays the major role at all other genes. We also uncovered an unexpected, protein homeostasis-dependent binding property of Hmo1 at a large subset of RPG promoters. Finally, we show that the Ifh1 paralog Crf1, previously described as a transcriptional repressor, can act as a constitutive RPG activator in the W303 strain background when overexpressed. Our study thus provides a more complete picture of RPG regulation and may serve as a paradigm for unravelling RPG regulation in multicellular eukaryotes.
SC-GAN: 3D self-attention conditional GAN with spectral normalization for multi-modal neuroimaging synthesis
Authors: Lan Haoyu ,   the Alzheimer Disease Neuroimaging Initiative, Toga Arthur W , Sepehrband Farshid 
Published: June 2020

AbstractImage synthesis is one of the key applications of deep learning in neuroimaging, which enables shortening of the scan time and/or improve image quality; therefore, reducing the imaging cost and improving patient experience. Given the multi-modal and large-scale nature of neuroimaging data, the synthesis task is computationally challenging. 2D image synthesis networks do not take advantage of multi-dimensional spatial information and the 3D implementation has dimensionality problem, negatively affecting the network reliability. These limitations hinder the research and clinical applicability of deep learning-based neuroimaging synthesis. In this paper, we proposed a new network that is designed and optimized for the application of multi-modal 3D synthesis of neuroimaging data. The network is based on 3D conditional generative adversarial network (GAN), and employs spectral normalization and feature matching to stabilize the training process and ensure optimization convergence. We also added a self-attention module to model relationships between widely separated voxels. The performance of the network was evaluated by predicting positron emission tomography (PET) images, Fractional anisotropy (FA) and mean diffusivity (MD) maps from multi-modal magnetic resonance images (MRI) of 265 and 497 individuals correspondingly. The proposed network, called self-attention conditional GAN (SC-GAN), significantly outperformed conventional 2D conditional GAN and the 3D implementation, enabling robust 3D deep learning-based neuroimaging synthesis.